Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000422.1 Hibiscus syriacus cultivar Beakdansim tig00000773_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2457469
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:443788 original size:46 final size:45
Alignment explanation
Indices: 443690--443795 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
443680 GTGCACTAAG
* *
443690 AGTGCATCGATGCATCAAGTACATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATACATTCGATGTTTCAAAATAGCCAC
* * * *
443735 AGTGCATCGATGCGTCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATACATTCGATG-TTTCA-AAATAGCCAC
*
443781 AGTGCATCGGTGCAT
1 AGTGCATCGATGCAT
443796 GGTATATGCA
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
45 27 0.53
46 21 0.41
47 3 0.06
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATACATTCGATGTTTCAAAATAGCCAC
Found at i:452770 original size:23 final size:23
Alignment explanation
Indices: 452736--452804 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
452726 CATTATTATA
*
452736 TGGCACTACGGTGTAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
*
452759 CT-GCACTCCGGTGCAATTCTACG
1 -TGGCACTACGGTGCAATTCTACG
* *
452782 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTCTACG
452805 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
22 1 0.03
23 38 0.95
24 1 0.03
ACGTcount: A:0.20, C:0.26, G:0.25, T:0.29
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:455358 original size:18 final size:17
Alignment explanation
Indices: 455304--455352 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
455294 TTGGACCCTT
* *
455304 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
455322 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
455340 AGTGCATTCGATG
1 AGTGCA-TCGATG
455353 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:455457 original size:65 final size:64
Alignment explanation
Indices: 455300--455483 Score: 194
Period size: 65 Copynumber: 2.8 Consensus size: 64
455290 ACCGTTGGAC
* *
455300 CCTTAGTGCATCGGTGCACTAAG-AGTGCATCGATGCATCAAGTGCATTCGATG-TTTCAAAATA
1 CCTTAGTGCATCGGTGCA-T-GGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATA
455363 G
64 G
** *** * *
455364 CCAGAGTGCATTAATGCATGGCTGGTGCATCGATGCATTAAATGCATTCGATGTTTTCATAAA-A
1 CCTTAGTGCATCGGTGCATGG-TAGTGCATCGATGCATCAAATGCATTCGATGTTTTCA-AAATA
*
455428 T
64 G
* *
455429 CCTTAGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTCAATGTT
1 CCTTAGTGCATCGGTGCATGGTA-GTGCATCGATGCATCAAATGCATTCGATGTT
455484 CAATTTAATT
Statistics
Matches: 97, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 41 0.42
65 51 0.53
66 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.31
Consensus pattern (64 bp):
CCTTAGTGCATCGGTGCATGGTAGTGCATCGATGCATCAAATGCATTCGATGTTTTCAAAATAG
Found at i:455522 original size:65 final size:64
Alignment explanation
Indices: 455324--455531 Score: 197
Period size: 65 Copynumber: 3.2 Consensus size: 64
455314 TGCACTAAGA
* * * * * ** *
455324 GTGCATCGATGCATCAAGTGCATTCGATGTTTCA-AAATAGCCAGAGTGCATTAATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCAATGTTTCATAAA-ATCCATAGTGCATCGATGCATGGTTG
* * * *
455388 GTGCATCGATGCATTAAATGCATTCGATGTTTTCATAAAATCCTTAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATGAAATGCATTCAATG-TTTCATAAAATCCATAGTGCATCGATGCATGGT-T
455453 -
64 G
** * *
455453 GTGCATCGATGCATGAAATGCATTCAATG-TTCAATTTAATTCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATGAAATGCATTCAATGTTTC-ATAAAATCCATAGTGCATCGATGCATGG-TT
455517 G
64 G
*
455518 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
455532 CACTTTGATA
Statistics
Matches: 120, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
63 3 0.03
64 50 0.42
65 63 0.52
66 4 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCAATGTTTCATAAAATCCATAGTGCATCGATGCATGGTTG
Found at i:457127 original size:30 final size:30
Alignment explanation
Indices: 457060--457134 Score: 100
Period size: 30 Copynumber: 2.5 Consensus size: 30
457050 GAAAAAATTG
*
457060 AATACTTTATGTA-TCTATTTTGATCAAAA
1 AATACTTTAGGTACTCTATTTTGATCAAAA
*
457089 GATAACTTTAGGTACT-TATTTTGATCAAAAA
1 AAT-ACTTTAGGTACTCTATTTTGATC-AAAA
457120 AATACTTTAGGTACT
1 AATACTTTAGGTACT
457135 AAAATGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
29 2 0.05
30 31 0.77
31 7 0.17
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (30 bp):
AATACTTTAGGTACTCTATTTTGATCAAAA
Found at i:459651 original size:42 final size:44
Alignment explanation
Indices: 459562--459658 Score: 135
Period size: 43 Copynumber: 2.2 Consensus size: 44
459552 TACGTTTAAA
* *
459562 AAAATATTTTATTGAAAATATTATTATTATTTTAATATTTTTAGT
1 AAAATA-TTTATTGAAAATATTAATATTATTTTAATATTTTCAGT
* *
459607 AAAA-ATTTATTTAAAATATTAATATT-TTTTAATATTTTCGGT
1 AAAATATTTATTGAAAATATTAATATTATTTTAATATTTTCAGT
459649 AAAATATTTA
1 AAAATATTTA
459659 ATATTAACAT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 18 0.38
43 24 0.51
44 1 0.02
45 4 0.09
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (44 bp):
AAAATATTTATTGAAAATATTAATATTATTTTAATATTTTCAGT
Found at i:459764 original size:21 final size:21
Alignment explanation
Indices: 459738--459777 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
459728 TAAAGCGTCC
*
459738 AATAATAATATTTTCGGTAGA
1 AATAATAATATTTTAGGTAGA
*
459759 AATAATAATGTTTTAGGTA
1 AATAATAATATTTTAGGTA
459778 ATTTTTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (21 bp):
AATAATAATATTTTAGGTAGA
Found at i:469773 original size:176 final size:176
Alignment explanation
Indices: 469464--469814 Score: 558
Period size: 176 Copynumber: 2.0 Consensus size: 176
469454 AGGCAAATGT
* *
469464 TGCCTCGCATAATGAGAATGGTGCTTATGTTGGGAAGAATTCGTCTGGATTTCATTTTTCCTCTG
1 TGCCTCGCATAATGAGAATGGTGCTTATGCTGGGAAGAATTCGTCTGGATTTCATCTTTCCTCTG
* * * * * * * * *
469529 AAACGTTAGACACGTCTCAAGGCAATCGTGGTGGTGGTGGCCGTGGTGGTAACCGTGGACAGTTT
66 AAACATCAGACACGTCTCAAGGCAATCGTCGTGGTGGTGGCCATAGTCGCAACCGCGGACAATTT
469594 AATAATCGACCACAGTGTCAGTTGTGTGGAAAATATGGGCATCTGC
131 AATAATCGACCACAGTGTCAGTTGTGTGGAAAATATGGGCATCTGC
*
469640 TGCCTCGTATAATGAGAATGGTGCTTATGCTGGGAAGAATTCGTCTGGATTTCATCTTTCCTCTG
1 TGCCTCGCATAATGAGAATGGTGCTTATGCTGGGAAGAATTCGTCTGGATTTCATCTTTCCTCTG
* * **
469705 GAACATCGGACACGTCTCAAGGCAATCGTCGTGGTGGTGGCCATAGTCGCGGCCGCGGACAATTT
66 AAACATCAGACACGTCTCAAGGCAATCGTCGTGGTGGTGGCCATAGTCGCAACCGCGGACAATTT
469770 AATAATCGACCACAGTGTCAGTTGTGTGGAAAATATGGGCATCTG
131 AATAATCGACCACAGTGTCAGTTGTGTGGAAAATATGGGCATCTG
469815 GTTCAGAAGT
Statistics
Matches: 159, Mismatches: 16, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
176 159 1.00
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.29
Consensus pattern (176 bp):
TGCCTCGCATAATGAGAATGGTGCTTATGCTGGGAAGAATTCGTCTGGATTTCATCTTTCCTCTG
AAACATCAGACACGTCTCAAGGCAATCGTCGTGGTGGTGGCCATAGTCGCAACCGCGGACAATTT
AATAATCGACCACAGTGTCAGTTGTGTGGAAAATATGGGCATCTGC
Found at i:478966 original size:5 final size:5
Alignment explanation
Indices: 478956--478996 Score: 55
Period size: 5 Copynumber: 7.8 Consensus size: 5
478946 AACGGTCAAC
*
478956 GGTCG GGTCG GGTCAG CGGTTG GGTCG GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC-G -GGTCG GGTCG GGTCG GGTCG GGTC
478997 AGACCGGTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 27 0.84
6 2 0.06
7 3 0.09
ACGTcount: A:0.02, C:0.20, G:0.56, T:0.22
Consensus pattern (5 bp):
GGTCG
Found at i:478975 original size:17 final size:17
Alignment explanation
Indices: 478949--478996 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
478939 AACGGTCAAC
*
478949 GGTCAACGGTCGGGTCG
1 GGTCAGCGGTCGGGTCG
*
478966 GGTCAGCGGTTGGGTCG
1 GGTCAGCGGTCGGGTCG
478983 GGTC-G-GGTCGGGTC
1 GGTCAGCGGTCGGGTC
478997 AGACCGGTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 8 0.29
16 1 0.04
17 19 0.68
ACGTcount: A:0.06, C:0.21, G:0.52, T:0.21
Consensus pattern (17 bp):
GGTCAGCGGTCGGGTCG
Found at i:479022 original size:10 final size:10
Alignment explanation
Indices: 479009--479056 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
478999 ACCGGTTCAG
479009 ACCGGTCAAA
1 ACCGGTCAAA
479019 ACCGGTC-AA
1 ACCGGTCAAA
*
479028 ACCAGTCAAA
1 ACCGGTCAAA
*
479038 ACCGGTTGAAA
1 ACCGG-TCAAA
479049 ACCGGTCA
1 ACCGGTCA
479057 GACCGGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 8 0.25
10 15 0.47
11 9 0.28
ACGTcount: A:0.38, C:0.29, G:0.21, T:0.12
Consensus pattern (10 bp):
ACCGGTCAAA
Found at i:479035 original size:19 final size:19
Alignment explanation
Indices: 478999--479043 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
478989 GTCGGGTCAG
* *
478999 ACCGGTTCAGACCGGTCAAA
1 ACCGG-TCAAACCAGTCAAA
479019 ACCGGTCAAACCAGTCAAA
1 ACCGGTCAAACCAGTCAAA
479038 ACCGGT
1 ACCGGT
479044 TGAAAACCGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 18 0.78
20 5 0.22
ACGTcount: A:0.33, C:0.31, G:0.22, T:0.13
Consensus pattern (19 bp):
ACCGGTCAAACCAGTCAAA
Found at i:479063 original size:9 final size:9
Alignment explanation
Indices: 478993--479063 Score: 52
Period size: 10 Copynumber: 7.3 Consensus size: 9
478983 GGTCGGGTCG
*
478993 GGTCAGACC
1 GGTCAAACC
*
479002 GGTTCAGACC
1 GG-TCAAACC
479012 GGTCAAAACC
1 GGTC-AAACC
479022 GGTCAAACC
1 GGTCAAACC
*
479031 AGTCAAAACC
1 GGTC-AAACC
*
479041 GGTTGAAAACC
1 GG-T-CAAACC
*
479052 GGTCAGACC
1 GGTCAAACC
479061 GGT
1 GGT
479064 TTTCTAGCCC
Statistics
Matches: 51, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
9 19 0.37
10 24 0.47
11 8 0.16
ACGTcount: A:0.31, C:0.28, G:0.27, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:480152 original size:2 final size:2
Alignment explanation
Indices: 480145--480173 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
480135 GTTGATGAAG
480145 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
480174 TCAATGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:485511 original size:39 final size:39
Alignment explanation
Indices: 485464--485552 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
485454 AATTCTTATC
485464 CAAAATACAATGAAACCAAAACCCTTCCTCCTCCAATCA
1 CAAAATACAATGAAACCAAAACCCTTCCTCCTCCAATCA
* *
485503 CAAAATACAATGAAACCAAAATCCTTTCTCCTCCAATCA
1 CAAAATACAATGAAACCAAAACCCTTCCTCCTCCAATCA
*
485542 CAAACTACAAT
1 CAAAATACAAT
485553 ATCATTCAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 47 1.00
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (39 bp):
CAAAATACAATGAAACCAAAACCCTTCCTCCTCCAATCA
Found at i:491138 original size:13 final size:13
Alignment explanation
Indices: 491120--491146 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
491110 AGTATGCATC
491120 TAAATAAATAAAA
1 TAAATAAATAAAA
491133 TAAATAAATAAAA
1 TAAATAAATAAAA
491146 T
1 T
491147 GAATTAATCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAATAAATAAAA
Found at i:497162 original size:22 final size:22
Alignment explanation
Indices: 497111--497162 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
497101 CTTATAGGAA
*
497111 AAATA-TAAAAGATAATTAAAT
1 AAATATTAAAAGATAAATAAAT
* * * *
497132 TAATTTTAAAATATAAATATAT
1 AAATATTAAAAGATAAATAAAT
497154 AAATATTAA
1 AAATATTAA
497163 GATTTAAACC
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
AAATATTAAAAGATAAATAAAT
Found at i:499014 original size:17 final size:17
Alignment explanation
Indices: 498989--499022 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
498979 ATACTCCTTC
*
498989 AAGGGGTATCGATACTG
1 AAGGAGTATCGATACTG
499006 AAGGAGTATCGATACTG
1 AAGGAGTATCGATACTG
499023 CCCTCATGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (17 bp):
AAGGAGTATCGATACTG
Found at i:503567 original size:11 final size:11
Alignment explanation
Indices: 503551--503593 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
503541 GGTCTTTGTA
503551 AATAATAATAT
1 AATAATAATAT
*
503562 AATAATATTAT
1 AATAATAATAT
*
503573 -ATAATATTTAT
1 AATAATA-ATAT
503584 AATAATAATA
1 AATAATAATA
503594 ACACTCGGAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 6 0.21
11 16 0.57
12 6 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
AATAATAATAT
Found at i:503978 original size:33 final size:33
Alignment explanation
Indices: 503915--503978 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 33
503905 AGACACGAAG
503915 TTGATACTTCACTATCTTCTGTGAAGGTTGAAT
1 TTGATACTTCACTATCTTCTGTGAAGGTTGAAT
*
503948 TTGATTACTTCACTACTGTTC-GTGAA-GTTGA
1 TTGA-TACTTCACTA-TCTTCTGTGAAGGTTGA
503979 TCTTGAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 9 0.32
34 15 0.54
35 4 0.14
ACGTcount: A:0.23, C:0.16, G:0.19, T:0.42
Consensus pattern (33 bp):
TTGATACTTCACTATCTTCTGTGAAGGTTGAAT
Found at i:504019 original size:118 final size:115
Alignment explanation
Indices: 503874--504093 Score: 288
Period size: 118 Copynumber: 1.9 Consensus size: 115
503864 GATTGACTTG
* *
503874 AGAAGAATCGTTTCACTATTTCGTGAAGATCAGACACGAAGTT-G-ATACTTC-ACTATCTTCTG
1 AGAAGAATCGTTTCACTATTTCATGAAGATCAAACACGAAGTTGGAATACTTCAACTAT-TT-TG
*
503936 TGAAGGTTGAATTTGA-TTACTTCACTACTGTT-CGTGAAGTTGATCTTGAATA
64 TGAAGGTTG--TTTGATTTACTTCACTACTCTTCCGTGAAGTTGATCTTGAATA
*
503988 AGAAGAATCTGTTTCACTACACTTTCATGAAGATCAAACTCGAAGTTGGAATACTTCATACTATT
1 AGAAGAATC-GTTTCACT--A-TTTCATGAAGATCAAACACGAAGTTGGAATACTTCA-ACTATT
504053 TTGTGAAGGTTGTTTGATTTACTTCACTACTCTTCCGTGAA
61 TTGTGAAGGTTGTTTGATTTACTTCACTACTCTTCCGTGAA
504094 TGTTTGATTG
Statistics
Matches: 92, Mismatches: 4, Indels: 14
0.84 0.04 0.13
Matches are distributed among these distances:
114 9 0.10
115 8 0.09
117 1 0.01
118 27 0.29
119 16 0.17
120 24 0.26
121 2 0.02
122 5 0.05
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (115 bp):
AGAAGAATCGTTTCACTATTTCATGAAGATCAAACACGAAGTTGGAATACTTCAACTATTTTGTG
AAGGTTGTTTGATTTACTTCACTACTCTTCCGTGAAGTTGATCTTGAATA
Found at i:505913 original size:157 final size:157
