Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
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: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 135 of 182
Found at i:41555749 original size:28 final size:27
Alignment explanation
Indices: 41555717--41555782 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 27
41555707 AAAATTCGGT
41555717 TCGGTTAACGGTTA-AAAAATTTGAGAGG
1 TCGGTTAACGGTTACAAAAATTT-AG-GG
* *
41555745 TCGGTTAATTCGGTTACAAGAATTTCGGG
1 TCGGTTAA--CGGTTACAAAAATTTAGGG
41555774 TCGGTTAAC
1 TCGGTTAAC
41555783 CGACTGAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
27 1 0.03
28 8 0.24
29 10 0.30
30 7 0.21
31 7 0.21
ACGTcount: A:0.29, C:0.12, G:0.27, T:0.32
Consensus pattern (27 bp):
TCGGTTAACGGTTACAAAAATTTAGGG
Found at i:41557423 original size:15 final size:16
Alignment explanation
Indices: 41557403--41557437 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41557393 ATCCTAATAC
*
41557403 ATATTATT-ATATTTT
1 ATATTATTAAAATTTT
41557418 ATATTATTAAAATTTT
1 ATATTATTAAAATTTT
41557434 ATAT
1 ATAT
41557438 ATTTTTATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTATTAAAATTTT
Found at i:41557452 original size:18 final size:17
Alignment explanation
Indices: 41557403--41557452 Score: 50
Period size: 18 Copynumber: 2.9 Consensus size: 17
41557393 ATCCTAATAC
*
41557403 ATATTATT-ATATTT-T
1 ATATTATTAAAATTTAT
41557418 ATATTATTAAAATTTTAT
1 ATATTATTAAAA-TTTAT
*
41557436 ATATTTTTATAAATTTA
1 ATATTATTA-AAATTTA
41557453 ATCATATTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 8 0.28
16 2 0.07
17 3 0.10
18 13 0.45
19 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATTATTAAAATTTAT
Found at i:41557459 original size:20 final size:18
Alignment explanation
Indices: 41557417--41557460 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
41557407 TATTATATTT
*
41557417 TATATTATTAAAATTTTA
1 TATATTATTAAAATTTAA
*
41557435 TATATTTTTATAAATTTAA
1 TATATTATTA-AAATTTAA
41557454 TCATATT
1 T-ATATT
41557461 CAGATTGCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 9 0.41
19 8 0.36
20 5 0.23
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TATATTATTAAAATTTAA
Found at i:41557490 original size:15 final size:15
Alignment explanation
Indices: 41557470--41557506 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
41557460 TCAGATTGCG
41557470 TATTTTT-ATATTATT
1 TATTTTTAATATTA-T
41557485 TATTTTTAATATTAT
1 TATTTTTAATATTAT
41557500 TATTTTT
1 TATTTTT
41557507 CTTTTATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TATTTTTAATATTAT
Found at i:41558005 original size:14 final size:15
Alignment explanation
Indices: 41557985--41558025 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
41557975 TTTGATTGCC
41557985 AGTAAAATGTTTTC-
1 AGTAAAATGTTTTCT
* *
41557999 CGTAAAATGATTTCT
1 AGTAAAATGTTTTCT
41558014 AG-AAAATGTTTT
1 AGTAAAATGTTTT
41558026 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (15 bp):
AGTAAAATGTTTTCT
Found at i:41561738 original size:19 final size:19
Alignment explanation
Indices: 41561702--41561772 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
41561692 ATTTGAGATG
* *
41561702 AGTTT-AAAACTATAAAAA
1 AGTTTAAAAATTATTAAAA
41561720 AGTTTAAAAATTATTAAAA
1 AGTTTAAAAATTATTAAAA
* *
41561739 A-TATTAATAATTACTAAAA
1 AGT-TTAAAAATTATTAAAA
*
41561758 AGTTGTAAAAGTTAT
1 AGTT-TAAAAATTAT
41561773 CTAAGAAATT
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
18 6 0.14
19 28 0.67
20 8 0.19
ACGTcount: A:0.55, C:0.03, G:0.07, T:0.35
Consensus pattern (19 bp):
AGTTTAAAAATTATTAAAA
Found at i:41566252 original size:21 final size:21
Alignment explanation
Indices: 41566226--41566266 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
41566216 ATCTGCTCAA
* *
41566226 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
41566247 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
41566267 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:41572374 original size:2 final size:2
Alignment explanation
Indices: 41572367--41572412 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
41572357 AGAAAATAAG
41572367 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
41572409 GA GA
1 GA GA
41572413 TTCCCACTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41582351 original size:20 final size:21
Alignment explanation
Indices: 41582312--41582353 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
41582302 AAACTATATT
* *
41582312 AAAAGAGATGGAGAAGGTAGA
1 AAAACAGATGAAGAAGGTAGA
41582333 AAAACAGATGAAGAA-GTAGA
1 AAAACAGATGAAGAAGGTAGA
41582353 A
1 A
41582354 GATAATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.57, C:0.02, G:0.31, T:0.10
Consensus pattern (21 bp):
AAAACAGATGAAGAAGGTAGA
Found at i:41588593 original size:21 final size:21
Alignment explanation
Indices: 41588567--41588608 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
41588557 GCAATTTTGT
41588567 AATTAAATG-GAAATTAAAACA
1 AATT-AATGAGAAATTAAAACA
41588588 AATTAATGAGAAATTAAAACA
1 AATTAATGAGAAATTAAAACA
41588609 TTTTAACTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (21 bp):
AATTAATGAGAAATTAAAACA
Found at i:41591665 original size:13 final size:14
Alignment explanation
Indices: 41591645--41591684 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
41591635 GTAACGTTTT
41591645 TGTTTTATTTTGGA
1 TGTTTTATTTTGGA
*
41591659 T-TTTTATTTTGGGT
1 TGTTTTATTTT-GGA
41591673 TGTTTTATTTTG
1 TGTTTTATTTTG
41591685 TTTATAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
13 9 0.39
14 5 0.22
15 9 0.39
ACGTcount: A:0.10, C:0.00, G:0.20, T:0.70
Consensus pattern (14 bp):
TGTTTTATTTTGGA
Found at i:41591680 original size:15 final size:15
Alignment explanation
Indices: 41591644--41591684 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
41591634 TGTAACGTTT
41591644 TTGTTTTATTTT-GG
1 TTGTTTTATTTTGGG
*
41591658 AT-TTTTATTTTGGG
1 TTGTTTTATTTTGGG
41591672 TTGTTTTATTTTG
1 TTGTTTTATTTTG
41591685 TTTATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 10 0.43
ACGTcount: A:0.10, C:0.00, G:0.20, T:0.71
Consensus pattern (15 bp):
TTGTTTTATTTTGGG
Found at i:41601580 original size:37 final size:37
Alignment explanation
Indices: 41601530--41601608 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
41601520 TTATTACGAA
* * *
41601530 GTCTTACCCGGACATAATCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
*
41601567 GTCTTACCCGGACAAAATCCCCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
41601604 GTCTT
1 GTCTT
41601609 TAGAGCTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATCCCCACACGAAGTCATCGG
Found at i:41602120 original size:24 final size:23
Alignment explanation
Indices: 41602072--41602129 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
41602062 TAATCAAACA
41602072 TTATTATATATATATCATATCATT
1 TTATTAT-TATATATCATATCATT
*
41602096 TTATTATTAT-TATCATTATTTATT
1 TTATTATTATATATCA-TA-TCATT
41602120 TTATT-TTATA
1 TTATTATTATA
41602130 CTTTTCAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
22 5 0.17
23 9 0.30
24 16 0.53
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (23 bp):
TTATTATTATATATCATATCATT
Found at i:41612287 original size:23 final size:23
Alignment explanation
Indices: 41612261--41612307 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
41612251 GTAATTATAA
41612261 ATACATGTGTAATAAATATATGT
1 ATACATGTGTAATAAATATATGT
* *
41612284 ATACATTTGTAATTAATATATGT
1 ATACATGTGTAATAAATATATGT
41612307 A
1 A
41612308 CATACTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.43
Consensus pattern (23 bp):
ATACATGTGTAATAAATATATGT
Found at i:41613340 original size:25 final size:25
Alignment explanation
Indices: 41613310--41613400 Score: 119
Period size: 25 Copynumber: 3.6 Consensus size: 25
41613300 CTTTAGCGCA
* *
41613310 CTCTCTAATTCTTAGCACATCAGCG
1 CTCTCTGATTATTAGCACATCAGCG
*
41613335 CTCTCTGATTATTAGCACATCAGTG
1 CTCTCTGATTATTAGCACATCAGCG
* *
41613360 CTCTCTGATTATTAGCACGTCAGTG
1 CTCTCTGATTATTAGCACATCAGCG
* *
41613385 TTCTCTGATTACTAGC
1 CTCTCTGATTATTAGC
41613401 TGATAACACT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 60 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.36
Consensus pattern (25 bp):
CTCTCTGATTATTAGCACATCAGCG
Found at i:41613695 original size:15 final size:15
Alignment explanation
Indices: 41613670--41613704 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
41613660 GACTCTATTT
*
41613670 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
41613684 TAATTAATATTAAGA
1 TAATTAATATTAAGA
41613699 TAATTA
1 TAATTA
41613705 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:41614800 original size:24 final size:22
Alignment explanation
Indices: 41614738--41614803 Score: 96
Period size: 22 Copynumber: 3.0 Consensus size: 22
41614728 ACCGCATCAC
* *
41614738 TAGCACGTCAATGCTCTCTGTT
1 TAGCACATCAGTGCTCTCTGTT
*
41614760 TAGCACATCTGTGCTCTCTGTT
1 TAGCACATCAGTGCTCTCTGTT
*
41614782 TAGCACTTCAGTGCTCTCTGTT
1 TAGCACATCAGTGCTCTCTGTT
41614804 CATTAGTGCA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.15, C:0.27, G:0.18, T:0.39
Consensus pattern (22 bp):
TAGCACATCAGTGCTCTCTGTT
Found at i:41614887 original size:6 final size:6
Alignment explanation
Indices: 41614876--41614901 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
41614866 TACTTTGGGC
41614876 TAAGAA TAAGAA TAAGAA TAAGAA TA
1 TAAGAA TAAGAA TAAGAA TAAGAA TA
41614902 TGAGATAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.19
Consensus pattern (6 bp):
TAAGAA
Found at i:41614949 original size:18 final size:18
Alignment explanation
Indices: 41614923--41614964 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
41614913 ATTGAAAATA
41614923 GAATGTGAAAA-ACAATAGT
1 GAAT-TGAAAATACAAT-GT
*
41614942 GAATTGAAAATAGAATGT
1 GAATTGAAAATACAATGT
41614960 GAATT
1 GAATT
