Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001279.1 Hibiscus syriacus cultivar Beakdansim tig00002511_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: 6984689
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 29
Found at i:1684889 original size:20 final size:20
Alignment explanation
Indices: 1684866--1684921 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
1684856 TCTGAAACTT
1684866 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
1684886 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** *
1684906 ACTATCGCAACGCGAA
1 AAAATCGCAACACGAA
1684922 GCATTGCGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.50, C:0.23, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:1685362 original size:22 final size:22
Alignment explanation
Indices: 1685307--1685363 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
1685297 GATGGAGATA
* *
1685307 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGTCAGAGATGGG
* *
1685329 GGCTGATTTCGTCAGAGATGGG
1 GACGGATTTCGTCAGAGATGGG
*
1685351 GACGGATGTCGTC
1 GACGGATTTCGTC
1685364 TTAGAGAGTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.18, C:0.18, G:0.42, T:0.23
Consensus pattern (22 bp):
GACGGATTTCGTCAGAGATGGG
Found at i:1685641 original size:20 final size:20
Alignment explanation
Indices: 1685528--1685665 Score: 161
Period size: 20 Copynumber: 6.9 Consensus size: 20
1685518 GCGCTTTGAA
1685528 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* * *
1685548 CATCGCGTTGCGACAGTCAG
1 AATCGCATTGCGATAGTCAG
1685568 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
1685588 AATCTCGTTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
1685608 AATCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* * *
1685628 AATCGCATTACGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
*
1685648 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
1685666 GAAAAATTGC
Statistics
Matches: 100, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
19 1 0.01
20 98 0.98
21 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:1685659 original size:60 final size:60
Alignment explanation
Indices: 1685528--1685665 Score: 179
Period size: 60 Copynumber: 2.3 Consensus size: 60
1685518 GCGCTTTGAA
* *
1685528 AATCGCATTGCGATAGTCAGCATCGCGTTGCGACAGTCAGAATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTACGATAGTCAG
* * * * * *
1685588 AATCTCGTTGCGATAGTCAGAATCGCGTTGCGATAGTCATAATCGCATTACGAT-TTACAT
1 AATCGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTACGATAGT-CAG
*
1685648 ATTCGCATTGCGATAGTC
1 AATCGCATTGCGATAGTC
1685666 GAAAAATTGC
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
59 1 0.02
60 65 0.98
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (60 bp):
AATCGCATTGCGATAGTCAGAATCGCGTTGCGACAGTCAGAATCGCATTACGATAGTCAG
Found at i:1686394 original size:39 final size:39
Alignment explanation
Indices: 1686345--1686490 Score: 181
Period size: 39 Copynumber: 3.7 Consensus size: 39
1686335 ATATATATTA
1686345 ATATAATATATAGTTGTTGAAAATA-TTTTGAAAACATAT
1 ATATAATATATAGTT-TTGAAAATATTTTTGAAAACATAT
* * * *
1686384 ATATAGTATATAGTTTTTGAAAATATTTTTTAATATATAT
1 ATATAATATATAG-TTTTGAAAATATTTTTGAAAACATAT
* *
1686424 ATATAATATATAGATTTGAAAATATTTTTTGAAAAC--GT
1 ATATAATATATAGTTTTGAAAATA-TTTTTGAAAACATAT
1686462 ATATAATATATAGTTTTGGAAAATATTTT
1 ATATAATATATAGTTTT-GAAAATATTTT
1686491 CAAATTTTGA
Statistics
Matches: 92, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
38 21 0.23
39 38 0.41
40 33 0.36
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (39 bp):
ATATAATATATAGTTTTGAAAATATTTTTGAAAACATAT
Found at i:1686629 original size:15 final size:14
Alignment explanation
Indices: 1686592--1686644 Score: 70
Period size: 15 Copynumber: 3.6 Consensus size: 14
1686582 TTATATTATA
*
1686592 TTATTTTGTTTATTCT
1 TTATTTT-TTTAAT-T
1686608 TTATTTTTTTAATT
1 TTATTTTTTTAATT
1686622 TTATTTTTTTAATTT
1 TTATTTTTTTAA-TT
1686637 TTATTTTT
1 TTATTTTT
1686645 AGGTCCAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
14 13 0.37
15 15 0.43
16 7 0.20
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (14 bp):
TTATTTTTTTAATT
Found at i:1687902 original size:26 final size:26
Alignment explanation
Indices: 1687873--1687929 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
1687863 TTCTACTTCC
* *
1687873 TTTTAATATTTTTTGTTCTTTT-CAAA
1 TTTTAAT-TTTTTTATTATTTTCCAAA
* *
1687899 TTTTAGTTTTTTTATTATTTTCCTAA
1 TTTTAATTTTTTTATTATTTTCCAAA
1687925 TTTTA
1 TTTTA
1687930 TTTAATTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (26 bp):
TTTTAATTTTTTTATTATTTTCCAAA
Found at i:1687909 original size:25 final size:26
Alignment explanation
Indices: 1687881--1687929 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
1687871 CCTTTTAATA
* *
1687881 TTTTTTGTTCTTTT-CAAATTTTAGT
1 TTTTTTATTATTTTCCAAATTTTAGT
*
1687906 TTTTTTATTATTTTCCTAATTTTA
1 TTTTTTATTATTTTCCAAATTTTA
1687930 TTTAATTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.69
Consensus pattern (26 bp):
TTTTTTATTATTTTCCAAATTTTAGT
Found at i:1694285 original size:201 final size:201
Alignment explanation
Indices: 1693932--1694436 Score: 735
Period size: 201 Copynumber: 2.5 Consensus size: 201
1693922 TATAACATAG
* ** * ** *
1693932 CTCAAGGCGAGAAGGGTTAGATGTCAACAAAAACTTTCGAGTTCGATTAGATTCAGTTCGATGAC
1 CTCAAGGCGAAAAGGGTTATCTGTCAACAAAACCTTTCGAGTTCGATTCCATTCAGCTCGATGAC
* *
1693997 ATATCAACTGCATGGTAGCAGCGAGGAACTACTTTCCGGTTGAAGCTTAAACTGAGGTCTTTAAG
66 ATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGATTGAAGCTTAAACTGAGGTCTTTAAG
* * * *
1694062 TTAAGAAGAAGACTTGGGTTGGTTGCGATTTAGCAACAAGAAACTATATCCTAGTCAAATTTATA
131 TCAAGAAGAAGACTTAGGTTGGTTGCGATTTAGCAACAAGAAACTATATCCCAGTCAAATTTACA
1694127 GAATAA
196 GAATAA
1694133 CTCAAGGCGAAAAGGGTTATCTGTCAACAAAACCTTTCGAGTTCGATTCCATTCAGCTCGATGAC
1 CTCAAGGCGAAAAGGGTTATCTGTCAACAAAACCTTTCGAGTTCGATTCCATTCAGCTCGATGAC
*
1694198 ATATCAACCGCATGGTAGCAGCGAGGAACTACTTTTCGATTGAAGCTTAAACTGAGGTCTTTAAG
66 ATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGATTGAAGCTTAAACTGAGGTCTTTAAG
* * *
1694263 TCAAGAAGAATACTTAGGTTGGTTGTGATTTAGCAACAAGGAACTATATCCCAGTCAAATTTACA
131 TCAAGAAGAAGACTTAGGTTGGTTGCGATTTAGCAACAAGAAACTATATCCCAGTCAAATTTACA
* *
1694328 GCATAG
196 GAATAA
* ** * *
1694334 CTCAAGGTGAGAAA-GACTATCTGTCAACAAAAACC-TTCGAGTTTGATTCCATTCAGCTCGAGG
1 CTCAAGGCGA-AAAGGGTTATCTGTCAAC-AAAACCTTTCGAGTTCGATTCCATTCAGCTCGATG
* * *
1694397 GCATATCAACCACATGGTAGCATCGAGGAACTACTTTCCG
64 ACATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCG
1694437 GTCAAATTTT
Statistics
Matches: 274, Mismatches: 28, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
201 265 0.97
202 9 0.03
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (201 bp):
CTCAAGGCGAAAAGGGTTATCTGTCAACAAAACCTTTCGAGTTCGATTCCATTCAGCTCGATGAC
ATATCAACCGCATGGTAGCAGCGAGGAACTACTTTCCGATTGAAGCTTAAACTGAGGTCTTTAAG
TCAAGAAGAAGACTTAGGTTGGTTGCGATTTAGCAACAAGAAACTATATCCCAGTCAAATTTACA
GAATAA
Found at i:1694912 original size:47 final size:45
Alignment explanation
Indices: 1694822--1694911 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 45
1694812 TATTAAGATA
1694822 ATATATAGTTGTTGAAAACATTTTGAAAACATGTATATAATATATT
1 ATATATAGTTGTTGAAAACATTTTGAAAACA-GTATATAATATATT
1694868 ATATATAGTT-TTGAAAACATTTTTTGAAAAC-GTATATAATATAT
1 ATATATAGTTGTTGAAAACA--TTTTGAAAACAGTATATAATATAT
1694912 AGTTTTGGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
45 22 0.52
46 10 0.24
47 10 0.24
ACGTcount: A:0.43, C:0.04, G:0.10, T:0.42
Consensus pattern (45 bp):
ATATATAGTTGTTGAAAACATTTTGAAAACAGTATATAATATATT
Found at i:1695021 original size:5 final size:5
Alignment explanation
Indices: 1695004--1695329 Score: 607
Period size: 5 Copynumber: 64.2 Consensus size: 5
1694994 ATAATTTTAT
1695004 TATTA TAATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA T-ATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1695055 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1695105 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1695155 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1695205 TATTA TATTA TATTA TATTATA TATTA TATTA TATTA TATTA TATTATA
1 TATTA TATTA TATTA TA-T-TA TATTA TATTA TATTA TATTA TA-T-TA
1695254 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
1695304 TATTA TATTA TATTA TATTA TATTA T
1 TATTA TATTA TATTA TATTA TATTA T
1695330 TTTGTTTATT
Statistics
Matches: 316, Mismatches: 0, Indels: 10
0.97 0.00 0.03
Matches are distributed among these distances:
5 299 0.95
6 9 0.03
7 8 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TATTA
Found at i:1695354 original size:15 final size:16
Alignment explanation
Indices: 1695326--1695359 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1695316 TTATATTATA
1695326 TTATTTTGTTTATTGT
1 TTATTTTGTTTATTGT
*
1695342 TTATTTT-TTTATTTT
1 TTATTTTGTTTATTGT
1695357 TTA
1 TTA
1695360 GGTCCAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.15, C:0.00, G:0.06, T:0.79
Consensus pattern (16 bp):
TTATTTTGTTTATTGT
Found at i:1697219 original size:163 final size:163
Alignment explanation
Indices: 1696944--1697270 Score: 546
Period size: 163 Copynumber: 2.0 Consensus size: 163
1696934 ATCAACCTAA
*
1696944 ATATTGTTTTTAAAATGATCGGTGGCGGCTCTAACGTGTTTTATTTAAGTCGAAGTCCAATTTCA
1 ATATTGTTTTTAAAATGATCGGTGGCGGCTCTAACGTGTTTTATTTAAGTCAAAGTCCAATTTCA
* ** *
1697009 GACCCACCCGAAATACGGTTGCGACAATATTAAATTTAAATAAATATAGCCTAGTAAATAAAATT
66 GACCCACCCAAAATACAATTGCGACAATATTAAATTTAAAAAAATATAGCCTAGTAAATAAAATT
*
1697074 ATAACTTGAATAAATAATACGGTTATAAATGCT
131 ATAACTTGAATAAATAATACGATTATAAATGCT
* * *
1697107 ATATTGTTTTTAAAATGATTGGTGGGGGCTCTAACGTGTTTTATTTAAGTCAAAGTCCAATTTCG
1 ATATTGTTTTTAAAATGATCGGTGGCGGCTCTAACGTGTTTTATTTAAGTCAAAGTCCAATTTCA
* * *
1697172 GGCCCACCCAAAATACAATTGCGATAATATTAAATTTAAAAAAATATAGCCTTGTAAATAAAATT
66 GACCCACCCAAAATACAATTGCGACAATATTAAATTTAAAAAAATATAGCCTAGTAAATAAAATT
1697237 ATAACTTGAATAAATAATACGATTATAAATGCT
131 ATAACTTGAATAAATAATACGATTATAAATGCT
1697270 A
1 A
1697271 CACAAGTATA
Statistics
Matches: 152, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
163 152 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (163 bp):
ATATTGTTTTTAAAATGATCGGTGGCGGCTCTAACGTGTTTTATTTAAGTCAAAGTCCAATTTCA
GACCCACCCAAAATACAATTGCGACAATATTAAATTTAAAAAAATATAGCCTAGTAAATAAAATT
ATAACTTGAATAAATAATACGATTATAAATGCT
Found at i:1700360 original size:25 final size:24
Alignment explanation
Indices: 1700325--1700417 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 24
1700315 ATTAAATATC
1700325 AATTCAAATTTAACATAAAATATTT
1 AATT-AAATTTAACATAAAATATTT
1700350 ATATTAAATTTTAA-ATATGAACATTAAATATT
1 A-ATTAAA-TTTAACATA--AA-A-T--AT-TT
1700382 AATTTAAATTTAACATAAAATATTT
1 AA-TTAAATTTAACATAAAATATTT
1700407 AGATTAAATTT
1 A-ATTAAATTT
1700418 TAAACGTGAC
Statistics
Matches: 56, Mismatches: 0, Indels: 24
0.70 0.00 0.30
Matches are distributed among these distances:
25 18 0.32
26 11 0.20
27 2 0.04
28 2 0.04
29 2 0.04
30 2 0.04
31 8 0.14
32 11 0.20
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
AATTAAATTTAACATAAAATATTT
Found at i:1700391 original size:57 final size:56
Alignment explanation
Indices: 1700305--1700481 Score: 228
Period size: 57 Copynumber: 3.1 Consensus size: 56
1700295 TCATTAATCT
*
1700305 AACATTGAGCATTAAATATCAATTCAAATTTAACATAAAATATTTATATTAAATTTTA
1 AACA-TGA-CATTAAATATCAATTCAAATTTAACATAAAATATTTAAATTAAATTTTA
* * * *
1700363 AATATGAACATTAAATATTAATTTAAATTTAACATAAAATATTTAGATTAAATTTTA
1 AACATG-ACATTAAATATCAATTCAAATTTAACATAAAATATTTAAATTAAATTTTA
* ** * *
1700420 AACGTGACTATTAAATATCAGCTCAAACTTAACATAAAATGTTTAAATTAAATTTTA
1 AACATGAC-ATTAAATATCAATTCAAATTTAACATAAAATATTTAAATTAAATTTTA
1700477 AACAT
1 AACAT
1700482 TTATATTTAT
Statistics
Matches: 103, Mismatches: 14, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
56 2 0.02
57 97 0.94
58 4 0.04
ACGTcount: A:0.49, C:0.08, G:0.05, T:0.38
Consensus pattern (56 bp):