Alignment explanation
Indices: 505612--505926 Score: 582
Period size: 157 Copynumber: 2.0 Consensus size: 157
505602 AATCTAAACG
505612 ACGTTCATCTCCGTTGTCTAGCCTCTATAGCTGTGAGATGGGACTCCATGGATGCAAACCTCAAA
1 ACGTTCATCTCCGTTGTCTAGCCTCTATAGCTGTGAGATGGGACTCCATGGATGCAAACCTCAAA
505677 TTAAACGTCTCTAAGAATATCAAAAATATGGAGGCGTTTGATCCTCTTGTTGTGCCGGCGCGTCC
66 TTAAACGTCTCTAAGAATATCAAAAATATGGAGGCGTTTGATCCTCTTGTTGTGCCGGCGCGTCC
505742 TTGGGTGCTTATCTTCATATCGTCGAT
131 TTGGGTGCTTATCTTCATATCGTCGAT
505769 ACGTTCATCTCCCGTTGTCTAGCCTCTATAGCTGTGAGAT-GGACTCCATGGATGCAAACCTCAA
1 ACGTTCATCT-CCGTTGTCTAGCCTCTATAGCTGTGAGATGGGACTCCATGGATGCAAACCTCAA
505833 ATTAAACGTCTCTAAGAATTATC-AAAA-ATGGAGGCGTTTGATCCTCTTGTTGTGCCGGCGCGT
65 ATTAAACGTCTCTAAGAA-TATCAAAAATATGGAGGCGTTTGATCCTCTTGTTGTGCCGGCGCGT
505896 CCTTGGGTGCTTCATCTTCATATCGTCGAT
129 CCTTGGGTGCTT-ATCTTCATATCGTCGAT
505926 A
1 A
505927 TCTTTTATTA
Statistics
Matches: 155, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
156 48 0.31
157 74 0.48
158 33 0.21
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (157 bp):
ACGTTCATCTCCGTTGTCTAGCCTCTATAGCTGTGAGATGGGACTCCATGGATGCAAACCTCAAA
TTAAACGTCTCTAAGAATATCAAAAATATGGAGGCGTTTGATCCTCTTGTTGTGCCGGCGCGTCC
TTGGGTGCTTATCTTCATATCGTCGAT
Found at i:506874 original size:26 final size:28
Alignment explanation
Indices: 506845--506900 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
506835 AATGGGCATA
506845 GTTTTG-AAAACTATTTAT-AAAACAAT
1 GTTTTGAAAAACTATTTATGAAAACAAT
* *
506871 G-TTTGAAAAATTATTTTTGAAAACAAT
1 GTTTTGAAAAACTATTTATGAAAACAAT
506898 GTT
1 GTT
506901 CCAACAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
25 4 0.16
26 11 0.44
27 9 0.36
28 1 0.04
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (28 bp):
GTTTTGAAAAACTATTTATGAAAACAAT
Found at i:506900 original size:27 final size:25
Alignment explanation
Indices: 506847--506900 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
506837 TGGGCATAGT
506847 TTTGAAAACTATTTATAAAACAATG
1 TTTGAAAACTATTTATAAAACAATG
* *
506872 TTTGAAAAATTATTTTTGAAAACAATG
1 TTTG-AAAACTATTTAT-AAAACAATG
506899 TT
1 TT
506901 CCAACAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.16
26 10 0.40
27 11 0.44
ACGTcount: A:0.44, C:0.06, G:0.09, T:0.41
Consensus pattern (25 bp):
TTTGAAAACTATTTATAAAACAATG
Found at i:513259 original size:65 final size:64
Alignment explanation
Indices: 513184--513337 Score: 202
Period size: 65 Copynumber: 2.4 Consensus size: 64
513174 TACACTAGGG
* * *
513184 GTGCATCGATGCATTAATTACATTCAATGTTTCTAA-AAAGCCAAGAGTGCATCGATGCATGGTC
1 GTGCATCGATGCATAAAATACATTCAATGTTTC-AATAAAACCAAGAGTGCATCGATGCATGG-C
513248 T
64 T
* * * *
513249 GTGCATCGATGCATAAAATGCATTCGATGTTTCAATAAAATCATGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATAAAATACATTCAATGTTTCAATAAAACCAAGAGTGCATCGATGCATGGCT
* *
513313 GTGCATCGGTGCATAAAATTCATTC
1 GTGCATCGATGCATAAAATACATTC
513338 GAAATGGGGT
Statistics
Matches: 79, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
64 27 0.34
65 52 0.66
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATACATTCAATGTTTCAATAAAACCAAGAGTGCATCGATGCATGGCT
Found at i:513889 original size:20 final size:20
Alignment explanation
Indices: 513866--514112 Score: 341
Period size: 20 Copynumber: 12.3 Consensus size: 20
513856 CAAAAGATTC
** *
513866 ACAAATTACCCAAAGGTTTT
1 ACAAATTACCCGGAGGCTTT
* *
513886 ACAAATGACCTGGAGGCTTT
1 ACAAATTACCCGGAGGCTTT
513906 ACAAATTACCCGGAGGCTTT
1 ACAAATTACCCGGAGGCTTT
*
513926 ACAAATGACCCGGAGGCTTT
1 ACAAATTACCCGGAGGCTTT
* *
513946 ACAAATGACCCGAAGGCTTT
1 ACAAATTACCCGGAGGCTTT
* * *
513966 ATAAATTACTCGGAGGATTT
1 ACAAATTACCCGGAGGCTTT
*
513986 ACAAATGACCCGGAGGCTTT
1 ACAAATTACCCGGAGGCTTT
* *
514006 ACAAATTACCTGGTGGCTTT
1 ACAAATTACCCGGAGGCTTT
*
514026 ACAAATTACCTGGAGGCTTT
1 ACAAATTACCCGGAGGCTTT
514046 ACAAATTACCCGGAGGCTTT
1 ACAAATTACCCGGAGGCTTT
*
514066 ACAAATTACCCAGAGGCTTT
1 ACAAATTACCCGGAGGCTTT
*
514086 ACAAATTACTCGGAGGCTTT
1 ACAAATTACCCGGAGGCTTT
514106 ACAAATT
1 ACAAATT
514113 TAAGGAAAAT
Statistics
Matches: 201, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 201 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.27
Consensus pattern (20 bp):
ACAAATTACCCGGAGGCTTT
Found at i:513895 original size:40 final size:40
Alignment explanation
Indices: 513850--513936 Score: 93
Period size: 40 Copynumber: 2.2 Consensus size: 40
513840 AGACTGACAG
*
513850 ATGACCCAAAAGATTCACAAATTACCCAAAGGTTTTACAA
1 ATGACCCAAAAGATTCACAAATTACCCAAAGGCTTTACAA
*** * * * **
513890 ATGACCTGGAGGCTTTACAAATTACCCGGAGGCTTTACAA
1 ATGACCCAAAAGATTCACAAATTACCCAAAGGCTTTACAA
513930 ATGACCC
1 ATGACCC
513937 GGAGGCTTTA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.37, C:0.24, G:0.16, T:0.23
Consensus pattern (40 bp):
ATGACCCAAAAGATTCACAAATTACCCAAAGGCTTTACAA
Found at i:522755 original size:28 final size:28
Alignment explanation
Indices: 522723--522783 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 28
522713 TTTAAGGCTT
* *
522723 AGGTTAACTTGGGAATGTGGAGTATTTC
1 AGGTTAACTTGGGAAGGTAGAGTATTTC
* * * *
522751 AGGTTGATTTGGGGAGGTAGAGTGTTTC
1 AGGTTAACTTGGGAAGGTAGAGTATTTC
522779 AGGTT
1 AGGTT
522784 GGGTTATTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.21, C:0.05, G:0.38, T:0.36
Consensus pattern (28 bp):
AGGTTAACTTGGGAAGGTAGAGTATTTC
Found at i:530667 original size:17 final size:17
Alignment explanation
Indices: 530645--530689 Score: 72
Period size: 17 Copynumber: 2.6 Consensus size: 17
530635 GGCTCGTTAA
* *
530645 GAACTCGAGTCAAGCTC
1 GAACTCAAGTCAAACTC
530662 GAACTCAAGTCAAACTC
1 GAACTCAAGTCAAACTC
530679 GAACTCAAGTC
1 GAACTCAAGTC
530690 GAGTCCATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.18
Consensus pattern (17 bp):
GAACTCAAGTCAAACTC
Found at i:531313 original size:20 final size:21
Alignment explanation
Indices: 531272--531322 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
531262 TTTAAATATA
* *
531272 TAAAATTTTAAATTTCATTTT
1 TAAAATTATAAATATCATTTT
531293 TAAAATTATAAATAT-ATTTT
1 TAAAATTATAAATATCATTTT
531313 TAAAATTATA
1 TAAAATTATA
531323 TTTAAAACTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
TAAAATTATAAATATCATTTT
Found at i:531338 original size:33 final size:33
Alignment explanation
Indices: 531277--531339 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
531267 ATATATAAAA
* * *
531277 TTTTAAATTTCATTTTTAAAATTATAAATATAT
1 TTTTAAAATTCATATTTAAAACTATAAATATAT
531310 TTTTAAAATT-ATATTTAAAACTATTAAATA
1 TTTTAAAATTCATATTTAAAACTA-TAAATA
531340 AAAGTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 11 0.42
33 15 0.58
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (33 bp):
TTTTAAAATTCATATTTAAAACTATAAATATAT
Found at i:531384 original size:38 final size:38
Alignment explanation
Indices: 531335--531453 Score: 204
Period size: 38 Copynumber: 3.1 Consensus size: 38
531325 TAAAACTATT
531335 AAATAAAAGTTAAATAATTATTA-ATGTGTTTGATAAACA
1 AAAT-AAAGTTAAATAATTATTACA-GTGTTTGATAAACA
531374 AAATAAAGTTAAATAATTATTACAGTGTTTGATAAACA
1 AAATAAAGTTAAATAATTATTACAGTGTTTGATAAACA
*
531412 AAATAAAGTTAAATAATTATTACAGTTTTTGATAAACA
1 AAATAAAGTTAAATAATTATTACAGTGTTTGATAAACA
531450 AAAT
1 AAAT
531454 TGATTTTATT
Statistics
Matches: 78, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
38 73 0.94
39 5 0.06
ACGTcount: A:0.51, C:0.04, G:0.09, T:0.35
Consensus pattern (38 bp):
AAATAAAGTTAAATAATTATTACAGTGTTTGATAAACA
Found at i:532138 original size:50 final size:49
Alignment explanation
Indices: 532083--532185 Score: 152
Period size: 50 Copynumber: 2.1 Consensus size: 49
532073 TTATAAAGAT
* *
532083 TTAAAATTAGTTAAAAATTTCAAGGTAAATTATTTAAAATAAAATAGTAA
1 TTAAAATTA-TTAAAAATTTAAAGATAAATTATTTAAAATAAAATAGTAA
* *
532133 TTAAAAATTATTTAAAATTTAAAGATAAATTATTTAAAATAAAATATTAA
1 TT-AAAATTATTAAAAATTTAAAGATAAATTATTTAAAATAAAATAGTAA
532183 TTA
1 TTA
532186 CATTATTTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
49 1 0.02
50 40 0.83
51 7 0.15
ACGTcount: A:0.55, C:0.01, G:0.05, T:0.39
Consensus pattern (49 bp):
TTAAAATTATTAAAAATTTAAAGATAAATTATTTAAAATAAAATAGTAA
Found at i:532140 original size:28 final size:27
Alignment explanation
Indices: 532109--532193 Score: 83
Period size: 22 Copynumber: 3.3 Consensus size: 27
532099 ATTTCAAGGT
532109 AAATTATTTAAAATAAAATAGTAATTAA
1 AAATTATTTAAAATAAAATAGTAATT-A
**
532137 AAATTATTTAAAATTTAA-AG--A-T-
1 AAATTATTTAAAATAAAATAGTAATTA
*
532159 AAATTATTTAAAATAAAATATTAATT-
1 AAATTATTTAAAATAAAATAGTAATTA
*
532185 ACATTATTT
1 AAATTATTT
532194 TCCATATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
22 16 0.34
23 1 0.02
24 1 0.02
25 2 0.04
26 9 0.19
27 2 0.04
28 16 0.34
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.41
Consensus pattern (27 bp):
AAATTATTTAAAATAAAATAGTAATTA
Found at i:533798 original size:21 final size:21
Alignment explanation
Indices: 533772--533824 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
533762 AGAATAGAGG
*
533772 GTATCGACACTCCTAAAGGAA
1 GTATCGGCACTCCTAAAGGAA
533793 GTATCGGCACTCCTAAAGGAA
1 GTATCGGCACTCCTAAAGGAA
533814 GTATCGGCACT
1 GTATCGGCACT
533825 ACCTTTGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.32, C:0.25, G:0.23, T:0.21
Consensus pattern (21 bp):
GTATCGGCACTCCTAAAGGAA
Found at i:548466 original size:18 final size:19
Alignment explanation
Indices: 548443--548487 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
548433 TGTTTTCATA
*
548443 AATAGTATTATA-TGTATG
1 AATAGTACTATACTGTATG
548461 AATAGTACTATACTGTATG
1 AATAGTACTATACTGTATG
*
548480 AACAGTAC
1 AATAGTAC
548488 CATGAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 11 0.46
19 13 0.54
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (19 bp):
AATAGTACTATACTGTATG
Found at i:548545 original size:21 final size:21
Alignment explanation
Indices: 548519--548559 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
548509 TCATGAACAG
548519 TGCTACAGTGTACCGATGCAC
1 TGCTACAGTGTACCGATGCAC
548540 TGCTACAGTGTACCGATGCA
1 TGCTACAGTGTACCGATGCA
548560 TAATAACATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (21 bp):
TGCTACAGTGTACCGATGCAC
Found at i:549286 original size:22 final size:22
Alignment explanation
Indices: 549258--549318 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
549248 GGCATGTGAA
549258 ATTTGTCCCAAAGGACCTATGT
1 ATTTGTCCCAAAGGACCTATGT
* *
549280 ATTTGTCCCGAAGGACCTCTGT
1 ATTTGTCCCAAAGGACCTATGT
*
549302 ATATGTCCCAAAGGACC
1 ATTTGTCCCAAAGGACC
549319 ACGTAGACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (22 bp):
ATTTGTCCCAAAGGACCTATGT
Found at i:553568 original size:11 final size:11
Alignment explanation
Indices: 553552--553615 Score: 50
Period size: 11 Copynumber: 6.4 Consensus size: 11
553542 AATATATTTG
553552 ATTAAATTTAA
1 ATTAAATTTAA
*
553563 ATTAAATTT-C
1 ATTAAATTTAA
553573 A-TAAATTT-A
1 ATTAAATTTAA
* *
553582 ATTCAA-CTAA
1 ATTAAATTTAA
553592 A--AAATTTAA
1 ATTAAATTTAA
*
553601 ATAAAATTTAA
1 ATTAAATTTAA
553612 ATTA
1 ATTA
553616 TAAAATAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
8 2 0.05
9 13 0.32
10 6 0.15
11 20 0.49
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:563025 original size:17 final size:17
Alignment explanation
Indices: 563003--563035 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
562993 CCTGGACTGA
*
563003 GCCGTTGATTGTTGACC
1 GCCGTTGATCGTTGACC
563020 GCCGTTGATCGTTGAC
1 GCCGTTGATCGTTGAC
563036 TATTGACCGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.24, G:0.30, T:0.33
Consensus pattern (17 bp):
GCCGTTGATCGTTGACC
Found at i:563055 original size:21 final size:21
Alignment explanation
Indices: 563021--563063 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
563011 TTGTTGACCG
*
563021 CCGTTGATCGTTGACTA-TTGA
1 CCGTTGACCGTTGA-TAGTTGA
*
563042 CCGTTGACCTTTGATAGTTGA
1 CCGTTGACCGTTGATAGTTGA
563063 C
1 C
563064 TTTGACCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.37
Consensus pattern (21 bp):
CCGTTGACCGTTGATAGTTGA
Found at i:565108 original size:48 final size:49
Alignment explanation
Indices: 565056--565164 Score: 134
Period size: 48 Copynumber: 2.3 Consensus size: 49
565046 ATGTTTTATT
*
565056 TGATTTTC-GATTTGAATTCTGTTCTGATACCTGACCTGAATTTTGTTA
1 TGATTTTCTGATATGAATTCTGTTCTGATACCTGACCTGAATTTTGTTA
* * * * * *
565104 TGA-TTTCTTATATGGATTTTGTTCTGATATCTGATCTGAATTTTGTTT
1 TGATTTTCTGATATGAATTCTGTTCTGATACCTGACCTGAATTTTGTTA
565152 TGA-TTTCTGATAT
1 TGATTTTCTGATAT
565165 CTCCATTTAC
Statistics
Matches: 52, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
47 4 0.08
48 48 0.92
ACGTcount: A:0.20, C:0.11, G:0.17, T:0.52
Consensus pattern (49 bp):
TGATTTTCTGATATGAATTCTGTTCTGATACCTGACCTGAATTTTGTTA
Found at i:565122 original size:24 final size:24
Alignment explanation
Indices: 565092--565164 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
565082 ATACCTGACC
*
565092 TGAATTTTGTTATGATTTCTTATA
1 TGAATTTTGTTATGATTTCTGATA
* * * *
565116 TGGATTTTGTTCTGATATCTGATC
1 TGAATTTTGTTATGATTTCTGATA
*
565140 TGAATTTTGTTTTGATTTCTGATA
1 TGAATTTTGTTATGATTTCTGATA
565164 T
1 T
565165 CTCCATTTAC
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 40 1.00
ACGTcount: A:0.21, C:0.07, G:0.16, T:0.56
Consensus pattern (24 bp):
TGAATTTTGTTATGATTTCTGATA
Found at i:565518 original size:30 final size:28
Alignment explanation
Indices: 565482--565537 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 28
565472 CCTGAGATAT
565482 ATATAAACTATAAATTATACATATATAATA
1 ATATAAACTAT--ATTATACATATATAATA
* *
565512 ATATAAAGTATATTATATATATATAA
1 ATATAAACTATATTATACATATATAA
565538 AGTATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.58
30 10 0.42
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (28 bp):
ATATAAACTATATTATACATATATAATA
