Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold462
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: 1234098
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 4 of 8
Found at i:488522 original size:19 final size:19
Alignment explanation
Indices: 488475--488524 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
488465 GTTTTATTGT
** *
488475 TCAATACAATTGAGTATGTA
1 TCAATACAA-TGAACATGCA
*
488495 TCGATACAATGAACATGCA
1 TCAATACAATGAACATGCA
488514 TCAATACAATG
1 TCAATACAATG
488525 TATCGATATA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (19 bp):
TCAATACAATGAACATGCA
Found at i:496952 original size:97 final size:97
Alignment explanation
Indices: 496786--496974 Score: 292
Period size: 97 Copynumber: 1.9 Consensus size: 97
496776 GTGTTACGAC
*
496786 ATTTATGCAAAAATAAGATTTAAATCATGACAAGTTTAAAAATGGGGTTGGAGTATCCCCGTAAA
1 ATTTAAGCAAAAATAAGATTTAAATCATGACAAGTTTAAAAATGGGGTTGGAGTATCCCCGTAAA
* *
496851 AGAAT-AGAGTTGGAGTATCCTCGATGATGACA
66 AGAATAAG-GTTCGAGTATCCCCGATGATGACA
* **
496883 ATTTAAGCAAAAATAAGATTTAAATCTTGACAAGTTTAAAAATGGGGTTGGAGTATCCCC-TCGG
1 ATTTAAGCAAAAATAAGATTTAAATCATGACAAGTTTAAAAATGGGGTTGGAGTATCCCCGT-AA
496947 AAGAATAAGGTTCGAGTATCCCCGATGA
65 AAGAATAAGGTTCGAGTATCCCCGATGA
496975 ATAAAATTTT
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
96 1 0.01
97 81 0.96
98 2 0.02
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (97 bp):
ATTTAAGCAAAAATAAGATTTAAATCATGACAAGTTTAAAAATGGGGTTGGAGTATCCCCGTAAA
AGAATAAGGTTCGAGTATCCCCGATGATGACA
Found at i:499428 original size:21 final size:20
Alignment explanation
Indices: 499403--499454 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
499393 TACATAGTCT
499403 TGTATCAATACATTTCAAGCA
1 TGTATCAATACA-TTCAAGCA
* ***
499424 TGTATCGATACATTCACTTA
1 TGTATCAATACATTCAAGCA
499444 TGTATCAATAC
1 TGTATCAATAC
499455 GTTACCTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.35, C:0.19, G:0.10, T:0.37
Consensus pattern (20 bp):
TGTATCAATACATTCAAGCA
Found at i:499446 original size:20 final size:20
Alignment explanation
Indices: 499423--499476 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
499413 CATTTCAAGC
499423 ATGTATCGATACATT-CACTT
1 ATGTATCGATACATTAC-CTT
* *
499443 ATGTATCAATACGTTACCTT
1 ATGTATCGATACATTACCTT
499463 ATTGTATCGATACA
1 A-TGTATCGATACA
499477 AATTGTTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACATTACCTT
Found at i:505360 original size:80 final size:78
Alignment explanation
Indices: 505233--505730 Score: 376
Period size: 80 Copynumber: 6.2 Consensus size: 78
505223 AAGACATCAA
* * * * * *
505233 AAGGGATACTCCAACCACTGTTTTCACTTCTAAAACACCAAAATTTTCATCTTCGGCGATACTCC
1 AAGGGATACTCCAACC-CCGTTTTTACTTCCAAAACTCTAAATTTTTCATCTTCGG-GATACTCC
*
505298 AACCCTATCATCTCTG
64 AACCC-ACCATCTCTG
* * * * **
505314 AATGGATACACCAACCCCGTATTTACTTCTAAAACTCTAAATTTTTCAAAT-TTTAGGATACTCC
1 AAGGGATACTCCAACCCCGTTTTTACTTCCAAAACTCTAAATTTTTC--ATCTTCGGGATACTCC
* *
505378 AACCCTACAATCTTTG
64 AACCC-ACCATCTCTG
** * * *
505394 AAAAGATACTTCAACCCCGTTTTTACTTCCAAAA-TACCAAATTTTTCATCTTAGGGGATACTCC
1 AAGGGATACTCCAACCCCGTTTTTACTTCCAAAACT-CTAAATTTTTCATCTT-CGGGATACTCC
**
505458 AACCCCACCATCTCCA
64 AA-CCCACCATCTCTG
* * * * * * *
505474 AATGGATACTCCAATCCCATTTTTACTTCCAAAACGTC-AAATTTTTCATATCTAGAGATACTAC
1 AAGGGATACTCCAACCCCGTTTTTACTTCCAAAAC-TCTAAATTTTTCATCT-TCGGGATACTCC
505538 AACACCACCATCTCTG
64 AAC-CCACCATCTCTG
* * * ** * * ** *
505554 AGGGGATACTCAAATCTTGATTTTACTTCTAAAAAGCTAACTTTTTCATCTTCGAGGATACTCCA
1 AAGGGATACTCCAACCCCGTTTTTACTTCCAAAACTCTAAATTTTTCATCTTCG-GGATACTCCA
*
505619 ACCCCACCATCTTTG
65 A-CCCACCATCTCTG
* * * ** * *
505634 AGGGGATATTCTAACCTTGTTTTTACTTCCAAAACAT-TAAATTATTCATCTTTGAGGATACTCC
1 AAGGGATACTCCAACCCCGTTTTTACTTCCAAAAC-TCTAAATTTTTCATCTTCG-GGATACTCC
505698 AACCACACCATCTCTG
64 AACC-CACCATCTCTG
505714 -AGGAGATACTCCAACCC
1 AAGG-GATACTCCAACCC
505731 TAGTTTTCAC
Statistics
Matches: 333, Mismatches: 68, Indels: 33
0.77 0.16 0.08
Matches are distributed among these distances:
78 2 0.01
79 11 0.03
80 294 0.88
81 23 0.07
82 3 0.01
ACGTcount: A:0.32, C:0.28, G:0.10, T:0.31
Consensus pattern (78 bp):
AAGGGATACTCCAACCCCGTTTTTACTTCCAAAACTCTAAATTTTTCATCTTCGGGATACTCCAA
CCCACCATCTCTG
Found at i:508383 original size:45 final size:45
Alignment explanation
Indices: 508333--509113 Score: 589
Period size: 44 Copynumber: 17.7 Consensus size: 45
508323 CTAGACCCAC
* * * *
508333 CAAACTCCTTTCATTCCTATTTGATGTAATGGTTCTTGCCCTGGT
1 CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
* * * ** *
508378 CAAACTATTTTCATTCTTATTTGACGTGATGGCTCTCGCCTTGGT
1 CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
* * * * *
508423 CAAACTTTTTTCATTACTATTTGACATGATGGTT-ATGCCCTGGT
1 CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
* * * * *
508467 CAAACTATTTTCATTTC-GTTTGATGTGATGGTTC-TACCCTGCT
1 CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
** * * * *
508510 CAAACTAC-TTTCATTTTTGTTTAACATGATGGTTC-TACCATGGT
1 CAAACT-CTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
* * * * *
508554 TAAACTTTTTTCA-T-CTCATTCGACGTGATGGTTC-TACCTTGGC
1 CAAACTCTTTTCATTCCT-ATTTGACGTGATGGTTCTTACCCTGGT
** * * *
508597 CAAACTCTTTTCATTTTTGTTTGATGTCATGGTTC-TACCCTGGT
1 CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
* * * *
508641 TAAACTCTTTTGATTCC-AGTTTGACATGATGGTTCTCACCCTGGT
1 CAAACTCTTTTCATTCCTA-TTTGACGTGATGGTTCTTACCCTGGT
* * *
508686 CAAACTCATTTCATTCC-ATTTGACGTGATGGTTCTTGCCCTAGT
1 CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
* ** * * * *
508730 TAAACTCTTTTCATTTTTGTTTAACGTGATGGTT-TTGCCTTGGT
1 CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
** * * * *
508774 CAAACTCTTTTCATTCCGGTTTAATGTGATGGCTCTTACCCTAGT
1 CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
* * *
508819 CAAACTCTTTTCATTCAC-GTTTGACGTGATGGTTCTT-GCCTAGT
1 CAAACTCTTTTCATTC-CTATTTGACGTGATGGTTCTTACCCTGGT
* * * * **
508863 CAAGCAT-TTTGTCATTCC-ATTTGACATGATGGATCTCACCCTAAT
1 CAAAC-TCTTT-TCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
* * *
508908 CAAACTCTTTTCATT-CTGTTTGATGTGATGGTTCTCACCCTGGT
1 CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
* * *
508952 CAAACATCTTTTTATTCC-ATTTGACGTGATGATTC-T-CTCCTAGT
1 CAAAC-TCTTTTCATTCCTATTTGACGTGATGGTTCTTAC-CCTGGT
* * * *
508996 CAAACTCTTTTCATT-CTATTTGACATGATGGTTCTCACCTTAGT
1 CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
* * * **
509040 CAAACTTTTTTCATT-CTATTTGACATGATGGTTCTCACATTGGT
1 CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
* * *
509084 CAAACTCTTTTCATTTCGATTTGATGTGAT
1 CAAACTCTTTTCATTCCTATTTGACGTGAT
509114 AGTTTAGCCC
Statistics
Matches: 595, Mismatches: 117, Indels: 48
0.78 0.15 0.06
Matches are distributed among these distances:
42 2 0.00
43 92 0.15
44 302 0.51
45 197 0.33
46 2 0.00
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.43
Consensus pattern (45 bp):
CAAACTCTTTTCATTCCTATTTGACGTGATGGTTCTTACCCTGGT
Found at i:509095 original size:88 final size:88
Alignment explanation
Indices: 508341--509113 Score: 589
Period size: 89 Copynumber: 8.7 Consensus size: 88
508331 ACCAAACTCC
** * ** *
508341 TTTCATTCCTATTTGATGTAATGGTTCTTGCCCTGGTCAAACTATTTTCATTCTTATTTGACGTG
1 TTTCATT-CTATTTGACATGATGGTTCTCACCCTGGTCAAACTCTTTTCATTC-TATTTGACGTG
* *
508406 ATGGCTCTCGCCTTGGTCAAACTTT
64 ATGGTTCTCACCTTGGTCAAACTTT
* * * * *
508431 TTTCATTACTATTTGACATGATGGTTAT-GCCCTGGTCAAACTATTTTCATT-TCGTTTGATGTG
1 TTTCATT-CTATTTGACATGATGGTTCTCACCCTGGTCAAACTCTTTTCATTCT-ATTTGACGTG
* * **
508494 ATGGTTCT-ACCCTGCTCAAACTAC
64 ATGGTTCTCACCTTGGTCAAACTTT
* * * * * * *
508518 TTTCATTTTTGTTTAACATGATGGTTCT-ACCATGGTTAAACTTTTTTCA-TCTCATTCGACGTG
1 TTTCA-TTCTATTTGACATGATGGTTCTCACCCTGGTCAAACTCTTTTCATTCT-ATTTGACGTG
* *
508581 ATGGTTCT-ACCTTGGCCAAACTCT
64 ATGGTTCTCACCTTGGTCAAACTTT
* * ** * * * * *
508605 TTTCATTTTTGTTTGATGTCATGGTTCT-ACCCTGGTTAAACTCTTTTGATTCCAGTTTGACATG
1 TTTCA-TTCTATTTGACATGATGGTTCTCACCCTGGTCAAACTCTTTTCATTCTA-TTTGACGTG
* **
508669 ATGGTTCTCACCCTGGTCAAACTCA
64 ATGGTTCTCACCTTGGTCAAACTTT
* * ** * * * * *
508694 TTTCATTCCATTTGACGTGATGGTTCTTGCCCTAGTTAAACTCTTTTCATTTTTGTTTAACGTGA
1 TTTCATTCTATTTGACATGATGGTTCTCACCCTGGTCAAACTCTTTTCA-TTCTATTTGACGTGA
** *
508759 TGGTT-TTGCCTTGGTCAAACTCT
65 TGGTTCTCACCTTGGTCAAACTTT
** * ** * * *
508782 TTTCATTCCGGTTTAATGTGATGGCTCTTACCCTAGTCAAACTCTTTTCATTC-ACGTTTGACGT
1 TTTCATT-CTATTTGACATGATGGTTCTCACCCTGGTCAAACTCTTTTCATTCTA--TTTGACGT
** * *
508846 GATGGTTCTTGCC-TAGTCAAGCATTT
63 GATGGTTCTCACCTTGGTCAAAC-TTT
* * * ** * *
508872 TGTCATTCCATTTGACATGATGGATCTCACCCTAATCAAACTCTTTTCATTCTGTTTGATGTGAT
1 TTTCATTCTATTTGACATGATGGTTCTCACCCTGGTCAAACTCTTTTCATTCTATTTGACGTGAT
*
508937 GGTTCTCACCCTGGTCAAACATCTT
66 GGTTCTCACCTTGGTCAAAC-T-TT
* * * * * *
508962 TTT-ATTCCATTTGACGTGATGATTCTC-TCCTAGTCAAACTCTTTTCATTCTATTTGACATGAT
1 TTTCATTCTATTTGACATGATGGTTCTCACCCTGGTCAAACTCTTTTCATTCTATTTGACGTGAT
*
509025 GGTTCTCACCTTAGTCAAACTTT
66 GGTTCTCACCTTGGTCAAACTTT
** * *
509048 TTTCATTCTATTTGACATGATGGTTCTCACATTGGTCAAACTCTTTTCATTTCGATTTGATGTGA
1 TTTCATTCTATTTGACATGATGGTTCTCACCCTGGTCAAACTCTTTTCA-TTCTATTTGACGTGA
509113 T
65 T
509114 AGTTTAGCCC
Statistics
Matches: 556, Mismatches: 108, Indels: 39
0.79 0.15 0.06
Matches are distributed among these distances:
86 6 0.01
87 143 0.26
88 157 0.28
89 208 0.37
90 42 0.08
ACGTcount: A:0.20, C:0.21, G:0.16, T:0.43
Consensus pattern (88 bp):
TTTCATTCTATTTGACATGATGGTTCTCACCCTGGTCAAACTCTTTTCATTCTATTTGACGTGAT
GGTTCTCACCTTGGTCAAACTTT
Found at i:510420 original size:165 final size:164
Alignment explanation
Indices: 510224--510589 Score: 377
Period size: 165 Copynumber: 2.2 Consensus size: 164
510214 CATTACTTAT
* * * * *
510224 TTCAAATTAAATCATTTTTAAAAAATTTCTTTTATTTCATGAGTTATTGATTTTTT-TTTAGAAT
1 TTCAAATTAAATTAGTTTTGAAAAATTTCTTTTATTTCATGAATTATTGATTTTTTCTTGA-AAT
* * * * ** *
510288 TCCTCTTATTTTCAAAATACGAAGTTTTC-TTCCTTGTAAT-TTTTTTAGGAAGA-TTTTCATTT
65 TCCTC-TATTTTCAAAATACAAAATTTTCATTCCAT-AAATATTTTCAAGG-AGACTTTTC--TC
* *
510350 G-TTTATGAA-TTTTAAAATTTATCAAATATCACCATTTAA
125 GATTTAT-AATTTTTAAAATTCATCAAATAACACCATTTAA
* * * *
510389 TTCACATTAAATTAGTTTTGAAAATTTTCTTTTATTTCATGAATTTTTTATTTTTTCTTGAAATT
1 TTCAAATTAAATTAGTTTTGAAAAATTTCTTTTATTTCATGAATTATTGATTTTTTCTTGAAATT
* ** *
510454 TCTCTATTTTTGAAATACAAAATTTTCTATTCCATAAATATTTTCAAGGGGACTTTTCTCGATTT
66 CCTCTATTTTCAAAATACAAAATTTTC-ATTCCATAAATATTTTCAAGGAGACTTTTCTCGATTT
*
510519 ATAATTTTTAAAATTCATCAAATAACATCATTTAA
130 ATAATTTTTAAAATTCATCAAATAACACCATTTAA
* * *
510554 TTCATAGTAAATTAGTTTTGAAAAATTT-ATTTATTT
1 TTCAAATTAAATTAGTTTTGAAAAATTTCTTTTATTT
510590 TCAAAAGTTT
Statistics
Matches: 167, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
164 30 0.18
165 117 0.70
166 20 0.12
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.51
Consensus pattern (164 bp):
TTCAAATTAAATTAGTTTTGAAAAATTTCTTTTATTTCATGAATTATTGATTTTTTCTTGAAATT
CCTCTATTTTCAAAATACAAAATTTTCATTCCATAAATATTTTCAAGGAGACTTTTCTCGATTTA
TAATTTTTAAAATTCATCAAATAACACCATTTAA
Found at i:510445 original size:19 final size:21
Alignment explanation
Indices: 510410--510464 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 21
510400 TTAGTTTTGA
510410 AAATTT-TCT-TTTATTTCATG
1 AAATTTCTCTATTT-TTTCATG
* *
510430 -AATTT-TTTATTTTTTCTTG
1 AAATTTCTCTATTTTTTCATG
510449 AAATTTCTCTATTTTT
1 AAATTTCTCTATTTTT
510465 GAAATACAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 13 0.45
20 8 0.28
21 8 0.28
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.65
Consensus pattern (21 bp):
AAATTTCTCTATTTTTTCATG
Found at i:510603 original size:165 final size:167
Alignment explanation
Indices: 510351--510704 Score: 441
Period size: 165 Copynumber: 2.1 Consensus size: 167
510341 TTTTCATTTG
* * * *
510351 TTTATGAA-TTTTAAAATTTATCAAATATCACCATTTAATTCACATTAAATTAGTTTTGAAAATT
1 TTTAT-AATTTTTAAAATTCATCAAATAACACCATTTAATTCACAGTAAATTAGTTTTGAAAAAT
* * *
510415 TTCTTTTATTTCATGAATTTTTTATTTTTTCTT-GAAATTTCTCTATTTTTGAAATACAAAATTT
65 TTATTTTATTTCATAAATTTTTTATTTTTTCTTCGAAATTTCTCTATTTTTGAAAAACAAAATTT
* *
510479 TCTATTCCATAAATATTTTCAAG-GGGA-CTTTTCTCGA
130 TCTATTCAATAAATATTTTCAAGAGGGATC-TTTCTCAA
* *
510516 TTTATAATTTTTAAAATTCATCAAATAACATCATTTAATTCATAGTAAATTAGTTTTGAAAAATT
1 TTTATAATTTTTAAAATTCATCAAATAACACCATTTAATTCACAGTAAATTAGTTTTGAAAAATT
* * * * *
510581 TA-TTTATTTTCA-AAAGTTTTTTATTTTTTCTTCGATATTTTTCTGTTTTTGAAAAACCAAGTT
66 TATTTTA-TTTCATAAA-TTTTTTATTTTTTCTTCGAAATTTCTCTATTTTTGAAAAACAAAATT
* * * *
510644 TTCTATTCAATGAATGTTTTTAGGAGGGATCTTTCTCAA
129 TTCTATTCAATAAATATTTTCAAGAGGGATCTTTCTCAA
*
510683 TTTAAAATTTTTAAAATTCATC
1 TTTATAATTTTTAAAATTCATC
510705 TAACATTAGT
Statistics
Matches: 162, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
164 8 0.05
165 78 0.48
166 43 0.27
167 32 0.20
168 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.07, T:0.49
Consensus pattern (167 bp):
TTTATAATTTTTAAAATTCATCAAATAACACCATTTAATTCACAGTAAATTAGTTTTGAAAAATT
TATTTTATTTCATAAATTTTTTATTTTTTCTTCGAAATTTCTCTATTTTTGAAAAACAAAATTTT
CTATTCAATAAATATTTTCAAGAGGGATCTTTCTCAA
Found at i:510608 original size:18 final size:18
Alignment explanation
Indices: 510569--510607 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
510559 AGTAAATTAG
*
510569 TTTTGAAAAATTTATTTA
1 TTTTCAAAAATTTATTTA
*
510587 TTTTCAAAAGTTT-TTTA
1 TTTTCAAAAATTTATTTA
510604 TTTT
1 TTTT
510608 TTCTTCGATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.62
Consensus pattern (18 bp):
TTTTCAAAAATTTATTTA
