Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 98 of 204
Found at i:29646383 original size:20 final size:20
Alignment explanation
Indices: 29646358--29646406 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
29646348 AGGAGCAATT
*
29646358 AAATCAATTTGATTAAAATC
1 AAATCAAATTGATTAAAATC
**
29646378 AAATCAAATTGATTGGAATC
1 AAATCAAATTGATTAAAATC
*
29646398 AAATAAAAT
1 AAATCAAAT
29646407 CAGAATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.31
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATC
Found at i:29646893 original size:21 final size:21
Alignment explanation
Indices: 29646852--29646893 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29646842 ATTTTCGAAA
*
29646852 ACCACTTGACTTTATTGATTT
1 ACCACTTGACTTAATTGATTT
29646873 ACCACTTGAACTTAATT-ATTT
1 ACCACTTG-ACTTAATTGATTT
29646894 GTTCAAATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.29, C:0.19, G:0.07, T:0.45
Consensus pattern (21 bp):
ACCACTTGACTTAATTGATTT
Found at i:29648736 original size:25 final size:25
Alignment explanation
Indices: 29648706--29648812 Score: 117
Period size: 25 Copynumber: 4.3 Consensus size: 25
29648696 GGTCACCGAT
** *
29648706 TTCAGCTCTTATGAGCTTCCCGATA
1 TTCAGCTCACATGAGCTTCCCGTTA
* *
29648731 CTCAGCTCACATGAGCTTCCTGTTA
1 TTCAGCTCACATGAGCTTCCCGTTA
* *
29648756 TTCAGCTCGCATAAGCTTCCCGTTA
1 TTCAGCTCACATGAGCTTCCCGTTA
* *
29648781 TTCAGCTAATATGAGCTTCCCGTT-
1 TTCAGCTCACATGAGCTTCCCGTTA
*
29648805 TACAGCTC
1 TTCAGCTC
29648813 GTATGAGCAT
Statistics
Matches: 67, Mismatches: 15, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
24 6 0.09
25 61 0.91
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.34
Consensus pattern (25 bp):
TTCAGCTCACATGAGCTTCCCGTTA
Found at i:29648760 original size:50 final size:49
Alignment explanation
Indices: 29648705--29648820 Score: 142
Period size: 50 Copynumber: 2.3 Consensus size: 49
29648695 AGGTCACCGA
* * *
29648705 TTTCAGCTCTTATGAGCTTCCCGATACTCAGCTCACATGAGCTTCCTGT
1 TTTCAGCTCGTATGAGCTTCCCGATACTCAGCTAACATGAGCTTCCCGT
* * * * *
29648754 TATTCAGCTCGCATAAGCTTCCCGTTATTCAGCTAATATGAGCTTCCCGT
1 T-TTCAGCTCGTATGAGCTTCCCGATACTCAGCTAACATGAGCTTCCCGT
*
29648804 TTACAGCTCGTATGAGC
1 TTTCAGCTCGTATGAGC
29648821 ATACATGTAC
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
49 14 0.25
50 41 0.75
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (49 bp):
TTTCAGCTCGTATGAGCTTCCCGATACTCAGCTAACATGAGCTTCCCGT
Found at i:29661201 original size:69 final size:67
Alignment explanation
Indices: 29661041--29661270 Score: 196
Period size: 69 Copynumber: 3.3 Consensus size: 67
29661031 AGGCCGTAGC
* ** * *
29661041 CTTAAATCGACGTGCTAGGTAGATCAATTGTGATCTTAAATTAGTGAGA-TGCAAAATAGGGACA
1 CTTAAATCG-CGTGCTATGTAGATCTGTCGTGATCTTAAATTAGCG-GACTGCAAAATAGGGACA
29661105 CAAT
64 CAAT
* *
29661109 CTTAAATCTTCGTGCTATGTAGATCTGTCGTGATCTTAAATTAGCGGACTGTAAAATAAGGG-CA
1 CTTAAATC-GCGTGCTATGTAGATCTGTCGTGATCTTAAATTAGCGGACTGCAAAAT-AGGGACA
*
29661173 CGATT
64 C-AAT
* * * * * * **
29661178 TTTAAATCAGCGTGCTATGTAGAT-TAGTCATGATCTAAAATCAGCGGACTACAAAAAAAAAGAC
1 CTTAAATC-GCGTGCTATGTAGATCT-GTCGTGATCTTAAATTAGCGGACTGC-AAAATAGGGAC
*
29661242 ACTAT
63 ACAAT
*
29661247 ATTAAATCTGCGTGCTATGTAGAT
1 CTTAAATC-GCGTGCTATGTAGAT
29661271 TAGATGTGAG
Statistics
Matches: 132, Mismatches: 23, Indels: 13
0.79 0.14 0.08
Matches are distributed among these distances:
67 2 0.02
68 50 0.38
69 73 0.55
70 7 0.05
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (67 bp):
