Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 2 of 171
Found at i:415618 original size:23 final size:22
Alignment explanation
Indices: 415588--415634 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
415578 AGGTTGAGAC
* *
415588 AATAAATAATTTAAAATTATAAA
1 AATAAATAAATCAAAATTA-AAA
415611 AATAAATAAATCAAAATTAAAA
1 AATAAATAAATCAAAATTAAAA
415633 AA
1 AA
415635 GAATTATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AATAAATAAATCAAAATTAAAA
Found at i:416548 original size:2 final size:2
Alignment explanation
Indices: 416541--416582 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
416531 GGAATTTACC
416541 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
416583 TAAATAATCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:424419 original size:42 final size:42
Alignment explanation
Indices: 424357--424583 Score: 224
Period size: 43 Copynumber: 5.3 Consensus size: 42
424347 AGAAAAACAT
* * * *
424357 CGCTATAGAATATGGCCTTTAGCGGCGCTTTCTCAAAAACGC
1 CGCTAAAGAACATGGTCTTTAGCGGCGCTTTCTCACAAACGC
*
424399 CGCTATAA-AACATGGTCTTTAGTGGCGCTTTCTCACAAACGC
1 CGCTA-AAGAACATGGTCTTTAGCGGCGCTTTCTCACAAACGC
* *
424441 CGCTAAAGAACATGGTCTTTAGCGGCGCTTAT-TCTATAAATGC
1 CGCTAAAGAACATGGTCTTTAGCGGCGCTT-TCTC-ACAAACGC
* * *
424484 CGCTAAAGAGCATGGTCTTTAGCGACGCTTTTCCCACAAACGC
1 CGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCTCACAAACGC
* * * * ** * * *
424527 CGTTAAAGACCATGATCTTTAACGGCAAATTTCTCGCAAATGT
1 CGCTAAAGAACATGGTCTTTAGCGGC-GCTTTCTCACAAACGC
424570 CGCTAAAGAACATG
1 CGCTAAAGAACATG
424584 CTTTTTAGTG
Statistics
Matches: 152, Mismatches: 26, Indels: 13
0.80 0.14 0.07
Matches are distributed among these distances:
41 2 0.01
42 63 0.41
43 84 0.55
44 3 0.02
ACGTcount: A:0.29, C:0.25, G:0.20, T:0.27
Consensus pattern (42 bp):
CGCTAAAGAACATGGTCTTTAGCGGCGCTTTCTCACAAACGC
Found at i:424500 original size:43 final size:42
Alignment explanation
Indices: 424357--424552 Score: 207
Period size: 42 Copynumber: 4.6 Consensus size: 42
424347 AGAAAAACAT
* * *
424357 CGCTATAGAATATGGCCTTTAGCGGCGCTTTCTCAAAAACGC
1 CGCTAAAGAACATGGTCTTTAGCGGCGCTTTCTCAAAAACGC
* *
424399 CGCTATAA-AACATGGTCTTTAGTGGCGCTTTCTCACAAACGC
1 CGCTA-AAGAACATGGTCTTTAGCGGCGCTTTCTCAAAAACGC
* *
424441 CGCTAAAGAACATGGTCTTTAGCGGCGCTTAT-TCTATAAATGC
1 CGCTAAAGAACATGGTCTTTAGCGGCGCTT-TCTC-AAAAACGC
* * * *
424484 CGCTAAAGAGCATGGTCTTTAGCGACGCTTTTCCCACAAACGC
1 CGCTAAAGAACATGGTCTTTAGCGGCGC-TTTCTCAAAAACGC
* * * *
424527 CGTTAAAGACCATGATCTTTAACGGC
1 CGCTAAAGAACATGGTCTTTAGCGGC
424553 AAATTTCTCG
Statistics
Matches: 130, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
41 2 0.02
42 63 0.48
43 62 0.48
44 3 0.02
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (42 bp):
CGCTAAAGAACATGGTCTTTAGCGGCGCTTTCTCAAAAACGC
Found at i:424568 original size:86 final size:86
Alignment explanation
Indices: 424397--424618 Score: 234
Period size: 86 Copynumber: 2.6 Consensus size: 86
424387 TCTCAAAAAC
* *
424397 GCCGCTATAA-AACATGGTCTTTAGTGGCGC-TTTCTCACAAACGCCGCTAAAGAACATGGTCTT
1 GCCGCTA-AAGAACATGGTCTTTAGTGACGCTTTTCTCACAAACGCCGCTAAAGAACATGATCTT
* *** *
424460 TAGCGGCGCTTATTCTATAAAT
65 TAACGGCAAATATTCTACAAAT
* * * * *
424482 GCCGCTAAAGAGCATGGTCTTTAGCGACGCTTTTCCCACAAACGCCGTTAAAGACCATGATCTTT
1 GCCGCTAAAGAACATGGTCTTTAGTGACGCTTTTCTCACAAACGCCGCTAAAGAACATGATCTTT
*
424547 AACGGCAAAT-TTCTCGCAAAT
66 AACGGCAAATATTCT-ACAAAT
* * * ** *
424568 GTCGCTAAAGAACATGCTTTTTAGTGACATTTTTCTCACAAACGCCACTAA
1 GCCGCTAAAGAACATGGTCTTTAGTGACGCTTTTCTCACAAACGCCGCTAA
424619 TATTAACAAA
Statistics
Matches: 111, Mismatches: 23, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
84 2 0.02
85 28 0.25
86 81 0.73
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (86 bp):
GCCGCTAAAGAACATGGTCTTTAGTGACGCTTTTCTCACAAACGCCGCTAAAGAACATGATCTTT
AACGGCAAATATTCTACAAAT
Found at i:427328 original size:19 final size:19
Alignment explanation
Indices: 427300--427338 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
427290 AATTTTTACT
*
427300 TATCTGTAAATCAATTTTG
1 TATCTATAAATCAATTTTG
*
427319 TATCTATAAATCATTTTTG
1 TATCTATAAATCAATTTTG
427338 T
1 T
427339 CTAATGATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.51
Consensus pattern (19 bp):
TATCTATAAATCAATTTTG
Found at i:428980 original size:24 final size:24
Alignment explanation
Indices: 428953--429002 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
428943 CTTAGTGAAG
428953 TATGACTAAAAAAATGTAAATAAA
1 TATGACTAAAAAAATGTAAATAAA
428977 TATGACTAAAAAAATGTAAATAAA
1 TATGACTAAAAAAATGTAAATAAA
429001 TA
1 TA
429003 AACAAATGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.26
Consensus pattern (24 bp):
TATGACTAAAAAAATGTAAATAAA
Found at i:430545 original size:5 final size:5
Alignment explanation
Indices: 430535--430567 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
430525 AATTTATAAG
430535 AATCA AATCA AATCA AATCA AATCA AATCA AAT
1 AATCA AATCA AATCA AATCA AATCA AATCA AAT
430568 TTTTATGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.61, C:0.18, G:0.00, T:0.21
Consensus pattern (5 bp):
AATCA
Found at i:431771 original size:8 final size:8
Alignment explanation
Indices: 431760--431785 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
431750 TATTAAATTT
431760 ATTTAAAA
1 ATTTAAAA
431768 ATTTAAAA
1 ATTTAAAA
431776 ATTTAAAA
1 ATTTAAAA
431784 AT
1 AT
431786 ATATATTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (8 bp):
ATTTAAAA
Found at i:431785 original size:28 final size:27
Alignment explanation
Indices: 431724--431795 Score: 85
Period size: 27 Copynumber: 2.6 Consensus size: 27
431714 CAACATAATA
431724 TAAAAATATT-TTTAAAAATTAAAAAT
1 TAAAAATATTATTTAAAAATTAAAAAT
*
431750 TATTAAAT-TTATTTAAAAATTTAAAAATT
1 TA-AAAATATTATTTAAAAA-TTAAAAA-T
431779 TAAAAATATATATTTAA
1 TAAAAATAT-TATTTAA
431796 TATTTTTGAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
26 4 0.11
27 12 0.32
28 11 0.29
29 4 0.11
30 7 0.18
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAAAATATTATTTAAAAATTAAAAAT
Found at i:431964 original size:24 final size:24
Alignment explanation
Indices: 431922--431984 Score: 71
Period size: 23 Copynumber: 2.8 Consensus size: 24
431912 AATTGACAAA
*
431922 AAAT-AAAAATTTAAAAATA-TTT
1 AAATAAAAAATTAAAAAATATTTT
431944 AAATAAAAAATTAAAATAATATTTT
1 AAATAAAAAATTAAAA-AATATTTT
*
431969 TAAT--AAAATTAAAAAA
1 AAATAAAAAATTAAAAAA
431985 CCAAATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
22 6 0.17
23 20 0.56
24 4 0.11
25 6 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
AAATAAAAAATTAAAAAATATTTT
Found at i:455210 original size:16 final size:16
Alignment explanation
Indices: 455186--455226 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
455176 TAATAAAAAT
455186 ATAATTTTATTATTTTA
1 ATAATTTTA-TATTTTA
*
455203 AT-ATTTTATATTTTT
1 ATAATTTTATATTTTA
455218 ATAATTTTA
1 ATAATTTTA
455227 AAGGATTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 8 0.36
16 12 0.55
17 2 0.09
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (16 bp):
ATAATTTTATATTTTA
Found at i:456037 original size:6 final size:6
Alignment explanation
Indices: 456028--456055 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
456018 ATTTTTCGAA
456028 TGGCTG TGGCTG TGGCTG TGGCTG TGGC
1 TGGCTG TGGCTG TGGCTG TGGCTG TGGC
456056 GCTCTCTTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.50, T:0.32
Consensus pattern (6 bp):
TGGCTG
Found at i:456068 original size:3 final size:3
Alignment explanation
Indices: 456060--456091 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
456050 TGTGGCGCTC
456060 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
456092 ACCATCTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:465734 original size:26 final size:23
Alignment explanation
Indices: 465693--465749 Score: 69
Period size: 26 Copynumber: 2.3 Consensus size: 23
465683 TGACGGAAGT
465693 AATAAAATGTACACAACAAAATTAA
1 AATAAAATGTACAC-A-AAAATTAA
* *
465718 AATTAAAATGTATACAAATATTAA
1 AA-TAAAATGTACACAAAAATTAA
465742 AATAAAAT
1 AATAAAAT
465750 TTTAGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
23 6 0.21
24 9 0.31
25 3 0.10
26 11 0.38
ACGTcount: A:0.63, C:0.07, G:0.04, T:0.26
Consensus pattern (23 bp):
AATAAAATGTACACAAAAATTAA
Found at i:472141 original size:6 final size:7
Alignment explanation
Indices: 472123--472147 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
