Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 132 of 213
Found at i:38727301 original size:30 final size:28
Alignment explanation
Indices: 38727258--38727347 Score: 110
Period size: 30 Copynumber: 3.2 Consensus size: 28
38727248 CAGTAGTAGT
*
38727258 ACAGTGTGGGCCTTAGCCCATTACAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
*
38727286 ACAGTGTGTGTGCCTTAGCACAATACAGT-
1 ACAGTGTG-G-GCCTTAGCCCAATACAGTA
* * *
38727315 ACAGTGTGGACCTTAGACCAATAAAGTA
1 ACAGTGTGGGCCTTAGCCCAATACAGTA
38727343 ACAGT
1 ACAGT
38727348 ACAATGCAGT
Statistics
Matches: 53, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
27 14 0.26
28 14 0.26
29 9 0.17
30 16 0.30
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.24
Consensus pattern (28 bp):
ACAGTGTGGGCCTTAGCCCAATACAGTA
Found at i:38727727 original size:27 final size:26
Alignment explanation
Indices: 38727704--38728011 Score: 267
Period size: 27 Copynumber: 11.4 Consensus size: 26
38727694 AGTGGTATAA
*
38727704 TAGTCATTTTACCCTTTTGGGGTATT
1 TAGTCATTTTACCCTTTGGGGGTATT
* * *
38727730 TCGATTATTTTACCCTTCGGGGGTATTT
1 TAG-TCATTTTACCCTTTGGGGGTA-TT
*
38727758 TAGTCATTTTAACCTTTGGGGGTATT
1 TAGTCATTTTACCCTTTGGGGGTATT
***
38727784 TCAGTCATTTTACCCTTCAAGGGTATTT
1 T-AGTCATTTTACCCTTTGGGGGTA-TT
** *
38727812 TAGTCATTTTA-CCTTTCAAGGTTATTT
1 TAGTCATTTTACCCTTT-GGGGGTA-TT
*
38727839 TAGTCATTTTACCCTTTGAGGGTATT
1 TAGTCATTTTACCCTTTGGGGGTATT
* * *
38727865 TCGATCATTTTACCCTTCGAGGGTATTT
1 TAG-TCATTTTACCCTTTGGGGGTA-TT
*
38727893 TAGTCATTTTACCCTTTGAGGGTATT
1 TAGTCATTTTACCCTTTGGGGGTATT
* *
38727919 TTGATCATTTTACCATTTGGGGGTATT
1 TAG-TCATTTTACCCTTTGGGGGTATT
* * * *
38727946 TCGATCATTTTAACCTTCGAGGGTATT
1 TAG-TCATTTTACCCTTTGGGGGTATT
* * *
38727973 TCAATCATTTTACCCTTCGGGGTTATT
1 T-AGTCATTTTACCCTTTGGGGGTATT
*
38728000 TCGGTCATTTTA
1 T-AGTCATTTTA
38728012 GGCCCATTAC
Statistics
Matches: 237, Mismatches: 35, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
26 17 0.07
27 204 0.86
28 16 0.07
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (26 bp):
TAGTCATTTTACCCTTTGGGGGTATT
Found at i:38727763 original size:54 final size:55
Alignment explanation
Indices: 38727704--38728011 Score: 332
Period size: 54 Copynumber: 5.7 Consensus size: 55
38727694 AGTGGTATAA
* * *
38727704 TAGTCATTTTACCCTTTTGGGGTATTTCGA-TTATTTTACCCTTCGGGGGTATTT
1 TAGTCATTTTACCCTTTCGGGGTATTTCGAGTCATTTTACCCTTCGAGGGTATTT
* * *
38727758 TAGTCATTTTAACCTTTGGGGGTATTTC-AGTCATTTTACCCTTCAAGGGTATTT
1 TAGTCATTTTACCCTTTCGGGGTATTTCGAGTCATTTTACCCTTCGAGGGTATTT
* * * *
38727812 TAGTCATTTTA-CCTTTCAAGGTTATTT-TAGTCATTTTACCCTTTGAGGGTA-TT
1 TAGTCATTTTACCCTTTC-GGGGTATTTCGAGTCATTTTACCCTTCGAGGGTATTT
* * *
38727865 TCGATCATTTTACCC-TTCGAGGGTATTT-TAGTCATTTTACCCTTTGAGGGTATTT
1 TAG-TCATTTTACCCTTTCG-GGGTATTTCGAGTCATTTTACCCTTCGAGGGTATTT
* * *
38727920 T-GATCATTTTACCATTTGGGGGTATTTCGA-TCATTTTAACCTTCGAGGGTATTT
1 TAG-TCATTTTACCCTTTCGGGGTATTTCGAGTCATTTTACCCTTCGAGGGTATTT
* *
38727974 CAATCATTTTACCC-TTCGGGGTTATTTCG-GTCATTTTA
1 TAGTCATTTTACCCTTTCGGGG-TATTTCGAGTCATTTTA
38728012 GGCCCATTAC
Statistics
Matches: 220, Mismatches: 22, Indels: 24
0.83 0.08 0.09
Matches are distributed among these distances:
53 16 0.07
54 195 0.89
55 9 0.04
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (55 bp):
TAGTCATTTTACCCTTTCGGGGTATTTCGAGTCATTTTACCCTTCGAGGGTATTT
Found at i:38727838 original size:81 final size:81
Alignment explanation
Indices: 38727736--38728011 Score: 353
Period size: 81 Copynumber: 3.4 Consensus size: 81
38727726 TATTTCGATT
* * *
38727736 ATTTTACCCTTCGGGGGTATTTTAGTCATTTTAACCTTTGGGGGTATTTC-AGTCATTTTACCCT
1 ATTTTACCTTTCGAGGTTATTTTAGTCATTTTAACCTTTGGGGGTATTTCGA-TCATTTTACCCT
*
38727800 TCAAGGGTATTTTAGTC
65 TCGAGGGTATTTTAGTC
* * *
38727817 ATTTTACCTTTCAAGGTTATTTTAGTCATTTTACCCTTTGAGGGTATTTCGATCATTTTACCCTT
1 ATTTTACCTTTCGAGGTTATTTTAGTCATTTTAACCTTTGGGGGTATTTCGATCATTTTACCCTT
38727882 CGAGGGTATTTTAGTC
66 CGAGGGTATTTTAGTC
* *
38727898 ATTTTACCCTTT-GAGGGTATTTT-GATCATTTT-ACCATTTGGGGGTATTTCGATCATTTTAAC
1 ATTTTA-CCTTTCGAGGTTATTTTAG-TCATTTTAACC-TTTGGGGGTATTTCGATCATTTTACC
* *
38727960 CTTCGAGGGTATTTCAATC
63 CTTCGAGGGTATTTTAGTC
* * **
38727979 ATTTTACCCTTCGGGGTTATTTCGGTCATTTTA
1 ATTTTACCTTTCGAGGTTATTTTAGTCATTTTA
38728012 GGCCCATTAC
Statistics
Matches: 170, Mismatches: 18, Indels: 13
0.85 0.09 0.06
Matches are distributed among these distances:
80 7 0.04
81 156 0.92
82 7 0.04
ACGTcount: A:0.19, C:0.17, G:0.18, T:0.46
Consensus pattern (81 bp):
ATTTTACCTTTCGAGGTTATTTTAGTCATTTTAACCTTTGGGGGTATTTCGATCATTTTACCCTT
CGAGGGTATTTTAGTC
Found at i:38733998 original size:26 final size:27
Alignment explanation
Indices: 38733963--38734028 Score: 80
Period size: 26 Copynumber: 2.5 Consensus size: 27
38733953 TTTGGTGAAC
* *
38733963 CCCCCAGTTCACCGAAGTACTGG-AAA
1 CCCCTAGTTCACCGAAGTACAGGCAAA
* * *
38733989 CCCTTAGTTCACAGAAGTACAGGCGAA
1 CCCCTAGTTCACCGAAGTACAGGCAAA
38734016 CCCCTAGTTCACC
1 CCCCTAGTTCACC
38734029 AAAACACTGG
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
26 19 0.59
27 13 0.41
ACGTcount: A:0.29, C:0.35, G:0.18, T:0.18
Consensus pattern (27 bp):
CCCCTAGTTCACCGAAGTACAGGCAAA
Found at i:38749507 original size:27 final size:27
Alignment explanation
Indices: 38749477--38749654 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
38749467 ATATTGAGTC
* * * *
38749477 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
38749504 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38749531 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
38749559 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
38749586 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
38749613 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38749640 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38749655 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:38749616 original size:82 final size:81
Alignment explanation
Indices: 38749498--38749653 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
38749488 TGCTATATAA
* *
38749498 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
38749563 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
38749580 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
38749644 CACTTAGTGC
65 CACTTAGTGC
38749654 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:38751562 original size:51 final size:51
Alignment explanation
Indices: 38751501--38751611 Score: 136
Period size: 51 Copynumber: 2.2 Consensus size: 51
38751491 TTGGGCTGTC
*
38751501 ACACACGTGACCA-AAGCCT-TCCGGTACACATAGTAGCCTGCACATAGTACT
1 ACACACGTGACCATAA-CCTAT-CGATACACATAGTAGCCTGCACATAGTACT
* * * * *
38751552 ACACATGTGACCATTATCTATCGATACACGTAGTAGCCTGCACCTAGTACT
1 ACACACGTGACCATAACCTATCGATACACATAGTAGCCTGCACATAGTACT
38751603 ACACACGTG
1 ACACACGTG
38751612 TTTATAGGCA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
51 49 0.96
52 2 0.04
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.23
Consensus pattern (51 bp):
ACACACGTGACCATAACCTATCGATACACATAGTAGCCTGCACATAGTACT
Found at i:38754590 original size:29 final size:29
Alignment explanation
Indices: 38754551--38754628 Score: 106
Period size: 29 Copynumber: 2.7 Consensus size: 29
38754541 CTTAATAATC
38754551 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCC-TGTACATTTA
*
38754581 AACTCGCACACTTAGTG-CTGTACATTTTA
1 AACCCGCACACTTAGTGCCTGTACA-TTTA
38754610 AACCCGCACACTTAGTGCC
1 AACCCGCACACTTAGTGCC
38754629 GAAAACCAGC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.27, C:0.31, G:0.15, T:0.27
Consensus pattern (29 bp):
AACCCGCACACTTAGTGCCTGTACATTTA
Found at i:38756558 original size:83 final size:83
Alignment explanation
Indices: 38756437--38756604 Score: 336
Period size: 83 Copynumber: 2.0 Consensus size: 83
38756427 AGTTAACCCC
38756437 GTGAATCCGTTTCTCACTAAGCTCAGTCCAATACAAAAGGATTCTACACTTACGTCCATATAATG
1 GTGAATCCGTTTCTCACTAAGCTCAGTCCAATACAAAAGGATTCTACACTTACGTCCATATAATG
38756502 TTTCATACGGTGCCATTT
66 TTTCATACGGTGCCATTT
38756520 GTGAATCCGTTTCTCACTAAGCTCAGTCCAATACAAAAGGATTCTACACTTACGTCCATATAATG
1 GTGAATCCGTTTCTCACTAAGCTCAGTCCAATACAAAAGGATTCTACACTTACGTCCATATAATG
38756585 TTTCATACGGTGCCATTT
66 TTTCATACGGTGCCATTT
38756603 GT
1 GT
38756605 ATACTCGACT
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
83 85 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (83 bp):
GTGAATCCGTTTCTCACTAAGCTCAGTCCAATACAAAAGGATTCTACACTTACGTCCATATAATG
TTTCATACGGTGCCATTT
Found at i:38759156 original size:69 final size:70
Alignment explanation
Indices: 38759024--38759156 Score: 205
Period size: 69 Copynumber: 1.9 Consensus size: 70
38759014 TAGTTTATTA
* * * * * *
38759024 CTAATTAATTTGCTGCTGTAATGCTGTAAATTATTGGCTGTCGAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
38759089 CTTAG
66 CTTAG
38759094 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
38759157 GTTATGTACT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 34 0.60
70 23 0.40
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTGTAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:38760598 original size:47 final size:47
Alignment explanation
Indices: 38760544--38760994 Score: 697
Period size: 47 Copynumber: 9.6 Consensus size: 47
38760534 TATTTGAATA
*
38760544 AATGTGAAAGTGTATATATGTGATAAGACCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38760591 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
38760638 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * *
38760687 AATGTGAAAGTGTATATATCTGATAAGGCATAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
38760734 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
38760781 AATGTGAAACTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38760828 AATGTGAAAGTGTATATATGTGACAAGGCCTAATAGCCGATG-GATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* **