CTTAAATCGCGTGCTATGTAGATCTGTCGTGATCTTAAATTAGCGGACTGCAAAATAGGGACACA
AT
Found at i:29661288 original size:69 final size:69
Alignment explanation
Indices: 29661101--29661302 Score: 203
Period size: 69 Copynumber: 2.9 Consensus size: 69
29661091 GCAAAATAGG
* * * **
29661101 GACACAATCTTAAATCTTCGTGCTATGTAGATCT-GTCGTGATCTTAAATTAGCGGACT-GTAAA
1 GACACAATATTAAATCTGCGTGCTATGTAGAT-TAGTCGTGATCTTAAATCAGCGGACTACAAAA
* *
29661164 ATAAG
65 AAAAA
* * * * * *
29661169 GGCACGATTTTTAAATCAGCGTGCTATGTAGATTAGTCATGATCTAAAATCAGCGGACTACAAAA
1 GACAC-AATATTAAATCTGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAGCGGACTACAAAA
29661234 AAAAA
65 AAAAA
* * **
29661239 GACACTATATTAAATCTGCGTGCTATGTAGATTAGAT-GTGAGCTTAAATCAGCGGGTTACAAAA
1 GACACAATATTAAATCTGCGTGCTATGTAGATTAG-TCGTGATCTTAAATCAGCGGACTACAAAA
29661303 TAGGGAAGCG
Statistics
Matches: 108, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
68 5 0.05
69 92 0.85
70 11 0.10
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (69 bp):
GACACAATATTAAATCTGCGTGCTATGTAGATTAGTCGTGATCTTAAATCAGCGGACTACAAAAA
AAAA
Found at i:29667618 original size:21 final size:21
Alignment explanation
Indices: 29667588--29667628 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
29667578 CCAGTTTATA
29667588 TCCTGCACA-TTCGAGTGCAAT
1 TCCTGCACATTTCGA-TGCAAT
*
29667609 TCCTGGACATTTCGATGCAA
1 TCCTGCACATTTCGATGCAA
29667629 GGCATCCACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (21 bp):
TCCTGCACATTTCGATGCAAT
Found at i:29669205 original size:82 final size:80
Alignment explanation
Indices: 29669066--29669215 Score: 192
Period size: 82 Copynumber: 1.9 Consensus size: 80
29669056 AATCATCCAC
* * * ** *
29669066 ATCTATACTACTATATAAAAGATAGGCCTAAGGCCTTCCTTAAAAGATATTTTTCCATTCTTTTC
1 ATCTATACTACCATATAAAAGATAGCCCTAAGGCCTTCCTAAAAAGATACATGTCCATTCTTTTC
29669131 TTTTGCATCAAAAAA
66 TTTTGCATCAAAAAA
* * * *
29669146 ATCTATACTTACCGTATAAAAGTTAAGCCCTAGGGCCTTCGTAAAAAGATACATGTCCATTCTTT
1 ATCTATAC-TACCATATAAAAGAT-AGCCCTAAGGCCTTCCTAAAAAGATACATGTCCATTCTTT
29669211 TCTTT
64 TCTTT
29669216 CACATGAGAA
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 8 0.14
81 12 0.21
82 38 0.66
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (80 bp):
ATCTATACTACCATATAAAAGATAGCCCTAAGGCCTTCCTAAAAAGATACATGTCCATTCTTTTC
TTTTGCATCAAAAAA
Found at i:29671716 original size:25 final size:25
Alignment explanation
Indices: 29671685--29671746 Score: 81
Period size: 25 Copynumber: 2.5 Consensus size: 25
29671675 ATCTTAGTGC
* * *
29671685 GCTCTCTAATTATTAGCACGT-TAGT
1 GCTCTCTGATTATTAACAC-TCCAGT
29671710 GCTCTCTGATTATTAACACTCCAGT
1 GCTCTCTGATTATTAACACTCCAGT
29671735 GCTCTCTGATTA
1 GCTCTCTGATTA
29671747 GCACATTTGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 1 0.03
25 32 0.97
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.39
Consensus pattern (25 bp):
GCTCTCTGATTATTAACACTCCAGT
Found at i:29674841 original size:17 final size:17
Alignment explanation
Indices: 29674799--29674841 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
29674789 ATGGAATTAG
* *
29674799 AATTAGATTGAGAAAAT
1 AATTAAATTGAAAAAAT
* *
29674816 GATTGAATTGAAAAAAT
1 AATTAAATTGAAAAAAT
29674833 AATTAAATT
1 AATTAAATT
29674842 AAATTAAATC
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.33
Consensus pattern (17 bp):
AATTAAATTGAAAAAAT
Found at i:29686862 original size:174 final size:179
Alignment explanation
Indices: 29686550--29686869 Score: 470
Period size: 174 Copynumber: 1.8 Consensus size: 179