AACATGACATTAAATATCAATTCAAATTTAACATAAAATATTTAAATTAAATTTTA
Found at i:1700402 original size:24 final size:27
Alignment explanation
Indices: 1700350--1700405 Score: 73
Period size: 24 Copynumber: 2.2 Consensus size: 27
1700340 TAAAATATTT
*
1700350 ATATTAAATTTTAAATATGAACATTAA
1 ATATTAAATTTTAAATATGAACATAAA
*
1700377 ATATT-AA-TTTAAAT-TTAACATAAA
1 ATATTAAATTTTAAATATGAACATAAA
1700401 ATATT
1 ATATT
1700406 TAGATTAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 13 0.48
25 7 0.26
26 2 0.07
27 5 0.19
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (27 bp):
ATATTAAATTTTAAATATGAACATAAA
Found at i:1701040 original size:30 final size:30
Alignment explanation
Indices: 1700983--1701040 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1700973 ACGAGCCGGT
** *
1700983 TGGGAACCGGGAAAACTGGTGGGAACCGAC
1 TGGGAACCGGGAAAACCAGTGGAAACCGAC
*
1701013 TGGGAACCGGGAAAACCAGTGTAAACCG
1 TGGGAACCGGGAAAACCAGTGGAAACCG
1701041 TCGGTTCTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.33, C:0.21, G:0.36, T:0.10
Consensus pattern (30 bp):
TGGGAACCGGGAAAACCAGTGGAAACCGAC
Found at i:1710054 original size:33 final size:32
Alignment explanation
Indices: 1709989--1710057 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 32
1709979 GTTTTTTTTG
** *
1709989 TGTTTGTTTTGTTCGTTTAATGTGTTCATTTA
1 TGTTTGTTTTGTTAATTTAATATGTTCATTTA
* *
1710021 TGTTTGTTTATGTTAATTTATTATGTTCGTTTA
1 TGTTTGTTT-TGTTAATTTAATATGTTCATTTA
1710054 TGTT
1 TGTT
1710058 CATTCGTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
32 9 0.29
33 22 0.71
ACGTcount: A:0.14, C:0.04, G:0.17, T:0.64
Consensus pattern (32 bp):
TGTTTGTTTTGTTAATTTAATATGTTCATTTA
Found at i:1710094 original size:10 final size:10
Alignment explanation
Indices: 1710041--1710097 Score: 60
Period size: 10 Copynumber: 5.3 Consensus size: 10
1710031 TGTTAATTTA
1710041 TTATGTTCGT
1 TTATGTTCGT
1710051 TTATGTTCATTCGT
1 TTATG----TTCGT
*
1710065 TTGTGTTCGT
1 TTATGTTCGT
1710075 TTATGTTCGT
1 TTATGTTCGT
*
1710085 TTATGATCGT
1 TTATGTTCGT
1710095 TTA
1 TTA
1710098 AATGAACGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 31 0.77
14 9 0.22
ACGTcount: A:0.12, C:0.11, G:0.19, T:0.58
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:1710175 original size:16 final size:16
Alignment explanation
Indices: 1710154--1710186 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1710144 ATTTTTTTTT
*
1710154 TGTTCGTTTATGTTCA
1 TGTTCGTTTATGCTCA
1710170 TGTTCGTTTATGCTCA
1 TGTTCGTTTATGCTCA
1710186 T
1 T
1710187 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGCTCA
Found at i:1710681 original size:21 final size:21
Alignment explanation
Indices: 1710652--1710699 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1710642 TATTCCGAAT
*
1710652 AAGGAATAAAGACTCTAAGGG
1 AAGGAATAAAAACTCTAAGGG
* *
1710673 AAGGGATAAAAACTCTAGGGG
1 AAGGAATAAAAACTCTAAGGG
1710694 AAGGAA
1 AAGGAA
1710700 AGGAAGGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.08, G:0.31, T:0.12
Consensus pattern (21 bp):
AAGGAATAAAAACTCTAAGGG
Found at i:1715367 original size:44 final size:43
Alignment explanation
Indices: 1715251--1715380 Score: 147
Period size: 44 Copynumber: 3.0 Consensus size: 43
1715241 AGTATGAATT
* * *
1715251 CCAAACTAACAATCCACAAATACACCAAACTAGCATATTAAAA
1 CCAAAGTAACAATCCACAAATACACAAAACTAACATATTAAAA
* * * * *
1715294 CTAAAGTAAAAATCCATAAATTTGC-CAAAACTAATATATTAAAA
1 CCAAAGTAACAATCCACAAA--TACACAAAACTAACATATTAAAA
1715338 CCAAAGTAACAATCCACAAATACATCAAAA-TAACATATTAAAA
1 CCAAAGTAACAATCCACAAATACA-CAAAACTAACATATTAAAA
1715381 GAATTCTTAA
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
42 2 0.03
43 28 0.40
44 38 0.54
45 2 0.03
ACGTcount: A:0.55, C:0.21, G:0.03, T:0.21
Consensus pattern (43 bp):
CCAAAGTAACAATCCACAAATACACAAAACTAACATATTAAAA
Found at i:1716911 original size:75 final size:74
Alignment explanation
Indices: 1716740--1716920 Score: 186
Period size: 75 Copynumber: 2.4 Consensus size: 74
1716730 ATGAGGTACC
* * * * * *
1716740 ATCGATACCATGGTA-AAGGTATCAATACCAAGCAACATCGAATCTAAATTTGGTATCGATACCG
1 ATCGATACCATGGTATAAAGTATCGATACCAGGAAACATCAAACCTAAATTTGGTATCGATACCG
1716804 GAAAGGGGT
66 GAAAGGGGT
* * * * *
1716813 A-CCACTATCATAGTATTATAGTATCGATACCAGGAAACATCAAACCTAAATTTGGTATCGATAT
1 ATCGA-TACCATGGTA-TAAAGTATCGATACCAGGAAACATCAAACCTAAATTTGGTATCGATAC
* *
1716877 TGGAAGGGGGT
64 CGGAAAGGGGT
* *
1716888 ATCGGTACCATGGTATAGAAGTATCGGTACCAG
1 ATCGATACCATGGTATA-AAGTATCGATACCAG
1716921 AATAACAGTA
Statistics
Matches: 84, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
72 2 0.02
73 9 0.11
74 2 0.02
75 70 0.83
76 1 0.01
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (74 bp):
ATCGATACCATGGTATAAAGTATCGATACCAGGAAACATCAAACCTAAATTTGGTATCGATACCG
GAAAGGGGT
Found at i:1717325 original size:54 final size:54
Alignment explanation
Indices: 1717260--1717597 Score: 500
Period size: 54 Copynumber: 6.3 Consensus size: 54
1717250 TTACCAAATA
* * *
1717260 GGCACTGAGTGTGCATTTCACAGAATTCATCATATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
*
1717314 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * *
1717368 GACACTAAGTGTGCATTTCACAGAATT-ATCCTATGTGGATTAATAACCATTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
*
1717421 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTT
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* * * * *
1717475 GTCACTAAGTGTGCATTTCACGGAATTCATTCTATGTGAATGAATAATCGTTTC
1 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
* *
1717529 GACACTAAGTGTGCATTTCA-TGAAATTCATCCTATGTGGATGAATAACCGTTTC
1 GGCACTAAGTGTGCATTTCACAG-AATTCATCCTATGTGGATGAATAACCGTTTC
* *
1717583 GGCAATATGTGTGCA
1 GGCACTAAGTGTGCA
1717598 AAACATGAAA
Statistics
Matches: 258, Mismatches: 24, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
53 52 0.20
54 206 0.80
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTC
Found at i:1717532 original size:161 final size:162
Alignment explanation
Indices: 1717260--1717597 Score: 536
Period size: 161 Copynumber: 2.1 Consensus size: 162
1717250 TTACCAAATA
*
1717260 GGCACTGAGTGTGCATTTCACAGAATTCATCATATGTGGATGAATAACCGTTTTGGCACTAAGTG
1 GGCACTAAGTGTGCATTTCACAGAATTCATCATATGTGGATGAATAACCGTTTTGGCACTAAGTG
*
1717325 TGCATTTCACAGAATTCATCCTATGTGGATGAATAACCATTTCGACACTAAGTGTGCATTTCACA
66 TGCATTTCACAGAATTCATCCTATGTGAATGAATAACCATTTCGACACTAAGTGTGCATTTCA-A
*
1717390 G-AATT-ATCCTATGTGGATTAATAACCATTTC
130 GAAATTCATCCTATGTGGATGAATAACCATTTC
* *
1717421 GGCACTAAGTGTGCATTTCACAGAATTCATCCTATGTGGATGAATAACCGTTTTGTCACTAAGTG
1 GGCACTAAGTGTGCATTTCACAGAATTCATCATATGTGGATGAATAACCGTTTTGGCACTAAGTG
* * * * *
1717486 TGCATTTCACGGAATTCATTCTATGTGAATGAATAATCGTTTCGACACTAAGTGTGCATTTCATG
66 TGCATTTCACAGAATTCATCCTATGTGAATGAATAACCATTTCGACACTAAGTGTGCATTTCAAG
*
1717551 AAATTCATCCTATGTGGATGAATAACCGTTTC
131 AAATTCATCCTATGTGGATGAATAACCATTTC
* *
1717583 GGCAATATGTGTGCA
1 GGCACTAAGTGTGCA
1717598 AAACATGAAA
Statistics
Matches: 162, Mismatches: 13, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
160 1 0.01
161 124 0.77
162 37 0.23
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (162 bp):
GGCACTAAGTGTGCATTTCACAGAATTCATCATATGTGGATGAATAACCGTTTTGGCACTAAGTG
TGCATTTCACAGAATTCATCCTATGTGAATGAATAACCATTTCGACACTAAGTGTGCATTTCAAG
AAATTCATCCTATGTGGATGAATAACCATTTC
Found at i:1717626 original size:108 final size:106
Alignment explanation
Indices: 1717279--1717653 Score: 387
Period size: 108 Copynumber: 3.5 Consensus size: 106
1717269 TGTGCATTTC
* * *
1717279 ACAGAATTCAT-CATATGTGGATGAATAACCGTTTTGGCACTAAGTGTGCATTTCACAGAATTCA
1 ACAGAATTTATAC-TATGTGAATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACAGAATTCA
* *
1717343 TCCTATGTGGATGAATAACCATTTCGACACTAAGTGTGCATTTC
65 TCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCA--TA
* * * *
1717387 ACAGAA-TTATCCTATGTGGATTAATAACCATTTCGGCACTAAGTGTGCATTTCACAGAATTCAT
1 ACAGAATTTATACTATGTGAATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACAGAATTCAT
* * *
1717451 CCTATGTGGATGAATAACCGTTTTGTCACTAAGTGTGCATTTC
66 CCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCA--TA
* * * * * *
1717494 ACGGAATTCATTCTATGTGAATGAATAATCGTTTCGACACTAAGTGTGCATTTCA-TGAAATTCA
1 ACAGAATTTATACTATGTGAATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACAG-AATTCA
* * * *
1717558 TCCTATGTGGATGAATAACCGTTTCGGCAATATGTGTGCAAA
65 TCCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATA
* ** * * * * *
1717600 ACATGAAATTTATAATATGTTTATGAATGACTGTTTGGGCACTACGGGTGCATT
1 ACA-G-AATTTATACTATGTGAATGAATAACCGTTTCGGCACTAAGTGTGCATT
1717654 ACAAAGAAAT
Statistics
Matches: 227, Mismatches: 35, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
106 2 0.01
107 99 0.44
108 126 0.56
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (106 bp):
ACAGAATTTATACTATGTGAATGAATAACCGTTTCGGCACTAAGTGTGCATTTCACAGAATTCAT
CCTATGTGGATGAATAACCGTTTCGACACTAAGTGTGCATA
Found at i:1717722 original size:2 final size:2
Alignment explanation
Indices: 1717715--1717750 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1717705 GAAAAATGAA
1717715 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
1717751 TGATTGCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1737649 original size:5 final size:5
Alignment explanation
Indices: 1737641--1737670 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
1737631 ATACCTGATC
1737641 TTTTA TTTTA TTTTA TTTTA TTTGTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTT-TA TTTT
1737671 TTTAACATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:1738342 original size:25 final size:24
Alignment explanation
Indices: 1738294--1738339 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
1738284 AAAAATTAGG
1738294 GTTTTTGAAAATAAAATATTTTAA
1 GTTTTTGAAAATAAAATATTTTAA
*
1738318 GTTTTTTAAAATAAAATATTTT
1 GTTTTTGAAAATAAAATATTTT
1738340 TAAACATGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (24 bp):
GTTTTTGAAAATAAAATATTTTAA
Found at i:1740140 original size:19 final size:20
Alignment explanation
Indices: 1740108--1740157 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
1740098 ATTTTAATTG
*
1740108 TTAAGGTATATTTT-ATTATAT
1 TTAA-GTATTTTTTAATT-TAT
1740129 TTAA-TATTTTTTAATTTAT
1 TTAAGTATTTTTTAATTTAT
1740148 TTAAGTATTT
1 TTAAGTATTT
1740158 AAATTTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 14 0.54
20 8 0.31
21 4 0.15
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (20 bp):
TTAAGTATTTTTTAATTTAT
Found at i:1740184 original size:27 final size:27
Alignment explanation
Indices: 1740126--1740178 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
1740116 TATTTTATTA
*
1740126 TATTTAATATTTTTTAATTTATTTAAG
1 TATTTAATATTTTTAAATTTATTTAAG
1740153 TATTTAA-ATTTTTAATATTTATTTAA
1 TATTTAATATTTTTAA-ATTTATTTAA
1740179 TAATTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (27 bp):
TATTTAATATTTTTAAATTTATTTAAG
Found at i:1745871 original size:185 final size:186
Alignment explanation
Indices: 1745527--1745887 Score: 539
Period size: 185 Copynumber: 1.9 Consensus size: 186
1745517 TTCATAAAAT
*
1745527 ATTAAATGAGAAACTTTGGAAATTGCTTTCTCATTTTCACAATTCATGTGAAAACATCCTACCCG
1 ATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTCACAATTCATGTGAAAACATCCTACCCG
* * *
1745592 AAGGATTTACGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGACTTATAAAAGACCCGAAGG
66 AAGGATTTACGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAAAAGACCCAAAGG
* * * *
1745657 ATTTAATGATCATTCTCGAATGACTTACTGATGGCC-GATAGGACTTTTCAGAAGAG
131 ATTTAATCATCATGCTCAAAAGACTTACTGATGGCCTGA-AGGACTTTTCAGAAGAG
* *
1745713 ATTAAATGAGAAACTTTGGAAATCGCTTTCTCTTTTTCATAATTCATGTGAAAACATCCTACCC-
1 ATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTCACAATTCATGTGAAAACATCCTACCCG
* ** * * *
1745777 AATG-TCTTGTGGATTGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGACCCAAAG
66 AAGGAT-TTACGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAAAAGACCCAAAG
1745841 GATTTAATCATCATGCTCAAAAGACTTACTGATGGCCTGAAGGACTT
130 GATTTAATCATCATGCTCAAAAGACTTACTGATGGCCTGAAGGACTT
1745888 ACCAATTTTG
Statistics
Matches: 157, Mismatches: 16, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
184 1 0.01
185 93 0.59
186 63 0.40
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (186 bp):
ATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTCACAATTCATGTGAAAACATCCTACCCG
AAGGATTTACGGATGGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAAAAGACCCAAAGG
ATTTAATCATCATGCTCAAAAGACTTACTGATGGCCTGAAGGACTTTTCAGAAGAG
Found at i:1745884 original size:42 final size:41
Alignment explanation
Indices: 1745793--1745888 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
1745783 TTGTGGATTG
*
1745793 CCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAGATGA
1 CCCGAAGGACTTATCATCATGCTCAAAAGACTTATAGATGA
* * *
1745834 CCCAAAGGATTTAATCATCATGCTCAAAAGACTTACT-GATGG
1 CCCGAAGGACTT-ATCATCATGCTCAAAAGACTTA-TAGATGA
*
1745876 CCTGAAGGACTTA
1 CCCGAAGGACTTA
1745889 CCAATTTTGG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
41 11 0.24
42 34 0.74
43 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (41 bp):
CCCGAAGGACTTATCATCATGCTCAAAAGACTTATAGATGA
Found at i:1746121 original size:42 final size:41
Alignment explanation
Indices: 1746049--1746145 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 41
1746039 TCTACGGATT
* * * * *
1746049 GCCCAAAGGACTTATCATCTTGTTCGAAAGACTTACAGATG
1 GCCCGAAGGACTTATCATCATGCTCAAAAGACTTACAGATA
* *
1746090 GCCCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATA
1 GCCCGAAGGACTT-ATCATCATGCTCAAAAGACTTACAGATA
1746132 GCCCGAAGGACTTA
1 GCCCGAAGGACTTA
1746146 CAAATTTTGG
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 12 0.26
42 35 0.74
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (41 bp):
GCCCGAAGGACTTATCATCATGCTCAAAAGACTTACAGATA
Found at i:1746163 original size:257 final size:256
Alignment explanation
Indices: 1745701--1746779 Score: 1474
Period size: 257 Copynumber: 4.2 Consensus size: 256
1745691 CCGATAGGAC
* * *
1745701 TTTTCAGAAGAGATTAAATGAGAAACTTTGGAAATCGCTTTCTCTTTTTCATAATTCATGTGAAA
1 TTTTCAGAAAAGATTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTCA-AATTCATGTGAAA
* ** * * * *
1745766 ACATCCTACCC-AATGTCTTGTGGATTGCCCGAAGGACTTATCATCTTGCTCAAAAGACTTATAG
65 ACATCCTACCCGAAGGTCTTACGGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAG
* * * *
1745830 ATGACCCAAAGGATTTAATCATCATGCTCAAAAGACTTACTGATGGCCTGAAGGACTTACCAATT
130 ATGACCCAAAGGATTTAATCATCATGCTCAAAAGACTTACTGATAGCCCGAAGAACTTACTAA-T
* *
1745895 TTGGAAAATAATTTACTT-GGTAAGAAACTTTGGTAATCACTTTCTTACTTTTCAAAAATTTCA
194 TTGGGAAATAATTTA-TTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCA
* * *
1745958 TTTTCAGAAGAGATTAAATGAGAAACTTTGGAAATCACTTTCACATTTTCACAATTAATGTGAAA
1 TTTTCAGAAAAGATTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTCA-AATTCATGTGAAA
* *
1746023 ACATCCTACCCGAAGGTC-TACGGATTGCCCAAAGGACTTATCATCTTGTTCGAAAGACTTACAG
65 ACATCCTACCCGAAGGTCTTACGGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAG
* * * *
1746087 ATGGCCCGAAGGATTTAATCATCATGCTCAAAAGACTTACTGATAGCCCGAAGGACTTACAAATT
130 ATGACCCAAAGGATTTAATCATCATGCTCAAAAGACTTACTGATAGCCCGAAGAACTTACTAA-T
* * * **
1746152 TTGGGAAATAATGTATTAGGTAAGAAACTTTGGTAATCGTTTTCTTACTTTTCAAAAATTTCA
194 TTGGGAAATAATTTATTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCA
* *
1746215 TTTTCAGAAAAGATTAAATGAGAAACTTTGGAAATCGCTTTCTCATTTTTCAAATTCTTGTGAAA
1 TTTTCAGAAAAGATTAAATGAGAAACTTTGGAAATCACTTTCTCA-TTTTCAAATTCATGTGAAA
* * * * *
1746280 ACATTCTACCTGAAGGTCTTACGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTGACAT
65 ACATCCTACCCGAAGGTCTTACGGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAG
* * *
1746345 ATGACCTAAAGGATTTAATCATCTTGCTCGAAAGACTTACTGATAGCCCGAAGAACTTACTAATT
130 ATGACCCAAAGGATTTAATCATCATGCTCAAAAGACTTACTGATAGCCCGAAGAACTTACTAATT
* *
1746410 TGGGAAATAATTTATTGGGTAAAAAACTTTGGAAATCGCTTTCTTACTTTTCAAAAATTTCA
195 TGGGAAATAATTTATTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCA
* ** *
1746472 TTTTCTGAAAACTTTAAATGAGAAACTTTGGAAA-AATCTTTCT-ATTTTTTCAAATTCATGTGA
1 TTTTCAGAAAAGATTAAATGAGAAACTTTGGAAATCA-CTTTCTCA--TTTTCAAATTCATGTGA
*
1746535 AATCATCCTACCCGAAGGTCTTACGGATGGCCCGAAA-GACTTATCATCTTGCTCGAAAGACTTA
63 AAACATCCTACCCGAAGGTCTTACGGATGGCCC-AAAGGACTTATCATCTTGCTCGAAAGACTTA
* * * * * *
1746599 CATATAACCCAAAGGATTTAGTCATCATGCTCGAAAGATTTACTGAT-GTCTCGAAGAACTTACT
127 CAGATGACCCAAAGGATTTAATCATCATGCTCAAAAGACTTACTGATAG-CCCGAAGAACTTACT
* * *
1746663 AATTTAGGAAATAGTTTATTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATATC
191 AATTTGGGAAATAATTTATTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTC
1746728 A
256 A
* *
1746729 TTTT--TAAAACATTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTCAAA
1 TTTTCAGAAAAGATTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTCAAA
1746780 ACAACTTAAT
Statistics
Matches: 742, Mismatches: 70, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
254 8 0.01
255 32 0.04
256 6 0.01
257 586 0.79
258 110 0.15
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (256 bp):
TTTTCAGAAAAGATTAAATGAGAAACTTTGGAAATCACTTTCTCATTTTCAAATTCATGTGAAAA
CATCCTACCCGAAGGTCTTACGGATGGCCCAAAGGACTTATCATCTTGCTCGAAAGACTTACAGA
TGACCCAAAGGATTTAATCATCATGCTCAAAAGACTTACTGATAGCCCGAAGAACTTACTAATTT
GGGAAATAATTTATTGGGTAAGAAACTTTGGAAATCACTTTCTTACTTTTCAAAAATTTCA
Found at i:1754976 original size:10 final size:10
Alignment explanation
Indices: 1754961--1754985 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1754951 TTTTTAGTGA
1754961 TTGTTGGTTG
1 TTGTTGGTTG
1754971 TTGTTGGTTG
1 TTGTTGGTTG
1754981 TTGTT
1 TTGTT
1754986 TTTTCCCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (10 bp):
TTGTTGGTTG
Found at i:1766315 original size:17 final size:18
Alignment explanation
Indices: 1766281--1766335 Score: 85
Period size: 18 Copynumber: 3.1 Consensus size: 18
1766271 CTTTGCTACA
1766281 CAAAACGAGTCTAATACC
1 CAAAACGAGTCTAATACC
*
1766299 CAAAACGAGT-GAATACC
1 CAAAACGAGTCTAATACC
*
1766316 CAAAATGAGTCTAATACC
1 CAAAACGAGTCTAATACC
1766334 CA
1 CA
1766336 TGAAACTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
17 15 0.45
18 18 0.55
ACGTcount: A:0.45, C:0.25, G:0.13, T:0.16
Consensus pattern (18 bp):
CAAAACGAGTCTAATACC
Found at i:1769195 original size:21 final size:21
Alignment explanation
Indices: 1769152--1769195 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1769142 AGATGAACTA
* *
1769152 TGGCTTTGTAAAAGTGTTGCT
1 TGGCTTTGTAAAAATGTTCCT
1769173 TGGCTTTGTAACAAAT-TTCCT
1 TGGCTTTGTAA-AAATGTTCCT
1769194 TG
1 TG
1769196 ATTTTTAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.43
Consensus pattern (21 bp):
TGGCTTTGTAAAAATGTTCCT
Found at i:1769264 original size:21 final size:20
Alignment explanation
Indices: 1769231--1769270 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
1769221 TGCATCAAAG
*
1769231 TCTTTATGGAGGCCATAAAA
1 TCTTTATCGAGGCCATAAAA
1769251 TCTTTCATCGAGGCCATAAA
1 TCTTT-ATCGAGGCCATAAA
1769271 TTCCTGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (20 bp):
TCTTTATCGAGGCCATAAAA
Found at i:1779114 original size:22 final size:20
Alignment explanation
Indices: 1779064--1779135 Score: 74
Period size: 22 Copynumber: 3.5 Consensus size: 20
1779054 GCAAAAAAGA
* *
1779064 TATCGATTCCATAG-GAGGG
1 TATCGATACCATAGTAAGGG
* *
1779083 TATCGGTACCATAGTATGGTAG
1 TATCGATACCATAGTAAGG--G
*
1779105 TATCGATACCATGGTAAGGG
1 TATCGATACCATAGTAAGGG
1779125 TATCGATACCA
1 TATCGATACCA
1779136 GGTAACATCG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 12 0.28
20 14 0.33
22 17 0.40
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.28
Consensus pattern (20 bp):
TATCGATACCATAGTAAGGG
Found at i:1779120 original size:17 final size:18
Alignment explanation
Indices: 1779098--1779139 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
1779088 GTACCATAGT
1779098 ATGGTA-GTATCGATACC
1 ATGGTAGGTATCGATACC
1779115 ATGGTAAGGGTATCGATACC
1 ATGGT-A-GGTATCGATACC
1779135 A-GGTA
1 ATGGTA
1779140 ACATCGAATC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
17 5 0.23
18 2 0.09
19 3 0.14
20 12 0.55
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (18 bp):
ATGGTAGGTATCGATACC
Found at i:1779623 original size:59 final size:59
Alignment explanation
Indices: 1779549--1779960 Score: 612
Period size: 59 Copynumber: 7.0 Consensus size: 59
1779539 ATTTCCAAAT
* * * *
1779549 GGCACTAAGAGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCATATTG
1 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
*
1779608 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTA
1 GGCACTATGTGTGCT-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * *
1779668 GGCACTATGTGTGCTAAAATATTAAGAATTTCATACTAAGTGTATGAATTTCTGTATTG
1 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
*
1779727 GGCACTATATGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
*
1779786 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTTTATGAATTTCCGTATTG
1 GGCACTATGTGTGCT-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * * * *
1779846 GGCACTATATGTCCTAAAATGTTAATAAATGCATACTAAGTGTATG-ATTTTCATATTG
1 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * *
1779904 GGCACTTTGTGTGC-AAACATGTTAAGAAATTCATACTAGGTGTATGAATTTCTGTAT
1 GGCACTATGTGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1779961 GGGAAATATA
Statistics
Matches: 318, Mismatches: 31, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
57 3 0.01
58 46 0.14
59 157 0.49
60 112 0.35
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.36
Consensus pattern (59 bp):
GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
Found at i:1779741 original size:119 final size:118
Alignment explanation
Indices: 1779549--1779995 Score: 627
Period size: 119 Copynumber: 3.8 Consensus size: 118
1779539 ATTTCCAAAT
* * *
1779549 GGCACTAAGAGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTT-TCATATTGGGCAC
1 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCT-GTATTGGGCAC
* *
1779613 TATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTA
65 TATATGTGCT-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
1779668 GGCACTATGTGTGCTAAAATATTAAGAATTTCATACTAAGTGTATGAATTTCTGTATTGGGCACT
1 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACT
1779733 ATATGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
66 ATATGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
1779786 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTTTATGAATTTCCGTATTGGGCAC
1 GGCACTATGTGTGCT-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCAC
* * * * *
1779851 TATATGTCCTAAAATGTTAATAAATGCATACTAAGTGTATG-ATTTTCATATTG
65 TATATGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * *
1779904 GGCACTTTGTGTGC-AAACATGTTAAGAAATTCATACTAGGTGTATGAATTTCTGTA-TGGGAAA
1 GGCACTATGTGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCAC
**
1779967 TATATGTG-TATAAA-CATAAGAAATTCATA
65 TATATGTGCTA-AAATGTTAAGAAATTCATA
1779996 ACAAGGAAAT
Statistics
Matches: 297, Mismatches: 27, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
115 13 0.04
116 18 0.06
117 35 0.12
118 81 0.27
119 149 0.50
120 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.36
Consensus pattern (118 bp):
GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCTGTATTGGGCACT
ATATGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
Found at i:1779852 original size:178 final size:177
Alignment explanation
Indices: 1779559--1779960 Score: 635
Period size: 178 Copynumber: 2.3 Consensus size: 177
1779549 GGCACTAAGA
* *
1779559 GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTTCATATTGGGCACTATGTGTGCTA
1 GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGCTA
* *
1779624 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTATGTGTGCTAAAATA
66 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTATATGTCCTAAAATA
* * *