Found at i:510742 original size:167 final size:163
Alignment explanation
Indices: 510359--510758 Score: 414
Period size: 165 Copynumber: 2.4 Consensus size: 163
510349 TGTTTATGAA
* * * * * *
510359 TTTTAAAATTTATCAAATATCACCATTTAATTCACATTAAATTAGTTTTGAAAATTTTCTTT-TA
1 TTTTAAAATTCATC--ATAACATCATTTAATTCATAGTAAATTAGTTTTGAAAATTTTATTTAT-
* * *
510423 TTTCATGAATTTTTTATTTTTTCTTGAAATTTCTCTATTTTTGAAATACAAAATTTTCTATTCCA
63 TTTCATAAATTTTTTATTTTTTCTTGAAATTTCTCTATTTTTGAAAAACAAAATTTTCTATTCAA
* *
510488 TAAATATTTTCAAGGGGACTTTTCTCGATTTATAAT
128 TAAATATTTTCAAGGGGACTTTTCTCAATTTAAAAT
*
510524 TTTTAAAATTCATCAAATAACATCATTTAATTCATAGTAAATTAGTTTTGAAAAATTTATTTATT
1 TTTTAAAATTCATC--ATAACATCATTTAATTCATAGTAAATTAGTTTTGAAAATTTTATTTATT
* * * * *
510589 TTCA-AAAGTTTTTTATTTTTTCTTCGATATTTTTCTGTTTTTGAAAAACCAAGTTTTCTATTCA
64 TTCATAAA-TTTTTTATTTTTTCTT-GAAATTTCTCTATTTTTGAAAAACAAAATTTTCTATTCA
* * * *
510653 ATGAATGTTTTTAGGAGGGA-TCTTTCTCAATTTAAAAT
127 ATAAATATTTTCAAG-GGGACT-TTTCTCAATTTAAAAT
* ** *
510691 TTTTAAAATTCATC-TAACATTAGTATTAGACTT-ATTTTGAATTAGTTTTGAAAATTTTGATTT
1 TTTTAAAATTCATCATAACATCA-T-TTA-A-TTCATAGTAAATTAGTTTTGAAAATTTT-ATTT
510754 ATTTT
61 ATTTT
510759 ATGAGTTTTA
Statistics
Matches: 199, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
164 9 0.05
165 77 0.39
166 48 0.24
167 54 0.27
168 11 0.06
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.50
Consensus pattern (163 bp):
TTTTAAAATTCATCATAACATCATTTAATTCATAGTAAATTAGTTTTGAAAATTTTATTTATTTT
CATAAATTTTTTATTTTTTCTTGAAATTTCTCTATTTTTGAAAAACAAAATTTTCTATTCAATAA
ATATTTTCAAGGGGACTTTTCTCAATTTAAAAT
Found at i:510832 original size:153 final size:153
Alignment explanation
Indices: 510675--511082 Score: 378
Period size: 153 Copynumber: 2.7 Consensus size: 153
510665 AGGAGGGATC
* * * *
510675 TTTCTCAA-TTTAAAATTTTTAAAATTCATCTAA-CAT-TAGTATTAGACTTATTTTGAATTAGT
1 TTTCT-AAGTTTAAAATTTTTAAAATTCATCAAATAATGTAGT-TTA-ACTTATATTAAATTAGT
** * * * * *
510737 TTTGAAAATTTTGATTTATTTTATGAGTTTTAGAATTTTTCCTATTATCGAAATAAGAAGTTTTT
63 TTCAAAAAATTTAATTTATTTTATGAATTTTAGAATTTTTCCTATTATCAAAATAAGAAATTTTT
510802 TACTCCATAAATTTTTCAACAAGTTT
128 TACTCCATAAATTTTTCAACAAGTTT
* * * * *
510828 TTTCTAAGTTTATAATTTTTCAAATTCTTCAAATAATGTTGTTTAATTTATATTAAATTAGTTTC
1 TTTCTAAGTTTAAAATTTTTAAAATTCATCAAATAATGTAGTTTAACTTATATTAAATTAGTTTC
* * *
510893 AAAAAATTTAATTTATTTTATGAATTTTAGAATTTTTCCTGTTTTCAAAATACGAAATTTTTTAC
66 AAAAAATTTAATTTATTTTATGAATTTTAGAATTTTTCCTATTATCAAAATAAGAAATTTTTTAC
* * ** *** *
510958 TTCGTAAAATTTTTTGATTGGATT
131 TCCAT-AAATTTTTCAACAAGTTT
* * * * * * * *
510982 TTTCTTAGTTCAAAATTTTTAAAATTTATCAAATATTTTCA--TTAAATTCATAGTAAATCAGTT
1 TTTCTAAGTTTAAAATTTTTAAAATTCATCAAATAATGT-AGTTTAACTT-ATATTAAATTAGTT
* * *
511045 TTAAAAAATTCAATTTATTTTTTGAATTTT-GAATTTTT
64 TCAAAAAATTTAATTTATTTTATGAATTTTAGAATTTTT
511083 TCACATGCAT
Statistics
Matches: 207, Mismatches: 42, Indels: 12
0.79 0.16 0.05
Matches are distributed among these distances:
152 2 0.01
153 115 0.56
154 87 0.42
155 3 0.01
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (153 bp):
TTTCTAAGTTTAAAATTTTTAAAATTCATCAAATAATGTAGTTTAACTTATATTAAATTAGTTTC
AAAAAATTTAATTTATTTTATGAATTTTAGAATTTTTCCTATTATCAAAATAAGAAATTTTTTAC
TCCATAAATTTTTCAACAAGTTT
Found at i:511045 original size:154 final size:153
Alignment explanation
Indices: 510741--511082 Score: 375
Period size: 154 Copynumber: 2.2 Consensus size: 153
510731 ATTAGTTTTG
* * * * *
510741 AAAATTTTGATTTATTTTATGAGTTTTAGAATTTTTCCTATTATCGAAATAAGAAGTTTTTTACT
1 AAAAATTTAATTTATTTTATGAATTTTAGAATTTTTCCTATTATCAAAATAAGAAATTTTTTACT
* * * * *
510806 CCATAAATTTTTCAACAAGTTTTTTCTAAGTTTATAATTTTTCAAATTCTTCAAATAATGTTGTT
66 CCATAAATTTTTCAACAAGATTTTTCTAAGTTCAAAATTTTTAAAATTCTTCAAATAATGTTATT
* * * *
510871 TAATTTATATTAAATTAGTTTCA
131 AAATTCATAGTAAATCAGTTTCA
* * *
510894 AAAAATTTAATTTATTTTATGAATTTTAGAATTTTTCCTGTTTTCAAAATACGAAATTTTTTACT
1 AAAAATTTAATTTATTTTATGAATTTTAGAATTTTTCCTATTATCAAAATAAGAAATTTTTTACT
* * ** *** * *
510959 TCGTAAAATTTTTTGATTGGATTTTTCTTAGTTCAAAATTTTTAAAATT-TATCAAAT-ATTTTC
66 CCAT-AAATTTTTCAACAAGATTTTTCTAAGTTCAAAATTTTTAAAATTCT-TCAAATAATGTT-
*
511022 ATTAAATTCATAGTAAATCAGTTTTA
128 ATTAAATTCATAGTAAATCAGTTTCA
* *
511048 AAAAATTCAATTTATTTTTTGAATTTT-GAATTTTT
1 AAAAATTTAATTTATTTTATGAATTTTAGAATTTTT
511083 TCACATGCAT
Statistics
Matches: 157, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
153 72 0.46
154 85 0.54
ACGTcount: A:0.34, C:0.08, G:0.07, T:0.51
Consensus pattern (153 bp):
AAAAATTTAATTTATTTTATGAATTTTAGAATTTTTCCTATTATCAAAATAAGAAATTTTTTACT
CCATAAATTTTTCAACAAGATTTTTCTAAGTTCAAAATTTTTAAAATTCTTCAAATAATGTTATT
AAATTCATAGTAAATCAGTTTCA
Found at i:511240 original size:25 final size:26
Alignment explanation
Indices: 511203--511252 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
511193 TTAATTTTAA
511203 CTTTTTTTAATTTTAAA-TTTATTTT
1 CTTTTTTTAATTTTAAATTTTATTTT
511228 CTTTATTTT-ATTTTAAATTTTATTT
1 CTTT-TTTTAATTTTAAATTTTATTT
511253 GCCAAATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (26 bp):
CTTTTTTTAATTTTAAATTTTATTTT
Found at i:518103 original size:13 final size:13
Alignment explanation
Indices: 518065--518103 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
518055 CATTTTTCTT
*
518065 TGTATCGATACAT
1 TGTATCGATACAG
518078 TGTATCGATACAG
1 TGTATCGATACAG
518091 TGTATCGATACAG
1 TGTATCGATACAG
518104 GGGGATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:518266 original size:20 final size:20
Alignment explanation
Indices: 518223--518268 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
518213 AAATCTTTTG
518223 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
518244 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
518264 CAAAA
1 CAAAA
518269 CTAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:520651 original size:13 final size:13
Alignment explanation
Indices: 520633--520658 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
520623 TACACCAAGT
520633 ATGTATCGATACA
1 ATGTATCGATACA
520646 ATGTATCGATACA
1 ATGTATCGATACA
520659 CAAAAAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:524509 original size:19 final size:21
Alignment explanation
Indices: 524485--524531 Score: 64
Period size: 19 Copynumber: 2.3 Consensus size: 21
524475 ATTAGAAAAG
524485 TTTAAAA-GATCATTT-TTT-T
1 TTTAAAATGATC-TTTATTTGT
524504 TTTAAAATGATCTTTATTTGT
1 TTTAAAATGATCTTTATTTGT
524525 TTTAAAA
1 TTTAAAA
524532 AAATAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 10 0.40
20 7 0.28
21 8 0.32
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (21 bp):
TTTAAAATGATCTTTATTTGT
Found at i:532563 original size:21 final size:21
Alignment explanation
Indices: 532530--532574 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
532520 TTGCAAGTTG
*
532530 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
532552 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
532572 AAA
1 AAA
532575 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:534389 original size:15 final size:15
Alignment explanation
Indices: 534369--534399 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
534359 TAAAAATGTC
*
534369 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
534384 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
534399 C
1 C
534400 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:536660 original size:20 final size:20
Alignment explanation
Indices: 536617--536662 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
536607 AAATCTTTTG
536617 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
536638 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
536658 CAAAA
1 CAAAA
536663 CCAGCATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:539055 original size:13 final size:13
Alignment explanation
Indices: 539037--539062 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
539027 TACAGCAAGT
539037 ATGTATCGATACA
1 ATGTATCGATACA
539050 ATGTATCGATACA
1 ATGTATCGATACA
539063 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:540212 original size:23 final size:24
Alignment explanation
Indices: 540160--540205 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
540150 CCTTTAAATG
*
540160 ACAAAAAAAGTCAAAAGCAAAAGC
1 ACAAAAAAAGTCAAAAGAAAAAGC
*
540184 ACAAAAAAA-TGAAAAGAAAAAG
1 ACAAAAAAAGTCAAAAGAAAAAG
540206 TGCAAAAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.72, C:0.11, G:0.13, T:0.04
Consensus pattern (24 bp):
ACAAAAAAAGTCAAAAGAAAAAGC
Found at i:541576 original size:27 final size:27
Alignment explanation
Indices: 541537--542844 Score: 1884
Period size: 27 Copynumber: 48.0 Consensus size: 27
541527 ACTGTGACCT
* *
541537 CTTTAAAGCCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
541564 CTTTTAAGTCCACAACTCCGTTGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
541591 CTTTTAAGTCCACAACTTCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
541618 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
541645 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
541672 CTTTTAAGTCCACAAGTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
541699 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
541726 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
**
541753 CTTTTAAGTCCACAACTTTGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
* *
541781 CTTTTAAGACCACAACTCCATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
541808 CTTTTAAGTCCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
541835 CTTTTAAGTCCATAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
541863 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
541890 CTTTTAAGTCCATAACTCCGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* ** *
541917 CTTTTAAGTCCATAACTCAATGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
541945 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
541972 CTTTTAAAGTCCACAACTCCGCGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
542000 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
542027 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
542054 CTTTTAAGTCCGCAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
542081 CTTTTAAGTCCACAACTCCGTGGCATCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
** *
542109 CTTTTAAGTCCACAACTTTGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
542136 CTTTTAAAGTCCACAACTCCGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
542164 CTTTTAAGACCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
542191 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
542218 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
542246 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
542273 CTTTTAAAGTCCACAACT-C-T-GCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
542298 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
542326 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
542353 CTTTTAAGTCCACAACTTCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
542380 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
542407 CTTTTAAGGCCACAACTCCATGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
542434 CTTTTAAGACCGCAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
542461 ATTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
542488 CTTTTAAGTCCATAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
542516 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
542543 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
542570 CTTTTAAAGTCCACAACTCTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
542598 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
542625 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
542652 CTTTTAAATCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
542679 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * **
542706 CTTTTAAGACCGCAACTCTATGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* * *
542733 CTTTTAAGTCCATAACTCTGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
542761 CTTTTAAGTCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
542788 CTTTTAAAATCCACAACTCCGTGGCACT
1 CTTTT-AAGTCCACAACTCCGTGGCACC
* **
542816 CTTTTAAAATCCACAACTTTGTGGCACC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
542844 C
1 C
542845 AAAGCCCACA
Statistics
Matches: 1163, Mismatches: 103, Indels: 29
0.90 0.08 0.02
Matches are distributed among these distances:
25 23 0.02
26 1 0.00
27 827 0.71
28 312 0.27
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:541831 original size:82 final size:82
Alignment explanation
Indices: 541537--542833 Score: 1898
Period size: 82 Copynumber: 15.9 Consensus size: 82
541527 ACTGTGACCT
* * *
541537 CTTTAAAGCCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTTGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
541602 ACAACTTCGTGGCAT-C
66 ACAACTCCGTGGCATCC
* *
541618 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
541683 ACAAGTCCGTGGCAT-C
66 ACAACTCCGTGGCATCC
*
541699 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
**
541764 ACAACTTTGTGGCATCC
66 ACAACTCCGTGGCATCC
* * *
541781 CTTTTAAGACCACAACTCCATGGCACCCTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
541846 ATAACTCCGTGGCATCC
66 ACAACTCCGTGGCATCC
* * *
541863 CTTTTAAGACCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGTACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* ** *
541928 ATAACTCAATGGCATCT
66 ACAACTCCGTGGCATCC
* * *