29686540 GTATCACTAG
* * * * * *
29686550 TTATGCCTTTTTAGGCCTCTTAAATCTGTCAACTGCTTGTACTTCTTTCAATTTTTCTTGTATTG
1 TTATGCCTTTCTAGGCCTCTCAAATATATCAACTGCTTCTACTTCTTTCAATTTTTCTTATATTG
* * * *
29686615 GGACTTTGCTGCATTTGGCTTGTCTGTCTGTATAATTAGAATGACTAGTGATTACTTTAGACGGT
66 AGACTTTGCTGCATTTGGCTTATCTCTCTGTATAATTAGAATGACTAGTGATTACTTTAGACGGA
*
29686680 TTGATGATTCATCATTGATATGATATGTCTTTAATTATTTTAGTCTGTA
131 TGGATGATTCATCATTGATATGATATGTCTTTAATTATTTTAGTCTGTA
*
29686729 TTATGCCTTTCTAGGCCTCTCAAATATATCAATTGCTTCTAC-T-TTTCAA-TTTTCTTATATTG
1 TTATGCCTTTCTAGGCCTCTCAAATATATCAACTGCTTCTACTTCTTTCAATTTTTCTTATATTG
* * *
29686791 AGACTTTGCTGCATTTGGCTTATTTCTTTGTAT-A-TAGAATGACTAGTGATTACTTTTGACGGA
66 AGACTTTGCTGCATTTGGCTTATCTCTCTGTATAATTAGAATGACTAGTGATTACTTTAGACGGA
29686854 TGGATGATTCATCATT
131 TGGATGATTCATCATT
29686870 ATTTATATGA
Statistics
Matches: 126, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
174 42 0.33
175 1 0.01
176 40 0.32
177 6 0.05
178 1 0.01
179 36 0.29
ACGTcount: A:0.22, C:0.15, G:0.16, T:0.46
Consensus pattern (179 bp):
TTATGCCTTTCTAGGCCTCTCAAATATATCAACTGCTTCTACTTCTTTCAATTTTTCTTATATTG
AGACTTTGCTGCATTTGGCTTATCTCTCTGTATAATTAGAATGACTAGTGATTACTTTAGACGGA
TGGATGATTCATCATTGATATGATATGTCTTTAATTATTTTAGTCTGTA
Found at i:29702476 original size:28 final size:28
Alignment explanation
Indices: 29702428--29702482 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
29702418 CAACACCCAT
29702428 TTTACTATTTTTTTATTAAAATTTAATC
1 TTTACTATTTTTTTATTAAAATTTAATC
29702456 TTTA-TATTTTTATT-TTCAAAATTTAAT
1 TTTACTATTTTT-TTATT-AAAATTTAAT
29702483 TCCTCTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.36
28 16 0.64
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (28 bp):
TTTACTATTTTTTTATTAAAATTTAATC
Found at i:29703138 original size:2 final size:2
Alignment explanation
Indices: 29703131--29703165 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
29703121 TTAGTATAGA
*
29703131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29703166 AGATAAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:29711957 original size:18 final size:18
Alignment explanation
Indices: 29711934--29711968 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
29711924 CATTAGACCA
29711934 TTTAAATAGTTAGTGGAG
1 TTTAAATAGTTAGTGGAG
29711952 TTTAAATAGTTAGTGGA
1 TTTAAATAGTTAGTGGA
29711969 CTTTTATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.34, C:0.00, G:0.26, T:0.40
Consensus pattern (18 bp):
TTTAAATAGTTAGTGGAG
Found at i:29717187 original size:15 final size:16
Alignment explanation
Indices: 29717167--29717196 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29717157 TGGTGCCTTG
29717167 TTGAT-ATGTGTTAAT
1 TTGATAATGTGTTAAT
29717182 TTGATAATGTGTTAA
1 TTGATAATGTGTTAA
29717197 AGCATGTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (16 bp):
TTGATAATGTGTTAAT
Found at i:29720048 original size:18 final size:17
Alignment explanation
Indices: 29720016--29720075 Score: 56
Period size: 17 Copynumber: 3.7 Consensus size: 17
29720006 ATAATATTAT
29720016 TTTAATATTAAATTAAA
1 TTTAATATTAAATTAAA
*
29720033 TTTAATACTTATATT-AA
1 TTTAATA-TTAAATTAAA
**
29720050 --TAATATTTTATT-AA
1 TTTAATATTAAATTAAA
29720064 TTTAATATTAAA
1 TTTAATATTAAA
29720076 GTGATTATCT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
14 8 0.22
15 5 0.14
16 8 0.22
17 9 0.25
18 6 0.17
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (17 bp):
TTTAATATTAAATTAAA
Found at i:29720199 original size:58 final size:61
