Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 38
Found at i:914778 original size:17 final size:17
Alignment explanation
Indices: 914752--914784 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
914742 ATTTATATAT
914752 ATATTATTAATTTAATC
1 ATATTATTAATTTAATC
*
914769 ATATTTTTAATTTAAT
1 ATATTATTAATTTAAT
914785 TTTATAAATT
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:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
ATATTATTAATTTAATC
Found at i:915258 original size:23 final size:22
Alignment explanation
Indices: 915228--915271 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
915218 ACTAATAATA
*
915228 TAATTAATAATATTTACTATTT
1 TAATTAATAATATTTAATATTT
*
915250 TAATATAATATTATTTAATATT
1 TAAT-TAATAATATTTAATATT
915272 AAAATATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATTAATAATATTTAATATTT
Found at i:915277 original size:23 final size:23
Alignment explanation
Indices: 915232--915279 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
915222 ATAATATAAT
* **
915232 TAATAATATTTACTATTTTAATA
1 TAATAATATTTAATATTAAAATA
*
915255 TAATATTATTTAATATTAAAATA
1 TAATAATATTTAATATTAAAATA
915278 TA
1 TA
915280 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (23 bp):
TAATAATATTTAATATTAAAATA
Found at i:915287 original size:14 final size:14
Alignment explanation
Indices: 915268--915309 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 14
915258 TATTATTTAA
915268 TATTAAAATATATT
1 TATTAAAATATATT
*
915282 TATTAAAA-ATAAT
1 TATTAAAATATATT
915295 TATT--AATATATT
1 TATTAAAATATATT
915307 TAT
1 TAT
915310 ATTATATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 2 0.08
12 7 0.28
13 8 0.32
14 8 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TATTAAAATATATT
Found at i:915313 original size:17 final size:17
Alignment explanation
Indices: 915293--915326 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
915283 ATTAAAAATA
915293 ATTAT-TAATATATTTAT
1 ATTATATAA-ATATTTAT
915310 ATTATATAAATATTTAT
1 ATTATATAAATATTTAT
915327 TTTTTAGATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTATATAAATATTTAT
Found at i:916625 original size:13 final size:13
Alignment explanation
Indices: 916590--916627 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
916580 GTATACCGCT
916590 ATATATTATTAAA
1 ATATATTATTAAA
*
916603 ATGACA-TATTAAA
1 AT-ATATTATTAAA
916616 ATATATTATTAA
1 ATATATTATTAA
916628 CTAAAATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
12 2 0.10
13 17 0.81
14 2 0.10
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (13 bp):
ATATATTATTAAA
Found at i:921449 original size:20 final size:20
Alignment explanation
Indices: 921426--921463 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
921416 AGATAGAATC
* *
921426 AAATACAATTGTATAAAATA
1 AAATAAAATTATATAAAATA
921446 AAATAAAATTATATAAAA
1 AAATAAAATTATATAAAA
921464 AAATTAGCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.29
Consensus pattern (20 bp):
AAATAAAATTATATAAAATA
Found at i:922287 original size:32 final size:31
Alignment explanation
Indices: 922249--922325 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
922239 CGGGGCTGTG
*
922249 GGGCCTACCTAAGAACACATCTTAGGGCCACA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCACA
** ** *
922281 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCACA
*
922312 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
922326 GTCACATTAG
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCACA
Found at i:928150 original size:2 final size:2
Alignment explanation
Indices: 928143--928171 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
928133 ACTATCAAAC
928143 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
928172 GATAAAATAT
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:928256 original size:2 final size:2
Alignment explanation
Indices: 928249--928278 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
928239 AACTTTATTC
928249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
928279 GATAAAATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:930488 original size:52 final size:55
Alignment explanation
Indices: 930422--930609 Score: 184
Period size: 56 Copynumber: 3.4 Consensus size: 55
930412 AAAAAATGAC
* *
930422 TGAGCACCTCTGTGCTTCAGTCTAGAATCTGGCACCTCTGTGC-TTT-GGG-GAT
1 TGAGCACCTATGTGCTTCAATCTAGAATCTGGCACCTCTGTGCTTTTAGGGAGAT
* * * *
930474 TGAGCACCTATGTGCTTCAATCTAGGATCTAGCACCTATGTTCTTTTAGGGATGAT
1 TGAGCACCTATGTGCTTCAATCTAGAATCTGGCACCTCTGTGCTTTTAGGGA-GAT
* * * * * * * *
930530 TAAGCACCTATGTGCTTCAATCTAAAATCCGGCATCTCTGTGCATTAAGGAAACGGT
1 TGAGCACCTATGTGCTTCAATCTAGAATCTGGCACCTCTGTGCTTTTAGG-GA-GAT
* *
930587 TGAGCACCTTTGTGCATCAATCT
1 TGAGCACCTATGTGCTTCAATCT
930610 TTGAATTGGC
Statistics
Matches: 109, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
52 37 0.34
53 3 0.03
54 3 0.03
56 43 0.39
57 23 0.21
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (55 bp):
TGAGCACCTATGTGCTTCAATCTAGAATCTGGCACCTCTGTGCTTTTAGGGAGAT
Found at i:930544 original size:56 final size:52
Alignment explanation
Indices: 930424--930558 Score: 162
Period size: 52 Copynumber: 2.5 Consensus size: 52
930414 AAAATGACTG
* * * * *
930424 AGCACCTCTGTGCTTCAGTCTAGAATCTGGCACCTCTGTGCTTTGGGGATTG
1 AGCACCTATGTGCTTCAATCTAGAATCTAGCACCTATGTGCTTTGGGGATTA
* *
930476 AGCACCTATGTGCTTCAATCTAGGATCTAGCACCTATGTTCTTTTAGGGATGATTA
1 AGCACCTATGTGCTTCAATCTAGAATCTAGCACCTATGTGC-TTT-GGG--GATTA
*
930532 AGCACCTATGTGCTTCAATCTAAAATC
1 AGCACCTATGTGCTTCAATCTAGAATC
930559 CGGCATCTCT
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
52 35 0.50
53 3 0.04
54 3 0.04
56 29 0.41
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (52 bp):
AGCACCTATGTGCTTCAATCTAGAATCTAGCACCTATGTGCTTTGGGGATTA
Found at i:930629 original size:57 final size:57
Alignment explanation
Indices: 930560--930689 Score: 152
Period size: 57 Copynumber: 2.3 Consensus size: 57
930550 TCTAAAATCC
* * * * * * * * *
930560 GGCATCTCTGTGCATTAAGGAAACGGTTGAGCACCTTTGTGCATCAATCTTTGAATT
1 GGCACCTCTGTGCATTAAAGAAACGATAGAACACCTCTGTGCAACAATCTTTAAACT
* * *
930617 GGCACTTTTGTGCATTAAATAAACGATAGAACACCTCTGTGCAACAATCTTTAAACT
1 GGCACCTCTGTGCATTAAAGAAACGATAGAACACCTCTGTGCAACAATCTTTAAACT
930674 GGCACCTCTGTGCATT
1 GGCACCTCTGTGCATT
930690 TACCCCACTG
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.32
Consensus pattern (57 bp):
GGCACCTCTGTGCATTAAAGAAACGATAGAACACCTCTGTGCAACAATCTTTAAACT
Found at i:934689 original size:25 final size:23
Alignment explanation
Indices: 934623--934690 Score: 57
Period size: 28 Copynumber: 2.7 Consensus size: 23
934613 CTTAGATTAT
934623 TAAAAAAAACATAATTTAAAGAAAC
1 TAAAAAAAA-AT-ATTTAAAGAAAC
934648 -AAACAAAACAATTTATTTCATAAGAAAC
1 TAAA-AAAA-AA--TATTT-A-AAGAAAC
934676 TAAAAAAAAATATTT
1 TAAAAAAAAATATTT
934691 TTTAATACTT
Statistics
Matches: 36, Mismatches: 0, Indels: 14
0.72 0.00 0.28
Matches are distributed among these distances:
24 3 0.08
25 10 0.28
26 5 0.14
27 4 0.11
28 11 0.31
29 3 0.08
ACGTcount: A:0.63, C:0.09, G:0.03, T:0.25
Consensus pattern (23 bp):
TAAAAAAAAATATTTAAAGAAAC
Found at i:934988 original size:45 final size:45
Alignment explanation
Indices: 934937--935022 Score: 136
Period size: 45 Copynumber: 1.9 Consensus size: 45
934927 TCAGATTTGA
*
934937 GCAAAAATTCCAGAATGCAAAGAGGGTACCGATACCCCCTGGAAG
1 GCAAAAATTCCAGAATGCAAAGAAGGTACCGATACCCCCTGGAAG
** *
934982 GCAAAAATTCCAGAATGCTCATAAGGTACCGATACCCCCTG
1 GCAAAAATTCCAGAATGCAAAGAAGGTACCGATACCCCCTG
935023 CAGGGGTATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.16
Consensus pattern (45 bp):
GCAAAAATTCCAGAATGCAAAGAAGGTACCGATACCCCCTGGAAG
Found at i:938200 original size:21 final size:21
Alignment explanation
Indices: 938171--938211 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
938161 AGGTATCTTT
*
938171 TTAAGAATTGATATCCTTTTG
1 TTAACAATTGATATCCTTTTG
* *
938192 TTAACAATTGGTATCTTTTT
1 TTAACAATTGATATCCTTTT
938212 CATTAAACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.27, C:0.10, G:0.12, T:0.51
Consensus pattern (21 bp):
TTAACAATTGATATCCTTTTG
Found at i:938534 original size:20 final size:22
Alignment explanation
Indices: 938496--938535 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
938486 TTTGAGTAGA
938496 AAAATCATCCCCAAACGGCTCC
1 AAAATCATCCCCAAACGGCTCC
938518 AAAA-CATCCCC-AACGGCT
1 AAAATCATCCCCAAACGGCT
938536 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 7 0.39
22 4 0.22
ACGTcount: A:0.38, C:0.40, G:0.10, T:0.12