472113 GAAATATAGT
472123 TAAAAAC
1 TAAAAAC
472130 TAAAAAC
1 TAAAAAC
472137 TAAAAAC
1 TAAAAAC
472144 TAAA
1 TAAA
472148 TTAAAAACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.72, C:0.12, G:0.00, T:0.16
Consensus pattern (7 bp):
TAAAAAC
Found at i:479536 original size:27 final size:28
Alignment explanation
Indices: 479504--479568 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
479494 AAGTCAAATT
*
479504 AAAATA-AAGTTAACATTTTTTGTTTAA-
1 AAAATATAA-TTAACATTTATTGTTTAAC
*
479531 AAAATATTAATTATCATTTATTGTTTAAC
1 AAAATA-TAATTAACATTTATTGTTTAAC
479560 AAAAT-TAAT
1 AAAATATAAT
479569 ATTTTTAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 10 0.30
28 16 0.48
29 7 0.21
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (28 bp):
AAAATATAATTAACATTTATTGTTTAAC
Found at i:484834 original size:5 final size:5
Alignment explanation
Indices: 484824--484850 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
484814 TTCACTCCCA
484824 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
484851 CATCCTCGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:490653 original size:15 final size:15
Alignment explanation
Indices: 490633--490665 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
490623 CTCAAAAATG
490633 TTTAATAGATAAT-TT
1 TTTAATAGA-AATATT
490648 TTTAATAGAAATATT
1 TTTAATAGAAATATT
490663 TTT
1 TTT
490666 GAAAAAGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 3 0.18
15 14 0.82
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TTTAATAGAAATATT
Found at i:497979 original size:21 final size:21
Alignment explanation
Indices: 497910--497970 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
497900 AGACACCATC
497910 TGTGACGTCGATGACTCACCT
1 TGTGACGTCGATGACTCACCT
*
497931 TGTGACGGCGATGACTCACCT
1 TGTGACGTCGATGACTCACCT
497952 TGTGACGTCGATGACTCAC
1 TGTGACGTCGATGACTCAC
497971 TTCCCGACGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (21 bp):
TGTGACGTCGATGACTCACCT
Found at i:500505 original size:3 final size:3
Alignment explanation
Indices: 500497--500543 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
500487 CAATTAATAG
500497 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
500544 GTTCGGGAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:503202 original size:18 final size:19
Alignment explanation
Indices: 503176--503214 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
503166 AAAAACTAAA
503176 AATTCTAAAATAAT-TTTT
1 AATTCTAAAATAATGTTTT
*
503194 AATTTTAAAATAATGTTTT
1 AATTCTAAAATAATGTTTT
503213 AA
1 AA
503215 CGTTAAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (19 bp):
AATTCTAAAATAATGTTTT
Found at i:503222 original size:18 final size:18
Alignment explanation
Indices: 503181--503221 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
503171 CTAAAAATTC
**
503181 TAAAATAATTTTTAATTT
1 TAAAATAATTTTTAACGT
503199 TAAAATAATGTTTTAACGT
1 TAAAATAAT-TTTTAACGT
503218 TAAA
1 TAAA
503222 TTTAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (18 bp):
TAAAATAATTTTTAACGT
Found at i:506248 original size:2 final size:2
Alignment explanation
Indices: 506241--506268 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
506231 AAGAAATTAA
506241 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
506269 TAATAGTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:507155 original size:12 final size:13
Alignment explanation
Indices: 507129--507161 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
507119 TTCAAACTTC
507129 ATATGTACAATCT
1 ATATGTACAATCT
507142 ATATGTAC-ATCT
1 ATATGTACAATCT
507154 ATATGTAC
1 ATATGTAC
507162 GAAAACGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.60
13 8 0.40
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (13 bp):
ATATGTACAATCT
Found at i:513261 original size:4 final size:4
Alignment explanation
Indices: 513252--513283 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
513242 AACATCTACT
513252 CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA
513284 TAATTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:515216 original size:3 final size:3
Alignment explanation
Indices: 515208--515232 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
515198 AATTTTTAAT
515208 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
515233 AAGAAGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:517412 original size:24 final size:25
Alignment explanation
Indices: 517385--517432 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
517375 CAAAAGTTGC
517385 AAGTGAAAATAAT-AAAAATAAATA
1 AAGTGAAAATAATAAAAAATAAATA
* * *
517409 AAGTTAAAGTGATAAAAAATAAAT
1 AAGTGAAAATAATAAAAAATAAAT
517433 TTTAGAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (25 bp):
AAGTGAAAATAATAAAAAATAAATA
Found at i:524620 original size:21 final size:22
Alignment explanation
Indices: 524591--524632 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
524581 GTTTAAAATG
524591 TTTTAATTAT-TATTTGAATCT
1 TTTTAATTATATATTTGAATCT
*
524612 TTTTTATTATAATATTTGAAT
1 TTTTAATTAT-ATATTTGAAT
524633 TTATATTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
23 9 0.50
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTTAATTATATATTTGAATCT
Found at i:526293 original size:3 final size:3
Alignment explanation
Indices: 526285--526315 Score: 53
Period size: 3 Copynumber: 10.0 Consensus size: 3
526275 ATAAAAACAG
526285 TAA TAA TAA TAA TAA TAA TAA TAA TAGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
526316 AAGATCAAGC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 24 0.89
4 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:526346 original size:2 final size:2
Alignment explanation
Indices: 526339--526375 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
526329 TAGAGTTATA
*
526339 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
526376 TGAAAAGTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:538896 original size:21 final size:21
Alignment explanation
Indices: 538849--538897 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
538839 CAATTCAATC
*
538849 ATTATTACAAACAAAAAAAAT
1 ATTATTAAAAACAAAAAAAAT
* *
538870 AGTATTAAAAATAAAAATAAA-
1 ATTATTAAAAACAAAAA-AAAT
538891 ATTATTA
1 ATTATTA
538898 TTATAAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.29
Consensus pattern (21 bp):
ATTATTAAAAACAAAAAAAAT
Found at i:546190 original size:2 final size:2
Alignment explanation
Indices: 546183--546211 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
546173 ATTTCATTCT
546183 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA C
546212 GTCGTATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:553968 original size:2 final size:2
Alignment explanation
Indices: 553961--553992 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
553951 AAATAAATAA
553961 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
553993 TAAAATGGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:559080 original size:40 final size:40
Alignment explanation
Indices: 558994--559163 Score: 173
Period size: 40 Copynumber: 4.2 Consensus size: 40
558984 TTTGGAAACA
* *
558994 AAGCGCCGCAAAAGGTAAAGCATCAGCGGCGCTTTTCC-T
1 AAGCGCCGCAAAAGGTAAAGCATTAGCGGCGCTTTCCCAT
*
559033 AATGCGCCGCAAAAGGTAAAGCATTAGCGGCGCTTTCCCAC
1 AA-GCGCCGCAAAAGGTAAAGCATTAGCGGCGCTTTCCCAT
* *** ***
559074 AAGCGCCGCTAAAGGTCGGGTCATTAGCGGCGCTTTTATATT
1 AAGCGCCGCAAAAGGTAAAG-CATTAGCGGCGCTTTCCCA-T
* ** *
559116 AAGCGCCGCTAAAGGT-GTGCATTAGCGGCACTTTCCCAT
1 AAGCGCCGCAAAAGGTAAAGCATTAGCGGCGCTTTCCCAT
559155 AAGCGCCGC
1 AAGCGCCGC
559164 TAATTTATTT
Statistics
Matches: 111, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
39 12 0.11
40 63 0.57
41 20 0.18
42 16 0.14
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (40 bp):
AAGCGCCGCAAAAGGTAAAGCATTAGCGGCGCTTTCCCAT
Found at i:559130 original size:42 final size:39
Alignment explanation
Indices: 559053--559166 Score: 129
Period size: 41 Copynumber: 2.8 Consensus size: 39
559043 AAAAGGTAAA
* * *
559053 GCATTAGCGGCGCTTTCCCACAAGCGCCGCTAAAGGTCGG
1 GCATTAGCGGCACTTTCACATAAGCGCCGCTAAAGGT-GG
* * * *
559093 GTCATTAGCGGCGCTTTTATATTAAGCGCCGCTAAAGGTGT
1 G-CATTAGCGGCACTTTCACA-TAAGCGCCGCTAAAGGTGG
*
559134 GCATTAGCGGCACTTTCCCATAAGCGCCGCTAA
1 GCATTAGCGGCACTTTCACATAAGCGCCGCTAA
559167 TTTATTTAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