Alignment explanation
Indices: 29720085--29720200 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 61
29720075 AGTGATTATC
*
29720085 TTAATATTAAATTTTATTCAATATTTACCTTGTAGATAAATATTATATTAATTTAATAGAT
1 TTAATATTAAATTTAATTCAATATTTACCTTGTAGATAAATATTATATTAATTTAATAGAT
* *
29720146 TTAATATTAAATTTAA-TCTAATATTTATC-T-T-GATAAGTATTATATTAATTTAATA
1 TTAATATTAAATTTAATTC-AATATTTACCTTGTAGATAAATATTATATTAATTTAATA
29720201 TTAAAGTGAT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
58 23 0.45
59 1 0.02
60 3 0.06
61 24 0.47
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (61 bp):
TTAATATTAAATTTAATTCAATATTTACCTTGTAGATAAATATTATATTAATTTAATAGAT
Found at i:29721939 original size:46 final size:46
Alignment explanation
Indices: 29721872--29722056 Score: 264
Period size: 46 Copynumber: 4.0 Consensus size: 46
29721862 CATGGCAAAG
**
29721872 TGTGAAACTTAGGTATGGTATTCCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTCCAGTGAAGAAAACCATACTGAGT
* * *
29721918 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGCGT
1 TGTGAAAAGTAGGTATGGTATTCCAGTGAAGAAAACCATACTGAGT
* * * * *
29721964 TGTGAAAAGTAGGTATGGTGTTTCGGTAAAGAAAATCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTCCAGTGAAGAAAACCATACTGAGT
29722010 TGTGAAAAGTAGGTATGGTATTTCC-GTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTA-TTCCAGTGAAGAAAACCATACTGAGT
29722056 T
1 T
29722057 ATAGCCTTGT
Statistics
Matches: 123, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
46 120 0.98
47 3 0.02
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTCCAGTGAAGAAAACCATACTGAGT
Found at i:29728741 original size:21 final size:21
Alignment explanation
Indices: 29728712--29728756 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
29728702 GATGTATAGG
29728712 AAAAGTAAT-AAAAAATAAGA
1 AAAAGTAATCAAAAAATAAGA
*
29728732 AAAAGGTAATGCAAAAGATAAGA
1 AAAA-GTAAT-CAAAAAATAAGA
29728755 AA
1 AA
29728757 CTTTTTTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 5 0.24
23 12 0.57
ACGTcount: A:0.69, C:0.02, G:0.16, T:0.13
Consensus pattern (21 bp):
AAAAGTAATCAAAAAATAAGA
Found at i:29735569 original size:48 final size:48
Alignment explanation
Indices: 29735487--29735671 Score: 244
Period size: 48 Copynumber: 3.9 Consensus size: 48
29735477 AATAGATTTC
* * * * * * *
29735487 TCGGTGGCCTGCACACAGTTCGTACCAGCTTTGTATAATACCAGATTC
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGATTA
* * * *
29735535 TCGGTGGCCTGCACATAGTCTGTGCCACCCTTGTATCTTAACAGGTTA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGATTA
* *
29735583 TTGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGAATA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGATTA
*
29735631 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTGTCATAA
1 TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAA
29735672 TAGAATATTG
Statistics
Matches: 118, Mismatches: 19, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 118 1.00
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (48 bp):
TCGGTGGCCTGCACACAGTCCGTGCCACCCTTGTATCATAACAGATTA
Found at i:29742460 original size:3 final size:3
Alignment explanation
Indices: 29742454--29742480 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
29742444 CATCATCATC
29742454 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
29742481 TGGTTAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:29742616 original size:13 final size:14
Alignment explanation
