Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr7
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: 21614486
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1093914 characters in sequence are not A, C, G, or T
File 20 of 54
Found at i:8865922 original size:19 final size:19
Alignment explanation
Indices: 8865898--8865937 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
8865888 CCAAATGACC
8865898 CAAAAAGTATCACTAGAGG
1 CAAAAAGTATCACTAGAGG
* *
8865917 CAAAAAGTGTCACTAGCGG
1 CAAAAAGTATCACTAGAGG
8865936 CA
1 CA
8865938 GCACCAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
CAAAAAGTATCACTAGAGG
Found at i:8873063 original size:194 final size:194
Alignment explanation
Indices: 8872729--8873094 Score: 520
Period size: 194 Copynumber: 1.9 Consensus size: 194
8872719 CCAATTCCCC
* * * * * *
8872729 AAAAGAAGAAGAATCTTTTAGAGTTCGATGACTGCTTTATTGAAAGTGGGAATTTGCTTTCGGTG
1 AAAAGAACAAGAATCTTGTAAAGCTCGATGACTGCTTGATTGAAAGTGAGAATTTGCTTTCGGTG
**
8872794 ACTCACGGCCAGTTTCTTCCTTGTCTTTTTCCATCGGTACCGCTGGCTCCAACAAACCACATGGG
66 ACTCACGGCCAGTTTCTTCCTTGTCTTTTTCCATCACTACCGCTGGCTCCAACAAACCACATGGG
8872859 GTCATTCTTCGAAAGAGAAGTCGACGACTCCAAGTCAATACCCACCTCAATAAGCTGTTTGGTA
131 GTCATTCTTCGAAAGAGAAGTCGACGACTCCAAGTCAATACCCACCTCAATAAGCTGTTTGGTA
* *
8872923 AAAAGAACAAGAATCTTGTAAAGCTCGATTACTGCTTGATTGAAAGT-AGAATTTGCTTTGGGTG
1 AAAAGAACAAGAATCTTGTAAAGCTCGATGACTGCTTGATTGAAAGTGAGAATTTGCTTTCGGTG
** * * * * *
8872987 ACTCATTGCTAGTTTTTTCCTTGTCTTTTTCCATCACTACCAG-TGGCCTCTAAGAAACTACATG
66 ACTCACGGCCAGTTTCTTCCTTGTCTTTTTCCATCACTACC-GCTGG-CTCCAACAAACCACATG
* * *
8873051 GGGTCTTTCTTCGAATGAGAATTCGACGACTCCAAGTCAATACC
129 GGGTCATTCTTCGAAAGAGAAGTCGACGACTCCAAGTCAATACC
8873095 TTACTCAATT
Statistics
Matches: 150, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
193 53 0.35
194 97 0.65
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.31
Consensus pattern (194 bp):
AAAAGAACAAGAATCTTGTAAAGCTCGATGACTGCTTGATTGAAAGTGAGAATTTGCTTTCGGTG
ACTCACGGCCAGTTTCTTCCTTGTCTTTTTCCATCACTACCGCTGGCTCCAACAAACCACATGGG
GTCATTCTTCGAAAGAGAAGTCGACGACTCCAAGTCAATACCCACCTCAATAAGCTGTTTGGTA
Found at i:8891206 original size:16 final size:16
Alignment explanation
Indices: 8891185--8891218 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
8891175 TTAATATATT
*
8891185 TTAAATATATTATTAA
1 TTAAATATACTATTAA
*
8891201 TTAAATTTACTATTAA
1 TTAAATATACTATTAA
8891217 TT
1 TT
8891219 CGTCATGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATATACTATTAA
Found at i:8896135 original size:18 final size:17
Alignment explanation
Indices: 8896112--8896149 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
8896102 ACTTGATTTC
8896112 AATTTTTAATAAAATATT
1 AATTTTT-ATAAAATATT
*
8896130 AATTTTTTTAAAATATT
1 AATTTTTATAAAATATT
8896147 AAT
1 AAT
8896150 ATTAAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
AATTTTTATAAAATATT
Found at i:8896185 original size:23 final size:23
Alignment explanation
Indices: 8896140--8896185 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
8896130 AATTTTTTTA
*
8896140 AAATATTAATATTAAATTATAAT
1 AAATATTAATATTAAAATATAAT
8896163 AAATATTAATATTTAAAAT-TAAT
1 AAATATTAATA-TTAAAATATAAT
8896186 NNNNNNNNNN
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAATATTAATATTAAAATATAAT
Found at i:8896618 original size:22 final size:24
Alignment explanation
Indices: 8896569--8896663 Score: 61
Period size: 27 Copynumber: 3.8 Consensus size: 24
8896559 NNNNNNNNNN
* *
8896569 TAAATAAAATATTAATATTTTTAAAAA
1 TAAATCAAATATTAATA--TTT-GAAA
8896596 TAAAT-AAATATTAATA-TTGAAA
1 TAAATCAAATATTAATATTTGAAA
* * *
8896618 T-TATCAATTATTAATATTTTAAA
1 TAAATCAAATATTAATATTTGAAA
*
8896641 TAAATTATCAATTATTAATATTT
1 T-AA--ATCAAATATTAATATTT
8896664 TAAAAATAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
21 2 0.04
22 14 0.25
23 8 0.14
26 11 0.19
27 22 0.39
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (24 bp):
TAAATCAAATATTAATATTTGAAA
Found at i:8896647 original size:27 final size:27
Alignment explanation
Indices: 8896615--8896667 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
8896605 ATTAATATTG
8896615 AAATTATCAATTATTAATATTTTAAAT
1 AAATTATCAATTATTAATATTTTAAAT
8896642 AAATTATCAATTATTAATATTTTAAA
1 AAATTATCAATTATTAATATTTTAAA
8896668 AATAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (27 bp):
AAATTATCAATTATTAATATTTTAAAT
Found at i:8896786 original size:24 final size:26
Alignment explanation
Indices: 8896737--8896786 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
8896727 TAAATGATTT
*
8896737 ATTATTAATATTTTAATTAAATTCTAG
1 ATTATTAATATTTTAA-TAAAATCTAG
8896764 ATTATTAATA-TTTAA-AAAATCTA
1 ATTATTAATATTTTAATAAAATCTA
8896787 ATAAAATAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
26 5 0.23
27 10 0.45
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (26 bp):
ATTATTAATATTTTAATAAAATCTAG
Found at i:8900699 original size:66 final size:66
Alignment explanation
Indices: 8900624--8900803 Score: 209
Period size: 69 Copynumber: 2.7 Consensus size: 66
8900614 AATTGTGGGT
* * *
8900624 TGTCCGTCTCTACTATCATTAAGCATCAGTAACATATCTCTTCTTCAGCATCTGCG-AATTAAAG
1 TGTCGGTCTCTAATATCATTAAGCATCAGTAACATATCTCTTCTTAAGCATCTG-GAAATTAAAG
**
8900688 TG
65 AC
* * * * *
8900690 TGTCGGTCTCTAAGATCAGTAAGCATCAGCAACATATCTCCTCCTCTTAAGCATTTGGAAATTAG
1 TGTCGGTCTCTAATATCATTAAGCATCAGTAACATATCT-CT--TCTTAAGCATCTGGAAATTAA
8900755 AGAC
63 AGAC
* *
8900759 TGTGGGTCTCTAATATCATTAAGCATCAGTAACATTTCTCTTCTT
1 TGTCGGTCTCTAATATCATTAAGCATCAGTAACATATCTCTTCTT
8900804 GCGCATTTGA
Statistics
Matches: 95, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
66 38 0.40
67 2 0.02
68 3 0.03
69 52 0.55
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (66 bp):
TGTCGGTCTCTAATATCATTAAGCATCAGTAACATATCTCTTCTTAAGCATCTGGAAATTAAAGA
C
Found at i:8913927 original size:21 final size:21
Alignment explanation
Indices: 8913880--8913928 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
8913870 TGAAGAGTCC
8913880 AAGCTTGATGGAAGTGCTGAT
1 AAGCTTGATGGAAGTGCTGAT
** *
8913901 GCGCTTGATGGAATTGCTGAT
1 AAGCTTGATGGAAGTGCTGAT
8913922 AAGCTTG
1 AAGCTTG
8913929 TCTGACCTGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.33, T:0.31
Consensus pattern (21 bp):
AAGCTTGATGGAAGTGCTGAT
Found at i:8915984 original size:218 final size:220
Alignment explanation
Indices: 8915511--8916057 Score: 708
Period size: 218 Copynumber: 2.5 Consensus size: 220
8915501 TAAATTAAAC
* *
8915511 ATAAAAACTAAAGTGATAACTAATAAAGTTATTAAGTGTAATTATATAAATAAAGTTTATTATAA
1 ATAAAAACTAAAGTGATAACTAATAAAGTTATTAAGTGTAATCATATAAATAAAATTTATTATAA
* * * * * *
8915576 ATCATAATAATACTTATGTATAAATTAAATATATGTGTACATAATATATTATTTTATTATATACA
66 GTTATAGTAATACTTATGTATAAATTAAATATATGTATATATAATATATTACTTTATTATATACA
* * * *
8915641 TATGAAATTAATAACACAACTTATAGATTATAATGTTTTAATTTTTATATCAAAATTTGTATAAA
131 TATGAAATTAATAACACAAC-TACAGATTATAATATTATAATTTTTATATCAAAATTTATATAAA
*
8915706 TAATAACTAATTATAAATAATATGTT
195 TAATAACTAATTATAAACAATATGTT
* * * * * *
8915732 ATAAAAACTAAAGTGATAACTAACAAAATTATTAAATGTAGTCGTATAAATAAAATCTATTATAA
1 ATAAAAACTAAAGTGATAACTAATAAAGTTATTAAGTGTAATCATATAAATAAAATTTATTATAA
* * *
8915797 GTTGTAGTAATGA-TTATATATAAATTAAATATATGTATATATAATATATTACTTTATTATATAT
66 GTTATAGTAAT-ACTTATGTATAAATTAAATATATGTATATATAATATATTACTTTATTATATAC
* * ** * * *
8915861 ATAT-ATATATAATTA-ATGAC-ACAGTTTAT-ATATTATGATATTTTATATTAAAATTTATATA
130 ATATGAAAT-TAATAACACAACTACAGATTATAATATTATAAT-TTTTATATCAAAATTTATATA
8915922 AATAATAACTAATTATAAACAATATGTT
193 AATAATAACTAATTATAAACAATATGTT
* *
8915950 ATAAAAACTAAGGTGATAATTAATAAAGTTATTAAGTGTAATCATATAAATAAAATTTATTATAA
1 ATAAAAACTAAAGTGATAACTAATAAAGTTATTAAGTGTAATCATATAAATAAAATTTATTATAA
* * *
8916015 GTTATAGTAATATTTATGTATGAATTAAATATATATAATATAT
66 GTTATAGTAATACTTATGTATAAATTAAATATATGT-ATATAT
8916058 TTATACAATT
Statistics
Matches: 280, Mismatches: 41, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
217 8 0.03
218 140 0.50
219 6 0.02
220 6 0.02
221 119 0.43
222 1 0.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (220 bp):
ATAAAAACTAAAGTGATAACTAATAAAGTTATTAAGTGTAATCATATAAATAAAATTTATTATAA
GTTATAGTAATACTTATGTATAAATTAAATATATGTATATATAATATATTACTTTATTATATACA
TATGAAATTAATAACACAACTACAGATTATAATATTATAATTTTTATATCAAAATTTATATAAAT
AATAACTAATTATAAACAATATGTT
Found at i:8920796 original size:22 final size:22
Alignment explanation
Indices: 8920771--8920819 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
8920761 AAAATTGATT
8920771 AGACTGATTTTTAAGTATTGCG
1 AGACTGATTTTTAAGTATTGCG
*
8920793 AGACTGATTTTTAGGTATTGCG
1 AGACTGATTTTTAAGTATTGCG
*
8920815 TGACT
1 AGACT
8920820 TAATCACTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (22 bp):
AGACTGATTTTTAAGTATTGCG