541945 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTCCACAACTCCGCGGCACCCTTTTTAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
542010 CACAACTCCGTGGCA-CC
65 CACAACTCCGTGGCATCC
*
542027 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCGCAACTCCGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
542092 ACAACTCCGTGGCATCC
66 ACAACTCCGTGGCATCC
** * *
542109 CTTTTAAGTCCACAACTTTGTGGCATCCTTTTAAAGTCCACAACTCCGTGGCACCCTTTTAAGAC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGTC
542174 CACAACTCCGTGGCA-CC
65 CACAACTCCGTGGCATCC
* *
542191 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCATAACTCCGTGGCATCTCTTTTAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCA-CCCTTTTAAGTC
*
542256 CACAACTCTGTGGCA-CC
65 CACAACTCCGTGGCATCC
* *
542273 CTTTTAAAGTCCACAACT-C-T-GCACCCTTTTAAAGTCCACAACTCTGTGGCACCCTTTTTAGT
1 CTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTTAAGT
542335 CCACAACTCCGTGGCA-CC
64 CCACAACTCCGTGGCATCC
* *
542353 CTTTTAAGTCCACAACTTCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGGCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
*
542418 ACAACTCCATGGCAT-C
66 ACAACTCCGTGGCATCC
* * * *
542434 CTTTTAAGACCGCAACTCCGTGGCACCATTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* *
542499 ATAACTCCGTGGCATCT
66 ACAACTCCGTGGCATCC
* *
542516 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAGTC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTC
*
542581 CACAACTCTGTGGCA-CC
65 CACAACTCCGTGGCATCC
* *
542598 CTTTTTAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAATCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
542663 ACAACTCCGTGGCA-CC
66 ACAACTCCGTGGCATCC
* * * **
542679 CTTTTAAGTCCACAACTCCGTGGCATCCTTTTAAGACCGCAACTCTATGGCACCCTTTTAAGTCC
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
* * *
542744 ATAACTCTGTGGCATCT
66 ACAACTCCGTGGCATCC
* * * *
542761 CTTTTAAGTCCACAACTCTGTGGCACCCTTTTAAAATCCACAACTCCGTGGCACTCTTTTAAAAT
1 CTTTTAAGTCCACAACTCCGTGGCACCCTTTT-AAGTCCACAACTCCGTGGCACCCTTTT-AAGT
542826 CCACAACT
64 CCACAACT
542834 TTGTGGCACC
Statistics
Matches: 1099, Mismatches: 101, Indels: 29
0.89 0.08 0.02
Matches are distributed among these distances:
79 12 0.01
80 42 0.04
81 439 0.40
82 460 0.42
83 136 0.12
84 10 0.01
ACGTcount: A:0.23, C:0.34, G:0.14, T:0.29
Consensus pattern (82 bp):
CTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCCACAACTCCGTGGCACCCTTTTAAGTCC
ACAACTCCGTGGCATCC
Found at i:542885 original size:32 final size:32
Alignment explanation
Indices: 542844--543231 Score: 618
Period size: 32 Copynumber: 12.1 Consensus size: 32
542834 TTGTGGCACC
*
542844 CAAAGCCCACATAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
542876 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
542908 CAAAGCCCACACAAGTCGGTGGCAA-CCATTTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCA-TTT
*
542940 CAAAGCCCACACAAGTCGGTGGCAACCTATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
542972 CAAAGCCCACACAAGTCGGTGGCAA-CCATTTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCA-TTT
*
543004 CAAAGCCCACACAAGTCGGTGGCAACCCTTTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
543036 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
* *
543068 CAAAGCCCACACAAGTCGCTGGCAACCCATTC
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
*
543100 CAAAGCCCACATAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
*
543132 CAAAGCCCACACAAGTCGGTGGCAACCCTTTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
543164 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
* * ** ** *
543196 AAAAGCTCATGCAAGTCAATGGCAACCCTTTT
1 CAAAGCCCACACAAGTCGGTGGCAACCCATTT
543228 CAAA
1 CAAA
543232 TCACCATTTT
Statistics
Matches: 331, Mismatches: 21, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
31 5 0.02
32 322 0.97
33 4 0.01
ACGTcount: A:0.31, C:0.33, G:0.18, T:0.18
Consensus pattern (32 bp):
CAAAGCCCACACAAGTCGGTGGCAACCCATTT
Found at i:544996 original size:25 final size:24
Alignment explanation
Indices: 544964--545015 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 24
544954 AGAAAAGTTT
544964 AAAAGATCATGTT-TTT-TTTTAAAA
1 AAAAGATC-T-TTATTTGTTTTAAAA
544988 AAAATGATCTTTATTTGTTTTAAAA
1 AAAA-GATCTTTATTTGTTTTAAAA
545013 AAA
1 AAA
545016 TAAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 2 0.08
24 8 0.32
25 15 0.60
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (24 bp):
AAAAGATCTTTATTTGTTTTAAAA
Found at i:548356 original size:312 final size:311
Alignment explanation
Indices: 547791--548560 Score: 849
Period size: 312 Copynumber: 2.5 Consensus size: 311
547781 AAGGAAAAGC
* * * *
547791 GAACCTA-CGCTAAATACGTACCTTTAGCATAAAAGT-GACCCGGTGACAAACTAGGACTCAGTT
1 GAACCTATC-CTAAATACCTACCTTTAGCATAAAAGTGGACTCGGTGACAACCTAGGACTCGGTT
* * * ** * *
547854 TTAAAAAATTATGAAAATACCCCTATAGGATA-CCTTTGACTCAGAAATGTCCAAT-ACCCTTAA
65 CTAAAAAATTATGAAAATGCCCCTATA-GATATACTTTGA-TGTGAAATATCCAGTAACCC-TAA
* * * *
547917 AGGACTTAAAAATGATAATAGATATGATGAACCTATCTTAAATACCCCCTTTTGGCATAAAAACG
127 AGGACTTAAAAATGATAATAGATAGGATGAACCTATCCTAAATACCCCCGTTCGGCATAAAAACG
* * * * * * *
547982 GACCCGATGACAACTTAGGACTTAGTTCTAGAAAATTACAAAAAATGGTCTTATGGGTATACCTT
192 AACCCGATGACAACTTAGGACTCAATTCTAAAAAATTACAAAAAATAGTCCTATAGGTATACCTT
* * *
548047 CGACGTGAAAG-TATCCA-AGTAAC-CTTAAAAGACTTAAAAAAGTCATAGCTGGGGT
257 CAACGTG-AAGCTATCCAGA-TAACTC-TAAAAGACTTAAAAAAGTCATAGCTAGGAT
** *
548102 GAACCTATCCTAAATACCTACCTTCGGCATAAAAGTGGACTCGGTGTCAACCTAGGACTCGGTTC
1 GAACCTATCCTAAATACCTACCTTTAGCATAAAAGTGGACTCGGTGACAACCTAGGACTCGGTTC
** *
548167 TAAAAAATTATGAAAATGGTCTTATAGATATACTTTCGATGTGAAAGTATCACAGTAACCCTAAA
66 TAAAAAATTATGAAAATGCCCCTATAGATATACTTT-GATGTGAAA-TATC-CAGTAACCCTAAA
* * * * * * * *
548232 GGACTTAAAAA-GATTATAGCTAGGGTGAACTTATCCTAAATACTCGCGTTCGGTATAAAAGCGA
128 GGACTTAAAAATGATAATAGATAGGATGAACCTATCCTAAATACCCCCGTTCGGCATAAAAACGA
** * *
548296 ACCCGATGGTAACTTAGGACTCAATTTTAAAAAATTAC-GAAAATAGTCCTATAGGTATACCTTC
193 ACCCGATGACAACTTAGGACTCAATTCTAAAAAATTACAAAAAATAGTCCTATAGGTATACCTTC
* * * *
548360 AACGTGAAGCTATCCCGATAACTCTAAAGGACTTAAAAATGTTATAGCTAGGAT
258 AACGTGAAGCTATCCAGATAACTCTAAAAGACTTAAAAAAGTCATAGCTAGGAT
* * *
548414 GAACCTATCCTAAATACCCACATTTAGCATAAAAGCGGACTCGGTGACAACCTAGGACTCGGTTC
1 GAACCTATCCTAAATACCTACCTTTAGCATAAAAGTGGACTCGGTGACAACCTAGGACTCGGTTC
* * * *
548479 TAAAAAATTATGAAAATGCCCCTATAGGTATACCTTTGACGTGAAAATATCCCGGTAACCCTAAT
66 TAAAAAATTATGAAAATGCCCCTATAGATATA-CTTTGATGTG-AAATAT-CCAGTAACCCTAAA
*
548544 GGACACT-AAAATGATAA
128 GGAC-TTAAAAATGATAA
548561 GTAATAATGA
Statistics
Matches: 382, Mismatches: 62, Indels: 28
0.81 0.13 0.06
Matches are distributed among these distances:
311 38 0.10
312 230 0.60
313 92 0.24
314 18 0.05
315 4 0.01
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.26
Consensus pattern (311 bp):
GAACCTATCCTAAATACCTACCTTTAGCATAAAAGTGGACTCGGTGACAACCTAGGACTCGGTTC
TAAAAAATTATGAAAATGCCCCTATAGATATACTTTGATGTGAAATATCCAGTAACCCTAAAGGA
CTTAAAAATGATAATAGATAGGATGAACCTATCCTAAATACCCCCGTTCGGCATAAAAACGAACC
CGATGACAACTTAGGACTCAATTCTAAAAAATTACAAAAAATAGTCCTATAGGTATACCTTCAAC
GTGAAGCTATCCAGATAACTCTAAAAGACTTAAAAAAGTCATAGCTAGGAT
Found at i:548556 original size:156 final size:157
Alignment explanation
Indices: 547791--548547 Score: 694
Period size: 156 Copynumber: 4.9 Consensus size: 157
547781 AAGGAAAAGC
** * * *
547791 GAACCTA-CGCTAAATACGTACCTTTAGCATAAAAG-TGACCCGGTGACAAACTAGGACTCAGTT
1 GAACCTATC-CTAAATACCCACCTTTGGCATAAAAGCGGACCCGGTGACAACCTAGGACTCAGTT
* * * * * *
547854 TTAAAAAATTATGAAAATACCCCTATAGG-ATACCTTTGAC-TCAGAAATGT-CCAAT-ACCCTT
65 CTAAAAAATTATGAAAATGCTCCTATAGGTATACCTTTGACGTGA-AAATATCCCAGTAACCC-T
* * *
547915 AAAGGACTTAAAAATGATAATAGATATGAT
128 AAAGGACTTAAAAATGATTATAGCTAGGAT
* * * * *
547945 GAACCTATCTTAAATACCC-CCTTTTGGCATAAAAACGGACCCGATGACAACTTAGGACTTAGTT
1 GAACCTATCCTAAATACCCACC-TTTGGCATAAAAGCGGACCCGGTGACAACCTAGGACTCAGTT
* ** * * * * * * *
548009 CTAGAAAATTACAAAAAATGGTCTTATGGGTATACCTTCGACGTGAAAGTATCCAAGTAACCTTA
65 CTAAAAAATTA-TGAAAATGCTCCTATAGGTATACCTTTGACGTGAAAATATCCCAGTAACCCTA
* * * * *
548074 AAAGACTTAAAAAAG-TCATAGCTGGGGT
129 AAGGACTTAAAAATGATTATAGCTAGGAT
* * * * * *
548102 GAACCTATCCTAAATACCTACCTTCGGCATAAAAGTGGACTCGGTGTCAACCTAGGACTCGGTTC
1 GAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACCCGGTGACAACCTAGGACTCAGTTC
* * * * * *
548167 TAAAAAATTATGAAAATGGTCTTATAGATATA-CTTTCGATGTGAAAGTATCACAGTAACCCTAA
66 TAAAAAATTATGAAAATGCTCCTATAGGTATACCTTT-GACGTGAAAATATCCCAGTAACCCTAA
*
548231 AGGACTTAAAAA-GATTATAGCTAGGGT
130 AGGACTTAAAAATGATTATAGCTAGGAT
* * * * * * * * ** * * *
548258 GAACTTATCCTAAATACTCGCGTTCGGTATAAAAGCGAACCCGATGGTAACTTAGGACTCAATTT
1 GAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACCCGGTGACAACCTAGGACTCAGTTC
* ** ** *
548323 TAAAAAATTACGAAAATAG-TCCTATAGGTATACCTTCAACGTGAAGCTATCCC-GATAACTCTA
66 TAAAAAATTATGAAAAT-GCTCCTATAGGTATACCTTTGACGTGAAAATATCCCAG-TAACCCTA
548386 AAGGACTTAAAAATG-TTATAGCTAGGAT
129 AAGGACTTAAAAATGATTATAGCTAGGAT
* * * *
548414 GAACCTATCCTAAATACCCACATTTAGCATAAAAGCGGACTCGGTGACAACCTAGGACTCGGTTC
1 GAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACCCGGTGACAACCTAGGACTCAGTTC
* * *
548479 TAAAAAATTATGAAAATGCCCCTATAGGTATACCTTTGACGTGAAAATATCCCGGTAACCCTAAT
66 TAAAAAATTATGAAAATGCTCCTATAGGTATACCTTTGACGTGAAAATATCCCAGTAACCCTAAA
548544 GGAC
131 GGAC
548548 ACTAAAATGA
Statistics
Matches: 478, Mismatches: 108, Indels: 32
0.77 0.17 0.05
Matches are distributed among these distances:
153 2 0.00
154 25 0.05
155 39 0.08
156 299 0.63
157 88 0.18
158 22 0.05
159 3 0.01
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (157 bp):
GAACCTATCCTAAATACCCACCTTTGGCATAAAAGCGGACCCGGTGACAACCTAGGACTCAGTTC
TAAAAAATTATGAAAATGCTCCTATAGGTATACCTTTGACGTGAAAATATCCCAGTAACCCTAAA
GGACTTAAAAATGATTATAGCTAGGAT
Found at i:549642 original size:25 final size:24
Alignment explanation
Indices: 549606--549660 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
549596 TTTTGTCATC
*
549606 CTTTTT-CATTTTTTTATTTCTTTTT
1 CTTTTTACATTTTTTGA-TT-TTTTT
549631 CTTTTTAC-TTTTTTGATTTTTTT
1 CTTTTTACATTTTTTGATTTTTTT
549654 CTTTTTA
1 CTTTTTA
549661 TTTAATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 12 0.43
24 2 0.07
25 13 0.46
26 1 0.04
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.78
Consensus pattern (24 bp):
CTTTTTACATTTTTTGATTTTTTT
Found at i:549652 original size:23 final size:24
Alignment explanation
Indices: 549626--549674 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
549616 TTTTTATTTC
549626 TTTTTCTTTTTACTT-TTTTGATT
1 TTTTTCTTTTTACTTATTTTGATT
*
549649 TTTTTCTTTTTATTTAATTTTGATT
1 TTTTTCTTTTTACTT-ATTTTGATT
549674 T
1 T
549675 GATTTAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.61
25 9 0.39
ACGTcount: A:0.12, C:0.06, G:0.04, T:0.78
Consensus pattern (24 bp):
TTTTTCTTTTTACTTATTTTGATT
Found at i:550524 original size:166 final size:163
Alignment explanation
Indices: 550027--550534 Score: 497
Period size: 164 Copynumber: 3.1 Consensus size: 163
550017 ATGAGAGTTT
* * * * * ** *
550027 AATAACAATATTAGATGAATTTTAAAAATTTTAAAA-CGATAAAAATGCCTCCGAAAACATTTAT
1 AATAATAATATTTGATGAATTTTAAAAA--TTAAAACCAAGAAAAATCCCTCTAAAAACATTTAC
* * * * * *
550091 GGAGTAGAAAACTCCAT-TTTTTTGAAACATGAGAATTTTGAA-GAAAAATTCAAAGCTCATGAT
64 GGAGTAGAAAACTCCATATTTTAT-AAATAAGAGAA-TTTCAAGGAAAAA-TGAAAACTCATGA-
* * * *
550154 A-ATAAATTAATTTTTCAAATCA-AATGTAATATGAATTA
125 AGATGAATAAATTTTTCAAA-AATAATTTAATATGAATTA
* * ** * *
550192 AATAATAATATTTGATGATTTTTAAAAATTGAAACCAAGAAAAATCATTCTAAAAATATTTACAG
1 AATAATAATATTTGATGAATTTTAAAAATTAAAACCAAGAAAAATCCCTCTAAAAACATTTACGG
* * * * *
550257 AGTAGAAAACTTCGTATTTCAAAAATAAGAGAGTTTCAAGGAAAAAATGAAAACTCATGAAGATG
66 AGTAGAAAACTCCATATTTTATAAATAAGAGAATTTCAAGG-AAAAATGAAAACTCATGAAGATG
* * * * * * *
550322 AGTGAATTTTTGAAAACTGATTTTACATGAATTA
130 AATAAATTTTTCAAAAATAATTTAATATGAATTA
* * *
550356 AATAGTAATTTTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCTTAAAACATTTACG
1 AATAATAATATTTGATGAATTTTAAAAATT-AAAACCAAGAAAAATCCCTCTAAAAACATTTACG
*
550421 GAGTAAAAAACTCCATATTTTATAAATAAAGAGAATTTCAAGGAAAAATGAAAAACTCATGAAGA
65 GAGTAGAAAACTCCATATTTTATAAAT-AAGAGAATTTCAAGGAAAAATG-AAAACTCATGAAGA
550486 TGAATAAATTTTTCAAAAATAATTTAATAGTG-ATTA
128 TGAATAAATTTTTCAAAAATAATTTAATA-TGAATTA
*
550522 AATTATAATATTT
1 AATAATAATATTT
550535 AAAGAATGTT
Statistics
Matches: 273, Mismatches: 60, Indels: 19
0.78 0.17 0.05
Matches are distributed among these distances:
163 11 0.04
164 106 0.39
165 90 0.33
166 64 0.23
167 2 0.01
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (163 bp):
AATAATAATATTTGATGAATTTTAAAAATTAAAACCAAGAAAAATCCCTCTAAAAACATTTACGG
AGTAGAAAACTCCATATTTTATAAATAAGAGAATTTCAAGGAAAAATGAAAACTCATGAAGATGA
ATAAATTTTTCAAAAATAATTTAATATGAATTA
Found at i:555878 original size:52 final size:52
Alignment explanation
Indices: 555733--555858 Score: 234
Period size: 52 Copynumber: 2.4 Consensus size: 52
555723 AATATGAAAT
*
555733 TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
*
555785 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGTAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
555837 TTTGCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
555859 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:555885 original size:13 final size:13
Alignment explanation
Indices: 555867--555891 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
555857 CAAAGATCAG
555867 TGTATCGATACAA