38760874 AATGTGAAAGTGTATATATGTGGTAAGAACTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
38760921 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38760968 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
38760995 TCCCGAAGGG
Statistics
Matches: 368, Mismatches: 33, Indels: 6
0.90 0.08 0.01
Matches are distributed among these distances:
46 41 0.11
47 282 0.77
49 45 0.12
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:38762730 original size:40 final size:40
Alignment explanation
Indices: 38762407--38762718 Score: 489
Period size: 40 Copynumber: 7.8 Consensus size: 40
38762397 GAGAATTGAG
*
38762407 AGTGATGTATCTGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
38762447 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
38762487 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
38762527 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
*
38762567 AGTGATGTATCCGGGCTAAGTCTCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * *
38762607 AGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCATGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * **
38762647 AGTGATATATCCGTGCTAAACCCCGAAGAGCATTCGTGCT
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
* * * *
38762687 GGTGTTATATCCGGGCTAGGTCCCGAAGAGCA
1 AGTGATGTATCCGGGCTAAGTCCCGAAGAGCA
38762719 ATCATGCTGG
Statistics
Matches: 253, Mismatches: 19, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 253 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (40 bp):
AGTGATGTATCCGGGCTAAGTCCCGAAGAGCATTCGTGCT
Found at i:38765447 original size:69 final size:70
Alignment explanation
Indices: 38765315--38765447 Score: 205
Period size: 69 Copynumber: 1.9 Consensus size: 70
38765305 TAGTTTATTA
* * * * * *
38765315 CTAATTAATTTGCTGCTGTAATGCTATAAATTATTGGCTGTCGAAATTAGGACAAATTTATGGTA
1 CTAATTAATATGCTGCTGTAATACTATAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
38765380 CTTAG
66 CTTAG
38765385 CTAATTAATATGCTGCTGTAATACT-TAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
1 CTAATTAATATGCTGCTGTAATACTATAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGT
38765448 GTTATGTACT
Statistics
Matches: 57, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
69 34 0.60
70 23 0.40
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
CTAATTAATATGCTGCTGTAATACTATAAATTATTGGCTCTCCAAATTAGGACAAAATCATGGTA
CTTAG
Found at i:38766888 original size:47 final size:47
Alignment explanation
Indices: 38766834--38767285 Score: 733
Period size: 47 Copynumber: 9.6 Consensus size: 47
38766824 TATTTGAATA
*
38766834 AATGTGAAAGTGTATATATGTGATAAGACCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38766881 AATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
38766928 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
38766977 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
38767024 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
38767071 AATGTGAAACTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38767118 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGCGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
**
38767165 AATGTGAAAGTGTATATATGTGATAAGAACTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * *
38767212 AATGTGAAAGTGTATATATGTGATAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
38767259 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
38767286 TCCCGAAGGG
Statistics
Matches: 376, Mismatches: 27, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
47 331 0.88
49 45 0.12
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:38777611 original size:26 final size:26
Alignment explanation
Indices: 38777582--38777633 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
38777572 ATATAATTTC
38777582 CAAATCATGTATC-TATATATCATGTA
1 CAAATCAT-TATCATATATATCATGTA
* *
38777608 CAAATCATTTTCATATATCTCATGTA
1 CAAATCATTATCATATATATCATGTA
38777634 AATACCTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.37, C:0.17, G:0.06, T:0.40
Consensus pattern (26 bp):
CAAATCATTATCATATATATCATGTA
Found at i:38777843 original size:25 final size:25
Alignment explanation
Indices: 38777815--38777888 Score: 112
Period size: 25 Copynumber: 3.0 Consensus size: 25
38777805 CCGAGTTGAA
*
38777815 TAATGGTAAGCTTGTATGAGCTGAG
1 TAATGGTAAGCTTATATGAGCTGAG
38777840 TAATGGTAAGCTTATATGAGCTGAG
1 TAATGGTAAGCTTATATGAGCTGAG
* * *
38777865 CAATGGTAAGCTCATAAGAGCTGA
1 TAATGGTAAGCTTATATGAGCTGA
38777889 AACTGATAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.32, C:0.11, G:0.28, T:0.28
Consensus pattern (25 bp):
TAATGGTAAGCTTATATGAGCTGAG
Found at i:38780327 original size:18 final size:18
Alignment explanation
Indices: 38780304--38780340 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
38780294 CCGATGATGG
38780304 CTAAATTCCTCTAATCCT
1 CTAAATTCCTCTAATCCT
38780322 CTAAATTCCTCTAATCCT
1 CTAAATTCCTCTAATCCT
38780340 C
1 C
38780341 ACTCAACTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.35, G:0.00, T:0.38
Consensus pattern (18 bp):
CTAAATTCCTCTAATCCT
Found at i:38780331 original size:10 final size:10
Alignment explanation
Indices: 38780304--38780335 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
38780294 CCGATGATGG
38780304 CTAAATTCCT
1 CTAAATTCCT
38780314 CT-AA-TCCT
1 CTAAATTCCT
38780322 CTAAATTCCT
1 CTAAATTCCT
38780332 CTAA
1 CTAA
38780336 TCCTCACTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
8 6 0.30
9 4 0.20
10 10 0.50
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
CTAAATTCCT
Found at i:38786008 original size:8 final size:8
Alignment explanation
Indices: 38785988--38786018 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
38785978 TTTATCCTAG
38785988 AAAATTAAT
1 AAAATT-AT
38785997 AAAATTAT
1 AAAATTAT
38786005 AAAATTAT
1 AAAATTAT
38786013 AAAATT
1 AAAATT
38786019 CACCCCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.73
9 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
AAAATTAT
Found at i:38786121 original size:17 final size:17
Alignment explanation
Indices: 38786081--38786115 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38786071 CAGTACTAAT
* *
38786081 TCACATTTCCATCGTCA
1 TCACCTTTCCATCATCA
38786098 TCACCTTTCCATCATCA
1 TCACCTTTCCATCATCA
38786115 T
1 T
38786116 TTCCTTATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.23, C:0.37, G:0.03, T:0.37
Consensus pattern (17 bp):
TCACCTTTCCATCATCA
Found at i:38787636 original size:31 final size:31
Alignment explanation
Indices: 38787600--38787682 Score: 112
Period size: 31 Copynumber: 2.7 Consensus size: 31
38787590 GTAGTCTTGT
** * *
38787600 GTGTGAAAAATTGGCAATGAGGAGTCTTTAG
1 GTGTGAAAAATCAGCAATGAAGAGCCTTTAG
*
38787631 GTGTGAACAATCAGCAATGAAGAGCCTTTAG
1 GTGTGAAAAATCAGCAATGAAGAGCCTTTAG
*
38787662 GTGTGAACAATCAGCAATGAA
1 GTGTGAAAAATCAGCAATGAA
38787683 AAGTAAAGCA
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (31 bp):
GTGTGAAAAATCAGCAATGAAGAGCCTTTAG
Found at i:38789009 original size:6 final size:6
Alignment explanation
Indices: 38788991--38789020 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
38788981 GCAAATGGAT
38788991 CATTTC TCATTTC CATTTC CATTTC CATTT
1 CATTTC -CATTTC CATTTC CATTTC CATTT
38789021 TTATTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.17, C:0.30, G:0.00, T:0.53
Consensus pattern (6 bp):
CATTTC
Found at i:38793582 original size:40 final size:40
Alignment explanation
Indices: 38793537--38793635 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
38793527 ATTGCAGACC
* ** *
38793537 GAAGTGCAAATAAAGGCATGAATGTGCT-ATCAGAGCCACT
1 GAAGTGCAAATAGAGGCACAAATGTG-TGATCAAAGCCACT
* *
38793577 GAAGTGCAAACAGAGGCACAAATGTGTGATCAAAGGCACT
1 GAAGTGCAAATAGAGGCACAAATGTGTGATCAAAGCCACT
*
38793617 GAAGTACAAATAGAGGCAC
1 GAAGTGCAAATAGAGGCAC
38793636 CGAAGTGAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
39 1 0.02
40 49 0.98
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.16
Consensus pattern (40 bp):
GAAGTGCAAATAGAGGCACAAATGTGTGATCAAAGCCACT
Found at i:38794609 original size:16 final size:17
Alignment explanation
Indices: 38794584--38794616 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
38794574 AGATGATGAC
*
38794584 ATTATTGTTTT-ATTTA
1 ATTATAGTTTTAATTTA
38794600 ATTATAGTTTTAATTTA
1 ATTATAGTTTTAATTTA
38794617 TAAATTATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (17 bp):
ATTATAGTTTTAATTTA
Found at i:38805813 original size:27 final size:25
Alignment explanation
Indices: 38805783--38805871 Score: 88
Period size: 26 Copynumber: 3.4 Consensus size: 25
38805773 CGCCATGAAG
* *
38805783 GCTTCCATTTCATATATTGTCACAAAA
1 GCTTCCATTTCAGATA-T-CCACAAAA
* * *
38805810 GCTTTCATTTCAGATACACCACAAAG
1 GCTTCCATTTCAGATA-TCCACAAAA
*
38805836 GCTTCCATTTCAGATACTCCACAAAT
1 GCTTCCATTTCAGATA-TCCACAAAA
38805862 GCTTCCATTT
1 GCTTCCATTT
38805872 TCTGACATGT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 39 0.74
27 14 0.26
ACGTcount: A:0.30, C:0.27, G:0.09, T:0.34
Consensus pattern (25 bp):
GCTTCCATTTCAGATATCCACAAAA
Found at i:38805839 original size:26 final size:26
Alignment explanation
Indices: 38805803--38805871 Score: 102
Period size: 26 Copynumber: 2.7 Consensus size: 26
38805793 CATATATTGT
*
38805803 CACAAAAGCTTTCATTTCAGATACAC
1 CACAAAAGCTTCCATTTCAGATACAC
* *
38805829 CACAAAGGCTTCCATTTCAGATACTC
1 CACAAAAGCTTCCATTTCAGATACAC
*
38805855 CACAAATGCTTCCATTT
1 CACAAAAGCTTCCATTT
38805872 TCTGACATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.33, C:0.29, G:0.09, T:0.29
Consensus pattern (26 bp):
CACAAAAGCTTCCATTTCAGATACAC
Found at i:38808847 original size:29 final size:29
Alignment explanation
Indices: 38808814--38808871 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
38808804 TGAATTTTTT
38808814 TTTGTTCAAATTAGGCCCTGAACTTGGCA