41614965 ATGTTGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.50, C:0.02, G:0.21, T:0.26
Consensus pattern (18 bp):
GAATTGAAAATACAATGT
Found at i:41615514 original size:18 final size:19
Alignment explanation
Indices: 41615476--41615514 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41615466 GATGATAAGA
*
41615476 TTAAATCATGATGTGAATG
1 TTAAATAATGATGTGAATG
*
41615495 TTAAATAATTATGT-AATG
1 TTAAATAATGATGTGAATG
41615513 TT
1 TT
41615515 TGCATTTGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (19 bp):
TTAAATAATGATGTGAATG
Found at i:41617576 original size:22 final size:21
Alignment explanation
Indices: 41617546--41617591 Score: 51
Period size: 22 Copynumber: 2.1 Consensus size: 21
41617536 TTAAATAAGT
41617546 GAAATATGATG-TTTTAGATCCTA
1 GAAATATGA-GATTTT-GA-CCTA
41617569 GAAA-ATGAGATTTTGACCTA
1 GAAATATGAGATTTTGACCTA
41617589 GAA
1 GAA
41617592 TGGGAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.32
21 3 0.14
22 8 0.36
23 4 0.18
ACGTcount: A:0.39, C:0.09, G:0.20, T:0.33
Consensus pattern (21 bp):
GAAATATGAGATTTTGACCTA
Found at i:41618137 original size:44 final size:44
Alignment explanation
Indices: 41618050--41618144 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 44
41618040 TATCTCAAGT
* * *
41618050 TCCATGTTTATAACATGGCAATTAAGGAAGAATTGATGGAAAAG
1 TCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGAAAAAG
*
41618094 TCCATGTTTATAACATGGCAATTAAGAAAGAATTGGCGAAAAAG
1 TCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGAAAAAG
41618138 TACCATG
1 T-CCATG
41618145 GTTGATCCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
44 41 0.89
45 5 0.11
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (44 bp):
TCCATGTTTATAACATGGCAATTAAGAAAGAATTGACGAAAAAG
Found at i:41618223 original size:50 final size:50
Alignment explanation
Indices: 41618162--41618509 Score: 484
Period size: 50 Copynumber: 7.0 Consensus size: 50
41618152 CATGTAAACT
*
41618162 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATAGCGTTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
* * * *
41618212 CGAGATAAGAGGTCCCATGTTAGACCATGTCTGGGACATGGCATTGGCAT
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
*
41618262 CGAGATTAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
*
41618312 C-ATGATGAGAGGTCACATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
1 CGA-GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
*
41618362 CGAGATGAGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCAC
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
* ** * * * *
41618412 TGAGATGAGAGGTCCCCCGTCAGACCATGTCT-GGACATGGCATAGGCAT
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
* ** * * *
41618461 CGATATGAGAACTCCCATGTAAGACCATATCTGGGATATGGCATTGGCA
1 CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
41618510 GTACAGGAAA
Statistics
Matches: 264, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
49 39 0.15
50 224 0.85
51 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.22
Consensus pattern (50 bp):
CGAGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCAC
Found at i:41623574 original size:25 final size:26
Alignment explanation
Indices: 41623546--41623597 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
41623536 ACTTGCGAGT
*
41623546 TGTAGTCACCAGTGGGCCT-GTGAGC
1 TGTAGTCACCAGAGGGCCTAGTGAGC
**
41623571 TGTAGTTGCCAGAGGGCCTAGTGAGC
1 TGTAGTCACCAGAGGGCCTAGTGAGC
41623597 T
1 T
41623598 ACAGTCGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.17, C:0.21, G:0.37, T:0.25
Consensus pattern (26 bp):
TGTAGTCACCAGAGGGCCTAGTGAGC
Found at i:41626244 original size:15 final size:15
Alignment explanation
Indices: 41626226--41626256 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41626216 TTAAACCAAA
*
41626226 AAATTAATTTTTTAT
1 AAATTAAGTTTTTAT
41626241 AAATTAAGTTTTTAT
1 AAATTAAGTTTTTAT
41626256 A
1 A
41626257 TTTATTCTTT
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:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (15 bp):
AAATTAAGTTTTTAT
Found at i:41626906 original size:15 final size:15
Alignment explanation
Indices: 41626879--41626907 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
41626869 TCTCAACCTA
41626879 TAAACTTTATTTTTT
1 TAAACTTTATTTTTT
41626894 TAAA-TTTATTTTTT
1 TAAACTTTATTTTTT
41626908 CGATTCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TAAACTTTATTTTTT
Found at i:41630262 original size:61 final size:58
Alignment explanation
Indices: 41630196--41630311 Score: 137
Period size: 61 Copynumber: 1.9 Consensus size: 58
41630186 TTGAATTATC
* * *
41630196 TTAATA-TAATATTAAATTTACTATTTATCTTCTAGATACA-TATTGTATTAATTTAATAGAT
1 TTAATATTAA-ATTAAATCTAATATTTATC-T-T-GATA-AGTATTATATTAATTTAATAGAT
*
41630257 TTAATATTAAATTTAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATA
1 TTAATATTAAATTAAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATA
41630312 TTAAATTGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
57 1 0.02
58 21 0.43
59 1 0.02
60 1 0.02
61 22 0.45
62 3 0.06
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (58 bp):
TTAATATTAAATTAAATCTAATATTTATCTTGATAAGTATTATATTAATTTAATAGAT
Found at i:41634195 original size:68 final size:68
Alignment explanation
Indices: 41634104--41634234 Score: 199
Period size: 68 Copynumber: 1.9 Consensus size: 68
41634094 AGCTTGGTTA
* *
41634104 TGGCAACCAATAAAGTCTACCAGGATATTAAACACGGGGTTACAAAGTGTAAGAACATAGCTCGA
1 TGGCAACCAATAAAGTCCACCAGGACATTAAACACGGGGTTACAAAGTGTAAGAACATAGCTCGA
41634169 CTG
66 CTG
* * * * *
41634172 TGGCAACCAATAGAGTCCGCCAGGACATTAAACATGGGGTTACAAGGTGTAAGACCATAGCTC
1 TGGCAACCAATAAAGTCCACCAGGACATTAAACACGGGGTTACAAAGTGTAAGAACATAGCTC
41634235 AGCTATGACA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 56 1.00
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.20
Consensus pattern (68 bp):
TGGCAACCAATAAAGTCCACCAGGACATTAAACACGGGGTTACAAAGTGTAAGAACATAGCTCGA
CTG
Found at i:41637195 original size:44 final size:44
Alignment explanation
Indices: 41637130--41637249 Score: 222
Period size: 44 Copynumber: 2.7 Consensus size: 44
41637120 TAACCAACCA
41637130 CATATATCACATACAAGTATTCTCACATATTAAAATAAGTACAT
1 CATATATCACATACAAGTATTCTCACATATTAAAATAAGTACAT
* *
41637174 CATATATCACATACAAATATTCTCACATCTTAAAATAAGTACAT
1 CATATATCACATACAAGTATTCTCACATATTAAAATAAGTACAT
41637218 CATATATCACATACAAGTATTCTCACATATTA
1 CATATATCACATACAAGTATTCTCACATATTA
41637250 CCTATCATAA
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 72 1.00
ACGTcount: A:0.44, C:0.20, G:0.03, T:0.33
Consensus pattern (44 bp):
CATATATCACATACAAGTATTCTCACATATTAAAATAAGTACAT
Found at i:41647562 original size:71 final size:71
Alignment explanation
Indices: 41647439--41647601 Score: 247
Period size: 71 Copynumber: 2.3 Consensus size: 71
41647429 ACGAGATAAG
* * * *
41647439 GTTGCTCACACGAGTTCTGAGAATAAGCCTGCTCACACGAGTTGTGAGTCGGGATGGTAACTTTA
1 GTTGCTTACACGAGCTATGAAAATAAGCCTGCTCACACGAGTTGTGAGTCGGGATGGTAACTTTA
41647504 CATGAT
66 CATGAT
* *
41647510 TTTG-TTAACACGAGCTATGAAAATAAGCCTGCTCACACGAGTTGTGGGTCGGGATGGTAACTTT
1 GTTGCTT-ACACGAGCTATGAAAATAAGCCTGCTCACACGAGTTGTGAGTCGGGATGGTAACTTT
41647574 ACATGAT
65 ACATGAT
*
41647581 GTTGCTTACACGAGCTGTGAA
1 GTTGCTTACACGAGCTATGAA
41647602 GAATCCACAA
Statistics
Matches: 82, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
70 1 0.01
71 79 0.96
72 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.29
Consensus pattern (71 bp):
GTTGCTTACACGAGCTATGAAAATAAGCCTGCTCACACGAGTTGTGAGTCGGGATGGTAACTTTA
CATGAT
Found at i:41654702 original size:39 final size:38
Alignment explanation
Indices: 41654614--41654703 Score: 92
Period size: 39 Copynumber: 2.3 Consensus size: 38
41654604 AATCACGAAG
* *
41654614 AAAAAAAAAGAAATTTTGAAAAAAAGTTGAAAAGAAAAAG
1 AAAAAAAAA-AAATTTTGAAAAAAAATT-AAAAGAAAAAC
* **
41654654 AAAAGAAAAAAATTTTGAAAAAAAAATT-AAAGAATATTC
1 AAAAAAAAAAAATTTTG-AAAAAAAATTAAAAGAA-AAAC
41654693 AAAAAAAAAAA
1 AAAAAAAAAAA
41654704 GGTCCACATG
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
38 6 0.14
39 19 0.45
40 17 0.40
ACGTcount: A:0.72, C:0.01, G:0.10, T:0.17
Consensus pattern (38 bp):
AAAAAAAAAAAATTTTGAAAAAAAATTAAAAGAAAAAC
Found at i:41654999 original size:7 final size:7
Alignment explanation
Indices: 41654987--41655032 Score: 85
Period size: 7 Copynumber: 6.7 Consensus size: 7
41654977 GTTTGTTTGT
41654987 TTTTTTC
1 TTTTTTC
41654994 TTTTTTC
1 TTTTTTC
41655001 TTTTTTC
1 TTTTTTC
41655008 TTTTTTC
1 TTTTTTC
41655015 -TTTTTC
1 TTTTTTC
41655021 TTTTTTC
1 TTTTTTC
41655028 TTTTT
1 TTTTT
41655033 GTTCCTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
6 6 0.16
7 32 0.84
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTTTC
Found at i:41655011 original size:13 final size:13
Alignment explanation
Indices: 41654969--41655032 Score: 85
Period size: 13 Copynumber: 4.8 Consensus size: 13
41654959 AAAGCTAGTA
*
41654969 TTTTTCTTGTTTGT
1 TTTTTCTT-TTTCT
*
41654983 TTGTT-TTTTTCT
1 TTTTTCTTTTTCT
41654995 TTTTTCTTTTTTCT
1 TTTTTC-TTTTTCT
41655009 TTTTTCTTTTTCT
1 TTTTTCTTTTTCT
41655022 TTTTTCTTTTT
1 TTTTTCTTTTT
41655033 GTTCCTTTGT
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
12 8 0.18
13 20 0.44
14 17 0.38
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (13 bp):
TTTTTCTTTTTCT
Found at i:41659766 original size:23 final size:23
Alignment explanation
Indices: 41659740--41659797 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
41659730 AGCTCGTATG
*
41659740 AGCTTATCGTTTCAGCTCTATAA
1 AGCTTACCGTTTCAGCTCTATAA
*
41659763 AGCTTACCGTTTCAGCTCTATAG
1 AGCTTACCGTTTCAGCTCTATAA
41659786 AGCTTACCGTTT
1 AGCTTACCGTTT
41659798 ATCAGCTTGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (23 bp):
AGCTTACCGTTTCAGCTCTATAA
Found at i:41664898 original size:24 final size:25
Alignment explanation
Indices: 41664843--41664899 Score: 66