1779689 TTAAGAATTTCATACTAAGTGTATGAATTTCTGTATTGGGCACTATAT
131 TTAAGAAATGCATACTAAGTGTATGAATTTC-ATATTGGGCACTATAT
1779737 GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGCTA
1 GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGCTA
* * *
1779802 AAAATGTTAAGAAATTCATACTAAGTTTATGAATTTCCGTATTGGGCACTATATGTCCTAAAATG
66 AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTATATGTCCTAAAATA
* * * *
1779867 TTAATAAATGCATACTAAGTGTATGATTTTCATATTGGGCACTTTGT
131 TTAAGAAATGCATACTAAGTGTATGAATTTCATATTGGGCACTATAT
* *
1779914 GTGC-AAACATGTTAAGAAATTCATACTAGGTGTATGAATTTCTGTAT
1 GTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1779961 GGGAAATATA
Statistics
Matches: 207, Mismatches: 16, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
176 3 0.01
177 54 0.26
178 150 0.72
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.37
Consensus pattern (177 bp):
GTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTATGTGTGCTA
AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTAGGCACTATATGTCCTAAAATA
TTAAGAAATGCATACTAAGTGTATGAATTTCATATTGGGCACTATAT
Found at i:1787045 original size:57 final size:59
Alignment explanation
Indices: 1786648--1787051 Score: 542
Period size: 58 Copynumber: 7.0 Consensus size: 59
1786638 ATTAACAAAT
*
1786648 GGCACTAAGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
1 GGCACTATGTGTGCT-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * *
1786708 GGCACTA--TGTGCTAAAACTGTTAAGAAATTCATATTAAGTGTATGAATTACCGTAATG
1 GGCACTATGTGTGCTAAAA-TGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
*
1786766 GGCACTATGTGTGCTAAAA---TAAGAAATTCATACTAAGTGTATAAATTTCCGTATTG
1 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
1786822 GGC-CTATGTGTGCT-AAATGTTAAGAAATTCATATTAAGTGTATGAATTTCCGTTTTG
1 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* *
1786879 GGCACTATGTGTGCTAAAAATGTTAAGAAATTCATACTAAGTTTATGAATTTCAGTATTG
1 GGCACTATGTGTGCT-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * *
1786939 GGCACTATGTGCGCTAAAATGTTAAGAAA-TCATACTAAGTGTATAAATTT-TGTATTG
1 GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
* * * * *
1786996 GGCACTTTGTGTGC-AAATATGTTAA-AAAATCATACTAGGTGTAGGAATTTCTGTAT
1 GGCACTATGTGTGCTAAA-ATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
1787052 GGGAAATATA
Statistics
Matches: 309, Mismatches: 23, Indels: 26
0.86 0.06 0.07
Matches are distributed among these distances:
54 3 0.01
55 11 0.04
56 42 0.14
57 84 0.27
58 85 0.28
59 14 0.05
60 70 0.23
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.35
Consensus pattern (59 bp):
GGCACTATGTGTGCTAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTG
Found at i:1788226 original size:2 final size:2
Alignment explanation
Indices: 1788219--1788253 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1788209 CTTTTAATTG
1788219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1788254 ATTCAGAAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1798090 original size:40 final size:40
Alignment explanation
Indices: 1798035--1798116 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
1798025 ATCGTAGTGA
*
1798035 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATACACACCGAAGTGTAT
1798075 TACACATAAGGTCGTGCCCACCATACACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATACACACCGAAGTGTAT
1798115 TA
1 TA
1798117 TAAACCTGCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.33, C:0.28, G:0.17, T:0.22
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATACACACCGAAGTGTAT
Found at i:1800351 original size:34 final size:34
Alignment explanation
Indices: 1800308--1800373 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
1800298 AACAAGCCCA
** *
1800308 ACTCAATGCCATATCTATGCACATTCTCTTTTCT
1 ACTCAATGCCATAGATATGAACATTCTCTTTTCT
*
1800342 ACTCAATGCCATAGATATGAACATTCTTTTTT
1 ACTCAATGCCATAGATATGAACATTCTCTTTT
1800374 TACACTGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.27, C:0.24, G:0.08, T:0.41
Consensus pattern (34 bp):
ACTCAATGCCATAGATATGAACATTCTCTTTTCT
Found at i:1805181 original size:187 final size:188
Alignment explanation
Indices: 1804853--1805422 Score: 634
Period size: 182 Copynumber: 3.1 Consensus size: 188
1804843 AATTGTACCT
* * ** *
1804853 AAGAATG-CAATGATTCACTAAGAAAGTAGGTTGCGATTTGGAATGCTACTATTTTT-TTAATAA
1 AAGAATGTC-ATGATTCACTAAGAAAGTAGGTTGCGATCTGAAATAATAATATTTTTATTAATAA
* * *
1804916 AATGGGTTGCACCTAAAATGTTATCAGAGTTTAAGCTGATTGAGCCTTATATTTTTC-CACGAT-
65 AATGGGTTGCACCTAAAATGTTATCAGAGTTTAAACTGATGGAGCCTTAGATTTTTCTCACGATA
*
1804979 AACAAAATAAGTTAAAAGCTGAAAATGTTATGAATAACTATAATAAATACGGTTGCGCCC
130 AACAAAA-AAGTTAAAAGATGAAAATGTTATGAATAACTATAATAAATACGGTTGCGCCC
* * *
1805039 AAGAATTTCATGATTCACTAAGAAAGTAGGTTGCAATCTGAAAAAATAATATTTTTATTAATAAA
1 AAGAATGTCATGATTCACTAAGAAAGTAGGTTGCGATCTGAAATAATAATATTTTTATTAATAAA
* *
1805104 ATGGGTTGCACCTAAAATGTTA-CTAGAATTTAAACTG-TGGTGCCTTAGATTTTTCTCACGATA
66 ATGGGTTGCACCTAAAATGTTATC-AGAGTTTAAACTGATGGAGCCTTAGATTTTTCTCACGATA
* * **
1805167 AACAAAAAAGTTAAAAAGATG-AAATGTTA--AAT-A-TCT-ATAAATACAGTTGCGCTT
130 AACAAAAAAGTT-AAAAGATGAAAATGTTATGAATAACTATAATAAATACGGTTGCGCCC
* * * * *
1805221 AAGAATGTCATGGTTCACTAAGAAAGGAGGCTGTGATCT-AGAATATTAATATTTTTATTAATAA
1 AAGAATGTCATGATTCACTAAGAAAGTAGGTTGCGATCTGA-AATAATAATATTTTTATTAATAA
* * *
1805285 AATGGGTTATC-CCTAAAATGTTATCAGAGTTTAAGA-TGATGGAGTCTTAGA-ATTTCTCACGA
65 AATGGGTT-GCACCTAAAATGTTATCAGAGTTTAA-ACTGATGGAGCCTTAGATTTTTCTCACGA
* * * * * ** *
1805347 TAATA-AAAAAAGTTGAAAGTTAAAAATGTTATGAATATCTATAATAAATATGGTTGTACTC
128 TAA-ACAAAAAAGTTAAAAGATGAAAATGTTATGAATAACTATAATAAATACGGTTGCGCCC
*
1805408 AAGAATGTGATGATT
1 AAGAATGTCATGATT
1805423 GTCAATATTT
Statistics
Matches: 323, Mismatches: 43, Indels: 35
0.81 0.11 0.09
Matches are distributed among these distances:
181 6 0.02
182 129 0.40
183 16 0.05
184 4 0.01
185 3 0.01
186 64 0.20
187 87 0.27
188 14 0.04
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (188 bp):
AAGAATGTCATGATTCACTAAGAAAGTAGGTTGCGATCTGAAATAATAATATTTTTATTAATAAA
ATGGGTTGCACCTAAAATGTTATCAGAGTTTAAACTGATGGAGCCTTAGATTTTTCTCACGATAA
ACAAAAAAGTTAAAAGATGAAAATGTTATGAATAACTATAATAAATACGGTTGCGCCC
Found at i:1806195 original size:36 final size:36
Alignment explanation
Indices: 1806131--1806224 Score: 152
Period size: 36 Copynumber: 2.6 Consensus size: 36
1806121 TTTTGAAAAT
**
1806131 TATAATATATAGTTTTGAAAACATTTTTAAAAATGTA
1 TATAATATATAGTTTT-AAAACATTTTTAAAAACATA
1806168 TATAATATATAGTTTTAAAACATTTTTAAAAACATA
1 TATAATATATAGTTTTAAAACATTTTTAAAAACATA
1806204 TATAATATATAGTTTTTAAAA
1 TATAATATATAG-TTTTAAAA
1806225 AAATAATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
36 30 0.56
37 24 0.44
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (36 bp):
TATAATATATAGTTTTAAAACATTTTTAAAAACATA
Found at i:1806246 original size:38 final size:35
Alignment explanation
Indices: 1806131--1806257 Score: 148
Period size: 36 Copynumber: 3.5 Consensus size: 35
1806121 TTTTGAAAAT
*
1806131 TATAATATATAGTTTTGAAAACATTTTTAAAAATGTA
1 TATAATATATAGTTTT-AAAACATTTTT-AAAATCTA
*
1806168 TATAATATATAGTTTTAAAACATTTTTAAAAACATA
1 TATAATATATAGTTTTAAAACATTTTTAAAATC-TA
*
1806204 TATAATATATAGTTTTTAAAAAAATAATTTTAAAATCT-
1 TATAATATATAG-TTTT-AAAACAT--TTTTAAAATCTA
*
1806242 TATAATATATATTTTT
1 TATAATATATAGTTTT
1806258 TTTAAAATGA
Statistics
Matches: 80, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
35 4 0.05
36 25 0.31
37 24 0.30
38 17 0.21
39 1 0.01
40 9 0.11
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (35 bp):
TATAATATATAGTTTTAAAACATTTTTAAAATCTA
Found at i:1806271 original size:37 final size:37
Alignment explanation
Indices: 1806203--1806298 Score: 97
Period size: 37 Copynumber: 2.6 Consensus size: 37
1806193 TTAAAAACAT
1806203 ATATAATATATAGTTTTTAAAAAAATAA-TTTTAAAATC
1 ATATAATATATA-TTTTTAAAAAAATAATTTTTAAAA-C
* *** * *
1806241 TTATAATATATATTTTTTTTAAAATGATTTTTGAAAC
1 ATATAATATATATTTTTAAAAAAATAATTTTTAAAAC
*
1806278 ATATAATATA-ATTTTTGAAAA
1 ATATAATATATATTTTTAAAAA
1806299 TATATAGTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
36 8 0.17
37 21 0.45
38 18 0.38
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (37 bp):
ATATAATATATATTTTTAAAAAAATAATTTTTAAAAC
Found at i:1806373 original size:18 final size:18
Alignment explanation
Indices: 1806332--1806374 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1806322 TACATTATAT
1806332 TTATTTTATTTATTTATC
1 TTATTTTATTTATTTATC
* *
1806350 TCATTTTA-TTCTTTATTC
1 TTATTTTATTTATTTA-TC
1806368 TTATTTT
1 TTATTTT
1806375 TCTTTTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTTTATTTATTTATC
Found at i:1811213 original size:17 final size:17
Alignment explanation
Indices: 1811187--1811232 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
1811177 TATAGAATTG
*
1811187 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
1811204 GATTCTAATTCCTCACA
1 GATTCCAATTCCTCACA
1811221 GATTCCAATTCC
1 GATTCCAATTCC
1811233 CTCATAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:1811495 original size:13 final size:13
Alignment explanation
Indices: 1811477--1811506 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1811467 TTGACTAAAG
1811477 CTTCCGGTGAAAT
1 CTTCCGGTGAAAT
1811490 CTTCCGGTGAAAT
1 CTTCCGGTGAAAT
1811503 CTTC
1 CTTC
1811507 GGCCTCTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.20, C:0.27, G:0.20, T:0.33
Consensus pattern (13 bp):
CTTCCGGTGAAAT
Found at i:1813239 original size:21 final size:20
Alignment explanation
Indices: 1813209--1813252 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
1813199 GCATTGGCCA
1813209 ATCCCCGATGAAAACAATTG
1 ATCCCCGATGAAAACAATTG
* *
1813229 ATCCCTCGATGAAAGCGATTG
1 ATCCC-CGATGAAAACAATTG
1813250 ATC
1 ATC
1813253 TATACCCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCCCCGATGAAAACAATTG
Found at i:1814428 original size:407 final size:406
Alignment explanation
Indices: 1813627--1814553 Score: 1197
Period size: 407 Copynumber: 2.3 Consensus size: 406
1813617 TTTTTAATTG
* * * * *
1813627 ATTGAAAGAGCTAATAAATACAACTCAACTATTATATTATTAGTCTATTTTGAAATTATGGTTCT
1 ATTGAAAGAGTTAACAAATACAACTCAACTATTATATTATTGGTCCATTTTGAAATTATGATTCT
** * * * *
1813692 TACATTATCATCATAATCATAAAGAGATATTGGGAATAGCTCACTAAATTGAGATGTGTGAGATG
66 TACATTATCATCATAATCATCGA-AGATATTGGCAACAACTCACTAAATTGAGATGTGTGAGATC
* * *
1813757 ATAATAATTCAAATCATCAACATCAACATCAACTCATAATTTTTAGTGTATTTTCCCCCTCGATT
130 ATAATAATTCAAA-CAT-AACATCAACACCAACTAATAATTTTTAGTGTATTTTCCCCCTCAATT
* *
1813822 TCTTCAAATGTAATATTTTTAAAACATGTTTATAGACGTTTGAGATTCAAATACAATGTCAATAT
193 TCTTCAAATGTAATATTTTAAAAACATGTTTATAGACGTTTGAGATTCAAATACAATGTCAACAT
* * * *
1813887 CGATATCAATAATTTATCAATTAAAATGGACAATCAAGGAAAAAATATTATCAATGTTTTCTACA
258 AGATATCAAGAATTTATCAATTAAAATGGACAATCAAGAAAAAAATATTATCAATGTTCTCTACA
* ** * * * * *
1813952 ACTTTCATACGTAATTCAAATTAAAAACTCTATAGCTTTCATGTGTAAACGATCAATACACCACC
323 ACTTCCATACACAAATCAAATTAAAAACTCTACAACTTTCATGTGTAAAAGACCAATACACCACC
1814017 TCTTGACATATTTCGATTA
388 TCTTGACATATTTCGATTA
*
1814036 ATTGAAAGAGTTAACAAATACAACTTC-ACTATTATATTATTGGTCCGTTTTGAAATTATGATTC
1 ATTGAAAGAGTTAACAAATACAAC-TCAACTATTATATTATTGGTCCATTTTGAAATTATGATTC
* *
1814100 TTACATTATCATCATAATCATCGAATGATATTGGACAACAACTCACTAGATTGAGATGTTTGAGA
65 TTACATTATCATCATAATCATCGAA-GATATTGG-CAACAACTCACTAAATTGAGATGTGTGAGA
* * * *
1814165 TCCTAATACTTC-AA-AT-A-ATCAAGACCAACTAATAATTTTTAGTGTATTTTCTCCCTCAATT
128 TCATAATAATTCAAACATAACATCAACACCAACTAATAATTTTTAGTGTATTTTCCCCCTCAATT
*
1814226 TCTTTC-AATGTAATATGTTTAAAACATCATGTTTATAGATGTTTGAGATTCAAATACAATGTCA
193 TC-TTCAAATGTAATAT-TTTAAAA-A-CATGTTTATAGACGTTTGAGATTCAAATACAATGTCA
* *
1814290 ACATAGATATCAAGAATTTATCCATTAAAATGGACAATCAAGAAAAAAATTATTATTAATGTTCT
254 ACATAGATATCAAGAATTTATCAATTAAAATGGACAATCAAGAAAAAAA-TATTATCAATGTTCT
* ** * * *
1814355 CTACAACTTCCATGCACAAATCAAATTAAAATTTTTACAAC-TTCTATGTGTAAAAGGCCAATGC
318 CTACAACTTCCATACACAAATCAAATTAAAAACTCTACAACTTTC-ATGTGTAAAAGACCAATAC
* *