Found at i:565535 original size:20 final size:20
Alignment explanation
Indices: 565512--565586 Score: 82
Period size: 20 Copynumber: 3.6 Consensus size: 20
565502 ATATATAATA
565512 ATATAAAGTATATTATATAT
1 ATATAAAGTATATTATATAT
565532 ATATAAAGTATAATTATA-A-
1 ATATAAAGTAT-ATTATATAT
* *
565551 AGACTAAAGTATATAAGTATAT
1 ATA-TAAAGTATATTA-TATAT
565573 AATATAAAGTATAT
1 -ATATAAAGTATAT
565587 AAGAATATAA
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 5 0.11
20 22 0.48
21 7 0.15
22 10 0.22
23 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.37
Consensus pattern (20 bp):
ATATAAAGTATATTATATAT
Found at i:565543 original size:13 final size:14
Alignment explanation
Indices: 565527--565587 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
565517 AAGTATATTA
565527 TATATA-TATAAAG
1 TATATAGTATAAAG
*
565540 TATA-ATTATAAAG
1 TATATAGTATAAAG
*
565553 -ACTAAAGTATATAAG
1 TA-TATAGTATA-AAG
*
565568 TATATAATATAAAG
1 TATATAGTATAAAG
565582 TATATA
1 TATATA
565588 AGAATATAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
12 2 0.05
13 13 0.32
14 14 0.35
15 10 0.25
16 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.36
Consensus pattern (14 bp):
TATATAGTATAAAG
Found at i:565570 original size:8 final size:8
Alignment explanation
Indices: 565557--565596 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
565547 ATAAAGACTA
565557 AAGTATAT
1 AAGTATAT
565565 AAGTATAT
1 AAGTATAT
565573 AA-TATA-
1 AAGTATAT
565579 AAGTATAT
1 AAGTATAT
*
565587 AAGAATAT
1 AAGTATAT
565595 AA
1 AA
565597 ACTACATAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 2 0.07
7 8 0.28
8 19 0.66
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (8 bp):
AAGTATAT
Found at i:565571 original size:22 final size:22
Alignment explanation
Indices: 565509--565596 Score: 78
Period size: 22 Copynumber: 4.2 Consensus size: 22
565499 TACATATATA
* *
565509 ATAATATAAAGTATATTA-TAT
1 ATAAGATAAAGTATATAAGTAT
* *
565530 AT-ATATAAAG--TATAATTAT
1 ATAAGATAAAGTATATAAGTAT
565549 A-AAGACTAAAGTATATAAGTAT
1 ATAAGA-TAAAGTATATAAGTAT
* *
565571 ATAATATAAAGTATATAAGAAT
1 ATAAGATAAAGTATATAAGTAT
565593 ATAA
1 ATAA
565597 ACTACATAGT
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
18 4 0.07
19 6 0.11
20 13 0.23
21 2 0.04
22 28 0.50
23 3 0.05
ACGTcount: A:0.56, C:0.01, G:0.08, T:0.35
Consensus pattern (22 bp):
ATAAGATAAAGTATATAAGTAT
Found at i:565671 original size:20 final size:20
Alignment explanation
Indices: 565591--566218 Score: 158
Period size: 20 Copynumber: 30.7 Consensus size: 20
565581 GTATATAAGA
*
565591 ATATAAACTACATAGTTTAT
1 ATATAAACTATATAGTTTAT
* *
565611 ATTTATAA-TATTATA-TACTAT
1 ATATA-AACTA-TATAGT-TTAT
565632 ATATAAACTATATA-TATTAT
1 ATATAAACTATATAGT-TTAT
*
565652 GTATAAACTATATAGTTTATT
1 ATATAAACTATATAGTTTA-T
*
565673 AATATAAATTATATAGTTTAT
1 -ATATAAACTATATAGTTTAT
* *
565694 ATATAAATTATATATGAATTAT
1 ATATAAACTATATA-G-TTTAT
* * *
565716 ATTTGAA-TATATACATCTTAT
1 ATATAAACTATATA-GT-TTAT
* * **
565737 ATTTATA-TAT-TA-TGCAT
1 ATATAAACTATATAGTTTAT
** *
565754 AATTATAAGTTATATA-TACTAT
1 -A-TATAAACTATATAGT-TTAT
* *
565776 GTATAAATTATATAGTTTAT
1 ATATAAACTATATAGTTTAT
* *
565796 ATAGTTTAAA-TATAAAGTATAT
1 ATA---TAAACTATATAGTTTAT
* **
565818 ATATAAACTATAAATAATACAT
1 ATATAAACTAT--ATAGTTTAT
* *
565840 ATATAATAATATAAAGTATATTAT
1 ATATAA-ACTATATAG--T-TTAT
* *
565864 ATATATAA--AGTATAATTATAA
1 ATATA-AACTA-TATAGTT-TAT
* * *
565885 AGACTAAAGTATATAAGTATAT
1 ATA-TAAACTATAT-AGTTTAT
*
565907 AATATAAAGTATATAAG---A-
1 -ATATAAACTATAT-AGTTTAT
*
565925 ATATAAACTACATAGTTTAT
1 ATATAAACTATATAGTTTAT
* * * * *
565945 ATTTATATTATTATA-TACTCT
1 ATATAAACTA-TATAGT-TTAT
565966 ATATAAACTATATA-TATTAT
1 ATATAAACTATATAGT-TTAT
*
565986 GTATAAACTATATAG-TT-T
1 ATATAAACTATATAGTTTAT
**
566004 AT-T-AA-TATA-A-ACTAT
1 ATATAAACTATATAGTTTAT
* *
566019 ATATAAACTATAAAGTGTAT
1 ATATAAACTATATAGTTTAT
* * *
566039 ATATAAAGTATATAAACTATAT
1 ATATAAACTATAT--AGTTTAT
566061 ATATAAACTATATAGTTTAT
1 ATATAAACTATATAGTTTAT
* * * *
566081 ATTTATATTATTATA-TACTAT
1 ATATAAACTA-TATAGT-TTAT
*
566102 ATATAAACTATATATATATTAT
1 ATATAAACTATATA-GT-TTAT
* * *
566124 GTATAAACTATAGAGTCTAT
1 ATATAAACTATATAGTTTAT
* * **
566144 ATATGAA-T-TATTGAACTAT
1 ATATAAACTATATAG-TTTAT
566163 ATATAAACTATATAGTTTACT
1 ATATAAACTATATAGTTTA-T
*
566184 AATATAAATTATATAGTTTAT
1 -ATATAAACTATATAGTTTAT
*
566205 ATATAAATTATATA
1 ATATAAACTATATA
566219 TTAATTATAT
Statistics
Matches: 457, Mismatches: 92, Indels: 118
0.69 0.14 0.18
Matches are distributed among these distances:
14 2 0.00
15 7 0.02
16 5 0.01
17 16 0.04
18 11 0.02
19 23 0.05
20 159 0.35
21 82 0.18
22 126 0.28
23 17 0.04
24 8 0.02
25 1 0.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.43
Consensus pattern (20 bp):
ATATAAACTATATAGTTTAT
Found at i:565698 original size:11 final size:11
Alignment explanation
Indices: 565629--565717 Score: 64
Period size: 11 Copynumber: 8.5 Consensus size: 11
565619 TATTATATAC
*
565629 TATATATAAAC
1 TATATATAAAT
565640 TATATAT--AT
1 TATATATAAAT
* *
565649 TATGTATAAAC
1 TATATATAAAT
**
565660 TATATAGTTTAT
1 TATATA-TAAAT
565672 TA-ATATAAAT
1 TATATATAAAT
565682 TATATAGT---T
1 TATATA-TAAAT
565691 TATATATAAAT
1 TATATATAAAT
*
565702 TATATATGAAT
1 TATATATAAAT
565713 TATAT
1 TATAT
565718 TTGAATATAT
Statistics
Matches: 60, Mismatches: 10, Indels: 16
0.70 0.12 0.19
Matches are distributed among these distances:
8 1 0.02
9 14 0.23
10 5 0.08
11 35 0.58
12 5 0.08
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.47
Consensus pattern (11 bp):
TATATATAAAT
Found at i:565722 original size:11 final size:11
Alignment explanation
Indices: 565670--565728 Score: 54
Period size: 11 Copynumber: 5.7 Consensus size: 11
565660 TATATAGTTT
*
565670 ATTA-ATATAA
1 ATTATATATGA
565680 ATTATATA-G-
1 ATTATATATGA
* *
565689 TTTATATATAA
1 ATTATATATGA
565700 ATTATATATGA
1 ATTATATATGA
*
565711 ATTATATTTGA
1 ATTATATATGA
565722 A-TATATA
1 ATTATATA
565729 CATCTTATAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
9 7 0.18
10 9 0.23
11 23 0.59
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (11 bp):
ATTATATATGA
Found at i:565829 original size:7 final size:6
Alignment explanation
Indices: 565802--565919 Score: 53
Period size: 7 Copynumber: 18.3 Consensus size: 6
565792 TTATATAGTT
* * *
565802 TAAATA TAAAGTA TATATA TAAACTA TAAATAA TACATA TATA-A T-AATA
1 TAAATA TAAA-TA TAAATA TAAA-TA TAAAT-A TAAATA TAAATA TAAATA
* * * *
565851 TAAAGTA T-ATTA TATATA TAAAGTA TAATTA TAAAGA CTAAAGTA TATAAGTA
1 TAAA-TA TAAATA TAAATA TAAA-TA TAAATA TAAATA -TAAA-TA TA-AA-TA
565904 TATAATA TAAAGTA TA
1 TA-AATA TAAA-TA TA
565920 TAAGAATATA
Statistics
Matches: 87, Mismatches: 13, Indels: 23
0.71 0.11 0.19
Matches are distributed among these distances:
4 1 0.01
5 7 0.08
6 30 0.34
7 38 0.44
8 11 0.13
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.36
Consensus pattern (6 bp):
TAAATA
Found at i:565883 original size:24 final size:23
Alignment explanation
Indices: 565804--565884 Score: 65
Period size: 26 Copynumber: 3.3 Consensus size: 23
565794 ATATAGTTTA
*
565804 AATATAAAGTATATATATAAACTAT
1 AATAT-AA-TATATATATAAAATAT
*
565829 AA-ATAATACATATATAATAATAT
1 AATATAATATATATATAA-AATAT
* *
565852 AAAGTATATTATATATATAAAGTAT
1 -AA-TATAATATATATATAAAATAT
565877 AATTATAA
1 AA-TATAA
565885 AGACTAAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
22 10 0.22
23 6 0.13
24 10 0.22
25 6 0.13
26 13 0.29
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (23 bp):
AATATAATATATATATAAAATAT
Found at i:565904 original size:8 final size:8
Alignment explanation
Indices: 565891--565930 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
565881 ATAAAGACTA
565891 AAGTATAT
1 AAGTATAT
565899 AAGTATAT
1 AAGTATAT
565907 AA-TATA-
1 AAGTATAT
565913 AAGTATAT
1 AAGTATAT
*
565921 AAGAATAT
1 AAGTATAT
565929 AA
1 AA
565931 ACTACATAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
6 2 0.07
7 8 0.28
8 19 0.66
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (8 bp):
AAGTATAT
Found at i:565905 original size:22 final size:22
Alignment explanation
Indices: 565874--565930 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
565864 ATATATAAAG
*
565874 TATAATTATA-AAGACTAAAGTA
1 TATAAGTATATAAGA-TAAAGTA
*
565896 TATAAGTATATAATATAAAGTA
1 TATAAGTATATAAGATAAAGTA
*
565918 TATAAGAATATAA
1 TATAAGTATATAA
565931 ACTACATAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 28 0.90
23 3 0.10
ACGTcount: A:0.56, C:0.02, G:0.09, T:0.33
Consensus pattern (22 bp):
TATAAGTATATAAGATAAAGTA
Found at i:565970 original size:11 final size:11
Alignment explanation
Indices: 565942--566135 Score: 81
Period size: 11 Copynumber: 18.4 Consensus size: 11
565932 CTACATAGTT
* *
565942 TATATTTATAT
1 TATATATATAC
565953 TAT-TATATAC
1 TATATATATAC
* *
565963 TCTATATAAAC
1 TATATATATAC
565974 TATATATAT--
1 TATATATATAC
* *
565983 TATGTATAAAC
1 TATATATATAC
* *
565994 TATATAGTTTAT
1 TATATA-TATAC
*
566006 TA-ATATAAAC
1 TATATATATAC
*
566016 TATATATAAAC
1 TATATATATAC
*
566027 TATA-A-AGT-G
1 TATATATA-TAC
* *
566036 TATATATAAAG
1 TATATATATAC
566047 TATATA-A-AC
1 TATATATATAC
566056 TATATATATAAAC
1 TATATATAT--AC
566069 TATATAGT-T--
1 TATATA-TATAC
* *
566078 TATATTTATAT
1 TATATATATAC
566089 TAT-TATATAC
1 TATATATATAC
*
566099 TATATATAAAC
1 TATATATATAC
*
566110 TATATATATAT
1 TATATATATAC
* *
566121 TATGTATAAAC
1 TATATATATAC
566132 TATA
1 TATA
566136 GAGTCTATAT
Statistics
Matches: 136, Mismatches: 29, Indels: 36
0.68 0.14 0.18
Matches are distributed among these distances:
8 1 0.01
9 25 0.18
10 23 0.17
11 73 0.54
12 4 0.03
13 9 0.07
14 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (11 bp):
TATATATATAC
Found at i:566128 original size:22 final size:22
Alignment explanation
Indices: 566008--566356 Score: 121
Period size: 22 Copynumber: 16.7 Consensus size: 22
565998 TAGTTTATTA
*
566008 ATATAAACTATATATAAACTAT
1 ATATATACTATATATAAACTAT
* *
566030 A-A-AGT-GTATATATAAAGTAT
1 ATATA-TACTATATATAAACTAT
*
566050 ATAAACTA-TATATATAAACTAT
1 ATATA-TACTATATATAAACTAT
* * *
566072 ATAGT-T--TATATTTATATTAT
1 ATA-TATACTATATATAAACTAT
566092 -TATATACTATATATAAACTAT
1 ATATATACTATATATAAACTAT
* *
566113 ATATATATTATGTATAAACTAT
1 ATATATACTATATATAAACTAT
* * *
566135 AGA-GT-CTATATATGAA-T-T
1 ATATATACTATATATAAACTAT
566153 AT-TGA-ACTATATATAAACTAT
1 ATAT-ATACTATATATAAACTAT
*
566174 ATAGTTTACTA-ATATAAA-T-T
1 ATA-TATACTATATATAAACTAT
* *
566194 ATATAGT-TTATATATAAATTAT
1 ATATA-TACTATATATAAACTAT
* *
566216 ATAT-TAATTATATTTAAA-TAT
1 ATATAT-ACTATATATAAACTAT
* * **
566237 ATACA-ACT-TTTATTTA-TAT
1 ATATATACTATATATAAACTAT
* *
566256 AT-TAT-GTATAATTATAAATTAT
1 ATATATACTAT-A-TATAAACTAT
*
566278 ATATATACTATGTATAAA-T-T
1 ATATATACTATATATAAACTAT
* *
566298 ATATAGT-TTATATATAAAGTAT
1 ATATA-TACTATATATAAACTAT
*
566320 ATA-AGTA-TATCTATAAACTAT
1 ATATA-TACTATATATAAACTAT
*
566341 AAATTATA-TATATATA
1 ATA-TATACTATATATA
566357 TAAAGTGTAT
Statistics
Matches: 245, Mismatches: 45, Indels: 74
0.67 0.12 0.20
Matches are distributed among these distances:
18 5 0.02
19 27 0.11
20 65 0.27
21 50 0.20
22 86 0.35
23 9 0.04
24 3 0.01
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (22 bp):
ATATATACTATATATAAACTAT
Found at i:566129 original size:63 final size:61
Alignment explanation
Indices: 566036--566219 Score: 187
Period size: 61 Copynumber: 3.0 Consensus size: 61
566026 CTATAAAGTG
* *
566036 TATATATAAAGTATATAAACTATATATATAAACTATATAGTTTATATTTATATTATTATATAC
1 TATATATAAACTATATATA-TATATATATAAACTATATAGTTTATATTTA-ATTATTATATAC
* * * * *
566099 TATATATAAACTATATATATATTATGTATAAACTATAGAGTCTATATATGAATTATT-GA-AC
1 TATATATAAACTATATATATA-TATATATAAACTATATAGTTTATAT-TTAATTATTATATAC
* * *
566160 TATATATAAACTATATAGTTTACTA-ATATAAATTATATAGTTTATATATAAATTA-TATAT
1 TATATATAAACTATATA-TATA-TATATATAAACTATATAGTTTATAT-TTAATTATTATAT
566220 TAATTATATT
Statistics
Matches: 101, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
60 1 0.01
61 45 0.45
62 8 0.08
63 45 0.45
64 2 0.02
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (61 bp):
TATATATAAACTATATATATATATATATAAACTATATAGTTTATATTTAATTATTATATAC
Found at i:566163 original size:334 final size:332
Alignment explanation
Indices: 565478--566174 Score: 949
Period size: 334 Copynumber: 2.0 Consensus size: 332
565468 ACTACCTGAG
*
565478 ATATATATAAACTATAAATTATACATATATAATAATATAAAGTATATTATATATATATAAAGTAT
1 ATATATATAAACTATAAATAATACATATATAATAATATAAAGTATATTATATATATATAAAGTAT
565543 AATTATAAAGACTAAAGTATATAAGTATATAATATAAAGTATATAAGAATATAAACTACATAGTT
66 AATTATAAAGACTAAAGTATATAAGTATATAATATAAAGTATATAAGAATATAAACTACATAGTT
565608 TATATTTATAATATTATATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTATT
131 TATATTTATAATATTATATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTATT
* * * ** *
565673 AATATAAATTATATAGTTTATATATAAATTATATATGAATTATATTTGAATATATACATCTTATA
196 AATATAAACTATATA--TTAAATATAAATTATATATAAATTATAACTGAATATATACAACTTATA
* * * *** * *
565738 TTTATATATTATGCATAATTATAAGTTATATATACTATGTATAAATTATATAGTTTATATAGTTT
259 TTTATATATTAT-CATAATTATAACTTATATAAACTATATATAAATTATATAAACTATAGAGTCT
*
565803 AAATATAAAGT
323 -AATATAAAGA
565814 ATATATATAAACTATAAATAATACATATATAATAATATAAAGTATA-T-TATATATATAAAGTAT
1 ATATATATAAACTATAAATAATACATATATAATAATATAAAGTATATTATATATATATAAAGTAT
565877 AATTATAAAGACTAAAGTATATAAGTATATAATATAAAGTATATAAGAATATAAACTACATAGTT
66 AATTATAAAGACTAAAGTATATAAGTATATAATATAAAGTATATAAGAATATAAACTACATAGTT
* *
565942 TATATTTATATTATTATATACTCTATATAAACTATATATATTATGTATAAACTATATAGTTTATT
131 TATATTTATAATATTATATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTATT
566007 AATATAAACTATATA-TAAACTATAAAGTGTATATATAAAGTATATAAACT-ATATATATA-AAC