Found at i:8920892 original size:22 final size:22
Alignment explanation
Indices: 8920862--8920908 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
8920852 GTGATTGGTC
* *
8920862 TTAGGTATTGCGTGACTGATTT
1 TTAGATATTACGTGACTGATTT
8920884 TTAGATATTACGTGACTGATTT
1 TTAGATATTACGTGACTGATTT
8920906 TTA
1 TTA
8920909 AACAATGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (22 bp):
TTAGATATTACGTGACTGATTT
Found at i:8920953 original size:23 final size:23
Alignment explanation
Indices: 8920919--8920978 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
8920909 AACAATGCTT
8920919 AAGTCACACAATGCCTTACTAAC
1 AAGTCACACAATGCCTTACTAAC
* *
8920942 AAGTCACGCAATGCCTTACTAAT
1 AAGTCACACAATGCCTTACTAAC
8920965 AAGTCACACAATGC
1 AAGTCACACAATGC
8920979 TTATCAACTA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (23 bp):
AAGTCACACAATGCCTTACTAAC
Found at i:8921062 original size:21 final size:21
Alignment explanation
Indices: 8921038--8921092 Score: 92
Period size: 21 Copynumber: 2.6 Consensus size: 21
8921028 AAACTAGTCG
8921038 CGCAATGCCCAAAGTCAATCA
1 CGCAATGCCCAAAGTCAATCA
* *
8921059 CGCAATGCCCCAAGTCAGTCA
1 CGCAATGCCCAAAGTCAATCA
8921080 CGCAATGCCCAAA
1 CGCAATGCCCAAA
8921093 AATCACAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.35, C:0.36, G:0.16, T:0.13
Consensus pattern (21 bp):
CGCAATGCCCAAAGTCAATCA
Found at i:8921268 original size:9 final size:10
Alignment explanation
Indices: 8921234--8921268 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
8921224 TTCATATATC
8921234 AAAAATCACTT
1 AAAAAT-ACTT
8921245 AAAAATACTT
1 AAAAATACTT
*
8921255 AAAAATACTC
1 AAAAATACTT
8921265 AAAA
1 AAAA
8921269 CGTTCAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 17 0.74
11 6 0.26
ACGTcount: A:0.63, C:0.14, G:0.00, T:0.23
Consensus pattern (10 bp):
AAAAATACTT
Found at i:8931261 original size:2 final size:2
Alignment explanation
Indices: 8931254--8931285 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
8931244 TTCTTATTGA
8931254 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8931286 GTATGTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8931290 original size:4 final size:4
Alignment explanation
Indices: 8931283--8931313 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
8931273 TATATATATA
8931283 TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TAT
8931314 ATTTGAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:8936206 original size:17 final size:18
Alignment explanation
Indices: 8936173--8936206 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
8936163 CTCCTTTGAA
*
8936173 ATTTTTTTTTTTATCTTT
1 ATTTTTTTATTTATCTTT
8936191 ATTTTTTTATTT-TCTT
1 ATTTTTTTATTTATCTT
8936207 ATTAATTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (18 bp):
ATTTTTTTATTTATCTTT
Found at i:8937690 original size:61 final size:62
Alignment explanation
Indices: 8937577--8937705 Score: 163
Period size: 61 Copynumber: 2.1 Consensus size: 62
8937567 CACCCCCCGC
** *
8937577 AATTTTAAAATTTTTATAATTTATCGTTATTTTTTGAAATTTTATAATTTTGCC-CTTACAAA
1 AATTTTAAAATTTTTATAACATATCGTTATTTTTTGAAATTTTATAAGTTTGCCTC-TACAAA
* * * * *
8937639 AATTTTAAAATTTTTCTAACATA-CTTTTTTTTTTGTAATTTTATAAGTTTGCCTCTACAAT
1 AATTTTAAAATTTTTATAACATATCGTTATTTTTTGAAATTTTATAAGTTTGCCTCTACAAA
8937700 AATTTT
1 AATTTT
8937706 TTGCTTGGTG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
61 37 0.64
62 21 0.36
ACGTcount: A:0.32, C:0.09, G:0.05, T:0.54
Consensus pattern (62 bp):
AATTTTAAAATTTTTATAACATATCGTTATTTTTTGAAATTTTATAAGTTTGCCTCTACAAA
Found at i:8938585 original size:17 final size:17
Alignment explanation
Indices: 8938563--8938605 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
8938553 CATTTTTTAA
8938563 TGTAAAAGATTGACAAC
1 TGTAAAAGATTGACAAC
*
8938580 TGTAAAACATATTGACAAC
1 TGT-AAA-AGATTGACAAC
8938599 TGTAAAA
1 TGTAAAA
8938606 CATATGACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 4 0.17
18 6 0.26
19 13 0.57
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.26
Consensus pattern (17 bp):
TGTAAAAGATTGACAAC
Found at i:8938595 original size:19 final size:19
Alignment explanation
Indices: 8938571--8938610 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
8938561 AATGTAAAAG
8938571 ATTGACAACTGTAAAACAT
1 ATTGACAACTGTAAAACAT
8938590 ATTGACAACTGTAAAACAT
1 ATTGACAACTGTAAAACAT
8938609 AT
1 AT
8938611 GACTCATGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.28
Consensus pattern (19 bp):
ATTGACAACTGTAAAACAT
Found at i:8942808 original size:2 final size:2
Alignment explanation
Indices: 8942801--8942831 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8942791 GAATTTTTAT
8942801 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8942832 CGAGGGTGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8944187 original size:16 final size:17
Alignment explanation
Indices: 8944160--8944191 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
8944150 AGGCATCTCA
8944160 ATAAACAAAAAATTATT
1 ATAAACAAAAAATTATT
8944177 ATAAA-AAAAAATTAT
1 ATAAACAAAAAATTAT
8944192 AAAATTTCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
ATAAACAAAAAATTATT
Found at i:8955128 original size:2 final size:2
Alignment explanation
Indices: 8955123--8955201 Score: 74
Period size: 2 Copynumber: 40.0 Consensus size: 2
8955113 TATGCGTGTG
* * * *
8955123 TA TA TA TA TA TA TA TA TA TA TA TA TT TG TC T- TA TT TA TGA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
*
8955164 CT- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8955202 GGAATACACA
Statistics
Matches: 65, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
1 3 0.05
2 61 0.94
3 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8964337 original size:15 final size:15
Alignment explanation
Indices: 8964313--8964347 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
8964303 TAATAAATTT
*
8964313 TAAAATTAATAATAA
1 TAAAAATAATAATAA
*
8964328 TAAAAATAATTATAA
1 TAAAAATAATAATAA
8964343 TAAAA
1 TAAAA
8964348 CAAAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATAATAATAA
Found at i:8973285 original size:3 final size:3
Alignment explanation
Indices: 8973277--8973313 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
8973267 TTGAAGAGTT
8973277 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
8973314 AAAAGCAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:8978620 original size:2 final size:2
Alignment explanation
Indices: 8978613--8978649 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
8978603 TAATTTAATT
8978613 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8978650 TTAAAAGTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8979410 original size:34 final size:34
Alignment explanation
Indices: 8979284--8979413 Score: 127
Period size: 35 Copynumber: 3.8 Consensus size: 34
8979274 AAAAACCATG
* * *
8979284 GGTTTCGCTTTAT-CTGGTGAAAAGGCTATTGTAAA
1 GGTTTCGCTTGATCCT-GT-AAAAAGCTATTGTGAA
* * *
8979319 GGCTTCGCTTGATCCTGTTAAAAAGATATTGTGAG
1 GGTTTCGCTTGATCCTG-TAAAAAGCTATTGTGAA
* * * **
8979354 GGTTTCACTTAATCTTAAAAAAAGCTATTGTGAA
1 GGTTTCGCTTGATCCTGTAAAAAGCTATTGTGAA
8979388 GGTTTCGCTTGATCCTGTAAAAAGCT
1 GGTTTCGCTTGATCCTGTAAAAAGCT
8979414 CATTTTTGTT
Statistics
Matches: 74, Mismatches: 19, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
34 35 0.47
35 36 0.49
36 3 0.04
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.35
Consensus pattern (34 bp):
GGTTTCGCTTGATCCTGTAAAAAGCTATTGTGAA
Found at i:8984796 original size:17 final size:17
Alignment explanation
Indices: 8984742--8984797 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
8984732 CATTGGCTTG
8984742 GACTTTGATATTAGTTTC
1 GACTTTGATATT-GTTTC
* * *
8984760 GACTTTG---GTGTGTG
1 GACTTTGATATTGTTTC
8984774 GACTTTGATATTGTTTC
1 GACTTTGATATTGTTTC
8984791 GACTTTG
1 GACTTTG
8984798 GTGTTTGAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 7
0.69 0.14 0.17
Matches are distributed among these distances:
14 10 0.34
15 1 0.03
17 11 0.38
18 7 0.24
ACGTcount: A:0.16, C:0.11, G:0.25, T:0.48
Consensus pattern (17 bp):
GACTTTGATATTGTTTC
Found at i:8984834 original size:32 final size:32
Alignment explanation
Indices: 8984743--8984841 Score: 146
Period size: 32 Copynumber: 3.1 Consensus size: 32
8984733 ATTGGCTTGG
* * *
8984743 ACTTTGATATTAGTTTCGACTTTGGTGTGTGG
1 ACTTTAATATTAGTTTCGACTTTGGTGTTTGA
*
8984775 ACTTTGATATT-GTTTCGACTTTGGTGTTTGA
1 ACTTTAATATTAGTTTCGACTTTGGTGTTTGA
*
8984806 ATTTTAATATTAGTTTCGACTTTGGTGTTTGA
1 ACTTTAATATTAGTTTCGACTTTGGTGTTTGA
8984838 ACTT
1 ACTT
8984842 GAATTATTCG
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
31 27 0.44
32 34 0.56
ACGTcount: A:0.18, C:0.09, G:0.22, T:0.51
Consensus pattern (32 bp):