Period size: 24 Copynumber: 2.3 Consensus size: 25
41664833 CTAAACGATA
41664843 TATTCTTTTCTGTTTTTGAATCGTTTT
1 TATT-TTTTCTGTTTTTGAATC-TTTT
41664870 T-TTTTTT-TGTTTTTGAAT-TTTT
1 TATTTTTTCTGTTTTTGAATCTTTT
41664892 GTATTTTT
1 -TATTTTT
41664900 GTATTGATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
22 4 0.14
23 1 0.04
24 16 0.57
25 4 0.14
26 2 0.07
27 1 0.04
ACGTcount: A:0.11, C:0.05, G:0.11, T:0.74
Consensus pattern (25 bp):
TATTTTTTCTGTTTTTGAATCTTTT
Found at i:41675602 original size:239 final size:239
Alignment explanation
Indices: 41675177--41675653 Score: 900
Period size: 239 Copynumber: 2.0 Consensus size: 239
41675167 TAAGTAGAAT
41675177 GTGAATAATGAATCAAATGGTAGACATAATCGTCAAAAGCAGGTATTTGAAAGGATTCACAAGGT
1 GTGAATAATGAATCAAATGGTAGACATAATCGTCAAAAGCAGGTATTTGAAAGGATTCACAAGGT
*
41675242 TCACGGAGTTGCACAATCATACCATGCATTAGACGATTGATTATAGATTCATTCACACATGCATC
66 TCACGGAGTTGCACAATCATACCATGCATTAGACGATTGACTATAGATTCATTCACACATGCATC
41675307 ATAAAAATGATCAGAAACAATAATCTTATTATCAACAACCAAAACAGATAGATCATCGTCAAGCA
131 ATAAAAATGATCAGAAACAATAATCTTATTATCAACAACCAAAACAGATAGATCATCGTCAAGCA
41675372 AAATGGAACAACTAAGCACAACACGATCTAAGTGTTTTACAAAC
196 AAATGGAACAACTAAGCACAACACGATCTAAGTGTTTTACAAAC
* *
41675416 GTGAATAATGAATCAAATGGTAGACATAATCGTCACAAGCAGGTATTTGAAAGGATTCACACGGT
1 GTGAATAATGAATCAAATGGTAGACATAATCGTCAAAAGCAGGTATTTGAAAGGATTCACAAGGT
*
41675481 TCACGGAGTTGCACAATCATACCGTGCATTAGACGATTGACTATAGATTCATTCACACATGCATC
66 TCACGGAGTTGCACAATCATACCATGCATTAGACGATTGACTATAGATTCATTCACACATGCATC
* *
41675546 ATAAAAATGATCAGAAACAATAATCTTATTGTCAACAACCAAAACAGATGGATCATCGTCAAGCA
131 ATAAAAATGATCAGAAACAATAATCTTATTATCAACAACCAAAACAGATAGATCATCGTCAAGCA
41675611 AAATGGAACAACTAAGCACAACACGATCTAAGTGTTTTACAAA
196 AAATGGAACAACTAAGCACAACACGATCTAAGTGTTTTACAAA
41675654 AGATAAATCT
Statistics
Matches: 232, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
239 232 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (239 bp):
GTGAATAATGAATCAAATGGTAGACATAATCGTCAAAAGCAGGTATTTGAAAGGATTCACAAGGT
TCACGGAGTTGCACAATCATACCATGCATTAGACGATTGACTATAGATTCATTCACACATGCATC
ATAAAAATGATCAGAAACAATAATCTTATTATCAACAACCAAAACAGATAGATCATCGTCAAGCA
AAATGGAACAACTAAGCACAACACGATCTAAGTGTTTTACAAAC
Found at i:41680139 original size:23 final size:21
Alignment explanation
Indices: 41680092--41680139 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 21
41680082 AATGTAGGTT
*
41680092 ATATATTATTTTTATAATTTT
1 ATATATTATTTTTATAATTTC
41680113 ATATATTATGATTTTATTAA-TTC
1 ATATATTAT--TTTTA-TAATTTC
41680136 ATAT
1 ATAT
41680140 TTTAATAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 9 0.39
23 11 0.48
24 3 0.13
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (21 bp):
ATATATTATTTTTATAATTTC
Found at i:41680253 original size:61 final size:58
Alignment explanation
Indices: 41680114--41680270 Score: 174
Period size: 61 Copynumber: 2.6 Consensus size: 58
41680104 TATAATTTTA
* *
41680114 TATATTATGATTTTATT-AATTCATATTTTAATAATAATTATATTAAGAATATTATTAAAT
1 TATA-TATTATTTTATTAAATT-ATA-TTTAATAATAATTATATTAAGAATATGATTAAAT
* * * *
41680174 TATATATTATTTTATTAAATTGTGTTTAATGATAATTATGTTAA-AATATGATTAAAT
1 TATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAGAATATGATTAAAT
*
41680231 TATTTATTTTTATTTTTATTAAATTATATTTAATAATAAT
1 TA--TA-TATTA-TTTTATTAAATTATATTTAATAATAAT
41680271 CTTATTACAA
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
57 14 0.17
58 18 0.22
59 14 0.17
60 12 0.15
61 24 0.29
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (58 bp):
TATATATTATTTTATTAAATTATATTTAATAATAATTATATTAAGAATATGATTAAAT
Found at i:41685939 original size:19 final size:20
Alignment explanation
Indices: 41685901--41685939 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
41685891 TAAAAATATT
* *
41685901 TTTTATTTTTATTAATTAAA
1 TTTTATTTTGATTAAGTAAA
41685921 TTTTATTTTGA-TAAGTAAA
1 TTTTATTTTGATTAAGTAAA
41685940 ATTATTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
TTTTATTTTGATTAAGTAAA
Found at i:41688135 original size:44 final size:44
Alignment explanation
Indices: 41688087--41688182 Score: 174
Period size: 44 Copynumber: 2.2 Consensus size: 44
41688077 ACTCAGAAAT
* *
41688087 TCTTTCCTCTAATTCAAGTATCAAATGATATCATTTCTATGATA
1 TCTTTCCTCTAATTCAAGCATCAAATGAGATCATTTCTATGATA
41688131 TCTTTCCTCTAATTCAAGCATCAAATGAGATCATTTCTATGATA
1 TCTTTCCTCTAATTCAAGCATCAAATGAGATCATTTCTATGATA
41688175 TCTTTCCT
1 TCTTTCCT
41688183 TCCTCAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 50 1.00
ACGTcount: A:0.29, C:0.21, G:0.07, T:0.43
Consensus pattern (44 bp):
TCTTTCCTCTAATTCAAGCATCAAATGAGATCATTTCTATGATA
Found at i:41690915 original size:43 final size:43
Alignment explanation
Indices: 41690863--41691051 Score: 299
Period size: 43 Copynumber: 4.4 Consensus size: 43
41690853 TTTTAGAAAT
* *
41690863 AAACGCCGCTAAAGATCAGGACCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* * *
41690906 AAACGCCGCTATAGATCAAGACCTTTAACGGCGC-CTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
*
41690948 AAACGCCGCTATAGATCAGGATCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
* *
41690991 ATACGCCGCTATAGATCAGGACCTTTAGCAGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
41691034 AAACGCCGCTATAGATCA
1 AAACGCCGCTATAGATCA
41691052 ACGCTTTTCC
Statistics
Matches: 132, Mismatches: 13, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
42 37 0.28
43 95 0.72
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCAC
Found at i:41691006 original size:85 final size:86
Alignment explanation
Indices: 41690863--41691051 Score: 299
Period size: 85 Copynumber: 2.2 Consensus size: 86
41690853 TTTTAGAAAT
* *
41690863 AAACGCCGCTAAAGATCAGGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTATAGATCAAGAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
*
41690928 CTTTAACGGCGC-CTTCCCAC
66 CTTTAACAGCGCTCTTCCCAC
* * *
41690948 AAACGCCGCTATAGATCAGGATCTTTAGCGGCGCTTTTCCCACATACGCCGCTATAGATCAGGAC
1 AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
* *
41691013 CTTTAGCAGCGCTTTTCCCAC
66 CTTTAACAGCGCTCTTCCCAC
41691034 AAACGCCGCTATAGATCA
1 AAACGCCGCTATAGATCA
41691052 ACGCTTTTCC
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
85 70 0.74
86 25 0.26
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.23
Consensus pattern (86 bp):
AAACGCCGCTATAGATCAGGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCAAGAC
CTTTAACAGCGCTCTTCCCAC
Found at i:41691060 original size:31 final size:31
Alignment explanation
Indices: 41691022--41691082 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
41691012 CCTTTAGCAG
41691022 CGCTTTTCCCACAAACGCCGCTATAGATCAA
1 CGCTTTTCCCACAAACGCCGCTATAGATCAA
* *
41691053 CGCTTTTCCCACGAACGGCGCTATAGATCA
1 CGCTTTTCCCACAAACGCCGCTATAGATCA
41691083 GGACCTTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.34, G:0.16, T:0.23
Consensus pattern (31 bp):
CGCTTTTCCCACAAACGCCGCTATAGATCAA
Found at i:41691120 original size:43 final size:43
Alignment explanation
Indices: 41691052--41691211 Score: 203
Period size: 43 Copynumber: 3.7 Consensus size: 43
41691042 CTATAGATCA
* * *
41691052 ACGCTTTTCCCACGAACGGCGCTATAGATCAGGACCTTTAGCG
1 ACGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCG
* * * *
41691095 ACACTTTTCCCACAAACGCCACTATAGATCAAGACTTTTAGCA
1 ACGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCG
* *
41691138 ACGCTTTTCTCACAAATGCCGCTATAGATCAAGACCTTTAGCG
1 ACGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCG
* * * *
41691181 ACGCTTCTCTCACGAACACCGCTATAGATCA
1 ACGCTTTTCCCACAAACGCCGCTATAGATCA
41691212 TATTTTTATT
Statistics
Matches: 100, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 100 1.00
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.25
Consensus pattern (43 bp):
ACGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCG
Found at i:41691133 original size:74 final size:74
Alignment explanation
Indices: 41690979--41691126 Score: 237
Period size: 74 Copynumber: 2.0 Consensus size: 74
41690969 TCTTTAGCGG
* *
41690979 CGCTTTTCCCACATACGCCGCTATAGATCAGGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCT
1 CGCTTTTCCCACATACGCCGCTATAGATCAGGACCTTTAGCAGCACTTTTCCCACAAACGCCACT
41691044 ATAGATCAA
66 ATAGATCAA
*
41691053 CGCTTTTCCCACGA-ACGGCGCTATAGATCAGGACCTTTAGC-GACACTTTTCCCACAAACGCCA
1 CGCTTTTCCCAC-ATACGCCGCTATAGATCAGGACCTTTAGCAG-CACTTTTCCCACAAACGCCA
41691116 CTATAGATCAA
64 CTATAGATCAA
41691127 GACTTTTAGC
Statistics
Matches: 69, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
73 1 0.01
74 67 0.97
75 1 0.01
ACGTcount: A:0.27, C:0.33, G:0.16, T:0.24
Consensus pattern (74 bp):
CGCTTTTCCCACATACGCCGCTATAGATCAGGACCTTTAGCAGCACTTTTCCCACAAACGCCACT
ATAGATCAA
Found at i:41691152 original size:117 final size:117
Alignment explanation
Indices: 41690941--41691169 Score: 350
Period size: 117 Copynumber: 2.0 Consensus size: 117
41690931 TAACGGCGCC
* * * * *
41690941 TTCCCACAAACGCCGCTATAGATCAGGATCTTTAGCGGCGCTTTTCCCACATACGCCGCTATAGA
1 TTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGACACTTTTCCCACAAACGCCACTATAGA
* *
41691006 TCAGGACCTTTAGCAGCGCTTTTCCCACAAACGCCGCTATAGATCAACGCTT
66 TCAAGACCTTTAGCAACGCTTTTCCCACAAACGCCGCTATAGATCAACGCTT
* *
41691058 TTCCCACGAACGGCGCTATAGATCAGGACCTTTAGCGACACTTTTCCCACAAACGCCACTATAGA
1 TTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGACACTTTTCCCACAAACGCCACTATAGA
* * *
41691123 TCAAGACTTTTAGCAACGCTTTTCTCACAAATGCCGCTATAGATCAA
66 TCAAGACCTTTAGCAACGCTTTTCCCACAAACGCCGCTATAGATCAA
41691170 GACCTTTAGC
Statistics
Matches: 100, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
117 100 1.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.25
Consensus pattern (117 bp):
TTCCCACAAACGCCGCTATAGATCAGGACCTTTAGCGACACTTTTCCCACAAACGCCACTATAGA
TCAAGACCTTTAGCAACGCTTTTCCCACAAACGCCGCTATAGATCAACGCTT
Found at i:41691161 original size:160 final size:159
Alignment explanation