196 AATATAAACTATATATTAAA-TATAAA-T-TATATATAAA-T-TAT-AACTGA-ATATATACAAC
* *
566069 TATATAGTTTATAT-TTAT-ATTATTATATACTATATATAAACTATATATATATTATGTATAAAC
254 T-TATA-TTTATATATTATCATAATTATA-ACT-TATATAAACTATATATAAATTA--TATAAAC
566132 TATAGAGTCTATATATGAATTATTGA
313 TATAGAGTCTA-ATAT-AA--A--GA
566158 ACTATATATAAACTATA
1 A-TATATATAAACTATA
566175 TAGTTTACTA
Statistics
Matches: 321, Mismatches: 20, Indels: 31
0.86 0.05 0.08
Matches are distributed among these distances:
331 3 0.01
332 6 0.02
333 1 0.00
334 167 0.52
335 10 0.03
336 54 0.17
337 36 0.11
338 8 0.02
339 16 0.05
340 2 0.01
342 1 0.00
344 2 0.01
345 15 0.05
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.42
Consensus pattern (332 bp):
ATATATATAAACTATAAATAATACATATATAATAATATAAAGTATATTATATATATATAAAGTAT
AATTATAAAGACTAAAGTATATAAGTATATAATATAAAGTATATAAGAATATAAACTACATAGTT
TATATTTATAATATTATATACTATATATAAACTATATATATTATGTATAAACTATATAGTTTATT
AATATAAACTATATATTAAATATAAATTATATATAAATTATAACTGAATATATACAACTTATATT
TATATATTATCATAATTATAACTTATATAAACTATATATAAATTATATAAACTATAGAGTCTAAT
ATAAAGA
Found at i:566173 original size:11 final size:11
Alignment explanation
Indices: 565965--566239 Score: 88
Period size: 11 Copynumber: 26.4 Consensus size: 11
565955 TTATATACTC
565965 TATATAAACTA
1 TATATAAACTA
*
565976 TATAT--ATTA
1 TATATAAACTA
*
565985 TGTATAAACTA
1 TATATAAACTA
** *
565996 TATAGTTTATTA
1 TATA-TAAACTA
566008 -ATATAAACTA
1 TATATAAACTA
566018 TATATAAACTA
1 TATATAAACTA
***
566029 TA-A-AGTGTA
1 TATATAAACTA
*
566038 TATATAAA--G
1 TATATAAACTA
566047 TATATAAACTATA
1 TATATAAAC--TA
566060 TATATAAACTA
1 TATATAAACTA
*
566071 TATAGT---TTA
1 TATA-TAAACTA
* * *
566080 TATTTATATTA
1 TATATAAACTA
*
566091 T-TATATACTA
1 TATATAAACTA
566101 TATATAAACTA
1 TATATAAACTA
* *
566112 TATATATATTA
1 TATATAAACTA
*
566123 TGTATAAACTA
1 TATATAAACTA
*
566134 TAGAGT---CTA
1 TATA-TAAACTA
*
566143 TATATGAA-T-
1 TATATAAACTA
*
566152 TAT-TGAACTA
1 TATATAAACTA
566162 TATATAAACTA
1 TATATAAACTA
**
566173 TATAGTTTACTA
1 TATA-TAAACTA
566185 -ATATAAA-T-
1 TATATAAACTA
***
566193 TATATAGTTTA
1 TATATAAACTA
*
566204 TATATAAATTA
1 TATATAAACTA
* *
566215 TATATTAATTA
1 TATATAAACTA
*
566226 TATTTAAA-TA
1 TATATAAACTA
566236 TATA
1 TATA
566240 CAACTTTTAT
Statistics
Matches: 195, Mismatches: 43, Indels: 53
0.67 0.15 0.18
Matches are distributed among these distances:
8 6 0.03
9 41 0.21
10 26 0.13
11 102 0.52
12 11 0.06
13 9 0.05
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (11 bp):
TATATAAACTA
Found at i:566190 original size:61 final size:63
Alignment explanation
Indices: 566036--566215 Score: 206
Period size: 63 Copynumber: 2.9 Consensus size: 63
566026 CTATAAAGTG
* * * * *
566036 TATATATAAAGTATATAAACTA-TATATATAAACTATATAGTTTATATTTATATTATTATATAC
1 TATATATAAACTATATATA-TACTATATATAAACTATATAGTTTATATATAAATTATTAGATAC
* * * * *
566099 TATATATAAACTATATATATATTATGTATAAACTATAGAGTCTATATATGAATTATT-GA-AC
1 TATATATAAACTATATATATACTATATATAAACTATATAGTTTATATATAAATTATTAGATAC
* *
566160 TATATATAAACTATATAGTTTACTA-ATATAAATTATATAGTTTATATATAAATTAT
1 TATATATAAACTATATA-TATACTATATATAAACTATATAGTTTATATATAAATTAT
566216 ATATTAATTA
Statistics
Matches: 99, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
61 45 0.45
62 8 0.08
63 46 0.46
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (63 bp):
TATATATAAACTATATATATACTATATATAAACTATATAGTTTATATATAAATTATTAGATAC
Found at i:566216 original size:9 final size:10
Alignment explanation
Indices: 566185--566314 Score: 51
Period size: 11 Copynumber: 12.8 Consensus size: 10
566175 TAGTTTACTA
566185 ATATA-AATT
1 ATATATAATT
566194 ATATAGT--TT
1 ATATA-TAATT
566203 ATATATAAATT
1 ATATAT-AATT
566214 ATATATTAATT
1 ATATA-TAATT
* *
566225 ATATTTAAAT
1 ATATATAATT
*
566235 ATATACAACTTTT
1 ATATATAA---TT
*
566248 ATTTATATATT
1 ATATATA-ATT
*
566259 ATGTATAA-T
1 ATATATAATT
566268 -TATA-AATT
1 ATATATAATT
*
566276 ATATATATACT
1 ATATATA-ATT
*
566287 ATGTATAAATT
1 ATATAT-AATT
566298 ATATAGT--TT
1 ATATA-TAATT
566307 ATATATAA
1 ATATATAA
566315 AGTATATAAG
Statistics
Matches: 90, Mismatches: 13, Indels: 35
0.65 0.09 0.25
Matches are distributed among these distances:
7 2 0.02
8 6 0.07
9 24 0.27
10 12 0.13
11 36 0.40
12 3 0.03
13 6 0.07
14 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.49
Consensus pattern (10 bp):
ATATATAATT
Found at i:566260 original size:45 final size:45
Alignment explanation
Indices: 566200--566285 Score: 111
Period size: 45 Copynumber: 1.9 Consensus size: 45
566190 AATTATATAG
*
566200 TTTATATATAAATTATATATTAATTAT-ATTTAAATATATACAACT
1 TTTATATATAAATTATATA-TAATTATAAATTAAATATATACAACT
* * * *
566245 TTTATTTATATATTATGTATAATTATAAATTATATATATAC
1 TTTATATATAAATTATATATAATTATAAATTAAATATATAC
566286 TATGTATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 7 0.20
45 28 0.80
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (45 bp):
TTTATATATAAATTATATATAATTATAAATTAAATATATACAACT
Found at i:566277 original size:28 final size:29
Alignment explanation
Indices: 566246--566313 Score: 86
Period size: 28 Copynumber: 2.4 Consensus size: 29
566236 TATACAACTT
* *
566246 TTATTTATATATTATGTAT-AATTATAAA
1 TTATATATATACTATGTATAAATTATAAA
*
566274 TTATATATATACTATGTATAAATTATATAG
1 TTATATATATACTATGTATAAATTATA-AA
566304 TT-TATATATA
1 TTATATATATA
566314 AAGTATATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
28 17 0.49
29 15 0.43
30 3 0.09
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (29 bp):
TTATATATATACTATGTATAAATTATAAA
Found at i:566588 original size:13 final size:13
Alignment explanation
Indices: 566570--566596 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
566560 CATAGTTGAA
566570 CAGTCTTCATATG
1 CAGTCTTCATATG
566583 CAGTCTTCATATG
1 CAGTCTTCATATG
566596 C
1 C
566597 GCATCTGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:566634 original size:14 final size:15
Alignment explanation
Indices: 566615--566644 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
566605 AATGGGAATT
566615 AATCCTTGC-TAAAA
1 AATCCTTGCGTAAAA
566629 AATCCTTGCGTAAAA
1 AATCCTTGCGTAAAA
566644 A
1 A
566645 TCTCTGCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.27
Consensus pattern (15 bp):
AATCCTTGCGTAAAA
Found at i:570960 original size:2 final size:2
Alignment explanation
Indices: 570941--572289 Score: 232
Period size: 2 Copynumber: 676.5 Consensus size: 2
570931 TAAGTATTAA
* * * * * *
570941 AT AT AA AT AT AT AC AT AT AT AT AT AA AGT AC A- AA AGT AT AT AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT
*
570984 AGT AT AT AT AT AT AT AA AGT AT A- AGT AT AT -T AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT
* * * *
571025 AT AT AT AT AT AT AA AGT AT A- AT -T AT AA AG A- AT AA AGT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT
* *
571066 A- AGT AT AT A- AT AT AA AGT AT AT A- AGT AT AT A- AT AT AA AT
1 AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT
* * * *
571105 AT AT A- AGT AT -T A- AT AT A- AGT AT AT AC GT AT AT AT AA AC AT
1 AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
* *
571145 AA ACT AT AA AGT AT A- AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
571187 AT AT AT AT AT ACT TT AT AT -T AT AT -T CT -T AT AT ACT TT AT -T
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * * * *
571227 CT TT AT A- AT -T AT ACT CT CT CT AT AT AT AT ACT -T AT ACT TT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T AT
* * * *
571267 AT AT -T AT AT AT GT AT AT AT AT GT GT AT AT AT AT AT ACT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * * *
571309 AGT TT AT AT AT AT ACT -T AT AT ACT TT AT AT -T AT AT AC GT AT
1 A-T AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT AT AT AT
* *
571350 AT AT AT AT ACT -T AT AT -T TT AT AT AT AT CT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
571391 AT AT AT AC AT AT ACT TT AT AT -T AT -T AT AT AC GT GT AT AT AT
1 AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
571432 AT A- AT -T AT AT -T TT AT AT -T AT -T AT AT AT GT AT AT AC ACT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T
* * * *
571470 TT AT ACT A- AA AT -T AT AT AT AT AT AC ACT -T A- AT AGT TT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT
* * * *
571509 AT ACT -T AT AT AT -T TT AT AT TT A- AT ACT -T AT AT TT A- AT GT
1 AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* * * *
571548 TT AT AT ACT TT AT AT -T AT -T AT AT AT GT AT AT AT AT -T TT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
571588 AT TT AT AT ACT -T AT AT AC ACT -T TT AT AT AT AT AT AT AT A- AT
1 AT AT AT AT A-T AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
571629 AT ACT -T AT ACT -T AT ACT -T AT ACT TT AT AT -T AT -T AT AT AT
1 AT A-T AT AT A-T AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT
* * * *
571668 GT AT GT AT ACT TT AT ACT A- AA ACT AT AT AT AT AT AT ACT -T AT
1 AT AT AT AT A-T AT AT A-T AT AT A-T AT AT AT AT AT AT A-T AT AT
* * * *
571710 ACT TT GT AGT TT AT AT AT AT AT AT AT AT ACT -T AT ACT -T GT ACT
1 A-T AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT A-T
* * *
571753 TT AT AT ACT -T AT AT AC CT -T AT AT -T AT AT ACT -T AT AT ACT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T
* * * * *
571792 TT AGT CT TT AT A- AT -T GT AGT TT AT AT AT AT AT A- AT AT ACT
1 AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T
* * *
571832 -T AT ACT TT AT AT TT A- AT ACT -T AT AT ACT TT AT AT -T AT AT
1 AT AT A-T AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT AT AT AT
* * * * * *
571871 AC CT AT AT AC AT -T TT AT A- AT A- AA ACT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT
* *
571911 AT AT AT AT AT AT ACT TT AT AT ACT -T AT AT ACT TT AT AT A- AT
1 AT AT AT AT AT AT A-T AT AT AT A-T AT AT AT A-T AT AT AT AT AT
* *
571952 -T AT ACT TT AT AT AT AT AT AT AGT AT ACT -T AT ACT TT AT AT -T
1 AT AT A-T AT AT AT AT AT AT AT A-T AT A-T AT AT A-T AT AT AT AT
* * *
571993 AT -T AT AT AT GT AT AT AT ACT TT AT ACT A- AT ACT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT A-T AT AT AT AT
* * * *
572034 AT GT A- AGT AT AT A- AT AT AT A- AT AT AT AT AA AGT TT AT GT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
* * * *
572075 AA AGT AT AT AT AT -T TT AT AGT TT AT AT AT AT ACT -T AT ACT TT
1 AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT A-T AT
* * * *
572117 AT AGT TT AT AT AT AT AT AT AT AT ACT TT AT ACT TT AA AGT AT AT
1 AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT A-T AT AT
* * * *
572161 AT AC CT -T AT AGT TT AT AT AT AT AT AT ACT TT AT AGT AT A- AT
1 AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT
* * * * *
572202 AT AA AT AT AT AA AGT TT AT GT AT A- AGT AT AT AT AT -T TT AT AGT
1 AT AT AT AT AT AT A-T AT AT AT AT AT A-T AT AT AT AT AT AT AT A-T
* * *
572245 TT AT AT AT AT ACT -T AT ACT TT AT AGT TT AT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT
572287 AT A
1 AT A
572290 CTTTATACTT
Statistics
Matches: 970, Mismatches: 201, Indels: 352
0.64 0.13 0.23
Matches are distributed among these distances:
1 90 0.09
2 795 0.82
3 85 0.09
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:571050 original size:170 final size:169
Alignment explanation
Indices: 570816--571197 Score: 489
Period size: 170 Copynumber: 2.3 Consensus size: 169
570806 GAAAAGCGTA
*
570816 ATATATAATAATATAAAGTATAAGTATA-TATATATATATATAAATATATAAAAAGTATAATTAT
1 ATATAT-AT-ATATAAAGTATAAGTATATTATATATATATATATATATATAAAAAGTATAATTAT
* *
570880 AAAGACTAAAGTATATAAG-CTAT-A-ACAAAG-TACAA-TATATAATATAAATA-ATAAGTATT
64 AAAGAATAAAGTATATAAGTATATAATACAAAGATACAAGTATATAATATAAATATATAAGTATT
570939 AAATATAAATATATACATATATATATAA-AGTACAAAAGTATATAAAGT
129 -AATATAAATATATACATATATATA-AACA-T---AAA--ATATAAAGT
*
570987 ATATATATATATAAAGTATAAGTATATTATATATATATATATATATATATAAAGTATAATTATAA
1 ATATATATATATAAAGTATAAGTATATTATATATATATATATATATATAAAAAGTATAATTATAA
* *
571052 AGAATAAAGTATATAAGTATATAATATAAAGTATATAAGTATATAATATAAATATATAAGTATTA
66 AGAATAAAGTATATAAGTATATAATACAAAG-ATACAAGTATATAATATAAATATATAAGTATTA
* * *
571117 ATATAAGTATATACGTATATATAAACATAAACTATAAAGT
130 ATATAAATATATACATATATATAAACATAAAATATAAAGT
*
571157 ATA-ATATATATATA-TATATA-TATATTATATATATATATATA
1 ATATATATATATAAAGTATA-AGTATATTATATATATATATATA
571198 CTTTATATTA
Statistics
Matches: 191, Mismatches: 10, Indels: 23
0.85 0.04 0.10
Matches are distributed among these distances:
168 25 0.13
169 29 0.15
170 65 0.34
171 9 0.05
172 4 0.02
173 5 0.03
175 7 0.04
176 38 0.20
177 9 0.05
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.37
Consensus pattern (169 bp):
ATATATATATATAAAGTATAAGTATATTATATATATATATATATATATAAAAAGTATAATTATAA
AGAATAAAGTATATAAGTATATAATACAAAGATACAAGTATATAATATAAATATATAAGTATTAA
TATAAATATATACATATATATAAACATAAAATATAAAGT
Found at i:571775 original size:46 final size:45
Alignment explanation
Indices: 571725--572035 Score: 155
Period size: 45 Copynumber: 7.2 Consensus size: 45
571715 GTAGTTTATA
*
571725 TATATATATATATACTTATACTTGTACTTTATATACTTATATAC-C
1 TATATATATATATACTTATACTT-TACTTTATATACTTATATACTT
*
571770 T-TATAT-TATATACTTATATACTTTAGTCTTTATA-A-TTGTAGT--TT
1 TATATATATATATAC-T-TATACTTTA--CTTTATATACTTATA-TACTT
*
571814 ATATATATATAATATACTTATACTTTATATTTA-ATACTTATATAC-T
1 -TATATATAT-ATATACTTATACTTTA-CTTTATATACTTATATACTT
* * *
571860 T-TATAT-TATATACCTATA---TACATTT-TATA-ATA-AAACTT
1 TATATATATATATACTTATACTTTAC-TTTATATACTTATATACTT
571898 TATATATATATATA-TATATA-TATATACTTTATATACTTATATACTT
1 TATATATATATATACT-TATACT-T-TACTTTATATACTTATATACTT
*
571944 TATATA-AT-TATACTTTATA-TATATA-TATAGTATAC-T-TATACTT
1 TATATATATATATAC-TTATACT-T-TACTTTA-TATACTTATATACTT
*
571987 TATAT-TATTATATA-TGTATA-TATAC-TT-TATAC-TA-ATACTT