ACTTTAATATTAGTTTCGACTTTGGTGTTTGA
Found at i:8988316 original size:21 final size:21
Alignment explanation
Indices: 8988291--8988338 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
8988281 TTAAAAGGAT
8988291 TTTGAAGAACAAGTATCGATA
1 TTTGAAGAACAAGTATCGATA
* * *
8988312 TTTGATGAATATGTATCGATA
1 TTTGAAGAACAAGTATCGATA
*
8988333 CTTGAA
1 TTTGAA
8988339 ACTCAAGAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (21 bp):
TTTGAAGAACAAGTATCGATA
Found at i:8993533 original size:21 final size:21
Alignment explanation
Indices: 8993507--8993547 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
8993497 CCCTTTAACT
8993507 CAAACATGACATCATACCCAC
1 CAAACATGACATCATACCCAC
*
8993528 CAAACATGACGTCATACCCA
1 CAAACATGACATCATACCCA
8993548 ACTTCAGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.37, G:0.07, T:0.15
Consensus pattern (21 bp):
CAAACATGACATCATACCCAC
Found at i:9015863 original size:2 final size:2
Alignment explanation
Indices: 9015856--9015882 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9015846 TCTATGTATG
9015856 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
9015883 CCATCATCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9015954 original size:43 final size:42
Alignment explanation
Indices: 9015906--9016027 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 42
9015896 CACCCTCCCA
* * *
9015906 TCATCATCAGCTCATATGCACTCCCCACTAGCACATGGTTGGG
1 TCATCATCAGCTCATACGCACT-CCCACTAGCACATAGTTAGG
* * * *
9015949 TCATCATCGGCTTATACGCACTCCTACTCGCACATAGTTAGG
1 TCATCATCAGCTCATACGCACTCCCACTAGCACATAGTTAGG
* * * * * *
9015991 TCAGCATCGGCTTATGCGCACTCTCACTTGCACATAG
1 TCATCATCAGCTCATACGCACTCCCACTAGCACATAG
9016028 CCGGGTCAAT
Statistics
Matches: 67, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
42 48 0.72
43 19 0.28
ACGTcount: A:0.23, C:0.32, G:0.18, T:0.27
Consensus pattern (42 bp):
TCATCATCAGCTCATACGCACTCCCACTAGCACATAGTTAGG
Found at i:9015999 original size:42 final size:42
Alignment explanation
Indices: 9015931--9016027 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
9015921 ATGCACTCCC
* * * *
9015931 CACTAGCACATGGTTGGGTCATCATCGGCTTATACGCACTC-
1 CACTCGCACATAGTTAGGTCAGCATCGGCTTATACGCACTCT
*
9015972 CTACTCGCACATAGTTAGGTCAGCATCGGCTTATGCGCACTCT
1 C-ACTCGCACATAGTTAGGTCAGCATCGGCTTATACGCACTCT
*
9016015 CACTTGCACATAG
1 CACTCGCACATAG
9016028 CCGGGTCAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (42 bp):
CACTCGCACATAGTTAGGTCAGCATCGGCTTATACGCACTCT
Found at i:9027858 original size:20 final size:21
Alignment explanation
Indices: 9027835--9027874 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9027825 TAAAAACTTA
*
9027835 TTTA-AAATTTTTTTAAATAG
1 TTTAGAAATTTTTTCAAATAG
*
9027855 TTTAGAAGTTTTTTCAAATA
1 TTTAGAAATTTTTTCAAATA
9027875 TTATGCCATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTAGAAATTTTTTCAAATAG
Found at i:9029587 original size:41 final size:41
Alignment explanation
Indices: 9029530--9029613 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
9029520 GCTTCCGCTA
9029530 CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
1 CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
9029571 CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
1 CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
9029612 CT
1 CT
9029614 TTCTTCTTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (41 bp):
CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
Found at i:9030703 original size:27 final size:28
Alignment explanation
Indices: 9030647--9030713 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
9030637 AATCCATCAT
* *
9030647 TTCCGTTGAAAAACCATTTACCATGGAA
1 TTCCGTTGAAAAACCATTTACCACGAAA
* *
9030675 TTCCGTTGAAAAAGCATTT-CCCCGAAA
1 TTCCGTTGAAAAACCATTTACCACGAAA
*
9030702 TTCTGTTGAAAA
1 TTCCGTTGAAAA
9030714 TTTCCAATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
27 16 0.47
28 18 0.53
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (28 bp):
TTCCGTTGAAAAACCATTTACCACGAAA
Found at i:9030865 original size:24 final size:25
Alignment explanation
Indices: 9030836--9030886 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
9030826 TTAAAAAAAC
9030836 ATTTCCCACAAAATTT-TATTGAAA
1 ATTTCCCACAAAATTTCTATTGAAA
*
9030860 ATTTCCCACGAAATTTCTATTGAAA
1 ATTTCCCACAAAATTTCTATTGAAA
9030885 AT
1 AT
9030887 GCATTTCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 15 0.60
25 10 0.40
ACGTcount: A:0.39, C:0.18, G:0.06, T:0.37
Consensus pattern (25 bp):
ATTTCCCACAAAATTTCTATTGAAA
Found at i:9030914 original size:30 final size:29
Alignment explanation
Indices: 9030860--9030916 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
9030850 TTTATTGAAA
* * *
9030860 ATTTCCCACGAAATTTCTATTGAAAATGC
1 ATTTCCAACGAAAATTCAATTGAAAATGC
9030889 ATTTCCAACGAAAAATTCAATTGAAAAT
1 ATTTCCAACG-AAAATTCAATTGAAAAT
9030917 TTTCGACAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.32
Consensus pattern (29 bp):
ATTTCCAACGAAAATTCAATTGAAAATGC
Found at i:9042609 original size:72 final size:71
Alignment explanation
Indices: 9042485--9042641 Score: 199
Period size: 72 Copynumber: 2.2 Consensus size: 71
9042475 ATTCGCACCC
* * *
9042485 ATCTATCGATAGATGTAAGTATCTATCGATAGATTCAACTCAAGATCATTTTGAAGTATCCTTGG
1 ATCTATCGATAGATGTAAGCATCTATCAATAGATGCAACTCAAGATCATTTTGAAGTATCCTTGG
*
9042550 GTGGCT
66 GTGCCT
* * * * *
9042556 ATCTATCGATAGATGTCACA-CATCTATCAATAGATGCAAGTCAGGGTCCTTTTGAAGTATTCTT
1 ATCTATCGATAGATGT-A-AGCATCTATCAATAGATGCAACTCAAGATCATTTTGAAGTATCCTT
9042620 GGGTGCCT
64 GGGTGCCT
*
9042628 ATCTATCAATAGAT
1 ATCTATCGATAGAT
9042642 ACCATGTATT
Statistics
Matches: 74, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
71 16 0.22
72 57 0.77
73 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (71 bp):
ATCTATCGATAGATGTAAGCATCTATCAATAGATGCAACTCAAGATCATTTTGAAGTATCCTTGG
GTGCCT
Found at i:9042668 original size:72 final size:72
Alignment explanation
Indices: 9042505--9042680 Score: 199
Period size: 72 Copynumber: 2.4 Consensus size: 72
9042495 AGATGTAAGT
* * * *
9042505 ATCTATCGATAGATTCAACTCAAGATCATTTTGAAGTATCCTTGGGTGGCTATCTATCGATAGAT
1 ATCTATCAATAGATTCAAGTCAAGATCATTTTGAAGTATCCTTGGGTGCCTATCTATCAATAGAT
**
9042570 GTCACAC
66 ACCACAC
* * * * *
9042577 ATCTATCAATAGATGCAAGTCAGGGTCCTTTTGAAGTATTCTTGGGTGCCTATCTATCAATAGAT
1 ATCTATCAATAGATTCAAGTCAAGATCATTTTGAAGTATCCTTGGGTGCCTATCTATCAATAGAT
***
9042642 ACCATGT
66 ACCACAC
* *
9042649 ATTTATCAGTAGATTCAAGTCAAGATCCATTT
1 ATCTATCAATAGATTCAAGTCAAGAT-CATTT
9042681 ATTTTGTTAT
Statistics
Matches: 83, Mismatches: 20, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
72 79 0.95
73 4 0.05
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (72 bp):
ATCTATCAATAGATTCAAGTCAAGATCATTTTGAAGTATCCTTGGGTGCCTATCTATCAATAGAT
ACCACAC
Found at i:9044671 original size:25 final size:26
Alignment explanation
Indices: 9044628--9044685 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
9044618 ATTTTATTTT
9044628 TAAATTATTATTTTAAATAA-ATATTA
1 TAAATTATTATTTTAAATAACA-ATTA
* *
9044654 TTAATTA-TATTTTCAATAACAATTA
1 TAAATTATTATTTTAAATAACAATTA
9044679 TAAATTA
1 TAAATTA
9044686 ATAATAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
TAAATTATTATTTTAAATAACAATTA
Found at i:9048785 original size:63 final size:63
Alignment explanation
Indices: 9048717--9048873 Score: 235
Period size: 63 Copynumber: 2.5 Consensus size: 63
9048707 TGATGTAACT
* * *
9048717 GTGCATGTGCGGAGTGGGCAGTGCATATGCCGGTTGAATGACGATGTTGTGACAAC-TACAACC
1 GTGCATATGCGGAGTGGGCAGTGCATATGCCGGTCGAATGACGATGTTATGAC-ACTTACAACC
* *
9048780 GTGCATATGCAGAGTGGGCAGTGCATATGCCGGTCGAATGACGATGTTATGACACTTACAACT
1 GTGCATATGCGGAGTGGGCAGTGCATATGCCGGTCGAATGACGATGTTATGACACTTACAACC
* *
9048843 GTGCATATGCGGAGTGGGTAGTGCACATGCC
1 GTGCATATGCGGAGTGGGCAGTGCATATGCC
9048874 AGTAATGATG
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
62 2 0.02
63 83 0.98
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (63 bp):
GTGCATATGCGGAGTGGGCAGTGCATATGCCGGTCGAATGACGATGTTATGACACTTACAACC
Found at i:9052013 original size:15 final size:15
Alignment explanation
Indices: 9051995--9052050 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
9051985 AACTTCTCCT
9051995 TCATCTCCTTCCATG
1 TCATCTCCTTCCATG
* *
9052010 TCATCT-TTTCCATCT
1 TCATCTCCTTCCAT-G
*
9052025 TCATCTCCTTGCATG
1 TCATCTCCTTCCATG
* *
9052040 ACATCTTCTTC
1 TCATCTCCTTC
9052051 ATCCTCAATC
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
14 6 0.19
15 20 0.65
16 5 0.16
ACGTcount: A:0.14, C:0.36, G:0.05, T:0.45
Consensus pattern (15 bp):
TCATCTCCTTCCATG
Found at i:9059463 original size:63 final size:63
Alignment explanation
Indices: 9059387--9059510 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 63
9059377 TGATACCAAT
*