Indices: 41690894--41691211 Score: 415
Period size: 160 Copynumber: 2.0 Consensus size: 159
41690884 CCTTTAGCGG
* * * *
41690894 CGCTTTTCTCACAAACGCCGCTATAGATCAAGACCTTTAACGGCGCCTTCCCACAAACGCCGCTA
1 CGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAACGACACCTTCCCACAAACGCCACTA
* ** * *
41690959 TAGATCAGGATCTTTAGCGGCGCTTTTCCCACATACGCCGCTATAGATCAGGACCTTTAGC-AGC
66 TAGATCAAGATCTTTAGCAACGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGA-C
* *
41691023 GCTTTTCCCACAAACGCCGCTATAGATCAA
130 GCTTCTCCCACAAACACCGCTATAGATCAA
* * * * *
41691053 CGCTTTTCCCACGAACGGCGCTATAGATCAGGACCTTTAGCGACACTTTTCCCACAAACGCCACT
1 CGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAACGACAC-CTTCCCACAAACGCCACT
* *
41691118 ATAGATCAAGA-CTTTTAGCAACGCTTTTCTCACAAATGCCGCTATAGATCAAGACCTTTAGCGA
65 ATAGATCAAGATC-TTTAGCAACGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGA
* *
41691182 CGCTTCTCTCACGAACACCGCTATAGATCA
129 CGCTTCTCCCACAAACACCGCTATAGATCA
41691212 TATTTTTATT
Statistics
Matches: 136, Mismatches: 20, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
159 40 0.29
160 95 0.70
161 1 0.01
ACGTcount: A:0.27, C:0.32, G:0.17, T:0.25
Consensus pattern (159 bp):
CGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAACGACACCTTCCCACAAACGCCACTA
TAGATCAAGATCTTTAGCAACGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGACG
CTTCTCCCACAAACACCGCTATAGATCAA
Found at i:41691206 original size:86 final size:86
Alignment explanation
Indices: 41691050--41691211 Score: 225
Period size: 86 Copynumber: 1.9 Consensus size: 86
41691040 CGCTATAGAT
* * * * *
41691050 CAACGCTTTTCCCACGAACGGCGCTATAGATCAGGACCTTTAGCGACACTTTTCCCACAAACGCC
1 CAACGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGACACTTCTCCCACAAACACC
41691115 ACTATAGATCAAGACTTTTAG
66 ACTATAGATCAAGACTTTTAG
* * * * *
41691136 CAACGCTTTTCTCACAAATGCCGCTATAGATCAAGACCTTTAGCGACGCTTCTCTCACGAACACC
1 CAACGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGACACTTCTCCCACAAACACC
*
41691201 GCTATAGATCA
66 ACTATAGATCA
41691212 TATTTTTATT
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
86 65 1.00
ACGTcount: A:0.29, C:0.31, G:0.15, T:0.25
Consensus pattern (86 bp):
CAACGCTTTTCCCACAAACGCCGCTATAGATCAAGACCTTTAGCGACACTTCTCCCACAAACACC
ACTATAGATCAAGACTTTTAG
Found at i:41694143 original size:57 final size:57
Alignment explanation
Indices: 41694030--41694143 Score: 167
Period size: 57 Copynumber: 2.0 Consensus size: 57
41694020 CTCCACTCCA
* **
41694030 ACATTTACAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTGTGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
* *
41694087 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGACAG-GCTTTTCTTCAGCTGC
1 ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAG-CAGAGCTCTTATTCAGCTGC
41694144 TCTTCAATGA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 48 0.94
58 3 0.06
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (57 bp):
ACATTTAAAGTTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
Found at i:41695835 original size:7 final size:7
Alignment explanation
Indices: 41695825--41695925 Score: 51
Period size: 7 Copynumber: 14.4 Consensus size: 7
41695815 CACTAACTCT
*
41695825 TAACCTC
1 TAACCCC
41695832 TAACCCC
1 TAACCCC
41695839 TAACCCC
1 TAACCCC
* *
41695846 AAATCCC
1 TAACCCC
* *
41695853 AAACCCT
1 TAACCCC
41695860 TAACCCC
1 TAACCCC
* * *
41695867 AAATCTC
1 TAACCCC
41695874 TAA-CCC
1 TAACCCC
*
41695880 TAAACCC
1 TAACCCC
*
41695887 TAAACCCA
1 T-AACCCC
*
41695895 AAACCCC
1 TAACCCC
* *
41695902 AAACCCA
1 TAACCCC
**
41695909 TAACTAC
1 TAACCCC
41695916 TAACCCC
1 TAACCCC
41695923 TAA
1 TAA
41695926 ACCTTATTTA
Statistics
Matches: 69, Mismatches: 23, Indels: 4
0.72 0.24 0.04
Matches are distributed among these distances:
6 5 0.07
7 60 0.87
8 4 0.06
ACGTcount: A:0.40, C:0.45, G:0.00, T:0.16
Consensus pattern (7 bp):
TAACCCC
Found at i:41695857 original size:21 final size:21
Alignment explanation
Indices: 41695833--41695907 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
41695823 CTTAACCTCT
41695833 AACCCCTAACCCCAAATCCCA
1 AACCCCTAACCCCAAATCCCA
* * *
41695854 AACCCTTAACCCCAAATCTCT
1 AACCCCTAACCCCAAATCCCA
*
41695875 AA-CCCTAAACCCTAAA-CCCAA
1 AACCCCT-AACCCCAAATCCC-A
*
41695896 AACCCCAAACCC
1 AACCCCTAACCC
41695908 ATAACTACTA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
20 5 0.12
21 35 0.81
22 3 0.07
ACGTcount: A:0.40, C:0.48, G:0.00, T:0.12
Consensus pattern (21 bp):
AACCCCTAACCCCAAATCCCA
Found at i:41695992 original size:13 final size:13
Alignment explanation
Indices: 41695967--41696016 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 13
41695957 AATTAATCTA
41695967 AACCCTAAACCCT
1 AACCCTAAACCCT
41695980 AACCC-AAATCCCT
1 AACCCTAAA-CCCT
41695993 AATCCCT-AACCACT
1 AA-CCCTAAACC-CT
41696007 AACCCCTAAA
1 AA-CCCTAAA
41696017 TCACAACCCT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 3 0.10
13 13 0.42
14 13 0.42
15 2 0.06
ACGTcount: A:0.40, C:0.44, G:0.00, T:0.16
Consensus pattern (13 bp):
AACCCTAAACCCT
Found at i:41696568 original size:40 final size:41
Alignment explanation
Indices: 41696523--41696619 Score: 117
Period size: 39 Copynumber: 2.4 Consensus size: 41
41696513 TTGGGCTTAG
*
41696523 GTTTTTAGCGGCGTTTTTCAAAAAAATGCCGCTAATGCTCA
1 GTTTTTAGCGGCGTTTTTCAAAAAAACGCCGCTAATGCTCA
* *** *
41696564 -TTTTTGGCGGCG-TTTTCCTGAAAGCGCCGCTAATGCTCA
1 GTTTTTAGCGGCGTTTTTCAAAAAAACGCCGCTAATGCTCA
*
41696603 GTCTTTAGCGGCGTTTT
1 GTTTTTAGCGGCGTTTT
41696620 ATTTAAAGCG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
39 22 0.48
40 21 0.46
41 3 0.07
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.36
Consensus pattern (41 bp):
GTTTTTAGCGGCGTTTTTCAAAAAAACGCCGCTAATGCTCA
Found at i:41696593 original size:39 final size:39
Alignment explanation
Indices: 41696550--41696659 Score: 139
Period size: 40 Copynumber: 2.8 Consensus size: 39
41696540 TCAAAAAAAT
* *
41696550 GCCGCTAATGCTCATTTTTGGCGGCGTTTTCCTGAAAGC
1 GCCGCTAATGCTCATTTTTAGCGGCGTTTTACTGAAAGC
* * *
41696589 GCCGCTAATGCTCAGTCTTTAGCGGCGTTTTATTTAAAGC
1 GCCGCTAATGCTCA-TTTTTAGCGGCGTTTTACTGAAAGC
* *
41696629 GCCGCTAATACTTGATTTTTAGCGGCGTTTT
1 GCCGCTAATGC-TCATTTTTAGCGGCGTTTT
41696660 TTGTCCAAAC
Statistics
Matches: 61, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
39 14 0.23
40 45 0.74
41 2 0.03
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (39 bp):
GCCGCTAATGCTCATTTTTAGCGGCGTTTTACTGAAAGC
Found at i:41696628 original size:40 final size:40
Alignment explanation
Indices: 41696523--41696659 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 40
41696513 TTGGGCTTAG
* ** **
41696523 GTTTTTAGCGGCGTTTTTCAAAAAAATGCCGCTAATGCTCA
1 GTTTTTAGCGGCGTTTTAC-TGAAAGCGCCGCTAATGCTCA
* *
41696564 -TTTTTGGCGGCGTTTTCCTGAAAGCGCCGCTAATGCTCA
1 GTTTTTAGCGGCGTTTTACTGAAAGCGCCGCTAATGCTCA
* * * * *
41696603 GTCTTTAGCGGCGTTTTATTTAAAGCGCCGCTAATACT-T
1 GTTTTTAGCGGCGTTTTACTGAAAGCGCCGCTAATGCTCA
41696642 GATTTTTAGCGGCGTTTT
1 G-TTTTTAGCGGCGTTTT
41696660 TTGTCCAAAC
Statistics
Matches: 80, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
39 18 0.22
40 62 0.77
ACGTcount: A:0.20, C:0.20, G:0.23, T:0.37
Consensus pattern (40 bp):
GTTTTTAGCGGCGTTTTACTGAAAGCGCCGCTAATGCTCA
Found at i:41696686 original size:12 final size:12
Alignment explanation
Indices: 41696669--41696693 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41696659 TTTGTCCAAA
41696669 CGCCACTAAAAG
1 CGCCACTAAAAG
41696681 CGCCACTAAAAG
1 CGCCACTAAAAG
41696693 C
1 C
41696694 CTGTTTTGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.36, G:0.16, T:0.08
Consensus pattern (12 bp):
CGCCACTAAAAG
Found at i:41697113 original size:27 final size:26
Alignment explanation
Indices: 41697029--41697115 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 26
41697019 GCTGCAGGAA
*
41697029 AGAAGAAGAA-AATAAAAAGAGAA-G
1 AGAAGAAGAAGAAGAAAAAGAGAAGG
*
41697053 AGAAGAAGAAGAAG-AAGAG-GAAGG
1 AGAAGAAGAAGAAGAAAAAGAGAAGG
****
41697077 AGGCCTAGAAGGAAGAAAAAGAGAAGG
1 AGAAGAAGAA-GAAGAAAAAGAGAAGG
41697104 AGAAGAAGAAGA
1 AGAAGAAGAAGA
41697116 GGGAGGGAAG
Statistics
Matches: 47, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
23 3 0.06
24 21 0.45
25 6 0.13
26 6 0.13
27 11 0.23
ACGTcount: A:0.61, C:0.02, G:0.34, T:0.02
Consensus pattern (26 bp):
AGAAGAAGAAGAAGAAAAAGAGAAGG
Found at i:41697125 original size:17 final size:16
Alignment explanation
Indices: 41697083--41697150 Score: 52
Period size: 17 Copynumber: 4.2 Consensus size: 16
41697073 AAGGAGGCCT
41697083 AGAA-GGAAGAAAAAG
1 AGAAGGGAAGAAAAAG
*
41697098 AGAAGGAGAAGAAGAAG
1 AGAAGG-GAAGAAAAAG
*
41697115 AGGGAGGGAAGGAAAAAG
1 A-GAAGGGAA-GAAAAAG
* *
41697133 A-AA-GGAAAAAAAAA
1 AGAAGGGAAGAAAAAG
41697147 AGAA
1 AGAA
41697151 AGGTAATTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
14 6 0.14
15 10 0.24
16 2 0.05
17 13 0.31
18 11 0.26
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
AGAAGGGAAGAAAAAG
Found at i:41697412 original size:30 final size:30
Alignment explanation
Indices: 41697352--41697422 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
41697342 CATAATTTAA
**
41697352 TTTTAATT-TTTATGTTATGTACATTCTATG
1 TTTT-ATTATTTATGTTATGTACATAATATG
*
41697382 TTTTATTATTTATGTTATGTTCATAATATG
1 TTTTATTATTTATGTTATGTACATAATATG
*
41697412 TCTTATTATTT
1 TTTTATTATTT
41697423 TATTATTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 3 0.08
30 33 0.92
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.62
Consensus pattern (30 bp):
TTTTATTATTTATGTTATGTACATAATATG
Found at i:41697435 original size:38 final size:37
Alignment explanation
Indices: 41697382--41697501 Score: 111
Period size: 38 Copynumber: 3.2 Consensus size: 37
41697372 ACATTCTATG
*
41697382 TTTTATTATTTATGTTATGTTCATAATATGTCTTATTA
1 TTTTATTATTTATGTTATGTTCAT-ATATGTATTATTA
* * *