1 TATATATA-TATATACT-TATACTTTACTTTATATACTTATATACTT
572027 TATATATAT
1 TATATATAT
572036 GTAAGTATAT
Statistics
Matches: 215, Mismatches: 14, Indels: 79
0.70 0.05 0.26
Matches are distributed among these distances:
37 3 0.01
38 4 0.02
39 13 0.06
40 28 0.13
41 2 0.01
42 13 0.06
43 25 0.12
44 39 0.18
45 42 0.20
46 38 0.18
47 2 0.01
48 6 0.03
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.51
Consensus pattern (45 bp):
TATATATATATATACTTATACTTTACTTTATATACTTATATACTT
Found at i:571788 original size:61 final size:59
Alignment explanation
Indices: 571507--572017 Score: 118
Period size: 59 Copynumber: 8.7 Consensus size: 59
571497 TTAATAGTTT
* * **
571507 ATATAC-TTATATAT-TTTATATTTAATACTTATA-TTTA-ATGTTTATATACTT-TAT-
1 ATATACTTTATATATATATATACTT-ATACTTATACTTTATATACTTATATACTTATATA
* * *
571561 AT-TA--TTATATATGTATATA--TAT-TTTATA-TTTATATACTTATATACACTTTTAT-
1 ATATACTTTATATATATATATACTTATACTTATACTTTATATACTTATAT--ACTTATATA
*
571614 ATATA-TATATATAATATACTTATACTTATACTTATACTTTATATTA-TTATATA-TGTATGTAT
1 ATATACTTTATAT-ATATA--TATACTTATACTTATACTTTATA-TACTTATATACT-TA--TAT
571676 A
59 A
* * * *
571677 CTTTATACTAAAACTATATATATATATACTTATACTTTGTAGTTTATATA-TATATATA-TATAC
1 --ATATACT----TTATATATATATATACTTATAC-TTATACTTTATATACT-TATATACT-TA-
571740 TTATA
56 -TATA
* * *
571745 CTTGTACTTTATATACT-TATATACCTTATATTATATAC-TTATATACTT-TAGT-CTT-TATA
1 -ATATACTTTATATA-TATATATA-CTTATACT-TATACTTTATATACTTATA-TACTTATATA
* *
571804 ATTGTAGTTTATATATATATA-A--TATACTTATACTTTATAT--TTA-ATACTTATATA
1 A-TATACTTTATATATATATATACTTATACTTATACTTTATATACTTATATACTTATATA
* * * * * * *
571858 CTTTA-TATTATATACCTATATACATTTTATAATAAAACTTTATATA--TATATA-TATATATA
1 ATATACT-TTATATA--TATATATA-CTTATACTTATACTTTATATACTTATATACT-TATATA
*
571918 TATATACTTTATATACT-TATATACTTTATATAATTATACTTTATATA--TATATA--TAGTATA
1 -ATATACTTTATATA-TATATATAC--T-TATACTTATACTTTATATACTTATATACTTA-TATA
*
571978 CTTATACTTTATAT-TATTATATA-TGTATA--TATACTTTATA
1 -ATATACTTTATATATA-TATATACT-TATACTTATACTTTATA
572018 CTAATACTTT
Statistics
Matches: 361, Mismatches: 38, Indels: 115
0.70 0.07 0.22
Matches are distributed among these distances:
49 9 0.02
50 10 0.03
51 1 0.00
52 14 0.04
53 28 0.08
54 13 0.04
55 33 0.09
56 5 0.01
57 5 0.01
58 7 0.02
59 46 0.13
60 39 0.11
61 38 0.11
62 19 0.05
63 25 0.07
64 11 0.03
65 4 0.01
66 1 0.00
67 20 0.06
68 23 0.06
69 5 0.01
70 5 0.01
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (59 bp):
ATATACTTTATATATATATATACTTATACTTATACTTTATATACTTATATACTTATATA
Found at i:572029 original size:129 final size:131
Alignment explanation
Indices: 571863--572199 Score: 311
Period size: 129 Copynumber: 2.5 Consensus size: 131
571853 ATATACTTTA
** * * *
571863 TATTATATACCTATATACATTTTATAATAAAACTTTATATATATATATATATATATATATACTTT
1 TATTATATATATATATATACTTTATACT-AAACTTTATATATATATATATATATATATATACTTT
*
571928 ATATACTTATATACTTTA-TAT-AA-T-TATACT-TTATATA-TATATATAGTATACTTATACTT
65 ATATA--TATAAACTTTAGTATAAAGTATATA-TATTATATAGTATATATA-TATACTTATACTT
571987 TATA-T
126 TATAGT
* *
571992 TATTATATATGTATATATACTTTATACTAATACTTTATATATATGTA-AGTATATA-ATATA--T
1 TATTATATATATATATATACTTTATACTAA-ACTTTATATATATATATA-TATATATATATACTT
* * * *
572053 AATATATATAAAGTTTATGTATAAAGTATATATATTTTATAGTTTATATATATACTTATACTTTA
64 TATATATATAAACTTTA-GTATAAAGTATATATATTATATAGTATATATATATACTTATACTTTA
572118 TAGT
128 TAGT
* * *
572122 T-TATATATATATATATATACTTTATACTTTAAAGTATATATACCTTATAGTTTATATATATATA
1 TAT-TATATATATATATATACTTTATAC--TAAACTTTATATA---TATA-TATATATATATATA
572186 TACTTTATAGTATA
59 TACTTTATA-TATA
572200 ATATAAATAT
Statistics
Matches: 169, Mismatches: 17, Indels: 34
0.77 0.08 0.15
Matches are distributed among these distances:
124 9 0.05
126 9 0.05
127 2 0.01
128 10 0.06
129 72 0.43
130 32 0.19
131 8 0.05
132 3 0.02
134 3 0.02
135 7 0.04
136 6 0.04
138 4 0.02
139 4 0.02
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (131 bp):
TATTATATATATATATATACTTTATACTAAACTTTATATATATATATATATATATATATACTTTA
TATATATAAACTTTAGTATAAAGTATATATATTATATAGTATATATATATACTTATACTTTATAG
T
Found at i:572255 original size:149 final size:153
Alignment explanation
Indices: 571944--572345 Score: 588
Period size: 149 Copynumber: 2.6 Consensus size: 153
571934 TTATATACTT
* * *
571944 TATATAATTATACTTTATA-TATATATATAGTATACT-TATACTTTATATTATTATATATGTATA
1 TATATACTTATACTTTATAGTTTATATATA-TATA-TATATACTTTATACT-TTA-A-A-GTATA
* * * * *
572007 TATACTTTATA-CTAATACTTTATATATA-TGTA-AGTATATAATATATAATATATATAAAGTTT
60 TATACCTTATAGTTTATA-TATATATATACTTTATAG--TATAATATATAATATATATAAAGTTT
572069 ATGTATAAAGTATATATATTTTATAGTTTATA
122 ATGTATAAAGTATATATATTTTATAGTTTATA
572101 TATATACTTATACTTTATAGTTTATATATATATATATATACTTTATACTTTAAAGTATATATACC
1 TATATACTTATACTTTATAGTTTATATATATATATATATACTTTATACTTTAAAGTATATATACC
572166 TTATAGTTTATATATATATATACTTTATAGTAT-A-ATATAA-ATATATAAAGTTTATGTAT-AA
66 TTATAGTTTATATATATATATACTTTATAGTATAATATATAATATATATAAAGTTTATGTATAAA
572227 GTATATATATTTTATAGTTTATA
131 GTATATATATTTTATAGTTTATA
572250 TATATACTTATACTTTATAGTTTATATATATATATATATACTTTATACTTTAAAGTATATATACC
1 TATATACTTATACTTTATAGTTTATATATATATATATATACTTTATACTTTAAAGTATATATACC
572315 TTATAGTTTATATATATATATACTTTATAGT
66 TTATAGTTTATATATATATATACTTTATAGT
572346 TTACACATTA
Statistics
Matches: 232, Mismatches: 8, Indels: 18
0.90 0.03 0.07
Matches are distributed among these distances:
149 121 0.52
150 19 0.08
151 6 0.03
152 1 0.00
153 27 0.12
154 8 0.03
155 3 0.01
156 4 0.02
157 34 0.15
158 9 0.04
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (153 bp):
TATATACTTATACTTTATAGTTTATATATATATATATATACTTTATACTTTAAAGTATATATACC
TTATAGTTTATATATATATATACTTTATAGTATAATATATAATATATATAAAGTTTATGTATAAA
GTATATATATTTTATAGTTTATA
Found at i:572669 original size:26 final size:25
Alignment explanation
Indices: 572633--572688 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 25
572623 CTTTATATAC
*
572633 ATATATAAAGTATAAAGTATATGTAT
1 ATATATAAAGTATAAAGTACAT-TAT
*
572659 ATATATAAAGTATAATGTACATTAT
1 ATATATAAAGTATAAAGTACATTAT
572684 ATATA
1 ATATA
572689 CATGCATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.50, C:0.02, G:0.09, T:0.39
Consensus pattern (25 bp):
ATATATAAAGTATAAAGTACATTAT
Found at i:572684 original size:19 final size:19
Alignment explanation
Indices: 572643--572686 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 19
572633 ATATATAAAG
*
572643 TATAAAGTATATGTATATA
1 TATAAAGTATATGTACATA
572662 TATAAAGTATAATGTACATTA
1 TATAAAGTAT-ATGTACA-TA
572683 TATA
1 TATA
572687 TACATGCATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.45
20 6 0.27
21 6 0.27
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (19 bp):
TATAAAGTATATGTACATA
Found at i:573069 original size:24 final size:24
Alignment explanation
Indices: 573040--573085 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
573030 TTAGTCCATT
573040 TTTTAT-ATTAATATCAACTTCACA
1 TTTTATAATTAAT-TCAACTTCACA
*
573064 TTTTATAATTAATTCAATTTCA
1 TTTTATAATTAATTCAACTTCA
573086 TCTCTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTATAATTAATTCAACTTCACA
Found at i:573197 original size:2 final size:2
Alignment explanation
Indices: 573190--573231 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
573180 AAAGTATAAG
573190 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
573232 AAGTATAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:573286 original size:20 final size:20
Alignment explanation
Indices: 573245--573292 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
573235 TATAATGTAC
573245 ATTATATATACATGCATCAT
1 ATTATATATACATGCATCAT
* *
573265 ATTATCATA-ACATTCATTAT
1 ATTAT-ATATACATGCATCAT
573285 A-TATATAT
1 ATTATATAT
573293 TATAATTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 3 0.12
19 3 0.12
20 15 0.62
21 3 0.12
ACGTcount: A:0.42, C:0.12, G:0.02, T:0.44
Consensus pattern (20 bp):
ATTATATATACATGCATCAT
Found at i:573421 original size:544 final size:534
Alignment explanation
Indices: 572509--573759 Score: 1878
Period size: 540 Copynumber: 2.3 Consensus size: 534
572499 ATTATACATA
** * *
572509 TTATATTAATATCAGCTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGTGTGGTCC
1 TTATATTAATATCAGCTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGAATGTTGC
572574 TTAATTTATTCAATTTTTATTTCCAATTTCATGTTTGTTCAATTTGGTACTTTATATACATATAT
66 TTAATTTATTCAATTTTTATTTCCAATTTCATGTTTGTTCAATTTGGTACTTTATATACATATAT
* * * * **
572639 AAAGTATAAAGTATATGTATATATATA-A-A-GTATA-ATGTACAT-TATATATACATGCATCAT
131 AAACTATAAAGTATAAGTATATATATATATATGTATATATATATATATATATATACATAAATCAT
* **
572699 ATTATCATTACATTCATTATGCATATTACATATTATATATATATATATATATTATAATTATTTTA
196 ATTATCATTACATTCATCATGCATATTACATAACATATATATATATATATATTATAATTATTTTA
* * * *
572764 AGTTTCCTCAACTTTTGAAATTAATGCAATTCAGTTCATTTTACAATTTTTGTTTGATTTGATCC
261 AGTTTCCCCAACTTCTGAAATTAATGCAATTCAGTCCATTTTACAATTTTTGTTTGATTTGATAC
*
572829 TTTTATGTTGTTTATTGTATTTAAATTTTAATTTGTAATTTTATATTTGTTCAATTTAGTCCTTC
326 TTTTATGTTGTTTATTGTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTC
*
572894 AAACTATATTTGTATCTGAAATTGACCCATACTTATTTATATTTTTGTAATGTACTTAAAACAAA
391 AAACTATATTTGTATATGAAATTGACCCATACTTATTTATATTTTTGTAATGTACTT---A-AAA
* *
572959 CCCTATAAAATGTAAATCATATAATAAATTTCTTTTCAAATTATGTTAACCAAC-TTTTAAATGT
452 CCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTAACCAACTTTTTAAATGT
573023 ATGCAATTTAGTCCATTTT
517 ATGCAATTTAGTCCA-TTT
* * *
573042 TTATATTAATATCAACTTCACATTTTATAATTAATTCAATTTCATCTCTCATCAATGCATGTTGC
1 TTATATTAATATCAGCTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGAATGTTGC
573107 TTAATTTATTCAATTTGTTATTTCCAATTTCATGTTTGTTCAATTTGGTACTTTATATACATATA
66 TTAATTTATTCAATTT-TTATTTCCAATTTCATGTTTGTTCAATTTGGTACTTTATATACATATA
* *
573172 TAAACTATAAAGTATAAGTATATATATATATATATATATATATATATATATATATATATAAAGT-
130 TAAACTATAAAGTATAAGTATATATATATATATGTATATATATATATATATATATACATAAA-TC
*
573236 ATAATGTA-CATTATATATACATGCAT-CATATTATCATAACAT-TCAT-TATATATATATTATA
194 AT-AT-TATCATTACAT-T-CAT-CATGCATATTA-CATAACATAT-ATATATATATATATTATA
* * * *
573297 ATTGTTTTAATTTTCCCCCAACTTCTGAAATTAATGTAATTCAGTCCATTTTACAATTTTTTTTT
252 ATTATTTTAAGTTT-CCCCAACTTCTGAAATTAATGCAATTCAGTCCATTTTACAA-TTTTTGTT
*
573362 TGATTTGATATTTTTATGTTGTTTATTGTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAA
315 TGATTTGATACTTTTATGTTGTTTATTGTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAA
* * *
573427 TTTAGTCCTTCAAATTATATTTGTATATGAAATTGACCCATACTTATTTATATTTTTGTAGTTTA
380 TTTAGTCCTTCAAACTATATTTGTATATGAAATTGACCCATACTTATTTATATTTTTGTAATGTA
*
573492 CTTAAAACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTCACCAACTTTT
445 CTTAAAACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTAACCAACTTTT
573557 TAAATGTATGCAATTTAGTCCATTT
510 TAAATGTATGCAATTTAGTCCATTT
*
573582 TTATATTAATATCAGTTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAAT-AAGTGTTG
1 TTATATTAATATCAGCTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGAA-TGTTG
* *
573646 TTTAATTTATTCAATTTTTTATTTCCAATTTCATGTTTGTTCAATTTGATACTTTATATACATAT
65 CTTAATTTATTCAA-TTTTTATTTCCAATTTCATGTTTGTTCAATTTGGTACTTTATATACATAT
* * *
573711 ATAAACTATAAAGTATAAGTATATATGTATGTTTGTATATATATATATA
129 ATAAACTATAAAGTATAAGTATATATATATATATGTATATATATATATA
573760 AAGTATAAAG
Statistics
Matches: 654, Mismatches: 45, Indels: 31
0.90 0.06 0.04
Matches are distributed among these distances:
533 75 0.11
534 74 0.11
535 1 0.00
536 1 0.00
537 4 0.01
538 6 0.01
539 14 0.02
540 229 0.35
541 32 0.05
542 38 0.06
543 47 0.07
544 133 0.20
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (534 bp):
TTATATTAATATCAGCTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGAATGTTGC
TTAATTTATTCAATTTTTATTTCCAATTTCATGTTTGTTCAATTTGGTACTTTATATACATATAT
AAACTATAAAGTATAAGTATATATATATATATGTATATATATATATATATATATACATAAATCAT
ATTATCATTACATTCATCATGCATATTACATAACATATATATATATATATATTATAATTATTTTA
AGTTTCCCCAACTTCTGAAATTAATGCAATTCAGTCCATTTTACAATTTTTGTTTGATTTGATAC
TTTTATGTTGTTTATTGTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAGTCCTTC
AAACTATATTTGTATATGAAATTGACCCATACTTATTTATATTTTTGTAATGTACTTAAAACCCT
ATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTAACCAACTTTTTAAATGTATGC
AATTTAGTCCATTT
Found at i:573609 original size:24 final size:24
Alignment explanation
Indices: 573580--573625 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
573570 TTTAGTCCAT
*
573580 TTTTAT-ATTAATATCAGTTTCACA
1 TTTTATAATTAAT-TCAATTTCACA
573604 TTTTATAATTAATTCAATTTCA
1 TTTTATAATTAATTCAATTTCA
573626 TCCCTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.35, C:0.11, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTTATAATTAATTCAATTTCACA
Found at i:573773 original size:22 final size:21
Alignment explanation
Indices: 573748--573918 Score: 97
Period size: 22 Copynumber: 7.9 Consensus size: 21
573738 TATGTTTGTA
*
573748 TATATATATATAAAGTATAAAG
1 TATATAAATAT-AAGTATAAAG
573770 TATAT-AATATAAAGTAATAAAG
1 TATATAAATAT-AAGT-ATAAAG
* * **
573792 TGTTTGGATATAAGTATTAAAG
1 TATATAAATATAAGTA-TAAAG
573814 TATATAAATATAAGTATTAAA-
1 TATATAAATATAAGTA-TAAAG
*
573835 TATA-AAGTATATAAGTACATAAG
1 TATATAA--ATATAAGTATA-AAG
573858 TACTA-AAGTATATAA-TATAAAG
1 TA-TATAA--ATATAAGTATAAAG
*
573880 TAT-TAAACTATATAATAT-AAG
1 TATATAAA-TATA-AGTATAAAG
573901 TAT-TAAATATAAAGTATA
1 TATATAAATAT-AAGTATA
573919 TTAATTATCG
Statistics
Matches: 124, Mismatches: 11, Indels: 29
0.76 0.07 0.18
Matches are distributed among these distances:
19 1 0.01
20 13 0.10
21 30 0.24
22 59 0.48
23 9 0.07
24 12 0.10
ACGTcount: A:0.53, C:0.02, G:0.10, T:0.36
Consensus pattern (21 bp):
TATATAAATATAAGTATAAAG
Found at i:573780 original size:14 final size:14
Alignment explanation
Indices: 573763--573919 Score: 71
Period size: 14 Copynumber: 10.9 Consensus size: 14
573753 ATATATAAAG
573763 TATAAAGTATATAA