1 TTTGTTCAAATTAGGCCCTGAACTTGGCA
*
38808843 TTTGTTCAAATTAGGTCCTGAACTTGGCA
1 TTTGTTCAAATTAGGCCCTGAACTTGGCA
38808872 ATTATTCTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (29 bp):
TTTGTTCAAATTAGGCCCTGAACTTGGCA
Found at i:38809557 original size:15 final size:16
Alignment explanation
Indices: 38809537--38809566 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
38809527 TAAATAAAAT
38809537 AAAATTT-TAATTTTA
1 AAAATTTCTAATTTTA
38809552 AAAATTTCTAATTTT
1 AAAATTTCTAATTTT
38809567 TTCATTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
AAAATTTCTAATTTTA
Found at i:38809791 original size:20 final size:21
Alignment explanation
Indices: 38809754--38809793 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
38809744 ATTATTAGAA
* *
38809754 AATTTAAAAATTTTAAAAATC
1 AATTTAAAAAGTTCAAAAATC
38809775 AATTT-AAAAGTTCAAAAAT
1 AATTTAAAAAGTTCAAAAAT
38809794 TTACAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (21 bp):
AATTTAAAAAGTTCAAAAATC
Found at i:38811711 original size:15 final size:16
Alignment explanation
Indices: 38811691--38811723 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
38811681 TAATACAAAT
38811691 TTAAAAACTAAAA-AA
1 TTAAAAACTAAAATAA
*
38811706 TTAAAAATTAAAATAA
1 TTAAAAACTAAAATAA
38811722 TT
1 TT
38811724 TTTTTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAAAAACTAAAATAA
Found at i:38812156 original size:30 final size:30
Alignment explanation
Indices: 38812122--38812193 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
38812112 TTTCAAAATT
**
38812122 AATTTTAATTT-AGTGTAGTTATACACATAA
1 AATTTTAATTTGA-TGTAAATATACACATAA
*
38812152 AATTTTAATTGTGATGTAAATATATACATAA
1 AATTTTAATT-TGATGTAAATATACACATAA
*
38812183 AACTTTAATTT
1 AATTTTAATTT
38812194 CGATTTAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 11 0.31
31 24 0.67
32 1 0.03
ACGTcount: A:0.42, C:0.06, G:0.08, T:0.44
Consensus pattern (30 bp):
AATTTTAATTTGATGTAAATATACACATAA
Found at i:38812378 original size:29 final size:30
Alignment explanation
Indices: 38812335--38812393 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
38812325 AAATTGGATC
* *
38812335 AAATCAAATTTTCATGTATAAAATTACACA
1 AAATCAAATATTCATATATAAAATTACACA
* *
38812365 AAATCAAA-ATTCATATATACAATTGCACA
1 AAATCAAATATTCATATATAAAATTACACA
38812394 TTAAACTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 17 0.68
30 8 0.32
ACGTcount: A:0.51, C:0.15, G:0.03, T:0.31
Consensus pattern (30 bp):
AAATCAAATATTCATATATAAAATTACACA
Found at i:38814619 original size:139 final size:140
Alignment explanation
Indices: 38814288--38814637 Score: 427
Period size: 142 Copynumber: 2.5 Consensus size: 140
38814278 ATATTGTTTC
* * *
38814288 AAGCTTGAAGCAACATAAAATAAAAAAATACAAATGTGAGTAGTAGAGGAATTGAACTTGAGACT
1 AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTTGAGACT
* * * * * *
38814353 -AAGGATGTAATTGCAGCTATATAACCATCCAACGAAAGGACTAATATGTTAAAAACGTAATTAA
66 CAAGGATGTAATTACAACTATATAACCATCCAACGAAAGAACTAACATATTAAAAAAGTAATTAA
38814417 AATTTAAAAAAAA
131 AATTT---AAAAA
* * *
38814430 AAACTTGAAGCAACATGAAATAAAAAAATACAAATGTGAATAGGAAAGAAATTGAACTTGAGACT
1 AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTTGAGACT
* * * * * *
38814495 CAATGATGTATTTACAACTATCTAACCATCTAACTAAAGAACTAACATATTAAAAAAATTAATTA
66 CAAGGATGTAATTACAACTATATAACCATCCAACGAAAGAACTAACATATT-AAAAAAGTAATTA
*
38814560 AAATTT-GAAA
130 AAATTTAAAAA
* * * **
38814570 AAGCCTGAAGTAACATGAAAT-AAAAAATACAAATGTGAGTAGGAGAGAAATCGAACCCGAGACT
1 AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTTGAGACT
38814634 CAAG
66 CAAG
38814638 AATAAAAGAA
Statistics
Matches: 178, Mismatches: 28, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
139 41 0.23
140 21 0.12
142 59 0.33
143 40 0.22
144 17 0.10
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.23
Consensus pattern (140 bp):
AAGCTTGAAGCAACATGAAATAAAAAAATACAAATGTGAGTAGGAGAGAAATTGAACTTGAGACT
CAAGGATGTAATTACAACTATATAACCATCCAACGAAAGAACTAACATATTAAAAAAGTAATTAA
AATTTAAAAA
Found at i:38823748 original size:19 final size:19
Alignment explanation
Indices: 38823724--38823768 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
38823714 ATGCTACGGG
38823724 CGTGTGGAAAGGCCTAAGC
1 CGTGTGGAAAGGCCTAAGC
*
38823743 CGTGTGGAAAGGCCTAGGC
1 CGTGTGGAAAGGCCTAAGC
38823762 CGTGTGG
1 CGTGTGG
38823769 GGGTCAACAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.20, C:0.20, G:0.42, T:0.18
Consensus pattern (19 bp):
CGTGTGGAAAGGCCTAAGC
Found at i:38831887 original size:40 final size:40
Alignment explanation
Indices: 38831828--38832039 Score: 268
Period size: 40 Copynumber: 5.3 Consensus size: 40
38831818 CATTTGAATG
* *
38831828 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
38831868 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
38831908 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
38831948 TTATCCGGGCTAAGACCCGAAGACATTTGTGCAAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
38831988 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
38832028 ATATCC-GGCTAA
1 ATATCCGGGCTAA
38832040 ATTCCGAAGA
Statistics
Matches: 146, Mismatches: 22, Indels: 9
0.82 0.12 0.05
Matches are distributed among these distances:
39 10 0.07
40 131 0.90
41 5 0.03
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:38831965 original size:80 final size:80
Alignment explanation
Indices: 38831832--38832039 Score: 319
Period size: 80 Copynumber: 2.6 Consensus size: 80
38831822 TGAATGATAT
* *
38831832 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGACATTTG
* *
38831897 TGCGAGTTGCTATAC
66 TGCAAGTTGATATAC
*
38831912 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGACATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGACATTTG
*
38831977 TGCAAGTTGATATAT
66 TGCAAGTTGATATAC
* * * *
38831992 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAA
38832040 ATTCCGAAGA
Statistics
Matches: 117, Mismatches: 11, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
79 6 0.05
80 111 0.95
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGACATTTG
TGCAAGTTGATATAC
Found at i:38839953 original size:40 final size:40
Alignment explanation
Indices: 38839894--38840105 Score: 277
Period size: 40 Copynumber: 5.3 Consensus size: 40
38839884 CATTTGAATG
* *
38839894 ATATCCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
38839934 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
38839974 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
38840014 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
38840054 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
38840094 ATATCC-GGCTAA
1 ATATCCGGGCTAA
38840106 ATTCCGAAGA
Statistics
Matches: 148, Mismatches: 20, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
39 10 0.07
40 133 0.90
41 5 0.03
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.27
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:38840031 original size:80 final size:80
Alignment explanation
Indices: 38839898--38840105 Score: 337
Period size: 80 Copynumber: 2.6 Consensus size: 80
38839888 TGAATGATAT
*
38839898 CCGGGCTAAGTCCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
*
38839963 TGCGAGTTGCTATAC
66 TGCGAGTTGATATAC
*
38839978 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
*
38840043 TGCGAGTTGATATAT
66 TGCGAGTTGATATAC
* * * *
38840058 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAA
38840106 ATTCCGAAGA
Statistics
Matches: 119, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
79 6 0.05
80 113 0.95
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
TGCGAGTTGATATAC
Found at i:38856505 original size:14 final size:14
Alignment explanation
Indices: 38856486--38856547 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
38856476 GGTAGGCAAC
*
38856486 TTTTTTTTGCGGTT
1 TTTTTTTTGCGATT
*
38856500 TTTTTTTTGCGCTT
1 TTTTTTTTGCGATT
*
38856514 TTTGCTTTTT-C-TTT
1 TTT--TTTTTGCGATT
*
38856528 TTTTTTTTGCTATT
1 TTTTTTTTGCGATT
38856542 TTTTTT
1 TTTTTT
38856548 AGCTTCAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
12 5 0.12
13 1 0.02
14 29 0.71
15 1 0.02
16 5 0.12
ACGTcount: A:0.02, C:0.10, G:0.11, T:0.77
Consensus pattern (14 bp):
TTTTTTTTGCGATT
Found at i:38857930 original size:72 final size:71
Alignment explanation
Indices: 38857848--38857986 Score: 167
Period size: 72 Copynumber: 1.9 Consensus size: 71
38857838 CTTTCCCCCC
* * * **
38857848 AAAAATTTTACTTTCC-CTCAAA-CCACACAACTTTTTTTCCTTTTATTTTTCCCCCAAAAC-TT
1 AAAAAATTTAC-TTCCTCCCAAACCCACAAAACTTTTTTT-C-TTT-TGCTTCCCCCAAAACTTT
38857910 TACTTCTCTT
62 TACTTCTCTT
*
38857920 AAAAAATTTACTTCCTCCCAAACCCTCAAAACTTTTTTTCTTTTGCTTCCCCCAAAACTTTTACT
1 AAAAAATTTACTTCCTCCCAAACCCACAAAACTTTTTTTCTTTTGCTTCCCCCAAAACTTTTACT
38857985 TC
66 TC
38857987 CTCCTAAACC
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
70 13 0.22
71 15 0.26
72 16 0.28
73 14 0.24
ACGTcount: A:0.27, C:0.30, G:0.01, T:0.42
Consensus pattern (71 bp):
AAAAAATTTACTTCCTCCCAAACCCACAAAACTTTTTTTCTTTTGCTTCCCCCAAAACTTTTACT
TCTCTT
Found at i:38859026 original size:21 final size:21
Alignment explanation
Indices: 38859002--38859060 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
38858992 TGTCAATTTT
*
38859002 CACATGGGCGTGTGCCTTGGA
1 CACACGGGCGTGTGCCTTGGA
* * * *
38859023 CACACGGCCGTGTTCCTTTGC
1 CACACGGGCGTGTGCCTTGGA
*
38859044 CACACGGGTGTGTGCCT
1 CACACGGGCGTGTGCCT
38859061 CTTTTCACCT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.12, C:0.31, G:0.32, T:0.25
Consensus pattern (21 bp):
CACACGGGCGTGTGCCTTGGA
Found at i:38869536 original size:265 final size:266
Alignment explanation
Indices: 38869036--38869564 Score: 997
Period size: 265 Copynumber: 2.0 Consensus size: 266
38869026 CACAGTGCTC
* *
38869036 TTTGCTCCCTTCCGGTCATTCTCCTCTAGTTGGTGGTGTATTTCAACAAAGTTTTTTTTTGTGTG