Consensus pattern (22 bp):
AAAATCATCCCCAAACGGCTCC
Found at i:938789 original size:34 final size:32
Alignment explanation
Indices: 938750--938819 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
938740 TTTTGTAAAG
*
938750 GGGAAAAGTTCTAGCTTAGCCCATGTAAAAGCTA
1 GGGAAAAGTTCTAGCTTAGCCCA-G-AAAAACTA
* *
938784 GGGAAAGGTTCTAGTTTAGCCCAGAAAAACTA
1 GGGAAAAGTTCTAGCTTAGCCCAGAAAAACTA
938816 GGGA
1 GGGA
938820 GTCGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.36, C:0.16, G:0.27, T:0.21
Consensus pattern (32 bp):
GGGAAAAGTTCTAGCTTAGCCCAGAAAAACTA
Found at i:939811 original size:21 final size:22
Alignment explanation
Indices: 939762--939813 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
939752 CAAAATGTGC
*
939762 ATGTAGTATCAATATTATTCTT
1 ATGTAGTATCAATATTATTCTG
*
939784 AAG-AGTATCAATATT-TAT-TG
1 ATGTAGTATCAATATTAT-TCTG
939804 ATGTAGTATC
1 ATGTAGTATC
939814 GATACTAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 4 0.16
21 19 0.76
22 2 0.08
ACGTcount: A:0.35, C:0.08, G:0.13, T:0.44
Consensus pattern (22 bp):
ATGTAGTATCAATATTATTCTG
Found at i:939978 original size:21 final size:21
Alignment explanation
Indices: 939952--940006 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
939942 CATATTCTCC
939952 GTTGAGTATCCATACTCCCTA
1 GTTGAGTATCCATACTCCCTA
939973 GTTGAGTATCCATACTCCCTA
1 GTTGAGTATCCATACTCCCTA
939994 GTTGAGTATCCAT
1 GTTGAGTATCCAT
940007 GCTCTCCAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.25, G:0.16, T:0.35
Consensus pattern (21 bp):
GTTGAGTATCCATACTCCCTA
Found at i:940213 original size:20 final size:19
Alignment explanation
Indices: 940169--940218 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
940159 AAAATGTTGT
*
940169 TATGAATAGTATTATACTA
1 TATGAATAGTATAATACTA
* *
940188 TATGAATAGTATCAATATTG
1 TATGAATAGTAT-AATACTA
940208 TATGAATAGTA
1 TATGAATAGTA
940219 CCGATACTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.42, C:0.04, G:0.14, T:0.40
Consensus pattern (19 bp):
TATGAATAGTATAATACTA
Found at i:943418 original size:21 final size:20
Alignment explanation
Indices: 943366--943423 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
943356 CAACAATTGG
*
943366 TAACGATTGGTAT-C-TTTT
1 TAACAATTGGTATCCTTTTT
* *
943384 TAACAATCGATATCCTTTTGT
1 TAACAATTGGTATCCTTTT-T
943405 TAACAATTGGTAT-CTTTTT
1 TAACAATTGGTATCCTTTTT
943424 CATTAAACAT
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
18 10 0.31
19 2 0.06
20 8 0.25
21 12 0.38
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (20 bp):
TAACAATTGGTATCCTTTTT
Found at i:943659 original size:19 final size:20
Alignment explanation
Indices: 943635--943679 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 20
943625 AAAATGTTTT
**
943635 TATGAATAGTATTG-TACTG
1 TATGAATAGTACCGATACTG
943654 TATGAATAGTACCGATACTG
1 TATGAATAGTACCGATACTG
943674 TATGAA
1 TATGAA
943680 CAGTGATGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (20 bp):
TATGAATAGTACCGATACTG
Found at i:943748 original size:20 final size:20
Alignment explanation
Indices: 943723--943764 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
943713 AGAATGTTAA
*
943723 AGGGGTATCGATACTACTAC
1 AGGGGTACCGATACTACTAC
*
943743 AGGGGTACCGATACTGCTAC
1 AGGGGTACCGATACTACTAC
943763 AG
1 AG
943765 TAATTTCAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (20 bp):
AGGGGTACCGATACTACTAC
Found at i:947901 original size:16 final size:17
Alignment explanation
Indices: 947880--947915 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
947870 TTAACGTTAT
947880 TTTAAAATTAAATT-AA
1 TTTAAAATTAAATTGAA
*
947896 TTTAAATTTAAATTGAA
1 TTTAAAATTAAATTGAA
947913 TTT
1 TTT
947916 TTCTCATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAAAATTAAATTGAA
Found at i:947997 original size:18 final size:18
Alignment explanation
Indices: 947974--948016 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
947964 AAGTATCATA
947974 ATTATATGTTTATTTATT
1 ATTATATGTTTATTTATT
947992 ATTATATGTTTATTTATT
1 ATTATATGTTTATTTATT
*
948010 TTTATAT
1 ATTATAT
948017 AAATTTTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
ATTATATGTTTATTTATT
Found at i:948139 original size:24 final size:23
Alignment explanation
Indices: 948112--948167 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
948102 ATCTAATATT
948112 TAATATAAAGAAT-AAATAAATAAA
1 TAATATAAA-AATAAAATAAA-AAA
*
948136 TAATATTATAAATAAAATAAAAAA
1 TAATA-TAAAAATAAAATAAAAAA
948160 TGAATATA
1 T-AATATA
948168 TTCCTTGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.29
Consensus pattern (23 bp):
TAATATAAAAATAAAATAAAAAA
Found at i:950054 original size:24 final size:24
Alignment explanation
Indices: 950027--950072 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
950017 AGATATAGAA
* *
950027 TTTTTATATTTGT-AGTTATGTAT
1 TTTTTTTATTTCTAAGTTATGTAT
*
950050 TTTTTTTCTTTCTAAGTTATGTA
1 TTTTTTTATTTCTAAGTTATGTA
950073 AAATGAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.04, G:0.11, T:0.65
Consensus pattern (24 bp):
TTTTTTTATTTCTAAGTTATGTAT
Found at i:951793 original size:2 final size:2
Alignment explanation
Indices: 951786--951820 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
951776 TTTCTTAAAT
951786 TA TA TA 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 TA TA TA T
951821 TAAAAGAACC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:959869 original size:37 final size:37
Alignment explanation
Indices: 959782--959879 Score: 106
Period size: 37 Copynumber: 2.6 Consensus size: 37
959772 GTCCTATTAC
* *
959782 GATTTAAACTCCTAAAAATAGGATAAAATTTTGCTAG
1 GATTTAAACTCCTAAAAATAGGATAAAATTCTACTAG
* * * * * *
959819 GATTCAAATTCCTAAAAATATGATAGAGTTCTACTAT
1 GATTTAAACTCCTAAAAATAGGATAAAATTCTACTAG
* *
959856 TATTTAAACTCCTAAAGATAGGAT
1 GATTTAAACTCCTAAAAATAGGAT
959880 CCACAAGTAT
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 48 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.34
Consensus pattern (37 bp):
GATTTAAACTCCTAAAAATAGGATAAAATTCTACTAG
Found at i:960329 original size:22 final size:21
Alignment explanation
Indices: 960304--960348 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
960294 TATATATATA
960304 TTATTATA-TTTTATTTATTTAT
1 TTATTATACTTTT-TTT-TTTAT
960326 TTATTATACTTTTTTTTTTAT
1 TTATTATACTTTTTTTTTTAT
960347 TT
1 TT
960349 TTCTTTGTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 7 0.32
22 11 0.50
23 4 0.18
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATTATACTTTTTTTTTTAT
Found at i:960387 original size:2 final size:2
Alignment explanation
Indices: 960380--960420 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
960370 ATTTTCTTAT
960380 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
960421 TATTTTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:960446 original size:21 final size:20
Alignment explanation
Indices: 960420--960468 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
960410 TATATATATA
*
960420 TTATTTTTTATCTATGTTTAC
1 TTATTTTTTATAT-TGTTTAC
* *
960441 TTATTTATTATATTTTTTAC
1 TTATTTTTTATATTGTTTAC
960461 TATATTTT
1 T-TATTTT
960469 CTTAATGTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.69
Consensus pattern (20 bp):
TTATTTTTTATATTGTTTAC
Found at i:960483 original size:30 final size:29
Alignment explanation
Indices: 960416--960483 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 29
960406 TATATATATA
*
960416 TATATTATTTTTTATCTATGTTTACTTATT
1 TATA-TATTTTTTATCTATATTTACTTATT
*
960446 TATTATATTTTTTA-CTATATTTTCTTAATGT
1 TA-TATATTTTTTATCTATATTTACTT-AT-T
960477 TATATAT
1 TATATAT
960484 ATATTCTTAC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
29 10 0.30
30 18 0.55
31 5 0.15
ACGTcount: A:0.26, C:0.06, G:0.03, T:0.65
Consensus pattern (29 bp):
TATATATTTTTTATCTATATTTACTTATT
Found at i:960646 original size:11 final size:11
Alignment explanation
Indices: 960613--960665 Score: 63
Period size: 11 Copynumber: 4.7 Consensus size: 11
960603 TATACATACA
960613 TTTTTATATTT
1 TTTTTATATTT
960624 TTTATATATATTT
1 TTT-T-TATATTT
*
960637 TTTTTTTATTT
1 TTTTTATATTT
960648 TTTTT-TATTT
1 TTTTTATATTT
*
960658 TATTTATA
1 TTTTTATA
960666 CTATTTATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 9 0.24
11 16 0.43
12 2 0.05
13 10 0.27
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTATATTT
Found at i:960650 original size:13 final size:13
Alignment explanation
Indices: 960613--960653 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