Indices: 29742586--29742620 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
29742576 TGTTTTATTG
*
29742586 AAAATGGTTTTTGA
1 AAAATGATTTTTGA
*
29742600 AAAATGATTTTTAA
1 AAAATGATTTTTGA
29742614 AAAATGA
1 AAAATGA
29742621 CTTACTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (14 bp):
AAAATGATTTTTGA
Found at i:29742843 original size:21 final size:20
Alignment explanation
Indices: 29742791--29742859 Score: 61
Period size: 21 Copynumber: 3.5 Consensus size: 20
29742781 TTATTTCATA
29742791 AATCTT-ATTATATTTTAATT
1 AATCTTAATT-TATTTTAATT
* **
29742811 AATCATGTTTTAGTTTTAATT
1 AATCTTAATTTA-TTTTAATT
*
29742832 AATCTTAATTTA-CTTAATT
1 AATCTTAATTTATTTTAATT
*
29742851 AAGCTTAAT
1 AATCTTAAT
29742860 CATTAATTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
19 14 0.35
20 7 0.17
21 19 0.47
ACGTcount: A:0.35, C:0.07, G:0.04, T:0.54
Consensus pattern (20 bp):
AATCTTAATTTATTTTAATT
Found at i:29744761 original size:49 final size:49
Alignment explanation
Indices: 29744688--29744784 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
29744678 TCTAGAAGGG
* * *
29744688 ATAAATAGTGATAAGAGTGTAGACAGTGGAAGACTAAGTTTAGCAATGT
1 ATAAATAGTGATAAGAGTGCAGACAGTGGAAGACCAAGTTTAGAAATGT
29744737 ATAAATAGTGATAAGAGTGCAGACAGTGGAAGACCAAGTTTAGAAATG
1 ATAAATAGTGATAAGAGTGCAGACAGTGGAAGACCAAGTTTAGAAATG
29744785 CATAGCATAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.42, C:0.07, G:0.27, T:0.24
Consensus pattern (49 bp):
ATAAATAGTGATAAGAGTGCAGACAGTGGAAGACCAAGTTTAGAAATGT
Found at i:29767987 original size:21 final size:21
Alignment explanation
Indices: 29767948--29767999 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
29767938 GGTCTACAAA
29767948 CCCGTGTGGAAAGAGACACACG
1 CCCGTGT-GAAAGAGACACACG
**
29767970 CCCGTGTGAAAGTTACACACG
1 CCCGTGTGAAAGAGACACACG
* *
29767991 ACAGTGTGA
1 CCCGTGTGA
29768000 TCGAGTTACA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
21 19 0.73
22 7 0.27
ACGTcount: A:0.31, C:0.25, G:0.29, T:0.15
Consensus pattern (21 bp):
CCCGTGTGAAAGAGACACACG
Found at i:29768117 original size:21 final size:21
Alignment explanation
Indices: 29768093--29768147 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
29768083 TAGGAAACTC
29768093 ACACGTCTGTGTGGCT-AAGGA
1 ACACGTC-GTGTGGCTCAAGGA
*
29768114 ACACGGTCGTGT-GCTCAAGGC
1 ACAC-GTCGTGTGGCTCAAGGA
29768135 ACACGTCCGTGTG
1 ACACGT-CGTGTG
29768148 AAAATTGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
20 5 0.17
21 21 0.72
22 3 0.10
ACGTcount: A:0.20, C:0.25, G:0.33, T:0.22
Consensus pattern (21 bp):
ACACGTCGTGTGGCTCAAGGA
Found at i:29773364 original size:15 final size:16
Alignment explanation
Indices: 29773336--29773365 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
29773326 TTTATTACAT
29773336 TTGCATTTATGTTAAC
1 TTGCATTTATGTTAAC
29773352 TTGCATTTA-GTTAA
1 TTGCATTTATGTTAA
29773366 TTAATTTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.10, G:0.13, T:0.50
Consensus pattern (16 bp):
TTGCATTTATGTTAAC
Found at i:29787521 original size:47 final size:47
Alignment explanation
Indices: 29787452--29787544 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
29787442 GGTTCGGCCC
29787452 CAATTGCCTACTCCACTACCTTAGCTTTCCACAACTAAATATTTTCT
1 CAATTGCCTACTCCACTACCTTAGCTTTCCACAACTAAATATTTTCT
*
29787499 CAATTGCCTACTCCACTACCTTAGCTTTCCACAACTAGATATTTTC
1 CAATTGCCTACTCCACTACCTTAGCTTTCCACAACTAAATATTTTC
29787545 CCAAATTCAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.27, C:0.32, G:0.05, T:0.35
Consensus pattern (47 bp):