9059387 ATTAAGGACTTTTACAAGCAAAAGACAAGTTTTTGTTACCTAGAGATTTTGCTTAGTTTCAAA
1 ATTAAGGACTTTTACAAGCAAAAGACAAGTTTTTGTTACCTAGAGATTTTGCCTAGTTTCAAA
*
9059450 ATTAAGGACTTTTACAAGCAAAAGACAAGTTTTTGTTACCTAGAGATTTTGCCTATTTTCA
1 ATTAAGGACTTTTACAAGCAAAAGACAAGTTTTTGTTACCTAGAGATTTTGCCTAGTTTCA
9059511 TGCAATTGTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (63 bp):
ATTAAGGACTTTTACAAGCAAAAGACAAGTTTTTGTTACCTAGAGATTTTGCCTAGTTTCAAA
Found at i:9060763 original size:21 final size:21
Alignment explanation
Indices: 9060737--9060793 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
9060727 TTGGGTGGCT
9060737 ATCTATCGATAGATGTCACGC
1 ATCTATCGATAGATGTCACGC
9060758 ATCTATCGATAGATGTCACGC
1 ATCTATCGATAGATGTCACGC
*
9060779 ATCTATCAATAGATG
1 ATCTATCGATAGATG
9060794 CAAGTCAGGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.30
Consensus pattern (21 bp):
ATCTATCGATAGATGTCACGC
Found at i:9060833 original size:93 final size:92
Alignment explanation
Indices: 9060665--9060836 Score: 211
Period size: 93 Copynumber: 1.9 Consensus size: 92
9060655 AATTTGCACC
* * * * *
9060665 CATCTATCGATAGATGTAAGTATTTATCAATAGATTCAACTCAAGATCATTTTAAAGTATTCTTG
1 CATCTATCGATAGATGTAAGCATCTATCAATAGATGCAACTCAAGATCATTTCAAAGTATTCTCG
*
9060730 GGTGGCTATCTATCGATAGATGTCACG
66 AGTGGCTATCTATCGATAGATGTCACG
* * * * * *
9060757 CATCTATCGATAGATGTCACGCATCTATCAATAGATGCAAGTCAGGGTCCTTTCGAAGTATTCTC
1 CATCTATCGATAGATGT-AAGCATCTATCAATAGATGCAACTCAAGATCATTTCAAAGTATTCTC
9060822 GAGT-GCGTATCTATC
65 GAGTGGC-TATCTATC
9060837 AATAAATATC
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
92 19 0.29
93 47 0.71
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (92 bp):
CATCTATCGATAGATGTAAGCATCTATCAATAGATGCAACTCAAGATCATTTCAAAGTATTCTCG
AGTGGCTATCTATCGATAGATGTCACG
Found at i:9061019 original size:20 final size:21
Alignment explanation
Indices: 9060975--9061027 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
9060965 AAACAATCAA
***
9060975 CTATCGATAGATTTTCTTCAT
1 CTATCGATAGATGAGCTTCAT
9060996 CTATCGATAGATGAGCTT-AT
1 CTATCGATAGATGAGCTTCAT
9061016 CTATCGATAGAT
1 CTATCGATAGAT
9061028 TGCGAGCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 14 0.48
21 15 0.52
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (21 bp):
CTATCGATAGATGAGCTTCAT
Found at i:9062635 original size:27 final size:27
Alignment explanation
Indices: 9062597--9062911 Score: 116
Period size: 27 Copynumber: 11.7 Consensus size: 27
9062587 TCCTTAGGCA
*
9062597 CTTCTATACTTGGAACACCCCTGGGCG
1 CTTCTATGCTTGGAACACCCCTGGGCG
*
9062624 CTTCTATGCTTGGAATA-CCCTCGGGCG
1 CTTCTATGCTTGGAACACCCCT-GGGCG
* * * * *
9062651 CTTCTGTGCTTGGAACGCCCCTAGACA
1 CTTCTATGCTTGGAACACCCCTGGGCG
* * * *
9062678 CTTCTACT-CTTGAAACACCCTTAGGCA
1 CTTCTA-TGCTTGGAACACCCCTGGGCG
** * *
9062705 CTT-TCGCGCTTGGAACACCCCTTGGTG
1 CTTCT-ATGCTTGGAACACCCCTGGGCG
** * *
9062732 CTTCCGCT-CTTGGAACGCCCCTAGGCG
1 CTT-CTATGCTTGGAACACCCCTGGGCG
**** * * *
9062759 CTTCCGCACTTGAAACGCCCCTGGGCA
1 CTTCTATGCTTGGAACACCCCTGGGCG
* * * * *
9062786 CTTCCATGCTTGGAATACCCTTGGACA
1 CTTCTATGCTTGGAACACCCCTGGGCG
* * * *
9062813 CTTCTGTGCTTAGAACACTCTTGGGCG
1 CTTCTATGCTTGGAACACCCCTGGGCG
* *** * ** **
9062840 ATTCTGCACTTAGAACACCTTTGGATG
1 CTTCTATGCTTGGAACACCCCTGGGCG
* ** *
9062867 CTTCTATGCTTGGAATACCCCTAAGTG
1 CTTCTATGCTTGGAACACCCCTGGGCG
* *
9062894 CTTCCATGCTTGTAACAC
1 CTTCTATGCTTGGAACAC
9062912 TTCCACGCTT
Statistics
Matches: 212, Mismatches: 68, Indels: 16
0.72 0.23 0.05
Matches are distributed among these distances:
26 6 0.03
27 201 0.95
28 5 0.02
ACGTcount: A:0.19, C:0.32, G:0.21, T:0.29
Consensus pattern (27 bp):
CTTCTATGCTTGGAACACCCCTGGGCG
Found at i:9062664 original size:54 final size:53
Alignment explanation
Indices: 9062577--9062844 Score: 137
Period size: 54 Copynumber: 5.0 Consensus size: 53
9062567 GTTTTCTGCG
* * ***
9062577 CTTGTAACACTCCTTAGGCACTTCTATACTTGGAACACCCCTGGGCGCTTCTAT
1 CTTGGAACAC-CCTCAGGCACTTCTGCGCTTGGAACACCCCTGGGCGCTTCTAT
* * * * * * * *
9062631 GCTTGGAATACCCTCGGGCGCTTCTGTGCTTGGAACGCCCCTAGACACTTCTACT
1 -CTTGGAACACCCTCAGGCACTTCTGCGCTTGGAACACCCCTGGGCGCTTCTA-T
* * * * **
9062686 CTTGAAACACCCTTAGGCACTT-TCGCGCTTGGAACACCCCTTGGTGCTTCCGCT
1 CTTGGAACACCCTCAGGCACTTCT-GCGCTTGGAACACCCCTGGGCGCTT-CTAT
* * * * * * * *
9062740 CTTGGAACGCCC-CTAGGCGCTTCCGCACTTGAAACGCCCCTGGGCACTTCCAT
1 CTTGGAACACCCTC-AGGCACTTCTGCGCTTGGAACACCCCTGGGCGCTTCTAT
* * * * * * *
9062793 GCTTGGAATACCCT-TGGACACTTCTGTGCTTAGAACACTCTTGGGCGATTCT
1 -CTTGGAACACCCTCAGG-CACTTCTGCGCTTGGAACACCCCTGGGCGCTTCT
9062845 GCACTTAGAA
Statistics
Matches: 153, Mismatches: 52, Indels: 17
0.69 0.23 0.08
Matches are distributed among these distances:
53 5 0.03
54 138 0.90
55 10 0.07
ACGTcount: A:0.18, C:0.33, G:0.21, T:0.28
Consensus pattern (53 bp):
CTTGGAACACCCTCAGGCACTTCTGCGCTTGGAACACCCCTGGGCGCTTCTAT
Found at i:9062695 original size:81 final size:81
Alignment explanation
Indices: 9062595--9062828 Score: 215
Period size: 81 Copynumber: 2.9 Consensus size: 81
9062585 ACTCCTTAGG
* *
9062595 CACTTCTA-TACTTGGAACACCCCTGGGCGCTTCTATGCTTGGAATACCCTCGGGCGCTTCTGTG
1 CACTTCTACT-CTTGAAACACCCCTGGGCACTTCTATGCTTGGAATACCCTCGGGCGCTTCTGTG
9062659 CTTGGAACGCCCCTAGA
65 CTTGGAACGCCCCTAGA
* * ** * * * *
9062676 CACTTCTACTCTTGAAACACCCTTAGGCACTT-TCGCGCTTGGAACACCC-CTTGGTGCTTCCGC
1 CACTTCTACTCTTGAAACACCCCTGGGCACTTCT-ATGCTTGGAATACCCTC-GGGCGCTTCTG-
*
9062739 T-CTTGGAACGCCCCTAGG
63 TGCTTGGAACGCCCCTAGA
* ** * * * * * *
9062757 CGCTTCCGCACTTGAAACGCCCCTGGGCACTTCCATGCTTGGAATACCCTTGGACACTTCTGTGC
1 CACTTCTACTCTTGAAACACCCCTGGGCACTTCTATGCTTGGAATACCCTCGGGCGCTTCTGTGC
*
9062822 TTAGAAC
66 TTGGAAC
9062829 ACTCTTGGGC
Statistics
Matches: 117, Mismatches: 29, Indels: 14
0.73 0.18 0.09
Matches are distributed among these distances:
80 3 0.03
81 112 0.96
82 2 0.02
ACGTcount: A:0.18, C:0.34, G:0.21, T:0.27
Consensus pattern (81 bp):
CACTTCTACTCTTGAAACACCCCTGGGCACTTCTATGCTTGGAATACCCTCGGGCGCTTCTGTGC
TTGGAACGCCCCTAGA
Found at i:9062958 original size:26 final size:26
Alignment explanation
Indices: 9062929--9063023 Score: 109
Period size: 26 Copynumber: 3.7 Consensus size: 26
9062919 CTTAGGGCGT
* *
9062929 TTCTACGCTTGAAACACCTTAGGCGC
1 TTCTACGCTTGGAACACCTTAGGCAC
* * * * *
9062955 TTCTGCACTTGGAACGCCTTGGGTAC
1 TTCTACGCTTGGAACACCTTAGGCAC
* *
9062981 TTCCACGCTTGGAACACCCTAGGCAC
1 TTCTACGCTTGGAACACCTTAGGCAC
9063007 TTCTACGCTTGGAACAC
1 TTCTACGCTTGGAACAC
9063024 TTCTAATGTA
Statistics
Matches: 54, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.21, C:0.32, G:0.21, T:0.26
Consensus pattern (26 bp):
TTCTACGCTTGGAACACCTTAGGCAC
Found at i:9063158 original size:2 final size:2
Alignment explanation
Indices: 9063151--9063205 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
9063141 AGACAATGCT
9063151 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
9063193 TA AA TA TA TA TA T
1 TA TA TA TA TA TA T
9063206 TCATCTTTGA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:9064321 original size:25 final size:26
Alignment explanation
Indices: 9064278--9064335 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
9064268 ATTTTATTTT
9064278 TAAATTATTATTTTAAATAA-ATATTA
1 TAAATTATTATTTTAAATAACA-ATTA
* *
9064304 TTAATTA-TATTTTCAATAACAATTA
1 TAAATTATTATTTTAAATAACAATTA
9064329 TAAATTA
1 TAAATTA
9064336 ATAATAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
TAAATTATTATTTTAAATAACAATTA
Found at i:9065407 original size:25 final size:26
Alignment explanation
Indices: 9065364--9065421 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
9065354 ATTTTATTTT
9065364 TAAATTATTATTTTAAATAA-ATATTA
1 TAAATTATTATTTTAAATAACA-ATTA
* *
9065390 TTAATTA-TATTTTCAATAACAATTA
1 TAAATTATTATTTTAAATAACAATTA
9065415 TAAATTA
1 TAAATTA
9065422 ATAATAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 21 0.75
26 7 0.25
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
TAAATTATTATTTTAAATAACAATTA
Found at i:9067671 original size:41 final size:41
Alignment explanation
Indices: 9067614--9067738 Score: 250
Period size: 41 Copynumber: 3.0 Consensus size: 41
9067604 GCTTCCGCTA
9067614 CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
1 CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
9067655 CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
1 CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
9067696 CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
1 CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
9067737 CT
1 CT
9067739 TTCTTCTTCC
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.34
Consensus pattern (41 bp):
CTAAAACATGGGGAGAGGAATACAATCTATTTGGTATTTTT
Found at i:9069017 original size:24 final size:24
Alignment explanation