1814419 ACC-CCTCTTGACATATTTTGGTTA
382 ACCACCTCTTGACATATTTCGATTA
* * * * * *
1814443 ACTGAAAGCGTTAACAAGTACAACTCAACTATTATATTATTGTTCCATTATGAAATTAT-AATCT
1 ATTGAAAGAGTTAACAAATACAACTCAACTATTATATTATTGGTCCATTTTGAAATTATGATTCT
1814507 TACATTATCATCATAATCATCGAGAGATATTAGGCAACAACTCACTA
66 TACATTATCATCATAATCATCGA-AGATATT-GGCAACAACTCACTA
1814554 TATTAAATGT
Statistics
Matches: 453, Mismatches: 53, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
404 51 0.11
405 10 0.02
406 49 0.11
407 157 0.35
408 63 0.14
409 87 0.19
410 36 0.08
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.35
Consensus pattern (406 bp):
ATTGAAAGAGTTAACAAATACAACTCAACTATTATATTATTGGTCCATTTTGAAATTATGATTCT
TACATTATCATCATAATCATCGAAGATATTGGCAACAACTCACTAAATTGAGATGTGTGAGATCA
TAATAATTCAAACATAACATCAACACCAACTAATAATTTTTAGTGTATTTTCCCCCTCAATTTCT
TCAAATGTAATATTTTAAAAACATGTTTATAGACGTTTGAGATTCAAATACAATGTCAACATAGA
TATCAAGAATTTATCAATTAAAATGGACAATCAAGAAAAAAATATTATCAATGTTCTCTACAACT
TCCATACACAAATCAAATTAAAAACTCTACAACTTTCATGTGTAAAAGACCAATACACCACCTCT
TGACATATTTCGATTA
Found at i:1815216 original size:20 final size:20
Alignment explanation
Indices: 1815188--1815226 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1815178 TTTTTAAACA
*
1815188 AAATTTTTCAATACTACTTC
1 AAATATTTCAATACTACTTC
*
1815208 AAATATTTCAATATTACTT
1 AAATATTTCAATACTACTT
1815227 TACTAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.15, G:0.00, T:0.46
Consensus pattern (20 bp):
AAATATTTCAATACTACTTC
Found at i:1816000 original size:26 final size:26
Alignment explanation
Indices: 1815951--1816002 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
1815941 GATGGAGCCT
* *
1815951 AATATTTTTTTTATTTTTTCAAAAAA
1 AATATTTTTTATATTTGTTCAAAAAA
1815977 AATATTTTTTAATATTTGTT-AAAAAA
1 AATATTTTTT-ATATTTGTTCAAAAAA
1816003 TAAAAATAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (26 bp):
AATATTTTTTATATTTGTTCAAAAAA
Found at i:1818619 original size:78 final size:75
Alignment explanation
Indices: 1818474--1818619 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 75
1818464 ATGGTATATA
* * * * *
1818474 AAATGACCTTTGAGATATAGTAAATATCATCTATAGTTGTTACATAGGCAATTAATGGTTGAGTC
1 AAATGACCTTTGAGATATAATAAATATCATCTACAGTTGTTACATAGGCAATTAATAGTAGAATC
1818539 AGCTTAGATT
66 AGCTTAGATT
* *
1818549 AAATGACCTTTGAGATAATACAATGAATATCATCTACAGTTGTTACCA-AGGTAATTAATAGTAG
1 AAATGACCTTTGAGAT-AT--AATAAATATCATCTACAGTTGTTA-CATAGGCAATTAATAGTAG
1818613 AATCAGC
62 AATCAGC
1818620 AGCACATTCT
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
75 16 0.27
76 2 0.03
78 40 0.67
79 2 0.03
ACGTcount: A:0.38, C:0.12, G:0.17, T:0.33
Consensus pattern (75 bp):
AAATGACCTTTGAGATATAATAAATATCATCTACAGTTGTTACATAGGCAATTAATAGTAGAATC
AGCTTAGATT
Found at i:1826552 original size:14 final size:14
Alignment explanation
Indices: 1826533--1826566 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1826523 GTATGATGAA
1826533 TTCATGAATAAATC
1 TTCATGAATAAATC
**
1826547 TTCATGAATGTATC
1 TTCATGAATAAATC
1826561 TTCATG
1 TTCATG
1826567 GCTGAATCCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (14 bp):
TTCATGAATAAATC
Found at i:1831098 original size:23 final size:23
Alignment explanation
Indices: 1831079--1831124 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
1831069 TTTTTTTTTC
1831079 CTTGTATATTCGTGCATTTTCTT
1 CTTGTATATTCGTGCATTTTCTT
1831102 CTTGTATATTCGTGCATTTTCTT
1 CTTGTATATTCGTGCATTTTCTT
1831125 ATGCTTGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57
Consensus pattern (23 bp):
CTTGTATATTCGTGCATTTTCTT
Found at i:1834578 original size:22 final size:21
Alignment explanation
Indices: 1834538--1834578 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1834528 TCGATATCGT
*
1834538 AAGGGAGTATCGGTACCATAG
1 AAGGGAGTATCGATACCATAG
*
1834559 AAGGGTAGTATCGATGCCAT
1 AAGGG-AGTATCGATACCAT
1834579 GTTAAGGTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.32, C:0.15, G:0.32, T:0.22
Consensus pattern (21 bp):
AAGGGAGTATCGATACCATAG
Found at i:1834676 original size:20 final size:20
Alignment explanation
Indices: 1834648--1834689 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1834638 TATCGGTACC
*
1834648 CTAGTGTAGAAGTATCGATA
1 CTAGGGTAGAAGTATCGATA
*
1834668 CTAGGGTAGTAGTATCGATA
1 CTAGGGTAGAAGTATCGATA
1834688 CT
1 CT
1834690 TTATAACTAG
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:0.31, C:0.12, G:0.26, T:0.31
Consensus pattern (20 bp):
CTAGGGTAGAAGTATCGATA
Found at i:1835154 original size:45 final size:45
Alignment explanation
Indices: 1835135--1835466 Score: 502
Period size: 45 Copynumber: 7.4 Consensus size: 45
1835125 AAAGGATGCC
*
1835135 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
* *
1835180 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAATTATACT
1 ATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
* *
1835225 ATAGTTGAAATGTATATGGGTACATTATCAACAGAAAAATATACT
1 ATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
**
1835270 ATAGTTGAAATTTATATGGGTACATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
* **
1835315 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATGTT
1 ATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
*
1835360 ATAGTTGAAATGCATATGGGTGCATTATCAACAGAAAAGTATACT
1 ATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
* * * * *
1835405 ATAGTTGAAATGCATATGAGTGCATTATCATCAGAAAAATATGCT
1 ATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
*
1835450 ATAGTTTAAAGTGCATA
1 ATAGTTGAAA-TGCATA
1835467 ATGGTGTATT
Statistics
Matches: 270, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
45 264 0.98
46 6 0.02
ACGTcount: A:0.41, C:0.09, G:0.18, T:0.32
Consensus pattern (45 bp):
ATAGTTGAAATGCATATGGGTACATTATCAACAGAAAAGTATACT
Found at i:1844817 original size:2 final size:2
Alignment explanation
Indices: 1844798--1844887 Score: 74
Period size: 2 Copynumber: 45.5 Consensus size: 2
1844788 GCATGTGTTC
* * * * * *
1844798 TA TA TA TT TA TA TG TA TA TA TA TA -A TA TT TT TT TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
1844839 CA TA CA TA CA TA CA TA TA TA TA TA TA TA CA 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
1844881 TA TA TA T
1 TA TA TA T
1844888 TAAAGATCTC
Statistics
Matches: 69, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
1 1 0.01
2 68 0.99
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1847372 original size:29 final size:28
Alignment explanation
Indices: 1847272--1847482 Score: 160
Period size: 29 Copynumber: 7.4 Consensus size: 28
1847262 GGATAAACCT
* * * *
1847272 TTATCATAACTTATAAATAGTTTAGTAC
1 TTATTATAATTTAGAAATAGTTTTGTAC
*
1847300 TTATTATAATTTAGAAATAG-TTTGCAC
1 TTATTATAATTTAGAAATAGTTTTGTAC
* **
1847327 TTATTGTGTTTTAGAAATAGTTTTGTAC
1 TTATTATAATTTAGAAATAGTTTTGTAC
* * *
1847355 TTTATTTTAATTTCGAAATAGTTTTGCAC
1 -TTATTATAATTTAGAAATAGTTTTGTAC
* *
1847384 TTTCTTATAATTTAGAAATAGTTATGTACC
1 -TTATTATAATTTAGAAATAGTTTTGTA-C
* * *
1847414 TTATTGTAATTTATAAATA-TTTTTTACC
1 TTATTATAATTTAGAAATAGTTTTGTA-C
* *
1847442 TTATTTGTAATTTA-ATAA-AATTTTGTACC
1 TTA-TTATAATTTAGA-AATAGTTTTGTA-C
*
1847471 TTATTGTAATTT
1 TTATTATAATTT
1847483 CTAAAAAGAT
Statistics
Matches: 152, Mismatches: 25, Indels: 12
0.80 0.13 0.06
Matches are distributed among these distances:
27 22 0.14
28 44 0.29
29 85 0.56
30 1 0.01
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (28 bp):
TTATTATAATTTAGAAATAGTTTTGTAC
Found at i:1847418 original size:58 final size:55
Alignment explanation
Indices: 1847272--1847511 Score: 169
Period size: 58 Copynumber: 4.2 Consensus size: 55
1847262 GGATAAACCT
* * *
1847272 TTATCATAACTTATAAATAGTTTAGTA-CTTATTATAATTTAGAAATAGTTTGCAC
1 TTATTATAATTTAGAAATAGTTT-GTACCTTATTATAATTTAGAAATAGTTTGCAC
* ** * * *
1847327 TTATTGTGTTTTAGAAATAGTTTTGTACTTTATTTTAATTTCGAAATAGTTTTGCAC
1 TTATTATAATTTAGAAATAG-TTTGTACCTTATTATAATTTAGAAATAG-TTTGCAC
* * * * **
1847384 TTTCTTATAATTTAGAAATAGTTATGTACCTTATTGTAATTTATAAATATTTTTTACC
1 -TTATTATAATTTAGAAATAGTT-TGTACCTTATTATAATTTAGAAATAGTTTGCA-C
* * * * ** * *
1847442 TTATTTGTAATTTA-ATAAAATTTTGTACCTTATTGTAATTTCTAAAAAGATTTGCCC
1 TTA-TTATAATTTAGA-AATAGTTTGTACCTTATTATAATTTAGAAATAG-TTTGCAC
1847499 TTCATTATAATTT
1 TT-ATTATAATTT
1847512 CTAAAATATT
Statistics
Matches: 144, Mismatches: 31, Indels: 18
0.75 0.16 0.09
Matches are distributed among these distances:
55 17 0.12
56 21 0.15
57 50 0.35
58 56 0.39
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (55 bp):
TTATTATAATTTAGAAATAGTTTGTACCTTATTATAATTTAGAAATAGTTTGCAC
Found at i:1847489 original size:28 final size:28
Alignment explanation
Indices: 1847408--1847523 Score: 110
Period size: 29 Copynumber: 4.0 Consensus size: 28
1847398 GAAATAGTTA
* *
1847408 TGTACCTTATTGTAATTTATAAATATTT
1 TGTACCTTATTGTAATTTCTAAAAATTT
* *
1847436 TTTACCTTATTTGTAATTT-AATAAAATTT
1 TGTACCTTA-TTGTAATTTCTA-AAAATTT
*
1847465 TGTACCTTATTGTAATTTCTAAAAAGATT
1 TGTACCTTATTGTAATTTCTAAAAA-TTT
* *
1847494 TG-CCCTTCATTATAATTTCTAAAATATTT
1 TGTACCTT-ATTGTAATTTCTAAAA-ATTT
1847523 T
1 T
1847524 TTTCCTTTGT
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
28 26 0.36
29 46 0.63
30 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (28 bp):
TGTACCTTATTGTAATTTCTAAAAATTT
Found at i:1847510 original size:57 final size:58
Alignment explanation
Indices: 1847336--1847511 Score: 171
Period size: 58 Copynumber: 3.1 Consensus size: 58
1847326 CTTATTGTGT
* * * * *
1847336 TTTAGAAATAGTTTTGTACTTTATTTTAATTTCGAAATAGTTTTGCACTTTC-TTATAA
1 TTTAGAAATAATTTTGTACCTTATTGTAATTTCTAAATAGTTTTGC-CCTTCATTATAA
* * * * ** *
1847394 TTTAGAAATAGTTATGTACCTTATTGTAATTTATAAATATTTTTTACCTT-ATTTGTAA
1 TTTAGAAATAATTTTGTACCTTATTGTAATTTCTAAATAGTTTTGCCCTTCA-TTATAA
* *
1847452 TTTA-ATAA-AATTTTGTACCTTATTGTAATTTCTAAAAAGATTTGCCCTTCATTATAA
1 TTTAGA-AATAATTTTGTACCTTATTGTAATTTCTAAATAGTTTTGCCCTTCATTATAA
1847509 TTT
1 TTT
1847512 CTAAAATATT
Statistics
Matches: 95, Mismatches: 19, Indels: 9
0.77 0.15 0.07
Matches are distributed among these distances:
57 45 0.47
58 50 0.53
ACGTcount: A:0.32, C:0.09, G:0.09, T:0.51
Consensus pattern (58 bp):
TTTAGAAATAATTTTGTACCTTATTGTAATTTCTAAATAGTTTTGCCCTTCATTATAA
Found at i:1848644 original size:13 final size:13
Alignment explanation
Indices: 1848626--1848652 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1848616 TGTATTGGGG
1848626 TATTGGTAATAAT
1 TATTGGTAATAAT
1848639 TATTGGTAATAAT
1 TATTGGTAATAAT
1848652 T
1 T
1848653 CTCTCTATAA
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:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TATTGGTAATAAT
Found at i:1851168 original size:43 final size:43
Alignment explanation
Indices: 1851095--1851222 Score: 123
Period size: 43 Copynumber: 3.0 Consensus size: 43
1851085 CTATCTAGAT
* * * * * *
1851095 CTATGTTGGAGCTATTACCAGCTTTTCAACTTATTTCCTAACA
1 CTATGCTGGAGATATTACAAACTTTCCAACTTATTTCCTAAAA
* ** *
1851138 CTATGTTGGAGATATTGTAAACTTTCCAACTTATTCCCTAAAA
1 CTATGCTGGAGATATTACAAACTTTCCAACTTATTTCCTAAAA
** *
1851181 CTATGCTGGATCTATTACCAACTTTTCCAACTTA-TTCCTAAA
1 CTATGCTGGAGATATTACAAAC-TTTCCAACTTATTTCCTAAA
1851223 TTTCAAAAAA
Statistics
Matches: 69, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
43 58 0.84
44 11 0.16
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.38
Consensus pattern (43 bp):
CTATGCTGGAGATATTACAAACTTTCCAACTTATTTCCTAAAA
Found at i:1857081 original size:17 final size:17
Alignment explanation
Indices: 1857059--1857120 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
1857049 TTTAGGGAAA
1857059 TAGTTCATTCATGAATT
1 TAGTTCATTCATGAATT
**
1857076 TAGTTCATTCAAT-AAAG
1 TAGTTCATTC-ATGAATT
* *
1857093 TAGTTAATTCATGCATT
1 TAGTTCATTCATGAATT
1857110 TAGTTCATTCA
1 TAGTTCATTCA
1857121 ATAAACTACT
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
16 2 0.06
17 32 0.89
18 2 0.06
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (17 bp):
TAGTTCATTCATGAATT
Found at i:1857137 original size:34 final size:34