41697420 TTTTATTATTAATGTTA--TT-ATTTATTTATTATTTA
1 TTTTATTATTTATGTTATGTTCATATATGTATTA-TTA
* * *
41697455 TGTTTTATTATTTATGTTATGTACATTCTATGTTTTATTA
1 --TTTTATTATTTATGTTATGTTCA-TATATGTATTATTA
41697495 TTTTATT
1 TTTTATT
41697502 TAATTTATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
34 7 0.11
35 5 0.08
36 2 0.03
37 16 0.24
38 23 0.35
39 1 0.02
40 4 0.06
41 8 0.12
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (37 bp):
TTTTATTATTTATGTTATGTTCATATATGTATTATTA
Found at i:41697474 original size:23 final size:22
Alignment explanation
Indices: 41697408--41697474 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
41697398 ATGTTCATAA
*
41697408 TATGTCTTATTATTT-TATTATT
1 TATGTTTTATTATTTAT-TTATT
*
41697430 AATGTTATTATTTATTTA-TTATT
1 TATGTT-TTA-TTATTTATTTATT
41697453 TATGTTTTATTATTTATGTTAT
1 TATGTTTTATTATTTAT-TTAT
41697475 GTACATTCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 7 0.19
22 7 0.19
23 17 0.46
24 6 0.16
ACGTcount: A:0.25, C:0.01, G:0.06, T:0.67
Consensus pattern (22 bp):
TATGTTTTATTATTTATTTATT
Found at i:41697805 original size:30 final size:30
Alignment explanation
Indices: 41697745--41697815 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
41697735 CATAATTTAA
**
41697745 TTTTAATT-TTTATGTTATGTACATTCTATG
1 TTTT-ATTATTTATGTTATGTACATAATATG
*
41697775 TTTTATTATTTATGTTATGTTCATAATATG
1 TTTTATTATTTATGTTATGTACATAATATG
*
41697805 TCTTATTATTT
1 TTTTATTATTT
41697816 TATTATTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 3 0.08
30 33 0.92
ACGTcount: A:0.24, C:0.06, G:0.08, T:0.62
Consensus pattern (30 bp):
TTTTATTATTTATGTTATGTACATAATATG
Found at i:41697828 original size:38 final size:37
Alignment explanation
Indices: 41697775--41697894 Score: 111
Period size: 38 Copynumber: 3.2 Consensus size: 37
41697765 ACATTCTATG
*
41697775 TTTTATTATTTATGTTATGTTCATAATATGTCTTATTA
1 TTTTATTATTTATGTTATGTTCAT-ATATGTATTATTA
* * *
41697813 TTTTATTATTAATGTTA--TT-ATTTATTTATTATTTA
1 TTTTATTATTTATGTTATGTTCATATATGTATTA-TTA
* * *
41697848 TGTTTTATTATTTATGTTATGTACATTCTATGTTTTATTA
1 --TTTTATTATTTATGTTATGTTCA-TATATGTATTATTA
41697888 TTTTATT
1 TTTTATT
41697895 TAATTTATTT
Statistics
Matches: 66, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
34 7 0.11
35 5 0.08
36 2 0.03
37 16 0.24
38 23 0.35
39 1 0.02
40 4 0.06
41 8 0.12
ACGTcount: A:0.25, C:0.03, G:0.07, T:0.65
Consensus pattern (37 bp):
TTTTATTATTTATGTTATGTTCATATATGTATTATTA
Found at i:41697867 original size:23 final size:22
Alignment explanation
Indices: 41697801--41697867 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
41697791 ATGTTCATAA
*
41697801 TATGTCTTATTATTT-TATTATT
1 TATGTTTTATTATTTAT-TTATT
*
41697823 AATGTTATTATTTATTTA-TTATT
1 TATGTT-TTA-TTATTTATTTATT
41697846 TATGTTTTATTATTTATGTTAT
1 TATGTTTTATTATTTAT-TTAT
41697868 GTACATTCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 7 0.19
22 7 0.19
23 17 0.46
24 6 0.16
ACGTcount: A:0.25, C:0.01, G:0.06, T:0.67
Consensus pattern (22 bp):
TATGTTTTATTATTTATTTATT
Found at i:41698049 original size:393 final size:395
Alignment explanation
Indices: 41697301--41698088 Score: 1463
Period size: 393 Copynumber: 2.0 Consensus size: 395
41697291 AAAAAGAGAT
41697301 ATTAAGGTATGTTTATATTTATCTATATTTTTTCATTCATTCATAATTTAATTTTAATTTTTATG
1 ATTAAGGTATGTTTATATTTA-CTATATTTTTTCATTCATTCATAATTTAATTTTAATTTTTATG
41697366 TTATGTACATTCTATGTTTTATTATTTATGTTATGTTCATAATATGTCTTATTATTTTATTATTA
65 TTATGTACATTCTATGTTTTATTATTTATGTTATGTTCATAATATGTCTTATTATTTTATTATTA
41697431 ATGTTATTATTTATTTATTATTTATGTTTTATTATTTATGTTATGTACATTCTATGTTTTATTAT
130 ATGTTATTATTTATTTATTATTTATGTTTTATTATTTATGTTATGTACATTCTATGTTTTATTAT
41697496 TTTATTTAATTTATTTGTTAAGTGTGTTTTATGTTGATTAGATATATTTTTTATGAAATTTATTT
195 TTTATTTAATTTATTTGTTAAGTGTGTTTTATGTTGATTAGATATATTTTTTATGAAATTTATTT
** **
41697561 AGCATGTTGTAATGAGATTTTTTTACAAAAATAGTATTAAAAATAAAATTTCTTAAAAATATGTT
260 AGCATGTTGTAATGAGATTTTTTTACAAAAATAGTATTAAAAATAAAATACCGAAAAAATATGTT
*
41697626 TATGAAAAAATAAAATACAAAAAGAAAT-AAAAAATGAAAATAGTATATTTACTGAAAGTAATAA
325 TATGAAAAAATAAAATACAAAAAGAAATAAAAAAACGAAAATAGTATATTTACTGAAAGTAATAA
41697690 AATCCG
390 AATCCG
41697696 ATTAAGGTATGTTTATATTTA-TATATTTTTTCATTCATTCATAATTTAATTTTAATTTTTATGT
1 ATTAAGGTATGTTTATATTTACTATATTTTTTCATTCATTCATAATTTAATTTTAATTTTTATGT
41697760 TATGTACATTCTATGTTTTATTATTTATGTTATGTTCATAATATGTCTTATTATTTTATTATTAA
66 TATGTACATTCTATGTTTTATTATTTATGTTATGTTCATAATATGTCTTATTATTTTATTATTAA
41697825 TGTTATTATTTATTTATTATTTATGTTTTATTATTTATGTTATGTACATTCTATGTTTTATTATT
131 TGTTATTATTTATTTATTATTTATGTTTTATTATTTATGTTATGTACATTCTATGTTTTATTATT
41697890 TTATTTAATTTATTTGTTAAGTGTGTTTTATGTTGATTAGATATATTTTTTATGAAATTTATTTA
196 TTATTTAATTTATTTGTTAAGTGTGTTTTATGTTGATTAGATATATTTTTTATGAAATTTATTTA
41697955 GCATGTTGTAATGAGATTTTTTTACAAAAATAGTATTAAAAATAAAATACCGAAAAAATATGTTT
261 GCATGTTGTAATGAGATTTTTTTACAAAAATAGTATTAAAAATAAAATACCGAAAAAATATGTTT
* **
41698020 ATGAAAAAATAAAATACGAAAAGAAATAAAAAAAAACGAAAATAGTATATTTTTTGAAAGTAATA
326 ATGAAAAAATAAAATACAAAAAGAAAT--AAAAAAACGAAAATAGTATATTTACTGAAAGTAATA
41698085 AAAT
389 AAAT
41698089 TCGAAAATAA
Statistics
Matches: 382, Mismatches: 8, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
393 325 0.85
395 21 0.05
396 36 0.09
ACGTcount: A:0.36, C:0.04, G:0.09, T:0.51
Consensus pattern (395 bp):
ATTAAGGTATGTTTATATTTACTATATTTTTTCATTCATTCATAATTTAATTTTAATTTTTATGT
TATGTACATTCTATGTTTTATTATTTATGTTATGTTCATAATATGTCTTATTATTTTATTATTAA
TGTTATTATTTATTTATTATTTATGTTTTATTATTTATGTTATGTACATTCTATGTTTTATTATT
TTATTTAATTTATTTGTTAAGTGTGTTTTATGTTGATTAGATATATTTTTTATGAAATTTATTTA
GCATGTTGTAATGAGATTTTTTTACAAAAATAGTATTAAAAATAAAATACCGAAAAAATATGTTT
ATGAAAAAATAAAATACAAAAAGAAATAAAAAAACGAAAATAGTATATTTACTGAAAGTAATAAA
ATCCG
Found at i:41698325 original size:157 final size:157
Alignment explanation
Indices: 41698102--41698554 Score: 748
Period size: 157 Copynumber: 2.9 Consensus size: 157
41698092 AAAATAAAAG
41698102 GGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAAACACACTAAAATAATACATTTCAAAC
1 GGCCAAAATAAGGGTTTTTTACTAAATTTATAT-AAAAAACACACTAAAATAATACATTTCAAAC
41698167 ATTATGTACTAAAATAATATAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAA
65 ATTATGTACTAAAATAATATAAAATAATAAAATACGAAAATA-TATATTTTTTGAAAGTAATAAA
* *
41698232 ATCTGAAAATAAAAAAAATATGAACAAAT
129 ATATGAAAATAAAAAAAATACGAACAAAT
* *
41698261 GGCCAAAATAAGGGTTTTTTACTAAATTTATAT-AAAAATACACTAAAATAATGCATTTCAAACA
1 GGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAAATAATACATTTCAAACA
* *
41698325 TTATGTACTAAAATAATATAAAATAATAAAATACGAAAATA-ACATTTTTTTAAAGTAATAAAAT
66 TTATGTACTAAAATAATATAAAATAATAAAATACGAAAATATATATTTTTTGAAAGTAATAAAAT
*
41698389 ATGAAAATAAGAAAAATACGAACAAAT
131 ATGAAAATAAAAAAAATACGAACAAAT
* *
41698416 GGCCAAAATAAGGGGTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATACATTTCAAAC
1 GGCCAAAATAAGGGTTTTTTACTAAATTTATAT-AAAAAACACACTAAAATAATACATTTCAAAC
* *
41698481 TTTATGTACTAAAATAATATAAAATAATAAAATATGAAAATAATATATTTTTTGAAAGTAATAAA
65 ATTATGTACTAAAATAATATAAAATAATAAAATACGAAAAT-ATATATTTTTTGAAAGTAATAAA
*
41698546 ATAAGAAAA
129 ATATGAAAA
41698555 ATCTGAAAAT
Statistics
Matches: 274, Mismatches: 16, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
155 77 0.28
157 136 0.50
158 1 0.00
159 60 0.22
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.30
Consensus pattern (157 bp):
GGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAAAATAATACATTTCAAACA
TTATGTACTAAAATAATATAAAATAATAAAATACGAAAATATATATTTTTTGAAAGTAATAAAAT
ATGAAAATAAAAAAAATACGAACAAAT
Found at i:41698522 original size:16 final size:15
Alignment explanation
Indices: 41698496--41698525 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41698486 GTACTAAAAT
41698496 AATATAAAATAATAA
1 AATATAAAATAATAA
41698511 AATATGAAAATAATA
1 AATAT-AAAATAATA
41698526 TATTTTTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:41699069 original size:14 final size:14
Alignment explanation
Indices: 41699037--41699063 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41699027 CCAATCGACG
41699037 GGAGTCCCGTAACA
1 GGAGTCCCGTAACA
41699051 GGAGTCCCGTAAC
1 GGAGTCCCGTAAC
41699064 GAGAGTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (14 bp):
GGAGTCCCGTAACA
Found at i:41706820 original size:41 final size:41
Alignment explanation
Indices: 41706762--41706867 Score: 158
Period size: 41 Copynumber: 2.6 Consensus size: 41
41706752 AATGAGATAA
* * * *
41706762 TTCAGACTTTACATCTAGGAGGCTTGATGCCGGTGAAATGT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
*
41706803 TTCAGACTTTACGTCTAGCAGGCTTGACGCTGGTGAAATAT
1 TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
*
41706844 TTCGGACTTTACGTCTAGCAGGCT
1 TTCAGACTTTACGTCTAGCAGGCT
41706868 AATTGCCAGT
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 59 1.00
ACGTcount: A:0.23, C:0.20, G:0.25, T:0.32
Consensus pattern (41 bp):
TTCAGACTTTACGTCTAGCAGGCTTGACGCCGGTGAAATAT
Found at i:41708840 original size:25 final size:23
Alignment explanation
Indices: 41708763--41708865 Score: 95
Period size: 22 Copynumber: 4.4 Consensus size: 23
41708753 GCACTAATGA
*
41708763 ACAGAGAGCACTAAAGTGCT-AT
1 ACAGAGAGCACTAACGTGCTAAT
* *
41708785 ACAAAGAGCAC-AGATGTGCTAA-
1 ACAGAGAGCACTA-ACGTGCTAAT
*
41708807 ACAGAGAGCACTGACGTGCTAAAT
1 ACAGAGAGCACTAACGTGCT-AAT
*
41708831 ATCAGAGAGCACCAACGTGCTAAT
1 A-CAGAGAGCACTAACGTGCTAAT
41708855 AATCAGAGAGC
1 -A-CAGAGAGC
41708866 GCGCTAAAGT
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
21 1 0.01
22 32 0.48
23 3 0.04
24 4 0.06
25 27 0.40
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.16
Consensus pattern (23 bp):
ACAGAGAGCACTAACGTGCTAAT
Found at i:41708864 original size:27 final size:25
Alignment explanation
Indices: 41708808--41708865 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 25
41708798 ATGTGCTAAA
**
41708808 CAGAGAGCACTGACGTGCTAAATAT