1 TATAAAGTATATAA
573777 TATAAAGTA-ATAA
1 TATAAAGTATATAA
*** *
573790 -AGTGTTTGGATATAA
1 TA-T-AAAGTATATAA
573805 GTATTAAAGTATATAA
1 -TA-TAAAGTATATAA
573821 -ATATAAGTAT-TAAA
1 TATA-AAGTATAT-AA
573835 TATAAAGTATATAA
1 TATAAAGTATATAA
*
573849 GTACATAAGTACTA-AA
1 -TATA-AAGTA-TATAA
573865 GTATATAA-TATA-AA
1 -TATA-AAGTATATAA
*
573879 GTATTAAACTATATAA
1 -TA-TAAAGTATATAA
573895 TAT-AAGTAT-TAAA
1 TATAAAGTATAT-AA
573908 TATAAAGTATAT
1 TATAAAGTATAT
573920 TAATTATCGT
Statistics
Matches: 113, Mismatches: 12, Indels: 35
0.71 0.08 0.22
Matches are distributed among these distances:
12 2 0.02
13 18 0.16
14 44 0.39
15 22 0.19
16 23 0.20
17 4 0.04
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.36
Consensus pattern (14 bp):
TATAAAGTATATAA
Found at i:573816 original size:8 final size:7
Alignment explanation
Indices: 573803--573918 Score: 73
Period size: 8 Copynumber: 16.0 Consensus size: 7
573793 GTTTGGATAT
573803 AAGTATTA
1 AAGTA-TA
573811 AAGTATA
1 AAGTATA
*
573818 TAAATAT-
1 -AAGTATA
573825 AAGTATTA
1 AAGTA-TA
573833 AA-TATA
1 AAGTATA
573839 AAGTATA
1 AAGTATA
*
573846 TAAGTACA
1 -AAGTATA
573854 TAAGTACTA
1 -AAGTA-TA
573863 AAGTATA
1 AAGTATA
573870 TAA-TATA
1 -AAGTATA
573877 AAGTATTA
1 AAGTA-TA
*
573885 AACTATA
1 AAGTATA
573892 TAA-TAT-
1 -AAGTATA
573898 AAGTATTA
1 AAGTA-TA
573906 AA-TATA
1 AAGTATA
573912 AAGTATA
1 AAGTATA
573919 TTAATTATCG
Statistics
Matches: 89, Mismatches: 5, Indels: 29
0.72 0.04 0.24
Matches are distributed among these distances:
5 2 0.02
6 16 0.18
7 29 0.33
8 41 0.46
9 1 0.01
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (7 bp):
AAGTATA
Found at i:573866 original size:52 final size:49
Alignment explanation
Indices: 573801--573919 Score: 143
Period size: 52 Copynumber: 2.3 Consensus size: 49
573791 GTGTTTGGAT
573801 ATAAGTATTAAAGTATATAA-ATATAAGTATTAAA-TATAAAGTATATAAGTA
1 ATAAGTA-TAAAGTATATAATATA-AAGTATTAAACTATAAA--ATATAAGTA
*
573852 CATAAGTACTAAAGTATATAATATAAAGTATTAAACTATATAATATAAGTA
1 -ATAAGTA-TAAAGTATATAATATAAAGTATTAAACTATAAAATATAAGTA
* *
573903 TTAAATATAAAGTATAT
1 ATAAGTATAAAGTATAT
573920 TAATTATCGT
Statistics
Matches: 61, Mismatches: 4, Indels: 7
0.85 0.06 0.10
Matches are distributed among these distances:
49 10 0.16
50 5 0.08
51 9 0.15
52 29 0.48
53 8 0.13
ACGTcount: A:0.54, C:0.03, G:0.08, T:0.35
Consensus pattern (49 bp):
ATAAGTATAAAGTATATAATATAAAGTATTAAACTATAAAATATAAGTA
Found at i:573946 original size:540 final size:540
Alignment explanation
Indices: 572509--573946 Score: 1341
Period size: 540 Copynumber: 2.7 Consensus size: 540
572499 ATTATACATA
* ** * *
572509 TTATATTAATATCAGCTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGTGTGGTCC
1 TTATATTAATATCAACTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGAATGTTGC
*
572574 TTAATTTATTCAATTT-TTATTTCCAATTTCATGTTTGTTCAATTTGGTACTTTATATACATATA
66 TTAATTTATTCAATTTGTTATTTCCAATTTCATGTTTGTTCAATTTGATACTTTATATACATATA
* * * * * *
572638 TAAAGTATAAAGTATATGTATATATATA-A-AGTATA-ATGTACAT-T--ATATATACAT---GC
131 TAAACTATAAAGTATAAGTATATATATATATA-TATATATATAAATATAAATATATATATAAAGT
* * * * * * ** *
572694 ATCATATTATCATTACAT-T-CAT-TATGCATATTA-CATATTATAT-ATATATATATATATTAT
195 AT-AAAGTA-CATTAGATATACATGCAT-CAAAGTATCATAACAT-TCATA-ATATATATAATAT
* * * ** * ** * ** ** *
572754 AATTA-TTTTAAGTTTC-CTCAACTTTTGAAATTAATGCAATTCAGTTCATTTTACAAT-TTTTG
255 AA-TAGTTATAA-TGTCACACAACTACTGAAAGTAATATAATTAAG-TCATTAAACAATATAATA
** ** * ** * ** * * * *
572816 TTTGATTTGATCCT-TTTATGTTGTTTATTGTATTTAAATTTTAATTTGTAATTTTATATTTGTT
317 TAAGATTAAAT-ATAAGTATATTAATTATCGTAATTAAATATTAATTTGTAATTTCATATTTGTT
*
572880 CAATTTAGTCCTTCAAACTATATTTGTATCTGAAATTGACCCATACTTATTTATATTTTTGTAAT
381 CAATTTAGTCCTTCAAACTATATTTGTATATGAAATTGACCCATACTTATTTATATTTTTGTAAT
* *
572945 GTACTTAAAACAAACCCTATAAAATGTAAATCATATAATAAATTTCTTTTCAAATTATGTTAACC
446 GTACTT--AACAAACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTAACC
573010 AACTTTTAAATGTATGCAATTTAGTCCATTTT
509 AACTTTTAAATGTATGCAATTTAGTCCATTTT
* *
573042 TTATATTAATATCAACTTCACATTTTATAATTAATTCAATTTCATCTCTCATCAATGCATGTTGC
1 TTATATTAATATCAACTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGAATGTTGC
*
573107 TTAATTTATTCAATTTGTTATTTCCAATTTCATGTTTGTTCAATTTGGTACTTTATATACATATA
66 TTAATTTATTCAATTTGTTATTTCCAATTTCATGTTTGTTCAATTTGATACTTTATATACATATA
* *
573172 TAAACTATAAAGTATAAGTATATATATATATATATATATATATATATATATATATATATAAAGTA
131 TAAACTATAAAGTATAAGTATATATATATATATATATATATAAATATAAATATATATATAAAGTA
* * * * * * *
573237 TAATGTACATTATATATACATGCATCATATTATCATAACATTCATTATATATATATTATAATTGT
196 TAAAGTACATTAGATATACATGCATCAAAGTATCATAACATTCATAATATATATAATATAATAGT
* * * * * * * * ** * ** * **
573302 TTTAATTTTCCCCCAACTTCTGAAATTAATGTAATTCAGTCCATTTTACAATTTTTTTTTTGATT
261 TATAA-TGTCACACAACTACTGAAAGTAATATAATTAAGT-CATTAAACAATATAATATAAGATT
** *** * ** * * *
573367 TGATATTTTTATGTTGTTTATTGTATTTAAATTTTAATTTGTAATTTCATATTTGTTCAATTTAG
324 AAATATAAGTATATTAATTATCGTAATTAAATATTAATTTGTAATTTCATATTTGTTCAATTTAG
* * *
573432 TCCTTCAAATTATATTTGTATATGAAATTGACCCATACTTATTTATATTTTTGTAGTTTACTT-A
389 TCCTTCAAACTATATTTGTATATGAAATTGACCCATACTTATTTATATTTTTGTAATGTACTTAA
*
573496 -AAACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTCACCAACTTTTTAA
454 CAAACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTAACCAAC-TTTTAA
573560 ATGTATGCAATTTAGTCCA-TTT
518 ATGTATGCAATTTAGTCCATTTT
**
573582 TTATATTAATATCAGTTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAAT-AAGTGTTG
1 TTATATTAATATCAACTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGAA-TGTTG
* *
573646 TTTAATTTATTCAATTTTTTATTTCCAATTTCATGTTTGTTCAATTTGATACTTTATATACATAT
65 CTTAATTTATTCAATTTGTTATTTCCAATTTCATGTTTGTTCAATTTGATACTTTATATACATAT
*
573711 ATAAACTATAAAGTATAAGTATATATGTATGTTTGTATATATATATATAAAGTATAAAGTATATA
130 ATAAACTATAAAGTATAAGTATATA--TA----TATATATATATATATAAA-TATAAA-TATAT-
** * * *
573776 ATATAAAGTAATAAAGT-GTTTGGATATA-A-GTATTAAAGTAT-ATAA-A-T-ATAAGTAT-TA
186 ATATAAAGT-ATAAAGTACATTAGATATACATGCATCAAAGTATCATAACATTCATAA-TATATA
* * *
573833 -AATATAA-AGTATATAA-GT-ACATAAGTACT-AAAGT-ATATAATATAAAGT-ATTAAACTAT
249 TAATATAATAGT-TATAATGTCACACAACTACTGAAAGTAATATAAT-T-AAGTCATTAAACAAT
573891 ATAATATAAGTATTAAATATAAAGTATATTAATTATCGTAATTAATATATTAATTT
311 ATAATATAAG-ATTAAATAT-AAGTATATTAATTATCGTAATTAA-ATATTAATTT
573947 TATTTATTAA
Statistics
Matches: 779, Mismatches: 87, Indels: 71
0.83 0.09 0.08
Matches are distributed among these distances:
533 75 0.10
534 74 0.09
535 5 0.01
536 7 0.01
537 18 0.02
538 12 0.02
539 35 0.04
540 219 0.28
541 33 0.04
542 52 0.07
543 52 0.07
544 135 0.17
545 1 0.00
546 20 0.03
547 13 0.02
548 6 0.01
549 16 0.02
550 6 0.01
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.46
Consensus pattern (540 bp):
TTATATTAATATCAACTTCACATTTTATAATTAATTCAATTTCATCCCTCATCAATGAATGTTGC
TTAATTTATTCAATTTGTTATTTCCAATTTCATGTTTGTTCAATTTGATACTTTATATACATATA
TAAACTATAAAGTATAAGTATATATATATATATATATATATAAATATAAATATATATATAAAGTA
TAAAGTACATTAGATATACATGCATCAAAGTATCATAACATTCATAATATATATAATATAATAGT
TATAATGTCACACAACTACTGAAAGTAATATAATTAAGTCATTAAACAATATAATATAAGATTAA
ATATAAGTATATTAATTATCGTAATTAAATATTAATTTGTAATTTCATATTTGTTCAATTTAGTC
CTTCAAACTATATTTGTATATGAAATTGACCCATACTTATTTATATTTTTGTAATGTACTTAACA
AACCCTATAAAATGTAAATCACATAATAAATTTATTTTCAAATTATGTTAACCAACTTTTAAATG
TATGCAATTTAGTCCATTTT
Found at i:574694 original size:39 final size:39
Alignment explanation
Indices: 574651--574736 Score: 111
Period size: 39 Copynumber: 2.2 Consensus size: 39
574641 GTACTCCACA
* * *
574651 CGTCTTCAAGCTAAAT-ATGAAGATTCCACGATTGCATAG
1 CGTCTTCAAGC-AAATGAAGAAGACTCCACGACTGCATAG
* *
574690 CGTCTTCAAGCAAATGAAGAAGACTCCATGACTGCATGG
1 CGTCTTCAAGCAAATGAAGAAGACTCCACGACTGCATAG
574729 CGTCTTCA
1 CGTCTTCA
574737 GAAAAATTGA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
38 4 0.10
39 37 0.90
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (39 bp):
CGTCTTCAAGCAAATGAAGAAGACTCCACGACTGCATAG
Found at i:577831 original size:16 final size:17
Alignment explanation
Indices: 577806--577839 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
577796 CCGAGGTGTC
577806 ACATTGACTTTT-CAAA
1 ACATTGACTTTTACAAA
*
577822 ACATTTACTTTTACAAA
1 ACATTGACTTTTACAAA
577839 A
1 A
577840 GAATGAAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
ACATTGACTTTTACAAA
Found at i:578520 original size:22 final size:21
Alignment explanation
Indices: 578491--578556 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 21
578481 CATGTGAAAT
578491 CTATGTCCCGAAGGACCTATA
1 CTATGTCCCGAAGGACCTATA
578512 CATATGTCCCGAAGGACCTATGTTA
1 C-TATGTCCCGAAGGACCTA---TA
*
578537 CTATGTCCCGAAGCACCTAT
1 CTATGTCCCGAAGGACCTAT
578557 GTAACCCTCG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
21 2 0.05
22 18 0.45
24 17 0.43
25 3 0.08
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (21 bp):
CTATGTCCCGAAGGACCTATA
Found at i:578546 original size:24 final size:24
Alignment explanation
Indices: 578491--578558 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
578481 CATGTGAAAT
578491 CTATGTCCCGAAGGACCTA---TA
1 CTATGTCCCGAAGGACCTATGTTA
578512 CATATGTCCCGAAGGACCTATGTTA
1 C-TATGTCCCGAAGGACCTATGTTA
*
578537 CTATGTCCCGAAGCACCTATGT
1 CTATGTCCCGAAGGACCTATGT
578559 AACCCTCGAC
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
21 1 0.02
22 18 0.43
24 20 0.48
25 3 0.07
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (24 bp):
CTATGTCCCGAAGGACCTATGTTA
Found at i:581347 original size:20 final size:21
Alignment explanation
Indices: 581294--581347 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
581284 TATTTCCAAA
581294 AAAGGATCGATCCCTTGACTG
1 AAAGGATCGATCCCTTGACTG
* * *
581315 AAAAGATCAATCCCTTGCCT-
1 AAAGGATCGATCCCTTGACTG
581335 AAAGGATCGATCC
1 AAAGGATCGATCC
581348 AAAACTCACT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (21 bp):
AAAGGATCGATCCCTTGACTG
Found at i:584984 original size:17 final size:17
Alignment explanation
Indices: 584962--584999 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
584952 AAAGAAAGAA
584962 AAAGAGGTTAAAAGGAG
1 AAAGAGGTTAAAAGGAG
584979 AAAGAGGTTAAAAGGAG
1 AAAGAGGTTAAAAGGAG
584996 AAAG
1 AAAG
585000 TGACTAGATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.34, T:0.11
Consensus pattern (17 bp):
AAAGAGGTTAAAAGGAG
Found at i:596705 original size:22 final size:22
Alignment explanation
Indices: 596680--596723 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
596670 AAATCACTAG
596680 TCATTCATTCTTACTCAAAGAT
1 TCATTCATTCTTACTCAAAGAT
596702 TCATTCATTCTTACTCAAAGAT
1 TCATTCATTCTTACTCAAAGAT
596724 GTTGGCAGGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.23, G:0.05, T:0.41
Consensus pattern (22 bp):
TCATTCATTCTTACTCAAAGAT
Found at i:601159 original size:144 final size:144
Alignment explanation
Indices: 600899--601332 Score: 861
Period size: 144 Copynumber: 3.0 Consensus size: 144
600889 TTCACATACA
600899 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
1 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
600964 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
66 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
601029 CATTGAAAGAGAAT
131 CATTGAAAGAGAAT
601043 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
1 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
601108 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
66 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
601173 CATTGAAAGAG-AT
131 CATTGAAAGAGAAT
601186 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
1 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
601251 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
66 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
601316 CATTGAAAGAGAAT
131 CATTGAAAGAGAAT
601330 ATA
1 ATA
601333 GACTTCTTGG
Statistics
Matches: 289, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
143 143 0.49
144 146 0.51
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (144 bp):
ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
CATTGAAAGAGAAT
Found at i:601299 original size:143 final size:143
Alignment explanation
Indices: 600899--601333 Score: 854
Period size: 143 Copynumber: 3.0 Consensus size: 143
600889 TTCACATACA
600899 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
1 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
600964 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
66 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
601029 CATTGAAAGAGAAT
131 CATTGAAAGAG-AT
601043 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
1 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
601108 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
66 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
601173 CATTGAAAGAGAT
131 CATTGAAAGAGAT
601186 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
1 ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
601251 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
66 GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
601316 CATTGAAAGAGA-
131 CATTGAAAGAGAT
601328 ATATAG
1 ATATAG
601334 ACTTCTTGGT
Statistics
Matches: 291, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
142 6 0.02
143 144 0.49
144 141 0.48
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (143 bp):
ATATAGGGGCTCATAATAAAATTTTACTGAAATAAATAGGATCAACTAGAACTTTGGAGAGTGGA
GACCACCAATCAATGAACAAAAGTATGAAAGAAACGCGCCATTTCTAAAAGACATCCACATGTGA
CATTGAAAGAGAT
Found at i:615445 original size:54 final size:55
Alignment explanation
Indices: 615387--615658 Score: 341
Period size: 55 Copynumber: 5.0 Consensus size: 55
615377 GATGCATGAA
* * * * *
615387 ACTCGCACAATCTTCAACAAACGTCTCTGCTCTCTA-TGCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* *