1 TGTATCGATACAA
555880 TGTATCGATACA
1 TGTATCGATACA
555892 TTTAAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:557136 original size:141 final size:142
Alignment explanation
Indices: 556809--557332 Score: 567
Period size: 141 Copynumber: 3.7 Consensus size: 142
556799 CTTAGGAATG
* * * * *
556809 TTAAAGATGAAGGTACCAATGTGCTGATTCAAGGCCATCGACATTGGACTTAAAAGATGACAAAG
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGAAGGTG---AAG
*
556874 GCGCCAATATGCTGATTCAAGGCTAGCGATATTGGGTTTCAAGTTGAAGGTGCCAATGTGCTGAT
63 GTGCCAATATGCTGATTCAAGGCTAGCGATATTGGG---C---TTGAAGGTGCCAATGTGCTGAT
556939 TCAAGGCCAGCGACATTGGAC
122 TCAAGGCCAGCGACATTGGAC
* *
556960 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-GAAGGTGAAGATG
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGAAGGTGAAGGTG
* * * *
557024 CCAATATGCTGATTCACGACCAACGATATTGGGCTTGAAGGTGCCAATGTGCTGATTCAAGGCCA
66 CCAATATGCTGATTCAAGGCTAGCGATATTGGGCTTGAAGGTGCCAATGTGCTGATTCAAGGCCA
*
557089 GCTACATTGGAC
131 GCGACATTGGAC
* * * *
557101 TTAAAGATGAAGGTGCCAATATGCTGGTTCAAGGCCAGCGACATTGGTCTTAAAGATGGTTAAGG
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTT--AGAAGGTGAAGG
* * * * * *
557166 TGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTCTTCAAGGTGTCAATATGCTGATTCAAGGC
64 TGCCAATATGCTGATTCAAGGCTAGCGATATTGGGCTTGAAGGTGCCAATGTGCTGATTCAAGGC
* *
557231 CAGCGATATCGGAC
129 CAGCGACATTGGAC
* * * ** * * * *
557245 TTTAAGAT----GT--CAATATGCTGATTCAAGGCTAGCGATATTGGGTTTAAAAGATAAAGGCG
1 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGAAGGTGAAGGTG
* * *
557304 CCAATATGCTGGTTTAAGGCCAGCGATAT
66 CCAATATGCTGATTCAAGGCTAGCGATAT
557333 CAGACTTAGA
Statistics
Matches: 322, Mismatches: 48, Indels: 21
0.82 0.12 0.05
Matches are distributed among these distances:
136 33 0.10
138 30 0.09
140 2 0.01
141 90 0.28
144 82 0.25
147 33 0.10
150 5 0.02
151 47 0.15
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (142 bp):
TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGACATTGGACTTAGAAGGTGAAGGTG
CCAATATGCTGATTCAAGGCTAGCGATATTGGGCTTGAAGGTGCCAATGTGCTGATTCAAGGCCA
GCGACATTGGAC
Found at i:557193 original size:52 final size:49
Alignment explanation
Indices: 556809--557329 Score: 434
Period size: 49 Copynumber: 10.8 Consensus size: 49
556799 CTTAGGAATG
* * *
556809 TTAAAGATGAAGGTACCAATGTGCTGATTCAAGGCCATCGACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
* * * *
556858 TTAAAAGATGACAAAGGCGCCAATATGCTGATTCAAGGCTAGCGATATTGGGT-
1 TT-AAAGATG---AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGTC
* * *
556911 TTCAAGTTGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
* * *
556960 TTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
* * * * * * * * *
557009 TTGAAGGTGAAGATGCCAATATGCTGATTCACGACCAACGATATTGGGC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
* *
557058 -T-----TGAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
* *
557101 TTAAAGATGAAGGTGCCAATATGCTGGTTCAAGGCCAGCGACATTGGTC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
*
557150 TTAAAGATGGTTAAGGTGCCAATGTGCTGATTCAAGGCTAGCGACATTGGTC
1 TTAAAGAT-G--AAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
* * * * * *
557202 -T-----TCAAGGTGTCAATATGCTGATTCAAGGCCAGCGATATCGGAC
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
* * * *
557245 TTTAAGAT----GT--CAATATGCTGATTCAAGGCTAGCGATATTGGGT-
1 TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATT-GGTC
* * * * *
557288 TTAAAAGATAAAGGCGCCAATATGCTGGTTTAAGGCCAGCGA
1 TT-AAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
557330 TATCAGACTT
Statistics
Matches: 388, Mismatches: 55, Indels: 57
0.78 0.11 0.11
Matches are distributed among these distances:
43 97 0.25
44 9 0.02
45 2 0.01
46 1 0.00
48 4 0.01
49 168 0.43
50 30 0.08
51 1 0.00
52 42 0.11
53 32 0.08
54 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.26
Consensus pattern (49 bp):
TTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
Found at i:557228 original size:21 final size:21
Alignment explanation
Indices: 557202--557272 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
557192 GACATTGGTC
557202 TTCAAGGTGTCAATATGCTGA
1 TTCAAGGTGTCAATATGCTGA
* * *
557223 TTCAAGGCCAG-CGATAT-CGGA
1 TTCAAGG--TGTCAATATGCTGA
* *
557244 CTTTAAGATGTCAATATGCTGA
1 -TTCAAGGTGTCAATATGCTGA
557266 TTCAAGG
1 TTCAAGG
557273 CTAGCGATAT
Statistics
Matches: 35, Mismatches: 10, Indels: 10
0.64 0.18 0.18
Matches are distributed among these distances:
20 1 0.03
21 20 0.57
22 13 0.37
23 1 0.03
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.30
Consensus pattern (21 bp):
TTCAAGGTGTCAATATGCTGA
Found at i:557419 original size:28 final size:28
Alignment explanation
Indices: 557357--557628 Score: 219
Period size: 28 Copynumber: 9.4 Consensus size: 28
557347 GATGCCACCA
**
557357 ACTTGTGTGGACTTTTGAAAGGGTTG-CACCA
1 ACTTGTG-GG-CTTTT-AAA-GGTTGCCACTG
*
557388 ACTTGTGTGCTTTTAAAGGTTGCCACTG
1 ACTTGTGGGCTTTTAAAGGTTGCCACTG
* *
557416 ACTTGTGGGCTTTTGAAAGGATTG-CATTA
1 ACTTGTGGGCTTTT-AAAGG-TTGCCACTG
* *
557445 ACTTGTGTGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTAAAGGTTGCCACTG
* *
557473 ACTTGTGGGCTTTTGAAGGTTGCTACTG
1 ACTTGTGGGCTTTTAAAGGTTGCCACTG
* *
557501 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTT--AAAGGTTGCCACTG
* ** *
557531 ACTTGTAGGCTTCGGAAAAGGGTGCCACT-
1 ACTTGTGGGCTT--TTAAAGGTTGCCACTG
* *
557560 AGTTTGTGGGC-TTTGAAGGTTGCCACTG
1 A-CTTGTGGGCTTTTAAAGGTTGCCACTG
* * * *
557588 ACTTGTGGACTTTGAAAAAGATGCCACTG
1 ACTTGTGGGCTTT-TAAAGGTTGCCACTG
557617 ACTTGTGGGCTT
1 ACTTGTGGGCTT
557629 CGAAAAAGAT
Statistics
Matches: 197, Mismatches: 32, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
27 26 0.13
28 69 0.35
29 50 0.25
30 45 0.23
31 7 0.04
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.34
Consensus pattern (28 bp):
ACTTGTGGGCTTTTAAAGGTTGCCACTG
Found at i:557441 original size:57 final size:56
Alignment explanation
Indices: 557357--557628 Score: 253
Period size: 57 Copynumber: 4.7 Consensus size: 56
557347 GATGCCACCA
* *
557357 ACTTGTGTGGACTTTTGAAAGGGTTGCACCAACTTGTGTGCTTTTAAAGGTTGCCACTG
1 ACTTGTG-GG-CTTTTGAAA-GGTTGCACTAACTTGTGGGCTTTTAAAGGTTGCCACTG
* * *
557416 ACTTGTGGGCTTTTGAAAGGATTGCATTAACTTGTGTGCTTTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTGAAAGG-TTGCACTAACTTGTGGGCTTTTAAAGGTTGCCACTG
* * *
557473 ACTTGTGGGCTTTTG-AAGGTTGCTACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGCTTTTGAAAGGTTGC-ACTAACTTGTGGGCTTTT--AAAGGTTGCCACTG
* ** * ** *
557531 ACTTGTAGGCTTCGGAAAAGGGTGCCACTAGTTTGTGGGC-TTTGAAGGTTGCCACTG
1 ACTTGTGGGCTTTTG-AAAGGTTG-CACTAACTTGTGGGCTTTTAAAGGTTGCCACTG
* * * *
557588 ACTTGTGGAC-TTTGAAAAAGATGCCACTGACTTGTGGGCTT
1 ACTTGTGGGCTTTTG-AAAGGTTG-CACTAACTTGTGGGCTT
557629 CGAAAAAGAT
Statistics
Matches: 177, Mismatches: 28, Indels: 18
0.79 0.13 0.08
Matches are distributed among these distances:
55 4 0.02
56 43 0.24
57 77 0.44
58 25 0.14
59 10 0.06
60 17 0.10
61 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.34
Consensus pattern (56 bp):
ACTTGTGGGCTTTTGAAAGGTTGCACTAACTTGTGGGCTTTTAAAGGTTGCCACTG
Found at i:557621 original size:29 final size:29
Alignment explanation
Indices: 557388--557658 Score: 195
Period size: 29 Copynumber: 9.4 Consensus size: 29
557378 GGTTGCACCA
* * *
557388 ACTTGTGTGCTTT-TAAAGGTTGCCACTG
1 ACTTGTGGGCTTTGAAAAGGATGCCACTG
* *
557416 ACTTGTGGGCTTTTG-AAAGGATTG-CATTA
1 ACTTGTGGGC-TTTGAAAAGGA-TGCCACTG
* *
557445 ACTTGTGTGCTTTTG--AAGGTTGCCACTG
1 ACTTGTGGGC-TTTGAAAAGGATGCCACTG
* *
557473 ACTTGTGGGCTTTTG--AAGGTTGCTACTG
1 ACTTGTGGGC-TTTGAAAAGGATGCCACTG
* *
557501 ACTTGTGGGCTTTTGAAAAGGGTGCCACTA
1 ACTTGTGGGC-TTTGAAAAGGATGCCACTG
* * *
557531 ACTTGTAGGCTTCGGAAAAGGGTGCCACT-
1 ACTTGTGGGCTT-TGAAAAGGATGCCACTG
* *
557560 AGTTTGTGGGCTTTG--AAGGTTGCCACTG
1 A-CTTGTGGGCTTTGAAAAGGATGCCACTG
* *
557588 ACTTGTGGACTTTGAAAAAGATGCCACTG
1 ACTTGTGGGCTTTGAAAAGGATGCCACTG
* * *
557617 ACTTGTGGGCTTCGAAAAAGATGTCACT-
1 ACTTGTGGGCTTTGAAAAGGATGCCACTG
*
557645 AGTTTGTGGGCTTT
1 A-CTTGTGGGCTTT
557659 TGAAGGGTGA
Statistics
Matches: 203, Mismatches: 28, Indels: 23
0.80 0.11 0.09
Matches are distributed among these distances:
27 24 0.12
28 59 0.29
29 75 0.37
30 45 0.22
ACGTcount: A:0.21, C:0.16, G:0.29, T:0.34
Consensus pattern (29 bp):
ACTTGTGGGCTTTGAAAAGGATGCCACTG
Found at i:557636 original size:86 final size:87
Alignment explanation
Indices: 557390--557664 Score: 287
Period size: 85 Copynumber: 3.2 Consensus size: 87
557380 TTGCACCAAC
* * * * *
557390 TTGTGTGCTTTTAAAGGTTGCCACTGACTTGTGGGCTTTTG-AAAGGATTG-CATTAACTTGT-G
1 TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGACTTTTGAAAAAGA-TGCCACTAACTTGTAG
* * * *
557452 TGCTTTTG--AAGGTTGCCACT-GAC
65 -GC-TTCGAAAAAGATGCCACTAG-T
* * * *
557475 TTGTGGGCTTTTGAAGGTTGCTACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTAGG
1 TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGACTTTTGAAAAAGATGCCACTAACTTGTAGG
* *
557540 CTTCGGAAAAGGGTGCCACTAGT
66 CTTC-GAAAAAGATGCCACTAGT
* *
557563 TTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGAC-TTTGAAAAAGATGCCACTGACTTGTGGG
1 TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGACTTTTGAAAAAGATGCCACTAACTTGTAGG
*
557626 CTTCGAAAAAGATGTCACTAGT
66 CTTCGAAAAAGATGCCACTAGT
557648 TTGTGGGCTTTTGAAGG
1 TTGTGGGCTTTTGAAGG
557665 GTGAGGAATG
Statistics
Matches: 165, Mismatches: 17, Indels: 15
0.84 0.09 0.08
Matches are distributed among these distances:
85 65 0.39
86 54 0.33
87 26 0.16
88 19 0.12
89 1 0.01
ACGTcount: A:0.21, C:0.15, G:0.30, T:0.34
Consensus pattern (87 bp):
TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGACTTTTGAAAAAGATGCCACTAACTTGTAGG
CTTCGAAAAAGATGCCACTAGT
Found at i:559105 original size:1 final size:1
Alignment explanation
Indices: 559101--559193 Score: 69
Period size: 1 Copynumber: 93.0 Consensus size: 1
559091 CTTTTTGTTG
* * * * * * * * * *
559101 TTTTTTTGTTTTGTTTTTGTTTTTGTTGTTTTTTTTTCTTCTTTTTTTTTGTTTTTTTGTTTATT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
559166 TTTTGTTGTTTTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
559194 GCGGAGGACG
Statistics
Matches: 66, Mismatches: 26, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 66 1.00
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (1 bp):
T
Found at i:559108 original size:11 final size:10
Alignment explanation
Indices: 559092--559190 Score: 96
Period size: 11 Copynumber: 9.5 Consensus size: 10
559082 ATCCGGACCC
559092 TTTTTGTTGTT
1 TTTTTGTT-TT
559103 TTTTTGTTTT
1 TTTTTGTTTT
559113 GTTTTTG-TTT
1 -TTTTTGTTTT
*
559123 TTGTTGTTTT
1 TTTTTGTTTT
*
559133 TTTTTCTTCTT
1 TTTTTGTT-TT
559144 TTTTT-TTGTT
1 TTTTTGTT-TT
559154 TTTTTGTTTAT
1 TTTTTGTTT-T
559165 TTTTTGTTGTT
1 TTTTTGTT-TT
559176 TTTTT-TTTCT
1 TTTTTGTTT-T
559186 TTTTT
1 TTTTT
559191 TTTGCGGAGG
Statistics
Matches: 77, Mismatches: 4, Indels: 15
0.80 0.04 0.16
Matches are distributed among these distances:
9 6 0.08
10 32 0.42
11 38 0.49
12 1 0.01
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:559137 original size:32 final size:32
Alignment explanation
Indices: 559101--559191 Score: 114
Period size: 32 Copynumber: 2.8 Consensus size: 32
559091 CTTTTTGTTG
559101 TTTTT-TTGTTTTGTTTTTGTTTTTGTTGTTT-T
1 TTTTTCTTGTTTT-TTTTTGTTTTT-TTGTTTAT
*
559133 TTTTTCTTCTTTTTTTTTGTTTTTTTGTTTAT
1 TTTTTCTTGTTTTTTTTTGTTTTTTTGTTTAT
* *
559165 TTTTTGTTGTTTTTTTTTTCTTTTTTT
1 TTTTTCTTG-TTTTTTTTTGTTTTTTT
559192 TTGCGGAGGA
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
31 6 0.12
32 24 0.46
33 22 0.42
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (32 bp):
TTTTTCTTGTTTTTTTTTGTTTTTTTGTTTAT
Found at i:559149 original size:43 final size:43
Alignment explanation
Indices: 559092--559194 Score: 138
Period size: 43 Copynumber: 2.4 Consensus size: 43
559082 ATCCGGACCC
*
559092 TTTTTGTTGTTTTTTTGTTTTGTT-TTT-GTTTTTGTTGTTTTTT
1 TTTTTCTT-TTTTTTTGTTTTGTTGTTTAGTTTTTGTTG-TTTTT
* *
559135 TTTCTTCTTTTTTTTTGTTTTTTTGTTTATTTTTTGTTGTTTTT
1 TTT-TTCTTTTTTTTTGTTTTGTTGTTTAGTTTTTGTTGTTTTT
559179 TTTTTCTTTTTTTTTG
1 TTTTTCTTTTTTTTTG
559195 CGGAGGACGC
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
43 30 0.56
44 15 0.28
45 9 0.17
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (43 bp):
TTTTTCTTTTTTTTTGTTTTGTTGTTTAGTTTTTGTTGTTTTT
Found at i:559153 original size:51 final size:45
Alignment explanation
Indices: 559101--559193 Score: 138
Period size: 45 Copynumber: 2.1 Consensus size: 45
559091 CTTTTTGTTG
* *
559101 TTTTTTTGTTTTGTT-TTT-GTTTTTGTTG-TTTTTTTTTCTTCTT
1 TTTTTTTGTTTTTTTGTTTATTTTTTGTTGTTTTTTTTTTCTT-TT
559144 TTTTTTTGTTTTTTTGTTTATTTTTTGTTGTTTTTTTTTTCTTTT
1 TTTTTTTGTTTTTTTGTTTATTTTTTGTTGTTTTTTTTTTCTTTT
559189 TTTTT
1 TTTTT
559194 GCGGAGGACG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 14 0.31
44 3 0.07
45 16 0.36
46 12 0.27
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.86
Consensus pattern (45 bp):
TTTTTTTGTTTTTTTGTTTATTTTTTGTTGTTTTTTTTTTCTTTT
Found at i:572971 original size:52 final size:52
Alignment explanation
Indices: 572896--573021 Score: 234
Period size: 52 Copynumber: 2.4 Consensus size: 52
572886 AAAATGAAAT
572896 TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
*
572948 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
*
573000 TTTTCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
573022 AAGACCAGTG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