Indices: 9068965--9069017 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
9068955 AGAATTCCAT
*
9068965 AAATTCTGTAAGAAAATTCCCATA
1 AAATTCTGTAAGAAAATTCCCACA
* ** *
9068989 GAATTCTGTTGGAAATTTCCCACA
1 AAATTCTGTAAGAAAATTCCCACA
9069013 AAATT
1 AAATT
9069018 TCCATTAGAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.17, G:0.11, T:0.32
Consensus pattern (24 bp):
AAATTCTGTAAGAAAATTCCCACA
Found at i:9073414 original size:2 final size:2
Alignment explanation
Indices: 9073407--9073449 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
9073397 ATATTAAGAA
9073407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9073449 A
1 A
9073450 NNNNNNNNNN
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9073475 original size:2 final size:2
Alignment explanation
Indices: 9073468--9073514 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
9073458 NNNNNTAATA
9073468 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9073510 AT AT A
1 AT AT A
9073515 GTTGTTTCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:9078437 original size:63 final size:63
Alignment explanation
Indices: 9078361--9078484 Score: 230
Period size: 63 Copynumber: 2.0 Consensus size: 63
9078351 TGATACCAAT
*
9078361 ATTAAGGACTTTTACAAGCAAAAGACAAGTTTTTGTTACCTAGAGATTTTGCTTAGTTTCAAA
1 ATTAAGGACTTTTACAAGCAAAAGACAAGTTTTTGTTACCTAGAGATTTTGCCTAGTTTCAAA
*
9078424 ATTAAGGACTTTTACAAGCAAAAGACAAGTTTTTGTTACCTAGAGATTTTGCCTATTTTCA
1 ATTAAGGACTTTTACAAGCAAAAGACAAGTTTTTGTTACCTAGAGATTTTGCCTAGTTTCA
9078485 TGCAATTGTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (63 bp):
ATTAAGGACTTTTACAAGCAAAAGACAAGTTTTTGTTACCTAGAGATTTTGCCTAGTTTCAAA
Found at i:9082541 original size:31 final size:31
Alignment explanation
Indices: 9082503--9082561 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
9082493 CAACATATGC
*
9082503 AGAACCCAATGCAATCTGTAGACAGAGATGT
1 AGAACCCAATGCAATCAGTAGACAGAGATGT
9082534 AGAACCCAATGCAATCAGTAGACAGAGA
1 AGAACCCAATGCAATCAGTAGACAGAGA
9082562 CATTAATACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.20, G:0.22, T:0.15
Consensus pattern (31 bp):
AGAACCCAATGCAATCAGTAGACAGAGATGT
Found at i:9085344 original size:6 final size:6
Alignment explanation
Indices: 9085333--9085358 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
9085323 AGCTGGCTGA
9085333 TGGTGC TGGTGC TGGTGC TGGTGC TG
1 TGGTGC TGGTGC TGGTGC TGGTGC TG
9085359 TGGAGGAGGA
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:0.00, C:0.15, G:0.50, T:0.35
Consensus pattern (6 bp):
TGGTGC
Found at i:9095335 original size:25 final size:25
Alignment explanation
Indices: 9095275--9095336 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
9095265 AATAAACGTG
**
9095275 ATTATAGAAATTAGAAATCACCATA
1 ATTATAGGGATTAGAAATCACCATA
* * *
9095300 ATTATAAGGATTAGGAATCATCATA
1 ATTATAGGGATTAGAAATCACCATA
9095325 ATTATAGGGATT
1 ATTATAGGGATT
9095337 TTATTTTTTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.45, C:0.08, G:0.15, T:0.32
Consensus pattern (25 bp):
ATTATAGGGATTAGAAATCACCATA
Found at i:9095356 original size:23 final size:23
Alignment explanation
Indices: 9095329--9095375 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
9095319 ATCATAATTA
* *
9095329 TAGGGATTTTATTTTTTTTATTC
1 TAGGGAATTTATTTTCTTTATTC
9095352 TAGGGAATTTATTTTCTTTATTC
1 TAGGGAATTTATTTTCTTTATTC
9095375 T
1 T
9095376 TTTTCTATTT
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:0.19, C:0.06, G:0.13, T:0.62
Consensus pattern (23 bp):
TAGGGAATTTATTTTCTTTATTC
Found at i:9099858 original size:25 final size:25
Alignment explanation
Indices: 9099826--9099881 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
9099816 AAAAAACGTG
9099826 ATTATAAGAATTAAAAATCACCATA
1 ATTATAAGAATTAAAAATCACCATA
* *** *
9099851 ATTATAAGGATTGGGAATCATCATA
1 ATTATAAGAATTAAAAATCACCATA
9099876 ATTATA
1 ATTATA
9099882 GGGATTTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.48, C:0.09, G:0.11, T:0.32
Consensus pattern (25 bp):
ATTATAAGAATTAAAAATCACCATA
Found at i:9099907 original size:23 final size:23
Alignment explanation
Indices: 9099880--9099926 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
9099870 ATCATAATTA
*
9099880 TAGGGATTTTATTTTCTTTATTC
1 TAGGGATCTTATTTTCTTTATTC
9099903 TAGGGATCTTATTTTCTTTATTC
1 TAGGGATCTTATTTTCTTTATTC
9099926 T
1 T
9099927 TTTCCTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.11, G:0.13, T:0.60
Consensus pattern (23 bp):
TAGGGATCTTATTTTCTTTATTC
Found at i:9104124 original size:21 final size:21
Alignment explanation
Indices: 9104100--9104144 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
9104090 AAAAAATTTT
9104100 AATTTAAAATAAAAAT-ATAAA
1 AATTT-AAATAAAAATAATAAA
* *
9104121 AATTTAATTAAATATAATAAA
1 AATTTAAATAAAAATAATAAA
9104142 AAT
1 AAT
9104145 AAAAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
AATTTAAATAAAAATAATAAA
Found at i:9104128 original size:26 final size:28
Alignment explanation
Indices: 9104091--9104160 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 28
9104081 TAATTATAAA
*
9104091 AAAAATTTTAATTTAAA-ATAA-AAATAT
1 AAAAA-TTTAATTTAAATATAATAAAAAT
9104118 AAAAATTTAA-TTAAATATAATAAAAAT
1 AAAAATTTAATTTAAATATAATAAAAAT
9104145 AAAAATTT-ATTTAAAT
1 AAAAATTTAATTTAAAT
9104161 TTTATAGAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
25 5 0.13
26 10 0.26
27 24 0.62
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAAATTTAATTTAAATATAATAAAAAT
Found at i:9105394 original size:29 final size:30
Alignment explanation
Indices: 9105322--9105396 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
9105312 ATTGATGAAC
**
9105322 ATAAGTTTATTTTATTTAAAATAAAAATATA
1 ATAA-TTTATTTTAAATAAAATAAAAATATA
* * *
9105353 AAAATTTA-ATTAAATATAATAAAAA-ATA
1 ATAATTTATTTTAAATAAAATAAAAATATA
9105381 ATAATTTATTTTAAAT
1 ATAATTTATTTTAAAT
9105397 TTACTAACTA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
28 10 0.28
29 19 0.53
30 4 0.11
31 3 0.08
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (30 bp):
ATAATTTATTTTAAATAAAATAAAAATATA
Found at i:9115321 original size:28 final size:28
Alignment explanation
Indices: 9115290--9115356 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
9115280 TGAGTTAAAC
9115290 TTATAATTTTTAGGTAACCTAAAACTCA
1 TTATAATTTTTAGGTAACCTAAAACTCA
*
9115318 TTATAATTTTTAGGTACCCTAAAACTCA
1 TTATAATTTTTAGGTAACCTAAAACTCA
9115346 TTATAATTTTT
1 TTATAATTTTT
9115357 TTAAAGAGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (28 bp):
TTATAATTTTTAGGTAACCTAAAACTCA
Found at i:9132940 original size:85 final size:85
Alignment explanation
Indices: 9132788--9132952 Score: 246
Period size: 85 Copynumber: 1.9 Consensus size: 85
9132778 AAAAGAAATC
* * * *
9132788 ATTGAACAAAGTAATTATGATCGAAGAACTGATTCATTAGTTAAATCTGCAATTTCAACTTTTCT
1 ATTGAACAAAGTAATTATGATCCAAGAACTCATTCATTAGTTAAAACTGCAATTTCAACTTTGCT
9132853 TTTTCTTTTCAAATTATGTT
66 TTTTCTTTTCAAATTATGTT
9132873 ATTGAACAAAGTAAATTATGCA-CCAAGAACTCATTCATTAG-TAGAAACTGC-ATTTCAACTTT
1 ATTGAACAAAGT-AATTATG-ATCCAAGAACTCATTCATTAGTTA-AAACTGCAATTTCAACTTT
9132935 GCTTTTTCTTTTCAAATT
63 GCTTTTTCTTTTCAAATT
9132953 CATTACAGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
85 42 0.58
86 30 0.41
87 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (85 bp):
ATTGAACAAAGTAATTATGATCCAAGAACTCATTCATTAGTTAAAACTGCAATTTCAACTTTGCT
TTTTCTTTTCAAATTATGTT
Found at i:9145944 original size:22 final size:22
Alignment explanation
Indices: 9145864--9145944 Score: 67
Period size: 22 Copynumber: 3.6 Consensus size: 22
9145854 AAAATTGATA
* *
9145864 ATTTTTTATAAGAATTTTAAT-AA
1 ATTTTTTATAA-AATTAT-ATCAG
* *
9145887 ATTTTTGATAAAACTATATC-G
1 ATTTTTTATAAAATTATATCAG
* *
9145908 AATTTTCTATAAAATTCTATCAG
1 -ATTTTTTATAAAATTATATCAG
9145931 ATTTTTTATAAAAT
1 ATTTTTTATAAAAT
9145945 CTCAACAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
21 2 0.04
22 33 0.72
23 11 0.24
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (22 bp):
ATTTTTTATAAAATTATATCAG
Found at i:9147876 original size:23 final size:23
Alignment explanation
Indices: 9147846--9147891 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
9147836 TATTAACTTA
9147846 TTAATTATTTGTAT-AAAGTGTTG
1 TTAATTATTTGTATGAAA-TGTTG
9147869 TTAATTATTTGTATGAAATGTTG
1 TTAATTATTTGTATGAAATGTTG
9147892 ATATATCACG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 19 0.86
24 3 0.14
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.52
Consensus pattern (23 bp):
TTAATTATTTGTATGAAATGTTG
Found at i:9148189 original size:27 final size:27
Alignment explanation
Indices: 9148120--9148335 Score: 168
Period size: 27 Copynumber: 7.9 Consensus size: 27
9148110 TTATTAACGC
* * *
9148120 CATGTTGAAAAATATAG-TGTTATATGT
1 CATGTTG-AAAATTTAGTTGTTACACGT
* * *