615441 ACTCGAACAATCTTCAACAATCGTTTCTGCTCCCTATTTCTTCAGAGAGTATTAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* * *
615496 ACTCGAACAATTTTCAACATTTGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* * * *
615551 ACTCGAACATTCTTCAACAATCGTGTTTGTTCCCTATTTCTTCAAAGAGTATAAG
1 ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
* * * * * *
615606 ACTCGAACGATCTTCAATAATCGGGT-TCGCTCCCTCTTTCTTTAGGGAGTATA
1 ACTCGAACAATCTTCAACAATCGTGTCT-GCTCCCTATTTCTTCAGAGAGTATA
615659 GAACCCTAAT
Statistics
Matches: 189, Mismatches: 27, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
54 33 0.17
55 156 0.83
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (55 bp):
ACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAG
Found at i:615762 original size:54 final size:53
Alignment explanation
Indices: 615524--616620 Score: 1051
Period size: 55 Copynumber: 20.3 Consensus size: 53
615514 ATTTGTGTCT
* * ** * * *
615524 GCTCCCTATTTCTTCAGAGAGTATA-AGACTCGAACATTCTTCAACAATCGTGTTT
1 GCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCG-ACA-TCTTCTTCAAACGGGTTC
* * ** * *
615579 GTTCCCTATTTCTTCAAAGAGTATA-AGACTCGAACGATCTTCAAT-AATCGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGA-ACTCG-AC-ATCTTC-TTCAAACGGGTTC
* * * * *
615634 GCTCCCTCTTTCTTTAGGGAGTATAGAACCCTAATAATCTTCTGT-AAACAGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTC-GA-CATCTTCT-TCAAACGGGTTC
* *
615689 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCAGACATTTTCTTCAAACGAGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTC-GACATCTTCTTCAAACGGGTTC
* * *
615743 TCTCCCTCTTTC-TCTAGGGAGTATAGAACTTGGACATCTTCTTCAAACAGGTTC
1 GCTCCCTCTTTCTTC-AGGGAGTATAGAAC-TCGACATCTTCTTCAAACGGGTTC
* *
615797 GCTCCCTCTTTCTTCAGGGAGTATAGAACTTGGAAAT-TTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAAC-TCGACATCTTCTTCAAACGGGTTC
*
615850 GCTCCCTCTTTC-TCTAGGGAGTAT-GTAACTCAAACATCTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTC-AGGGAGTATAG-AACTC-GACATCTTCTTCAAACGGGTTC
* * **
615904 ACTTCGCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTC
1 GC-TCCCTCTTTCTTCAGGGAGTATAGAACTCG-AC-ATCTTCTTCAAACGGGTTC
* * **
615960 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGATAATCTTCTTCTTACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGA-CATCTTCTTCAAACGGGTTC
616014 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCG--ATCTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGACATCTTCTTCAAACGGGTTC
* ** * *
616065 TCTCCCTCTTTCTTCAATGAATATAGAACTCGAAAATCTTC-T--AACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCG-ACATCTTCTTCAAACGGGTTC
* * ** *
616116 GCTCCCTCTTTCTTTAGAGAGTATAGAACTCGTACAATCTTCTGAAAATGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCG-AC-ATCTTCTTCAAACGGGTTC
* * **
616171 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCTTCTTCTTACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGA-CATCTTCTTCAAACGGGTTC
* * * * *
616225 GCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACAGGTTC
1 GC-TCCCTCTTTCTTCAGGGAGTATAGAACTCG-A-CATCTTCTTCAAACGGGTTC
* *
616281 GCTCCCTCTTTC-TCTAGGGAGTATGGAACTCAAACATCTTCTTCAAACGGGTTC
1 GCTCCCTCTTTCTTC-AGGGAGTATAGAACTC-GACATCTTCTTCAAACGGGTTC
* *
616335 GCTCCCTCTTTC-TCTAGGGAGTATGGAACTCGAACATCTTCTTTAAACGGGTTC
1 GCTCCCTCTTTCTTC-AGGGAGTATAGAACTCG-ACATCTTCTTCAAACGGGTTC
* ** *
616389 TCTCCCTCTTTCTTCAATGAGTATAGAACTCGAAAATCTTC-T--AACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCG-ACATCTTCTTCAAACGGGTTC
* * **
616440 GCTCCCTCTTTCTTTAGAGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCG-AC-ATCTTCTTCAAACGGGTTC
* * **
616495 GCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCTTCTTCTTACGGGTTC
1 GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGA-CATCTTCTTCAAACGGGTTC
* * * * *
616549 GCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACAGGTTC
1 GC-TCCCTCTTTCTTCAGGGAGTATAGAACTCG-A-CATCTTCTTCAAACGGGTTC
616605 GCTCCCTCTTTCTTCA
1 GCTCCCTCTTTCTTCA
616621 TACACGAAAA
Statistics
Matches: 887, Mismatches: 114, Indels: 82
0.82 0.11 0.08
Matches are distributed among these distances:
51 121 0.14
52 16 0.02
53 47 0.05
54 298 0.34
55 343 0.39
56 62 0.07
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (53 bp):
GCTCCCTCTTTCTTCAGGGAGTATAGAACTCGACATCTTCTTCAAACGGGTTC
Found at i:616479 original size:324 final size:323
Alignment explanation
Indices: 615629--616618 Score: 1430
Period size: 324 Copynumber: 3.1 Consensus size: 323
615619 TCAATAATCG
* * *
615629 GGTTCGCTCCCTCTTTCTTTAGGGAGTATAGAACCCTAATAATCTTCTGT-AAACAGGTTCGCTC
1 GGTTCGCTCCCTCTTTC-TTAGGGAGTATAGAACTCGAA-AATCTTCT-TCAAACGGGTTCGCTC
* *
615693 CCTCTTTCTTCAGGGAGTATAGAACTC-AGACATTTTCTTCAAACGAGTTCTCTCCCTCTTTC-T
63 CCTCTTTCTTCAGGGAGTATAGAACTCGA-ACATCTTCTTCAAACGGGTTCTCTCCCTCTTTCTT
** * * * * * *
615756 CTAGGGAGTATAGAACTTGGACATCTTCTTCAAACAGGTTCGCTCCCTCTTTCTTCAGGGAGTAT
127 C-AATGAGTATAGAACTCGAAAATCTTC-T--AACGGGTTCGCTCCCTCTTTCTTTAGAGAGTAT
* * ** *
615821 AGAACTTGGA-AAT-TTCTTCAAACGGGTTCGCTCCCTCTTTC-TCTAGGGAGTAT-GTAACTC-
188 AGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTC-AGGAAGTATAG-AACTCG
* ** * * *
615881 AAACATCTTCTTCAAACGGGTTCACTTCGCTCTTTCTTCAGGGAGTATAGAACTCGAACAATCTT
251 AGA-ATCTTCTTCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTT
* *
615946 CTGAAAACG
315 CTGCAAACA
* * **
615955 GGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGATAATCTTCTTCTTACGGGTTCGCTCCC
1 GGTTCGCTCCCTCTTTCTT-AGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCC
616020 TCTTTCTTCAGGGAGTATAGAACTCG---ATCTTCTTCAAACGGGTTCTCTCCCTCTTTCTTCAA
65 TCTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCTCTCCCTCTTTCTTCAA
*
616082 TGAATATAGAACTCGAAAATCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAGAACTC
130 TGAGTATAGAACTCGAAAATCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAGAACTC
* *
616147 GTACAATCTTCTGAAAATGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCTTC
195 GAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCTTC
616212 TTCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACA
260 TTCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACA
*
616276 GGTTCGCTCCCTCTTTCTCTAGGGAGTATGGAACTC-AAACATCTTCTTCAAACGGGTTCGCTCC
1 GGTTCGCTCCCTCTTTCT-TAGGGAGTATAGAACTCGAAA-ATCTTCTTCAAACGGGTTCGCTCC
* *
616340 CTCTTTC-TCTAGGGAGTATGGAACTCGAACATCTTCTTTAAACGGGTTCTCTCCCTCTTTCTTC
64 CTCTTTCTTC-AGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCTCTCCCTCTTTCTTC
616404 AATGAGTATAGAACTCGAAAATCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAGAAC
128 AATGAGTATAGAACTCGAAAATCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAGAAC
616469 TCGAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCT
193 TCGAACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCT
616534 TCTTCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAAC
258 TCTTCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAAC
616599 A
323 A
616600 GGTTCGCTCCCTCTTTCTT
1 GGTTCGCTCCCTCTTTCTT
616619 CATACACGAA
Statistics
Matches: 607, Mismatches: 42, Indels: 33
0.89 0.06 0.05
Matches are distributed among these distances:
319 38 0.06
320 7 0.01
321 179 0.29
322 55 0.09
323 3 0.00
324 245 0.40
325 48 0.08
326 32 0.05
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (323 bp):
GGTTCGCTCCCTCTTTCTTAGGGAGTATAGAACTCGAAAATCTTCTTCAAACGGGTTCGCTCCCT
CTTTCTTCAGGGAGTATAGAACTCGAACATCTTCTTCAAACGGGTTCTCTCCCTCTTTCTTCAAT
GAGTATAGAACTCGAAAATCTTCTAACGGGTTCGCTCCCTCTTTCTTTAGAGAGTATAGAACTCG
AACAATCTTCTGAAAACGGGTTCGCTCCCTCTTTCTTCAGGAAGTATAGAACTCGAGAATCTTCT
TCTTACGGGTTCGCTTCGCTCTTTCTTCAGGAAGTATAGAACTCGAATAATCTTCTGCAAACA
Found at i:619304 original size:21 final size:22
Alignment explanation
Indices: 619280--619330 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
619270 TGTTTGATCG
619280 ATTTTCTTTCATTTTC-TTTTT
1 ATTTTCTTTCATTTTCATTTTT
*
619301 ATTTTC-CTCATTTTCAATTTTT
1 ATTTTCTTTCATTTTC-ATTTTT
619323 -TTTTCTTT
1 ATTTTCTTT
619331 TCTTTCTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 8 0.32
21 11 0.44
22 6 0.24
ACGTcount: A:0.12, C:0.16, G:0.00, T:0.73
Consensus pattern (22 bp):
ATTTTCTTTCATTTTCATTTTT
Found at i:619331 original size:17 final size:17
Alignment explanation
Indices: 619323--619362 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
619313 TTCAATTTTT
619323 TTTTCTTTTCTTTCTTC
1 TTTTCTTTTCTTTCTTC
*
619340 TTTTCTTTTCCTT-TTC
1 TTTTCTTTTCTTTCTTC
619356 TCTTTCT
1 T-TTTCT
619363 ACATTTCTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTCTTTTCTTTCTTC
Found at i:619340 original size:12 final size:11
Alignment explanation
Indices: 619286--619362 Score: 57
Period size: 12 Copynumber: 6.5 Consensus size: 11
619276 ATCGATTTTC
619286 TTTCATTTTCTT
1 TTTC-TTTTCTT
*
619298 TTTATTTTCCTCAT
1 TTTCTTTT-CT--T
619312 TTTCAATTTT-TT
1 TTTC--TTTTCTT
619324 TTTCTTTTCTT
1 TTTCTTTTCTT
619335 TCTTCTTTTCTT
1 T-TTCTTTTCTT
* *
619347 TTCCTTTTCTC
1 TTTCTTTTCTT
619358 TTTCT
1 TTTCT
619363 ACATTTCTCT
Statistics
Matches: 53, Mismatches: 5, Indels: 15
0.73 0.07 0.21
Matches are distributed among these distances:
10 4 0.08
11 19 0.36
12 21 0.40
14 5 0.09
16 4 0.08
ACGTcount: A:0.06, C:0.21, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:619369 original size:25 final size:23
Alignment explanation
Indices: 619325--619382 Score: 64
Period size: 25 Copynumber: 2.5 Consensus size: 23
619315 CAATTTTTTT
* * *
619325 TTCTTT-TCTTTCTTCTTTTCTT
1 TTCTTTCTCTTTCTACATTTCTC
619347 TTCCTTTTCTCTTTCTACATTTCTC
1 TT-C-TTTCTCTTTCTACATTTCTC
619372 TTCTTTCTCTT
1 TTCTTTCTCTT
619383 CATAATGACA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
22 2 0.07
23 9 0.30
24 4 0.13
25 15 0.50
ACGTcount: A:0.03, C:0.28, G:0.00, T:0.69
Consensus pattern (23 bp):
TTCTTTCTCTTTCTACATTTCTC
Found at i:621991 original size:21 final size:21
Alignment explanation
Indices: 621943--622059 Score: 164
Period size: 21 Copynumber: 5.6 Consensus size: 21
621933 CCATGCGACG
* *
621943 TGGTCTTCTCGTCTTTACGAA
1 TGGTCTTCTCGTCTTGATGAA
*
621964 T-GTCTTCTCGTCTTTATGAA
1 TGGTCTTCTCGTCTTGATGAA
*
621984 GGGTCTTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
622005 TGGTCTTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
**
622026 TGCCCTTCTCGTCTTGATGAA
1 TGGTCTTCTCGTCTTGATGAA
*
622047 TGCTCTTCTCGTC
1 TGGTCTTCTCGTC
622060 CTTGGTACGA
Statistics
Matches: 88, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
20 18 0.20
21 70 0.80
ACGTcount: A:0.13, C:0.24, G:0.21, T:0.43
Consensus pattern (21 bp):
TGGTCTTCTCGTCTTGATGAA
Found at i:627580 original size:64 final size:65
Alignment explanation
Indices: 627420--627581 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
627410 GAATTAATTG
* * **** *
627420 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTCA
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
* * **
627485 AAACATCGAATGCATTTGATGCATCCATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTC-
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
627549 AAACATCGAATGCATTTCATGCATCGATGCACA
1 AAACATCGAATGCATTTCATGCATCGATGCACA
627582 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
64 31 0.37
65 53 0.63
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (65 bp):
AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTCA
Found at i:634883 original size:21 final size:21
Alignment explanation
Indices: 634841--634884 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
634831 ACCCCGTGAG
*
634841 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
634862 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
634883 CT
1 CT
634885 CCTCCTCTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:635669 original size:20 final size:21
Alignment explanation
Indices: 635632--635671 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
635622 AAATTAAGTT
635632 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
635653 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
635672 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:635957 original size:65 final size:64
Alignment explanation
Indices: 635888--636049 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 64
635878 GAATTAATTG
* * **** *
635888 AAACATCGAATGCATTCCATGCACCGATGCATTCTCCATGCATCGATGCACTCTGAATATTTTC
1 AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTC
* * **
635952 AAAACATTGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTTTC
1 -AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTC
*
636017 AAACATCGAATGCATTTCATGCATCGATACACA
1 AAACATCGAATGCATTTCATGCATCGATGCACA
636050 CTTGGTGCAC
Statistics
Matches: 83, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 30 0.36
65 53 0.64
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (64 bp):
AAACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCGATGCACTCAGAATATTTTC
Found at i:640284 original size:19 final size:19
Alignment explanation
Indices: 640260--640301 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
640250 CGACTCCTAG
640260 TAAAATACTAATAAACTGA
1 TAAAATACTAATAAACTGA
640279 TAAAATACTAATAAACTGA
1 TAAAATACTAATAAACTGA
640298 TAAA
1 TAAA
640302 CAAATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.60, C:0.10, G:0.05, T:0.26
Consensus pattern (19 bp):
TAAAATACTAATAAACTGA
Found at i:640309 original size:19 final size:19
Alignment explanation
Indices: 640260--640311 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
640250 CGACTCCTAG
*
640260 TAAAATACTAATAAACTGA
1 TAAAATAATAATAAACTGA
*
640279 TAAAATACTAATAAACTGA
1 TAAAATAATAATAAACTGA
640298 TAAACA-AATAATAA
1 TAAA-ATAATAATAA
640312 TAAGATAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 30 0.97
20 1 0.03
ACGTcount: A:0.62, C:0.10, G:0.04, T:0.25