1 TTTGCTCCCTTCCAGTCATTCTCCTCTAATTGGTGGTGTATTTCAACAAAGTTTTTTTTTGTGTG
*
38869101 GGATCTCTTTTGTGTTTTTATGAGTGGTTTTTGTTATAATTTTTCCAAGCAGATTTTTTTTTGGG
66 GGATCTCTTTTGTGTTTTTATGAGTGGTTTCTGTTATAATTTTTCCAAGCAGATTTTTTTTTGGG
38869166 TATTAGTTAATTTTTTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCAC
131 TATTAGTTAATTTTTTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCAC
38869231 TCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACTT
196 TCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACTT
38869296 GTTTTT
261 GTTTTT
* *
38869302 TTTGCTCCCTTCCAGTCATTCTCCTCTAATTGGTGGTGTATTTCAGCTAAGTTTTTTTTTGTGTG
1 TTTGCTCCCTTCCAGTCATTCTCCTCTAATTGGTGGTGTATTTCAACAAAGTTTTTTTTTGTGTG
38869367 GGATCTCTTTTGTGTTTTTATGAGTGGTTTCTGTTATAATTTTTCCAAGCAGATTTTTTTTT-GG
66 GGATCTCTTTTGTGTTTTTATGAGTGGTTTCTGTTATAATTTTTCCAAGCAGATTTTTTTTTGGG
*
38869431 TATTAGTTAATTTTTTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCCC
131 TATTAGTTAATTTTTTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCAC
38869496 TCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACTT
196 TCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACTT
38869561 GTTT
261 GTTT
38869565 ATCAAGGCTC
Statistics
Matches: 257, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
265 135 0.53
266 122 0.47
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (266 bp):
TTTGCTCCCTTCCAGTCATTCTCCTCTAATTGGTGGTGTATTTCAACAAAGTTTTTTTTTGTGTG
GGATCTCTTTTGTGTTTTTATGAGTGGTTTCTGTTATAATTTTTCCAAGCAGATTTTTTTTTGGG
TATTAGTTAATTTTTTCAGCATTATGTTGAAAGACAAGAAGCTTGTGATTCCAACCAATAATCAC
TCATTGCAAATTAGTCCTGTTAAGCTTGATGGACATAATTACCTTGCTTGGTCAAGGTCCTACTT
GTTTTT
Found at i:38870593 original size:52 final size:49
Alignment explanation
Indices: 38870513--38870610 Score: 142
Period size: 52 Copynumber: 1.9 Consensus size: 49
38870503 CAAAAGTTTA
*
38870513 TTTAACTATACTAGTCCATCTAAAAATAGTGTATGAATAGACATATCAC
1 TTTAACTATACTAGTCCATCTAAAAATAGTGTACGAATAGACATATCAC
* *
38870562 TTTAACTATACTACTTGTTCATCTAAAAATAGTGTGCGAATAGACATAT
1 TTTAACTATACTA---GTCCATCTAAAAATAGTGTACGAATAGACATAT
38870611 GACAGGGTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 13 0.30
52 30 0.70
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.35
Consensus pattern (49 bp):
TTTAACTATACTAGTCCATCTAAAAATAGTGTACGAATAGACATATCAC
Found at i:38872278 original size:37 final size:37
Alignment explanation
Indices: 38872236--38872314 Score: 106
Period size: 37 Copynumber: 2.1 Consensus size: 37
38872226 TTATTACGAA
* *
38872236 GTCTTACCCGGACATAA-TCTCCACACGAAGTTATCGG
1 GTCTTACCCGGACAAAATTCT-CACACGAAGTCATCGG
* *
38872273 GTCTTACCCGGATAAAATTCTCACACGTAGTCATCGG
1 GTCTTACCCGGACAAAATTCTCACACGAAGTCATCGG
38872310 GTCTT
1 GTCTT
38872315 TAGAGCTCGG
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
37 34 0.92
38 3 0.08
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (37 bp):
GTCTTACCCGGACAAAATTCTCACACGAAGTCATCGG
Found at i:38872504 original size:47 final size:47
Alignment explanation
Indices: 38872433--38872877 Score: 737
Period size: 47 Copynumber: 9.4 Consensus size: 47
38872423 CCCTTCGGGA
* * * * * * *
38872433 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38872480 CCTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38872527 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
38872574 CTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38872621 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38872668 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38872715 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
38872764 CTTATCACATATATACACTTTCACATTCATCACATCGACTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
38872811 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
38872858 CTTATCACATATATACACTT
1 CTTATCACATATATACACTT
38872878 CCTTGGCTGA
Statistics
Matches: 375, Mismatches: 21, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
47 329 0.88
49 46 0.12
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:38872796 original size:190 final size:188
Alignment explanation
Indices: 38872433--38872877 Score: 764
Period size: 190 Copynumber: 2.4 Consensus size: 188
38872423 CCCTTCGGGA
** * * * * * * *
38872433 CTTATCACATTTATGCACTTTCACATCCATCACGTTGGCCACTCGGCCCTATCACATATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
38872498 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
* *
38872563 GGCCATTAGGCCTTATTACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
131 GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGACTATTAGGC
*
38872621 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
38872686 TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTCACATTCATCACA
66 TTTCACATTCATCACATCGGCCATTAGGCCTTATCAC--ATATATACACTTTCACATTCATCACA
38872751 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGACTATTAGGC
129 TCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGACTATTAGGC
38872811 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
1 CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
38872876 TT
66 TT
38872878 CCTTGGCTGA
Statistics
Matches: 242, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
188 92 0.38
190 150 0.62
ACGTcount: A:0.29, C:0.30, G:0.08, T:0.32
Consensus pattern (188 bp):
CTTATCACACATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACAC
TTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATC
GGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGACTATTAGGC
Found at i:38881111 original size:13 final size:13
Alignment explanation
Indices: 38881090--38881166 Score: 66
Period size: 13 Copynumber: 5.9 Consensus size: 13
38881080 AGTTTTTAGT
38881090 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
* *
38881103 TGTTTTTGAGAAG
1 TGCTTTTGAAAAG
*
38881116 TG-TTGTGAAAAAG
1 TGCTTTTG-AAAAG
* *
38881129 TACTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
38881142 TGCTTTTGAGAGG
1 TGCTTTTGAAAAG
*
38881155 TGCTTTTTAAAA
1 TGCTTTTGAAAA
38881167 TTTTGAGTGT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
12 4 0.08
13 42 0.84
14 4 0.08
ACGTcount: A:0.29, C:0.05, G:0.26, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:38881160 original size:26 final size:26
Alignment explanation
Indices: 38881090--38881161 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
38881080 AGTTTTTAGT
*
38881090 TGCTTTTGAAAAGTGTTTTTGAGAAG
1 TGCTTTTGAAAAGTGCTTTTGAGAAG
* *
38881116 TG-TTGTGAAAAAGTACTTTTGAGAAG
1 TGCTTTTG-AAAAGTGCTTTTGAGAAG
* *
38881142 TGCTTTTGAGAGGTGCTTTT
1 TGCTTTTGAAAAGTGCTTTT
38881162 TAAAATTTTG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
25 4 0.11
26 29 0.78
27 4 0.11
ACGTcount: A:0.25, C:0.06, G:0.28, T:0.42
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGCTTTTGAGAAG
Found at i:38883297 original size:71 final size:72
Alignment explanation
Indices: 38883207--38883379 Score: 201
Period size: 71 Copynumber: 2.4 Consensus size: 72
38883197 AAAATCACAT
** * * *
38883207 ATAAACAACTATCGATAAAACTAATTTAGTA-A-AAATAAGTAAAATATAAATTCAATATCTAAA
1 ATAAACAACTATTAATAAAACTAATTTAGCACATAAATAAGTAAAACAT-AATTCAATATCCAAA
*
38883270 GACCAAAC
65 AACCAAAC
* *
38883278 ATAAACAACTTTTAATAAAACTAGA-TTA-CACATAAATAAGTAGAACATAATTCAATATCCAAA
1 ATAAACAACTATTAATAAAACTA-ATTTAGCACATAAATAAGTAAAACATAATTCAATATCCAAA
38883341 AACCAAAC
65 AACCAAAC
* * *
38883349 ATAAATAACTGTTAATAAAACTAGTTTAGCA
1 ATAAACAACTATTAATAAAACTAATTTAGCA
38883380 TTGTTGTTTA
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
70 1 0.01
71 69 0.80
72 16 0.19
ACGTcount: A:0.54, C:0.14, G:0.06, T:0.26
Consensus pattern (72 bp):
ATAAACAACTATTAATAAAACTAATTTAGCACATAAATAAGTAAAACATAATTCAATATCCAAAA
ACCAAAC
Found at i:38883399 original size:71 final size:71
Alignment explanation
Indices: 38883239--38883372 Score: 205
Period size: 71 Copynumber: 1.9 Consensus size: 71
38883229 AATTTAGTAA
* * * * *
38883239 AAATAAGTAAAATATAAATTCAATATCTAAAGACCAAACATAAACAACTTTTAATAAAACTAGAT
1 AAATAAGTAGAACAT-AATTCAATATCCAAAAACCAAACATAAACAACTGTTAATAAAACTAGAT
38883304 TACACAT
65 TACACAT
*
38883311 AAATAAGTAGAACATAATTCAATATCCAAAAACCAAACATAAATAACTGTTAATAAAACTAG
1 AAATAAGTAGAACATAATTCAATATCCAAAAACCAAACATAAACAACTGTTAATAAAACTAG
38883373 TTTAGCATTG
Statistics
Matches: 56, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
71 43 0.77
72 13 0.23
ACGTcount: A:0.56, C:0.14, G:0.05, T:0.25
Consensus pattern (71 bp):
AAATAAGTAGAACATAATTCAATATCCAAAAACCAAACATAAACAACTGTTAATAAAACTAGATT
ACACAT
Found at i:38883822 original size:18 final size:18
Alignment explanation
Indices: 38883801--38883866 Score: 114
Period size: 18 Copynumber: 3.7 Consensus size: 18
38883791 TCCATCAATT
38883801 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
* *
38883819 TGAACATCACTTGAAATC
1 TGAACATCATTTGAAATG
38883837 TGAACATCATTTGAAATG
1 TGAACATCATTTGAAATG
38883855 TGAACATCATTT
1 TGAACATCATTT
38883867 TTCATATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (18 bp):
TGAACATCATTTGAAATG
Found at i:38885200 original size:23 final size:23
Alignment explanation
Indices: 38885174--38885245 Score: 69
Period size: 20 Copynumber: 3.2 Consensus size: 23
38885164 ACGCCTCCTC
38885174 CTTTTATCAATTGCTATCTTCTT
1 CTTTTATCAATTGCTATCTTCTT
* * **
38885197 CTTTT-TC-ATT-TTTTCCCCTT
1 CTTTTATCAATTGCTATCTTCTT
*
38885217 CTTTTACCTAATTGCTATCTTCTT
1 CTTTTATC-AATTGCTATCTTCTT
38885241 CTTTT
1 CTTTT
38885246 TCTTTTTGTC
Statistics
Matches: 36, Mismatches: 9, Indels: 7
0.69 0.17 0.13
Matches are distributed among these distances:
20 11 0.31
21 4 0.11
22 2 0.06
23 8 0.22
24 11 0.31
ACGTcount: A:0.12, C:0.25, G:0.03, T:0.60
Consensus pattern (23 bp):
CTTTTATCAATTGCTATCTTCTT
Found at i:38885236 original size:44 final size:44
Alignment explanation
Indices: 38885174--38885360 Score: 306
Period size: 44 Copynumber: 4.2 Consensus size: 44