Found at i:573032 original size:52 final size:52
Alignment explanation
Indices: 572896--573041 Score: 186
Period size: 52 Copynumber: 2.8 Consensus size: 52
572886 AAAATGAAAT
*** * *
572896 TTTGCCTGCATGTATCGATACATTTCATAATGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACAAGACACAGTGTATCGATACATCTGGGCAAA
*** *
572948 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACAAGACACAGTGTATCGATACATCTGGGCAAA
*
573000 TTTTCCTGCATGTATCGATACAAAGAC-CAGTGTATCGATACA
1 TTTGCCTGCATGTATCGATAC-AAGACACAGTGTATCGATACA
573042 ATGTTGTCGT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
52 85 0.98
53 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACAAGACACAGTGTATCGATACATCTGGGCAAA
Found at i:576193 original size:52 final size:52
Alignment explanation
Indices: 576108--576253 Score: 224
Period size: 52 Copynumber: 2.8 Consensus size: 52
576098 ATATGAAAAG
* *
576108 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
576160 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
576212 TTGCCTGCATGTATCGATACA--AAGATCAATGTATCGATACAT
1 TTGCCTGCATGTATCGATACATTTA-AT-AATGTATCGATACAT
576254 TTTTTGGCAG
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:576312 original size:13 final size:13
Alignment explanation
Indices: 576294--576318 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
576284 TAAAAAAATA
576294 TGTATCGATACAT
1 TGTATCGATACAT
576307 TGTATCGATACA
1 TGTATCGATACA
576319 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:577111 original size:52 final size:52
Alignment explanation
Indices: 577009--577607 Score: 252
Period size: 43 Copynumber: 11.8 Consensus size: 52
576999 GATATTGGGT
* * * * *
577009 TTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCACGGTCAGCGACATTAGAC
1 TTAAAGATGAG-AAAA--ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * **
577064 TTGAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAACAACATTGGGTT
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATT-GGAC
** * *
577117 TTAAAGATGATG-AAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGAC
1 TTAAAGATGA-GAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * ** ** *
577169 TTAAAGATGAAGATGAGAAAAGTGATAAAGATGCCAAT-ATGTTGATTCACGGCCAACGATATTG
1 TTAAAGAT---GA-GA-AAAA-TGCCAATG-TG-C--TGAT-TCAAGGC-CAG-CAAC---ATTG
*
577233 GGC
50 GAC
* * * * *
577236 TTAAAGATGAGAAAAAGGATGTCAATGTGCTAATTCAAGGCTAGCTACATTGAAC
1 TTAAAGATGAG-AAAA--ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * * *
577291 TTAAAGATG-GAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAA-ATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * *
577343 TT-AA-A-G-G-----TGCCAATGTGCTAATTTAAGGCC-GCTACATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* * * *
577385 TTAAAGA--AG-AAGATGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
* *
577434 TT-AA-A-G-G-----TGCCAATGTGTTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** * * *
577477 TTAAAGAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
*
577526 TT-AA-A-G-G-----TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGAC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
** *
577569 TTAAAGA--AG-AAGGTGCCAATATGCTGATTCAAGGCCAGC
1 TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGC
577608 TATATTGGGC
Statistics
Matches: 430, Mismatches: 66, Indels: 102
0.72 0.11 0.17
Matches are distributed among these distances:
42 13 0.03
43 93 0.22
44 6 0.01
45 3 0.01
47 3 0.01
48 24 0.06
49 75 0.17
50 1 0.00
51 2 0.00
52 71 0.17
53 45 0.10
54 6 0.01
55 28 0.07
57 2 0.00
58 7 0.02
59 3 0.01
60 5 0.01
61 4 0.01
62 5 0.01
63 8 0.02
64 11 0.03
65 1 0.00
67 14 0.03
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (52 bp):
TTAAAGATGAGAAAAATGCCAATGTGCTGATTCAAGGCCAGCAACATTGGAC
Found at i:577241 original size:67 final size:68
Alignment explanation
Indices: 577119--577245 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
577109 ATTGGGTTTT
* * *
577119 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
577184 AGA
66 AGA
* * * *
577187 AAAG-TGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
577246 GAAAAAGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.13, G:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:577313 original size:227 final size:228
Alignment explanation
Indices: 576904--577330 Score: 605
Period size: 227 Copynumber: 1.9 Consensus size: 228
576894 GTCTCGCAGT
* * * *
576904 GTGCCACTATGCAGATTCAAGGCCTACCACACTGGACTTAAAGATGATGAGGATGAAGAGCGATA
1 GTGCCAATATGCAGATTCAAGGCCTACAACACTGGACTTAAAGATGAAGAGGATGAAAAGCGATA
*
576969 AAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGTTTAAAGATGAGAAAAAGGATGTCAA
66 AAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAA
* * * *
577034 TGTGCTGATTCACGGTCAGCGACATTAGACTTGAAGATGAGAAAAATGCCAATGTGCTGATTCAA
131 TGTGCTAATTCAAGGTCAGCGACATTAGACTTAAAGATGAGAAAAATGCCAATATGCTGATTCAA
577099 GGCCAACAACATTGGGTTTTAAAGATGATGAAG
196 GGCCAACAACATTGGGTTTTAAAGATGATGAAG
* * * * *
577132 GTGCCAATATGCTGATTCAAGGCC-AGCAATATTGGACTTAAAGATGAAGATGA-GAAAAGTGAT
1 GTGCCAATATGCAGATTCAAGGCCTA-CAACACTGGACTTAAAGATGAAGAGGATGAAAAGCGAT
* *
577195 AAAGATG-CCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTC
65 AAA-AGGACCAATACGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTC
* *
577259 AATGTGCTAATTCAAGG-CTAGCTACATT-GAACTTAAAGATG-GAAAAGGTGCCAATATGCTGA
129 AATGTGCTAATTCAAGGTC-AGCGACATTAG-ACTTAAAGATGAGAAAA-ATGCCAATATGCTGA
577321 TTCAAGGCCA
191 TTCAAGGCCA
577331 GCTATATTGG
Statistics
Matches: 176, Mismatches: 18, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
226 7 0.04
227 123 0.70
228 46 0.26
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.23
Consensus pattern (228 bp):
GTGCCAATATGCAGATTCAAGGCCTACAACACTGGACTTAAAGATGAAGAGGATGAAAAGCGATA
AAAGGACCAATACGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATGTCAA
TGTGCTAATTCAAGGTCAGCGACATTAGACTTAAAGATGAGAAAAATGCCAATATGCTGATTCAA
GGCCAACAACATTGGGTTTTAAAGATGATGAAG
Found at i:577439 original size:49 final size:48
Alignment explanation
Indices: 577258--577620 Score: 391
Period size: 43 Copynumber: 7.8 Consensus size: 48
577248 AAAAGGATGT
* * * * * *
577258 CAATGTGCTAATTCAAGGCTAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA---AGAA-GTGC
577310 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-AAG--GTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGTGC
* * * *
577353 CAATGTGCTAATTTAAGGCC-GCTACATTGGACTTAAAGAAGAAGATGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAG-TGC
577401 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-AAG--GTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGTGC
* * *
577444 CAATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGA-AGAA-GTGC
577493 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-AAG--GTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGTGC
* *
577536 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAA-GTGC
*
577585 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
577621 GAAGGGTTGC
Statistics
Matches: 265, Mismatches: 25, Indels: 45
0.79 0.07 0.13
Matches are distributed among these distances:
42 13 0.05
43 93 0.35
44 2 0.01
45 6 0.02
46 9 0.03
47 4 0.02
48 20 0.08
49 87 0.33
50 1 0.00
52 30 0.11
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (48 bp):
CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAAGAAGTGC
Found at i:577440 original size:22 final size:22
Alignment explanation
Indices: 577415--577482 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 22
577405 ATGCTGATTC
577415 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
* * * *
577437 AAGGTGCCA-ATGTGTT-GA-TTC
1 AA-G-GCCAGCTATATTGGACTTA
*
577458 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTATATTGGACTTA
577480 AAG
1 AAG
577483 ATAAAGGTGC
Statistics
Matches: 32, Mismatches: 9, Indels: 10
0.63 0.18 0.20
Matches are distributed among these distances:
19 4 0.12
20 4 0.12
21 6 0.19
22 9 0.28
23 5 0.16
24 4 0.12
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (22 bp):
AAGGCCAGCTATATTGGACTTA
Found at i:577529 original size:92 final size:92
Alignment explanation
Indices: 577249--577625 Score: 596
Period size: 92 Copynumber: 4.1 Consensus size: 92
577239 AAGATGAGAA
* * * *
577249 AAAGGATGTCAATGTGCTAATTCAAGGCTAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAAT
1 AAAGG-TGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGA---AGAAGGTGCCAAT
577314 ATGCTGATTCAAGGCCAGCTATATTGGACTT
62 ATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
577345 AAAGGTGCCAATGTGCTAATTTAAGGCC-GCTACATTGGACTTAAAGAAGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
577409 TGATTCAAGGCCAGCTATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
577436 AAAGGTGCCAATGTGTTGATTCAAGGCCAGCTACATTGGACTTAAAGATA-AAGGTGCCAATATG
1 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGA-AGAAGGTGCCAATATG
577500 CTGATTCAAGGCCAGCTATATTGGACTT
65 CTGATTCAAGGCCAGCTATATTGGACTT
*
577528 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
*
577593 TGATTCAAGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCTATATTGGACTT
577620 AGAAGG
1 A-AAGG
577626 GTTGCCACCA
Statistics
Matches: 265, Mismatches: 12, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
91 68 0.26
92 149 0.56
93 5 0.02
94 18 0.07
95 20 0.08
96 5 0.02
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTAATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:577699 original size:32 final size:32
Alignment explanation
Indices: 577613--577880 Score: 323
Period size: 32 Copynumber: 8.3 Consensus size: 32
577603 CCAGCTATAT
*
577613 TGGGC-TTAGA-AGGGTTGCCACCAACTTATG
1 TGGGCTTTAGAGAGGGTTGCCACCAACTTGTG
*
577643 TGGGCTTTAGAGAGTGGTTGCCACCAACTTGTA
1 TGGGCTTTAGAGAG-GGTTGCCACCAACTTGTG
*
577676 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCAACTTGTG
*
577708 TGGGCTTT-GAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCAACTTGTG
*
577740 TGGGCTTT-GAGAAGGGTTGCCACTAACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCAACTTGTG
*
577772 TGGGCTTTTGAGAGGGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGA-GGGTTGCCACCAACTTGTG
* * *
577805 TGGG-TTGT-GGGAAGGGTTGCCACCGACTTATG
1 TGGGCTT-TAGAG-AGGGTTGCCACCAACTTGTG
* * *
577837 TGGGCTTTAGAAGAAGGTTGCGACCGACTTGTG
1 TGGGCTTTAG-AGAGGGTTGCCACCAACTTGTG
577870 TGGGCTTTAGA
1 TGGGCTTTAGA
577881 AGGAGAGAGA
Statistics
Matches: 213, Mismatches: 14, Indels: 20
0.86 0.06 0.08
Matches are distributed among these distances:
30 5 0.02
31 8 0.04
32 112 0.53
33 87 0.41
34 1 0.00
ACGTcount: A:0.18, C:0.17, G:0.35, T:0.29
Consensus pattern (32 bp):
TGGGCTTTAGAGAGGGTTGCCACCAACTTGTG
Found at i:577699 original size:65 final size:65
Alignment explanation
Indices: 577620--577880 Score: 334
Period size: 65 Copynumber: 4.0 Consensus size: 65
577610 TATTGGGCTT
*
577620 AGAAGGGTTGCCACCAACTTATGTGGGCTTTAGAGAGTGGTTGCCACCAACTTGTATGGGCTTTA
1 AGAAGGGTTGCCACCAACTTATGTGGGCTTTAGAGAG-GGTTGCCACCAACTTGTGTGGGCTTTA
577685 G
65 G
* * *
577686 AG-AGGGTTGCCACCGACTTGTGTGGGCTTT-GAGAAGGGTTGCCACCGACTTGTGTGGGCTTT-
1 AGAAGGGTTGCCACCAACTTATGTGGGCTTTAGAG-AGGGTTGCCACCAACTTGTGTGGGCTTTA
577748 G
65 G
* * *
577749 AGAAGGGTTGCCACTAACTTGTGTGGGCTTTTGAGAGGGGTTGCCACCAACTTGTGTGGG-TTGT
1 AGAAGGGTTGCCACCAACTTATGTGGGCTTTAGAGA-GGGTTGCCACCAACTTGTGTGGGCTT-T
577813 -G
64 AG
* * * * *
577814 GGAAGGGTTGCCACCGACTTATGTGGGCTTTAGAAGAAGGTTGCGACCGACTTGTGTGGGCTTTA
1 AGAAGGGTTGCCACCAACTTATGTGGGCTTTAG-AGAGGGTTGCCACCAACTTGTGTGGGCTTTA
577879 G
65 G
577880 A
1 A
577881 AGGAGAGAGA
Statistics
Matches: 171, Mismatches: 16, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
63 3 0.02
64 56 0.33
65 104 0.61
66 8 0.05
ACGTcount: A:0.19, C:0.17, G:0.35, T:0.29
Consensus pattern (65 bp):
AGAAGGGTTGCCACCAACTTATGTGGGCTTTAGAGAGGGTTGCCACCAACTTGTGTGGGCTTTAG
Found at i:577921 original size:27 final size:28
Alignment explanation
Indices: 577886--578128 Score: 170
Period size: 27 Copynumber: 8.0 Consensus size: 28
577876 TTAGAAGGAG
* *
577886 AGAGATGCCACGGAGTTGTAGACTTAAA
1 AGAGGTGCCACGGAGTTGTGGACTTAAA
*
577914 AG-GGTGCCACGGAATTGTGGACTTAAA
1 AGAGGTGCCACGGAGTTGTGGACTTAAA
* *
577941 AGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAA
1 A--G----AG-GTGCCACGGAGTTGTGGACTTAAA
* *
577976 CG-GGTGCCACGGAGTTGTGGGCTTTGAAA
1 AGAGGTGCCACGGAGTTGTGGAC-TT-AAA
*
578005 AGAAGGTGCCACGGAGTCGTGGACTTAAA
1 AG-AGGTGCCACGGAGTTGTGGACTTAAA
578034 AGGAACAAGGTGCCAC-GAGGTTGTGGACTTTAAA
1 A-G----AGGTGCCACGGA-GTTGTGGAC-TTAAA
578068 AG-GGTGCCACGGAGTTGTGGACTTAAAA
1 AGAGGTGCCACGGAGTTGTGGACTT-AAA
*
578096 AGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
1 AG----AG-GTGCCACGGAGTTGTGGACTTAAA
578129 CGGATAAAAG
Statistics
Matches: 176, Mismatches: 13, Indels: 47
0.75 0.06 0.20
Matches are distributed among these distances:
27 43 0.24
28 27 0.15
29 11 0.06
30 3 0.02
31 18 0.10
32 2 0.01
33 24 0.14
34 27 0.15
35 21 0.12
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.20
Consensus pattern (28 bp):
AGAGGTGCCACGGAGTTGTGGACTTAAA
Found at i:577957 original size:35 final size:34
Alignment explanation
Indices: 577911--578269 Score: 315
Period size: 34 Copynumber: 11.0 Consensus size: 34
577901 TTGTAGACTT
* * *
577911 AAAAGGGTGCCACGGAATTGTGGACTTAAAAGGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAA-GGA
* *
577946 AAAAGAGTGCCACAGAGTTGTGGGCTT-AAACG-
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
**
577978 ----G-GTGCCACGGAGTTGTGGGCTTTGAA--A