960603 TATACATACA
960613 TTTTTATATTTTT
1 TTTTTATATTTTT
* *
960626 TATATATATTTTT
1 TTTTTATATTTTT
960639 TTTTTAT-TTTTT
1 TTTTTATATTTTT
960651 TTT
1 TTT
960654 ATTTTATTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTTTATATTTTT
Found at i:961997 original size:19 final size:20
Alignment explanation
Indices: 961961--961998 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
961951 ACATTACTAA
*
961961 CTCTTTTCATTTTTTTTCCT
1 CTCTTTTCATTTTATTTCCT
961981 CTCTTTT-ATTTTATTTCC
1 CTCTTTTCATTTTATTTCC
961999 ATCATCTGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
CTCTTTTCATTTTATTTCCT
Found at i:965396 original size:13 final size:13
Alignment explanation
Indices: 965380--965410 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
965370 CAAAAAAGGG
965380 AAAAAAAAAGAAC
1 AAAAAAAAAGAAC
*
965393 AAAAAGAAAGAAC
1 AAAAAAAAAGAAC
965406 AAAAA
1 AAAAA
965411 TTGAAAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.84, C:0.06, G:0.10, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAC
Found at i:965398 original size:32 final size:32
Alignment explanation
Indices: 965340--965400 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
965330 CAATCATAAC
*
965340 AAAAAGGGCAAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGGGCAAAAAGAAAAAAAAAAAGAAGCA
965372 AAAAAGGG-AAAAA-AAAAGAACAAAAAGAA
1 AAAAAGGGCAAAAAGAAAA-AA-AAAAAGAA
965401 AGAACAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 4 0.15
31 7 0.27
32 15 0.58
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (32 bp):
AAAAAGGGCAAAAAGAAAAAAAAAAAGAAGCA
Found at i:965409 original size:23 final size:23
Alignment explanation
Indices: 965347--965410 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 23
965337 AACAAAAAGG
*
965347 GCAAAAAGAAA-AAAGAAAAGAA
1 GCAAAAAGAAAGAAAAAAAAGAA
**
965369 GCAAAAA-AGGGAAAAAAAAAGAA
1 GCAAAAAGAAAG-AAAAAAAAGAA
*
965392 -CAAAAAGAAAGAACAAAAA
1 GCAAAAAGAAAGAAAAAAAA
965411 TTGAAAGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 1 0.03
22 20 0.61
23 12 0.36
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (23 bp):
GCAAAAAGAAAGAAAAAAAAGAA
Found at i:966053 original size:22 final size:22
Alignment explanation
Indices: 966025--966079 Score: 110
Period size: 22 Copynumber: 2.5 Consensus size: 22
966015 GCTACCCCAT
966025 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
966047 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
966069 CAAACCTTTGA
1 CAAACCTTTGA
966080 CCAAACACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:967167 original size:106 final size:106
Alignment explanation
Indices: 967038--968301 Score: 1936
Period size: 106 Copynumber: 12.0 Consensus size: 106
967028 ATATCGTGCC
* * * * * *
967038 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTTAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
967103 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
967144 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
967209 AATTTCAGAGCCAATTTCAACTTCAC-GACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
* * *
967250 ACTCCAGACAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
967315 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
967356 ACTCAAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
967421 AATTTCATAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
967462 ACTCCAGACAACGCAAGTTCAACATCACGACGAAGGGACCGCTGGTTGTTAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
967527 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
967568 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCACTGGTTGTCAACAAATAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
967633 AATTTCATAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
967674 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAAAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
967739 AATTTCGGAGCCAATTTCAACTTCACAACGAAAGATATTGT
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
967780 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
967845 AATTTTGGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
967886 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
967951 AATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
967992 ACTCCAG---A--CAA---CAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
968049 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
968090 ACTCGAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
968155 AATTTCTGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * *
968196 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
968261 GATTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
968302 TCTCGGAGCA
Statistics
Matches: 1065, Mismatches: 82, Indels: 22
0.91 0.07 0.02
Matches are distributed among these distances:
98 89 0.08
101 4 0.00
103 4 0.00
105 1 0.00
106 966 0.91
107 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:969149 original size:37 final size:37
Alignment explanation
Indices: 969055--969151 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
969045 CATTTTCGTC
969055 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * *
969092 TTGCTAGGATTCAAATTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
** *
969129 CTACTATTATTTAAACTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
969152 GATATGATCC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:969574 original size:2 final size:2
Alignment explanation
Indices: 969561--969609 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
969551 TCTTATTATT
*
969561 TA TA TG TA TA TA 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 TA TA TA TA TA TA TA
969602 TA T- TA TA T
1 TA TA TA TA T
969610 TTTATTTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:969628 original size:24 final size:25
Alignment explanation
Indices: 969601--969684 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 25
969591 TATATATATA
969601 TTATTATATTTTATTTATTTTT-TT
1 TTATTATATTTTATTTATTTTTCTT
* * *
969625 TTATAATTTTTTTTTTATTTTTCTT
1 TTATTATATTTTATTTATTTTTCTT
* * * *
969650 TGTGTTATATTATA-TTATTTTCCTA
1 T-TATTATATTTTATTTATTTTTCTT
969675 TTATATATAT
1 TTAT-TATAT
969685 ATATATATAT
Statistics
Matches: 46, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
24 21 0.46
25 18 0.39
26 7 0.15
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (25 bp):
TTATTATATTTTATTTATTTTTCTT
Found at i:969646 original size:10 final size:11
Alignment explanation
Indices: 969604--969646 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
969594 ATATATATTA
*
969604 TTATATTTTAT
1 TTATATTTTTT
969615 TTAT-TTTTTT
1 TTATATTTTTT
969625 TTATAATTTTTT
1 TTAT-ATTTTTT
*
969637 TTTTATTTTT
1 TTATATTTTT
969647 CTTTGTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.32
11 10 0.36
12 9 0.32
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
TTATATTTTTT
Found at i:969683 original size:2 final size:2
Alignment explanation
Indices: 969676--969702 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
969666 ATTTTCCTAT
969676 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 T
969703 TTTTTTTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:969929 original size:30 final size:30
Alignment explanation
Indices: 969894--969957 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
969884 TTAAACATAC
*
969894 ATTTTTATATTTTTATATATA-TATTT-TTT
1 ATTTTTTTA-TTTTATATATACTATTTATTT
*
969923 ATTTTTTTATTTTATTTATACTATTTATTT
1 ATTTTTTTATTTTATATATACTATTTATTT
969953 ATTTT
1 ATTTT
969958 CATTATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
28 10 0.32
29 13 0.42
30 8 0.26
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (30 bp):
ATTTTTTTATTTTATATATACTATTTATTT
Found at i:970066 original size:18 final size:19
Alignment explanation
Indices: 970042--970085 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
970032 TGTATATATA
*
970042 TTTTTTTCTTC-ATTT-AT
1 TTTTTTTATTCAATTTCAT
970059 TTTATTTTATTCAATTTCAT
1 TTT-TTTTATTCAATTTCAT
970079 TTTTTTT
1 TTTTTTT
970086 TTGTATTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 3 0.13
18 7 0.30
19 8 0.35
20 5 0.22
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTTTTTATTCAATTTCAT
Found at i:970182 original size:3 final size:3
Alignment explanation
Indices: 970174--970203 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
970164 TTACTTTCTT
970174 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