1 CAGAGAGCACCAACGTGCTAAATAT
41708833 CAGAGAGCACCAACGTGCT-AATAAT
1 CAGAGAGCACCAACGTGCTAAAT-AT
41708858 CAGAGAGC
1 CAGAGAGC
41708866 GCGCTAAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 3 0.10
25 27 0.90
ACGTcount: A:0.38, C:0.22, G:0.24, T:0.16
Consensus pattern (25 bp):
CAGAGAGCACCAACGTGCTAAATAT
Found at i:41709963 original size:5 final size:5
Alignment explanation
Indices: 41709953--41710052 Score: 55
Period size: 5 Copynumber: 20.2 Consensus size: 5
41709943 TATATATAAG
* * * * * * *
41709953 AATAT AATAT AATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT
* * *
41710003 TATAT AATA- AA-AT AACAT ACTTATT AAT-T AAGTA- AATAT AATAT
1 AATAT AATAT AATAT AATAT A-ATA-T AATAT AA-TAT AATAT AATAT
41710047 AATAT A
1 AATAT A
41710053 TATTTTAAAT
Statistics
Matches: 83, Mismatches: 5, Indels: 14
0.81 0.05 0.14
Matches are distributed among these distances:
3 1 0.01
4 9 0.11
5 69 0.83
6 2 0.02
7 2 0.02
ACGTcount: A:0.51, C:0.02, G:0.01, T:0.46
Consensus pattern (5 bp):
AATAT
Found at i:41709972 original size:15 final size:15
Alignment explanation
Indices: 41709954--41710011 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
41709944 ATATATAAGA
*
41709954 ATATAATATAATATT
1 ATATTATATAATATT
*
41709969 ATATTATATTATATT
1 ATATTATATAATATT
*
41709984 ATATTATATTATATT
1 ATATTATATAATATT
41709999 ATATTATATAATA
1 ATATTATATAATA
41710012 AAATAACATA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTATATAATATT
Found at i:41712606 original size:40 final size:38
Alignment explanation
Indices: 41712522--41712740 Score: 128
Period size: 40 Copynumber: 5.6 Consensus size: 38
41712512 CCACTAATCC
**
41712522 TAATAACTAACACAATAATAATACTAGTTTTTTACTAAAAA
1 TAATAACT-A-ACAATAATAATA-TAGGGTTTTACTAAAAA
41712563 TAATACTAGCTAACAATAATAAT-TAGGGTTTTACTAAAAA
1 TAATA--A-CTAACAATAATAATATAGGGTTTTACTAAAAA
* ***
41712603 TAATAACTAAC---AATAATATAGTGTAAAAGCTAACAATCA
1 TAATAACTAACAATAATAATATAGGGTTTTA-CTAA-AA--A
* * * * ***
41712642 TACTAACTAA-AATAAT-ATTTAGGATTTTTATTAATCC
1 TAATAACTAACAATAATAATATAGG-GTTTTACTAAAAA
*
41712679 TAATAACTAACACAATAATAATACTA-GTTTCTTACTAAAAA
1 TAATAACT-A-ACAATAATAATA-TAGGGTT-TTACTAAAAA
41712720 TAATAACTAACAATAATAATA
1 TAATAACTAACAATAATAATA
41712741 CTAACTAACA
Statistics
Matches: 137, Mismatches: 23, Indels: 38
0.69 0.12 0.19
Matches are distributed among these distances:
34 6 0.04
35 6 0.04
36 4 0.03
37 14 0.10
38 2 0.01
39 23 0.17
40 38 0.28
41 27 0.20
42 13 0.09
43 2 0.01
44 2 0.01
ACGTcount: A:0.50, C:0.12, G:0.05, T:0.33
Consensus pattern (38 bp):
TAATAACTAACAATAATAATATAGGGTTTTACTAAAAA
Found at i:41712702 original size:157 final size:148
Alignment explanation
Indices: 41712516--41712847 Score: 411
Period size: 157 Copynumber: 2.2 Consensus size: 148
41712506 ATTTAACCAC
*
41712516 TAATCCTAATAACTAACACAATAATAATACTAGTTTTTTACTAAAAATAATACTAGCTAACAATA
1 TAATCCTAATAACTAACACAATAATAATACTAGTTTCTTACTAAAAATAATA--A-CTAACAATA
* * * *** * *
41712581 ATAATTAGGGTTTTACTAAAAATAATAACTAACAATAA-TATAGTGTAAAAGCTAAC-AATCATA
63 ATAA-TA----CTAACTAAAAATAAT---TAACAATAACTAAACCCTAAAAACTAACAAATAATA
41712644 CTAACTAAAATAATATTTAGGATTTTTAT
120 CTAACTAAAATAATATTTAGGATTTTTAT
41712673 TAATCCTAATAACTAACACAATAATAATACTAGTTTCTTACTAAAAATAATAACTAACAATAATA
1 TAATCCTAATAACTAACACAATAATAATACTAGTTTCTTACTAAAAATAATAACTAACAATAATA
* **
41712738 ATACTAACTAACAATAATTATTAATAACTAAACCCTAAAAACTAACAATAATAATACTAACTAAA
66 ATACTAACTAAAAATAATTAACAATAACTAAACCCTAAAAACTAAC-A-AATAATACTAACTAAA
41712803 ATAATATTTAGGATTTTTAT
129 ATAATATTTAGGATTTTTAT
41712823 TAATCCTAATAACT-A-ACAATAATAA
1 TAATCCTAATAACTAACACAATAATAA
41712848 CTAAACTAAC
Statistics
Matches: 159, Mismatches: 12, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
146 7 0.04
147 13 0.08
148 10 0.06
149 13 0.08
150 49 0.31
153 2 0.01
154 13 0.08
155 1 0.01
157 51 0.32
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.33
Consensus pattern (148 bp):
TAATCCTAATAACTAACACAATAATAATACTAGTTTCTTACTAAAAATAATAACTAACAATAATA
ATACTAACTAAAAATAATTAACAATAACTAAACCCTAAAAACTAACAAATAATACTAACTAAAAT
AATATTTAGGATTTTTAT
Found at i:41712745 original size:19 final size:19
Alignment explanation
Indices: 41712718--41712808 Score: 77
Period size: 19 Copynumber: 5.1 Consensus size: 19
41712708 TCTTACTAAA
41712718 AATAATAACTAACAATAAT
1 AATAATAACTAACAATAAT
*
41712737 AATACTAACTAACAATAATT
1 AATAATAACTAACAATAA-T
* ***
41712757 ATTAATAACT-A-AACCCT
1 AATAATAACTAACAATAAT
41712774 -A-AA-AACTAACAATAAT
1 AATAATAACTAACAATAAT
*
41712790 AATACTAACTAA-AATAAT
1 AATAATAACTAACAATAAT
41712808 A
1 A
41712809 TTTAGGATTT
Statistics
Matches: 55, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
16 3 0.05
17 2 0.04
18 10 0.18
19 24 0.44
20 9 0.16
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.26
Consensus pattern (19 bp):
AATAATAACTAACAATAAT
Found at i:41713044 original size:3 final size:3
Alignment explanation
Indices: 41713038--41713068 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
41713028 CCTCCTCCTC
41713038 CTT CTT CTT -TT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
41713069 CCTTTCCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
CTT
Found at i:41713366 original size:21 final size:20
Alignment explanation
Indices: 41713342--41713380 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41713332 TAAGTTATTG
*
41713342 AATTTTTATGAATTAAAAAAT
1 AATTATTAT-AATTAAAAAAT
*
41713363 AATTATTATATTTAAAAA
1 AATTATTATAATTAAAAA
41713381 TATATAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (20 bp):
AATTATTATAATTAAAAAAT
Found at i:41716096 original size:14 final size:15
Alignment explanation
Indices: 41716065--41716104 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
41716055 AGATCACTAC
41716065 AAATAAAAATATAAT
1 AAATAAAAATATAAT
*
41716080 AAATAAAAA-ATATT
1 AAATAAAAATATAAT
*
41716094 AAATTAAAATA
1 AAATAAAAATA
41716105 ATTACAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (15 bp):
AAATAAAAATATAAT
Found at i:41716105 original size:24 final size:23
Alignment explanation
Indices: 41716077--41716134 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
41716067 ATAAAAATAT
41716077 AATAAATAAAAAATATTAAATTAA
1 AATAAATAAAAAATA-TAAATTAA
* **
41716101 AATAATTACAAAAATATATTTTAA
1 AATAAATA-AAAAATATAAATTAA
41716125 AATAATATAA
1 AATAA-ATAA
41716135 TATTCTTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 19 0.68
25 9 0.32
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AATAAATAAAAAATATAAATTAA
Found at i:41718670 original size:24 final size:24
Alignment explanation
Indices: 41718643--41718690 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
41718633 TCTAAGCTTC
41718643 CTTAAACTTAATCATCCATAAGGA
1 CTTAAACTTAATCATCCATAAGGA
41718667 CTTAAACTTAATCATCCATAAGGA
1 CTTAAACTTAATCATCCATAAGGA
41718691 TTCAAAGGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.08, T:0.29
Consensus pattern (24 bp):
CTTAAACTTAATCATCCATAAGGA
Found at i:41721952 original size:16 final size:16
Alignment explanation
Indices: 41721928--41721963 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
41721918 AAAATTAAAA
*
41721928 AAATGTATGTAGACAT
1 AAATATATGTAGACAT
*
41721944 AAATATATGTATACAT
1 AAATATATGTAGACAT
41721960 AAAT
1 AAAT
41721964 TATAAAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.50, C:0.06, G:0.11, T:0.33
Consensus pattern (16 bp):
AAATATATGTAGACAT
Found at i:41722256 original size:3 final size:3
Alignment explanation
Indices: 41722248--41722319 Score: 87
Period size: 3 Copynumber: 24.3 Consensus size: 3
41722238 GTAAATGATC
*
41722248 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA GCTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
*
41722296 ATTA AT- TTA ATA ATA ATA A-A ATA A
1 A-TA ATA ATA ATA ATA ATA ATA ATA A
41722320 CGAGACTAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
2 5 0.08
3 50 0.83
4 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:41738601 original size:72 final size:72
Alignment explanation
Indices: 41738484--41738627 Score: 252
Period size: 72 Copynumber: 2.0 Consensus size: 72
41738474 TTCTTTCCTA
*
41738484 TATATTCACTGAGTTCACAAGAGCTCACACACCCATTTTTAACACTGCAGATAGTTAGACCGAAT
1 TATATTCACTAAGTTCACAAGAGCTCACACACCCATTTTTAACACTGCAGATAGTTAGACCGAAT
41738549 GGGGTGT
66 GGGGTGT
* * *
41738556 TATATTCACTAAGTTTACAAGAGCTCACACACCCCTTTTTAACACTGCAGATAGTTAGATCGAAT
1 TATATTCACTAAGTTCACAAGAGCTCACACACCCATTTTTAACACTGCAGATAGTTAGACCGAAT
41738621 GGGGTGT
66 GGGGTGT
41738628 AACGGCGAGG
Statistics
Matches: 68, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.29
Consensus pattern (72 bp):
TATATTCACTAAGTTCACAAGAGCTCACACACCCATTTTTAACACTGCAGATAGTTAGACCGAAT
GGGGTGT
Found at i:41742424 original size:34 final size:31
Alignment explanation
Indices: 41742386--41742455 Score: 95
Period size: 34 Copynumber: 2.2 Consensus size: 31
41742376 TGTTACTGTC
* *
41742386 ACTGTAATGGGCTGAGGCCCACACTGATACTGA
1 ACTGTAATGGGCTAAGACCCA-ACTGA-ACTGA
41742419 TACTGTAATGGGCTAAGACCCAACTGAACTGA
1 -ACTGTAATGGGCTAAGACCCAACTGAACTGA
41742451 ACTGT
1 ACTGT
41742456 TATTGAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
31 5 0.15
32 5 0.15
33 5 0.15
34 19 0.56
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (31 bp):
ACTGTAATGGGCTAAGACCCAACTGAACTGA
Found at i:41745900 original size:17 final size:16
Alignment explanation
Indices: 41745878--41745909 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41745868 TTATAGATAA
41745878 TTGGAAGCTCGATCGGT
1 TTGGAAGCTCG-TCGGT
41745895 TTGGAAGCTCGTCGG
1 TTGGAAGCTCGTCGG
41745910 AGATCTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.16, C:0.19, G:0.38, T:0.28
Consensus pattern (16 bp):
TTGGAAGCTCGTCGGT
Found at i:41746047 original size:30 final size:31
Alignment explanation
Indices: 41746011--41746072 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