Alignment explanation
Indices: 1857062--1857137 Score: 116
Period size: 34 Copynumber: 2.2 Consensus size: 34
1857052 AGGGAAATAG
* *
1857062 TTCATTCATGAATTTAGTTCATTCAATAAAGTAG
1 TTCATTCATGAATTTAGTTCATTCAATAAACTAC
* *
1857096 TTAATTCATGCATTTAGTTCATTCAATAAACTAC
1 TTCATTCATGAATTTAGTTCATTCAATAAACTAC
1857130 TTCATTCA
1 TTCATTCA
1857138 AGTCAGCAAG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (34 bp):
TTCATTCATGAATTTAGTTCATTCAATAAACTAC
Found at i:1857196 original size:17 final size:17
Alignment explanation
Indices: 1857110--1857215 Score: 74
Period size: 17 Copynumber: 6.1 Consensus size: 17
1857100 TTCATGCATT
1857110 TAGTTCATTCAAT-AAAC
1 TAGTTCATT-AATCAAAC
* *
1857127 TACTTCATTCAAGTC-AGC
1 TAGTTCATT-AA-TCAAAC
* *
1857145 AAGTTCATTGAAT-AAAGT
1 TAGTTCATT-AATCAAA-C
*
1857163 TAGTTGATTAATCAAAC
1 TAGTTCATTAATCAAAC
* * *
1857180 TAGTTTATTCATTAAAC
1 TAGTTCATTAATCAAAC
1857197 TAGTTCATTAATCAAAC
1 TAGTTCATTAATCAAAC
1857214 TA
1 TA
1857216 ACTCTTAATT
Statistics
Matches: 68, Mismatches: 16, Indels: 10
0.72 0.17 0.11
Matches are distributed among these distances:
17 46 0.68
18 22 0.32
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (17 bp):
TAGTTCATTAATCAAAC
Found at i:1872686 original size:21 final size:19
Alignment explanation
Indices: 1872658--1872703 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1872648 TCATTAAATC
1872658 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
1872678 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
1872697 ACTTAGT
1 A-TTAGT
1872704 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:1888546 original size:81 final size:81
Alignment explanation
Indices: 1888004--1888536 Score: 814
Period size: 81 Copynumber: 6.6 Consensus size: 81
1887994 CGCCTTTTTC
* * * *
1888004 TGCATTTGACAGAAATGTGTCAATCATACGAGTTAGATGAAAGGTTAAATATCTTTGAGTAAAAG
1 TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
*
1888069 ATTAATTGACTAGTTG
66 ATTAATTGCCTAGTTG
* *
1888085 TGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAG
1 TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* * *
1888150 ATTAATTGCCAAGCTA
66 ATTAATTGCCTAGTTG
*
1888166 TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAATGTTAAATACCTTTGAGTAAAAG
1 TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* *
1888231 ATTAATTGCCTAGCTA
66 ATTAATTGCCTAGTTG
* * **
1888247 TGCATTTGAAAAAAAGGTGTCAATCATGTTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
1 TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* *
1888312 ACTAATTGTCTAGTTG
66 ATTAATTGCCTAGTTG
1888328 TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
1 TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* * *
1888393 ACTAATTGCTTAGTCG
66 ATTAATTGCCTAGTTG
* *
1888409 TGCATTTGACATAAAGGTATCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
1 TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
*
1888474 ATTAATTTCCTAGTTG
66 ATTAATTGCCTAGTTG
* * *
1888490 TGCATTTGACTGAAAGGTGTCAATCATGCTAGTTAAATGAAAGGTTA
1 TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTA
1888537 CATGTCTTTG
Statistics
Matches: 413, Mismatches: 39, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 413 1.00
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (81 bp):
TGCATTTGACAGAAAGGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
ATTAATTGCCTAGTTG
Found at i:1888598 original size:46 final size:46
Alignment explanation
Indices: 1888546--1888813 Score: 347
Period size: 46 Copynumber: 5.8 Consensus size: 46
1888536 ACATGTCTTT
* * *
1888546 GGCATGAAAAGATGCCATAAATAAAAATGCATAATGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGCATTATA
* *
1888592 GACATGAAAGGATTCCATAAATGAAAATGCATAATGGTGCATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGCATTATA
* * * *
1888638 GGCATGAAAGGATGTCTTAAATAAAAATGCATAATGGTGCATTATC
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGCATTATA
* *
1888684 GGCATGAAAGGATACCATAAATGAAAATGCATAATGGTACATTATA
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGCATTATA
* * * * *
1888730 GGCATGAAAGGATGTCATAAATGAAAATGCTTAACGGTGCATAATT
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGCATTATA
* ** * *
1888776 GGCATGAAAGGATGACACCAATGAAAATACGTAATGGT
1 GGCATGAAAGGATGCCATAAATGAAAATGCATAATGGT
1888814 ATATTAACTG
Statistics
Matches: 192, Mismatches: 30, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
46 192 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (46 bp):
GGCATGAAAGGATGCCATAAATGAAAATGCATAATGGTGCATTATA
Found at i:1888661 original size:92 final size:92
Alignment explanation
Indices: 1888546--1888819 Score: 388
Period size: 92 Copynumber: 3.0 Consensus size: 92
1888536 ACATGTCTTT
* * * *
1888546 GGCATGAAAAGATGCCATAAATAAAAATGCATAATGGTGCATTATCGACATGAAAGGATTCCATA
1 GGCATGAAAGGATGTCATAAATAAAAATGCATAATGGTGCATTATCGGCATGAAAGGATACCATA
*
1888611 AATGAAAATGCATAATGGTGCATTATA
66 AATGAAAATGCATAATGGTACATTATA
*
1888638 GGCATGAAAGGATGTCTTAAATAAAAATGCATAATGGTGCATTATCGGCATGAAAGGATACCATA
1 GGCATGAAAGGATGTCATAAATAAAAATGCATAATGGTGCATTATCGGCATGAAAGGATACCATA
1888703 AATGAAAATGCATAATGGTACATTATA
66 AATGAAAATGCATAATGGTACATTATA
* * * * * *
1888730 GGCATGAAAGGATGTCATAAATGAAAATGCTTAACGGTGCATAATTGGCATGAAAGGATGA-CAC
1 GGCATGAAAGGATGTCATAAATAAAAATGCATAATGGTGCATTATCGGCATGAAAGGAT-ACCAT
* * * *
1888794 CAATGAAAATACGTAATGGTATATTA
65 AAATGAAAATGCATAATGGTACATTA
1888820 ACTGCATATC
Statistics
Matches: 164, Mismatches: 17, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
92 163 0.99
93 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.25
Consensus pattern (92 bp):
GGCATGAAAGGATGTCATAAATAAAAATGCATAATGGTGCATTATCGGCATGAAAGGATACCATA
AATGAAAATGCATAATGGTACATTATA
Found at i:1890229 original size:95 final size:96
Alignment explanation
Indices: 1890052--1890251 Score: 305
Period size: 95 Copynumber: 2.1 Consensus size: 96
1890042 ATATAGACTA
* * *
1890052 GGTAGTATCGATACCATGGTAAGGGTATCGATACTAGGAAAACATCGAATCTAAAACTGATATCG
1 GGTAGTATCGATACCATGGTAAGAGTATCGATACTAGGAAAACATCGAACCTAAAACAGATATCG
* *
1890117 ATACTAGAAGGGGGTATCGGTACCATAGTAT
66 ATACCAGAAGGGGGTATCGATACCATAGTAT
*
1890148 GGTAGTATCGATACCATGGTAAGAGTATCGATACTAGG-CAACATCGAACCTAAAATCAG-TATC
1 GGTAGTATCGATACCATGGTAAGAGTATCGATACTAGGAAAACATCGAACCTAAAA-CAGATATC
1890211 GATACCAGAAGGGGGTATCGATACCATAGTAT
65 GATACCAGAAGGGGGTATCGATACCATAGTAT
* *
1890243 AGAAGTATC
1 GGTAGTATC
1890252 TGTACTAGTG
Statistics
Matches: 95, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
95 56 0.59
96 39 0.41
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.24
Consensus pattern (96 bp):
GGTAGTATCGATACCATGGTAAGAGTATCGATACTAGGAAAACATCGAACCTAAAACAGATATCG
ATACCAGAAGGGGGTATCGATACCATAGTAT
Found at i:1891115 original size:68 final size:68
Alignment explanation
Indices: 1890978--1891115 Score: 177
Period size: 68 Copynumber: 2.0 Consensus size: 68
1890968 AAAGATTAAT
* * * *
1890978 AGGCCTAACTGTGCATTTGAAAAAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAACTGTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATACCG
1891043 TTG
66 TTG
* * ** * * *
1891046 AGGCCTAACTGTGCATTTGACATAATTGTGTCAATTATGCCAGTTAGATGAAGGGTTAAATATCG
1 AGGCCTAACTGTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATACCG
1891111 TTG
66 TTG
1891114 AG
1 AG
1891116 TAAAATAATA
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
68 59 1.00
ACGTcount: A:0.30, C:0.14, G:0.25, T:0.31
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGAAAAAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAATACCG
TTG
Found at i:1891184 original size:81 final size:81
Alignment explanation
Indices: 1891077--1891363 Score: 423
Period size: 81 Copynumber: 3.5 Consensus size: 81
1891067 ATAATTGTGT
* * *
1891077 CAATTATGCCAGTTAGATGAAGGGTTAAATATCGTTGAGTAAAATAATAATGGCCTAACTGTGCA
1 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAACAATAATGGCCTAACTGTGCA
*
1891142 ATTAGTAGAAAGGTAC
66 ATTGGTAGAAAGGTAC
* * * **
1891158 CAATTTTGCCAGTTAGATGAATGGTTAAATACCGTTGAGTAAAACAATAATGGCCTAAATGTATA
1 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAACAATAATGGCCTAACTGTGCA
1891223 ATTGGTAGAAAGGTAC
66 ATTGGTAGAAAGGTAC
* ** * *
1891239 CAATTATGCCGGTTAGATGAACGGTTAAATAATGTTGACT-AAACGAATAATGACCTAACTGTGC
1 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAC-AATAATGGCCTAACTGTGC
1891303 AATTGGTAGAAAGGTAC
65 AATTGGTAGAAAGGTAC
*
1891320 CAATTATGCTAGTTAGATGAACGGTTAAATACCGTTGAGTAAAA
1 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAA
1891364 GACGAAAGGT
Statistics
Matches: 181, Mismatches: 23, Indels: 3
0.87 0.11 0.01
Matches are distributed among these distances:
80 4 0.02
81 174 0.96
82 3 0.02
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.29
Consensus pattern (81 bp):
CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAACAATAATGGCCTAACTGTGCA
ATTGGTAGAAAGGTAC
Found at i:1897572 original size:20 final size:20
Alignment explanation
Indices: 1897547--1897585 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1897537 TAACTTACTT
* *
1897547 TCAAAAGTAAATTATGATCA
1 TCAAAAGAAAATAATGATCA
1897567 TCAAAAGAAAATAATGATC
1 TCAAAAGAAAATAATGATC
1897586 TTAAAGCTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (20 bp):
TCAAAAGAAAATAATGATCA
Found at i:1900435 original size:21 final size:21
Alignment explanation
Indices: 1900410--1900458 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
1900400 ATCTAAAAGC
1900410 CCTTAAGTGAATCTTTAGATA
1 CCTTAAGTGAATCTTTAGATA
1900431 CCTTAAGTGAATCTTTAGATA
1 CCTTAAGTGAATCTTTAGATA
1900452 CCTTAAG
1 CCTTAAG
1900459 GACACTCCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (21 bp):
CCTTAAGTGAATCTTTAGATA
Found at i:1901330 original size:23 final size:21
Alignment explanation
Indices: 1901275--1901331 Score: 53
Period size: 23 Copynumber: 2.6 Consensus size: 21
1901265 ACCCCCTTGC
*
1901275 TATGCATCGATACACCTTGAA
1 TATGTATCGATACACCTTGAA
*
1901296 TATTTA-CTGATACATTCCTTGAA
1 TATGTATC-GATACA--CCTTGAA
*
1901319 TGTGTATCGATAC
1 TATGTATCGATAC
1901332 CCCCAATGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
20 1 0.04
21 10 0.36
23 16 0.57
24 1 0.04
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (21 bp):
TATGTATCGATACACCTTGAA
Found at i:1905340 original size:58 final size:58
Alignment explanation
Indices: 1905278--1905405 Score: 186
Period size: 59 Copynumber: 2.2 Consensus size: 58
1905268 ATTACCAAAT
*
1905278 GGCACTAAGTGTGC-AAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCATATTG
1 GGCACTAAGTGTGCTAAAATATTAAGAAATTCATACTAAGTGTATGAATTTCCATA-TG
** * *
1905336 GGCACTTTGTGTGCTAAAATATTAAGAAATTCATACTAAGTGTATGAATTTTCGTATG
1 GGCACTAAGTGTGCTAAAATATTAAGAAATTCATACTAAGTGTATGAATTTCCATATG
*
1905394 GGCACTAGGTGT
1 GGCACTAAGTGT
1905406 ACGAAATAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
58 24 0.39
59 38 0.61
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (58 bp):
GGCACTAAGTGTGCTAAAATATTAAGAAATTCATACTAAGTGTATGAATTTCCATATG
Found at i:1905865 original size:81 final size:81
Alignment explanation
Indices: 1905757--1906289 Score: 753
Period size: 81 Copynumber: 6.6 Consensus size: 81
1905747 AAAAAGGTGT
*
1905757 CAATTATGCCAGTTAGATGAACGGTTAAATACAGTTGAGTAAAAGAATAATGGACTAACTGTGCA
1 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGACTAACTGTGCA
* *
1905822 ATTGGTAAAAAGGTAC
66 ATTGGTAGAAATGTAC
* * * *
1905838 CAATTATGTCAGTTAGATGAACGGTTAAATACCATTGAGTAAAAGAATAATGGTCTAACTATGCA
1 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGACTAACTGTGCA
*
1905903 ATTAGTAGAAATGTAC
66 ATTGGTAGAAATGTAC
* ** * * *
1905919 CAATCATGCCAGTTAGATGAACGGTTAAATATTGTTGAGTAAAAAAAATAATGGCCTAACTATGC
1 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGT-AAAAGAATAATGGACTAACTGTGC
1905984 AATTGGTAGAAATGTAC
65 AATTGGTAGAAATGTAC
* * * *
1906001 CAATAATGCGAGTTAGATGAACGGTTAAATACCGTTGAGAAAAAGAATAATGGTCTAACTGTGCA
1 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGACTAACTGTGCA
1906066 ATTGGTAGAAATGTAC