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
* * *
578005 AGAAG-GTGCCACGGAGTCGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
* *
578038 ACAAG-GTGCCAC-GAGGTTGTGGACTTTAAAA-G-
1 AAAAGAGTGCCACGGA-GTTGTGGGC-TTAAAAGGA
* *
578070 ----G-GTGCCACGGAGTTGTGGACTTAAAAAGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
*
578099 AAAAGAGTGCCACGGAGTTGTGGGCTTAAACGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
*
578133 TAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGA
1 -AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
* * * ** *
578168 AATAGAGCGCCACAGAGTTGTGGGCTTAACCGGGT
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAA-AAGGA
*
578203 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
* *
578237 AAAAGAATGCCACAGAGTTGTGGGCTTAAAAGG
1 AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG
578270 GTGCCACGGA
Statistics
Matches: 269, Mismatches: 35, Indels: 41
0.78 0.10 0.12
Matches are distributed among these distances:
27 26 0.10
28 21 0.08
29 2 0.01
31 22 0.08
32 2 0.01
33 23 0.09
34 91 0.34
35 82 0.30
ACGTcount: A:0.32, C:0.14, G:0.34, T:0.19
Consensus pattern (34 bp):
AAAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGA
Found at i:578084 original size:28 final size:28
Alignment explanation
Indices: 577946--578097 Score: 130
Period size: 28 Copynumber: 5.2 Consensus size: 28
577936 TTAAAAGGGA
* * *
577946 AAAAGAGTGCCACAGAGTTGTGGGC-TT
1 AAAAGGGTGCCACGGAGTTGTGGACTTT
* *
577973 AAACGGGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTT
*
578001 GAAAAGAAGGTGCCACGGAGTCGTGGAC-TT
1 -AAAAG--GGTGCCACGGAGTTGTGGACTTT
578031 AAAAGGAACAAGGTGCCAC-GAGGTTGTGGACTTT
1 AAAA-G-----GGTGCCACGGA-GTTGTGGACTTT
*
578065 AAAAGGGTGCCACGGAGTTGTGGACTTA
1 AAAAGGGTGCCACGGAGTTGTGGACTTT
578093 AAAAG
1 AAAAG
578098 AAAAAGAGTG
Statistics
Matches: 106, Mismatches: 8, Indels: 21
0.79 0.06 0.16
Matches are distributed among these distances:
27 22 0.21
28 26 0.25
29 10 0.09
30 3 0.03
31 18 0.17
32 2 0.02
33 19 0.18
34 6 0.06
ACGTcount: A:0.30, C:0.15, G:0.35, T:0.20
Consensus pattern (28 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTT
Found at i:578180 original size:69 final size:69
Alignment explanation
Indices: 578064--578266 Score: 316
Period size: 69 Copynumber: 2.9 Consensus size: 69
578054 TTGTGGACTT
* * *
578064 TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAA
1 TAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAA
578129 CGGA
66 CGGA
* * * * *
578133 TAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAATAGAGCGCCACAGAGTTGTGGGCTTAAC
1 TAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAA
*
578198 CGGG
66 CGGA
*
578202 TAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAATGCCACAGAGTTGTGGGCTTAAA
1 TAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAA
578267 AGGGTGCCAC
Statistics
Matches: 119, Mismatches: 15, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
69 119 1.00
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.19
Consensus pattern (69 bp):
TAAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACAGAGTTGTGGGCTTAAA
CGGA
Found at i:578233 original size:27 final size:27
Alignment explanation
Indices: 578202--578286 Score: 80
Period size: 34 Copynumber: 2.9 Consensus size: 27
578192 CTTAACCGGG
578202 TAAAAGAGTGCCACGGAGTTGTGGACT
1 TAAAAGAGTGCCACGGAGTTGTGGACT
* *
578229 TAAAAGGAAAAAGAATGCCACAGAGTTGTGGGCT
1 TAAAA-G----AG--TGCCACGGAGTTGTGGACT
*
578263 TAAAAGGGTGCCACGGAGTTGTGG
1 TAAAAGAGTGCCACGGAGTTGTGG
578287 GCTTTGAAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
27 20 0.43
28 1 0.02
29 1 0.02
32 2 0.04
33 1 0.02
34 22 0.47
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (27 bp):
TAAAAGAGTGCCACGGAGTTGTGGACT
Found at i:578411 original size:34 final size:33
Alignment explanation
Indices: 578356--578542 Score: 162
Period size: 30 Copynumber: 5.8 Consensus size: 33
578346 GGATTTTTAG
578356 GACAAAATGCCACTGAGTCGTGGGCTTTGAGAA
1 GACAAAATGCCACTGAGTCGTGGGCTTTGAGAA
* * *
578389 GA-AAAAGGTGCCACGGATTCGTGGACTTT-AG--
1 GACAAAA--TGCCACTGAGTCGTGGGCTTTGAGAA
* *
578420 GATAAAATGCCACTGAATCGTGGGCTTTGAGAA
1 GACAAAATGCCACTGAGTCGTGGGCTTTGAGAA
*
578453 GA-AAAAGGTGCCA-TGGAGTCGTGGACTTT-AG--
1 GACAAAA--TGCCACT-GAGTCGTGGGCTTTGAGAA
*
578484 GACAAAATGCCACTGATTCGTGGGCTTTGAGAA
1 GACAAAATGCCACTGAGTCGTGGGCTTTGAGAA
* * *
578517 -A-AGATTGCCACTGAGTCGTGGACTTT
1 GACAAAATGCCACTGAGTCGTGGGCTTT
578543 AAAAAGGTAT
Statistics
Matches: 126, Mismatches: 14, Indels: 30
0.74 0.08 0.18
Matches are distributed among these distances:
30 35 0.28
31 30 0.24
32 17 0.13
33 9 0.07
34 35 0.28
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (33 bp):
GACAAAATGCCACTGAGTCGTGGGCTTTGAGAA
Found at i:578427 original size:64 final size:64
Alignment explanation
Indices: 578351--578543 Score: 293
Period size: 64 Copynumber: 3.1 Consensus size: 64
578341 ATTATGGATT
* *
578351 TTTAGGACAAAATGCCACTGAGTCGTGGGCTTTGAGAAGAAAAAGGTGCCACGGATTCGTGGAC
1 TTTAGGACAAAATGCCACTGAATCGTGGGCTTTGAGAAGAAAAAGGTGCCACGGAGTCGTGGAC
* *
578415 TTTAGGATAAAATGCCACTGAATCGTGGGCTTTGAGAAGAAAAAGGTGCCATGGAGTCGTGGAC
1 TTTAGGACAAAATGCCACTGAATCGTGGGCTTTGAGAAGAAAAAGGTGCCACGGAGTCGTGGAC
* * * *
578479 TTTAGGACAAAATGCCACTGATTCGTGGGCTTTGAG-A-AAAGA-TTGCCACTGAGTCGTGGAC
1 TTTAGGACAAAATGCCACTGAATCGTGGGCTTTGAGAAGAAAAAGGTGCCACGGAGTCGTGGAC
578540 TTTA
1 TTTA
578544 AAAAGGTATT
Statistics
Matches: 119, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
61 20 0.17
62 4 0.03
63 1 0.01
64 94 0.79
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.25
Consensus pattern (64 bp):
TTTAGGACAAAATGCCACTGAATCGTGGGCTTTGAGAAGAAAAAGGTGCCACGGAGTCGTGGAC
Found at i:578661 original size:24 final size:24
Alignment explanation
Indices: 578622--578680 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 24
578612 ACATGTGGTG
*
578622 ATGATGTGAGTGCATGATGCAAATA
1 ATGATGT-TGTGCATGATGCAAATA
578647 ATGATGTTGTGCATGATGCAAATA
1 ATGATGTTGTGCATGATGCAAATA
578671 ATGATGTTGT
1 ATGATGTTGT
578681 TGATGTTATG
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 26 0.79
25 7 0.21
ACGTcount: A:0.32, C:0.07, G:0.27, T:0.34
Consensus pattern (24 bp):
ATGATGTTGTGCATGATGCAAATA
Found at i:579540 original size:24 final size:24
Alignment explanation
Indices: 579513--579574 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
579503 GGTTTTTCCC
579513 TTCTTCTTCTTTTTTTTTTTTTGT
1 TTCTTCTTCTTTTTTTTTTTTTGT
*
579537 TTCTTCTT-TTTTTTCTTTTTTGT
1 TTCTTCTTCTTTTTTTTTTTTTGT
579560 TT-TGT-TTCTTTTTTT
1 TTCT-TCTTCTTTTTTT
579575 GGAAAAGAAC
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 3 0.09
23 23 0.68
24 8 0.24
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (24 bp):
TTCTTCTTCTTTTTTTTTTTTTGT
Found at i:579564 original size:28 final size:26
Alignment explanation
Indices: 579512--579574 Score: 83
Period size: 27 Copynumber: 2.3 Consensus size: 26
579502 GGGTTTTTCC
*
579512 CTTCTTCTTCTTTTTTTTTTTTTGTTT
1 CTTCTT-TTTTTTTTTTTTTTTTGTTT
579539 CTTCTTTTTTTTCTTTTTTGTTTTGTTT
1 CTTCTTTTTTTT-TTTTTT-TTTTGTTT
579567 CTT-TTTTT
1 CTTCTTTTT
579575 GGAAAAGAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
26 5 0.15
27 17 0.52
28 11 0.33
ACGTcount: A:0.00, C:0.13, G:0.05, T:0.83
Consensus pattern (26 bp):
CTTCTTTTTTTTTTTTTTTTTTGTTT
Found at i:579575 original size:17 final size:16
Alignment explanation
Indices: 579519--579573 Score: 60
Period size: 16 Copynumber: 3.6 Consensus size: 16
579509 TCCCTTCTTC
579519 TTCTTTTTT-TTTT-T
1 TTCTTTTTTGTTTTGT
* * * *
579533 TTGTTTCTTCTTTTTT
1 TTCTTTTTTGTTTTGT
579549 TTCTTTTTTGTTTTGT
1 TTCTTTTTTGTTTTGT
579565 TTCTTTTTT
1 TTCTTTTTT
579574 TGGAAAAGAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
14 7 0.21
15 4 0.12
16 22 0.67
ACGTcount: A:0.00, C:0.09, G:0.05, T:0.85
Consensus pattern (16 bp):
TTCTTTTTTGTTTTGT
Found at i:586706 original size:52 final size:52
Alignment explanation
Indices: 586626--586745 Score: 204
Period size: 52 Copynumber: 2.3 Consensus size: 52
586616 AAAAGTTGCT
* *
586626 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGTAAATTTACC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTACC
* *
586678 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTACC
586730 TGCATGTATCGATACA
1 TGCATGTATCGATACA
586746 AAGATCAGTG
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTACC
Found at i:586758 original size:52 final size:51
Alignment explanation
Indices: 586621--586765 Score: 193
Period size: 52 Copynumber: 2.8 Consensus size: 51
586611 ATATGAAAAG
* *
586621 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGTAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
* * *
586673 TTACCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAAT
*
586725 TTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 TTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
586766 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAAT
Found at i:586772 original size:13 final size:13
Alignment explanation
Indices: 586754--586802 Score: 98
Period size: 13 Copynumber: 3.8 Consensus size: 13
586744 CAAAGATCAG
586754 TGTATCGATACAA
1 TGTATCGATACAA
586767 TGTATCGATACAA
1 TGTATCGATACAA
586780 TGTATCGATACAA
1 TGTATCGATACAA
586793 TGTATCGATA
1 TGTATCGATA
586803 TATTTGAGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 36 1.00
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:586872 original size:20 final size:20
Alignment explanation
Indices: 586843--586898 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
586833 GCAGTAGCTT
586843 AAAT-TGTATCGATACAGAA
1 AAATATGTATCGATACAGAA
586862 AAATATGTATCGATACAGAA
1 AAATATGTATCGATACAGAA
586882 AAATATGTATCGATACA
1 AAATATGTATCGATACA
586899 TTGTATCGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.11
20 32 0.89
ACGTcount: A:0.48, C:0.11, G:0.14, T:0.27
Consensus pattern (20 bp):
AAATATGTATCGATACAGAA
Found at i:586905 original size:13 final size:13
Alignment explanation
Indices: 586887--586911 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
586877 CAGAAAAATA
586887 TGTATCGATACAT
1 TGTATCGATACAT
586900 TGTATCGATACA
1 TGTATCGATACA
586912 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:587564 original size:43 final size:43
Alignment explanation
Indices: 587493--587821 Score: 226
Period size: 43 Copynumber: 7.1 Consensus size: 43
587483 CCGGGCGTTG
* *
587493 TTGGTCTTCAAGGTGTCAATATGTTGATTCAAGGCCAGCGATA
1 TTGGTCTTCAAGATGTCAATATGCTGATTCAAGGCCAGCGATA
* *
587536 TCGGACTTCAAGATGTCAATATGCTGATTCAAGGCCAGCGATA
1 TTGGTCTTCAAGATGTCAATATGCTGATTCAAGGCCAGCGATA
* * * *
587579 TTGGTCTTAAAGATGGTTAAGGTGCCAATGTGCTGGTTCAAGGCCAGCGACA
1 TTGGTCTTCAAGA----T---GT--CAATATGCTGATTCAAGGCCAGCGATA
* * * * ** * * *
587631 TTGGTCTTCATGGTGCCAATGTATTGATTCAAGGCGAGCTACA
1 TTGGTCTTCAAGATGTCAATATGCTGATTCAAGGCCAGCGATA
* *
587674 TTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATA
1 TTGGTCTTCAAGAT----GT--CAATATGCTGATTCAAGGCCAGCGATA
* * *
587723 TTGGTCTTAAAGATGGTTAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACA
1 TTGGTCTTCAAGA----T---GT--CAATATGCTGATTCAAGGCCAGCGATA
* *
587775 TTGGTCTTCAAGGTGTCAATATGCTAATTCAAGGCCAGCGATA
1 TTGGTCTTCAAGATGTCAATATGCTGATTCAAGGCCAGCGATA
587818 TTGG
1 TTGG
587822 GTTTAAAAGA
Statistics
Matches: 229, Mismatches: 38, Indels: 38
0.75 0.12 0.12
Matches are distributed among these distances:
43 109 0.48
45 3 0.01
47 2 0.01
48 2 0.01
49 33 0.14
50 2 0.01
52 77 0.34
53 1 0.00
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.29
Consensus pattern (43 bp):
TTGGTCTTCAAGATGTCAATATGCTGATTCAAGGCCAGCGATA
Found at i:587635 original size:52 final size:50
Alignment explanation
Indices: 587552--587865 Score: 275
Period size: 52 Copynumber: 6.5 Consensus size: 50
587542 TTCAAGATGT
* *
587552 CAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGGTTAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT-G-TAAGGTGC
* *
587604 CAATGTGCTGGTTCAAGGCCAGCGACATTGGTCTT---CA--T--GGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGTAAGGTGC
** * * *
587647 CAATGTATTGATTCAAGGCGAGCTACATTGGACTTAAAGATG-AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGTAAGGTGC
* *
587696 CAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGGTTAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGAT-G-TAAGGTGC
*
587748 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTCAAG--GT---GT--
1 CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGTAAGGTGC
* * * * *
587791 CAATATGCTAATTCAAGGCCAGCGATATTGGGT-TTAAAAGAT-AAAGGCGC
1 CAATGTGCTGATTCAAGGCCAGCGACATT-GGTCTT-AAAGATGTAAGGTGC
* * *
587841 CAATATGCTGGTTTAAGGCCAGCGA
1 CAATGTGCTGATTCAAGGCCAGCGA
587866 TATCGGACTT
Statistics
Matches: 213, Mismatches: 30, Indels: 40
0.75 0.11 0.14
Matches are distributed among these distances:
43 62 0.29
44 6 0.03
45 3 0.01
46 1 0.00
48 2 0.01
49 41 0.19
50 23 0.11
52 75 0.35
ACGTcount: A:0.28, C:0.18, G:0.27, T:0.27
Consensus pattern (50 bp):
CAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTAAAGATGTAAGGTGC
Found at i:587747 original size:144 final size:145
Alignment explanation
Indices: 587552--587868 Score: 483
Period size: 144 Copynumber: 2.2 Consensus size: 145
587542 TTCAAGATGT
*
587552 CAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGGTTAAGGTGCCAATGTGCTGGTT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGGTTAAGGTGCCAATGTGCTGATT