CAATTGCCTACTCCACTACCTTAGCTTTCCACAACTAAATATTTTCT
Found at i:29790782 original size:12 final size:13
Alignment explanation
Indices: 29790749--29790793 Score: 51
Period size: 12 Copynumber: 3.6 Consensus size: 13
29790739 TAAATATAAT
29790749 TAAAATTTA-TAA
1 TAAAATTTATTAA
29790761 TAAAA-TTATTAA
1 TAAAATTTATTAA
29790773 -AAAATTTATTAGA
1 TAAAATTTATTA-A
*
29790786 TATAATTT
1 TAAAATTT
29790794 TATGCACTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
11 7 0.25
12 14 0.50
13 1 0.04
14 6 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (13 bp):
TAAAATTTATTAA
Found at i:29791838 original size:19 final size:20
Alignment explanation
Indices: 29791785--29791839 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 20
29791775 TGATATAGAT
29791785 TAAAAAT-A-AATATTTCACA
1 TAAAAATAATAATATTT-ACA
* *
29791804 TATAAA-AATTATATTTAC-
1 TAAAAATAATAATATTTACA
29791822 TAAAAATAATAATATTTA
1 TAAAAATAATAATATTTA
29791840 TAATATTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
18 5 0.17
19 18 0.62
20 6 0.21
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAAAATAATAATATTTACA
Found at i:29796111 original size:21 final size:20
Alignment explanation
Indices: 29796087--29796146 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
29796077 ATTGTTATTT
29796087 TCTTAACAATAAAATTTAAAA
1 TCTTAA-AATAAAATTTAAAA
* *
29796108 TCTTAAAGTAAAATTTGAAA
1 TCTTAAAATAAAATTTAAAA
* * *
29796128 TGTTTAGAT-AAATTTAAAA
1 TCTTAAAATAAAATTTAAAA
29796147 AATTTACATA
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
19 9 0.28
20 17 0.53
21 6 0.19
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.37
Consensus pattern (20 bp):
TCTTAAAATAAAATTTAAAA
Found at i:29800837 original size:18 final size:18
Alignment explanation
Indices: 29800811--29800858 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
29800801 ACTAAACTCA
* **
29800811 AACCAAACCCAAGTATTC
1 AACCCAACCCAAGTACCC
* *
29800829 AACCCAACCTAATTACCC
1 AACCCAACCCAAGTACCC
29800847 AACCCAACCCAA
1 AACCCAACCCAA
29800859 TCATAAAAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.44, C:0.42, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAACCCAAGTACCC
Found at i:29800976 original size:9 final size:9
Alignment explanation
Indices: 29800962--29801016 Score: 74
Period size: 9 Copynumber: 6.1 Consensus size: 9
29800952 GTAGTGATTC
29800962 AATTCGGTT
1 AATTCGGTT
*
29800971 AATTCGGGT
1 AATTCGGTT
29800980 AATTCGGTT
1 AATTCGGTT
*
29800989 AATTCGGGT
1 AATTCGGTT
*
29800998 AATTAGGTT
1 AATTCGGTT
*
29801007 AATTCAGTT
1 AATTCGGTT
29801016 A
1 A
29801017 TTTTTAACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.27, C:0.09, G:0.24, T:0.40
Consensus pattern (9 bp):
AATTCGGTT
Found at i:29800985 original size:18 final size:18
Alignment explanation
Indices: 29800962--29801011 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
29800952 GTAGTGATTC
29800962 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
29800980 AATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGGT
*
29800998 AATTAGGTTAATTC
1 AATTCGGTTAATTC
29801012 AGTTATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.26, C:0.10, G:0.24, T:0.40
Consensus pattern (18 bp):
AATTCGGTTAATTCGGGT
Found at i:29807046 original size:18 final size:18
Alignment explanation
Indices: 29807023--29807059 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
29807013 TACCGAGGAG
29807023 ACTACTTCAAACCGTATA
1 ACTACTTCAAACCGTATA
29807041 ACTACTTCAAACCGTATA