9148147 CATATTTTAAAATTTAGTTGTTATACGT
1 CAT-GTTGAAAATTTAGTTGTTACACGT
* * *
9148175 TATGTTGAAATTTTAATTGTTACACGT
1 CATGTTGAAAATTTAGTTGTTACACGT
* *
9148202 CATGATGAAAATTTAATTGTTACACGT
1 CATGTTGAAAATTTAGTTGTTACACGT
* * **
9148229 CATATTGAAAAATATAGTTGTTACACAC
1 CATGTTG-AAAATTTAGTTGTTACACGT
* *
9148257 CATGTT-AAAGACTTAGTTGTTACATGT
1 CATGTTGAAA-ATTTAGTTGTTACACGT
* * **
9148284 TATGTTGAAAATTTAGTTATTACACAC
1 CATGTTGAAAATTTAGTTGTTACACGT
9148311 CATGTT-AACCAATTTAGTTGTTACA
1 CATGTTGAA--AATTTAGTTGTTACA
9148336 TGCTATGATG
Statistics
Matches: 149, Mismatches: 33, Indels: 13
0.76 0.17 0.07
Matches are distributed among these distances:
26 5 0.03
27 93 0.62
28 51 0.34
ACGTcount: A:0.35, C:0.10, G:0.14, T:0.41
Consensus pattern (27 bp):
CATGTTGAAAATTTAGTTGTTACACGT
Found at i:9148204 original size:55 final size:54
Alignment explanation
Indices: 9148121--9148360 Score: 161
Period size: 55 Copynumber: 4.4 Consensus size: 54
9148111 TATTAACGCC
* * * *
9148121 ATGTTGAAAAATATAG-TGTTATATGTCATATTTTAAAATTTAGTTGTTATACGTT
1 ATGTTG-AAAATTTAGTTGTTACACGTCATA-TTTAAAATTTAGTTGTTACACGTT
* * * * *
9148176 ATGTTGAAATTTTAATTGTTACACGTCATGA-TGAAAATTTAATTGTTACACGTC
1 ATGTTGAAAATTTAGTTGTTACACGTCAT-ATTTAAAATTTAGTTGTTACACGTT
* * ** * * *
9148230 ATATTGAAAAATATAGTTGTTACACACCAT-GTTAAAGACTTAGTTGTTACATGTT
1 ATGTTG-AAAATTTAGTTGTTACACGTCATATTTAAA-ATTTAGTTGTTACACGTT
* ** * * *
9148285 ATGTTGAAAATTTAGTTATTACACACCAT-GTTAACCAATTTAGTTGTTACATGCT
1 ATGTTGAAAATTTAGTTGTTACACGTCATATTTAA--AATTTAGTTGTTACACGTT
*
9148340 ATGATGAAAA---AGTTGTTACAC
1 ATGTTGAAAATTTAGTTGTTACAC
9148361 ATCACATCAT
Statistics
Matches: 151, Mismatches: 27, Indels: 17
0.77 0.14 0.09
Matches are distributed among these distances:
52 10 0.07
54 60 0.40
55 79 0.52
56 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (54 bp):
ATGTTGAAAATTTAGTTGTTACACGTCATATTTAAAATTTAGTTGTTACACGTT
Found at i:9148661 original size:17 final size:16
Alignment explanation
Indices: 9148645--9148692 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
9148635 GTGGGCAAAT
9148645 TAAAATAATGGGAAAA
1 TAAAATAATGGGAAAA
* *
9148661 TGAAATGATGGGAATAA
1 TAAAATAATGGGAA-AA
*
9148678 TCAAATAA-GGGAAAA
1 TAAAATAATGGGAAAA
9148693 CAAAGTCGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 2 0.07
16 17 0.63
17 8 0.30
ACGTcount: A:0.56, C:0.02, G:0.23, T:0.19
Consensus pattern (16 bp):
TAAAATAATGGGAAAA
Found at i:9149562 original size:14 final size:15
Alignment explanation
Indices: 9149514--9149572 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 15
9149504 TTAATAATTA
*
9149514 TAATAAA-AAATATT
1 TAATAAATACATATT
9149528 TCAAT-AAT-CATCATT
1 T-AATAAATACAT-ATT
9149543 TAATAAATACATATT
1 TAATAAATACATATT
*
9149558 T-ATAAATATATATT
1 TAATAAATACATATT
9149572 T
1 T
9149573 TTGATATTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.55
15 14 0.37
16 3 0.08
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATAAATACATATT
Found at i:9150794 original size:22 final size:22
Alignment explanation
Indices: 9150742--9150798 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
9150732 TTAAATAAAA
*
9150742 TTTTGATAAAACTATATCAAAT
1 TTTTGATAAAATTATATCAAAT
* * *
9150764 TTTCGATAAAATTCTATCAGAT
1 TTTTGATAAAATTATATCAAAT
*
9150786 TTTTTATAAAATT
1 TTTTGATAAAATT
9150799 TTAACAAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (22 bp):
TTTTGATAAAATTATATCAAAT
Found at i:9151356 original size:5 final size:5
Alignment explanation
Indices: 9151346--9151373 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
9151336 TATTCAAAAA
9151346 TATTT TATTT TATTT TATTT TATTT TAT
1 TATTT TATTT TATTT TATTT TATTT TAT
9151374 AAGTAACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
TATTT
Found at i:9152750 original size:23 final size:23
Alignment explanation
Indices: 9152720--9152764 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
9152710 GTTAACTTAT
* *
9152720 TAATGATTTGTATGAAGTGTTGC
1 TAATGATTTGTACGAAATGTTGC
9152743 TAATGATTTGTACGAAATGTTG
1 TAATGATTTGTACGAAATGTTG
9152765 ATATATCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.42
Consensus pattern (23 bp):
TAATGATTTGTACGAAATGTTGC
Found at i:9153089 original size:52 final size:55
Alignment explanation
Indices: 9153030--9153191 Score: 190
Period size: 55 Copynumber: 3.0 Consensus size: 55
9153020 TTATGCTTTC
*
9153030 AAATTTAATTGTTACATATCATGTTAG-AAA-TAATTGTTACATGTCATGTTG-A
1 AAATTTAATTGTTACATATCATGTTAGAAAATTAATTGTTACACGTCATGTTGAA
**
9153082 AAATTTAATTGTTACACGTCATGTT-GAAAATTTAATTGTTACACGTCATGTTGAA
1 AAATTTAATTGTTACATATCATGTTAGAAAA-TTAATTGTTACACGTCATGTTGAA
* * * * * *
9153137 AAATATAGTTGTTACATATCATGTTA-AAGACTTAGTTGTTACACGCCATATTGAA
1 AAATTTAATTGTTACATATCATGTTAGAA-AATTAATTGTTACACGTCATGTTGAA
9153192 GATTTAGTTG
Statistics
Matches: 93, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
51 1 0.01
52 26 0.28
54 20 0.22
55 45 0.48
56 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (55 bp):
AAATTTAATTGTTACATATCATGTTAGAAAATTAATTGTTACACGTCATGTTGAA
Found at i:9153097 original size:27 final size:27
Alignment explanation
Indices: 9153030--9153233 Score: 175
Period size: 27 Copynumber: 7.6 Consensus size: 27
9153020 TTATGCTTTC
**
9153030 AAATTTAATTGTTACATATCATGTT-A
1 AAATTTAATTGTTACACGTCATGTTGA
*
9153056 GAAA--TAATTGTTACATGTCATGTTGA
1 -AAATTTAATTGTTACACGTCATGTTGA
9153082 AAATTTAATTGTTACACGTCATGTTGA
1 AAATTTAATTGTTACACGTCATGTTGA
9153109 AAATTTAATTGTTACACGTCATGTTGAA
1 AAATTTAATTGTTACACGTCATGTTG-A
* * **
9153137 AAATATAGTTGTTACATATCATGTT-A
1 AAATTTAATTGTTACACGTCATGTTGA
* * * *
9153163 AAGACTTAGTTGTTACACGCCATATTGA
1 AA-ATTTAATTGTTACACGTCATGTTGA
* * * * * *
9153191 AGATTTAGTTGTCACAC-ACTAGGTTCAA
1 AAATTTAATTGTTACACGTC-ATGTT-GA
9153219 AAATTTAATTGTTAC
1 AAATTTAATTGTTAC
9153234 CCGCTATGAT
Statistics
Matches: 147, Mismatches: 22, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
25 22 0.15
26 5 0.03
27 83 0.56
28 37 0.25
ACGTcount: A:0.35, C:0.11, G:0.14, T:0.39
Consensus pattern (27 bp):
AAATTTAATTGTTACACGTCATGTTGA
Found at i:9153178 original size:82 final size:79
Alignment explanation
Indices: 9153030--9153208 Score: 216
Period size: 82 Copynumber: 2.2 Consensus size: 79
9153020 TTATGCTTTC
* * * *
9153030 AAATTTAATTGTTACATATCATGTTAGAAATAATTGTTACATGTCATGTTGAAAATTTAATTGTT
1 AAATTTAATTGTTACACATCATGTTAAAAATAATTGTTACATATCATGTTGAAAACTTAATTGTT
* *
9153095 ACACGTCATGTTGA
66 ACACGCCATATTGA
* *
9153109 AAATTTAATTGTTACACGTCATGTTGAAAAATATAGTTGTTACATATCATGTT-AAAGACTTAGT
1 AAATTTAATTGTTACACATCATGTT-AAAAATA-A-TTGTTACATATCATGTTGAAA-ACTTAAT
9153173 TGTTACACGCCATATTGA
62 TGTTACACGCCATATTGA
* * *
9153191 AGATTTAGTTGTCACACA
1 AAATTTAATTGTTACACA
9153209 CTAGGTTCAA
Statistics
Matches: 84, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
79 23 0.27
80 6 0.07
81 4 0.05
82 51 0.61
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.39
Consensus pattern (79 bp):
AAATTTAATTGTTACACATCATGTTAAAAATAATTGTTACATATCATGTTGAAAACTTAATTGTT
ACACGCCATATTGA
Found at i:9153221 original size:82 final size:82
Alignment explanation
Indices: 9153059--9153233 Score: 201
Period size: 82 Copynumber: 2.1 Consensus size: 82
9153049 CATGTTAGAA
* * * * *
9153059 ATAATTGTTACATGTCATGTTGAAAATTTAATTGTTACACGTCATGTTGAAAATTTAATTGTTAC
1 ATAATTGTTACATATCATGTTGAAAACTTAATTGTTACACGCCATATTGAAAATTTAATTGTCAC
* * *
9153124 ACGTCATGTTGAAAAAT
66 ACCTCAGGTTCAAAAAT
* * * *
9153141 ATAGTTGTTACATATCATGTT-AAAGACTTAGTTGTTACACGCCATATTGAAGATTTAGTTGTCA
1 ATAATTGTTACATATCATGTTGAAA-ACTTAATTGTTACACGCCATATTGAAAATTTAATTGTCA
9153205 CACACT-AGGTTCAAAAAT
65 CAC-CTCAGGTTCAAAAAT
*
9153223 TTAATTGTTAC
1 ATAATTGTTAC
9153234 CCGCTATGAT
Statistics
Matches: 77, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
81 3 0.04
82 73 0.95
83 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (82 bp):
ATAATTGTTACATATCATGTTGAAAACTTAATTGTTACACGCCATATTGAAAATTTAATTGTCAC
ACCTCAGGTTCAAAAAT
Found at i:9153231 original size:55 final size:55
Alignment explanation
Indices: 9153060--9153233 Score: 138
Period size: 55 Copynumber: 3.2 Consensus size: 55
9153050 ATGTTAGAAA
* * * * * * * * *
9153060 TAATTGTTACATGTCATGTTG-AAAATTTAATTGTTACACGTCATGTTGAAAATT
1 TAATTGTTACACGCCATATTGAAAAATATAGTTGTCACACATCAGGTTAAAAATT
* * * * * * *
9153114 TAATTGTTACACGTCATGTTGAAAAATATAGTTGTTACATATCATGTTAAAGACT
1 TAATTGTTACACGCCATATTGAAAAATATAGTTGTCACACATCAGGTTAAAAATT
* * *
9153169 TAGTTGTTACACGCCATATTG-AAGATTTAGTTGTCACACA-CTAGGTTCAAAAATT
1 TAATTGTTACACGCCATATTGAAAAATATAGTTGTCACACATC-AGGTT-AAAAATT
9153224 TAATTGTTAC
1 TAATTGTTAC
9153234 CCGCTATGAT
Statistics
Matches: 98, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
53 1 0.01
54 39 0.40
55 58 0.59
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (55 bp):