* * * * * *
587617 CAAGGCCAGCGACATTGGTCTTCATGGTGCCAATGTATTGATTCAAGGCGAGCTACATTGGACTT
66 CAAGGCCAGCGACATTGGTCTTCAAGGTGCCAATATACTAATTCAAGGCCAGCGACATTGGACTT
* *
587682 -AAAGATGAAGGTGC
131 AAAAGATAAAGGCGC
587696 CAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGGTTAAGGTGCCAATGTGCTGATT
1 CAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGGTTAAGGTGCCAATGTGCTGATT
* * * **
587761 CAAGGCCAGCGACATTGGTCTTCAAGGTGTCAATATGCTAATTCAAGGCCAGCGATATTGGGTTT
66 CAAGGCCAGCGACATTGGTCTTCAAGGTGCCAATATACTAATTCAAGGCCAGCGACATTGGACTT
587826 AAAAGATAAAGGCGC
131 AAAAGATAAAGGCGC
* *
587841 CAATATGCTGGTTTAAGGCCAGCGATAT
1 CAATATGCTGATTCAAGGCCAGCGATAT
587869 CGGACTTAGA
Statistics
Matches: 156, Mismatches: 16, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
144 118 0.76
145 38 0.24
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (145 bp):
CAATATGCTGATTCAAGGCCAGCGATATTGGTCTTAAAGATGGTTAAGGTGCCAATGTGCTGATT
CAAGGCCAGCGACATTGGTCTTCAAGGTGCCAATATACTAATTCAAGGCCAGCGACATTGGACTT
AAAAGATAAAGGCGC
Found at i:587764 original size:101 final size:95
Alignment explanation
Indices: 587642--587821 Score: 234
Period size: 95 Copynumber: 1.8 Consensus size: 95
587632 TGGTCTTCAT
* * * * *
587642 GGTGCCAATGTATTGATTCAAGGCGAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGA
1 GGTGCCAATGTACTGATTCAAGGCCAGCGACATTGGAC-T-----TCAAGGTGCCAATATGCTAA
587707 TTCAAGGCCAGCGATATTGGTCTTAAAGATGGTTAA
60 TTCAAGGCCAGCGATATTGGTCTTAAAGATGGTTAA
* * *
587743 GGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCTTCAAGGTGTCAATATGCTAATTCAAG
1 GGTGCCAATGTACTGATTCAAGGCCAGCGACATTGGACTTCAAGGTGCCAATATGCTAATTCAAG
587808 GCCAGCGATATTGG
66 GCCAGCGATATTGG
587822 GTTTAAAAGA
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 37 0.52
100 1 0.01
101 33 0.46
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.27
Consensus pattern (95 bp):
GGTGCCAATGTACTGATTCAAGGCCAGCGACATTGGACTTCAAGGTGCCAATATGCTAATTCAAG
GCCAGCGATATTGGTCTTAAAGATGGTTAA
Found at i:587809 original size:95 final size:93
Alignment explanation
Indices: 587689--587865 Score: 248
Period size: 95 Copynumber: 1.9 Consensus size: 93
587679 CTTAAAGATG
* * * * *
587689 AAGGTGCCAATATGCTGATTCAAGGCCAGCGATATT-GGTCTTAAAGATGGTTAAGGTGCCAATG
1 AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGT-TTAAA-A-GATAAAGGCGCCAATA
587753 TGCTGATTCAAGGCCAGCGACATTGGTCTTC
63 TGCTGATTCAAGGCCAGCGACATTGGTCTTC
*
587784 AAGGTGTCAATATGCTAATTCAAGGCCAGCGATATTGGGTTTAAAAGATAAAGGCGCCAATATGC
1 AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGTTTAAAAGATAAAGGCGCCAATATGC
* *
587849 TGGTTTAAGGCCAGCGA
66 TGATTCAAGGCCAGCGA
587866 TATCGGACTT
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
93 30 0.41
94 1 0.01
95 39 0.53
96 3 0.04
ACGTcount: A:0.29, C:0.18, G:0.27, T:0.26
Consensus pattern (93 bp):
AAGGTGCCAATATGCTAATTCAAGGCCAGCGATATTGGGTTTAAAAGATAAAGGCGCCAATATGC
TGATTCAAGGCCAGCGACATTGGTCTTC
Found at i:587980 original size:30 final size:29
Alignment explanation
Indices: 587939--588085 Score: 136
Period size: 30 Copynumber: 5.1 Consensus size: 29
587929 TGTGCTTTTG
*
587939 AAGGTTGCCACTGACTTGTGGGCTTTTGAA
1 AAGGGTGCCACTGACTTGTGGGC-TTTGAA
* *
587969 AAGGGTGCCACTAACTTGTGGGCTTCGAAA
1 AAGGGTGCCACTGACTTGTGGGCTTTG-AA
* **
587999 AAGGGTGCCATTGGTTTGTGGGCTTTG--
1 AAGGGTGCCACTGACTTGTGGGCTTTGAA
* *
588026 AAGGTTGCCACTGACTTGTGGACTTTGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAA
*** * * *
588055 AAATATGCCACTGACTTATAGGCTTCGAA
1 AAGGGTGCCACTGACTTGTGGGCTTTGAA
588084 AA
1 AA
588086 AGATGTCACT
Statistics
Matches: 94, Mismatches: 20, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
27 22 0.23
29 27 0.29
30 45 0.48
ACGTcount: A:0.24, C:0.17, G:0.29, T:0.30
Consensus pattern (29 bp):
AAGGGTGCCACTGACTTGTGGGCTTTGAA
Found at i:588084 original size:29 final size:29
Alignment explanation
Indices: 588031--588095 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
588021 CTTTGAAGGT
* * *
588031 TGCCACTGACTTGTGGACTTTGAAAAATA
1 TGCCACTGACTTATGGACTTCGAAAAAGA
588060 TGCCACTGACTTATAGG-CTTCGAAAAAGA
1 TGCCACTGACTTAT-GGACTTCGAAAAAGA
*
588089 TGTCACT
1 TGCCACT
588096 AGTTTGTGGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 29 0.94
30 2 0.06
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (29 bp):
TGCCACTGACTTATGGACTTCGAAAAAGA
Found at i:588084 original size:86 final size:87
Alignment explanation
Indices: 587926--588115 Score: 249
Period size: 86 Copynumber: 2.2 Consensus size: 87
587916 TTACATCAAC
* * * * * *
587926 TTGTGTGCTTTTGAAGGTTGCCACTGACTTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGG
1 TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGACTTTTGAAAAAGATGCCACTAACTTATAGG
* * *
587991 CTTCGAAAAAGGGTGCCATTGGT
66 CTTCGAAAAA-GATGCCACTAGT
* *
588014 TTGTGGGC-TTTGAAGGTTGCCACTGACTTGTGGAC-TTTGAAAAATATGCCACTGACTTATAGG
1 TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGACTTTTGAAAAAGATGCCACTAACTTATAGG
*
588077 CTTCGAAAAAGATGTCACTAGT
66 CTTCGAAAAAGATGCCACTAGT
588099 TTGTGGGCTTTTGAAGG
1 TTGTGGGCTTTTGAAGG
588116 GTGAGGAATG
Statistics
Matches: 89, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
85 16 0.18
86 40 0.45
87 26 0.29
88 7 0.08
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.33
Consensus pattern (87 bp):
TTGTGGGCTTTTGAAGGTTGCCACTGACTTGTGGACTTTTGAAAAAGATGCCACTAACTTATAGG
CTTCGAAAAAGATGCCACTAGT
Found at i:589564 original size:1 final size:1
Alignment explanation
Indices: 589560--589685 Score: 90
Period size: 1 Copynumber: 126.0 Consensus size: 1
589550 CTTTTTGTTG
* * * * * * * * * *
589560 TTTTTTTGTTTTGTTTTTGTTTTTGTTGTTTTTTTTTCTTTTTTCTTCTTTCTTTTTTTTTTTGT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* ** * * * * *
589625 TTTTTTGTTTAATTTTTGTTTTTTTTTGTTTTTGTTTTTTTTTTCTTTCTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
589686 GCGGAGGACG
Statistics
Matches: 91, Mismatches: 34, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 91 1.00
ACGTcount: A:0.02, C:0.05, G:0.08, T:0.86
Consensus pattern (1 bp):
T
Found at i:589567 original size:11 final size:10
Alignment explanation
Indices: 589551--589682 Score: 115
Period size: 11 Copynumber: 12.5 Consensus size: 10
589541 ATCCGGACCC
589551 TTTTTGTTGTT
1 TTTTTGTT-TT
589562 TTTTTGTTTT
1 TTTTTGTTTT
589572 GTTTTTG-TTT
1 -TTTTTGTTTT
*
589582 TTGTTGTTTT
1 TTTTTGTTTT
*
589592 TTTTTCTTTT
1 TTTTTGTTTT
*
589602 TTCTTCTTTCTTT
1 TT-TT-TGT-TTT
*
589615 TTTTTTTTGTT
1 TTTTTGTT-TT
*
589626 TTTTTGTTTAA
1 TTTTTGTTT-T
589637 TTTTTGTTTT
1 TTTTTGTTTT
589647 TTTTTGTTTT
1 TTTTTGTTTT
589657 TGTTTT-TTTT
1 T-TTTTGTTTT
*
589667 TTCTTTCTTTT
1 TT-TTTGTTTT
589678 TTTTT
1 TTTTT
589683 TTTGCGGAGG
Statistics
Matches: 104, Mismatches: 7, Indels: 21
0.79 0.05 0.16
Matches are distributed among these distances:
9 6 0.06
10 42 0.40
11 47 0.45
12 4 0.04
13 5 0.05
ACGTcount: A:0.02, C:0.05, G:0.09, T:0.85
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:589632 original size:47 final size:46
Alignment explanation
Indices: 589568--589668 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 46
589558 TGTTTTTTTG
* *
589568 TTTTGTTTTTGTTTTTGTTG-TT-TTTTT-TTCTTTTTTCTTCTTTCT
1 TTTTTTTTTTGTTTTT-TTGTTTATTTTTGTTTTTTTTTCTT-TTTCT
* *
589613 TTTTTTTTTTGTTTTTTTGTTTAATTTTTGTTTTTTTTTGTTTTTGT
1 TTTTTTTTTTGTTTTTTTGTTT-ATTTTTGTTTTTTTTTCTTTTTCT
589660 TTTTTTTTT
1 TTTTTTTTT
589669 CTTTCTTTTT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
44 3 0.06
45 17 0.35
47 18 0.38
48 10 0.21
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (46 bp):
TTTTTTTTTTGTTTTTTTGTTTATTTTTGTTTTTTTTTCTTTTTCT
Found at i:589685 original size:64 final size:64
Alignment explanation
Indices: 589551--589684 Score: 195
Period size: 64 Copynumber: 2.1 Consensus size: 64
589541 ATCCGGACCC
* **
589551 TTTTTGTTGTTTTTTTGTTTTGTTTTTGTTTTTGTTGTTTTTTTTTCTTTTTTCTTCTTTCTTT
1 TTTTTTTTGTTTTTTTGTTTAATTTTTGTTTTTGTTGTTTTTTTTTCTTTTTTCTTCTTTCTTT
589615 TTTTTTTTGTTTTTTTGTTTAATTTTTGTTTTT-TT-TTGTTTTTGTT-TTTTTT-TTCTTTCTT
1 TTTTTTTTGTTTTTTTGTTTAATTTTTGTTTTTGTTGTT-TTTTT-TTCTTTTTTCTTCTTTCTT
589676 T
64 T
589677 TTTTTTTT
1 TTTTTTTT
589685 TGCGGAGGAC
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
62 20 0.31
63 13 0.20
64 32 0.49
ACGTcount: A:0.01, C:0.04, G:0.09, T:0.85
Consensus pattern (64 bp):
TTTTTTTTGTTTTTTTGTTTAATTTTTGTTTTTGTTGTTTTTTTTTCTTTTTTCTTCTTTCTTT
Found at i:597254 original size:13 final size:13
Alignment explanation
Indices: 597236--597263 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
597226 ATACATTACT
597236 CATTGTATCGATA
1 CATTGTATCGATA
597249 CATTGTATCGATA
1 CATTGTATCGATA
597262 CA
1 CA
597264 CTGATCTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (13 bp):
CATTGTATCGATA
Found at i:597261 original size:33 final size:33
Alignment explanation
Indices: 597219--597284 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
597209 GCCAAGAAAA
*
597219 TGTATCGATACA-TTACTCATTGTATCGATACAT
1 TGTATCGATACACTGA-TCATTGTATCGATACAT
*
597252 TGTATCGATACACTGATCTTTGTATCGATACAT
1 TGTATCGATACACTGATCATTGTATCGATACAT
597285 GCAAGCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (33 bp):
TGTATCGATACACTGATCATTGTATCGATACAT
Found at i:606701 original size:13 final size:13
Alignment explanation
Indices: 606683--606707 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
606673 CAAAGATCAG
606683 TGTATCGATACAA
1 TGTATCGATACAA
606696 TGTATCGATACA
1 TGTATCGATACA
606708 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:606773 original size:19 final size:19
Alignment explanation
Indices: 606749--606846 Score: 103
Period size: 19 Copynumber: 5.8 Consensus size: 19
606739 AGTAGCTTCA
606749 TATGTATCGATACAACACT
1 TATGTATCGATACAACACT
606768 TATGTATCGAT---ACA--
1 TATGTATCGATACAACACT
606782 T-TGTATCGATACAACACT
1 TATGTATCGATACAACACT
*
606800 TATGTATTGAT---ACA--
1 TATGTATCGATACAACACT
606814 T-TGTATCGATACAACACT
1 TATGTATCGATACAACACT
606832 TATGTATCGATACAA
1 TATGTATCGATACAA
606847 ATCGTTGACA
Statistics
Matches: 65, Mismatches: 2, Indels: 24
0.71 0.02 0.26
Matches are distributed among these distances:
13 17 0.26
14 2 0.03
16 12 0.18
18 2 0.03
19 32 0.49
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (19 bp):
TATGTATCGATACAACACT
Found at i:606788 original size:13 final size:13
Alignment explanation
Indices: 606770--606826 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
606760 ACAACACTTA
606770 TGTATCGATACAT
1 TGTATCGATACAT
606783 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
*
606801 ATGTATTGATACAT
1 -TGTATCGATACAT
606815 TGTATCGATACA
1 TGTATCGATACA
606827 ACACTTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
16 6 0.17
18 1 0.03
19 8 0.22
ACGTcount: A:0.33, C:0.16, G:0.14, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:606792 original size:32 final size:32
Alignment explanation
Indices: 606751--606845 Score: 181
Period size: 32 Copynumber: 3.0 Consensus size: 32
606741 TAGCTTCATA
606751 TGTATCGATACAACACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
*
606783 TGTATCGATACAACACTTATGTATTGATACAT
1 TGTATCGATACAACACTTATGTATCGATACAT
606815 TGTATCGATACAACACTTATGTATCGATACA
1 TGTATCGATACAACACTTATGTATCGATACA
606846 AATCGTTGAC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATGTATCGATACAT
Found at i:609572 original size:13 final size:13
Alignment explanation
Indices: 609554--609579 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
609544 ACATACAAGA
609554 TGTATCGATACAT
1 TGTATCGATACAT
609567 TGTATCGATACAT
1 TGTATCGATACAT
609580 GACCAAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:609595 original size:33 final size:32
Alignment explanation
Indices: 609537--609601 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 32
609527 TAACTGTTTA
609537 TATCGATACATACAAGATGTATCGATACATTG
1 TATCGATACATACAAGATGTATCGATACATTG
609569 TATCGATACATGACCAA-ATGTATCGATACATTG
1 TATCGATACAT-A-CAAGATGTATCGATACATTG
609602 GCTTTTAACG
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 11 0.35
33 17 0.55
34 3 0.10
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (32 bp):
TATCGATACATACAAGATGTATCGATACATTG
Found at i:612340 original size:13 final size:13
Alignment explanation
Indices: 612322--612347 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
612312 CAATTTTTTG
612322 TGTATCGATACAT
1 TGTATCGATACAT
612335 TGTATCGATACAT
1 TGTATCGATACAT
612348 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:618761 original size:1 final size:1
Alignment explanation
Indices: 618757--618817 Score: 59
Period size: 1 Copynumber: 61.0 Consensus size: 1
618747 CAAAAAAACC
* * * * * * *
618757 AAAAAAAAAACAAAAAAAAACAAAAAAAAAAAACAAAACAAAGAAAAAAGAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
618818 GAAGAAGAAT
Statistics
Matches: 46, Mismatches: 14, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.89, C:0.07, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:618764 original size:11 final size:10
Alignment explanation
Indices: 618748--618816 Score: 70
Period size: 11 Copynumber: 6.8 Consensus size: 10
618738 ATTCTTTTTC
*
618748 AAAAAAACCAA
1 AAAAAAAAC-A
618759 AAAAAAAACA
1 AAAAAAAACA
618769 AAAAAAAAC-
1 AAAAAAAACA
618778 AAAAAAAA-A
1 AAAAAAAACA
*
618787 AAACAAAACA
1 AAAAAAAACA
*
618797 AAGAAAAAAGA
1 AA-AAAAAACA
618808 GAAAAAAAA
1 -AAAAAAAA
618817 AGAAGAAGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
9 15 0.30
10 13 0.26
11 20 0.40
12 2 0.04