39 13 0.21
40 16 0.25
41 18 0.29
42 16 0.25
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (39 bp):
GCATTAGCGGCACTTTCACATAAGCGCCGCTAAAGGTGG
Found at i:560963 original size:15 final size:15
Alignment explanation
Indices: 560943--560975 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
560933 ATTTGAAGTT
560943 ATTGGTTGGATTTGA
1 ATTGGTTGGATTTGA
*
560958 ATTGGTTGGATTTTA
1 ATTGGTTGGATTTGA
560973 ATT
1 ATT
560976 TATAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.21, C:0.00, G:0.27, T:0.52
Consensus pattern (15 bp):
ATTGGTTGGATTTGA
Found at i:562258 original size:29 final size:32
Alignment explanation
Indices: 562221--562291 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
562211 TTTTAATAAT
*
562221 TTAT-ATCTTTA-TATTTTTAAAA-AATTAAA
1 TTATAATCTTTATTATTTTTAAAATAATCAAA
562250 TTA-AATCTTTATTATTTTTAAAATAATCAAA
1 TTATAATCTTTATTATTTTTAAAATAATCAAA
562281 TTATAAT-TTTA
1 TTATAATCTTTA
562292 ACATTAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
29 10 0.27
30 11 0.30
31 13 0.35
32 3 0.08
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (32 bp):
TTATAATCTTTATTATTTTTAAAATAATCAAA
Found at i:562532 original size:23 final size:24
Alignment explanation
Indices: 562506--562550 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
562496 ATCTTCTACC
* *
562506 TATG-ATTTTATTTAATTAAAAAG
1 TATGCATTTGATTGAATTAAAAAG
562529 TATGCATTTGATTGAATTAAAA
1 TATGCATTTGATTGAATTAAAA
562551 TTTTTATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (24 bp):
TATGCATTTGATTGAATTAAAAAG
Found at i:565167 original size:29 final size:31
Alignment explanation
Indices: 565122--565186 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
565112 GAACCCAATA
* *
565122 ATTTTTAGGATATCAAAATTA-AATTATA-T
1 ATTTTTAGGATAGCAAAAATATAATTATATT
* *
565151 ATTTTTAGTATAGCAAAAATATAATTTTATT
1 ATTTTTAGGATAGCAAAAATATAATTATATT
565182 ATTTT
1 ATTTT
565187 AATAGCTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 18 0.60
30 6 0.20
31 6 0.20
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (31 bp):
ATTTTTAGGATAGCAAAAATATAATTATATT
Found at i:566280 original size:2 final size:2
Alignment explanation
Indices: 566273--566298 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
566263 GACTTTTCAA
566273 GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT
566299 TCCATATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:569575 original size:24 final size:25
Alignment explanation
Indices: 569531--569577 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
569521 CATTACATGA
*
569531 TTAAAAAAATCTTATATTTAAAATT
1 TTAAAAAAATCTAATATTTAAAATT
569556 TTAAAATAAAT-TAATA-TTAAAA
1 TTAAAA-AAATCTAATATTTAAAA
569578 GAAAAATGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 6 0.30
25 10 0.50
26 4 0.20
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (25 bp):
TTAAAAAAATCTAATATTTAAAATT
Found at i:570510 original size:36 final size:36
Alignment explanation
Indices: 570450--570519 Score: 97
Period size: 36 Copynumber: 1.9 Consensus size: 36
570440 CATTTTTATC
* *
570450 AAATATAAATTTAAATATATAAATATTATATTAAAA
1 AAATATAAATTTAAATATACAAATAATATATTAAAA
*
570486 AAATACTAAATTTAAATA-CCAAATAATATATTAA
1 AAATA-TAAATTTAAATATACAAATAATATATTAA
570520 TTTTAAATAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
36 18 0.60
37 12 0.40
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (36 bp):
AAATATAAATTTAAATATACAAATAATATATTAAAA
Found at i:572054 original size:23 final size:23
Alignment explanation
Indices: 572012--572055 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
572002 TTTCTGTAAA
*
572012 TTAATTAAAAATCAACTAAATAT
1 TTAATTAAAAAGCAACTAAATAT
572035 TTAATTAAAAAGGCAA-TAAAT
1 TTAATTAAAAA-GCAACTAAAT
572056 TGAATCATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 16 0.84
24 3 0.16
ACGTcount: A:0.57, C:0.07, G:0.05, T:0.32
Consensus pattern (23 bp):
TTAATTAAAAAGCAACTAAATAT
Found at i:582074 original size:2 final size:2
Alignment explanation
Indices: 582067--582114 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
582057 GCGAAAACAA
582067 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
582109 AG AG AG
1 AG AG AG
582115 GCGTACTCTG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:583613 original size:3 final size:3
Alignment explanation
Indices: 583605--583629 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
583595 ATGAAAACAG
583605 ATC ATC ATC ATC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC A
583630 GCCTGAGATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.32, G:0.00, T:0.32
Consensus pattern (3 bp):
ATC
Found at i:596858 original size:15 final size:15
Alignment explanation
Indices: 596838--596870 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
596828 CACTTAATAA
596838 ATAAAATATAAAT-TT
1 ATAAAAT-TAAATATT
596853 ATAAAATTAAATATT
1 ATAAAATTAAATATT
596868 ATA
1 ATA
596871 TTAAATTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAAAATTAAATATT
Found at i:602708 original size:11 final size:11
Alignment explanation
Indices: 602694--602718 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
602684 TAAATAAAAA
602694 AAAATTAAATT
1 AAAATTAAATT
602705 AAAATTAAATT
1 AAAATTAAATT
602716 AAA
1 AAA
602719 TAAAACAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAAATTAAATT
Found at i:603008 original size:7 final size:7
Alignment explanation
Indices: 602996--603053 Score: 107
Period size: 7 Copynumber: 8.1 Consensus size: 7
602986 TTATTTCATT
602996 CTTCTCC
1 CTTCTCC
603003 CTTCTCC
1 CTTCTCC
603010 CTCTCTCC
1 CT-TCTCC
603018 CTTCTCC
1 CTTCTCC
603025 CTTCTCC
1 CTTCTCC
603032 CTTCTCC
1 CTTCTCC
603039 CTTCTCC
1 CTTCTCC
603046 CTTCTCC
1 CTTCTCC
603053 C
1 C
603054 GGTAGTTGCT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
7 43 0.86
8 7 0.14
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (7 bp):
CTTCTCC
Found at i:603701 original size:12 final size:12
Alignment explanation
Indices: 603657--603707 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
603647 CTAAATATTA
603657 TAAAAATATAAT
1 TAAAAATATAAT
*
603669 TAATAAA-AAAAT
1 TAA-AAATATAAT
*
603681 TATTTAAATATAAT
1 TA--AAAATATAAT
603695 TAAAAATATAAT
1 TAAAAATATAAT
603707 T
1 T
603708 TTTTTTATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 8
0.72 0.09 0.19
Matches are distributed among these distances:
12 19 0.61
13 6 0.19
14 6 0.19
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (12 bp):
TAAAAATATAAT
Found at i:609960 original size:3 final size:3
Alignment explanation
Indices: 609952--609978 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
609942 AAAGCTTTCA
609952 CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC
609979 AAGCCTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:618634 original size:30 final size:30
Alignment explanation
Indices: 618600--618661 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
618590 GTAAGTGCTA
* *
618600 ATTTTGTATATT-ATTTGAATATCTAAATAT
1 ATTTTATATATTAAGTT-AATATCTAAATAT
*
618630 ATTTTATATATTAAGTTAATATTTAAATAT
1 ATTTTATATATTAAGTTAATATCTAAATAT
618660 AT
1 AT
618662 ATATTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (30 bp):
ATTTTATATATTAAGTTAATATCTAAATAT
Found at i:632199 original size:16 final size:16
Alignment explanation
Indices: 632154--632200 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
632144 TGAATTATTG
*
632154 ATTATAATTTTATTTC
1 ATTATAATCTTATTTC
* *
632170 ATTACAA-CTCTATTTT
1 ATTATAATCT-TATTTC
632186 ATTATAATCTTATTT
1 ATTATAATCTTATTT
632201 AATTTCAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 1 0.04
16 22 0.88
17 2 0.08
ACGTcount: A:0.32, C:0.11, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTATAATCTTATTTC
Found at i:632246 original size:17 final size:17
Alignment explanation
Indices: 632224--632275 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
632214 TAAGAGTTTA
632224 AATTAT-TTTAAAATAAT
1 AATTATATTTAAAA-AAT
*
632241 AATTATATTTATAAAAT
1 AATTATATTTAAAAAAT
*
632258 AATT-TAATTAAAAAAT
1 AATTATATTTAAAAAAT
632274 AA
1 AA
632276 AATTTTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 12 0.39
17 13 0.42
18 6 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTATATTTAAAAAAT
Found at i:638551 original size:32 final size:32
Alignment explanation
Indices: 638515--638578 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