38885164 ACGCCTCCTC
*
38885174 CTTTTATC-AATTGCTATCTTCTTCTTTTTCATTTTT-TCCCCTT
1 CTTTTACCTAATTGCTATCTTCTTCTTTTTC-TTTTTGTCCCCTT
38885217 CTTTTACCTAATTGCTATCTTCTTCTTTTTCTTTTTGTCCCCTT
1 CTTTTACCTAATTGCTATCTTCTTCTTTTTCTTTTTGTCCCCTT
*
38885261 CTTTTACCTAATTGCTATTTTCTTCTTTTTCTTTTTGTCCCCTT
1 CTTTTACCTAATTGCTATCTTCTTCTTTTTCTTTTTGTCCCCTT
**
38885305 CTTTTACCTAATTGCTATCTTCTTCTTTTTCTTATTTCCCCCCTT
1 CTTTTACCTAATTGCTATCTTCTTCTTTTTCTT-TTTGTCCCCTT
38885350 CTTTTACCTAA
1 CTTTTACCTAA
38885361 ATCAGATTGC
Statistics
Matches: 136, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
43 12 0.09
44 104 0.76
45 20 0.15
ACGTcount: A:0.11, C:0.27, G:0.03, T:0.58
Consensus pattern (44 bp):
CTTTTACCTAATTGCTATCTTCTTCTTTTTCTTTTTGTCCCCTT
Found at i:38885243 original size:24 final size:24
Alignment explanation
Indices: 38885214--38885333 Score: 85
Period size: 24 Copynumber: 5.3 Consensus size: 24
38885204 ATTTTTTCCC
38885214 CTTCTTTTACCTAATTGCTATCTT
1 CTTCTTTTACCTAATTGCTATCTT
* * * **
38885238 CTTCTTTT-TCT--TT-TTGTCCC
1 CTTCTTTTACCTAATTGCTATCTT
*
38885258 CTTCTTTTACCTAATTGCTATTTT
1 CTTCTTTTACCTAATTGCTATCTT
* * * **
38885282 CTTCTTTT-TCT--TT-TTGTCCC
1 CTTCTTTTACCTAATTGCTATCTT
38885302 CTTCTTTTACCTAATTGCTATCTT
1 CTTCTTTTACCTAATTGCTATCTT
38885326 CTTCTTTT
1 CTTCTTTT
38885334 TCTTATTTCC
Statistics
Matches: 66, Mismatches: 22, Indels: 16
0.63 0.21 0.15
Matches are distributed among these distances:
20 21 0.32
21 8 0.12
23 8 0.12
24 29 0.44
ACGTcount: A:0.10, C:0.26, G:0.04, T:0.60
Consensus pattern (24 bp):
CTTCTTTTACCTAATTGCTATCTT
Found at i:38886704 original size:19 final size:19
Alignment explanation
Indices: 38886666--38886704 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
38886656 GTGGTGGAGA
*
38886666 AGAGGAACAAAGCACCAGC
1 AGAGGAACAAAGAACCAGC
*
38886685 AGAGGAACAAAGAACTAGC
1 AGAGGAACAAAGAACCAGC
38886704 A
1 A
38886705 CCAGTAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.51, C:0.21, G:0.26, T:0.03
Consensus pattern (19 bp):
AGAGGAACAAAGAACCAGC
Found at i:38886809 original size:19 final size:19
Alignment explanation
Indices: 38886781--38886822 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
38886771 GAACCAGCAC
38886781 CAGCAAAGGATCAAAGAAG
1 CAGCAAAGGATCAAAGAAG
*
38886800 CAGCAGAGGATCAAAGAAG
1 CAGCAAAGGATCAAAGAAG
38886819 CAGC
1 CAGC
38886823 GATGAGAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.48, C:0.19, G:0.29, T:0.05
Consensus pattern (19 bp):
CAGCAAAGGATCAAAGAAG
Found at i:38887134 original size:21 final size:20
Alignment explanation
Indices: 38887108--38887147 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
38887098 TTTTCTACTT
*
38887108 ATATTTATTTTATTTTGTTTC
1 ATATTTATATT-TTTTGTTTC
38887129 ATATTTATATTTTTTGTTT
1 ATATTTATATTTTTTGTTT
38887148 TATTTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (20 bp):
ATATTTATATTTTTTGTTTC
Found at i:38887172 original size:30 final size:30
Alignment explanation
Indices: 38887115--38887172 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
38887105 CTTATATTTA
*
38887115 TTTTATTTTGTTTCATATTTATATTTTTTG
1 TTTTATTTTGTTTCATATTTAAATTTTTTG
**
38887145 TTTTATTTTGTTTTGT-TTTAAATTTTTT
1 TTTTATTTTGTTTCATATTTAAATTTTTT
38887173 ATATTTTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.16, C:0.02, G:0.07, T:0.76
Consensus pattern (30 bp):
TTTTATTTTGTTTCATATTTAAATTTTTTG
Found at i:38887192 original size:15 final size:15
Alignment explanation
Indices: 38887172--38887224 Score: 56
Period size: 15 Copynumber: 3.5 Consensus size: 15
38887162 TTAAATTTTT
38887172 TATATTTTTAATTAA
1 TATATTTTTAATTAA
38887187 TATATTTTTAA-TATA
1 TATATTTTTAATTA-A
*
38887202 TCAATATTTTTAGTTAA
1 T--ATATTTTTAATTAA
38887219 -ATATTT
1 TATATTT
38887225 AAATAATAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 8 0.24
15 13 0.39
17 10 0.30
18 2 0.06
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
TATATTTTTAATTAA
Found at i:38888776 original size:46 final size:45
Alignment explanation
Indices: 38888720--38888810 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 45
38888710 TTTTTATTTC
38888720 ATATTGTTTCAAGTT-TTTTTTAACTAATATTTATAATTAATAAAT
1 ATATTGTTTCAA-TTGTTTTTTAACTAATATTTATAATTAATAAAT
* * * *
38888765 ATATTGTTTTCAATTGTTTTTTAATTCATCTTTTTAATTAATAAAT
1 ATATTG-TTTCAATTGTTTTTTAACTAATATTTATAATTAATAAAT
38888811 CTTTTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
45 8 0.20
46 32 0.80
ACGTcount: A:0.34, C:0.05, G:0.04, T:0.56
Consensus pattern (45 bp):
ATATTGTTTCAATTGTTTTTTAACTAATATTTATAATTAATAAAT
Found at i:38889621 original size:29 final size:28
Alignment explanation
Indices: 38889573--38889632 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
38889563 TGTATCCTGG
38889573 TAAATATAAAAAAAACAACATACTTATT
1 TAAATATAAAAAAAACAACATACTTATT
* *
38889601 TAAATATTAAAAAAAACAACATATTTCTT
1 TAAATA-TAAAAAAAACAACATACTTATT
38889630 TAA
1 TAA
38889633 TTCCACTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.32
Consensus pattern (28 bp):
TAAATATAAAAAAAACAACATACTTATT
Found at i:38891375 original size:23 final size:23
Alignment explanation
Indices: 38891348--38891417 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 23
38891338 CGCAGCACAC
*
38891348 AAAAGAACAAAAAAGGAAGAAAA
1 AAAAGAAGAAAAAAGGAAGAAAA
* * *
38891371 GAAAGGAGAAAAAATAGAA-AAAA
1 AAAAGAAGAAAAAA-GGAAGAAAA
*
38891394 AAAAGAAGAAAAAAGAACAGAAAA
1 AAAAGAAGAAAAAAGGA-AGAAAA
38891418 TAGGACGATG
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
22 1 0.03
23 28 0.78
24 7 0.19
ACGTcount: A:0.77, C:0.03, G:0.19, T:0.01
Consensus pattern (23 bp):
AAAAGAAGAAAAAAGGAAGAAAA
Found at i:38891416 original size:35 final size:35
Alignment explanation
Indices: 38891351--38891417 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 35
38891341 AGCACACAAA
* * **
38891351 AGAACAAAAAAGGAAGAAAAGAAAGGAGAAAAAAT
1 AGAAAAAAAAAAGAAGAAAAGAAAACAGAAAAAAT
38891386 AGAAAAAAAAAAGAAGAAAA-AAGAACAGAAAA
1 AGAAAAAAAAAAGAAGAAAAGAA-AACAGAAAA
38891418 TAGGACGATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.07
35 25 0.93
ACGTcount: A:0.76, C:0.03, G:0.19, T:0.01
Consensus pattern (35 bp):
AGAAAAAAAAAAGAAGAAAAGAAAACAGAAAAAAT
Found at i:38891949 original size:18 final size:18
Alignment explanation
Indices: 38891926--38891963 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
38891916 TTTGAAAAAG
38891926 AAGAAAAAATAAAATTTC
1 AAGAAAAAATAAAATTTC
**
38891944 AAGAAAAAATTTAATTTC
1 AAGAAAAAATAAAATTTC
38891962 AA
1 AA
38891964 TAATATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (18 bp):
AAGAAAAAATAAAATTTC
Found at i:38896070 original size:13 final size:13
Alignment explanation
Indices: 38896052--38896077 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
38896042 ACCCCAAATG
38896052 GCACAATGCGAAT
1 GCACAATGCGAAT
38896065 GCACAATGCGAAT
1 GCACAATGCGAAT
38896078 ATCATGCGGG
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:0.23, G:0.23, T:0.15
Consensus pattern (13 bp):
GCACAATGCGAAT
Found at i:38897234 original size:35 final size:36
Alignment explanation
Indices: 38897173--38897251 Score: 110
Period size: 35 Copynumber: 2.2 Consensus size: 36
38897163 GGGTTCAGAT
38897173 TCAAAAAAAAAAGAGAGAAAAAAATCAAAATCAAAG
1 TCAAAAAAAAAAGAGAGAAAAAAATCAAAATCAAAG
*
38897209 TCAAAACAAAAAA-A-AGAAAAAAATCAAAGTCAAA-
1 TCAAAA-AAAAAAGAGAGAAAAAAATCAAAATCAAAG
*
38897243 ACAAAAAAA
1 TCAAAAAAA
38897252 GAGAAATCAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
33 3 0.08
34 5 0.12
35 19 0.47
36 7 0.17
37 6 0.15
ACGTcount: A:0.75, C:0.10, G:0.08, T:0.08
Consensus pattern (36 bp):
TCAAAAAAAAAAGAGAGAAAAAAATCAAAATCAAAG
Found at i:38897257 original size:30 final size:29
Alignment explanation
Indices: 38897199--38897289 Score: 119
Period size: 30 Copynumber: 3.1 Consensus size: 29
38897189 GAAAAAAATC
38897199 AAAATCAAAGTCAAAACAAAAAAAAGAAA
1 AAAATCAAAGTCAAAACAAAAAAAAGAAA
38897228 AAAATCAAAGTCAAAACAAAAAAAGAGAAA
1 AAAATCAAAGTCAAAACAAAAAAA-AGAAA
** * * *
38897258 TCAATTAAAGTCAAAATAAAAAATATGAAA
1 AAAATCAAAGTCAAAACAAAAAA-AAGAAA
38897288 AA
1 AA
38897290 GAGAAAAAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 24 0.45
30 28 0.53
31 1 0.02
ACGTcount: A:0.71, C:0.09, G:0.08, T:0.12
Consensus pattern (29 bp):
AAAATCAAAGTCAAAACAAAAAAAAGAAA
Found at i:38899551 original size:87 final size:87
Alignment explanation
Indices: 38899396--38899740 Score: 448
Period size: 87 Copynumber: 4.0 Consensus size: 87
38899386 GTGAAGATAA
*
38899396 AAAATAAAGCCTTGCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* *
38899461 GCATTGACAGCGAAGCAGATCG
66 GCATTAACAGTGAAGCAGATCG
* * ** * * *
38899483 AAAACAAAGCCTTTCCTCCATTGGTTGTAGTAGAGCTGGTTAAAGATAGCAGATTTTGCCTTCTT
1 AAAACAAAGCCTTGCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
*
38899548 GCATTAACAGTGAAGTAGATCG
66 GCATTAACAGTGAAGCAGATCG
*
38899570 AAAACAAA-----GCCTCCATCGGTTACAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* *
38899630 GCGTTAACAGTGAAACAGATCG
66 GCATTAACAGTGAAGCAGATCG
* * * * *
38899652 AAAACAAAGTCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTAAAGATAGTAGATCTTGCCCTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* ** *
38899717 GCGTCGACAATGAAGCAGATCG
66 GCATTAACAGTGAAGCAGATCG
38899739 AA
1 AA
38899741 GATTACAAGT
Statistics
Matches: 222, Mismatches: 31, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
82 71 0.32
87 151 0.68
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (87 bp):
AAAACAAAGCCTTGCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
GCATTAACAGTGAAGCAGATCG
Found at i:38899739 original size:169 final size:169
Alignment explanation
Indices: 38899409--38899740 Score: 484
Period size: 169 Copynumber: 2.0 Consensus size: 169
38899399 ATAAAGCCTT
*
38899409 GCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGA
1 GCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGA
* * * * *
38899474 AGCAGATCGAAAACAAAGCCTTTCCTCCATTGGTTGTAGTAGAGCTGGTTAAAGATAGCAGATTT
66 AACAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGATAGCAGATCT
* * * * *
38899539 TGCCTTCTTGCATTAACAGTGAAGTAGATCGAAAACAAA
131 TGCCCTCCTGCATCAACAATGAAGCAGATCGAAAACAAA
* * *
38899578 GCCTCCATCGGTTACAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCGTTAACAGTGA
1 GCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGA
* * * *
38899643 AACAGATCGAAAACAAAGTCTTGCCTCTATCGGTTGCAGTGGAGCTGGTTAAAGATAGTAGATCT
66 AACAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGATAGCAGATCT
* *
38899708 TGCCCTCCTGCGTCGACAATGAAGCAGATCGAA
131 TGCCCTCCTGCATCAACAATGAAGCAGATCGAA
38899741 GATTACAAGT
Statistics
Matches: 143, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
169 143 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (169 bp):
GCCTCCATCGGTTACAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGA
AACAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTAGAGCTGGTTAAAGATAGCAGATCT
TGCCCTCCTGCATCAACAATGAAGCAGATCGAAAACAAA
Found at i:38900197 original size:50 final size:50
Alignment explanation
Indices: 38900138--38900301 Score: 159
Period size: 50 Copynumber: 3.3 Consensus size: 50
38900128 GTAGTGGAAC
* * * *
38900138 AGATTAAAGCCACATCGGTGAATCTTGCTTCCCCGACATTGCGGTTAAAA
1 AGATTAAAGCCACATCAGTGAATCTTGCCTCCCAGACATTGCAGTTAAAA
* * * * * * ** *
38900188 AGATTAAAGCTACAAT-AGCGAATTTTACCTCCCAGGCAATGCAGTGGAAT
1 AGATTAAAGCCAC-ATCAGTGAATCTTGCCTCCCAGACATTGCAGTTAAAA
* * * *
38900238 AGATTAAAGCCAAAACAGTGAATCTTGCCTCCCTGACATTGTAGTTAAAA
1 AGATTAAAGCCACATCAGTGAATCTTGCCTCCCAGACATTGCAGTTAAAA
38900288 AGATTAAAGCCACA
1 AGATTAAAGCCACA
38900302 ATGGCGACTC
Statistics
Matches: 85, Mismatches: 27, Indels: 4
0.73 0.23 0.03
Matches are distributed among these distances:
49 1 0.01
50 82 0.96
51 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.24
Consensus pattern (50 bp):
AGATTAAAGCCACATCAGTGAATCTTGCCTCCCAGACATTGCAGTTAAAA
Found at i:38900886 original size:23 final size:23
Alignment explanation
Indices: 38900860--38900908 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
38900850 GCAGCACACA
38900860 AAAGAACAAAAAAAG-AAGAAAAG
1 AAAGAACAAAAAAAGCAA-AAAAG
* * *
38900883 AAAGGAGAAAAATAGCAAAAAAG
1 AAAGAACAAAAAAAGCAAAAAAG
38900906 AAA
1 AAA
38900909 AAAGAACAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 20 0.91
24 2 0.09
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (23 bp):
AAAGAACAAAAAAAGCAAAAAAG
Found at i:38908632 original size:50 final size:50
Alignment explanation
Indices: 38908534--38908665 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 50
38908524 TATTGAGGTT
* * * * *
38908534 ATGAGAGGTCCCACGTAAGACCATTTCTGAGACATGGCGTTGGTACCGAG
1 ATGAGAGGTCCCACGTAAGACCATATCTGGGACATGGCATAGGCACCGAG
* * * * *
38908584 ATTAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGTATAGGCACCGAT
1 ATGAGAGGTCCCACGTAAGACCATATCTGGGACATGGCATAGGCACCGAG
** *
38908634 ATGAGAACTCCCATGTAAGACCATATCTGGGA
1 ATGAGAGGTCCCACGTAAGACCATATCTGGGA
38908666 TACGTCATTT
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 67 1.00
ACGTcount: A:0.28, C:0.23, G:0.27, T:0.22
Consensus pattern (50 bp):
ATGAGAGGTCCCACGTAAGACCATATCTGGGACATGGCATAGGCACCGAG
Found at i:38911300 original size:23 final size:19
Alignment explanation
Indices: 38911277--38911315 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 19
38911267 TAACCTATAA
38911277 AAATTAATAATAATATTAATT
1 AAATT-ATAAT-ATATTAATT
38911298 AAATTATAATATATTAAT
1 AAATTATAATATATTAAT
38911316 ACTCAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 5 0.28
21 5 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATTATAATATATTAATT
Found at i:38912961 original size:26 final size:26
Alignment explanation
Indices: 38912925--38912983 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
38912915 ATGAATTTTC
* * *
38912925 TCAAAAATTTAACGTGGTTAAAATCA
1 TCAAAATTTTAACGAGGGTAAAATCA
* *
38912951 TCAAAATTTTACCGAGGGTAAAATCG
1 TCAAAATTTTAACGAGGGTAAAATCA
38912977 TCAAAAT
1 TCAAAAT
38912984 ATTACCTAGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.29
Consensus pattern (26 bp):
TCAAAATTTTAACGAGGGTAAAATCA
Found at i:38912988 original size:26 final size:26
Alignment explanation
Indices: 38912943--38913000 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
38912933 TTAACGTGGT
*
38912943 TAAAATCATCAAAATTTTACCGAGGG
1 TAAAATCATCAAAATATTACCGAGGG
* * *
38912969 TAAAATCGTCAAAATATTACCTAGTG
1 TAAAATCATCAAAATATTACCGAGGG
38912995 TAAAAT
1 TAAAAT
38913001 TGGAGTGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (26 bp):
TAAAATCATCAAAATATTACCGAGGG
Found at i:38917101 original size:14 final size:14
Alignment explanation
Indices: 38917082--38917110 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38917072 TACATTTTGA
38917082 TGGAGTCATATGTT
1 TGGAGTCATATGTT
38917096 TGGAGTCATATGTT
1 TGGAGTCATATGTT
38917110 T
1 T
38917111 AACTTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.45
Consensus pattern (14 bp):
TGGAGTCATATGTT
Found at i:38918955 original size:40 final size:40
Alignment explanation
Indices: 38918911--38918990 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
38918901 GACTTTATAA
* * *
38918911 CTTTTATCAACCTCTTTAGCTTCAATTTCGATACTAAAAC
1 CTTTTATCAACCTCCTTAGCTACAATTTCAATACTAAAAC
*
38918951 CTTTTGTCAACCTCCTTAGCTACAATTTCAATACTAAAAC
1 CTTTTATCAACCTCCTTAGCTACAATTTCAATACTAAAAC
38918991 AAAAAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (40 bp):
CTTTTATCAACCTCCTTAGCTACAATTTCAATACTAAAAC
Found at i:38922009 original size:37 final size:37
Alignment explanation
Indices: 38921953--38922061 Score: 123
Period size: 37 Copynumber: 3.0 Consensus size: 37
38921943 TGTACACAAG
* *
38921953 TAATCCAACC-AAAACATGCCAAGTGCTCCA-AAGAGA
1 TAATCCAACCGATAACATGCCAAATGCT-CAGAAGAGA
** *
38921989 TAATCCAATTGATAACATGCCAAATGCTCAGAAGAGT
1 TAATCCAACCGATAACATGCCAAATGCTCAGAAGAGA
* * *
38922026 TAATCCAACCGATAACACGCCAAATGTTCCGAAGAG
1 TAATCCAACCGATAACATGCCAAATGCTCAGAAGAG
38922062 CTATACATCT
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
36 10 0.16
37 51 0.84
ACGTcount: A:0.41, C:0.25, G:0.16, T:0.18
Consensus pattern (37 bp):
TAATCCAACCGATAACATGCCAAATGCTCAGAAGAGA
Found at i:38931308 original size:20 final size:19
Alignment explanation
Indices: 38931247--38931306 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
38931237 GTCTCTCTCA
38931247 ATAAAAATTTCAAAATAATTT
1 ATAAAAA-TTCAAAAT-ATTT
*
38931268 -TTAAAATTCAAAATATTT
1 ATAAAAATTCAAAATATTT
*
38931286 ATAAAAATTCCAAA-ATTT
1 ATAAAAATTCAAAATATTT
38931304 ATA
1 ATA
38931307 TATTTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
18 11 0.31
19 19 0.54
20 5 0.14
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (19 bp):
ATAAAAATTCAAAATATTT
Found at i:38931311 original size:26 final size:26
Alignment explanation
Indices: 38931280--38931329 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
38931270 AAAATTCAAA
38931280 ATATTTATAAAAATTCCAAAATTTAT
1 ATATTTATAAAAATTCCAAAATTTAT
* **
38931306 ATATTTTTAAAAATTTTAAAATTT
1 ATATTTATAAAAATTCCAAAATTT
38931330 TTTTGCAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
ATATTTATAAAAATTCCAAAATTTAT
Found at i:38932845 original size:9 final size:9
Alignment explanation
Indices: 38932828--38932870 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
38932818 TTTTTCTAAA
*
38932828 CTCTTAACT
1 CTCTCAACT
38932837 CTCTCAACT
1 CTCTCAACT
*
38932846 CTCTCAATT
1 CTCTCAACT
*
38932855 CTCTCAATT
1 CTCTCAACT
38932864 CTCTCAA
1 CTCTCAA
38932871 GTTTTGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.23, C:0.37, G:0.00, T:0.40
Consensus pattern (9 bp):
CTCTCAACT
Found at i:38933102 original size:9 final size:9
Alignment explanation
Indices: 38933088--38933115 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
38933078 TTTATTTTTG
38933088 TAAATATTT
1 TAAATATTT
38933097 TAAATATTT
1 TAAATATTT
38933106 TAAATATTT
1 TAAATATTT
38933115 T
1 T
38933116 TTGTCAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (9 bp):
TAAATATTT
Found at i:38948792 original size:7 final size:7
Alignment explanation
Indices: 38948774--38948816 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
38948764 TTTCAGGTCA
38948774 TTTTCA-
1 TTTTCAT
38948780 TTTTCAT
1 TTTTCAT
38948787 TTTTCAT
1 TTTTCAT
38948794 TTTTCAT
1 TTTTCAT
38948801 TTTTCA-
1 TTTTCAT
38948807 TTTTCAT
1 TTTTCAT
38948814 TTT
1 TTT
38948817 GGAGAAAACC
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
6 12 0.34
7 23 0.66
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (7 bp):
TTTTCAT
Found at i:38948792 original size:13 final size:13
Alignment explanation
Indices: 38948774--38948816 Score: 77
Period size: 13 Copynumber: 3.2 Consensus size: 13
38948764 TTTCAGGTCA
38948774 TTTTCATTTTCAT
1 TTTTCATTTTCAT
38948787 TTTTCATTTTTCAT
1 TTTTCA-TTTTCAT
38948801 TTTTCATTTTCAT
1 TTTTCATTTTCAT
38948814 TTT
1 TTT
38948817 GGAGAAAACC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 16 0.55
14 13 0.45
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTCATTTTCAT
Found at i:38948864 original size:57 final size:58
Alignment explanation
Indices: 38948801--38948918 Score: 148
Period size: 57 Copynumber: 2.1 Consensus size: 58
38948791 CATTTTTCAT
* ** * **
38948801 TTTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATTA-TCTTATTTCTCCA
1 TTTTCATTTTAATTTTCAAGAAAACCACAATCATTTCCAAAAGATTCTTATTTCTCCA
** *
38948858 TTTTCATTTTAATTTTCAAGAAAACCTTAATCATTTCCAAAAGATTCTTATTTTTCCA
1 TTTTCATTTTAATTTTCAAGAAAACCACAATCATTTCCAAAAGATTCTTATTTCTCCA
38948916 TTT
1 TTT
38948919 CACCATTTCT
Statistics
Matches: 51, Mismatches: 9, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