1 ACTACTTCAAACCGTATA
29807059 A
1 A
29807060 TGATTTCTGA
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:0.41, C:0.27, G:0.05, T:0.27
Consensus pattern (18 bp):
ACTACTTCAAACCGTATA
Found at i:29819326 original size:29 final size:28
Alignment explanation
Indices: 29819276--29819348 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
29819266 TAGAGTCTCG
*
29819276 CCACAAAGG-TGTCCTTT-AAGAGGTTTA
1 CCACAAAGGTTGT-CTTTCTAGAGGTTTA
** * *
29819303 CCATGAAGGCTTGTCTTTCTAGAGTTTTG
1 CCACAAAGG-TTGTCTTTCTAGAGGTTTA
29819332 CCACAAAGGTTGTCTTT
1 CCACAAAGGTTGTCTTT
29819349 TTACAAGTGT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
27 7 0.19
28 12 0.33
29 17 0.47
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.36
Consensus pattern (28 bp):
CCACAAAGGTTGTCTTTCTAGAGGTTTA
Found at i:29820999 original size:25 final size:23
Alignment explanation
Indices: 29820971--29821037 Score: 62
Period size: 25 Copynumber: 2.7 Consensus size: 23
29820961 TAAAATTGAA
*
29820971 AAAAATAAAAGAATTACTTAAAATT
1 AAAAATAAAA-AATTA-TTAAAACT
*
29820996 AAAAACTAGAAAATTATTAAAACT
1 AAAAA-TAAAAAATTATTAAAACT
*
29821020 AGAAAATTATAAAATTAT
1 A-AAAA-TAAAAAATTAT
29821038 AGAAAAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
24 8 0.22
25 24 0.67
26 4 0.11
ACGTcount: A:0.63, C:0.04, G:0.04, T:0.28
Consensus pattern (23 bp):
AAAAATAAAAAATTATTAAAACT
Found at i:29821019 original size:17 final size:16
Alignment explanation
Indices: 29820990--29821033 Score: 72
Period size: 17 Copynumber: 2.8 Consensus size: 16
29820980 AGAATTACTT
29820990 AAAATTA-AAAACTAG
1 AAAATTATAAAACTAG
29821005 AAAATTATTAAAACTAG
1 AAAATTA-TAAAACTAG
29821022 AAAATTATAAAA
1 AAAATTATAAAA
29821034 TTATAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.26
16 5 0.19
17 15 0.56
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.25
Consensus pattern (16 bp):
AAAATTATAAAACTAG
Found at i:29821309 original size:15 final size:15
Alignment explanation
Indices: 29821272--29821309 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
29821262 ATTATTTTTT
29821272 ATTATTTAAATAATA
1 ATTATTTAAATAATA
29821287 ATTTATTTGAAATAA-A
1 A-TTATTT-AAATAATA
29821303 ATTATTT
1 ATTATTT
29821310 TTTATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 7 0.33
16 8 0.38
17 6 0.29
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (15 bp):
ATTATTTAAATAATA
Found at i:29821476 original size:17 final size:17
Alignment explanation
Indices: 29821443--29821476 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29821433 ATGTGATTTA
*
29821443 TAAAATTTTTAAAATAT
1 TAAAATTTCTAAAATAT
*
29821460 TAAAATTTCTAATATAT
1 TAAAATTTCTAAAATAT
29821477 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TAAAATTTCTAAAATAT
Found at i:29821503 original size:23 final size:22
Alignment explanation
Indices: 29821453--29821503 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
29821443 TAAAATTTTT
29821453 AAAATA-TTAAAATTTCTAATA
1 AAAATATTTAAAATTTCTAATA
* * *
29821474 TATATATTTAAAATTTTTAAATA
1 AAAATATTTAAAATTTCT-AATA
29821497 AAAATAT
1 AAAATAT
29821504 AATTTTCTCT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 4 0.17
22 10 0.43
23 9 0.39
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAATATTTAAAATTTCTAATA
Found at i:29821864 original size:94 final size:89
Alignment explanation
Indices: 29821603--29821922 Score: 361
Period size: 88 Copynumber: 3.6 Consensus size: 89
29821593 AAAAACTCTC
* * *