41746001 TGTTTGGTTG
*
41746011 AATGCTAAATGTTGATTTTGGTA-TGTATAT
1 AATGCTAAATGTTGATCTTGGTACTGTATAT
*
41746041 AATGCTAAATTTTGATCTTGGTACGTGTATAT
1 AATGCTAAATGTTGATCTTGGTAC-TGTATAT
41746073 GTTGGTACAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 21 0.75
32 7 0.25
ACGTcount: A:0.29, C:0.06, G:0.19, T:0.45
Consensus pattern (31 bp):
AATGCTAAATGTTGATCTTGGTACTGTATAT
Found at i:41749803 original size:19 final size:19
Alignment explanation
Indices: 41749781--41749817 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41749771 TTATTTAAAA
41749781 TTTAAAAATAAAAAATCAT
1 TTTAAAAATAAAAAATCAT
*
41749800 TTTAAATATAAAAAATCA
1 TTTAAAAATAAAAAATCA
41749818 AAATTTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (19 bp):
TTTAAAAATAAAAAATCAT
Found at i:41749821 original size:25 final size:26
Alignment explanation
Indices: 41749725--41749820 Score: 78
Period size: 25 Copynumber: 3.9 Consensus size: 26
41749715 AATTTTTCAT
*
41749725 ATTTTAAATA-AAAACAT-AAAAA-A
1 ATTTTAAATATAAAAAATAAAAAATA
* *
41749748 A-TTTAAAGTAT-AAAAATGAAAAATT
1 ATTTTAAA-TATAAAAAATAAAAAATA
* * *
41749773 ATTTAAAAT-TTAAAAATAAAAAATC
1 ATTTTAAATATAAAAAATAAAAAATA
*
41749798 ATTTTAAATATAAAAAATCAAAA
1 ATTTTAAATATAAAAAATAAAAA
41749821 TTTCTATGTG
Statistics
Matches: 58, Mismatches: 8, Indels: 11
0.75 0.10 0.14
Matches are distributed among these distances:
22 6 0.10
23 8 0.14
24 6 0.10
25 22 0.38
26 16 0.28
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (26 bp):
ATTTTAAATATAAAAAATAAAAAATA
Found at i:41767143 original size:37 final size:36
Alignment explanation
Indices: 41767081--41767156 Score: 93
Period size: 37 Copynumber: 2.1 Consensus size: 36
41767071 GATAGTTACT
*
41767081 TTAATATTAAATTAATAAAATACTATTAAGATAAATA
1 TTAATATTAAATTAATAAAATACTATTAAAAT-AATA
*
41767118 TTAA-ATTAAATATAATATTAA-ACTATTAAAATAATA
1 TTAATATTAAAT-TAATA-AAATACTATTAAAATAATA
41767154 TTA
1 TTA
41767157 TTTTTGGAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
36 14 0.40
37 19 0.54
38 2 0.06
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (36 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAATA
Found at i:41767591 original size:19 final size:19
Alignment explanation
Indices: 41767553--41767592 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
41767543 AGAATATCAT
* *
41767553 ATTAATTTTAATTGATTTG
1 ATTAATTTAAATTGACTTG
*
41767572 ATTAATTTAAATTTACTTG
1 ATTAATTTAAATTGACTTG
41767591 AT
1 AT
41767593 CAAAATTAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (19 bp):
ATTAATTTAAATTGACTTG
Found at i:41768770 original size:15 final size:15
Alignment explanation
Indices: 41768746--41768777 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41768736 TATGCATGCA
*
41768746 AAATATAAAAGACAT
1 AAATACAAAAGACAT
41768761 AAATACAAAAGACAT
1 AAATACAAAAGACAT
41768776 AA
1 AA
41768778 TAATGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:41770784 original size:26 final size:26
Alignment explanation
Indices: 41770755--41770812 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
41770745 TCATAGCTAG
41770755 TGTGAGCAGACCCATTTAACAGCTCA
1 TGTGAGCAGACCCATTTAACAGCTCA
* * * * *
41770781 TGTGAGCATACTCTTTTCACAGCTCG
1 TGTGAGCAGACCCATTTAACAGCTCA
41770807 TGTGAG
1 TGTGAG
41770813 TATATATGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (26 bp):
TGTGAGCAGACCCATTTAACAGCTCA
Found at i:41771116 original size:32 final size:32
Alignment explanation
Indices: 41771075--41771138 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
41771065 AAATTCAAAC
*
41771075 GAATTGTGTTTAATTGAACTGGTATGTGTTGT
1 GAATTGTGTTTAATTGAACTGGCATGTGTTGT
*
41771107 GAATTGTGTTTAATTGAATTGGCATGTGTTGT
1 GAATTGTGTTTAATTGAACTGGCATGTGTTGT
41771139 TGGTGTGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.22, C:0.03, G:0.28, T:0.47
Consensus pattern (32 bp):
GAATTGTGTTTAATTGAACTGGCATGTGTTGT
Found at i:41777115 original size:23 final size:23
Alignment explanation
Indices: 41777087--41777136 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
41777077 TTTTCACAAA
*
41777087 AATTACCAGTATAGTAATTTTAC
1 AATTACCAGTAGAGTAATTTTAC
* *
41777110 AATTACTAGTGGAGTAATTTTAC
1 AATTACCAGTAGAGTAATTTTAC
41777133 AATT
1 AATT
41777137 TCTCTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (23 bp):
AATTACCAGTAGAGTAATTTTAC
Found at i:41777497 original size:37 final size:35
Alignment explanation
Indices: 41777440--41777509 Score: 97
Period size: 37 Copynumber: 1.9 Consensus size: 35
41777430 TCACTTTAAT
41777440 ATTAAATTAATAAAATACTATTAAAATAAATATTCA
1 ATTAAATTAATAAAATACTATTAAAAT-AATATTCA
*
41777476 ATTAAATTTAATATTAA-ACTATTAAAATAATATT
1 ATTAAA-TTAATA-AAATACTATTAAAATAATATT
41777510 ATTTCTAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
36 12 0.39
37 17 0.55
38 2 0.06
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (35 bp):
ATTAAATTAATAAAATACTATTAAAATAATATTCA
Found at i:41785711 original size:13 final size:13
Alignment explanation
Indices: 41785693--41785718 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41785683 GTGCAAAAGT
41785693 TGATTCTACTTAA
1 TGATTCTACTTAA
41785706 TGATTCTACTTAA
1 TGATTCTACTTAA
41785719 ATTTGTTGTA
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:0.08, T:0.46
Consensus pattern (13 bp):
TGATTCTACTTAA
Found at i:41787314 original size:28 final size:28
Alignment explanation
Indices: 41787249--41787347 Score: 137
Period size: 28 Copynumber: 3.5 Consensus size: 28
41787239 CATGAGATTG
* * *
41787249 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGAGTTC-GATTATATA
41787278 GCACTAAGTGTGCGAGTTCGATTATATA
1 GCACTAAGTGTGCGAGTTCGATTATATA
*
41787306 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCGAGTTCGATTATAT-A
41787334 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
41787348 GGCTTATTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
27 1 0.02
28 46 0.71
29 18 0.28
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTCGATTATATA
Found at i:41798009 original size:15 final size:15
Alignment explanation
Indices: 41797989--41798020 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41797979 ACGTTTTGAA
41797989 GGTTCTTTGTTTTTG
1 GGTTCTTTGTTTTTG
*
41798004 GGTTCTTTTTTTTTG
1 GGTTCTTTGTTTTTG
41798019 GG
1 GG
41798021 GTTTTCGGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.06, G:0.28, T:0.66
Consensus pattern (15 bp):
GGTTCTTTGTTTTTG
Found at i:41811620 original size:12 final size:12
Alignment explanation
Indices: 41811603--41811631 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
41811593 AAAATTACTA
41811603 TCGTGATAATAG
1 TCGTGATAATAG
41811615 TCGTGATAATAG
1 TCGTGATAATAG
41811627 TCGTG
1 TCGTG
41811632 CTCACGACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.28, T:0.34
Consensus pattern (12 bp):
TCGTGATAATAG
Found at i:41814010 original size:22 final size:22
Alignment explanation
Indices: 41813969--41814012 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
41813959 ACACCAAAAT
* *
41813969 AGGCTTTTAGCGGCGCTTTTTA
1 AGGCCTTTAGCGGCACTTTTTA
*
41813991 AGGCCTTTAGCGGCATTTTTTA
1 AGGCCTTTAGCGGCACTTTTTA
41814013 GCGCCGCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.16, C:0.18, G:0.25, T:0.41
Consensus pattern (22 bp):
AGGCCTTTAGCGGCACTTTTTA
Found at i:41814236 original size:42 final size:42
Alignment explanation
Indices: 41814177--41814381 Score: 230
Period size: 43 Copynumber: 4.8 Consensus size: 42
41814167 TAAAGACATT
* *
41814177 GACCTTTAGCGGCACTTTCCCAAAAACGCCACTATAGCTCAA
1 GACCTTTAGCGGCGCTTTCCCACAAACGCCACTATAGCTCAA
* * *
41814219 GACCTTTAGCGGCACTTTTCCACAAACGCCACTATAGCCCAA
1 GACCTTTAGCGGCGCTTTCCCACAAACGCCACTATAGCTCAA
* * * *
41814261 GACATTTAGCGACGCTTTTCTCACAAACGCCGCTATAGCTCAA
1 GACCTTTAGCGGCGC-TTTCCCACAAACGCCACTATAGCTCAA
* * * * *
41814304 GAGCTTTAGCAGCGCTTTTACCACAAACGCCGCTATAGTTCAA
1 GACCTTTAGCGGCGC-TTTCCCACAAACGCCACTATAGCTCAA
* * *
41814347 TACCTTTAGCGGCGCTTCTCACAAAAACGCCACTA
1 GACCTTTAGCGGCGCTT-TCCCACAAACGCCACTA
41814382 AAAATATAAC
Statistics
Matches: 137, Mismatches: 24, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
42 53 0.39
43 84 0.61
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (42 bp):
GACCTTTAGCGGCGCTTTCCCACAAACGCCACTATAGCTCAA
Found at i:41814375 original size:86 final size:84
Alignment explanation
Indices: 41814177--41814381 Score: 257
Period size: 86 Copynumber: 2.4 Consensus size: 84
41814167 TAAAGACATT
* * *
41814177 GACCTTTAGCGGCACTTTCCCAAAAACGCCACTATAGCTCAAGACCTTTAGCGGCACTTTTCCAC
1 GACCTTTAGCGGCGCTTTCACAAAAACGCCACTATAGCTCAAGACCTTTAGCAGCACTTTTCCAC
41814242 AAACGCCACTATAGCCCAA
66 AAACGCCACTATAGCCCAA
* * * * * * *
41814261 GACATTTAGCGACGCTTTTCTCACAAACGCCGCTATAGCTCAAGAGCTTTAGCAGCGCTTTTACC
1 GACCTTTAGCGGCGC-TTTCACAAAAACGCCACTATAGCTCAAGACCTTTAGCAGCACTTTT-CC
* **
41814326 ACAAACGCCGCTATAGTTCAA
64 ACAAACGCCACTATAGCCCAA
*
41814347 TACCTTTAGCGGCGCTTCTCACAAAAACGCCACTA
1 GACCTTTAGCGGCGCTT-TCACAAAAACGCCACTA
41814382 AAAATATAAC
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
84 12 0.12
85 42 0.42
86 46 0.46
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (84 bp):
GACCTTTAGCGGCGCTTTCACAAAAACGCCACTATAGCTCAAGACCTTTAGCAGCACTTTTCCAC
AAACGCCACTATAGCCCAA
Found at i:41816076 original size:28 final size:28
Alignment explanation
Indices: 41816043--41816096 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
41816033 GAATCAAATT
41816043 AGTTCAA-CTCCAAGTCCTTAGTCAAACC
1 AGTTCAACCT-CAAGTCCTTAGTCAAACC
* *
41816071 AGTTCAACCTCAAGTTCTTTGTCAAA
1 AGTTCAACCTCAAGTCCTTAGTCAAA
41816097 AGAAAAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.30
Consensus pattern (28 bp):
AGTTCAACCTCAAGTCCTTAGTCAAACC
Found at i:41817649 original size:252 final size:252
Alignment explanation
Indices: 41817204--41817960 Score: 1487
Period size: 252 Copynumber: 3.0 Consensus size: 252