638505 GAATTAGAGA
638515 AAGGGAAAAGAATTAAAAGATGAAAATATCAT
1 AAGGGAAAAGAATTAAAAGATGAAAATATCAT
638547 AAGGGAAAAGAATTAAAAGATGAAAATATCAT
1 AAGGGAAAAGAATTAAAAGATGAAAATATCAT
638579 CTTTTCTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.59, C:0.03, G:0.19, T:0.19
Consensus pattern (32 bp):
AAGGGAAAAGAATTAAAAGATGAAAATATCAT
Found at i:639931 original size:23 final size:23
Alignment explanation
Indices: 639899--640026 Score: 125
Period size: 23 Copynumber: 5.4 Consensus size: 23
639889 ACACTAGCGC
639899 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTCT-GT
* *
639922 GCTCTATGTTATTAGCACTGTGTGT
1 GCTCTCTG-T-TTAGCACTGTCTGT
* * *
639947 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTCTGT
* *
639970 GCTCTCTGATTAGCACT-TTTGT
1 GCTCTCTGTTTAGCACTGTCTGT
*
639992 GTACTCTCTGTTTAGCACTGTGTGT
1 G--CTCTCTGTTTAGCACTGTCTGT
640017 GCTCTCTGTT
1 GCTCTCTGTT
640027 GCCCAGCACT
Statistics
Matches: 91, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.05
23 46 0.51
24 16 0.18
25 21 0.23
26 3 0.03
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTCTGT
Found at i:640007 original size:47 final size:47
Alignment explanation
Indices: 639900--640025 Score: 148
Period size: 47 Copynumber: 2.7 Consensus size: 47
639890 CACTAGCGCG
* * *
639900 CTCTCTGTTTAGCACGTCT-CGTGCTCTATGTTATTAGCACTGTGTGTG
1 CTCTCTGTTTAGCAC-TCTGTGTGCTCTCTG-TATTAGCACTGTGTGTA
* * *
639948 CTCTCTGATTAGCACTTTGTGTGCTCTCTG-ATTAGCACTTTTGTGTA
1 CTCTCTGTTTAGCACTCTGTGTGCTCTCTGTATTAGCAC-TGTGTGTA
*
639995 CTCTCTGTTTAGCACTGTGTGTGCTCTCTGT
1 CTCTCTGTTTAGCACTCTGTGTGCTCTCTGT
640026 TGCCCAGCAC
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
46 8 0.12
47 36 0.54
48 23 0.34
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (47 bp):
CTCTCTGTTTAGCACTCTGTGTGCTCTCTGTATTAGCACTGTGTGTA
Found at i:640017 original size:70 final size:66
Alignment explanation
Indices: 639933--640073 Score: 185
Period size: 70 Copynumber: 2.0 Consensus size: 66
639923 CTCTATGTTA
*
639933 TTAGCACTGTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGCACTTTTGTGTACT
1 TTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGCAC-TTTG-GTACT
639997 CTCTGT
61 CTCTGT
*
640003 TTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCT
1 TTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGCACTTTGGTACTCT
640068 CTGT
63 CTGT
640072 TT
1 TT
640074 GTTCCGTATA
Statistics
Matches: 65, Mismatches: 2, Indels: 9
0.86 0.03 0.12
Matches are distributed among these distances:
69 15 0.23
70 26 0.40
71 6 0.09
72 13 0.20
73 5 0.08
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (66 bp):
TTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGCACTTTGGTACTCTCTG
T
Found at i:642588 original size:58 final size:58
Alignment explanation
Indices: 642542--642694 Score: 204
Period size: 57 Copynumber: 2.6 Consensus size: 58
642532 ATATTGTTAT
642542 TTTTATT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTA
1 TTTTATTAAATT-ATA-TTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTA
* * * * *
642601 TTTTATTAAATTGTATTTAATAATAATTATGTT-AAAATATAATTAAATTATTTATTA
1 TTTTATTAAATTATATTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTA
*
642658 TTTTATTAAATTGTATTTAATAATAATCT-TATTAAAA
1 TTTTATTAAATTATATTTAATAATAAT-TATATTAAAA
642695 TTTAATAACA
Statistics
Matches: 85, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
57 51 0.60
58 21 0.25
59 9 0.11
60 4 0.05
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (58 bp):
TTTTATTAAATTATATTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTA
Found at i:642695 original size:57 final size:57
Alignment explanation
Indices: 642558--642700 Score: 216
Period size: 57 Copynumber: 2.5 Consensus size: 57
642548 TAATTCATAT
* *
642558 TTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTATTTTATTAAATTGTA
1 TTTAATAATAATTATATT-AAAATATAATTAAATTATATATTATTTTATTAAATTGTA
* *
642616 TTTAATAATAATTATGTTAAAATATAATTAAATTATTTATTATTTTATTAAATTGTA
1 TTTAATAATAATTATATTAAAATATAATTAAATTATATATTATTTTATTAAATTGTA
*
642673 TTTAATAATAATCT-TATTAAAATTTAAT
1 TTTAATAATAAT-TATATTAAAATATAAT
642701 AACAATAATC
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
57 60 0.77
58 18 0.23
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.52
Consensus pattern (57 bp):
TTTAATAATAATTATATTAAAATATAATTAAATTATATATTATTTTATTAAATTGTA
Found at i:642843 original size:44 final size:46
Alignment explanation
Indices: 642780--642874 Score: 140
Period size: 44 Copynumber: 2.1 Consensus size: 46
642770 TATTACAGCA
642780 CCATTCCATTCAACCAAAC-ACAAAAATACT-ATTACAGCTCTATT
1 CCATTCCATTCAACCAAACAACAAAAATACTAATTACAGCTCTATT
** * *
642824 CCATTCCATTCAACCAAACAACTGAATTACTAATTATAGCTCTATT
1 CCATTCCATTCAACCAAACAACAAAAATACTAATTACAGCTCTATT
642870 CCATT
1 CCATT
642875 ACAGCGAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 19 0.42
45 8 0.18
46 18 0.40
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (46 bp):
CCATTCCATTCAACCAAACAACAAAAATACTAATTACAGCTCTATT
Found at i:652730 original size:18 final size:16
Alignment explanation
Indices: 652693--652733 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
652683 TCTAAATAGG
652693 ATTAGAATAAATTTTTA
1 ATTA-AATAAATTTTTA
652710 ATTAAATAAATTTAATTA
1 ATTAAATAAATTT--TTA
652728 ATTAAA
1 ATTAAA
652734 AATTTTAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 9 0.41
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (16 bp):
ATTAAATAAATTTTTA
Found at i:653297 original size:31 final size:29
Alignment explanation
Indices: 653233--653301 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
653223 ATACTAATAT
** *
653233 AAGTGACTAAAATGTAACATTTCAAACAT
1 AAGTGACTAAAATGTAACATAACAAACAA
*
653262 AAGTGACTAAAATGTAACCTGAAACAAACAA
1 AAGTGACTAAAATGTAACAT--AACAAACAA
653293 AAGTGACTA
1 AAGTGACTA
653302 TTTTTATAGT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.51, C:0.14, G:0.13, T:0.22
Consensus pattern (29 bp):
AAGTGACTAAAATGTAACATAACAAACAA
Found at i:662346 original size:22 final size:23
Alignment explanation
Indices: 662321--662364 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
662311 GTTTAAAAAA
*
662321 TTATAAATTTTTA-TTAAATTAT
1 TTATAAAATTTTATTTAAATTAT
662343 TTATAAAATTTTATTTAAATTA
1 TTATAAAATTTTATTTAAATTA
662365 GTGAACTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATAAAATTTTATTTAAATTAT
Found at i:662515 original size:146 final size:146
Alignment explanation
Indices: 662251--662538 Score: 540
Period size: 146 Copynumber: 2.0 Consensus size: 146
662241 GATATTTTCC
*
662251 TGCTGTCAATTTCAAAAAGATAATAGTAATAAAATAAAAACACTATGTTTTAGTATTTAAGTTTA
1 TGCTGTCAATTTCAAAAAGATAATAGCAATAAAATAAAAACACTATGTTTTAGTATTTAAGTTTA
* *
662316 AAAAATTATAAATTTTTATTAAATTATTTATAAAATTTTATTTAAATTAGTGAACTATTAAAATC
66 AAAAATTATAAATTTTTATTAAATTATTTAAAAAAATTTATTTAAATTAGTGAACTATTAAAATC
662381 ATTGATGTATAATTTT
131 ATTGATGTATAATTTT
662397 TGCTGTCAATTTCAAAAAGATAATAGCAATAAAATAAAAACACTATGTTTTAGTATTTAAGTTTA
1 TGCTGTCAATTTCAAAAAGATAATAGCAATAAAATAAAAACACTATGTTTTAGTATTTAAGTTTA
*
662462 AAAAATTATAAATTTTTATTAAATTATTTAAAAAAATTTATTTAAATTAGTGAACTATTAAAATT
66 AAAAATTATAAATTTTTATTAAATTATTTAAAAAAATTTATTTAAATTAGTGAACTATTAAAATC
662527 ATTGATGTATAA
131 ATTGATGTATAA
662539 CTTTAGTTGT
Statistics
Matches: 138, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
146 138 1.00
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.42
Consensus pattern (146 bp):
TGCTGTCAATTTCAAAAAGATAATAGCAATAAAATAAAAACACTATGTTTTAGTATTTAAGTTTA
AAAAATTATAAATTTTTATTAAATTATTTAAAAAAATTTATTTAAATTAGTGAACTATTAAAATC
ATTGATGTATAATTTT
Found at i:665812 original size:20 final size:20
Alignment explanation
Indices: 665779--665832 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
665769 AACTCATTCA
665779 AATTCAAT-TCAAATATTATT
1 AATTCAATAT-AAATATTATT
665799 AATTCAATATAAAT-TT-TT
1 AATTCAATATAAATATTATT
*
665817 -ATTC-ATATCAATATTA
1 AATTCAATATAAATATTA
665833 ACGCTTACCT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
16 7 0.23
17 6 0.20
18 2 0.07
19 2 0.07
20 12 0.40
21 1 0.03
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTCAATATAAATATTATT
Found at i:688668 original size:18 final size:20
Alignment explanation
Indices: 688645--688694 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 20
688635 TCATGATTTT
688645 TTTTTTAATTTTTAT-AA-A
1 TTTTTTAATTTTTATGAATA
688663 TTTTTT-ATTTTT-TGAATA