66 ATTGGTAGAAATGTAC
** ** * * *
1906082 CAATTATGCCAGTTAGATGAATAGTTAAATGTCGTTGAGTAAAAGAATAATGGCCTAAATGTACA
1 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGACTAACTGTGCA
*
1906147 ATTGGTAGAAATGTAT
66 ATTGGTAGAAATGTAC
* *
1906163 CAATTATGCCAGTTACATGAACGGTTAAATGCCGTTGAGTAAAAGAATAAT-GACCTAACTGTGC
1 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGA-CTAACTGTGC
* *
1906227 AATTGGTAAAAAGGTAC
65 AATTGGTAGAAATGTAC
* *
1906244 CAATTATACCAGTTAGATGAACGATTAAATACCGTTGAGTAAAAGA
1 CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGA
1906290 CGAAAGGTTA
Statistics
Matches: 401, Mismatches: 49, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
80 1 0.00
81 327 0.82
82 73 0.18
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.28
Consensus pattern (81 bp):
CAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGACTAACTGTGCA
ATTGGTAGAAATGTAC
Found at i:1906157 original size:244 final size:243
Alignment explanation
Indices: 1905747--1906289 Score: 780
Period size: 244 Copynumber: 2.2 Consensus size: 243
1905737 TGCATTTTAC
** *
1905747 AAAAAGGTGTCAATTATGCCAGTTAGATGAACGGTTAAATACAGTTGAGTAAAAGAATAATGGAC
1 AAAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGAC
* *
1905812 TAACTGTGCAATTGGTAAAAAGGTACCAATTATGTCAGTTAGATGAACGGTTAAATACCATTGAG
66 TAACTGTGCAATTGGTAAAAAGGTACCAATTATGCCAGTTAGATGAACAGTTAAATACCATTGAG
* * * *
1905877 TAAAAGAATAATGGTCTAACTATGCAATTAGTAGAAATGTACCAATCATGCCAGTTAGATGAACG
131 TAAAAGAATAATGGCCTAAATATACAATTAGTAGAAATGTACCAATCATGCCAGTTACATGAACG
** *
1905942 GTTAAATATTGTTGAGTAAAAAAAATAATGGCCTAACTATGCAATTGGT
196 GTTAAATACCGTTGAGT-AAAAAAATAATGACCTAACTATGCAATTGGT
* * * * * *
1905991 AGAAATGTACCAATAATGCGAGTTAGATGAACGGTTAAATACCGTTGAGAAAAAGAATAATGGTC
1 AAAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGAC
* * * ** *
1906056 TAACTGTGCAATTGGTAGAAATGTACCAATTATGCCAGTTAGATGAATAGTTAAATGTCGTTGAG
66 TAACTGTGCAATTGGTAAAAAGGTACCAATTATGCCAGTTAGATGAACAGTTAAATACCATTGAG
* * * *
1906121 TAAAAGAATAATGGCCTAAATGTACAATTGGTAGAAATGTATCAATTATGCCAGTTACATGAACG
131 TAAAAGAATAATGGCCTAAATATACAATTAGTAGAAATGTACCAATCATGCCAGTTACATGAACG
* * *
1906186 GTTAAATGCCGTTGAGTAAAAGAATAATGACCTAACTGTGCAATTGGT
196 GTTAAATACCGTTGAGTAAAAAAATAATGACCTAACTATGCAATTGGT
* *
1906234 AAAAAGGTACCAATTATACCAGTTAGATGAACGATTAAATACCGTTGAGTAAAAGA
1 AAAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGA
1906290 CGAAAGGTTA
Statistics
Matches: 261, Mismatches: 38, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
243 77 0.30
244 184 0.70
ACGTcount: A:0.40, C:0.11, G:0.21, T:0.27
Consensus pattern (243 bp):
AAAAAGGTACCAATTATGCCAGTTAGATGAACGGTTAAATACCGTTGAGTAAAAGAATAATGGAC
TAACTGTGCAATTGGTAAAAAGGTACCAATTATGCCAGTTAGATGAACAGTTAAATACCATTGAG
TAAAAGAATAATGGCCTAAATATACAATTAGTAGAAATGTACCAATCATGCCAGTTACATGAACG
GTTAAATACCGTTGAGTAAAAAAATAATGACCTAACTATGCAATTGGT
Found at i:1908628 original size:46 final size:46
Alignment explanation
Indices: 1908578--1909055 Score: 668
Period size: 46 Copynumber: 10.4 Consensus size: 46
1908568 TAATATACCA
* * * * *
1908578 TTATGTATTTTCATTTGTGGCATTCTTTCATGCCGATTATACACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
**
1908624 TTATGCATTTTCATTTATGGCATCCTTTCACACCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * * *
1908670 TTATGCGTTTTTATTTATGGCATCCTTTCATGCCAATAATGCACCA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* *
1908716 TTATGCATTTTCATTTATGGCATCATTTCATGTCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* ** *
1908762 TTATGCATTTTTATTTATGGCATCCTTTCATGTTGATAATGCATCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* *
1908808 TTATGCATTTTCATTTGTGGCATCCTTTCATGCCGATAATGCATCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* *
1908854 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATACACCA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
** * **
1908900 TTATGCATTTTCATTTATGGCATCCTTTCATGTTGATAATACACTA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* **
1908946 TTATGCATTTTCATTTATGGCATCCTTTCATGTCGATAATGCATTG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* *
1908992 TTATACATTTTCATTTATGACATCCTTTCATGCCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
*
1909038 TTATGCATTTTCTTTTAT
1 TTATGCATTTTCATTTAT
1909056 TCCTTCATTT
Statistics
Matches: 387, Mismatches: 45, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 387 1.00
ACGTcount: A:0.23, C:0.20, G:0.13, T:0.43
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
Found at i:1913541 original size:419 final size:418
Alignment explanation
Indices: 1912730--1913563 Score: 1236
Period size: 419 Copynumber: 2.0 Consensus size: 418
1912720 TCATGTTTTA
*
1912730 TTTCATAGATAATTAGAACCCCACCATGACTAACCTTATTTGGTGGGGTTGATTTTATGGATGTT
1 TTTCATAGATAATTAGAACCCCACCATGACTAACCTTATTTGGTGGAGTTGATTTTATGGATGTT
* * * * * *
1912795 TGATATTATTTTAATGGTATATTTAAATTTATCTTTTGCATTTACTTGTTTTGCTTATGAATGTT
66 TAACATTATTTTAATGGTAGATTTAAAGTTATCTTTTGCATTTACTTGTTTTGCGTATGAATGCT
** *
1912860 TCATCTTCTAAGTTTGTAGGAGGCATGAGAGTGTCCATTACTTAGATGAAGGCTATGTGATCAAA
131 TCATCGCCTAAGTTTGTAGGAGGCATGAGAGTGTCCATTACTTAGATGAAGGCTAGGTGATCAAA
* * *
1912925 AGAAACTTAGTTATTAATACTTGTAGTATTCGAGAGAAACACAAGTAAGATCCGCATAAACAATG
196 AGAAACTTAGTCATTAATACTTGTAGTATTCGAGAGAAACACAAGAAAGATCCACATAAACAATG
* * * * * *
1912990 GGGTATAGTAATTTCTTGAGCTTTGAACCGACATAATAATACTATATCCTAATCCCTTAGTGCTT
261 GGGTATAGTAATTTCTTAAGATTAGAACCGACATAATAATAATATATCCTAACCCCTTAATGCTT
* * * **
1913055 AAGAGAGACTAAGATAGGATTTCAATGACTAAGAGGGGTAGTTTTTATCAATAGTGTAGGATGCC
326 AAGAGAGACTAAGATAAGATTTCAACGACTAAGAGGGGTAGTTTTTATAAATAGCATAGGATGCC
*
1913120 ATAGTTGAGACTGAGAGGAGATGTCTTG
391 ATAGTTGAGACTAAGAGGAGATGTCTTG
* * *
1913148 TTTCATGGATGATTCGAACCCCACCATGAACTAACCTTATTTGGTGGAGTTGATTTTATGGATGT
1 TTTCATAGATAATTAGAACCCCACCATG-ACTAACCTTATTTGGTGGAGTTGATTTTATGGATGT
* * * *
1913213 TTAACATTATTTTAATGGTGGATTTATAGTTATCTTTTGTATTTACTTGTTTTTCGTATGAATGC
65 TTAACATTATTTTAATGGTAGATTTAAAGTTATCTTTTGCATTTACTTGTTTTGCGTATGAATGC
* *
1913278 TTCATCGCCTAAGTTTGTAGGAGGCATGAGAGTGTCCATTACTTAGATGAAGGCTAGGTGTTCGA
130 TTCATCGCCTAAGTTTGTAGGAGGCATGAGAGTGTCCATTACTTAGATGAAGGCTAGGTGATCAA
* * *
1913343 GAGAAACTTAGTCATTAATACTTGTATTATTCGAGAGAAACACAAGAAAGATCCACATAAGCAAT
195 AAGAAACTTAGTCATTAATACTTGTAGTATTCGAGAGAAACACAAGAAAGATCCACATAAACAAT
* * * * * *
1913408 GGGGTGTAGTATTTTCTTAAGATTAGAACTGGCCTAGTAATAATATATCCTAACCCCTTAATGCT
260 GGGGTATAGTAATTTCTTAAGATTAGAACCGACATAATAATAATATATCCTAACCCCTTAATGCT
* * * *
1913473 TGAGAGAGACTAAGATAAGATTTCAACGACTAAGAGGGGTGGTTTTTGTAAATAGCATAGGCTGC
325 TAAGAGAGACTAAGATAAGATTTCAACGACTAAGAGGGGTAGTTTTTATAAATAGCATAGGATGC
1913538 CATAGTTGAGACTAAGAGGAGATGTC
390 CATAGTTGAGACTAAGAGGAGATGTC
1913564 GTGGCATTAT
Statistics
Matches: 368, Mismatches: 47, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
418 25 0.07
419 343 0.93
ACGTcount: A:0.31, C:0.13, G:0.21, T:0.35
Consensus pattern (418 bp):
TTTCATAGATAATTAGAACCCCACCATGACTAACCTTATTTGGTGGAGTTGATTTTATGGATGTT
TAACATTATTTTAATGGTAGATTTAAAGTTATCTTTTGCATTTACTTGTTTTGCGTATGAATGCT
TCATCGCCTAAGTTTGTAGGAGGCATGAGAGTGTCCATTACTTAGATGAAGGCTAGGTGATCAAA
AGAAACTTAGTCATTAATACTTGTAGTATTCGAGAGAAACACAAGAAAGATCCACATAAACAATG
GGGTATAGTAATTTCTTAAGATTAGAACCGACATAATAATAATATATCCTAACCCCTTAATGCTT
AAGAGAGACTAAGATAAGATTTCAACGACTAAGAGGGGTAGTTTTTATAAATAGCATAGGATGCC
ATAGTTGAGACTAAGAGGAGATGTCTTG
Found at i:1915551 original size:18 final size:18
Alignment explanation
Indices: 1915528--1915565 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1915518 TATGTTAAGT
*
1915528 AACATTTAATCATACTCA
1 AACATTTAAACATACTCA
*
1915546 AACATTTAAACATATTCA
1 AACATTTAAACATACTCA
1915564 AA
1 AA
1915566 ACAAACTCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (18 bp):
AACATTTAAACATACTCA
Found at i:1915776 original size:229 final size:229
Alignment explanation
Indices: 1915375--1915834 Score: 902
Period size: 229 Copynumber: 2.0 Consensus size: 229
1915365 AGAATGATAT
1915375 TCATAGTTTAGGAATTAAATTAAAATATTTAAAAGTTTAAGGACTACCTTAATATAAGAGTCATA
1 TCATAGTTTAGGAATTAAATTAAAATATTTAAAAGTTTAAGGACTACCTTAATATAAGAGTCATA
1915440 ATTTGAGTACATGTGATACAATTAACTCCTGATAATAAAACTAAAAAACTTTATAAGTAAAATCA
66 ATTTGAGTACATGTGATACAATTAACTCCTGATAATAAAACTAAAAAACTTTATAAGTAAAATCA
1915505 AATGAATATTATGTATGTTAAGTAACATTTAATCATACTCAAACATTTAAACATATTCAAAACAA
131 AATGAATATTATGTATGTTAAGTAACATTTAATCATACTCAAACATTTAAACATATTCAAAACAA
1915570 ACTCCATAAACACATGTTAAGTCTACGAGCACCA
196 ACTCCATAAACACATGTTAAGTCTACGAGCACCA
1915604 TCATAGTTTAGGAATTAAATTAAAATATTTAAAAGTTTAAGGACTACCTTAATATAAGAGTCATA
1 TCATAGTTTAGGAATTAAATTAAAATATTTAAAAGTTTAAGGACTACCTTAATATAAGAGTCATA
1915669 ATTTGAGTACATGTGATACAATTAACTCCTGATAATAAAACTAAAAAACTTTATAAGTAAAATCA
66 ATTTGAGTACATGTGATACAATTAACTCCTGATAATAAAACTAAAAAACTTTATAAGTAAAATCA
*
1915734 AATGAATATTATGTCTGTTAAGTAACATTTAATCATACTCAAACATTTAAACATATTCAAAACAA
131 AATGAATATTATGTATGTTAAGTAACATTTAATCATACTCAAACATTTAAACATATTCAAAACAA
*
1915799 ACTCCGTAAACACATGTTAAGTCTACGAGCACCA
196 ACTCCATAAACACATGTTAAGTCTACGAGCACCA
1915833 TC
1 TC
1915835 CGTGTTGACT
Statistics
Matches: 229, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 229 1.00
ACGTcount: A:0.45, C:0.14, G:0.10, T:0.32
Consensus pattern (229 bp):
TCATAGTTTAGGAATTAAATTAAAATATTTAAAAGTTTAAGGACTACCTTAATATAAGAGTCATA
ATTTGAGTACATGTGATACAATTAACTCCTGATAATAAAACTAAAAAACTTTATAAGTAAAATCA
AATGAATATTATGTATGTTAAGTAACATTTAATCATACTCAAACATTTAAACATATTCAAAACAA
ACTCCATAAACACATGTTAAGTCTACGAGCACCA
Found at i:1915780 original size:18 final size:18
Alignment explanation
Indices: 1915757--1915794 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1915747 TCTGTTAAGT
*
1915757 AACATTTAATCATACTCA
1 AACATTTAAACATACTCA
*
1915775 AACATTTAAACATATTCA
1 AACATTTAAACATACTCA
1915793 AA
1 AA
1915795 ACAAACTCCG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (18 bp):
AACATTTAAACATACTCA
Found at i:1917575 original size:27 final size:26
Alignment explanation
Indices: 1917516--1917573 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
1917506 TGTTAAAGTG
* *
1917516 AATTTTTAAAATTTTAAGAAAAGATA
1 AATTTATAAAATTTTAAGAAAAAATA
1917542 AATTTATAAAATTTTAAAGATAAAAATA
1 AATTTATAAAATTTT-AAGA-AAAAATA
1917570 AATT
1 AATT
1917574 ATCAATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 14 0.50
27 4 0.14
28 10 0.36
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (26 bp):
AATTTATAAAATTTTAAGAAAAAATA
Found at i:1917599 original size:17 final size:18
Alignment explanation
Indices: 1917579--1917617 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
1917569 AAATTATCAA
1917579 TAAAAATATA-AAAAATT
1 TAAAAATATATAAAAATT
*
1917596 T-AAAATATATAATAATT
1 TAAAAATATATAAAAATT
1917613 TAAAA
1 TAAAA
1917618 TTTTTAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 8 0.42
17 8 0.42
18 3 0.16
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAAATATATAAAAATT
Found at i:1917626 original size:17 final size:17
Alignment explanation
Indices: 1917581--1917618 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
1917571 ATTATCAATA
*
1917581 AAAATATA-AAAAATTT
1 AAAATATATAATAATTT
1917597 AAAATATATAATAATTT
1 AAAATATATAATAATTT
1917614 AAAAT
1 AAAAT
1917619 TTTTAATAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATATATAATAATTT
Found at i:1917866 original size:3 final size:3
Alignment explanation
Indices: 1917858--1917964 Score: 63
Period size: 3 Copynumber: 33.7 Consensus size: 3
1917848 TTTTATTCGA
* * * * *
1917858 ATT ATT ATT AAT ATT AAT ATT AATA ATT ATT AATT GCTT ATG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT -ATT -ATT ATT ATT ATT
* * * *
1917906 ATT ATC ATT AATT ATT AGT ATTT ATA ATT ATT AGTT ACT ATT ATT AATT
1 ATT ATT ATT -ATT ATT ATT A-TT ATT ATT ATT A-TT ATT ATT ATT -ATT
1917955 A-T ATT ATT AT
1 ATT ATT ATT AT
1917965 AGTTAAATAT
Statistics
Matches: 78, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
2 2 0.03
3 58 0.74
4 18 0.23