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:618783 original size:23 final size:22
Alignment explanation
Indices: 618748--618794 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
618738 ATTCTTTTTC
*
618748 AAAAAAACCAAAAAAAAAACAA
1 AAAAAAACAAAAAAAAAAACAA
618770 AAAAAAACAAAAAAAAAAAACAA
1 AAAAAAAC-AAAAAAAAAAACAA
618793 AA
1 AA
618795 CAAAGAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (22 bp):
AAAAAAACAAAAAAAAAAACAA
Found at i:618812 original size:18 final size:18
Alignment explanation
Indices: 618748--618805 Score: 75
Period size: 17 Copynumber: 3.3 Consensus size: 18
618738 ATTCTTTTTC
*
618748 AAAAAAACCAAAA-AAAA
1 AAAAAAAACAAAACAAAA
*
618765 AACAAAAA-AAAACAAAA
1 AAAAAAAACAAAACAAAA
618782 AAAAAAAACAAAACAAAGA
1 AAAAAAAACAAAACAAA-A
618801 AAAAA
1 AAAAA
618806 GAGAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.11
17 17 0.49
18 8 0.23
19 6 0.17
ACGTcount: A:0.88, C:0.10, G:0.02, T:0.00
Consensus pattern (18 bp):
AAAAAAAACAAAACAAAA
Found at i:618812 original size:28 final size:27
Alignment explanation
Indices: 618757--618817 Score: 86
Period size: 29 Copynumber: 2.2 Consensus size: 27
618747 CAAAAAAACC
618757 AAAAAAAAAACAAAAAAAAACAAAAAA
1 AAAAAAAAAACAAAAAAAAACAAAAAA
* *
618784 AAAAAACAAAACAAAGAAAAAAGAGAAAA
1 AAAAAA-AAAACAAA-AAAAAACAAAAAA
618813 AAAAA
1 AAAAA
618818 GAAGAAGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 6 0.20
28 8 0.27
29 16 0.53
ACGTcount: A:0.89, C:0.07, G:0.05, T:0.00
Consensus pattern (27 bp):
AAAAAAAAAACAAAAAAAAACAAAAAA
Found at i:618816 original size:22 final size:19
Alignment explanation
Indices: 618748--618816 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 19
618738 ATTCTTTTTC
*
618748 AAAAAAACCAAAAAAAAAA
1 AAAAAAAACAAAAAAAAAA
618767 CAAAAAAAA-ACAAAAAAAAA
1 -AAAAAAAACA-AAAAAAAAA
*
618787 AAACAAAACAAAGAAAAAAGA
1 AAAAAAAACAAA-AAAAAA-A
618808 GAAAAAAAA
1 -AAAAAAAA
618817 AGAAGAAGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
19 10 0.24
20 23 0.56
21 1 0.02
22 7 0.17
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (19 bp):
AAAAAAAACAAAAAAAAAA
Found at i:618817 original size:23 final size:20
Alignment explanation
Indices: 618748--618817 Score: 77
Period size: 21 Copynumber: 3.2 Consensus size: 20
618738 ATTCTTTTTC
*
618748 AAAAAAACCAAAAAAAAAACA
1 AAAAAAAACAAAAAAAAAA-A
618769 AAAAAAAACAAAAAAAAAAA
1 AAAAAAAACAAAAAAAAAAA
*
618789 ACAAAACAAAGAAAAAAGAGAAAA
1 A-AAAA-AAACAAAAAA-A-AAAA
618813 AAAAA
1 AAAAA
618818 GAAGAAGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.05
21 22 0.51
22 9 0.21
23 5 0.12
24 5 0.12
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (20 bp):
AAAAAAAACAAAAAAAAAAA
Found at i:618820 original size:10 final size:10
Alignment explanation
Indices: 618758--618820 Score: 65
Period size: 10 Copynumber: 6.2 Consensus size: 10
618748 AAAAAAACCA
*
618758 AAAAAAAAAC
1 AAAAAAAAAG
*
618768 AAAAAAAAAC
1 AAAAAAAAAG
*
618778 AAAAAAAAAA
1 AAAAAAAAAG
618788 AACAAAACAAAG
1 AA-AAAA-AAAG
*
618800 -AAAAAAGAG
1 AAAAAAAAAG
618809 AAAAAAAAAG
1 AAAAAAAAAG
618819 AA
1 AA
618821 GAAGAATCTA
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
9 3 0.07
10 35 0.76
11 5 0.11
12 3 0.07
ACGTcount: A:0.87, C:0.06, G:0.06, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:619874 original size:55 final size:55
Alignment explanation
Indices: 619785--620317 Score: 496
Period size: 55 Copynumber: 9.3 Consensus size: 55
619775 ACTTTTTAGC
* * * * *
619785 CCTCAAAGAGTAGGACGCCTTTTAAAGCCTACACAAGTTGGTGTCACCCTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
* * * * *
619840 CCTTAAAGAGCAGGACGTCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTCCCAAT
1 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TCAGT
** *
619895 CCTCAAAGAGCAGGACATCTTTCAAAGCCCACACAAGTTGGTGGCACCGTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
* * * * *
619950 CCTCAAAGAGCAAGACACCTTTTAAAGCCCACATAAGTTGGTGGCA-CTTCCCAGT
1 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTT-TCAGT
* * **
620005 CCTCAAAGAGTAGGACGCCTTTCAATGCCCACACAAGTTGGTGGCATTTTTCAGT
1 CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
* * * *
620060 CCTCAAAAAGCAAGATGTTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTTTAGT
1 CCTCAAAGAGCAGGACG----C-CTTT-CAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
*
620121 CCTCAAAGAGCAGGATGCCTCGCCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGT
1 CCTCAAAGAGCAGGA-----CGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGT
* * * *
620181 CCGCAAAGAGTAGGATGCTTTCTCTCTGCAAAGCCCACATAAGTTGGTGGCACCTTTCAGT
1 CCTCAAAGAGCAGGACGC---CT-T-T-CAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
** * *
620242 CCTCAAAGAGCAGGACGCCTTTCCGTTTCAAAGCCCACATGAGTTGGTGGCACTTTTTAGT
1 CCTCAAAGAGCAGGACG-----CC-TTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
620303 CCTCAAAGAGCAGGA
1 CCTCAAAGAGCAGGA
620318 TGCACCTTAT
Statistics
Matches: 397, Mismatches: 52, Indels: 52
0.79 0.10 0.10
Matches are distributed among these distances:
54 4 0.01
55 195 0.49
56 4 0.01
58 2 0.01
59 5 0.01
60 45 0.11
61 132 0.33
62 5 0.01
63 2 0.01
64 1 0.00
66 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (55 bp):
CCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGT
Found at i:623811 original size:51 final size:51
Alignment explanation
Indices: 623736--623956 Score: 205
Period size: 51 Copynumber: 4.3 Consensus size: 51
623726 TTATTTCTGA
* * * * *
623736 GGGGAGACTCCAACCCCGGCTTTATTTCCAAAATATTGA-TTTCTCATAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTC-CATAATC
* * ** **
623787 GAGGATACTCCAACCCTGGTTTTATTTCTTAAACACTAATTTTCCACCATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTCCATAATC
* * *
623838 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTCC-ATAATC
* * *
623890 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATCTTTCGC--AATC
1 GGGGATACTCCAACCCCGGTTTTATTTCC-AAAACACTAAT-TTTC-CATAATC
* *
623942 GAGGATACTCTAACC
1 GGGGATACTCCAACC
623957 TCATTATTTC
Statistics
Matches: 139, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
51 74 0.53
52 49 0.35
53 11 0.08
54 4 0.03
55 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTCCATAATC
Found at i:623913 original size:52 final size:51
Alignment explanation
Indices: 623775--623956 Score: 174
Period size: 52 Copynumber: 3.5 Consensus size: 51
623765 AAAATATTGA
* ** *
623775 TTTCTCATAATCGAGGATACTCCAACCCTGGTTTTA-TTTCTTAAACACTAAT
1 TTTC-CATAATCGGGGATACTCCAACCC-GGTTTTATTTTCAAAAACACCAAT
**
623827 TTTCCACCATCGGGGATACTCCAACCCCGGTTTTATTTTC-AAAACACCAAT
1 TTTCCATAATCGGGGATACTCCAA-CCCGGTTTTATTTTCAAAAACACCAAT
* * *
623878 TTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAAT
1 TTTCC-ATAATCGGGGATACTCCAAC-CCGGTTTTATTTTCAAAAACACCAAT
* *
623931 CTTTCGC--AATCGAGGATACTCTAACC
1 -TTTC-CATAATCGGGGATACTCCAACC
623957 TCATTATTTC
Statistics
Matches: 111, Mismatches: 12, Indels: 15
0.80 0.09 0.11
Matches are distributed among these distances:
51 40 0.36
52 55 0.50
53 11 0.10
54 4 0.04
55 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (51 bp):
TTTCCATAATCGGGGATACTCCAACCCGGTTTTATTTTCAAAAACACCAAT
Found at i:624019 original size:108 final size:106
Alignment explanation
Indices: 623890--624096 Score: 249
Period size: 107 Copynumber: 1.9 Consensus size: 106
623880 TCCTTTAATC
* *
623890 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATCTTTCGCAA-TCGAGGATACTCTA
1 GGGGATACTCCAACTCCGATTTTATTTCC-AAAACACCAATCTTTCACAACT-GAGGATACTCCA
*
623954 ACCTCATTA-TTTCATCGGGGATACTCCAACCCCGTTACCTCCGA
64 ACCTCATTATTTTCA--AGGGATACTCCAACCCCGTTACCTCCGA
* * * * * * *
623998 GGGGATACTCCAA-TCTTGATTTTATTTCCTAATCATCGATTTTTCACAACTGGGGATACTCCAA
1 GGGGATACTCCAACTC-CGATTTTATTTCCAAAACACCAATCTTTCACAACTGAGGATACTCCAA
*
624062 CCTCCTTATTTTCAAGGGATACTCCAACCCCGTTA
65 CCTCATTATTTTCAAGGGATACTCCAACCCCGTTA
624097 TTATCTCCAA
Statistics
Matches: 85, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
106 20 0.24
107 34 0.40
108 31 0.36
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.31
Consensus pattern (106 bp):
GGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATCTTTCACAACTGAGGATACTCCAAC
CTCATTATTTTCAAGGGATACTCCAACCCCGTTACCTCCGA
Found at i:629588 original size:20 final size:20
Alignment explanation
Indices: 629565--629615 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
629555 CCTTCAGATG
*
629565 TATCCATACATAATGCACAA
1 TATCGATACATAATGCACAA
* *
629585 TATCGATACATAATGCATAG
1 TATCGATACATAATGCACAA
629605 TATCGATACAT
1 TATCGATACAT
629616 TGTATCAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (20 bp):
TATCGATACATAATGCACAA
Found at i:629736 original size:13 final size:12
Alignment explanation
Indices: 629718--629762 Score: 53
Period size: 13 Copynumber: 4.0 Consensus size: 12
629708 CATACAAGAG
629718 GTATCGATACATT
1 GTATCGATACA-T
629731 GTATCGATACAT
1 GTATCGATACAT
629743 G-ATC-A-A-AT
1 GTATCGATACAT
629751 GTATCGATACAT
1 GTATCGATACAT
629763 TGGCTTGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
8 3 0.11
9 4 0.14
10 2 0.07
11 4 0.14
12 4 0.14
13 11 0.39
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.33
Consensus pattern (12 bp):
GTATCGATACAT
Found at i:630021 original size:64 final size:64
Alignment explanation
Indices: 629947--630074 Score: 247
Period size: 64 Copynumber: 2.0 Consensus size: 64
629937 AAGAGCTTCC
629947 AGCAGCAAAACACAAGTAGAACCAACCAAGAAACATCAAGAGATCGAAGATTTCAAGTTTTATT
1 AGCAGCAAAACACAAGTAGAACCAACCAAGAAACATCAAGAGATCGAAGATTTCAAGTTTTATT
*
630011 AGCAGCAAAACACAAGTAGAACCAACCAAGAAACATCAAGAGATCGAAGCTTTCAAGTTTTATT
1 AGCAGCAAAACACAAGTAGAACCAACCAAGAAACATCAAGAGATCGAAGATTTCAAGTTTTATT
630075 CATTTTCTCA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.19
Consensus pattern (64 bp):
AGCAGCAAAACACAAGTAGAACCAACCAAGAAACATCAAGAGATCGAAGATTTCAAGTTTTATT
Found at i:631061 original size:13 final size:13
Alignment explanation
Indices: 631043--631067 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
631033 CATTATGCTT
631043 TGTATCGATACAA
1 TGTATCGATACAA
631056 TGTATCGATACA
1 TGTATCGATACA
631068 TGTTCATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:631082 original size:19 final size:20
Alignment explanation
Indices: 631058--631108 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
631048 CGATACAATG
**
631058 TATCGATACATGTTC-ATTA
1 TATCGATACATGGACAATTA
*
631077 TATCGATACATGGACAATTG
1 TATCGATACATGGACAATTA
631097 TATCGATACATG
1 TATCGATACATG
631109 AAACTGGCAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.46
20 15 0.54
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (20 bp):
TATCGATACATGGACAATTA
Found at i:631102 original size:20 final size:20
Alignment explanation
Indices: 631052--631108 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 20
631042 TTGTATCGAT
*
631052 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* *
631071 TC-ATTATATCGATACATGG
1 ACAATTGTATCGATACATGG
631090 ACAATTGTATCGATACATG
1 ACAATTGTATCGATACATG
631109 AAACTGGCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.48
20 15 0.48
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:631981 original size:34 final size:35
Alignment explanation
Indices: 631943--632009 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
631933 CCTTACAACA
631943 CTATC-TTTC-AAGGCTAAGATAGAAACCTCTCTCT
1 CTATCTTTTCAAAGGCTAAGATA-AAACCTCTCTCT
631977 CTATCTTTTTCAAAGGCTAAGATAAAACCTCTC
1 CTATC-TTTTCAAAGGCTAAGATAAAACCTCTC
632010 AATCACTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 5 0.17
36 13 0.43
37 12 0.40
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.33
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAAAACCTCTCTCT
Found at i:632421 original size:20 final size:20
Alignment explanation
Indices: 632379--632417 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
632369 CGTGTAAATG
* *
632379 TATCGATACAATTTTTGATA
1 TATCGATACAATATTTGAAA
632399 TATCGATAC-ATATTTGAAA
1 TATCGATACAATATTTGAAA
632418 ATATAGCCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATACAATATTTGAAA
Found at i:632486 original size:13 final size:13
Alignment explanation
Indices: 632468--632492 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
632458 CAATTTTTTG
632468 TGTATCGATACAT
1 TGTATCGATACAT
632481 TGTATCGATACA
1 TGTATCGATACA
632493 AACTTGCTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:640890 original size:13 final size:13
Alignment explanation
Indices: 640872--640897 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
640862 TACAGCAAGT
640872 ATGTATCGATACA
1 ATGTATCGATACA
640885 ATGTATCGATACA
1 ATGTATCGATACA
640898 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:643147 original size:21 final size:21
Alignment explanation
Indices: 643114--643158 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
643104 TTGCAAGTTG
*
643114 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
643136 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
643156 AAA
1 AAA
643159 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:644655 original size:21 final size:21
Alignment explanation
Indices: 644614--644657 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
644604 CTCTCCTTTA
* *
644614 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
644635 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
644656 TC
1 TC
644658 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Done.