970204 ACATCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:976026 original size:10 final size:10
Alignment explanation
Indices: 976011--976041 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
976001 CACTATTCAC
976011 ATGAATAGTA
1 ATGAATAGTA
*
976021 ATGAATATTA
1 ATGAATAGTA
976031 ATGAATAGTA
1 ATGAATAGTA
976041 A
1 A
976042 CATCGCAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (10 bp):
ATGAATAGTA
Found at i:983230 original size:59 final size:59
Alignment explanation
Indices: 983167--983298 Score: 140
Period size: 59 Copynumber: 2.2 Consensus size: 59
983157 AGGGATAATG
* ** * * *
983167 GTTTCAAGGGAAACCGACTCAAAGA-TGATGTTTCAAAAGAAATATACTCAAAGACTTTT
1 GTTTCAAGAGAAACAAAATCAAAGATTGATGTTTCAAAAGAAACAGACTCAAAGA-TTTT
** *
983226 GTTTCAAGAGAAACAAAATCAAAGATTTTTGTTTCAAGAGAAACAGACTCAAAGATTTT
1 GTTTCAAGAGAAACAAAATCAAAGATTGATGTTTCAAAAGAAACAGACTCAAAGATTTT
** *
983285 CCTTCAAAAGAAAC
1 GTTTCAAGAGAAAC
983299 TGTCTCAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
59 36 0.60
60 24 0.40
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.27
Consensus pattern (59 bp):
GTTTCAAGAGAAACAAAATCAAAGATTGATGTTTCAAAAGAAACAGACTCAAAGATTTT
Found at i:983296 original size:29 final size:30
Alignment explanation
Indices: 983167--983426 Score: 161
Period size: 29 Copynumber: 8.4 Consensus size: 30
983157 AGGGATAATG
** * **
983167 GTTTCAAGGGAAACCGACTCAAAGA-TGAT
1 GTTTCAAAAGAAACAGACTCAAAGACTTTT
* *
983196 GTTTCAAAAGAAATATACTCAAAGACTTTT
1 GTTTCAAAAGAAACAGACTCAAAGACTTTT
* * * *
983226 GTTTCAAGAGAAACAAAATCAAAGATTTTT
1 GTTTCAAAAGAAACAGACTCAAAGACTTTT
*
983256 GTTTCAAGAGAAACAGACTCAAAGA-TTTT
1 GTTTCAAAAGAAACAGACTCAAAGACTTTT
** * *
983285 CCTTCAAAAGAAACTGTCTCAAAAGAGACAAAATTTT
1 GTTTCAAAAGAAACAGACTC--AA-AGAC----TTTT
* *
983322 GTTTCCAAAGAAACATACTCAAAGA-TTTT
1 GTTTCAAAAGAAACAGACTCAAAGACTTTT
* *
983351 -TCTTCAAAAGAAACTGTCTCAAGAGACAAAATTTT
1 GT-TTCAAAAGAAACAGACTCAA-AGAC----TTTT
* *
983386 GTTTCCAAAGAAACAGACTCAAATA-TTTT
1 GTTTCAAAAGAAACAGACTCAAAGACTTTT
*
983415 TTTTCAAAAGAA
1 GTTTCAAAAGAA
983427 TTTGTCTCGA
Statistics
Matches: 179, Mismatches: 35, Indels: 34
0.72 0.14 0.14
Matches are distributed among these distances:
28 1 0.01
29 73 0.41
30 53 0.30
31 2 0.01
32 3 0.02
34 5 0.03
35 23 0.13
36 1 0.01
37 18 0.10
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (30 bp):
GTTTCAAAAGAAACAGACTCAAAGACTTTT
Found at i:983424 original size:130 final size:129
Alignment explanation
Indices: 983252--983668 Score: 504
Period size: 130 Copynumber: 3.2 Consensus size: 129
983242 AATCAAAGAT
** *
983252 TTTTGTTTCAAGAGAAACAGACTCAAAGATTTTCCTTCAAAAGAAACTGTCTCAAAAGAGACAAA
1 TTTTGTTTCAAGAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAATTGTCTCAAAAGAGACAAA
* * *
983317 ATTTTGTTTCCAAAGAAACATACTCAAAGATTTTTCTTCAAAAGAAACTGTCTCAAGAGACAAAA
66 AATTTGTTTCCAAAGAAACAAACTCAAAGATTTTT-TTCAAAAGAAATTGTCTCAAGAGACAAAA
* * * *
983382 TTTTGTTTCCAA-AGAAACAGACTCAAATATTTTTTTTCAAAAGAATTTGTCTCGAGAGAGACAA
1 TTTTGTTT-CAAGAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAATTGTCTCAAAAGAGACAA
*
983446 AACTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGAGAC
65 AAATTTGTTTCCAAAGAAACAAACTCAAAGA-TTTTTT-TCAAAAGAAATTGTCTC-A-AGAGAC
983511 AAAA
126 AAAA
* * * *
983515 TTTTGTTTCCAA-ATAAACAAACTTAAAGA-TTTTTTTCAAAAGAAATTGTCTCAATAGAGACAA
1 TTTTGTTT-CAAGAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAATTGTCTCAAAAGAGACAA
* * * * * * * *
983578 AAATTTATTTCCAGAGAAACAGACTCAAAG-TGTTTTTCTAAAACAAATTATCTCGAGAGACCAA
65 AAATTTGTTTCCAAAGAAACAAACTCAAAGATTTTTTTC-AAAAGAAATTGTCTCAAGAGACAAA
983642 A
129 A
*
983643 -TTTGTTTCAAGAGAAGCA-ACTCAAAG
1 TTTTGTTTCAAGAGAAACAGACTCAAAG
983669 GATATTGATA
Statistics
Matches: 251, Mismatches: 29, Indels: 18
0.84 0.10 0.06
Matches are distributed among these distances:
126 10 0.04
127 12 0.05
128 9 0.04
129 2 0.01
130 101 0.40
131 24 0.10
132 58 0.23
133 35 0.14
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (129 bp):
TTTTGTTTCAAGAGAAACAGACTCAAAGATTTTTTTTCAAAAGAAATTGTCTCAAAAGAGACAAA
AATTTGTTTCCAAAGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTCAAGAGACAAAA
Found at i:983561 original size:65 final size:65
Alignment explanation
Indices: 983252--983668 Score: 501
Period size: 66 Copynumber: 6.4 Consensus size: 65
983242 AATCAAAGAT
* * *
983252 TTTTGTTT-CAAGAGAAACAGACTCAAAGATTTTCCTTCAAAAGAAACTGTCTCAAAAGAGACAA
1 TTTTGTTTCCAA-AGAAACAGACTCAAAGATTTT-TTTCAAAAGAAATTGTCTCAAGAGAGACAA
983316 AA
64 AA
* *
983318 TTTTGTTTCCAAAGAAACATACTCAAAGATTTTTCTTCAAAAGAAACTGTCTC-A-AGAGACAAA
1 TTTTGTTTCCAAAGAAACAGACTCAAAGATTTTT-TTCAAAAGAAATTGTCTCAAGAGAGACAAA
983381 A
65 A
* * *
983382 TTTTGTTTCCAAAGAAACAGACTCAAATATTTTTTTTCAAAAGAATTTGTCTCGAGAGAGACAAA
1 TTTTGTTTCCAAAGAAACAGACTCAAAGA-TTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAA
983447 A
65 A
* *
983448 CTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTTTCTCAAAAGAAATTGTCTCAAGAGAGACAA
1 TTTTGTTTCCAAAGAAACAGACTCAAAGA-TTTTTT-TCAAAAGAAATTGTCTCAAGAGAGACAA
983513 AA
64 AA
* * * *
983515 TTTTGTTTCCAAATAAACAAACTTAAAGATTTTTTTCAAAAGAAATTGTCTCAATAGAGACAAAA
1 TTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAA
* * * * * * *
983580 ATTTATTTCCAGAGAAACAGACTCAAAG-TGTTTTTCTAAAACAAATTATCTC--GAGAGACCAA
1 TTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTC-AAAAGAAATTGTCTCAAGAGAGACAAA
983642 A
65 A
*
983643 -TTTGTTT-CAAGAGAAGCA-ACTCAAAG
1 TTTTGTTTCCAA-AGAAACAGACTCAAAG
983669 GATATTGATA
Statistics
Matches: 314, Mismatches: 29, Indels: 21
0.86 0.08 0.06
Matches are distributed among these distances:
61 10 0.03
62 12 0.04
63 9 0.03
64 60 0.19
65 71 0.23
66 95 0.30
67 57 0.18
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (65 bp):
TTTTGTTTCCAAAGAAACAGACTCAAAGATTTTTTTCAAAAGAAATTGTCTCAAGAGAGACAAAA
Found at i:983801 original size:32 final size:32
Alignment explanation
Indices: 983738--983801 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
983728 TTCGCATCAA
*
983738 GATGTTGAATCCCCAAAGAAGCCCTAACATTC
1 GATGTTGAATCCCCAAAGAAGCCCCAACATTC
* *
983770 GATGTTGAATCCCCAAAGATGCCCCATCATTC
1 GATGTTGAATCCCCAAAGAAGCCCCAACATTC
983802 ATCGTTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (32 bp):
GATGTTGAATCCCCAAAGAAGCCCCAACATTC
Found at i:987775 original size:2 final size:2
Alignment explanation
Indices: 987768--987801 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
987758 TATTTGAAAT
987768 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
987802 ATTGTTGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:988888 original size:14 final size:14
Alignment explanation
Indices: 988869--988896 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
988859 GACGTTATCC
988869 AAGAGTCTCGAATA
1 AAGAGTCTCGAATA
988883 AAGAGTCTCGAATA
1 AAGAGTCTCGAATA
988897 TATACTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AAGAGTCTCGAATA
Found at i:989450 original size:2 final size:2
Alignment explanation
Indices: 989443--989486 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
989433 ATCTAACTTG
989443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
989485 AT
1 AT
989487 TATTTTGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:999219 original size:15 final size:14
Alignment explanation
Indices: 999193--999239 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
999183 TATTAGAACA
999193 ATTTATTTAATATT
1 ATTTATTTAATATT
*
999207 ATTTATGTTAATATC
1 ATTTAT-TTAATATT
*
999222 A-TTATTAAAATATT
1 ATTTATT-TAATATT
999236 ATTT
1 ATTT
999240 CTATAATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 1 0.04
14 16 0.59
15 10 0.37
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (14 bp):
ATTTATTTAATATT
Found at i:999289 original size:31 final size:33
Alignment explanation
Indices: 999231--999311 Score: 98
Period size: 32 Copynumber: 2.5 Consensus size: 33
999221 CATTATTAAA
* *
999231 ATATTATTTCTATAATAAATAATATAAT-TTAT
1 ATATTATTACTAAAATAAATAATATAATGTTAT
999263 -TATATATTACTAAAATAAA-AATATAATGTTAT
1 ATAT-TATTACTAAAATAAATAATATAATGTTAT
*
999295 ATATTATTA-TAATATAA
1 ATATTATTACTAAAATAA
999312 TTATTTTAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
31 18 0.42
32 22 0.51
33 3 0.07
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (33 bp):
ATATTATTACTAAAATAAATAATATAATGTTAT
Found at i:999308 original size:29 final size:31
Alignment explanation
Indices: 999235--999308 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 31
999225 ATTAAAATAT
*
999235 TATTTCTATAATAAATAATATAATTTATTATA