1 TTTTTTAATTTTTATGAATA
*
688681 TTTTATAATTTTTA
1 TTTTTTAATTTTTA
688695 AATTAATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 1 0.04
17 8 0.30
18 12 0.44
19 6 0.22
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTTTTAATTTTTATGAATA
Found at i:697658 original size:16 final size:16
Alignment explanation
Indices: 697637--697726 Score: 62
Period size: 16 Copynumber: 5.6 Consensus size: 16
697627 TCAAAAATTT
*
697637 TAAAATATTTAATATA
1 TAAAATATTAAATATA
697653 TAAAATATTAAATATA
1 TAAAATATTAAATATA
*
697669 TCAAATAAATTAAAT-TA
1 T-AAA-ATATTAAATATA
*
697686 -AATAATTTTAAATA-A
1 TAA-AATATTAAATATA
* *
697701 -AATATTAATTAATTATA
1 TAA-AAT-ATTAAATATA
697718 TAAAATATT
1 TAAAATATT
697727 CATCAATCAA
Statistics
Matches: 59, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
15 15 0.25
16 26 0.44
17 8 0.14
18 10 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (16 bp):
TAAAATATTAAATATA
Found at i:697713 original size:22 final size:20
Alignment explanation
Indices: 697652--697726 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
697642 TATTTAATAT
*
697652 ATAAAATATTAAATATATCAA
1 ATAAAATATTAAATA-ATTAA
*
697673 ATAAATTAAATTAAATAATTTTAA
1 ATAAA--ATATTAAATAA--TTAA
* *
697697 ATAAAATATTAATTAATTAT
1 ATAAAATATTAAATAATTAA
697717 ATAAAATATT
1 ATAAAATATT
697727 CATCAATCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
20 13 0.29
21 5 0.11
22 10 0.22
23 9 0.20
24 8 0.18
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (20 bp):
ATAAAATATTAAATAATTAA
Found at i:700640 original size:12 final size:12
Alignment explanation
Indices: 700623--700672 Score: 57
Period size: 12 Copynumber: 4.2 Consensus size: 12
700613 TCATTAATAA
700623 ATAAACGAGCTT
1 ATAAACGAGCTT
*
700635 ATAAACGAG-TCA
1 ATAAACGAGCT-T
* *
700647 ATAAATGAGTTT
1 ATAAACGAGCTT
700659 ATAAACGAGCTT
1 ATAAACGAGCTT
700671 AT
1 AT
700673 TCGTGAAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
11 1 0.03
12 29 0.94
13 1 0.03
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (12 bp):
ATAAACGAGCTT
Found at i:700660 original size:24 final size:24
Alignment explanation
Indices: 700622--700667 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
700612 ATCATTAATA
700622 AATAAACGAGCTTATAAACGAGTC
1 AATAAACGAGCTTATAAACGAGTC
* *
700646 AATAAATGAGTTTATAAACGAG
1 AATAAACGAGCTTATAAACGAG
700668 CTTATTCGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.11, G:0.17, T:0.24
Consensus pattern (24 bp):
AATAAACGAGCTTATAAACGAGTC
Found at i:713769 original size:15 final size:14
Alignment explanation
Indices: 713749--713785 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
713739 ACCTACCCTC
713749 CCTCTTGTTTTCTCT
1 CCTCTT-TTTTCTCT
713764 CCTC-TTTTTCTCT
1 CCTCTTTTTTCTCT
713777 CCTCTTTTT
1 CCTCTTTTT
713786 CTCCCATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.57
14 5 0.24
15 4 0.19
ACGTcount: A:0.00, C:0.35, G:0.03, T:0.62
Consensus pattern (14 bp):
CCTCTTTTTTCTCT
Found at i:713798 original size:14 final size:13
Alignment explanation
Indices: 713756--713788 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
713746 CTCCCTCTTG
713756 TTTTCTCTCCTCT
1 TTTTCTCTCCTCT
713769 TTTTCTCTCCTCT
1 TTTTCTCTCCTCT
713782 TTTTCTC
1 TTTTCTC
713789 CCATTCTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTCTCTCCTCT
Found at i:718504 original size:7 final size:7
Alignment explanation
Indices: 718487--718524 Score: 69
Period size: 7 Copynumber: 5.6 Consensus size: 7
718477 AGAAGAGCCA
718487 AAAAAAG
1 AAAAAAG
718494 -AAAAAG
1 AAAAAAG
718500 AAAAAAG
1 AAAAAAG
718507 AAAAAAG
1 AAAAAAG
718514 AAAAAAG
1 AAAAAAG
718521 AAAA
1 AAAA
718525 GAATACCCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:718505 original size:14 final size:13
Alignment explanation
Indices: 718486--718524 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
718476 AAGAAGAGCC
718486 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
*
718499 GAAAAAAGAAAAA
1 AAAAAAAGAAAAA
718512 AGAAAAAAGAAAA
1 A-AAAAAAGAAAA
718525 GAATACCCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:726465 original size:18 final size:18
Alignment explanation
Indices: 726442--726479 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
726432 TCCGGTGAGA
726442 ACCGGCCACCATTCCAGC
1 ACCGGCCACCATTCCAGC
726460 ACCGGCCACCATTCCAGC
1 ACCGGCCACCATTCCAGC
726478 AC
1 AC
726480 TTGCTTCCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.50, G:0.16, T:0.11
Consensus pattern (18 bp):
ACCGGCCACCATTCCAGC
Found at i:727276 original size:20 final size:19
Alignment explanation
Indices: 727243--727283 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
727233 TATTATATCT
*
727243 TAAATTTTATAAATAAATA
1 TAAATTTTAAAAATAAATA
*
727262 TAAATATTTAAAAATATATA
1 TAAAT-TTTAAAAATAAATA
727282 TA
1 TA
727284 TATCGGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATTTTAAAAATAAATA
Found at i:742741 original size:72 final size:72
Alignment explanation
Indices: 742624--742771 Score: 251
Period size: 72 Copynumber: 2.1 Consensus size: 72
742614 CAATTTCTTC
* *
742624 CAAACTTGACATATTCCCCATCCACCTTGGTATGTCCCCAGAAAGCTCGTTATTGCTTAAATCCA
1 CAAACTGGACATATTCCCCATCCACCTTGGTATCTCCCCAGAAAGCTCGTTATTGCTTAAATCCA
742689 ATGTTGA
66 ATGTTGA
* * *
742696 CAAACTGGACATATTCTCCATCCACCTTGGTATCTCTCCAGAAAGCTCGTTCTTGCTTAAATCCA
1 CAAACTGGACATATTCCCCATCCACCTTGGTATCTCCCCAGAAAGCTCGTTATTGCTTAAATCCA
742761 ATGTTGA
66 ATGTTGA
742768 CAAA
1 CAAA
742772 AAGGAGCAAT
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 71 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (72 bp):
CAAACTGGACATATTCCCCATCCACCTTGGTATCTCCCCAGAAAGCTCGTTATTGCTTAAATCCA
ATGTTGA
Found at i:745909 original size:20 final size:20
Alignment explanation
Indices: 745866--745909 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
745856 ATTATATTAT
* *
745866 TGTTTTGATGTTTTTTTTAC
1 TGTTTTGATGTTATTTTGAC
745886 TGTTTTGATTGTTATTTTGA-
1 TGTTTTGA-TGTTATTTTGAC
745906 TGTT
1 TGTT
745910 GTTTTAGTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.11, C:0.02, G:0.18, T:0.68
Consensus pattern (20 bp):
TGTTTTGATGTTATTTTGAC
Found at i:745909 original size:32 final size:33
Alignment explanation
Indices: 745868--745931 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
745858 TATATTATTG
*
745868 TTTTGATGTT-TTTT-TTACTGTTTTGATTGTTA
1 TTTTGATGTTGTTTTAGTACT-TTTTGATTGTTA
*
745900 TTTTGATGTTGTTTTAGTACTTTTTTATTGTT
1 TTTTGATGTTGTTTTAGTACTTTTTGATTGTT
745932 TTAGCGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
32 10 0.36
33 14 0.50
34 4 0.14
ACGTcount: A:0.12, C:0.03, G:0.16, T:0.69
Consensus pattern (33 bp):
TTTTGATGTTGTTTTAGTACTTTTTGATTGTTA
Found at i:746680 original size:11 final size:12
Alignment explanation
Indices: 746663--746736 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 12
746653 GTATAATCTC
746663 ATATATTATATT
1 ATATATTATATT
746675 -TATATTA-ATT
1 ATATATTATATT
* *
746685 ATATATTATCTAC
1 ATATATTATAT-T
746698 ATATTATTATTAATT
1 ATA-TATTA-T-ATT
746713 ATATATTATAATCT
1 ATATATTAT-AT-T
746727 CATATATTAT
1 -ATATATTAT
746737 CTGCATATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
10 3 0.06
11 14 0.28
12 1 0.02
13 7 0.14
14 11 0.22
15 13 0.26
16 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (12 bp):
ATATATTATATT
Found at i:754821 original size:28 final size:27
Alignment explanation
Indices: 754762--754830 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 27
754752 AAAAATCTTG
*
754762 AATTTT-TTTAATTAAAATTCAATATT
1 AATTTTATTTAATTAAAATTCAATATA
**
754788 AATTTTATTTAATTAAATATTTTATATA
1 AATTTTATTTAATTAAA-ATTCAATATA
754816 AATTTTAATTTAATT
1 AATTTT-ATTTAATT
754831 TATAATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 6 0.16
27 10 0.27
28 13 0.35
29 8 0.22
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (27 bp):
AATTTTATTTAATTAAAATTCAATATA
Found at i:757402 original size:2 final size:2
Alignment explanation
Indices: 757395--757423 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
757385 ATTTACAGAA
757395 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 A
757424 CCTGATATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:765000 original size:29 final size:28
Alignment explanation
Indices: 764946--765000 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
764936 TATTTTTATA
**
764946 ATTTTTAAAAGATTAAATATTTTTTTTC
1 ATTTTTAAAAGATTAAATATAATTTTTC