57 36 0.71
58 15 0.29
ACGTcount: A:0.30, C:0.19, G:0.04, T:0.47
Consensus pattern (58 bp):
TTTTCATTTTAATTTTCAAGAAAACCACAATCATTTCCAAAAGATTCTTATTTCTCCA
Found at i:38951803 original size:57 final size:58
Alignment explanation
Indices: 38951712--38951829 Score: 170
Period size: 57 Copynumber: 2.1 Consensus size: 58
38951702 CATTTTTTCT
*
38951712 TTTTCATTTTCATTTTGGAGAAAACTACATTCATTTCCAAATGATTT-C-ATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAACTACATTCATTTCAAAATG-TTTCCTATTTCTCCA
**
38951769 TTTTCATTTTCATTTTGGAGAAAACCTTTA-TCATTTCAAAATGTTTCCTATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAA-CTACATTCATTTCAAAATGTTTCCTATTTCTCCA
38951827 TTT
1 TTT
38951830 CACCGTTTCT
Statistics
Matches: 55, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
56 3 0.05
57 37 0.67
58 15 0.27
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (58 bp):
TTTTCATTTTCATTTTGGAGAAAACTACATTCATTTCAAAATGTTTCCTATTTCTCCA
Found at i:38960278 original size:27 final size:27
Alignment explanation
Indices: 38960248--38960425 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
38960238 ATATTGAGTC
* * * *
38960248 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
38960275 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
38960302 CGCACACTTAGTGCTACATAGTCAATCT
1 CGCACACTTAGTGCTACATAGTCAA-AT
** * *
38960330 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
38960357 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
38960384 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
38960411 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38960426 GTAAAATTTA
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 105 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:38960387 original size:82 final size:81
Alignment explanation
Indices: 38960269--38960424 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
38960259 TGCTATATAA
* * *
38960269 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAATCTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAA-ATCGCA
38960334 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
38960351 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
38960415 CACTTAGTGC
65 CACTTAGTGC
38960425 TGTAAAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:38965861 original size:16 final size:16
Alignment explanation
Indices: 38965840--38965877 Score: 76
Period size: 16 Copynumber: 2.4 Consensus size: 16
38965830 TACAAAATCA
38965840 ATCAAATATTCATACT
1 ATCAAATATTCATACT
38965856 ATCAAATATTCATACT
1 ATCAAATATTCATACT
38965872 ATCAAA
1 ATCAAA
38965878 CTAGCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.34
Consensus pattern (16 bp):
ATCAAATATTCATACT
Found at i:38977324 original size:15 final size:16
Alignment explanation
Indices: 38977304--38977338 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
38977294 AAGCAATTAC
38977304 GACATG-AAAATATAT
1 GACATGAAAAATATAT
38977319 GACATGAAAAAATATAT
1 GACATG-AAAAATATAT
38977336 GAC
1 GAC
38977339 CATGTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.33
17 12 0.67
ACGTcount: A:0.54, C:0.09, G:0.14, T:0.23
Consensus pattern (16 bp):
GACATGAAAAATATAT
Found at i:38981893 original size:16 final size:16
Alignment explanation
Indices: 38981872--38981903 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38981862 AAAATCAGAG
38981872 TTCAATTCAAAACAAC
1 TTCAATTCAAAACAAC
38981888 TTCAATTCAAAACAAC
1 TTCAATTCAAAACAAC
38981904 GAAGAAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (16 bp):
TTCAATTCAAAACAAC
Found at i:38983422 original size:13 final size:13
Alignment explanation
Indices: 38983406--38983471 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
38983396 TTTAAACCAA
*
38983406 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
38983419 ACTTCTT-AAAAGC
1 ACTT-TTCAAAAGC
* *
38983432 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
*
38983445 ACTTTTCAAAAGT
1 ACTTTTCAAAAGC
38983458 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
38983471 A
1 A
38983472 ATGAAGAATT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
12 2 0.05
13 40 0.91
14 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:38987925 original size:5 final size:6
Alignment explanation
Indices: 38987909--38987933 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
38987899 GAATGTCGTG
38987909 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
38987934 CAAATACATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:38988364 original size:21 final size:21
Alignment explanation
Indices: 38988331--38988370 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
38988321 TATAGTTTCT
*
38988331 AAAATAATAAAAAAATTTATG
1 AAAAAAATAAAAAAATTTATG
* *
38988352 AAAAAAATTAAAATATTTA
1 AAAAAAATAAAAAAATTTA
38988371 AAACTCAAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (21 bp):
AAAAAAATAAAAAAATTTATG
Found at i:38988642 original size:15 final size:15
Alignment explanation
Indices: 38988622--38988651 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38988612 ATAAATTATT
38988622 AAAACATCAAAAATA
1 AAAACATCAAAAATA
*
38988637 AAAACATTAAAAATA
1 AAAACATCAAAAATA
38988652 TATAAAATTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.10, G:0.00, T:0.17
Consensus pattern (15 bp):
AAAACATCAAAAATA
Found at i:38989136 original size:6 final size:6
Alignment explanation
Indices: 38989125--38989191 Score: 134
Period size: 6 Copynumber: 11.2 Consensus size: 6
38989115 ATTTTTAATA
38989125 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
1 TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT TATTTT
38989173 TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT T
38989192 TAATAATTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 61 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:38989447 original size:27 final size:27
Alignment explanation
Indices: 38989417--38989504 Score: 94
Period size: 25 Copynumber: 3.4 Consensus size: 27
38989407 TTTTTTCTTA
38989417 ATTTTTTTAAATTTTTAAAAAAATTAT
1 ATTTTTTTAAATTTTTAAAAAAATTAT
* *
38989444 ATTTTTTT--ATTTTTTAAAAGATTAT
1 ATTTTTTTAAATTTTTAAAAAAATTAT
** *
38989469 ATTTATTTTTTATTTTTAAAAATA-TA-
1 ATTT-TTTTAAATTTTTAAAAAAATTAT
38989495 ATTTTTTTAA
1 ATTTTTTTAA
38989505 TTGTTATGTT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
25 23 0.44
26 8 0.15
27 10 0.19
28 11 0.21
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (27 bp):
ATTTTTTTAAATTTTTAAAAAAATTAT
Found at i:38989455 original size:25 final size:25
Alignment explanation
Indices: 38989417--38989503 Score: 88
Period size: 28 Copynumber: 3.4 Consensus size: 25
38989407 TTTTTTCTTA
38989417 ATTTTTTTAAATTTTTAAAAAAATTAT
1 ATTTTTTT--ATTTTTAAAAAAATTAT
* *
38989444 ATTTTTTTATTTTTTAAAAGATTAT
1 ATTTTTTTATTTTTAAAAAAATTAT
*
38989469 ATTTATTTTTTATTTTTAAAAATA-TA-
1 A--T-TTTTTTATTTTTAAAAAAATTAT
38989495 ATTTTTTTA
1 ATTTTTTTA
38989504 ATTGTTATGT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
23 7 0.13
24 1 0.02
25 16 0.30
26 1 0.02
27 11 0.21
28 17 0.32
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (25 bp):
ATTTTTTTATTTTTAAAAAAATTAT
Found at i:38989893 original size:21 final size:21
Alignment explanation
Indices: 38989867--38989908 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
38989857 TATTAGTTTT
38989867 TAAAAAA-AATTTAATGAATTTC
1 TAAAAAATAA-TTAAT-AATTTC
38989889 TAAAAAATAATTAATAATTT
1 TAAAAAATAATTAATAATTT
38989909 GAAAACTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 12 0.63
23 2 0.11
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (21 bp):
TAAAAAATAATTAATAATTTC
Found at i:38989996 original size:17 final size:17
Alignment explanation
Indices: 38989970--38990002 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
38989960 TAAAAAATAA
38989970 TTAATAATTTG-AAAAC
1 TTAATAATTTGTAAAAC
38989986 TTAATTAATTTGTAAAA
1 TTAA-TAATTTGTAAAA
38990003 GTATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 7 0.47
18 4 0.27
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
TTAATAATTTGTAAAAC
Found at i:38990525 original size:14 final size:15
Alignment explanation
Indices: 38990497--38990525 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38990487 TATAAAAGTG
38990497 TTATAAAATATTTAT
1 TTATAAAATATTTAT
38990512 TTATAAAA-ATTTAT
1 TTATAAAATATTTAT
38990526 ATGGAATGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATAAAATATTTAT
Found at i:38996468 original size:31 final size:31
Alignment explanation
Indices: 38996398--38996471 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
38996388 GAGTTGGTAC
* * * *
38996398 AATTATACACATGAAACTTTGATTGTGGTTT
1 AATTATATACATGAAACTTTAATTGTGATTG
** *
38996429 AAAAATATACATGAAACTTTAATTTTGATTG
1 AATTATATACATGAAACTTTAATTGTGATTG
38996460 AATTATATACAT
1 AATTATATACAT
38996472 TTAAAGAAAT
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (31 bp):
AATTATATACATGAAACTTTAATTGTGATTG
Found at i:39000606 original size:15 final size:15
Alignment explanation
Indices: 39000586--39000615 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
39000576 CCCAGTAGGT
39000586 GTAACTTTTTGTAAC
1 GTAACTTTTTGTAAC
39000601 GTAACTTTTTGTAAC
1 GTAACTTTTTGTAAC
39000616 ACCCCTAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.13, T:0.47
Consensus pattern (15 bp):
GTAACTTTTTGTAAC
Found at i:39002315 original size:42 final size:42
Alignment explanation
Indices: 39002219--39002413 Score: 202
Period size: 42 Copynumber: 4.6 Consensus size: 42
39002209 CAATGTCATA
* * * *
39002219 TCCCAGATATGGTCTTACATGCTATCATATATCGATGCCAATAG
1 TCCCAGACATGGTCTTACACG-AATCATATAACGATGCCAAT-G
39002263 --CCA-ACTATGGTCTTACACGAATC-TCATAACGATGCCAATG
1 TCCCAGAC-ATGGTCTTACACGAATCAT-ATAACGATGCCAATG
* *
39002303 TCCCAGACATGGTCTTACACGAATC-TCATATCAATGCCAATG
1 TCCCAGACATGGTCTTACACGAATCAT-ATAACGATGCCAATG