1 TATTACTATAATAAATAATATAA-TTATTATA
* *
999267 TATTACTAAAATAAA-AATATAA-TGTTATA
1 TATTACTATAATAAATAATATAATTATTATA
*
999296 TATTATTATAATA
1 TATTACTATAATA
999309 TAATTATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
29 17 0.46
31 7 0.19
32 13 0.35
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (31 bp):
TATTACTATAATAAATAATATAATTATTATA
Found at i:1007154 original size:27 final size:27
Alignment explanation
Indices: 1007116--1007226 Score: 159
Period size: 27 Copynumber: 4.1 Consensus size: 27
1007106 GTTTGCATGT
1007116 GGCTTTGATGATACCGGAGGCCTTTGG
1 GGCTTTGATGATACCGGAGGCCTTTGG
* *
1007143 GGCTTTGATGATACTGGAGGCCTTTGT
1 GGCTTTGATGATACCGGAGGCCTTTGG
* *
1007170 GGCTTTGATGACACCGGAGGCCTTTGT
1 GGCTTTGATGATACCGGAGGCCTTTGG
* **
1007197 GGCTTTGATGAAAGTGGAGGCCTTTGG
1 GGCTTTGATGATACCGGAGGCCTTTGG
1007224 GGC
1 GGC
1007227 ATCATTTTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 76 1.00
ACGTcount: A:0.15, C:0.17, G:0.37, T:0.31
Consensus pattern (27 bp):
GGCTTTGATGATACCGGAGGCCTTTGG
Found at i:1007176 original size:54 final size:54
Alignment explanation
Indices: 1007113--1007222 Score: 184
Period size: 54 Copynumber: 2.0 Consensus size: 54
1007103 CTTGTTTGCA
* *
1007113 TGTGGCTTTGATGATACCGGAGGCCTTTGGGGCTTTGATGATACTGGAGGCCTT
1 TGTGGCTTTGATGACACCGGAGGCCTTTGGGGCTTTGATGAAACTGGAGGCCTT
* *
1007167 TGTGGCTTTGATGACACCGGAGGCCTTTGTGGCTTTGATGAAAGTGGAGGCCTT
1 TGTGGCTTTGATGACACCGGAGGCCTTTGGGGCTTTGATGAAACTGGAGGCCTT
1007221 TG
1 TG
1007223 GGGCATCATT
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.15, C:0.16, G:0.35, T:0.33
Consensus pattern (54 bp):
TGTGGCTTTGATGACACCGGAGGCCTTTGGGGCTTTGATGAAACTGGAGGCCTT
Found at i:1007486 original size:36 final size:36
Alignment explanation
Indices: 1007417--1007487 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
1007407 TTAGGGCCAA
* * *
1007417 CAGGCCGGCCATACCCAGTATCGCTGCTAGAACCAG
1 CAGGCCGGCCAGACCCAGTACCACTGCTAGAACCAG
* *
1007453 CAGGCCGGCCAGACCCAGTACCATTGCTTGAACCA
1 CAGGCCGGCCAGACCCAGTACCACTGCTAGAACCA
1007488 ACTGGATGGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.25, C:0.37, G:0.24, T:0.14
Consensus pattern (36 bp):
CAGGCCGGCCAGACCCAGTACCACTGCTAGAACCAG
Found at i:1009950 original size:6 final size:6
Alignment explanation
Indices: 1009939--1009964 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
1009929 TCTGGTTTCT
1009939 TCTTCC TCTTCC TCTTCC TCTTCC TC
1 TCTTCC TCTTCC TCTTCC TCTTCC TC
1009965 ATATCCCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTTCC
Found at i:1015027 original size:38 final size:39
Alignment explanation
Indices: 1014976--1015064 Score: 146
Period size: 38 Copynumber: 2.3 Consensus size: 39
1014966 AAATGACCAA
1014976 CAAATTCGCAACGCGATCTCAAATTCGCAACGC-GA-TC
1 CAAATTCGCAACGCGATCTCAAATTCGCAACGCGGACTC
1015013 TCAAATTCGCAACGCGATCTCAAATTCGCAACGCGGACTC
1 -CAAATTCGCAACGCGATCTCAAATTCGCAACGCGGACTC
*
1015053 CAATTTCGCAAC
1 CAAATTCGCAAC
1015065 CCAGTTTCCA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
38 33 0.69
39 13 0.27
40 2 0.04
ACGTcount: A:0.31, C:0.33, G:0.16, T:0.20
Consensus pattern (39 bp):
CAAATTCGCAACGCGATCTCAAATTCGCAACGCGGACTC
Found at i:1015057 original size:19 final size:19
Alignment explanation
Indices: 1014976--1015047 Score: 144
Period size: 19 Copynumber: 3.8 Consensus size: 19
1014966 AAATGACCAA
1014976 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGATCT
1014995 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGATCT
1015014 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACGCGATCT
1015033 CAAATTCGCAACGCG
1 CAAATTCGCAACGCG
1015048 GACTCCAATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 53 1.00
ACGTcount: A:0.32, C:0.32, G:0.17, T:0.19
Consensus pattern (19 bp):
CAAATTCGCAACGCGATCT
Found at i:1015142 original size:20 final size:20
Alignment explanation
Indices: 1015119--1015158 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1015109 AATTTATAAA
1015119 TCGCAACAC-AGAAGTCAAAT
1 TCGCAACACGA-AAGTCAAAT
*
1015139 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
1015159 GTTTTTACGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAGTCAAAT
Found at i:1015675 original size:20 final size:19
Alignment explanation
Indices: 1015640--1015693 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1015630 AAATCGCAAC
1015640 GCGATTTTAGTTTCGCGTT
1 GCGATTTTAGTTTCGCGTT
* *
1015659 GCGATTTTCATTTTCGCTTT
1 GCGATTTT-AGTTTCGCGTT
*
1015679 GCGAATTTAAGTTTC
1 GCG-ATTTTAGTTTC
1015694 AGAAACTTCT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 8 0.28
20 17 0.59
21 4 0.14
ACGTcount: A:0.15, C:0.17, G:0.20, T:0.48
Consensus pattern (19 bp):
GCGATTTTAGTTTCGCGTT
Found at i:1017823 original size:21 final size:21
Alignment explanation
Indices: 1017799--1017874 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
1017789 TGCACCTCCT
1017799 ATCATTCAAGAGGCCCCTCTC
1 ATCATTCAAGAGGCCCCTCTC
* * *
1017820 ATCA-TCGAAAAAGCCCCTCCC
1 ATCATTC-AAGAGGCCCCTCTC
* * *
1017841 ACCGTTCAAGAGGCCCCTTTC
1 ATCATTCAAGAGGCCCCTCTC
**
1017862 ATTGTTCAAGAGG
1 ATCATTCAAGAGG
1017875 TCCCGCCCGC
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 2 0.05
21 38 0.90
22 2 0.05
ACGTcount: A:0.26, C:0.34, G:0.17, T:0.22
Consensus pattern (21 bp):
ATCATTCAAGAGGCCCCTCTC
Found at i:1019347 original size:14 final size:14
Alignment explanation
Indices: 1019301--1019337 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1019291 TTTTGATTAA
*
1019301 TTGATTTGCAAAAG
1 TTGATTTGTAAAAG
1019315 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
1019329 TTGATTTGT
1 TTGATTTGT
1019338 TTAATTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.30, C:0.03, G:0.22, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:1019397 original size:80 final size:74
Alignment explanation
Indices: 1019251--1019403 Score: 207
Period size: 80 Copynumber: 2.0 Consensus size: 74
1019241 TTTTACATTT
*
1019251 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTATTTTTTGATTAATTGATTTGCAAAAGT
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGATTAATTGATTTGCAAAAGT
1019316 TGATTTGTA
66 TGATTTGTA
* * **
1019325 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTGTTTTGCATGTTTAATTGATTTTT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTATT-TTTTG-A---TTAATTGATTTGC
1019390 AAAAGTTGATTTGT
60 AAAAGTTGATTTGT
1019404 TGTTTCTAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
74 17 0.25
75 20 0.29
76 5 0.07
77 1 0.01
80 25 0.37
ACGTcount: A:0.32, C:0.01, G:0.18, T:0.48
Consensus pattern (74 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTGATTAATTGATTTGCAAAAGT
TGATTTGTA
Found at i:1019517 original size:20 final size:20
Alignment explanation
Indices: 1019463--1019518 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1019453 GTTGAAGGTA
*
1019463 CAAATTCGCAACGCAAAAGT
1 CAAATTCGCAACGCGAAAGT
*
1019483 TAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
1019503 CAAATTTGCAACGCGA
1 CAAATTCGCAACGCGA
1019519 TTTTCGATTT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.41, C:0.23, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:1019814 original size:39 final size:39
Alignment explanation
Indices: 1019759--1019845 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
1019749 TCAAGTTGTA
1019759 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* * *
1019798 GATTTTGATTTTCTTTTTCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1019837 GATTTTGAT
1 GATTTTGAT
1019846 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:1020210 original size:24 final size:24
Alignment explanation
Indices: 1020147--1020199 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1020137 AGTGGAGCCG
*
1020147 AAATTTATATTGAAATTCAAACTC
1 AAATTTAAATTGAAATTCAAACTC
*
1020171 AAATTTAAATTTAAATTCAAACTC
1 AAATTTAAATTGAAATTCAAACTC
*
1020195 CAATT
1 AAATT
1020200 ACATATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.47, C:0.13, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATTTAAATTGAAATTCAAACTC
Found at i:1020657 original size:20 final size:20
Alignment explanation
Indices: 1020613--1020650 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1020603 AAATAATGTA
* *
1020613 CAACATGAAAGTTAAATTCG
1 CAACGTGAAAGTCAAATTCG
1020633 CAACGTGAAAGTCAAATT
1 CAACGTGAAAGTCAAATT
1020651 TGTAACGCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.45, C:0.16, G:0.16, T:0.24
Consensus pattern (20 bp):
CAACGTGAAAGTCAAATTCG