764974 ATTTTTAAAA-ATTAAAAGTATAATTTT
1 ATTTTTAAAAGATT-AAA-TATAATTTT
765001 ACAATTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 3 0.13
28 13 0.57
29 7 0.30
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (28 bp):
ATTTTTAAAAGATTAAATATAATTTTTC
Found at i:769447 original size:23 final size:23
Alignment explanation
Indices: 769379--769448 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 23
769369 CTACTAATTT
*
769379 TTTTAATTATTTAAATTATATACA
1 TTTTAATTA-TTAAATTATTTACA
* * *
769403 TTACTAAATTATT-AATAAATTTATA
1 TT--TTAATTATTAAAT-TATTTACA
769428 TTTTAATTATTAAATTATTTA
1 TTTTAATTATTAAATTATTTA
769449 AATCATAACA
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
23 13 0.36
24 8 0.22
25 9 0.25
26 6 0.17
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (23 bp):
TTTTAATTATTAAATTATTTACA
Found at i:769482 original size:36 final size:35
Alignment explanation
Indices: 769426--769504 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 35
769416 AATAAATTTA
* * *
769426 TATTTT-AATTATTAAATTATTTAAATCA-TAACAT
1 TATTTTAAAGTATTAAATTATTGAAAT-ATTAAAAT
769460 TATTTTAAAGTATTCAAATTATTGAAATATTAAAAT
1 TATTTTAAAGTATT-AAATTATTGAAATATTAAAAT
769496 TCATTTTAA
1 T-ATTTTAA
769505 GTTCGACAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
34 6 0.16
35 7 0.18
36 18 0.47
37 7 0.18
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (35 bp):
TATTTTAAAGTATTAAATTATTGAAATATTAAAAT
Found at i:769495 original size:17 final size:17
Alignment explanation
Indices: 769429--769501 Score: 60
Period size: 17 Copynumber: 4.2 Consensus size: 17
769419 AAATTTATAT
*
769429 TTTAATTATT-AAATTA
1 TTTAAATATTAAAATTA
*
769445 TTTAAATCA-TAACATTA
1 TTTAAAT-ATTAAAATTA
*
769462 TTTTAAAGTATTCAAATTA
1 -TTTAAA-TATTAAAATTA
*
769481 TTGAAATATTAAAATTCA
1 TTTAAATATTAAAATT-A
769499 TTT
1 TTT
769502 TAAGTTCGAC
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
16 7 0.16
17 15 0.34
18 15 0.34
19 7 0.16
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAAATATTAAAATTA
Found at i:773520 original size:23 final size:23
Alignment explanation
Indices: 773494--773540 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
773484 TCTCGAAAAT
*
773494 AAGTGGCAGATTTTTATTTGAGC
1 AAGTGGCAAATTTTTATTTGAGC
*
773517 AAGTGGTAAATTTTTATTTGAGC
1 AAGTGGCAAATTTTTATTTGAGC
773540 A
1 A
773541 TCCTATGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.06, G:0.23, T:0.40
Consensus pattern (23 bp):
AAGTGGCAAATTTTTATTTGAGC
Found at i:774600 original size:25 final size:24
Alignment explanation
Indices: 774561--774635 Score: 100
Period size: 25 Copynumber: 3.1 Consensus size: 24
774551 GAGGTACATA
*
774561 AGTGCTGGGGAAACAGAAGCATACAC
1 AGTGCT-GGG-AACAGAAGCACACAC
774587 AGTGCTGGGTAACAGAAGCACACAC
1 AGTGCTGGG-AACAGAAGCACACAC
774612 AGTGCT--GAACAGAAGCACACAC
1 AGTGCTGGGAACAGAAGCACACAC
774634 AG
1 AG
774636 GTCCTAATTC
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
22 17 0.36
23 1 0.02
25 23 0.49
26 6 0.13
ACGTcount: A:0.39, C:0.23, G:0.28, T:0.11
Consensus pattern (24 bp):
AGTGCTGGGAACAGAAGCACACAC
Found at i:784475 original size:35 final size:33
Alignment explanation
Indices: 784429--784504 Score: 109
Period size: 32 Copynumber: 2.3 Consensus size: 33
784419 AGCCGTACAT
784429 GCCTTTTCCCTTCTTCTTTTCCTTTATTTCTTTAA
1 GCCTTTTCCC--CTTCTTTTCCTTTATTTCTTTAA
*
784464 GCCTTTT-CCCTTCTTTTCTTTTATTTCTTTAA
1 GCCTTTTCCCCTTCTTTTCCTTTATTTCTTTAA
*
784496 GCCTCTTCC
1 GCCTTTTCC
784505 ATTTTTATTG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
32 28 0.74
33 1 0.03
34 2 0.05
35 7 0.18
ACGTcount: A:0.08, C:0.30, G:0.04, T:0.58
Consensus pattern (33 bp):
GCCTTTTCCCCTTCTTTTCCTTTATTTCTTTAA
Found at i:784487 original size:32 final size:32
Alignment explanation
Indices: 784441--784504 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
784431 CTTTTCCCTT
*
784441 CTTCTTTTCCTTTATTTCTTTAAGCCTTTTCC
1 CTTCTTTTCCTTTATTTCTTTAAGCCTCTTCC
*
784473 CTTCTTTTCTTTTATTTCTTTAAGCCTCTTCC
1 CTTCTTTTCCTTTATTTCTTTAAGCCTCTTCC
784505 ATTTTTATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.09, C:0.28, G:0.03, T:0.59
Consensus pattern (32 bp):
CTTCTTTTCCTTTATTTCTTTAAGCCTCTTCC
Found at i:786359 original size:17 final size:17
Alignment explanation
Indices: 786319--786394 Score: 75
Period size: 17 Copynumber: 4.5 Consensus size: 17
786309 CAATGAGATA
*
786319 TAAATTTAGTTTT-AAGT
1 TAAATTTA-TTTTAAATT
*
786336 TAGATTTATTTTAAATT
1 TAAATTTATTTTAAATT
* *
786353 TAAATTT-TCATAAAATT
1 TAAATTTAT-TTTAAATT
*
786370 TAAATTTATTATAAATT
1 TAAATTTATTTTAAATT
786387 TAAATTTA
1 TAAATTTA
786395 AAATTAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
16 5 0.10
17 42 0.88
18 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
TAAATTTATTTTAAATT
Found at i:786405 original size:5 final size:6
Alignment explanation
Indices: 786345--786404 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
786335 TTAGATTTAT
** *
786345 TTTAAA TTTAAA TTTTCA -TAAAA TTTAAA TTT--A TTATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAAA
*
786391 TTTAAA ATTAAA TT
1 TTTAAA TTTAAA TT
786405 AGATAAACTA
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
4 3 0.07
5 3 0.07
6 33 0.79
7 3 0.07
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTAAA
Found at i:788243 original size:29 final size:28
Alignment explanation
Indices: 788206--788363 Score: 128
Period size: 28 Copynumber: 5.5 Consensus size: 28
788196 TAGGTCCTTG
* *
788206 AACTGTCCAAAAATTATATTTTACCCCCA
1 AACTTTCCAAAAATTACATTTTA-CCCCA
** * *
788235 AACTTTCC-AAAATCCCATTTTAACCCT
1 AACTTTCCAAAAATTACATTTTACCCCA
788262 AA-TTTCACCAAAAATTACCATTTTACCCCA
1 AACTTT--CCAAAAATTA-CATTTTACCCCA
*
788292 AACTTTCC-CAAATTACATTTTAACCCC-
1 AACTTTCCAAAAATTACATTTT-ACCCCA
*
788319 GA-TTTCACCAAAAATTACCATTTTACCCCTA
1 AACTTT--CCAAAAATTA-CATTTTACCCC-A
788350 AACTTTCCAAAAAT
1 AACTTTCCAAAAAT
788364 CTATTTTTAA
Statistics
Matches: 102, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
26 6 0.06
27 12 0.12
28 26 0.25
29 25 0.25
30 26 0.25
31 4 0.04
32 3 0.03
ACGTcount: A:0.37, C:0.30, G:0.01, T:0.32
Consensus pattern (28 bp):
AACTTTCCAAAAATTACATTTTACCCCA
Found at i:788285 original size:30 final size:30
Alignment explanation
Indices: 788249--788350 Score: 122
Period size: 30 Copynumber: 3.5 Consensus size: 30
788239 TTCCAAAATC
788249 CCATTTTAACCCTAATTTCACCAAAAATTA
1 CCATTTTAACCCTAATTTCACCAAAAATTA
* *
788279 CCATTTTACCCCAAACTTTC-CC--AAATTA
1 CCATTTTAACCCTAA-TTTCACCAAAAATTA
**
788307 -CATTTTAACCCCGATTTCACCAAAAATTA
1 CCATTTTAACCCTAATTTCACCAAAAATTA
*
788336 CCATTTTACCCCTAA
1 CCATTTTAACCCTAA
788351 ACTTTCCAAA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
26 4 0.07
27 13 0.22
28 6 0.10
29 6 0.10
30 26 0.44
31 4 0.07
ACGTcount: A:0.35, C:0.31, G:0.01, T:0.32
Consensus pattern (30 bp):
CCATTTTAACCCTAATTTCACCAAAAATTA
Found at i:788290 original size:58 final size:56
Alignment explanation
Indices: 788212--788407 Score: 234
Period size: 57 Copynumber: 3.4 Consensus size: 56
788202 CTTGAACTGT
* *
788212 CCAAAAATTATATTTTACCCCCAAACTTTCCAAAATCCCATTTTAACCCTAATTTCA
1 CCAAAAATTACATTTTACCCCCAAACTTTCCAAAAT-CCATTTTAACCCTGATTTCA
* * *
788269 CCAAAAATTACCATTTTA-CCCCAAACTTTCCCAAATTACATTTTAACCCCGATTTCA
1 CCAAAAATTA-CATTTTACCCCCAAACTTT-CCAAAATCCATTTTAACCCTGATTTCA
* * *
788326 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAAATCTATTTTTAA-CCTCGGTTTCA
1 CCAAAAATTA-CATTTTACCCCCAAACTTTCC-AAAATCCA-TTTTAACCCT-GATTTCA
788385 CCAAAAATTACATTTTTACCCCC
1 CCAAAAATTACA-TTTTACCCCC
788408 GGAAGTTAAA
Statistics
Matches: 120, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
57 58 0.48
58 31 0.26
59 31 0.26
ACGTcount: A:0.35, C:0.30, G:0.02, T:0.33
Consensus pattern (56 bp):
CCAAAAATTACATTTTACCCCCAAACTTTCCAAAATCCATTTTAACCCTGATTTCA
Found at i:788400 original size:29 final size:29
Alignment explanation
Indices: 788250--788400 Score: 93
Period size: 29 Copynumber: 5.2 Consensus size: 29
788240 TCCAAAATCC
*
788250 CATTTTAACC-CTAATTTCACCAAAAATTA
1 CATTTTAACCTC-GATTTCACCAAAAATTA
* *
788279 CCATTTT-ACCCCAAACTTTC-CC--AAATTA
1 -CATTTTAACCTC-GA-TTTCACCAAAAATTA
*
788307 CATTTTAACCCCGATTTCACCAAAAATTA
1 CATTTTAACCTCGATTTCACCAAAAATTA
* **
788336 CCATTTTACCCCTAAACTTT--CCAAAAATCTA
1 -CATTTTA-ACCTCGA-TTTCACCAAAAAT-TA
* *
788367 -TTTTTAACCTCGGTTTCACCAAAAATTA
1 CATTTTAACCTCGATTTCACCAAAAATTA
788395 CATTTT
1 CATTTT