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:1917890 original size:16 final size:16
Alignment explanation
Indices: 1917860--1917938 Score: 54
Period size: 16 Copynumber: 4.9 Consensus size: 16
1917850 TTATTCGAAT
*
1917860 TATTATTAA-TATTAA
1 TATTAATAATTATTAA
1917875 TATTAATAATTATTAA
1 TATTAATAATTATTAA
* * *
1917891 T-TGCTTATGATTATTAT
1 TAT--TAATAATTATTAA
* * *
1917908 TATCATTAATTATTAG
1 TATTAATAATTATTAA
*
1917924 TATTTATAATTATTA
1 TATTAATAATTATTA
1917939 GTTACTATTA
Statistics
Matches: 48, Mismatches: 12, Indels: 7
0.72 0.18 0.10
Matches are distributed among these distances:
15 9 0.19
16 27 0.56
17 11 0.23
18 1 0.02
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (16 bp):
TATTAATAATTATTAA
Found at i:1917935 original size:20 final size:19
Alignment explanation
Indices: 1917900--1917963 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 19
1917890 ATTGCTTATG
* *
1917900 ATTATTATTATCATTAATT
1 ATTACTATTATAATTAATT
*
1917919 ATTAGTATTTATAATT-ATT
1 ATTACTA-TTATAATTAATT
1917938 AGTTACTATTATTAATTATATT
1 A-TTACTATTA-TAATTA-ATT
1917960 ATTA
1 ATTA
1917964 TAGTTAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
19 13 0.35
20 17 0.46
21 3 0.08
22 4 0.11
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (19 bp):
ATTACTATTATAATTAATT
Found at i:1923651 original size:14 final size:14
Alignment explanation
Indices: 1923628--1923668 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1923618 AGTCAAAGTC
*
1923628 AACGGGTTGACTCG
1 AACGAGTTGACTCG
*
1923642 AACGATTTGACTCG
1 AACGAGTTGACTCG
*
1923656 GACGAGTTGACTC
1 AACGAGTTGACTC
1923669 ATTCCAGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.29, T:0.24
Consensus pattern (14 bp):
AACGAGTTGACTCG
Found at i:1928889 original size:30 final size:29
Alignment explanation
Indices: 1928853--1928932 Score: 97
Period size: 30 Copynumber: 2.7 Consensus size: 29
1928843 ATAAAATTGA
*
1928853 TAAAAAATAATCGAAAATATTATTAGGTGT
1 TAAAAAAT-ATCGAAAATATTATTAGGCGT
*
1928883 TAAAAAATATCTGAAAACATTATTAGGCGT
1 TAAAAAATATC-GAAAATATTATTAGGCGT
* *
1928913 TAAAATATGACCGAAAATAT
1 TAAAAAAT-ATCGAAAATAT
1928933 AAAAAAATGA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
29 3 0.07
30 38 0.88
31 2 0.05
ACGTcount: A:0.50, C:0.07, G:0.12, T:0.30
Consensus pattern (29 bp):
TAAAAAATATCGAAAATATTATTAGGCGT
Found at i:1928969 original size:21 final size:20
Alignment explanation
Indices: 1928932--1928970 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1928922 ACCGAAAATA
* *
1928932 TAAAAAAATGATGTTTTAAG
1 TAAAAAAATAATATTTTAAG
1928952 TAAAAATAATAATATTTTA
1 TAAAAA-AATAATATTTTA
1928971 GATAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (20 bp):
TAAAAAAATAATATTTTAAG
Found at i:1930715 original size:20 final size:20
Alignment explanation
Indices: 1930690--1930728 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1930680 CACCAATTCC
1930690 ACCAACTCCACTAATGATGT
1 ACCAACTCCACTAATGATGT
1930710 ACCAACTCCACTAATGATG
1 ACCAACTCCACTAATGATG
1930729 CACACCACCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.31, G:0.10, T:0.23
Consensus pattern (20 bp):
ACCAACTCCACTAATGATGT
Found at i:1935106 original size:22 final size:22
Alignment explanation
Indices: 1935078--1935159 Score: 101
Period size: 22 Copynumber: 3.7 Consensus size: 22
1935068 ATCAGTGGCT
**
1935078 GTGCAGCCCGCTTCCAGCATTC
1 GTGCAGCCTACTTCCAGCATTC
* *
1935100 GTGCAGCCTACTTTCAACATTC
1 GTGCAGCCTACTTCCAGCATTC
* *
1935122 GTACAACCTACTTCCAGCATTC
1 GTGCAGCCTACTTCCAGCATTC
*
1935144 GTGCAGCCTTCTTCCA
1 GTGCAGCCTACTTCCA
1935160 CCATCCGTAC
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 49 1.00
ACGTcount: A:0.20, C:0.37, G:0.16, T:0.28
Consensus pattern (22 bp):
GTGCAGCCTACTTCCAGCATTC
Found at i:1935350 original size:27 final size:28
Alignment explanation
Indices: 1935311--1935385 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
1935301 AATGATAGTA
* * *
1935311 TTATTATAATTTAT-GAGAAGTTGTCCT
1 TTATTATAATTTATAAAAAAATTGTCCT
* *
1935338 TTATTGTATTTTATAAAAAAATTGTCCT
1 TTATTATAATTTATAAAAAAATTGTCCT
*
1935366 TTATCATAATTTATAAAAAA
1 TTATTATAATTTATAAAAAA
1935386 GTATACTTTA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 12 0.31
28 27 0.69
ACGTcount: A:0.39, C:0.07, G:0.08, T:0.47
Consensus pattern (28 bp):
TTATTATAATTTATAAAAAAATTGTCCT
Found at i:1935418 original size:22 final size:22
Alignment explanation
Indices: 1935375--1935419 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1935365 TTTATCATAA
*
1935375 TTTATAAAAAAGTATACTTTAT
1 TTTATAAAAAAGTATACATTAT
*
1935397 TTTAT-AAAAAGTTTTACATTAT
1 TTTATAAAAAAG-TATACATTAT
1935419 T
1 T
1935420 ATAATTTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
TTTATAAAAAAGTATACATTAT
Found at i:1935427 original size:27 final size:28
Alignment explanation
Indices: 1935397--1935461 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
1935387 TATACTTTAT
1935397 TTTATAAAAAGTTT-TACATT-ATTATAA
1 TTTATAAAAAGTTTGTAC-TTCATTATAA
*
1935424 TTTATAAACAATTTTGTACTTCATTATAA
1 TTTATAAA-AAGTTTGTACTTCATTATAA
*
1935453 TTCATAAAA
1 TTTATAAAA
1935462 CCTTTTGTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
27 8 0.24
28 8 0.24
29 17 0.52
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.46
Consensus pattern (28 bp):
TTTATAAAAAGTTTGTACTTCATTATAA
Found at i:1938527 original size:29 final size:30
Alignment explanation
Indices: 1938485--1938552 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 30
1938475 ATAAGCCTTA
* * * * *
1938485 GAAAATTTGGGGACCATTTTG-TAATTTTT
1 GAAAAGTTGGGGACCAATTCGATAACTTTG
1938514 GAAAAGTTGGGGACCAATTCGATAACTTTG
1 GAAAAGTTGGGGACCAATTCGATAACTTTG
1938544 GAAAAGTTG
1 GAAAAGTTG
1938553 TGAATGGTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
29 18 0.55
30 15 0.45
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (30 bp):
GAAAAGTTGGGGACCAATTCGATAACTTTG
Found at i:1940723 original size:12 final size:11
Alignment explanation
Indices: 1940704--1940794 Score: 67
Period size: 12 Copynumber: 7.7 Consensus size: 11
1940694 AGATCCAATC
*
1940704 AGAAAAAAAAT
1 AGAAAAAAAAA
*
1940715 AG-AAAAAAAG
1 AGAAAAAAAAA
*
1940725 AGAGAAAAACAA
1 AGA-AAAAAAAA
1940737 AGAAAAAACAAA
1 AGAAAAAA-AAA
1940749 TAGAAAATAAAAA
1 -AGAAAA-AAAAA
1940762 AGAAACAAAACAA
1 AGAAA-AAAA-AA
**
1940775 AGGAAAAAGTAA
1 A-GAAAAAAAAA
1940787 AGAAAAAA
1 AGAAAAAA
1940795 GAAGACAAGA
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
10 9 0.14
11 13 0.20
12 22 0.34
13 15 0.23
14 6 0.09
ACGTcount: A:0.78, C:0.04, G:0.13, T:0.04
Consensus pattern (11 bp):
AGAAAAAAAAA
Found at i:1947103 original size:4 final size:4
Alignment explanation
Indices: 1947094--1947126 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
1947084 TCTGATATCC
1947094 TATT TATT TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT TATT TATT T
1947127 TAGTTTAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:1953195 original size:3 final size:3
Alignment explanation
Indices: 1953187--1953252 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
1953177 TCTAATTGTA
1953187 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1953234 ATT ATT ATT ATT A-T ATT AT
1 ATT ATT ATT ATT ATT ATT AT
1953253 GCTTATTTAT
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.07
3 57 0.93
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:1956881 original size:31 final size:32
Alignment explanation
Indices: 1956845--1956906 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1956835 ATTTTACATG
1956845 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
1956876 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1956907 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:1959703 original size:43 final size:45
Alignment explanation
Indices: 1959625--1959719 Score: 140
Period size: 44 Copynumber: 2.2 Consensus size: 45
1959615 ATAAATGGTT
* *
1959625 ATGGCAAGTATATTGGTAAACTAAGCTTACGAGCTTATGGAAT-A
1 ATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAA
* *
1959669 ATGGTAAGTGTATTGGTAAAATAAG-TTACGAGCTTATGGGATAA
1 ATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAA
1959713 ATGGTAA
1 ATGGTAA
1959720 ATTTATTGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
43 16 0.35
44 30 0.65
ACGTcount: A:0.37, C:0.07, G:0.25, T:0.31
Consensus pattern (45 bp):
ATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAATAA
Found at i:1968822 original size:23 final size:23
Alignment explanation
Indices: 1968796--1968879 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
1968786 CTTGAATAAA
1968796 TGCACCGAAGTGCCACGTAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* *
1968819 TGCACCGAAGTGCCGCATAGAAT
1 TGCACCGAAGTGCCACGTAGAAT
* * *
1968842 TGCACTGAAGTGCCACGTAAAAA
1 TGCACCGAAGTGCCACGTAGAAT
1968865 TGCACCGAAGTGCCA
1 TGCACCGAAGTGCCA
1968880 TATAAGATGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 53 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
TGCACCGAAGTGCCACGTAGAAT
Found at i:1969692 original size:21 final size:21
Alignment explanation
Indices: 1969666--1969723 Score: 98
Period size: 21 Copynumber: 2.8 Consensus size: 21
1969656 AAATTGGTCT
1969666 TAGGGTATCGGTACCCATTCA
1 TAGGGTATCGGTACCCATTCA
*
1969687 TAGGGTATCGATACCCATTCA
1 TAGGGTATCGGTACCCATTCA
*
1969708 TAGGGTATCAGTACCC
1 TAGGGTATCGGTACCC
1969724 TTGCCTAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (21 bp):
TAGGGTATCGGTACCCATTCA
Found at i:1970506 original size:22 final size:21
Alignment explanation
Indices: 1970475--1970515 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
1970465 TTTACCCTTA
1970475 ATTTAATT-AAATTATTAAATT
1 ATTTAATTAAAATT-TTAAATT
1970496 ATTTATATTAAAATTTTAAA
1 ATTTA-ATTAAAATTTTAAA
1970516 CTTTAATCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.28
22 8 0.44
23 5 0.28
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTAATTAAAATTTTAAATT
Found at i:1977927 original size:20 final size:20
Alignment explanation
Indices: 1977902--1977963 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
1977892 TTTTTGTGCA
*
1977902 GAGGGAATCGATCCCCCCAT
1 GAGGGAACCGATCCCCCCAT
**
1977922 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGA-TCCCCCCAT
*
1977943 GAAGGGGAACCGATTCCCCCA
1 G-A-GGGAACCGATCCCCCCA
1977964 CAGGGAATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 10 0.30
21 8 0.24
22 6 0.18
23 9 0.27
ACGTcount: A:0.24, C:0.34, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATCCCCCCAT
Found at i:1978433 original size:2 final size:2
Alignment explanation
Indices: 1978426--1978464 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1978416 GTTATGAAAC
1978426 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 T
1978465 TGTTTCTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1980257 original size:16 final size:16
Alignment explanation
Indices: 1980236--1980268 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1980226 ATGTGTGTTT
1980236 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
1980252 TAAGTGTGTTTTAAAA
1 TAAGTGTGTTTTAAAA
1980268 T
1 T
1980269 GATAAATGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.45
Consensus pattern (16 bp):
TAAGTGTGTTTTAAAA
Found at i:1992338 original size:34 final size:34
Alignment explanation
Indices: 1992294--1992409 Score: 135
Period size: 35 Copynumber: 3.4 Consensus size: 34
1992284 TCTGATCTTG
*
1992294 CTTCACTACTC-TCCGTGAAGGCTGGATCGAATCA
1 CTTCACTACTCTTCCGTGAAGGCTGGAT-GAATTA
* * * *
1992328 CTTCATTACTCTTACGTGAAGGTTGGATTAAATTA
1 CTTCACTACTCTTCCGTGAAGGCTGGA-TGAATTA
* *
1992363 CTTCACTACTCTTCCGTGAAGGCTAGATGATTTA
1 CTTCACTACTCTTCCGTGAAGGCTGGATGAATTA
*
1992397 CTTCATTACTCTT
1 CTTCACTACTCTT
1992410 TAGTGAATGT
Statistics
Matches: 68, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
34 27 0.40
35 40 0.59
36 1 0.01
ACGTcount: A:0.24, C:0.23, G:0.16, T:0.36
Consensus pattern (34 bp):
CTTCACTACTCTTCCGTGAAGGCTGGATGAATTA
Done.