Found at i:1020662 original size:20 final size:20
Alignment explanation
Indices: 1020619--1020662 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1020609 TGTACAACAT
* *
1020619 GAAAGTTAAATTCGCAACGT
1 GAAAGTCAAATTCGCAACGC
* *
1020639 GAAAGTCAAATTTGTAACGC
1 GAAAGTCAAATTCGCAACGC
1020659 GAAA
1 GAAA
1020663 TAAGCGTTGC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (20 bp):
GAAAGTCAAATTCGCAACGC
Found at i:1023477 original size:12 final size:12
Alignment explanation
Indices: 1023456--1023489 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1023446 GGTTATGGGT
*
1023456 TTTGAGATTGTG
1 TTTGATATTGTG
1023468 TTTGATATTGTG
1 TTTGATATTGTG
*
1023480 TTTGGTATTG
1 TTTGATATTG
1023490 GAAATCTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1024078 original size:14 final size:15
Alignment explanation
Indices: 1024042--1024079 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
1024032 GAAATCATTG
1024042 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
1024057 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
1024072 AAAAATTA
1 AAAAATTA
1024080 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:1024230 original size:19 final size:21
Alignment explanation
Indices: 1024206--1024337 Score: 143
Period size: 19 Copynumber: 6.6 Consensus size: 21
1024196 ACTAAAACAT
*
1024206 GTTGCGAAATT-AAA-TTCGC
1 GTTGCGAATTTGAAATTTCGC
*
1024225 GTTGCGAATTTGAAA-TTC-A
1 GTTGCGAATTTGAAATTTCGC
*
1024244 GTTGCGAATTTGAAATTTTGC
1 GTTGCGAATTTGAAATTTCGC
*
1024265 GTTGCGAATTTGAAATTTTGC
1 GTTGCGAATTTGAAATTTCGC
*
1024286 GTTGCGAATTTG-AATTT-GT
1 GTTGCGAATTTGAAATTTCGC
* * *
1024305 GTTGCAAATTTG-ACTATCGC
1 GTTGCGAATTTGAAATTTCGC
1024325 GTTGCGAATTTGA
1 GTTGCGAATTTGA
1024338 CTTCTGTGTT
Statistics
Matches: 98, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
19 40 0.41
20 25 0.26
21 33 0.34
ACGTcount: A:0.26, C:0.11, G:0.23, T:0.39
Consensus pattern (21 bp):
GTTGCGAATTTGAAATTTCGC
Found at i:1024242 original size:20 final size:20
Alignment explanation
Indices: 1024206--1024417 Score: 150
Period size: 20 Copynumber: 10.6 Consensus size: 20
1024196 ACTAAAACAT
*
1024206 GTTGCGAAATT-AAATTCGC
1 GTTGCGAATTTGAAATTCGC
*
1024225 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGC
*
1024244 GTTGCGAATTTGAAATTTTGC
1 GTTGCGAATTTGAAA-TTCGC
*
1024265 GTTGCGAATTTGAAATTTTGC
1 GTTGCGAATTTGAAA-TTCGC
* *
1024286 GTTGCGAATTTG-AATTTGT
1 GTTGCGAATTTGAAATTCGC
* *
1024305 GTTGCAAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGC
* *
1024325 GTTGCGAATTTG-ACTTCTGT
1 GTTGCGAATTTGAAATTC-GC
*
1024345 GTTGCGAATTTGGAAAATCGC
1 GTTGCGAATTT-GAAATTCGC
**
1024366 AATGCG-ATTT-ACATATTCGC
1 GTTGCGAATTTGA-A-ATTCGC
* * * *
1024386 GTTGTGAAATTGGAGTTCGC
1 GTTGCGAATTTGAAATTCGC
*
1024406 GTTGTGAATTTG
1 GTTGCGAATTTG
1024418 TTGGTCATTT
Statistics
Matches: 158, Mismatches: 24, Indels: 21
0.78 0.12 0.10
Matches are distributed among these distances:
18 1 0.01
19 45 0.28
20 66 0.42
21 43 0.27
22 3 0.02
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGC
Found at i:1024270 original size:21 final size:21
Alignment explanation
Indices: 1024206--1024356 Score: 140
Period size: 19 Copynumber: 7.6 Consensus size: 21
1024196 ACTAAAACAT
* *
1024206 GTTGCGAAATT-AAA-TTCGC
1 GTTGCGAATTTGAAATTTTGC
1024225 GTTGCGAATTTGAAA--TT-C
1 GTTGCGAATTTGAAATTTTGC
1024243 AGTTGCGAATTTGAAATTTTGC
1 -GTTGCGAATTTGAAATTTTGC
1024265 GTTGCGAATTTGAAATTTTGC
1 GTTGCGAATTTGAAATTTTGC
*
1024286 GTTGCGAATTTG-AA-TTTGT
1 GTTGCGAATTTGAAATTTTGC
* * * *
1024305 GTTGCAAATTTG-ACTATCGC
1 GTTGCGAATTTGAAATTTTGC
* * *
1024325 GTTGCGAATTTG-ACTTCTGT
1 GTTGCGAATTTGAAATTTTGC
1024345 GTTGCGAATTTG
1 GTTGCGAATTTG
1024357 GAAAATCGCA
Statistics
Matches: 113, Mismatches: 13, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
18 1 0.01
19 42 0.37
20 34 0.30
21 35 0.31
22 1 0.01
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (21 bp):
GTTGCGAATTTGAAATTTTGC
Found at i:1025460 original size:16 final size:16
Alignment explanation
Indices: 1025435--1025465 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1025425 GTTCTAAATT
*
1025435 TTTTTTGAGTTCAAGC
1 TTTTTCGAGTTCAAGC
1025451 TTTTTCGAGTTCAAG
1 TTTTTCGAGTTCAAG
1025466 TTTCAATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.13, G:0.19, T:0.48
Consensus pattern (16 bp):
TTTTTCGAGTTCAAGC
Found at i:1026791 original size:6 final size:6
Alignment explanation
Indices: 1026780--1026810 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1026770 TTTGGCTGTT
1026780 GTGCAG GTGCAG GTGCAG GTGCAG GTGCAG G
1 GTGCAG GTGCAG GTGCAG GTGCAG GTGCAG G
1026811 ACGTTTACCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.52, T:0.16
Consensus pattern (6 bp):
GTGCAG
Found at i:1027276 original size:16 final size:17
Alignment explanation
Indices: 1027255--1027290 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
1027245 TTAATGTTAT
1027255 TTTAAAATTAAATT-AA
1 TTTAAAATTAAATTGAA
*
1027271 TTTAAATTTAAATTGAA
1 TTTAAAATTAAATTGAA
1027288 TTT
1 TTT
1027291 TTCTCATATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (17 bp):
TTTAAAATTAAATTGAA
Found at i:1029106 original size:19 final size:20
Alignment explanation
Indices: 1029062--1029106 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1029052 ATTTGGTTTT
*
1029062 AATAAATTTTTATATATGAA
1 AATAAATTTTTATATATCAA
* *
1029082 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATATATCAA
1029101 AATAAA
1 AATAAA
1029107 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATATATCAA
Found at i:1031412 original size:55 final size:55
Alignment explanation
Indices: 1031316--1031723 Score: 627
Period size: 55 Copynumber: 7.4 Consensus size: 55
1031306 TACCGAATGA
* * *
1031316 CACTGTGTGTGCAAAAATTTAAGAAATTCATACTAAGTGTATGAATTTTCGTATGGG
1 CACTATGTGTGC-AAAA-CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
*
1031373 CACTATGTGTGCAAAACTAAGAAATTCATACTAAATGTATGAATTTCCGTATGGG
1 CACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
* * * *
1031428 CACTATGTATGTAAAACTAAGAAATCCATACTATGTGTATGAATTTCCGTATGGG
1 CACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
* * * *
1031483 CACTATGTGTACAAAACTAAGAAATTCATAATATGTGTATGAATTTCTGTATGGG
1 CACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
* *
1031538 CACTATGTATACAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
1 CACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
** *
1031593 CACTATGTGTGCAAAACTAAGAAATTCATACTTTGTGTATGAATTTTCGTATGGG
1 CACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
*
1031648 CACTATGTGTGCAAAACAAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
1 CACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
*
1031703 TACTATGTGTGCAAAACTAAG
1 CACTATGTGTGCAAAACTAAG
1031724 GTGGTGTTTG
Statistics
Matches: 321, Mismatches: 30, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
55 306 0.95
56 4 0.01
57 11 0.03
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (55 bp):
CACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGG
Found at i:1031932 original size:12 final size:12
Alignment explanation
Indices: 1031915--1031959 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 12
1031905 TTCAAAGAGG
1031915 TTTTATATTTTA
1 TTTTATATTTTA
1031927 TTTTATA--TTA
1 TTTTATATTTTA
* *
1031937 TATTATATTTGA
1 TTTTATATTTTA
1031949 TTTTA-ATTTTA
1 TTTTATATTTTA
1031960 ATATTAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
10 9 0.33
11 5 0.19
12 13 0.48
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATATTTTA
Found at i:1031945 original size:22 final size:24
Alignment explanation
Indices: 1031917--1031970 Score: 69
Period size: 22 Copynumber: 2.4 Consensus size: 24
1031907 CAAAGAGGTT
1031917 TTATATTTTATTTT-ATATT-ATA
1 TTATATTTTATTTTAATATTAATA
* *
1031939 TTATATTTGATTTTAATTTTAATA
1 TTATATTTTATTTTAATATTAATA
1031963 TTA-ATTTT
1 TTATATTTT
1031971 TTAAATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.48
23 8 0.30
24 6 0.22
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (24 bp):
TTATATTTTATTTTAATATTAATA
Found at i:1031986 original size:24 final size:24
Alignment explanation
Indices: 1031959--1032027 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 24
1031949 TTTTAATTTT
1031959 AATATTAATTTTTTAAATAAATTA
1 AATATTAATTTTTTAAATAAATTA
1031983 AATATTAATTTTTTAATATTAATAAATTA
1 AATATTAA-TTTTT--TA--AATAAATTA
1032012 AATATTAATTTTTTAA
1 AATATTAATTTTTTAA
1032028 TATTATACTA
Statistics