TAATTGTTACACGCCATATTGAAAAATATAGTTGTCACACATCAGGTTAAAAATT
Found at i:9154204 original size:84 final size:82
Alignment explanation
Indices: 9154108--9154269 Score: 297
Period size: 84 Copynumber: 2.0 Consensus size: 82
9154098 AAGACATTTT
9154108 CCAGAGAACAACAAAAGCACTTTTATATTAAGTTTATGAGTATAAGTTTAATAAATATTAATATT
1 CCAGAGAACAACAAAAGCACTTTTATATTAAGTTTATGAGTATAAGTTTAATAAATATTAATATT
9154173 TAAATTAAAATATTAAAA
66 T-AATTAAAATATTAAAA
9154191 NCCAGAGAACAACAAAAGCACTTTTATATTAAGTTTATGAGTATAAGTTTAATAAATATTAATAT
1 -CCAGAGAACAACAAAAGCACTTTTATATTAAGTTTATGAGTATAAGTTTAATAAATATTAATAT
*
9154256 TTAATTTAAATATT
65 TTAATTAAAATATT
9154270 TAACTTAAAA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
83 11 0.14
84 66 0.86
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.36
Consensus pattern (82 bp):
CCAGAGAACAACAAAAGCACTTTTATATTAAGTTTATGAGTATAAGTTTAATAAATATTAATATT
TAATTAAAATATTAAAA
Found at i:9154269 original size:13 final size:13
Alignment explanation
Indices: 9154251--9154308 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
9154241 AATAAATATT
9154251 AATATTTAATTTA
1 AATATTTAATTTA
*
9154264 AATATTTAACTTAA
1 AATATTTAA-TTTA
* *
9154278 AAAAATTAATTTAA
1 AATATTTAATTT-A
*
9154292 AATATTAATATTTA
1 AATATTTA-ATTTA
9154306 AAT
1 AAT
9154309 TATACAACAC
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
13 11 0.31
14 20 0.57
15 4 0.11
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (13 bp):
AATATTTAATTTA
Found at i:9154496 original size:74 final size:74
Alignment explanation
Indices: 9154389--9154530 Score: 221
Period size: 74 Copynumber: 1.9 Consensus size: 74
9154379 ATAAATGGAA
* * * *
9154389 TAAATTTTACTTATAATTATAATAAAAAATATTTCAATAATCATCATTTGATGAATACACATTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATAATCATCATTTAATAAATACACATTTA
9154454 TAATAGGTT
66 TAATAGGTT
* * *
9154463 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATGATCGTCATTTAATAAATACATATTTA
1 TAAATCTTACTAATAATTATAATAAAAAATATTTCAATAATCATCATTTAATAAATACACATTTA
9154528 TAA
66 TAA
9154531 ATATAAGTTT
Statistics
Matches: 61, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.46, C:0.08, G:0.04, T:0.41
Consensus pattern (74 bp):
TAAATCTTACTAATAATTATAATAAAAAATATTTCAATAATCATCATTTAATAAATACACATTTA
TAATAGGTT
Found at i:9156361 original size:12 final size:12
Alignment explanation
Indices: 9156344--9156368 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9156334 TGCAAGCTAC
9156344 CGTACAGAGCGT
1 CGTACAGAGCGT
9156356 CGTACAGAGCGT
1 CGTACAGAGCGT
9156368 C
1 C
9156369 TTACCTTATG
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:0.24, C:0.28, G:0.32, T:0.16
Consensus pattern (12 bp):
CGTACAGAGCGT
Found at i:9159635 original size:22 final size:22
Alignment explanation
Indices: 9159610--9159658 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
9159600 TTTTAAGGAG
*
9159610 TTTTGGATAAAGTTGTATTAGAT
1 TTTTGG-TAAAGTTCTATTAGAT
* *
9159633 TTTTGGTAGATTTCTATTAGAT
1 TTTTGGTAAAGTTCTATTAGAT
9159655 TTTT
1 TTTT
9159659 ACTGAATTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.24, C:0.02, G:0.18, T:0.55
Consensus pattern (22 bp):
TTTTGGTAAAGTTCTATTAGAT
Found at i:9164407 original size:12 final size:12
Alignment explanation
Indices: 9164384--9164417 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
9164374 GACTTTTTCC
*
9164384 ACGACCATGATT
1 ACGACCACGATT
*
9164396 ACGACTACGATT
1 ACGACCACGATT
9164408 ACGACCACGA
1 ACGACCACGA
9164418 CCACGGCCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.35, C:0.29, G:0.18, T:0.18
Consensus pattern (12 bp):
ACGACCACGATT
Found at i:9169298 original size:22 final size:22
Alignment explanation
Indices: 9169275--9169358 Score: 71
Period size: 22 Copynumber: 3.8 Consensus size: 22
9169265 AAAATTCAAT
*
9169275 AATTTTTTATAAGAATTTTAATA
1 AATTTTTGATAA-AATTTTAATA
* * *
9169298 AATTTTTGATAAAATTATATTG
1 AATTTTTGATAAAATTTTAATA
* *
9169320 AATTTTCGATAAAATTCT-ATCA
1 AATTTTTGATAAAATTTTAAT-A
* *
9169342 GATTTTTTATAAAATTT
1 AATTTTTGATAAAATTT
9169359 CAACAAAACT
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
21 1 0.02
22 36 0.75
23 11 0.23
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.50
Consensus pattern (22 bp):
AATTTTTGATAAAATTTTAATA
Found at i:9171295 original size:23 final size:24
Alignment explanation
Indices: 9171264--9171330 Score: 84
Period size: 23 Copynumber: 2.7 Consensus size: 24
9171254 ATATTAACTT
9171264 ATTAATGATTTGTAT-AAAGTGTTG
1 ATTAATGATTTGTATGAAA-TGTTG
9171288 -TTAATGATTTGTATGAAATGTTG
1 ATTAATGATTTGTATGAAATGTTG
9171311 ATATATCATGATTTGTATGA
1 AT-TA--ATGATTTGTATGA
9171331 TTTTTAGGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
23 19 0.50
24 4 0.11
25 2 0.05
27 13 0.34
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.46
Consensus pattern (24 bp):
ATTAATGATTTGTATGAAATGTTG
Found at i:9185635 original size:15 final size:16
Alignment explanation
Indices: 9185604--9185646 Score: 54
Period size: 15 Copynumber: 2.7 Consensus size: 16
9185594 CTATTTTGTG
9185604 TTAACATTATAAAAATTA
1 TTAAC-TTAT-AAAATTA
9185622 -TAACTTATAAAATTA
1 TTAACTTATAAAATTA
9185637 TTAA-TTATAA
1 TTAACTTATAA
9185647 TAGATATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 13 0.54
16 7 0.29
17 4 0.17
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAACTTATAAAATTA
Found at i:9191711 original size:21 final size:22
Alignment explanation
Indices: 9191682--9191727 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
9191672 CTTTCTACCT
9191682 AAATCTTGATAAATTTTCAATG
1 AAATCTTGATAAATTTTCAATG
* *
9191704 AAAT-TTGATGATTTTTCAATG
1 AAATCTTGATAAATTTTCAATG
9191725 AAA
1 AAA
9191728 ATTCAATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (22 bp):
AAATCTTGATAAATTTTCAATG
Found at i:9191736 original size:22 final size:22
Alignment explanation
Indices: 9191695--9191742 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
9191685 TCTTGATAAA
**
9191695 TTTTCAATGAAATTTGATG-AT
1 TTTTCAATGAAATTCAATGAAT
9191716 TTTTCAATGAAAATTCAATGAAT
1 TTTTCAATG-AAATTCAATGAAT
9191739 TTTT
1 TTTT
9191743 TATAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 9 0.39
22 8 0.35
23 6 0.26
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (22 bp):
TTTTCAATGAAATTCAATGAAT
Found at i:9193179 original size:2 final size:2
Alignment explanation
Indices: 9193172--9193202 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9193162 GTGTTTCTAT
9193172 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
9193203 TATATATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:9195610 original size:57 final size:57
Alignment explanation
Indices: 9195522--9195639 Score: 193
Period size: 57 Copynumber: 2.1 Consensus size: 57
9195512 GCTTAATCAT
9195522 TTTAGCTTATTCTTTTTTTCAAATGGCTTTTCTTGCAGTATTGCAGATTCCTCACTC
1 TTTAGCTTATTCTTTTTTTCAAATGGCTTTTCTTGCAGTATTGCAGATTCCTCACTC
* **
9195579 TTTAGCTTATT-TCTTTTTTCAATTGGCTTTTCTTGCAGTATTGTGGATTCCTCACTC
1 TTTAGCTTATTCT-TTTTTTCAAATGGCTTTTCTTGCAGTATTGCAGATTCCTCACTC
9195636 TTTA
1 TTTA
9195640 TTAAATGCAG
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
56 1 0.02
57 56 0.98
ACGTcount: A:0.16, C:0.19, G:0.13, T:0.52
Consensus pattern (57 bp):
TTTAGCTTATTCTTTTTTTCAAATGGCTTTTCTTGCAGTATTGCAGATTCCTCACTC
Found at i:9196084 original size:19 final size:19
Alignment explanation
Indices: 9196047--9196084 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
9196037 CCATTTAACT
* *
9196047 TATTGGAGTATGATTTGAG
1 TATTGGAGTATAATCTGAG
9196066 TATTGGAGTATAATCTGAG
1 TATTGGAGTATAATCTGAG
9196085 GGTTTGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.29, T:0.39
Consensus pattern (19 bp):
TATTGGAGTATAATCTGAG
Found at i:9199781 original size:22 final size:22
Alignment explanation
Indices: 9199755--9199832 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
9199745 TATCGTCTCC
* *
9199755 CACAAACCAACATCAAGTCACT
1 CACAAACCAACAACAAATCACT
** * **
9199777 CACAAATTAGCAACAAATTTCT
1 CACAAACCAACAACAAATCACT
*
9199799 CACAAAACAACAACAAATCACT
1 CACAAACCAACAACAAATCACT
9199821 CACAAACCAACA
1 CACAAACCAACA
9199833 TCGAATTAGC
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.51, C:0.32, G:0.03, T:0.14
Consensus pattern (22 bp):
CACAAACCAACAACAAATCACT
Found at i:9200120 original size:2 final size:2
Alignment explanation
Indices: 9200115--9200139 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9200105 TCTCTCAACT
9200115 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
9200140 ATTTTCTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:9201075 original size:21 final size:20
Alignment explanation
Indices: 9201035--9201080 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
9201025 AAAACAAAAG
*