* * *
39002345 TCCCAGACATGGTCTTACATGAATCATGTAACGATGTCAATG
1 TCCCAGACATGGTCTTACACGAATCATATAACGATGCCAATG
* *
39002387 TCCCAAACATGATCTTACACGTAATCA
1 TCCCAGACATGGTCTTACACG-AATCA
39002414 CATCAAAGTA
Statistics
Matches: 130, Mismatches: 14, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
40 2 0.02
41 17 0.13
42 103 0.79
43 8 0.06
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.28
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACGAATCATATAACGATGCCAATG
Found at i:39009239 original size:42 final size:42
Alignment explanation
Indices: 39009140--39009327 Score: 186
Period size: 42 Copynumber: 4.5 Consensus size: 42
39009130 CAATGTCATA
* * *
39009140 TCCCAGATATGGTCTTACATGC-TATCATATATCGATGCCAATAG
1 TCCCAGACATGGTCTTACA--CAAATCTTATATCGATGCCAAT-G
* ** *
39009184 --CTAG-CTATGGTCTTACATGAATCTTATATCGATACCAATG
1 TCCCAGAC-ATGGTCTTACACAAATCTTATATCGATGCCAATG
*
39009224 TCCCAGACATAGTCTTACACAAATCTTATATCGATGCCAATG
1 TCCCAGACATGGTCTTACACAAATCTTATATCGATGCCAATG
* ** * *
39009266 TCCCAGGCATGGTCTTACACAAATCACATAACGATGCCAAAG
1 TCCCAGACATGGTCTTACACAAATCTTATATCGATGCCAATG
*
39009308 TCCAAGACATGGTCTTACAC
1 TCCCAGACATGGTCTTACAC
39009328 GTAATCACAT
Statistics
Matches: 120, Mismatches: 19, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
40 1 0.01
41 17 0.14
42 101 0.84
43 1 0.01
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (42 bp):
TCCCAGACATGGTCTTACACAAATCTTATATCGATGCCAATG
Found at i:39017211 original size:14 final size:14
Alignment explanation
Indices: 39017192--39017219 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
39017182 CACGTGTTAA
39017192 GAAAGCTTGCCTAG
1 GAAAGCTTGCCTAG
39017206 GAAAGCTTGCCTAG
1 GAAAGCTTGCCTAG
39017220 CTAGACGTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (14 bp):
GAAAGCTTGCCTAG
Found at i:39018939 original size:14 final size:14
Alignment explanation
Indices: 39018920--39018949 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
39018910 TGGATTTGAT
39018920 GTTGGCTCTATAGG
1 GTTGGCTCTATAGG
39018934 GTTGGCTCTATAGG
1 GTTGGCTCTATAGG
39018948 GT
1 GT
39018950 GCCCCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.13, G:0.37, T:0.37
Consensus pattern (14 bp):
GTTGGCTCTATAGG
Found at i:39022696 original size:4 final size:4
Alignment explanation
Indices: 39022687--39022712 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
39022677 ATTATTATTA
39022687 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
39022713 GCTTATTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:39023447 original size:40 final size:39
Alignment explanation
Indices: 39023384--39023479 Score: 138
Period size: 40 Copynumber: 2.4 Consensus size: 39
39023374 AAAACATCGG
*
39023384 TAAAAATCGAGCATTAGCGGTGTTTTATGGAAATCGCCAC
1 TAAAAAT-GAGCATTAGCGGTGTTTTATGAAAATCGCCAC
* * *
39023424 TAAAGATGGAGCATTAGCGGTGTTTTTTGAAAATCGCCGC
1 TAAAAAT-GAGCATTAGCGGTGTTTTATGAAAATCGCCAC
39023464 TAAAAATGAGCATTAG
1 TAAAAATGAGCATTAG
39023480 TGACGTTCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
39 9 0.18
40 41 0.82
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (39 bp):
TAAAAATGAGCATTAGCGGTGTTTTATGAAAATCGCCAC
Found at i:39023753 original size:23 final size:26
Alignment explanation
Indices: 39023700--39023754 Score: 62
Period size: 25 Copynumber: 2.2 Consensus size: 26
39023690 TCTTCAGAAA
* *
39023700 AAAATAATAGCACGTAGAAATAATTT
1 AAAATAATAACACATAGAAATAATTT
*
39023726 GAAATAA-AACACATAGAAA-AA-TT
1 AAAATAATAACACATAGAAATAATTT
39023749 AAAATA
1 AAAATA
39023755 CTATTATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 7 0.28
24 2 0.08
25 10 0.40
26 6 0.24
ACGTcount: A:0.62, C:0.07, G:0.09, T:0.22
Consensus pattern (26 bp):
AAAATAATAACACATAGAAATAATTT
Found at i:39024034 original size:8 final size:8
Alignment explanation
Indices: 39024013--39024047 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
39024003 TGGGATTTAA
39024013 GGTTTAGG
1 GGTTTAGG
39024021 GG-TTAGG
1 GGTTTAGG
39024028 GGTTTAGG
1 GGTTTAGG
*
39024036 GGTTTAGA
1 GGTTTAGG
39024044 GGTT
1 GGTT
39024048 AATGATTAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 7 0.28
8 18 0.72
ACGTcount: A:0.14, C:0.00, G:0.49, T:0.37
Consensus pattern (8 bp):
GGTTTAGG
Found at i:39024063 original size:22 final size:22
Alignment explanation
Indices: 39024031--39024076 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
39024021 GGTTAGGGGT
* * *
39024031 TTAGGGGTTTAGAGGTTAATGA
1 TTAGGGATTTAGGGTTTAATGA
39024053 TTAGGGATTTAGGGTTTAATGA
1 TTAGGGATTTAGGGTTTAATGA
39024075 TT
1 TT
39024077 TATGGGTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.33, T:0.41
Consensus pattern (22 bp):
TTAGGGATTTAGGGTTTAATGA
Found at i:39024146 original size:24 final size:24
Alignment explanation
Indices: 39024106--39024164 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
39024096 TTGGGTTTAG
* *
39024106 ATTAATTAT-TTTTTAATTTATAT
1 ATTAAATATATTTTTAATCTATAT
*
39024129 TTTAAATATATTTTTAATCTATAT
1 ATTAAATATATTTTTAATCTATAT
39024153 ATTAAATA-ATTT
1 ATTAAATATATTT
39024165 CACATATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 11 0.35
24 20 0.65
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTAAATATATTTTTAATCTATAT
Found at i:39024365 original size:20 final size:21
Alignment explanation
Indices: 39024340--39024380 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39024330 TTATGGCTTA
*
39024340 GTGA-TTATGGTTTAAGGGTT
1 GTGATTTAAGGTTTAAGGGTT
*
39024360 GTGATTTAAGGTTTAGGGGTT
1 GTGATTTAAGGTTTAAGGGTT
39024381 TAATGATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.44
Consensus pattern (21 bp):
GTGATTTAAGGTTTAAGGGTT
Found at i:39024686 original size:9 final size:9
Alignment explanation
Indices: 39024672--39024698 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
39024662 AATCTAAACC
39024672 ATTTGATAT
1 ATTTGATAT
39024681 ATTTGATAT
1 ATTTGATAT
39024690 ATTTGATAT
1 ATTTGATAT
39024699 GGATATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (9 bp):
ATTTGATAT
Found at i:39026353 original size:10 final size:10
Alignment explanation
Indices: 39026338--39026368 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
39026328 TCGGCCATGC
*
39026338 TTGCTTGACT
1 TTGCTTAACT
39026348 TTGCTTAACT
1 TTGCTTAACT
39026358 TTGCTTAACT
1 TTGCTTAACT
39026368 T
1 T
39026369 ACATTATTAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.16, C:0.19, G:0.13, T:0.52
Consensus pattern (10 bp):
TTGCTTAACT
Found at i:39028457 original size:49 final size:43
Alignment explanation
Indices: 39028285--39028557 Score: 357
Period size: 43 Copynumber: 6.3 Consensus size: 43
39028275 AGTGCATGTT
* *
39028285 TTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
39028328 TTTAGCGGCGTTTGTGGGAAAAGCGCCGTTGAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * *
39028371 TTTACCGGCGTTTGTGGAAAAAGCGCCGTTGAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
*
39028414 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTCTTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* *
39028457 TTTAGTGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
* * * ** * *
39028500 TTTAGTGGCATTTGTGAGAAAAGCGTTGCTAAAAATGTCCTGGTC
1 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCT--AAAGGTCTTGGTC
*
39028545 TTTAGTGGCGTTT
1 TTTAGCGGCGTTT
39028558 ATTTATAAAA
Statistics
Matches: 208, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
43 184 0.88
45 24 0.12
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCTTGGTC
Found at i:39031535 original size:61 final size:59
Alignment explanation
Indices: 39031428--39031543 Score: 169
Period size: 61 Copynumber: 1.9 Consensus size: 59
39031418 ATCATTTTAA
* * *
39031428 TATTAAATTAATATAATATTTATCAAGATAAAAATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTATCAAGATAAAAATTAAATTAAATTTAATATTAAATCT
* *
39031487 TATTAAAATAATAGAATATTATCTACAAGATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAGAATATT-TAT-CAAGATAAAAATTAAATTAAATTTAATATTAA
39031544 GATAATCTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
59 18 0.36
60 2 0.04
61 30 0.60
ACGTcount: A:0.53, C:0.04, G:0.03, T:0.40
Consensus pattern (59 bp):
TATTAAAATAATAGAATATTTATCAAGATAAAAATTAAATTAAATTTAATATTAAATCT
Found at i:39042687 original size:31 final size:31
Alignment explanation
Indices: 39042629--39043019 Score: 307
Period size: 31 Copynumber: 12.8 Consensus size: 31
39042619 CCTTTATCAT
** * *
39042629 CAAATCAA-TTCAACAATATATATTCATATA
1 CAAATCAATTTCGGCAATGTATAATCATATA
*
39042659 CGAATCAGA-TTCGGCAATGTATAATCATATA
1 CAAATCA-ATTTCGGCAATGTATAATCATATA
* *
39042690 CAAATCAATTT-GGCAATGGATAACCATATA
1 CAAATCAATTTCGGCAATGTATAATCATATA
** * *
39042720 TGAATCAAGTTCGGGAATGTATAATCATATA
1 CAAATCAATTTCGGCAATGTATAATCATATA
* *
39042751 CAAATTAA-TTCAGCAACT-TAT-ATCCATATA
1 CAAATCAATTTCGGCAA-TGTATAAT-CATATA
* ** * *
39042781 CAATTCAATTTCAACAATTTATAACCATATA
1 CAAATCAATTTCGGCAATGTATAATCATATA
* * *
39042812 CAAATTAATTTCAGCAAAGTATAATCATATA
1 CAAATCAATTTCGGCAATGTATAATCATATA
**
39042843 CAAATCAA-TTCGGCAACT-TATCTTCATATA
1 CAAATCAATTTCGGCAA-TGTATAATCATATA
* *
39042873 CAAATCAATTTCGACAATGTATAACCATATA
1 CAAATCAATTTCGGCAATGTATAATCATATA
* * *
39042904 CAAATAAATTTCAGCAATGTATAATTATATA
1 CAAATCAATTTCGGCAATGTATAATCATATA
* * ** *
39042935 CGAATCAA-TTCGACAACT-TATCTTCATAAA
1 CAAATCAATTTCGGCAA-TGTATAATCATATA
* ** *
39042965 TAAATCAATTTCGATAATGTATAACCATATA
1 CAAATCAATTTCGGCAATGTATAATCATATA
* **
39042996 CAAATAAATTTCAACAATGTATAA
1 CAAATCAATTTCGGCAATGTATAA
39043020 AACAATCAAA
Statistics
Matches: 285, Mismatches: 62, Indels: 27
0.76 0.17 0.07
Matches are distributed among these distances:
29 2 0.01
30 101 0.35
31 181 0.64
32 1 0.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.32
Consensus pattern (31 bp):
CAAATCAATTTCGGCAATGTATAATCATATA
Done.