Matches: 40, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
24 9 0.22
25 5 0.12
26 2 0.05
27 2 0.05
28 5 0.12
29 17 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AATATTAATTTTTTAAATAAATTA
Found at i:1032015 original size:15 final size:15
Alignment explanation
Indices: 1031974--1032020 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1031964 TAATTTTTTA
1031974 AATAAATTAAATATT
1 AATAAATTAAATATT
** *
1031989 AAT-TTTTTAATATT
1 AATAAATTAAATATT
1032003 AATAAATTAAATATT
1 AATAAATTAAATATT
1032018 AAT
1 AAT
1032021 TTTTTAATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
14 11 0.44
15 14 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTAAATATT
Found at i:1032052 original size:29 final size:29
Alignment explanation
Indices: 1031974--1032032 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1031964 TAATTTTTTA
1031974 AATAAATTAAATATTAATTTTTTAATATT
1 AATAAATTAAATATTAATTTTTTAATATT
1032003 AATAAATTAAATATTAATTTTTTAATATT
1 AATAAATTAAATATTAATTTTTTAATATT
1032032 A
1 A
1032033 TACTATAGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
AATAAATTAAATATTAATTTTTTAATATT
Found at i:1032108 original size:20 final size:19
Alignment explanation
Indices: 1032048--1032109 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
1032038 TAGATATTTA
*
1032048 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
1032067 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
1032085 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
1032105 ATTTT
1 ATTTT
1032110 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:1032631 original size:31 final size:31
Alignment explanation
Indices: 1032572--1032632 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
1032562 GTAGTTGTAT
* **
1032572 AAATTATTTAAATTTCAGTATTTTAAAACTA
1 AAATTATTTAAATCTCAGTATTGCAAAACTA
1032603 AAATTATTTAAATCTCAGTATTGCAAAACT
1 AAATTATTTAAATCTCAGTATTGCAAAACT
1032633 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
AAATTATTTAAATCTCAGTATTGCAAAACTA
Found at i:1033561 original size:54 final size:54
Alignment explanation
Indices: 1033476--1033740 Score: 410
Period size: 54 Copynumber: 4.9 Consensus size: 54
1033466 GGTAATTCAC
* * *
1033476 AACTTATTATGAATTAT-GTGGGTTTGCACACACAGTGCCAATATGGAAATTCATA
1 AACTTATTATGAATT-TCTTAGG-TTGCACACACAGTGCCAATACGGAAATTCATA
*
1033531 AACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGAAAATTCATA
1 AACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAATTCATA
*
1033585 AACTTATTATGAATTTCTTAGGTTGCACACACAGTGCTAATACGGAAATTCATA
1 AACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAATTCATA
* *
1033639 AACTTATTATGAATTTCTTAGGTTGCACACACAGTGACAATAC-G-AATCCATA
1 AACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAATTCATA
* *
1033691 AACTTATTATGAATTTCTTAGGTTGCACACACAGTGACAATACGGTAATT
1 AACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAATT
1033741 ACAATACATA
Statistics
Matches: 197, Mismatches: 10, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
52 50 0.25
53 2 0.01
54 127 0.64
55 18 0.09
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (54 bp):
AACTTATTATGAATTTCTTAGGTTGCACACACAGTGCCAATACGGAAATTCATA
Found at i:1034542 original size:22 final size:23
Alignment explanation
Indices: 1034514--1034566 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
1034504 AAAAAGGAAG
*
1034514 AAATAAAAAATAG-ACTAAATAA
1 AAATAAAAAATAGAACAAAATAA
1034536 AAAT-AAAAATAGAAACAAAATAA
1 AAATAAAAAATAG-AACAAAATAA
1034559 AACATAAA
1 AA-ATAAA
1034567 TATAAAAGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 8 0.31
22 4 0.15
23 10 0.38
24 2 0.08
25 2 0.08
ACGTcount: A:0.75, C:0.06, G:0.04, T:0.15
Consensus pattern (23 bp):
AAATAAAAAATAGAACAAAATAA
Found at i:1034703 original size:21 final size:21
Alignment explanation
Indices: 1034647--1034710 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 21
1034637 AAATAAAAGT
* * *
1034647 AAGAAGAAAATAACAAATAAG
1 AAGAAAAAAATAATAAATAAA
* *
1034668 TAGATAAATAA-AATAAATAAA
1 AAGA-AAAAAATAATAAATAAA
1034689 AAGAAAAAAATAAT-AATAAA
1 AAGAAAAAAATAATAAATAAA
1034709 AA
1 AA
1034711 ACAAATGAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
20 13 0.38
21 17 0.50
22 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.16
Consensus pattern (21 bp):
AAGAAAAAAATAATAAATAAA
Found at i:1034893 original size:15 final size:15
Alignment explanation
Indices: 1034853--1034893 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
1034843 AAAAAAAGTG
1034853 AAATAATAA-AAACA
1 AAATAATAATAAACA
*
1034867 AAA-AATATATAAAGA
1 AAATAATA-ATAAACA
1034882 AAATAATAATAA
1 AAATAATAATAA
1034894 TAATAATAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
13 4 0.17
14 4 0.17
15 11 0.48
16 4 0.17
ACGTcount: A:0.76, C:0.02, G:0.02, T:0.20
Consensus pattern (15 bp):
AAATAATAATAAACA
Found at i:1036084 original size:2 final size:2
Alignment explanation
Indices: 1036077--1036183 Score: 214
Period size: 2 Copynumber: 53.5 Consensus size: 2
1036067 ATAAATAAAT
1036077 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1036119 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1036161 AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC A
1036184 TATATATATA
Statistics
Matches: 105, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 105 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:1036188 original size:2 final size:2
Alignment explanation
Indices: 1036183--1036216 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1036173 ACACACACAC
1036183 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1036217 AAAATGTGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1037021 original size:120 final size:120
Alignment explanation
Indices: 1036858--1037082 Score: 335
Period size: 120 Copynumber: 1.9 Consensus size: 120
1036848 TGCTTGTGTG
* * *
1036858 CACGATATCCTTCATCATGAAGTTGAAATCGTGGCTGGCCCCTTCGTTGTGAAGTTGAGCCTTGG
1 CACGATATCCTTCATCATGAAGTTGAAATCATGGATGGCCCCTTCGTTGTGAAGTTGAGAC-TGG
* * *
1036923 -CTTGAATATCATTCGTCGTGAAGTTGAAATCCAAGTATTTTATGTTGTCAGTGGA
65 AATTGAATATCATTCATCGTGAAGTTGAAATCCAAATATTTTATGTTGTCAGTGGA
* * *
1036978 CACGATATCCTTCGTCGTGAAGTTGAAATCATGGATGGTCCCTTCGTTGTGAAGTTGAGACTGGA
1 CACGATATCCTTCATCATGAAGTTGAAATCATGGATGGCCCCTTCGTTGTGAAGTTGAGACTGGA
* *
1037043 ATTGGATATCCTTCATCGTGAAGTTGAAATCCAAATATTT
66 ATTGAATATCATTCATCGTGAAGTTGAAATCCAAATATTT
1037083 CGAGTCCAAT
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
119 3 0.03
120 90 0.97
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.34
Consensus pattern (120 bp):
CACGATATCCTTCATCATGAAGTTGAAATCATGGATGGCCCCTTCGTTGTGAAGTTGAGACTGGA
ATTGAATATCATTCATCGTGAAGTTGAAATCCAAATATTTTATGTTGTCAGTGGA
Found at i:1037270 original size:43 final size:43
Alignment explanation
Indices: 1037209--1037327 Score: 132
Period size: 43 Copynumber: 2.8 Consensus size: 43
1037199 ATGTTGTTGA
* * *
1037209 CACGATATCCTTCGTCGTGAAGTTAAAATCGTGG-TTGTATAGT
1 CACGATATCCTCCGTCGTGGAGTTAAAATCGTGGATT-TATAGG
* * * * * *
1037252 CATGATATCCTCCATCGTGGTGTTGAAATCGTGGATTTGTGGG
1 CACGATATCCTCCGTCGTGGAGTTAAAATCGTGGATTTATAGG
*
1037295 CACGATATCCTCCGTCGTGGAGTTCAAATCGTG
1 CACGATATCCTCCGTCGTGGAGTTAAAATCGTG
1037328 AATGACCCCT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
43 60 0.97
44 2 0.03
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (43 bp):
CACGATATCCTCCGTCGTGGAGTTAAAATCGTGGATTTATAGG
Found at i:1038246 original size:6 final size:6
Alignment explanation
Indices: 1038235--1038311 Score: 70
Period size: 6 Copynumber: 12.5 Consensus size: 6
1038225 TCACCTTATA
*
1038235 TTTCTT TTTCTT TTCTCTT TTTCTTT TGTTCTT TTT-TT CTTT-TT TCTCTT
1 TTTCTT TTTCTT TT-TCTT TTTC-TT T-TTCTT TTTCTT -TTTCTT TTTCTT
*
1038285 TTTCTGT GTTCTT TTTCTT TTT-TT TTT
1 TTTCT-T TTTCTT TTTCTT TTTCTT TTT
1038312 AATTTAGGGT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
5 9 0.15
6 32 0.52
7 17 0.28
8 3 0.05
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:1038258 original size:8 final size:7
Alignment explanation
Indices: 1038235--1038311 Score: 72
Period size: 7 Copynumber: 11.1 Consensus size: 7
1038225 TCACCTTATA
1038235 TTTC-TT
1 TTTCTTT
1038241 TTTCTTT
1 TTTCTTT
*
1038248 TCTC-TT
1 TTTCTTT
1038254 TTTCTTT
1 TTTCTTT
1038261 TGTTCTTTT
1 T-TTC-TTT
1038270 TTTCTTT
1 TTTCTTT
1038277 TTTCTCTT
1 TTTCT-TT
*
1038285 TTTCTGT
1 TTTCTTT
*
1038292 GTTC-TT
1 TTTCTTT
1038298 TTTCTTT
1 TTTCTTT
1038305 TTT-TTT
1 TTTCTTT
1038311 T
1 T