9201035 CCAGGCAAGCAGAAAGCCAA
1 CCAGCCAAGCAGAAAGCCAA
*
9201055 CCAGCCAAGCGAGAGAGCCAA
1 CCAGCCAAGC-AGAAAGCCAA
*
9201076 ACAGC
1 CCAGC
9201081 TGAAGGACCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.41, C:0.33, G:0.26, T:0.00
Consensus pattern (20 bp):
CCAGCCAAGCAGAAAGCCAA
Found at i:9201430 original size:2 final size:2
Alignment explanation
Indices: 9201423--9201489 Score: 102
Period size: 2 Copynumber: 34.0 Consensus size: 2
9201413 TGTATTCATA
9201423 AT AT AT AT -T AT AT AT AT AT AGT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT
*
9201464 NT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
9201490 TCAATATGGC
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
1 2 0.03
2 57 0.95
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9205098 original size:27 final size:29
Alignment explanation
Indices: 9205059--9205112 Score: 94
Period size: 28 Copynumber: 1.9 Consensus size: 29
9205049 ATTTACATAG
9205059 TTTTGATAAAAGAT-AAAACAATTAAAGA
1 TTTTGATAAAAGATAAAAACAATTAAAGA
9205087 TTTT-ATAAAAGATAAAAACAATTAAA
1 TTTTGATAAAAGATAAAAACAATTAAA
9205113 ATATCTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.30
Consensus pattern (29 bp):
TTTTGATAAAAGATAAAAACAATTAAAGA
Found at i:9206220 original size:27 final size:28
Alignment explanation
Indices: 9206190--9206247 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
9206180 TATAAGATGT
* *
9206190 AATAACA-TTTTGAATATAGCGTGTAAC
1 AATAACATTTTTCAATATAGCATGTAAC
9206217 AATAACATTTTTTCAATATAGCATGTAAC
1 AATAACA-TTTTTCAATATAGCATGTAAC
9206246 AA
1 AA
9206248 CTTTTTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 7 0.26
29 20 0.74
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.34
Consensus pattern (28 bp):
AATAACATTTTTCAATATAGCATGTAAC
Found at i:9206267 original size:32 final size:32
Alignment explanation
Indices: 9206224--9206287 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
9206214 AACAATAACA
* * *
9206224 TTTTTTCAATATAGCATGTAACAACTTTTTTT
1 TTTTTTAAATATAACATGTAACAACTGTTTTT
9206256 TTTTTTAAATATAACATGTAACAACTGTTTTT
1 TTTTTTAAATATAACATGTAACAACTGTTTTT
9206288 CAAAATAGTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (32 bp):
TTTTTTAAATATAACATGTAACAACTGTTTTT
Found at i:9206312 original size:26 final size:26
Alignment explanation
Indices: 9206253--9206339 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 26
9206243 AACAACTTTT
* * *
9206253 TTTTTTTTTAAATATAACATGTAACAA
1 TTTTTTTTCAAA-ATAGCGTGTAACAA
* * *
9206280 CTGTTTTTCAAAATAGTGTGTAA-ATA
1 TTTTTTTTCAAAATAGCGTGTAACA-A
* *
9206306 TTTTTTTTCAACATGGCGTGTAACAA
1 TTTTTTTTCAAAATAGCGTGTAACAA
9206332 TTTTTTTT
1 TTTTTTTT
9206340 TTCAACATGA
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
25 1 0.02
26 36 0.77
27 10 0.21
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.49
Consensus pattern (26 bp):
TTTTTTTTCAAAATAGCGTGTAACAA
Found at i:9206338 original size:28 final size:28
Alignment explanation
Indices: 9206302--9206369 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
9206292 ATAGTGTGTA
* *
9206302 AATATTTTTTTTCAACATGGCGTGTAAC
1 AATATTTTTTTTCAACATGACATGTAAC
* *
9206330 AATTTTTTTTTTCAACATGACATGTAAT
1 AATATTTTTTTTCAACATGACATGTAAC
9206358 AATATTTTTTTT
1 AATATTTTTTTT
9206370 ACAAGCACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.51
Consensus pattern (28 bp):
AATATTTTTTTTCAACATGACATGTAAC
Found at i:9206707 original size:2 final size:2
Alignment explanation
Indices: 9206688--9206739 Score: 79
Period size: 2 Copynumber: 26.5 Consensus size: 2
9206678 ATGAGGATTT
* *
9206688 TA TA TA -A TA GA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9206729 TA TA TA TA TA T
1 TA TA TA TA TA T
9206740 TATTAAAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:9212144 original size:22 final size:20
Alignment explanation
Indices: 9212094--9212146 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
9212084 GAAAATTAGA
*
9212094 CAGATTTTTGATAAAATTTT
1 CAGATTTTTGACAAAATTTT
*
9212114 AAGGAATTTTTGACAAAATTGTAT
1 CA-G-ATTTTTGACAAAATT-T-T
9212138 CAGATTTTT
1 CAGATTTTT
9212147 ACTGAATTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.04
21 1 0.04
22 20 0.77
23 2 0.08
24 2 0.08
ACGTcount: A:0.36, C:0.06, G:0.13, T:0.45
Consensus pattern (20 bp):
CAGATTTTTGACAAAATTTT
Found at i:9214778 original size:73 final size:73
Alignment explanation
Indices: 9214638--9214811 Score: 179
Period size: 73 Copynumber: 2.4 Consensus size: 73
9214628 TGCAGACAGA
* * * * * **
9214638 GAGCTCTTAATCTACTAACTTCCTTCTTAGTTGATTAAGTCAATTTTGTCTTCTGGTCTCAAATT
1 GAGCACTTAATCAACTAACTTCCTTCTTAGTCGATTAAGTCAATTCTATCTTCAAGTCTCAAATT
*
9214703 CTGGTAGT
66 CTGGCAGT
* ** * *
9214711 GAGCACTTAGTCAACTAACTTCCTTCTTAGTCGATTAAGTCGGTTCTATCTTGAAGTCT-AGATT
1 GAGCACTTAATCAACTAACTTCCTTCTTAGTCGATTAAGTCAATTCTATCTTCAAGTCTCA-AAT
9214775 TCTGGCAGT
65 TCTGGCAGT
* * * *
9214784 GGGCTCTTAATCGACTAACCTCCTTCTT
1 GAGCACTTAATCAACTAACTTCCTTCTT
9214812 GGTCAACTAA
Statistics
Matches: 82, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
72 1 0.01
73 81 0.99
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.40
Consensus pattern (73 bp):
GAGCACTTAATCAACTAACTTCCTTCTTAGTCGATTAAGTCAATTCTATCTTCAAGTCTCAAATT
CTGGCAGT
Found at i:9217688 original size:27 final size:28
Alignment explanation
Indices: 9217658--9217713 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
9217648 TTCTCTACAA
9217658 AATTACTGTT-AAAGTTATCGGAGGTTT
1 AATTACTGTTAAAAGTTATCGGAGGTTT
*
9217685 AATTACTGTTAAAAGTTATTGGAGGTTT
1 AATTACTGTTAAAAGTTATCGGAGGTTT
9217713 A
1 A
9217714 CCTAGGCTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.41
Consensus pattern (28 bp):
AATTACTGTTAAAAGTTATCGGAGGTTT
Found at i:9218116 original size:37 final size:37
Alignment explanation
Indices: 9218075--9218154 Score: 97
Period size: 37 Copynumber: 2.2 Consensus size: 37
9218065 AAATGAAACC
* **
9218075 GAGAAGGCGACTAGGCGAGAAGTCGAGAAGCTGTAGT
1 GAGAAGGCGACAAGGCGAGAAGTCGAGAAGCTACAGT
** * *
9218112 GAGAAGTTGAGAAGGTGAGAAGTCGAGAAGCTACAGT
1 GAGAAGGCGACAAGGCGAGAAGTCGAGAAGCTACAGT
9218149 GAGAAG
1 GAGAAG
9218155 TCAAGATTCT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.36, C:0.10, G:0.40, T:0.14
Consensus pattern (37 bp):
GAGAAGGCGACAAGGCGAGAAGTCGAGAAGCTACAGT
Found at i:9218117 original size:21 final size:20
Alignment explanation
Indices: 9218091--9218156 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
9218081 GCGACTAGGC
9218091 GAGAAGTCGAGAAGCTGTAGT
1 GAGAAGTCGAGAAGCTG-AGT
*
9218112 GAGAAGTTGAGAA---G-GT
1 GAGAAGTCGAGAAGCTGAGT
*
9218128 GAGAAGTCGAGAAGCTACAGT
1 GAGAAGTCGAGAAGCT-GAGT
9218149 GAGAAGTC
1 GAGAAGTC
9218157 AAGATTCTCG
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
16 14 0.38
18 1 0.03
21 22 0.59
ACGTcount: A:0.36, C:0.09, G:0.38, T:0.17
Consensus pattern (20 bp):
GAGAAGTCGAGAAGCTGAGT
Found at i:9218131 original size:16 final size:16
Alignment explanation
Indices: 9218110--9218141 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
9218100 AGAAGCTGTA
*
9218110 GTGAGAAGTTGAGAAG
1 GTGAGAAGTCGAGAAG
9218126 GTGAGAAGTCGAGAAG
1 GTGAGAAGTCGAGAAG
9218142 CTACAGTGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.44, T:0.16
Consensus pattern (16 bp):
GTGAGAAGTCGAGAAG
Found at i:9221422 original size:23 final size:23
Alignment explanation
Indices: 9221392--9221435 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
9221382 CTAAGATTGT
*
9221392 AACAAGCTACATGCCATGACTCC
1 AACAAGCTACATGCCAAGACTCC
*
9221415 AACAAGCTATATGCCAAGACT
1 AACAAGCTACATGCCAAGACT
9221436 GTTACATGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.39, C:0.30, G:0.14, T:0.18
Consensus pattern (23 bp):
AACAAGCTACATGCCAAGACTCC
Found at i:9221543 original size:23 final size:22
Alignment explanation
Indices: 9221507--9221584 Score: 84
Period size: 23 Copynumber: 3.4 Consensus size: 22
9221497 TCCATGATCA
* *
9221507 ATGTTACAAACCAAGGCTTTAAG
1 ATGTTACACACCAAGGCTTT-GG
* *
9221530 ATGTTACACGCCAAAGCTTCTGG
1 ATGTTACACACCAAGGCTT-TGG
*
9221553 ATGTTACACACCAAAGTCTTTGG
1 ATGTTACACACC-AAGGCTTTGG
9221576 ATGTTACAC
1 ATGTTACAC
9221585 CCCATGGCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
23 40 0.87
24 6 0.13
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (22 bp):
ATGTTACACACCAAGGCTTTGG
Found at i:9224712 original size:23 final size:23
Alignment explanation
Indices: 9224686--9224735 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
9224676 TGTTGGAAGC
* *
9224686 TACACTTCATGGCTTCAAGATGT
1 TACACATCATGGCTCCAAGATGT
9224709 TACACATCATGGCTCCAAGATGT
1 TACACATCATGGCTCCAAGATGT
9224732 TACA
1 TACA
9224736 AACCAAGGCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (23 bp):
TACACATCATGGCTCCAAGATGT
Done.