Consensus pattern (19 bp):
TAAAATAATAATAAACTGA
Found at i:642224 original size:36 final size:36
Alignment explanation
Indices: 642132--642413 Score: 201
Period size: 36 Copynumber: 8.0 Consensus size: 36
642122 GGTTTTTGAA
* *
642132 AAAATATATATAATATATGGTTTTGAAAACATGTTTG
1 AAAATATATATAATATATAGTTTTTAAAACAT-TTTG
* * * *
642169 AAAACATTTATATATTATATAATTTTTAAAATATTTTG
1 -AAA-ATATATATAATATATAGTTTTTAAAACATTTTG
* *
642207 AAAATAAATATAATATATAGTTTTTAAAACGTTTTTG
1 AAAATATATATAATATATAGTTTTTAAAAC-ATTTTG
* * * *
642244 AAAATTTATATAATACATAGTTTTGAAAATA-TTT-
1 AAAATATATATAATATATAGTTTTTAAAACATTTTG
*
642278 ---ATATAT-T-ATATA-A-TTTTTAAAAAACATTTTA
1 AAAATATATATAATATATAGTTTTT--AAAACATTTTG
* * * *
642309 AAAACATTTATAATATAAAGATTTTAAAACATTTTTG
1 AAAATATATATAATATATAGTTTTTAAAACA-TTTTG
* *
642346 -AAA-ATATATAATATATATTTTTTAAAACATTTTT
1 AAAATATATATAATATATAGTTTTTAAAACATTTTG
** * * *
642380 TTAATTTATATATTATAT-GTTTTTAAAATATTTT
1 AAAATATATATAATATATAGTTTTTAAAACATTTT
642414 TTTTTATTTT
Statistics
Matches: 192, Mismatches: 36, Indels: 35
0.73 0.14 0.13
Matches are distributed among these distances:
27 4 0.02
28 1 0.01
29 9 0.05
30 4 0.02
31 5 0.03
34 8 0.04
35 42 0.22
36 47 0.24
37 38 0.20
38 11 0.06
39 23 0.12
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (36 bp):
AAAATATATATAATATATAGTTTTTAAAACATTTTG
Found at i:642255 original size:37 final size:36
Alignment explanation
Indices: 642132--642407 Score: 168
Period size: 37 Copynumber: 7.8 Consensus size: 36
642122 GGTTTTTGAA
* * * *
642132 AAAATATATATAATATATGGTTTTGAAAACATGTTTG
1 AAAATTTATATAATATATAGTTTTTAAAAC-TTTTTG
* *
642169 AAAACATTTATATATTATATAATTTTTAAAA-TATTTTG
1 -AAA-ATTTATATAATATATAGTTTTTAAAACT-TTTTG
**
642207 AAAATAAATATAATATATAGTTTTTAAAACGTTTTTG
1 AAAATTTATATAATATATAGTTTTTAAAAC-TTTTTG
* *
642244 AAAATTTATATAATACATAGTTTTGAAAA-----T-
1 AAAATTTATATAATATATAGTTTTTAAAACTTTTTG
* * * *
642274 ---ATTTATATATTATATAATTTTTAAAAAACATTTTA
1 AAAATTTATATAATATATAGTTTTT--AAAACTTTTTG
* * *
642309 AAAACATT-TATAATATAAAGATTTTAAAACATTTTTG
1 AAAA-TTTATATAATATATAGTTTTTAAAAC-TTTTTG
*
642346 AAAA--TATATAATATATATTTTTTAAAACATTTTT-
1 AAAATTTATATAATATATAGTTTTTAAAAC-TTTTTG
** *
642380 TTAATTTATATATTATAT-GTTTTTAAAA
1 AAAATTTATATAATATATAGTTTTTAAAA
642408 TATTTTTTTT
Statistics
Matches: 186, Mismatches: 32, Indels: 43
0.71 0.12 0.16
Matches are distributed among these distances:
27 18 0.10
29 4 0.02
31 1 0.01
34 4 0.02
35 34 0.18
36 38 0.20
37 42 0.23
38 22 0.12
39 23 0.12
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (36 bp):
AAAATTTATATAATATATAGTTTTTAAAACTTTTTG
Found at i:642294 original size:27 final size:26
Alignment explanation
Indices: 642239--642300 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 26
642229 TTTAAAACGT
*
642239 TTTTG-AAAATTTATATAATACATAG
1 TTTTGAAAAATTTATATAATACATAA
* *
642264 TTTTGAAAATATTTATATATTATATAA
1 TTTTGAAAA-ATTTATATAATACATAA
*
642291 TTTTTAAAAA
1 TTTTGAAAAA
642301 ACATTTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
25 5 0.16
26 4 0.13
27 22 0.71
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (26 bp):
TTTTGAAAAATTTATATAATACATAA
Found at i:642391 original size:102 final size:99
Alignment explanation
Indices: 642165--642377 Score: 284
Period size: 100 Copynumber: 2.1 Consensus size: 99
642155 TGAAAACATG
* * * * *
642165 TTTGAAAACATTTATATATTATATAATTTTTAAAATATTTTGAAAATAAATATAATATATAGTTT
1 TTTGAAAACATTTATATATTATATAATTTTTAAAACATTTTAAAAACAAATATAATATAAAGATT
*
642230 TTAAAACGTTTTTGAAAATTTATATAATACATAGT
66 TTAAAACATTTTTGAAAA-TTATATAATACATAGT
* **
642265 TTTGAAAATATTTATATATTATATAATTTTTAAAAAACATTTTAAAAACATTTATAATATAAAGA
1 TTTGAAAACATTTATATATTATATAATTTTT--AAAACATTTTAAAAACAAATATAATATAAAGA
* *
642330 TTTTAAAACATTTTTGAAAA-TATATAATATATATT
64 TTTTAAAACATTTTTGAAAATTATATAATACATAGT
*
642365 TTTTAAAACATTT
1 TTTGAAAACATTT
642378 TTTTAATTTA
Statistics
Matches: 98, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
100 54 0.55
102 44 0.45
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (99 bp):
TTTGAAAACATTTATATATTATATAATTTTTAAAACATTTTAAAAACAAATATAATATAAAGATT
TTAAAACATTTTTGAAAATTATATAATACATAGT
Found at i:642403 original size:35 final size:36
Alignment explanation
Indices: 642277--642416 Score: 108
Period size: 35 Copynumber: 3.9 Consensus size: 36
642267 TGAAAATATT
* * **
642277 TATATATTATATAATTTTTAAAAAACA-TTTTAAAAACA
1 TATATAATATAT-ATTTTT-TAAAACATTTTTTTAAA-A
* * ** *
642315 TTTATAATATAAAGATTTTAAAACA-TTTTTGAAAA
1 TATATAATATATATTTTTTAAAACATTTTTTTAAAA
**
642350 TATATAATATATATTTTTTAAAACATTTTTTTAATT
1 TATATAATATATATTTTTTAAAACATTTTTTTAAAA
*
642386 TATAT-AT-TATATGTTTTTAAAATATTTTTTT
1 TATATAATATATAT-TTTTTAAAACATTTTTTT
642417 TTATTTTTTT
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
34 5 0.06
35 41 0.49
36 25 0.30
37 4 0.05
38 9 0.11
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (36 bp):
TATATAATATATATTTTTTAAAACATTTTTTTAAAA
Found at i:642435 original size:15 final size:14
Alignment explanation
Indices: 642408--642450 Score: 59
Period size: 15 Copynumber: 3.0 Consensus size: 14
642398 GTTTTTAAAA
*
642408 TATTTTTTTTTATT
1 TATTTATTTTTATT
*
642422 TTTTTATTTCTTATT
1 TATTTATTT-TTATT
642437 TATTTATTTTTATT
1 TATTTATTTTTATT
642451 CGATGTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.48
15 13 0.52
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.81
Consensus pattern (14 bp):
TATTTATTTTTATT
Found at i:643763 original size:2 final size:2
Alignment explanation
Indices: 643756--643813 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
643746 TTTTAATTTC
* *
643756 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
643798 AT AT AC AT AT AC AT AT
1 AT AT AT AT AT AT AT AT
643814 TTATTATTAT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:643903 original size:20 final size:20
Alignment explanation
Indices: 643865--643933 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
643855 TTTATTTTAT
* *
643865 TTTATCTTATATATATTTTTGG
1 TTTAT-TTA-ATATTTTTTTGA
*
643887 TTTATTTAATATTTTTTAT-T
1 TTTATTTAATATTTTTT-TGA
643907 TTTATTTAAT-TTTCTTTTGA
1 TTTATTTAATATTT-TTTTGA
643927 TTTATTT
1 TTTATTT
643934 TTTGATTTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
19 4 0.10
20 28 0.68
21 4 0.10
22 5 0.12
ACGTcount: A:0.22, C:0.03, G:0.04, T:0.71
Consensus pattern (20 bp):
TTTATTTAATATTTTTTTGA
Found at i:643946 original size:11 final size:12
Alignment explanation
Indices: 643896--643946 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
643886 GTTTATTTAA
643896 TATTTTTT-ATT
1 TATTTTTTGATT
* *
643907 T-TTATTTAATT
1 TATTTTTTGATT
*
643918 T-TCTTTTGATT
1 TATTTTTTGATT
643929 TATTTTTTGATT
1 TATTTTTTGATT
643941 TATTTT
1 TATTTT
643947 ACTTTCATTT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
10 5 0.15
11 13 0.39
12 15 0.45
ACGTcount: A:0.18, C:0.02, G:0.04, T:0.76
Consensus pattern (12 bp):
TATTTTTTGATT
Found at i:648064 original size:93 final size:92
Alignment explanation
Indices: 647897--648076 Score: 270
Period size: 93 Copynumber: 1.9 Consensus size: 92
647887 ATAATATTAT
* *
647897 TTATATACAATAAAGCTTGAGTTGTCCCTCTAAAGCAATTGGTTAAACGCCCCGACTTTATGGAT
1 TTATATACAATAAAGCTTGAGTTGTCCATCTAAAGCAATTGGTTAAACACCCCGACTTTATGGAT
* *
647962 AATATTCAGCTAGCCTGATAAAAGTGA
66 AAGATTCAGCTAACCTGATAAAAGTGA
* * * *
647989 TTATACTATAATAAAGCTTGAGTTGTCGATCTAAGGTAATTGGTTAAACACCCCGACTTTATGGA
1 TTATA-TACAATAAAGCTTGAGTTGTCCATCTAAAGCAATTGGTTAAACACCCCGACTTTATGGA
*
648054 TAAGATTCAGCTAACTTGATAAA
65 TAAGATTCAGCTAACCTGATAAA
648077 GGTATTTTCA
Statistics
Matches: 78, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
92 5 0.06
93 73 0.94
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (92 bp):
TTATATACAATAAAGCTTGAGTTGTCCATCTAAAGCAATTGGTTAAACACCCCGACTTTATGGAT
AAGATTCAGCTAACCTGATAAAAGTGA
Found at i:649422 original size:84 final size:84
Alignment explanation
Indices: 649287--650240 Score: 1059
Period size: 84 Copynumber: 11.5 Consensus size: 84
649277 GCTCAAGGCC
* * * *
649287 AGAAGGGTTATCTACC-ACC-AAGATCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
649350 TGCAGCATAACTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * *
649369 AGAAGGGTTATCTGCCAACCAAATACCTTTGAGTTCGACTACGCTCAGCTCCAACGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
649434 TGCAGCATAGCTTAAGTCA
66 TGCAGCATAACTTAAGTCG
* * * * * * * *
649453 AGAAGGGCTATCTG----CCAAAGACCTGCGAGTTTGATTACACTTAGCTTCGAGGGCACATCAT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
*
649514 TTGTAGCATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCG
* * * *
649534 AGAAGAGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACACTCAACTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
649599 TGCAGCATATCTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * * * * * *
649618 AGAAGGGCTATCTGCTAA--AGA-ACC-TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCAT
* * * *
649679 TTACAGCATAACTCAAGGCT
65 TTGCAGCATAACTTAAGTCG
* * * * *
649699 AGAAGGGTTATCTGTC-ACCAAAATACCTTCTAGTTTGACTACGCTCAGCTCCAAGGCATATCAT
1 AGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
*
649763 TTGCAGTATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCG
* * *
649783 AGAATGGTTATCTGCCAAGCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
649848 TGCAGTATATCTTAAGTCG
66 TGCAGCATAACTTAAGTCG
* * * * *
649867 AGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGA-TCACACTCAGCTACGAGGGCACATCA
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT-ACGCTCAGCT-CCAAGGCACATCA
* * * *
649927 TTTACAGCATAACTCAAGGCT
64 TTTGCAGCATAACTTAAGTCG
*** * * *
649948 AGAAGGGTTATCT-ATGACCAAAAGACCTTCGAGTTCGACGACGCTCAGCTCTAAGGCATATCAT
1 AGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
*
650012 TTGCAACATAACTTAAGTCG
65 TTGCAGCATAACTTAAGTCG
* * *
650032 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGACATATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * *
650097 TACAGTATAGCTTAAGTCA
66 TGCAGCATAACTTAAGTCG
* * *
650116 AGAAGGGATATCTG----CCAAAGACCTTCGAGTTCGACTACGCTAAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
650177 TGCAGCATAACTTAAGTCG
66 TGCAGCATAACTTAAGTCG
*
650196 AGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTACGCT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCT
650241 TAACTCAGAG
Statistics
Matches: 726, Mismatches: 119, Indels: 52
0.81 0.13 0.06
Matches are distributed among these distances:
79 1 0.00
80 143 0.20
81 122 0.17
82 17 0.02
83 5 0.01
84 365 0.50
85 73 0.10
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (84 bp):
AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAACTTAAGTCG
Found at i:649538 original size:165 final size:164
Alignment explanation
Indices: 649287--650240 Score: 1103
Period size: 165 Copynumber: 5.8 Consensus size: 164
649277 GCTCAAGGCC
* * * * *
649287 AGAAGGGTTATCTACCACCAAGATCTTCGAGTTCAACTACACTCAGCTCCAAGGCACATCATTTG
1 AGAAGGGCTATCTGCCA--AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
* *
649352 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTTTGAGTTCGACTACGCTCAG
64 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAG
* *
649417 CTCCAACGCACATCATTTGCAGCATAGCTTAAGTCA
129 CTCCAAGGCACATCATTTGCAGCATAACTTAAGTCA
* * * * * * * *
649453 AGAAGGGCTATCTGCCAAAGACCTGCGAGTTTGATTACACTTAGCTTCGAGGGCACATCATTTGT
1 AGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTGC
* * * *
649518 AGCATAACTTAAGTCGAGAAGAGTTATCTGCCAACTAAAGACCTTCGAGTTCGACTACACTCAAC
65 AGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC
* *
649583 TCCAAGGCACATCATTTGCAGCATATCTTAAGTCG
130 TCCAAGGCACATCATTTGCAGCATAACTTAAGTCA
* * * * * *
649618 AGAAGGGCTATCTGCTAAAGAACC-TCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTA
1 AGAAGGGCTATCTGCCAAAG-ACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTG
* * * * * * *
649682 CAGCATAACTCAAGGCTAGAAGGGTTATCTGTC-ACCAAAATACCTTCTAGTTTGACTACGCTCA
64 CAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTACGCTCA
* * *
649746 GCTCCAAGGCATATCATTTGCAGTATAACTTAAGTCG
128 GCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCA
* * *
649783 AGAATGGTTATCTGCCAAGCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGCTATCTG-C---CAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * * *
649848 TGCAGTATATCTTAAGTCGAGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGA-TCACACT
62 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT-ACGCT
* * * * * *
649908 CAGCTACGAGGGCACATCATTTACAGCATAACTCAAGGCT
126 CAGCT-CCAAGGCACATCATTTGCAGCATAACTTAAGTCA
* * * *
649948 AGAAGGGTTATCTATGACCAAAAGACCTTCGAGTTCGACGACGCTCAGCTCTAAGGCATATCATT
1 AGAAGGGCTATC--TG-CC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
650013 TGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGATTACGCTC
62 TGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTC
* * * * *
650078 AGCTCCAAGACATATCATTTACAGTATAGCTTAAGTCA
127 AGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCA
* * *
650116 AGAAGGGATATCTGCCAAAGACCTTCGAGTTCGACTACGCTAAGCTCCAAGGCATATCATTTGCA
1 AGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCA
*
650181 GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCAAGTTCGACTACGCT
66 GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCT
650241 TAACTCAGAG
Statistics
Matches: 676, Mismatches: 94, Indels: 38
0.84 0.12 0.05
Matches are distributed among these distances:
163 1 0.00
164 151 0.22
165 370 0.55
166 21 0.03
167 3 0.00
168 78 0.12
169 51 0.08
170 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (164 bp):
AGAAGGGCTATCTGCCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCA
GCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
CCAAGGCACATCATTTGCAGCATAACTTAAGTCA
Done.