1038312 AATTTAGGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
6 17 0.29
7 25 0.42
8 13 0.22
9 4 0.07
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.81
Consensus pattern (7 bp):
TTTCTTT
Found at i:1038297 original size:30 final size:32
Alignment explanation
Indices: 1038235--1038310 Score: 102
Period size: 31 Copynumber: 2.4 Consensus size: 32
1038225 TCACCTTATA
* *
1038235 TTTCTTTTTCTTTTCTCTTTTTCTTTTGTTCTT
1 TTTCTTCTT-TTTTCTCTTTTTCTTGTGTTCTT
1038268 TTT-TTCTTTTTTCTCTTTTTC-TGTGTTCTT
1 TTTCTTCTTTTTTCTCTTTTTCTTGTGTTCTT
*
1038298 TTTCTTTTTTTTT
1 TTTCTTCTTTTTT
1038311 TAATTTAGGG
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
30 11 0.28
31 21 0.54
32 4 0.10
33 3 0.08
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (32 bp):
TTTCTTCTTTTTTCTCTTTTTCTTGTGTTCTT
Found at i:1041657 original size:31 final size:31
Alignment explanation
Indices: 1041602--1041672 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
1041592 ATTTATTATT
*
1041602 CCATGTA-TACTTTTGATATCTTTTATAAAC
1 CCATGTATTACTTTTGAGATCTTTTATAAAC
*
1041632 CCATGTATTA-TTATTGAGATCTTTTATAAGC
1 CCATGTATTACTT-TTGAGATCTTTTATAAAC
1041663 CCATGTATTA
1 CCATGTATTA
1041673 ACCCAGTACA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
30 9 0.24
31 28 0.76
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (31 bp):
CCATGTATTACTTTTGAGATCTTTTATAAAC
Found at i:1041906 original size:42 final size:42
Alignment explanation
Indices: 1041820--1041920 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 42
1041810 ATAACTCCTT
* * * * *
1041820 AAGAATCACATATATATTCCAAAGGACCAGATATGTGTCTCG
1 AAGAACCACATATATGTTCCAAAGGACCAGATATATATCCCG
* ** *
1041862 AAGAACCGCATATATGTTCCAAAGGATTATATATATATCCCG
1 AAGAACCACATATATGTTCCAAAGGACCAGATATATATCCCG
* *
1041904 AAGGACCACATGTATGT
1 AAGAACCACATATATGT
1041921 CCTGAAGGAC
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.27
Consensus pattern (42 bp):
AAGAACCACATATATGTTCCAAAGGACCAGATATATATCCCG
Found at i:1041960 original size:38 final size:38
Alignment explanation
Indices: 1041898--1042007 Score: 139
Period size: 38 Copynumber: 2.9 Consensus size: 38
1041888 TTATATATAT
*** * * *
1041898 ATCCCGAAGGACCACATGTATGTCCTGAAGGACCTACC
1 ATCCCGAAGGATGTCATCTATGTCCCGTAGGACCTACC
* * *
1041936 ATCCCGCAGGATGTCATCTGTGTCCCGTAGGACCTATC
1 ATCCCGAAGGATGTCATCTATGTCCCGTAGGACCTACC
1041974 ATCCCGAAGGATGTCATCTATGTCCCGTAGGACC
1 ATCCCGAAGGATGTCATCTATGTCCCGTAGGACC
1042008 ACTCCTTAAG
Statistics
Matches: 61, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 61 1.00
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.23
Consensus pattern (38 bp):
ATCCCGAAGGATGTCATCTATGTCCCGTAGGACCTACC
Found at i:1041967 original size:21 final size:20
Alignment explanation
Indices: 1041937--1042005 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
1041927 GGACCTACCA
*
1041937 TCCCGCAGGATGTCATCTGTG
1 TCCCGTAGGATGTCATCT-TG
** *
1041958 TCCCGTAGGACCT-ATC--A
1 TCCCGTAGGATGTCATCTTG
*
1041975 TCCCGAAGGATGTCATCTATG
1 TCCCGTAGGATGTCATCT-TG
1041996 TCCCGTAGGA
1 TCCCGTAGGA
1042006 CCACTCCTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
17 10 0.29
18 3 0.09
20 3 0.09
21 19 0.54
ACGTcount: A:0.20, C:0.29, G:0.25, T:0.26
Consensus pattern (20 bp):
TCCCGTAGGATGTCATCTTG
Found at i:1043143 original size:18 final size:18
Alignment explanation
Indices: 1043119--1043168 Score: 68
Period size: 18 Copynumber: 2.8 Consensus size: 18
1043109 TTAAATACCG
1043119 GAAATTCCAGTAATTCCAA
1 GAAATTCCAGTAATT-CAA
1043138 -AAATTCCA-TAAATTCAA
1 GAAATTCCAGT-AATTCAA
1043155 GAAATTCCAGTAAT
1 GAAATTCCAGTAAT
1043169 GGAATTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 4 0.14
18 23 0.82
19 1 0.04
ACGTcount: A:0.46, C:0.18, G:0.08, T:0.28
Consensus pattern (18 bp):
GAAATTCCAGTAATTCAA
Found at i:1043407 original size:31 final size:29
Alignment explanation
Indices: 1043372--1043437 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
1043362 ATTCCAAACT
* * *
1043372 TTTTTACAAAATTACAAATTGGTCCCTCAAC
1 TTTTT-CAAAATTACAAAATGATCCCT-AAA
*
1043403 TTTTTGAAAATTACAAAATGATCCCTAAA
1 TTTTTCAAAATTACAAAATGATCCCTAAA
1043432 TTTTTC
1 TTTTTC
1043438 CAAAGCTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 7 0.23
30 18 0.60
31 5 0.17
ACGTcount: A:0.36, C:0.18, G:0.06, T:0.39
Consensus pattern (29 bp):
TTTTTCAAAATTACAAAATGATCCCTAAA
Found at i:1043415 original size:30 final size:29
Alignment explanation
Indices: 1043379--1043436 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
1043369 ACTTTTTTAC
* * *
1043379 AAAATTACAAATTGGTCCCTCAACTTTTTG
1 AAAATTACAAAATGATCCCT-AAATTTTTG
1043409 AAAATTACAAAATGATCCCTAAATTTTT
1 AAAATTACAAAATGATCCCTAAATTTTT
1043437 CCAAAGCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 7 0.28
30 18 0.72
ACGTcount: A:0.40, C:0.17, G:0.07, T:0.36
Consensus pattern (29 bp):
AAAATTACAAAATGATCCCTAAATTTTTG
Found at i:1045439 original size:6 final size:6
Alignment explanation
Indices: 1045430--1045469 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
1045420 ATCTTTTTTT
1045430 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1 TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTTCA TTTT
1045470 TTTTCAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTTCA
Found at i:1045475 original size:10 final size:10
Alignment explanation
Indices: 1045436--1045524 Score: 54
Period size: 10 Copynumber: 8.5 Consensus size: 10
1045426 TTTTTTTTCA
1045436 TTTTCATTTT
1 TTTTCATTTT
1045446 CATTTTCATTTT
1 --TTTTCATTTT
1045458 CATTTTCATTTT
1 --TTTTCATTTT
**
1045470 TTTTCAAATT
1 TTTTCATTTT
* **
1045480 GTTTCAAATT
1 TTTTCATTTT
* *
1045490 GTTTCAATTT
1 TTTTCATTTT
*
1045500 TTTTCTTTTTT
1 TTTTC-ATTTT
1045511 TTTTC-TTTT
1 TTTTCATTTT
1045520 TTTTC
1 TTTTC
1045525 CTCTCTTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
9 9 0.13
10 30 0.43
11 8 0.12
12 22 0.32
ACGTcount: A:0.15, C:0.12, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTCATTTT
Found at i:1045513 original size:11 final size:11
Alignment explanation
Indices: 1045497--1045538 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1045487 ATTGTTTCAA
1045497 TTTTTTTCTTT
1 TTTTTTTCTTT
1045508 TTTTTTTCTTT
1 TTTTTTTCTTT
* *
1045519 TTTTTCCTCTCT
1 TTTTT-TTCTTT
1045531 TTTTTTTC
1 TTTTTTTC
1045539 GCTCTTAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:1045543 original size:15 final size:14
Alignment explanation
Indices: 1045503--1045543 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
1045493 TCAATTTTTT
1045503 TCTTTTTTTT--T-
1 TCTTTTTTTTCCTC
1045514 TCTTTTTTTTCCTC
1 TCTTTTTTTTCCTC
1045528 TCTTTTTTTTCGCTC
1 TCTTTTTTTTC-CTC
1045543 T
1 T
1045544 TAGGCCTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 10 0.38
13 1 0.04
14 11 0.42
15 4 0.15
ACGTcount: A:0.00, C:0.22, G:0.02, T:0.76
Consensus pattern (14 bp):
TCTTTTTTTTCCTC
Found at i:1047062 original size:38 final size:38
Alignment explanation
Indices: 1047010--1047091 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 38
1047000 TATATCCCGA
* *
1047010 AGGACCTATCATCCCGCAA-GATGTCATGTATGTTCTGT
1 AGGACCTATCATCCCG-AAGGATGTCATCTATGTCCTGT
* * *
1047048 AGGACCTATTATCCCGAAGGTTGTCATCTGTGTCCTGT
1 AGGACCTATCATCCCGAAGGATGTCATCTATGTCCTGT
1047086 AGGACC
1 AGGACC
1047092 ACTCCTTAAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
37 2 0.05
38 36 0.95
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30
Consensus pattern (38 bp):
AGGACCTATCATCCCGAAGGATGTCATCTATGTCCTGT
Found at i:1047326 original size:33 final size:34
Alignment explanation
Indices: 1047288--1047354 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
1047278 TCACTTGTAT
*
1047288 CATTCTTATATGATCTCATAGATCATTGT-ATAA
1 CATTCTCATATGATCTCATAGATCATTGTCATAA
* *
1047321 CATTCTCGTATGATCTCATAGATCCTTGTCATAA
1 CATTCTCATATGATCTCATAGATCATTGTCATAA
1047355 AACCCATATC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.40
Consensus pattern (34 bp):
CATTCTCATATGATCTCATAGATCATTGTCATAA
Found at i:1048210 original size:9 final size:9
Alignment explanation
Indices: 1048188--1048241 Score: 63
Period size: 9 Copynumber: 6.0 Consensus size: 9
1048178 CTTAAATTTT
*
1048188 AAATACCAG
1 AAATTCCAG
*
1048197 TAATTCCAG
1 AAATTCCAG
*
1048206 AAATTCCAA
1 AAATTCCAG
*
1048215 AAATTCCAT
1 AAATTCCAG
*
1048224 AAATTCAAG
1 AAATTCCAG
1048233 AAATTCCAG
1 AAATTCCAG
1048242 TAATGGAATT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.48, C:0.20, G:0.07, T:0.24
Consensus pattern (9 bp):
AAATTCCAG
Done.