41817194 ACCACCAATC
*
41817204 AAATCAAGTTGCCCATAATTTTACTTAACAACCTACAGAATAAGGTATGGCACACTAGAGAACAT
1 AAATCAAGTTTCCCATAATTTTACTTAACAACCTACAGAATAAGGTATGGCACACTAGAGAACAT
41817269 GTACATGACATATTGCCACCATCATAACCACCTCGTCACAACTCTCAGCATCTCAACTCTCTTCA
66 GTACATGACATATTGCCACCATCATAACCACCTCGTCACAACTCTCAGCATCTCAACTCTCTTCA
41817334 ACAAAATTCATTTCAACCGAAAATAGAAGAACTAAGTTATCTACATTGATACAAAAGGCCACAGC
131 ACAAAATTCATTTCAACCGAAAATAGAAGAACTAAGTTATCTACATTGATACAAAAGGCCACAGC
41817399 TTTGATAAATTGAAATCATACTAAAATGGAGAGAAATTCCTTTGTTTCCAATAACAT
196 TTTGATAAATTGAAATCATACTAAAATGGAGAGAAATTCCTTTGTTTCCAATAACAT
41817456 AAATCAAGTTTCCCATAATTTTACTTAACAACCTACAGAATAAGGTATGGCACACTAGAGAACAT
1 AAATCAAGTTTCCCATAATTTTACTTAACAACCTACAGAATAAGGTATGGCACACTAGAGAACAT
41817521 GTACATGACATATTGCCACCATCATAACCACCTCGTCACAACTCTCAGCATCTCAACTCTCTTCA
66 GTACATGACATATTGCCACCATCATAACCACCTCGTCACAACTCTCAGCATCTCAACTCTCTTCA
41817586 ACAAAATTCATTTCAACCGAAAATAGAAGAACTAAGTTATCTACATTGATACAAAAGGCCACAGC
131 ACAAAATTCATTTCAACCGAAAATAGAAGAACTAAGTTATCTACATTGATACAAAAGGCCACAGC
41817651 TTTGATAAATTGAAATCATACTAAAATGGAGAGAAATTCCTTTGTTTCCAATAACAT
196 TTTGATAAATTGAAATCATACTAAAATGGAGAGAAATTCCTTTGTTTCCAATAACAT
41817708 AAATCAAGTTTCCCATAATTTTACTTAACAACCTACAGAATAAGGTATGGCACACTAGAGAACAT
1 AAATCAAGTTTCCCATAATTTTACTTAACAACCTACAGAATAAGGTATGGCACACTAGAGAACAT
*
41817773 GTACATGACATATTGCCACCATCATAACCACCTCGTCACAGCTCTCAGCATCTCAACTCTCTTCA
66 GTACATGACATATTGCCACCATCATAACCACCTCGTCACAACTCTCAGCATCTCAACTCTCTTCA
*
41817838 ACAAAATTCATTTCAACCGAAAATAGAAGAACTAAGTTATCTACTTTGATACAAAAGGCCACAGC
131 ACAAAATTCATTTCAACCGAAAATAGAAGAACTAAGTTATCTACATTGATACAAAAGGCCACAGC
41817903 TTTGATAAATTGAAATCATACTAAAATGGAGAGAAATTCCTTTGTTTCCAATAACAT
196 TTTGATAAATTGAAATCATACTAAAATGGAGAGAAATTCCTTTGTTTCCAATAACAT
41817960 A
1 A
41817961 GCAGCCATTC
Statistics
Matches: 502, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
252 502 1.00
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (252 bp):
AAATCAAGTTTCCCATAATTTTACTTAACAACCTACAGAATAAGGTATGGCACACTAGAGAACAT
GTACATGACATATTGCCACCATCATAACCACCTCGTCACAACTCTCAGCATCTCAACTCTCTTCA
ACAAAATTCATTTCAACCGAAAATAGAAGAACTAAGTTATCTACATTGATACAAAAGGCCACAGC
TTTGATAAATTGAAATCATACTAAAATGGAGAGAAATTCCTTTGTTTCCAATAACAT
Found at i:41819947 original size:13 final size:13
Alignment explanation
Indices: 41819929--41819953 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41819919 GTTTTTGCTG
41819929 AAAACGCCACTAA
1 AAAACGCCACTAA
41819942 AAAACGCCACTA
1 AAAACGCCACTA
41819954 CCTAAACTAT
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:0.52, C:0.32, G:0.08, T:0.08
Consensus pattern (13 bp):
AAAACGCCACTAA
Found at i:41820526 original size:22 final size:22
Alignment explanation
Indices: 41820500--41820552 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
41820490 ACCCTTGAAA
* * *
41820500 CCCTAAATCCCTAGCTCTTAAC
1 CCCTAAACCCCTAACTCCTAAC
*
41820522 CCCTAACCCCCTAACTCCTAAC
1 CCCTAAACCCCTAACTCCTAAC
41820544 CCCTAAACC
1 CCCTAAACC
41820553 TTAAATCTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.28, C:0.49, G:0.02, T:0.21
Consensus pattern (22 bp):
CCCTAAACCCCTAACTCCTAAC
Found at i:41821054 original size:15 final size:16
Alignment explanation
Indices: 41821028--41821059 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
41821018 CCTAACCTCT
41821028 AACCCTTAAATCCATA
1 AACCCTTAAATCCATA
41821044 AACCC-TAAATCCATA
1 AACCCTTAAATCCATA
41821059 A
1 A
41821060 TTGATCTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (16 bp):
AACCCTTAAATCCATA
Found at i:41821813 original size:41 final size:41
Alignment explanation
Indices: 41821767--41822130 Score: 532
Period size: 41 Copynumber: 8.9 Consensus size: 41
41821757 AAAAAATATT
* * * * *
41821767 ATTAGCGGCGTTTTTTTAAAAACGCTGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * * ** *
41821808 ATTAGCGGCGCTTTTTTAAAAACACCGCTAAAGATCTGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
41821849 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
41821890 ATTAGCGGCGCTTCTTCAAAAACG-CGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
41821930 ACTAGCGGTGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* * *
41821971 ACTAGTGGCGCTTCTTCAAAAATGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* *
41822012 ATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
* **
41822053 ATTAGCGGCGCTTATTCAAAAACGCCGCTAAAGGCTAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
41822094 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCC
41822131 CAAAAACTCA
Statistics
Matches: 296, Mismatches: 26, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 38 0.13
41 258 0.87
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGC
Found at i:41823081 original size:14 final size:15
Alignment explanation
Indices: 41823041--41823084 Score: 54
Period size: 14 Copynumber: 2.9 Consensus size: 15
41823031 TTTTCAACAT
41823041 AAATTAAACTAAAATCA
1 AAATTAAA-T-AAATCA
*
41823058 AAATTAAATAAATTA
1 AAATTAAATAAATCA
41823073 AAA-TAAATAAAT
1 AAATTAAATAAAT
41823085 ATGGGTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.35
15 8 0.31
16 1 0.04
17 8 0.31
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATTAAATAAATCA
Found at i:41841372 original size:23 final size:23
Alignment explanation
Indices: 41841342--41841400 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
41841332 CCAAGCTGAT
* *
41841342 AAACGGTAAGCTGTATCGAGCTG
1 AAACGGTAAGCTCTATAGAGCTG
*
41841365 AAACGGTAAGCTCTGTAGAGCTG
1 AAACGGTAAGCTCTATAGAGCTG
41841388 AAACGGTAAGCTC
1 AAACGGTAAGCTC
41841401 ATACAAGCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (23 bp):
AAACGGTAAGCTCTATAGAGCTG
Found at i:41841409 original size:23 final size:23
Alignment explanation
Indices: 41841319--41841410 Score: 80
Period size: 23 Copynumber: 3.9 Consensus size: 23
41841309 GAGCCATGAT
*
41841319 CGGTAAGCTCATTCCAAGCTGATAAA
1 CGGTAAGCTCA-TACAAGCTG--AAA
* *
41841345 CGGTAAGCT-GTATCGAGCTGAAA
1 CGGTAAGCTCATA-CAAGCTGAAA
* *
41841368 CGGTAAGCTCTGTA-GAGCTGAAA
1 CGGTAAGCTC-ATACAAGCTGAAA
41841391 CGGTAAGCTCATACAAGCTG
1 CGGTAAGCTCATACAAGCTG
41841411 TGGTGAGTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
22 2 0.04
23 36 0.63
24 1 0.02
25 9 0.16
26 9 0.16
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.22
Consensus pattern (23 bp):
CGGTAAGCTCATACAAGCTGAAA
Found at i:41843108 original size:23 final size:23
Alignment explanation
Indices: 41843078--41843136 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
41843068 CCAAGCTGAT
* *
41843078 AAACGGTAAGCTGTATCGAGCTG
1 AAACGGTAAGCTCTATAGAGCTG
*
41843101 AAACGGTAAGCTCTGTAGAGCTG
1 AAACGGTAAGCTCTATAGAGCTG
41843124 AAACGGTAAGCTC
1 AAACGGTAAGCTC
41843137 ATACAAGCTG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (23 bp):
AAACGGTAAGCTCTATAGAGCTG
Found at i:41843145 original size:23 final size:23
Alignment explanation
Indices: 41843055--41843146 Score: 80
Period size: 23 Copynumber: 3.9 Consensus size: 23
41843045 GAGCCATGAT
*
41843055 CGGTAAGCTCATTCCAAGCTGATAAA
1 CGGTAAGCTCA-TACAAGCTG--AAA
* *
41843081 CGGTAAGCT-GTATCGAGCTGAAA
1 CGGTAAGCTCATA-CAAGCTGAAA
* *
41843104 CGGTAAGCTCTGTA-GAGCTGAAA
1 CGGTAAGCTC-ATACAAGCTGAAA
41843127 CGGTAAGCTCATACAAGCTG
1 CGGTAAGCTCATACAAGCTG
41843147 TGGTGAGTCT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
22 2 0.04
23 36 0.63
24 1 0.02
25 9 0.16
26 9 0.16
ACGTcount: A:0.32, C:0.21, G:0.26, T:0.22
Consensus pattern (23 bp):
CGGTAAGCTCATACAAGCTGAAA
Found at i:41845128 original size:35 final size:35
Alignment explanation
Indices: 41845073--41845148 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
41845063 TTCTGCTGCC
* *
41845073 TATTGTCCTTTTTATGTTTTTTTATTTGTTTTTCTT
1 TATT-TCCTTTTTATATTTTTTTATTTGTTTGTCTT
*
41845109 TATTTCCTTTTTCTATTTTTTTATTTGTTTGTCTT
1 TATTTCCTTTTTATATTTTTTTATTTGTTTGTCTT
41845144 T-TTTC
1 TATTTC
41845149 TGTAATGGCG
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
34 4 0.11
35 29 0.78
36 4 0.11
ACGTcount: A:0.08, C:0.11, G:0.07, T:0.75
Consensus pattern (35 bp):
TATTTCCTTTTTATATTTTTTTATTTGTTTGTCTT
Found at i:41852009 original size:25 final size:25
Alignment explanation
Indices: 41851950--41852010 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
41851940 TATGCTCTTA
* *
41851950 CGAGCTATA-AACGGTAAGCTCCTC
1 CGAGCTAAATAACGATAAGCTCCTC
*
41851974 C-AGGCTGAATAACGATAAGCTCCTC
1 CGA-GCTAAATAACGATAAGCTCCTC
41851999 CGAGCTAAATAA
1 CGAGCTAAATAA
41852011 TGGTAAGCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
23 1 0.03
24 5 0.17
25 23 0.77
26 1 0.03
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (25 bp):
CGAGCTAAATAACGATAAGCTCCTC
Found at i:41852017 original size:25 final size:25
Alignment explanation
Indices: 41851959--41852045 Score: 95
Period size: 25 Copynumber: 3.5 Consensus size: 25
41851949 ACGAGCTATA
41851959 AACGGTAAGCTCCTCC-AGGCTGAAT
1 AACGGTAAGCTCCTCCGA-GCTGAAT
* *
41851984 AACGATAAGCTCCTCCGAGCTAAAT
1 AACGGTAAGCTCCTCCGAGCTGAAT
* * * * *
41852009 AATGGTAAGCACATGCGAGCTGAGT
1 AACGGTAAGCTCCTCCGAGCTGAAT
41852034 AACGGTAAGCTC
1 AACGGTAAGCTC
41852046 ATACGACCTG
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
25 49 0.98
26 1 0.02
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.20
Consensus pattern (25 bp):
AACGGTAAGCTCCTCCGAGCTGAAT
Found at i:41856021 original size:22 final size:20
Alignment explanation
Indices: 41855981--41856031 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 20
41855971 AACAAATAAT
41855981 AAAGAAAAAAATAGAAAAAA
1 AAAGAAAAAAATAGAAAAAA
41856001 AAAGAAAACCAAATA-ATAAAAA
1 AAAGAAAA--AAATAGA-AAAAA
*
41856023 AAGGAAAAA
1 AAAGAAAAA
41856032 CAATTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 9 0.33
21 1 0.04
22 17 0.63
ACGTcount: A:0.80, C:0.04, G:0.10, T:0.06
Consensus pattern (20 bp):
AAAGAAAAAAATAGAAAAAA
Done.