788401 TACCCCCGGA
Statistics
Matches: 96, Mismatches: 12, Indels: 27
0.71 0.09 0.20
Matches are distributed among these distances:
26 4 0.04
27 12 0.12
28 16 0.17
29 26 0.27
30 26 0.27
31 9 0.09
32 3 0.03
ACGTcount: A:0.35, C:0.28, G:0.02, T:0.35
Consensus pattern (29 bp):
CATTTTAACCTCGATTTCACCAAAAATTA
Found at i:792635 original size:13 final size:13
Alignment explanation
Indices: 792617--792645 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
792607 CCGACGTTTC
792617 AATGTGCGCGTGG
1 AATGTGCGCGTGG
792630 AATGTGCGCGTGG
1 AATGTGCGCGTGG
792643 AAT
1 AAT
792646 ACACGCTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.14, G:0.41, T:0.24
Consensus pattern (13 bp):
AATGTGCGCGTGG
Found at i:798569 original size:7 final size:7
Alignment explanation
Indices: 798557--798595 Score: 78
Period size: 7 Copynumber: 5.6 Consensus size: 7
798547 ATTCTTTGGT
798557 TGATTGC
1 TGATTGC
798564 TGATTGC
1 TGATTGC
798571 TGATTGC
1 TGATTGC
798578 TGATTGC
1 TGATTGC
798585 TGATTGC
1 TGATTGC
798592 TGAT
1 TGAT
798596 GCAAACAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.15, C:0.13, G:0.28, T:0.44
Consensus pattern (7 bp):
TGATTGC
Found at i:800344 original size:21 final size:21
Alignment explanation
Indices: 800318--800357 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
800308 AGTTACTAGC
800318 GAGTTCAG-TTCAATTAAATTT
1 GAGTTC-GTTTCAATTAAATTT
*
800339 GAGTTCGTTTGAATTAAAT
1 GAGTTCGTTTCAATTAAAT
800358 GGTTTACGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (21 bp):
GAGTTCGTTTCAATTAAATTT
Found at i:800414 original size:16 final size:16
Alignment explanation
Indices: 800377--800414 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
800367 GTTTAATTAA
800377 ATAT-TTTAAAATATT
1 ATATATTTAAAATATT
*
800392 TTATATTTAAAATATT
1 ATATATTTAAAATATT
*
800408 ATGTATT
1 ATATATT
800415 GATTTAATAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 3 0.16
16 16 0.84
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
ATATATTTAAAATATT
Found at i:806133 original size:23 final size:23
Alignment explanation
Indices: 806107--806323 Score: 204
Period size: 23 Copynumber: 9.3 Consensus size: 23
806097 AGTGCTGGGC
*
806107 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
806130 AACAGAGAGTACACAAAGTACTG
1 AACAGAGAGCACACAAAGTGCTA
* *
806153 ATCAGAGAGTACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
806176 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
806200 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
* *
806224 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACAAAGTGCTA
* *
806247 ATCAGAGATCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
806270 ATCAGAGAGAACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
*
806294 TAACAGAGAGCACA-AGACGTGCTA
1 -AACAGAGAGCACACA-AAGTGCTA
806318 AACAGA
1 AACAGA
806324 TAGCGCATTA
Statistics
Matches: 159, Mismatches: 28, Indels: 14
0.79 0.14 0.07
Matches are distributed among these distances:
22 1 0.01
23 120 0.75
24 5 0.03
25 32 0.20
26 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.13
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:806208 original size:94 final size:93
Alignment explanation
Indices: 806107--806323 Score: 348
Period size: 94 Copynumber: 2.3 Consensus size: 93
806097 AGTGCTGGGC
*
806107 AACAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTGATCAGAGAGT-ACACAAAG
1 AACAGAGAGCACA-ACAGTGCTAAACAGAGAGTACACAAAGTACTAATCAGAGA-TCACACAAAG
*
806171 TGCTAATCAGAGAGCACACACAGTGCTAAT
64 TGCTAATCAGAGAGAACACACAGTGCTAAT
806201 AACAGAGAGCACGAGAC-GTGCTAAACAGAGAGTACACAAAGTACTAATCAGAGATCACACAAAG
1 AACAGAGAGCAC-A-ACAGTGCTAAACAGAGAGTACACAAAGTACTAATCAGAGATCACACAAAG
806265 TGCTAATCAGAGAGAACACACAGTGCTAAT
64 TGCTAATCAGAGAGAACACACAGTGCTAAT
*
806295 AACAGAGAGCACAAGACGTGCTAAACAGA
1 AACAGAGAGCACAACA-GTGCTAAACAGA
806324 TAGCGCATTA
Statistics
Matches: 115, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
92 1 0.01
93 2 0.02
94 109 0.95
95 3 0.03
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.13
Consensus pattern (93 bp):
AACAGAGAGCACAACAGTGCTAAACAGAGAGTACACAAAGTACTAATCAGAGATCACACAAAGTG
CTAATCAGAGAGAACACACAGTGCTAAT
Found at i:806299 original size:71 final size:70
Alignment explanation
Indices: 806109--806303 Score: 236
Period size: 71 Copynumber: 2.8 Consensus size: 70
806099 TGCTGGGCAA
* * * *
806109 CAGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTGAT--CAGAGAGTACACAAAGT
1 CAGAGAGCACACACAGTGCTAATCAGAGAGAACACACAGTGCT-ATAACAGAGAGTACACAAAGT
*
806172 GCTAAT
65 ACTAAT
* *
806178 CAGAGAGCACACACAGTGCTAATAACAGAGAGCACGAGAC-GTGCTA-AACAGAGAGTACACAAA
1 CAGAGAGCACACACAGTGCTAAT--CAGAGAGAAC-ACACAGTGCTATAACAGAGAGTACACAAA
806241 GTACTAAT
63 GTACTAAT
* *
806249 CAGAGATCACACAAAGTGCTAATCAGAGAGAACACACAGTGCTAATAACAGAGAG
1 CAGAGAGCACACACAGTGCTAATCAGAGAGAACACACAGTGCT-ATAACAGAGAG
806304 CACAAGACGT
Statistics
Matches: 108, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
68 3 0.03
69 36 0.33
70 2 0.02
71 65 0.60
72 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.22, T:0.13
Consensus pattern (70 bp):
CAGAGAGCACACACAGTGCTAATCAGAGAGAACACACAGTGCTATAACAGAGAGTACACAAAGTA
CTAAT
Found at i:808914 original size:22 final size:21
Alignment explanation
Indices: 808872--808918 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
808862 AAGTCAATGA
*
808872 AAAAAATTAGAGTTTAATTATT
1 AAAAAATTAGAGATTAATTA-T
808894 AAAAAATTA-AGATTAATTTAT
1 AAAAAATTAGAGATTAA-TTAT
808915 AAAA
1 AAAA
808919 TGTGAAAGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 12 0.52
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.36
Consensus pattern (21 bp):
AAAAAATTAGAGATTAATTAT
Found at i:809904 original size:15 final size:15
Alignment explanation
Indices: 809884--809915 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
809874 TGGTACTTTT
809884 ACCTAAAATTAGGCG
1 ACCTAAAATTAGGCG
809899 ACCTAAAATTAGGCG
1 ACCTAAAATTAGGCG
809914 AC
1 AC
809916 TGATGTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (15 bp):
ACCTAAAATTAGGCG
Found at i:813234 original size:2 final size:2
Alignment explanation
Indices: 813227--813290 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
813217 TAGAAGAAAT
813227 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
813269 GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA
813291 ATCTTTAAGG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:814617 original size:13 final size:13
Alignment explanation
Indices: 814585--814634 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
814575 ATCTTTTAAA
*
814585 TATATTTAAGTTT
1 TATATTTAATTTT
* *
814598 AAGATTTAATTTT
1 TATATTTAATTTT
814611 TATATTTAATTTT
1 TATATTTAATTTT
*
814624 TA-ACTTAATTT
1 TATATTTAATTT
814635 GATTTTTATA
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
12 8 0.26
13 23 0.74
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (13 bp):
TATATTTAATTTT
Found at i:823701 original size:23 final size:23
Alignment explanation
Indices: 823661--823706 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
823651 AATCCCATTA
* *
823661 ATAAAAAAATGTTTATAT-TTTT
1 ATAAAAAAATATTCATATGTTTT
823683 ATAATAAAAATATTCATATGTTTT
1 ATAA-AAAAATATTCATATGTTTT
823707 CACTAAATGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 4 0.20
23 12 0.60
24 4 0.20
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
ATAAAAAAATATTCATATGTTTT
Found at i:825267 original size:125 final size:123
Alignment explanation
Indices: 824994--825680 Score: 785
Period size: 120 Copynumber: 5.6 Consensus size: 123
824984 TCTAAATATA
* *
824994 AACTATAAAATAGCCATGAAAAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCGATA
1 AACTATAAAATAGACATGAACAATAAAAAAA-TGAATGAGTTAATTGTATTAATCGGATCCGATA
* *
825059 TGTAATTACTT--AAAA-AAAATACATTTTAAAAAAATT-ACTTGAAACAC-TGAACATG
65 TGTAATTACTTAAAAAAGAAAATACCTTTTTAAAAAATTAACTTGAAAC-CTTGAACATG
* * * *
825114 AATTATAAAATA-AGTATGAATAATAAAAAAAATGAATGAGTTAATTGTATTAATCGAATCCGAT
1 AACTATAAAATAGA-CATGAACAAT-AAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGAT
* * *
825178 ATGTAATTACTTAAAAAAGAAAATGCTCTTTTTAAAAAATTGACTTGAAACCTTAAACATG
64 ATGTAATTACTTAAAAAAGAAAATAC-CTTTTTAAAAAATTAACTTGAAACCTTGAACATG
* *
825239 AACTATAAAATAGACATGAAGAATAAAAAAAATGAATGACTTAATTGTATTAATCGGATCCGATA
1 AACTATAAAATAGACATGAACAAT-AAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATA
* * * *
825304 TGTTATTACTTAAAAAAGAAAATGCC--TTTAAAAAA-AAACTTGAAA-CTCTAAACATG
65 TGTAATTACTTAAAAAAGAAAATACCTTTTTAAAAAATTAACTTGAAACCT-TGAACATG
* * * * * *
825360 AGCTATAAAATAAATATGAACAGTAAAAAAATAAACGAGTTAATTGTATTAATCGGATCCGATAT
1 AACTATAAAATAGACATGAACAATAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATAT
* * **
825425 GTAATTACTTAAAAAAGAAAATACCTTTTTTAAAAATTGACTCAAAACCTTGAA-ATG
66 GTAATTACTTAAAAAAGAAAATACCTTTTTAAAAAATTAACTTGAAACCTTGAACATG
** * * *
825482 AGTTATAAAATAGACATGAAGAATAAAAAAATGAATGAATTAATTGTATTAATTGGATCCGATAT
1 AACTATAAAATAGACATGAACAATAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATAT
* * *
825547 GTAATTTCTT--AAAA-AAAATACCTTTTAAAAAAAATTAACTT-AAAACTCTGAACATG
66 GTAATTACTTAAAAAAGAAAATACCTTTT-TAAAAAATTAACTTGAAACCT-TGAACATG
* * * * * * * *
825603 AACTATAATATAAATATAAACAGTAAAAAAATGAATGAGTTAATTTTATTAATCGGATTCAATAT
1 AACTATAAAATAGACATGAACAATAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATAT
*
825668 ATAATTAC-TAAAA
66 GTAATTACTTAAAA
825681 TACATTCTTA
Statistics
Matches: 485, Mismatches: 63, Indels: 36
0.83 0.11 0.06
Matches are distributed among these distances:
119 17 0.04
120 144 0.30
121 103 0.21
122 91 0.19
123 15 0.03
124 16 0.03
125 98 0.20
126 1 0.00
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (123 bp):
AACTATAAAATAGACATGAACAATAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATAT
GTAATTACTTAAAAAAGAAAATACCTTTTTAAAAAATTAACTTGAAACCTTGAACATG
Found at i:825424 original size:245 final size:242
Alignment explanation
Indices: 824994--825680 Score: 936
Period size: 245 Copynumber: 2.8 Consensus size: 242
824984 TCTAAATATA
* * * *
824994 AACTATAAAATAGCCATGAAAAATAAAAAAATTGAATGAGTTAATTGTATTAATCGGATCCGATA
1 AACTATAAAATAGACATGAAGAATAAAAAAAATGAATGAATTAATTGTATTAATCGGATCCGATA
* * *
825059 TGTAATTACTTAAAAAAAATACAT--TTTAAAAAAATTACTTGAAACACTGAACATGAATTATAA
66 TGTAATTACTTAAAAAAAA-A-ATCCTTTAAAAAAATAACTTGAAACTCTGAACATGAACTATAA
* * * *
825122 AATAAGTATGAATAATAAAAAAAATGAATGAGTTAATTGTATTAATCGAATCCGATATGTAATTA
129 AATAAATATGAACAGT-AAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATATGTAATTA
* **
825187 CTTAAAAAAGAAAATGCTCTTTTTAAAAAATTGACTTGAAACCTTAAACATG
193 CTTAAAAAAGAAAATAC-CTTTTTAAAAAATTGACTCAAAACCTTAAA-ATG
*
825239 AACTATAAAATAGACATGAAGAATAAAAAAAATGAATGACTTAATTGTATTAATCGGATCCGATA
1 AACTATAAAATAGACATGAAGAATAAAAAAAATGAATGAATTAATTGTATTAATCGGATCCGATA
* * *
825304 TGTTATTACTTAAAAAAGAAAATGCCTTTAAAAAAA-AACTTGAAACTCTAAACATGAGCTATAA
66 TGTAATTACTTAAAAAA-AAAAT-CCTTTAAAAAAATAACTTGAAACTCTGAACATGAACTATAA
* *
825368 AATAAATATGAACAGTAAAAAAATAAACGAGTTAATTGTATTAATCGGATCCGATATGTAATTAC
129 AATAAATATGAACAGTAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATATGTAATTAC
* *
825433 TTAAAAAAGAAAATACCTTTTTTAAAAATTGACTCAAAACCTTGAAATG
194 TTAAAAAAGAAAATACCTTTTTAAAAAATTGACTCAAAACCTTAAAATG
** *
825482 AGTTATAAAATAGACATGAAGAAT-AAAAAAATGAATGAATTAATTGTATTAATTGGATCCGATA
1 AACTATAAAATAGACATGAAGAATAAAAAAAATGAATGAATTAATTGTATTAATCGGATCCGATA
* * *
825546 TGTAATTTCTTAAAAAAAATA-CCTTTTAAAAAAAATTAACTTAAAACTCTGAACATGAACTATA
66 TGTAATTACTTAAAAAAAAAATCC-TTT-AAAAAAA-TAACTTGAAACTCTGAACATGAACTATA
* * * * * *
825610 ATATAAATATAAACAGTAAAAAAATGAATGAGTTAATTTTATTAATCGGATTCAATATATAATTA
128 AAATAAATATGAACAGTAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATATGTAATTA
825675 C-TAAAA
193 CTTAAAA
825681 TACATTCTTA
Statistics
Matches: 395, Mismatches: 39, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
239 2 0.01
240 3 0.01
241 10 0.03
242 58 0.15
243 107 0.27
244 28 0.07
245 139 0.35
246 38 0.10
247 10 0.03
ACGTcount: A:0.50, C:0.09, G:0.11, T:0.30
Consensus pattern (242 bp):
AACTATAAAATAGACATGAAGAATAAAAAAAATGAATGAATTAATTGTATTAATCGGATCCGATA
TGTAATTACTTAAAAAAAAAATCCTTTAAAAAAATAACTTGAAACTCTGAACATGAACTATAAAA
TAAATATGAACAGTAAAAAAATGAATGAGTTAATTGTATTAATCGGATCCGATATGTAATTACTT
AAAAAAGAAAATACCTTTTTAAAAAATTGACTCAAAACCTTAAAATG
Found at i:834756 original size:15 final size:16
Alignment explanation
Indices: 834738--834769 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
834728 CGAAAACTAT
834738 AAAAATTAAAAT-TAA
1 AAAAATTAAAATATAA
834753 AAAAATTAAAATATAA
1 AAAAATTAAAATATAA
834769 A
1 A
834770 GATTAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
AAAAATTAAAATATAA
Found at i:835004 original size:30 final size:29
Alignment explanation
Indices: 834968--835056 Score: 81
Period size: 30 Copynumber: 3.0 Consensus size: 29
834958 ATACATCACA
834968 AGTTTTTTTACTTTTAAAATTTTAAAATTT
1 AGTTTTTTTACTTTT-AAATTTTAAAATTT
**
834998 AGTTTTTATT-CTTTTATTTTTTAAGAATTT
1 AGTTTTT-TTACTTTTAAATTTTAA-AATTT
* * * *
835028 AATTTTTATACTTTTTAGATCTTAAAATT
1 AGTTTTTTTAC-TTTTAAATTTTAAAATT
835057 GAGATCTATT
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
29 8 0.17
30 28 0.58
31 12 0.25
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (29 bp):
AGTTTTTTTACTTTTAAATTTTAAAATTT
Found at i:840408 original size:2 final size:2
Alignment explanation
Indices: 840368--840392 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
840358 TTTATAGCCG
840368 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
840393 TCAGTTCTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:841348 original size:51 final size:51
Alignment explanation
Indices: 841275--841529 Score: 395
Period size: 51 Copynumber: 5.0 Consensus size: 51
841265 GATGCCGAAC
*
841275 CAGCAAGGTGGAAACATTGAATCCCAAACATACACTCAGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
* * *
841326 CAGCAAGGTGGTAACATCGAATCTCAAACATATACTCAGCTACCACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
* * * *
841377 CAGCAAGGTGGAAACGTTGAATACCAAACATATACTCAGCTGCCACAACAA
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
* *
841428 CATCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACAACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
*
841479 CAGCAAGGTGGAAACATTGAATCCCAAACATATACACAG-TCACCACAACAG
1 CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCT-ACCACAACAG
841530 TACTTAATGG
Statistics
Matches: 183, Mismatches: 20, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
50 1 0.01
51 182 0.99
ACGTcount: A:0.42, C:0.27, G:0.16, T:0.16
Consensus pattern (51 bp):
CAGCAAGGTGGAAACATTGAATCCCAAACATATACTCAGCTACCACAACAG
Found at i:860167 original size:12 final size:12
Alignment explanation
Indices: 860150--860175 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
860140 CAATCTAAAA
860150 AAGTACTAATAG
1 AAGTACTAATAG
860162 AAGTACTAATAG
1 AAGTACTAATAG
860174 AA
1 AA
860176 AACTATAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.15, T:0.23
Consensus pattern (12 bp):
AAGTACTAATAG
Found at i:865891 original size:21 final size:21
Alignment explanation
Indices: 865867--865908 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
865857 TAACAACCAT
865867 GCAACAAAATCCTTAAAATTG
1 GCAACAAAATCCTTAAAATTG
865888 GCAACAAAATCCTTAAAATTG
1 GCAACAAAATCCTTAAAATTG
865909 ACTTTCAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.19, G:0.10, T:0.24
Consensus pattern (21 bp):
GCAACAAAATCCTTAAAATTG
Found at i:866835 original size:20 final size:21
Alignment explanation
Indices: 866803--866841 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
866793 ACTAAAGATA
866803 TTTAAAAATTTTA-CTATTAT
1 TTTAAAAATTTTACCTATTAT
866823 TTTAACAAA-TTTACCTATT
1 TTTAA-AAATTTTACCTATT
866842 TAAATAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (21 bp):
TTTAAAAATTTTACCTATTAT
Found at i:872337 original size:23 final size:23
Alignment explanation
Indices: 872311--872354 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
872301 TACTCTTCGA
*
872311 AATATATATATTTTTTAAATTTT
1 AATATATATATTTTTCAAATTTT
* *
872334 AATATTTTTATTTTTCAAATT
1 AATATATATATTTTTCAAATT
872355 CTAAATAACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (23 bp):
AATATATATATTTTTCAAATTTT
Found at i:876781 original size:24 final size:23
Alignment explanation
Indices: 876746--876807 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
876736 TTTAATATTG
*
876746 TTTTTTTACTATTTTGGTTGCTA
1 TTTTTTTACTATTTTGGATGCTA
* *
876769 TTTTTTTTGCTATTTT-GATGTTA
1 -TTTTTTTACTATTTTGGATGCTA
876792 TTTTTTTACTATTTTG
1 TTTTTTTACTATTTTG
876808 ATTGTTGTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 14 0.42
23 5 0.15
24 14 0.42
ACGTcount: A:0.13, C:0.06, G:0.11, T:0.69
Consensus pattern (23 bp):
TTTTTTTACTATTTTGGATGCTA
Done.