29821603 AAACTTTTTCAAAAAAAGTAATTAAGCCC-CTGC--TTTTTTGCACTCAATTGGATACTTAAACT
1 AAACTTTTTCAAAAATAGAAATTAAGCCCTCTTCTTTTTTTTGCACTCAATTGGATACTTAAACT
*
29821665 TTCAAAATGCATCAAAAAGGCCTT
66 TTCAAAATGCATCAAAAAGGCCAT
*
29821689 AAACTTTTTCAAAAATAGAAATTAAG-CCTCTTCTTTTTTTCGCACTCAATTGGATACTTAAACT
1 AAACTTTTTCAAAAATAGAAATTAAGCCCTCTTCTTTTTTTTGCACTCAATTGGATACTTAAACT
*
29821753 TTCAAAATGCATCAAAAAGGCCCT
66 TTCAAAATGCATCAAAAAGGCCAT
* * *
29821777 AAACTTTTTCAAAAATAGAAATTAAGCCTCTGCTCTCTTTTTTTTTTACACTTAATTGGGTACTT
1 AAACTTTTTCAAAAATAGAAATTAAGCC-CT-CT-TC--TTTTTTTTGCACTCAATTGGATACTT
* * **
29821842 GAA-TTGCCAAAATGCAT-AAAAAAACCAT
61 AAACTT-TCAAAATGCATCAAAAAGGCCAT
* *
29821870 CAAAC-TTTTCAAAAA-AGCAATTAAGCCC-CTAATTTTTTTTTTGCACTCAATTG
1 -AAACTTTTTCAAAAATAGAAATTAAGCCCTCT--TCTTTTTTTTGCACTCAATTG
29821923 CCAAAATGCA
Statistics
Matches: 203, Mismatches: 19, Indels: 22
0.83 0.08 0.09
Matches are distributed among these distances:
85 2 0.01
86 27 0.13
88 94 0.46
89 3 0.01
90 3 0.01
91 3 0.01
92 13 0.06
93 20 0.10
94 38 0.19
ACGTcount: A:0.36, C:0.19, G:0.09, T:0.35
Consensus pattern (89 bp):
AAACTTTTTCAAAAATAGAAATTAAGCCCTCTTCTTTTTTTTGCACTCAATTGGATACTTAAACT
TTCAAAATGCATCAAAAAGGCCAT
Found at i:29822120 original size:30 final size:30
Alignment explanation
Indices: 29822070--29822142 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
29822060 AAAGATCAAT
*
29822070 AAAAGTTATAAAAATTATTAAATTTTAATA
1 AAAAGTTATAAAAATAATTAAATTTTAATA
* *
29822100 AAAAG-TATAAGAAATAATTAATTTTTATTA
1 AAAAGTTATAA-AAATAATTAAATTTTAATA
*
29822130 AAAA-TTAGAAAAA
1 AAAAGTTATAAAAA
29822143 GATTATAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 8 0.22
30 29 0.78
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (30 bp):
AAAAGTTATAAAAATAATTAAATTTTAATA
Found at i:29822195 original size:21 final size:21
Alignment explanation
Indices: 29822154--29822196 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
29822144 ATTATAAAAC
* * *
29822154 ATAAAAATGTAAAATTTTATA
1 ATAAAAAGGTAAAAATATATA
29822175 ATAAAAAGGTAAAAATATATA
1 ATAAAAAGGTAAAAATATATA
29822196 A
1 A
29822197 AATATATAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (21 bp):
ATAAAAAGGTAAAAATATATA
Found at i:29822274 original size:19 final size:21
Alignment explanation
Indices: 29822252--29822297 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
29822242 TAAGAAAATG
29822252 ATAAAAAAT-AT-AAAGAATT
1 ATAAAAAATCATAAAAGAATT
*
29822271 AT-AAAATTCATAAAAGAATT
1 ATAAAAAATCATAAAAGAATT
29822291 ATAAAAA
1 ATAAAAA
29822298 TTATCATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 5 0.22
19 4 0.17
20 10 0.43
21 4 0.17
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.26
Consensus pattern (21 bp):
ATAAAAAATCATAAAAGAATT
Found at i:29822299 original size:9 final size:9
Alignment explanation
Indices: 29822246--29822301 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
29822236 AAGTCGTAAG
*
29822246 AAAATGATA
1 AAAATTATA
*
29822255 AAAAATATA
1 AAAATTATA
29822264 AAGAATTAT-
1 AA-AATTATA
29822273 AAAATTCATAA
1 AAAATT-AT-A
29822284 AAGAATTATA
1 AA-AATTATA
29822294 AAAATTAT
1 AAAATTAT
29822302 CATATCATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
8 4 0.10
9 19 0.49
10 8 0.21
11 4 0.10
12 4 0.10
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.29
Consensus pattern (9 bp):
AAAATTATA
Found at i:29822334 original size:11 final size:11
Alignment explanation
Indices: 29822318--29822347 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
29822308 ATAAGAAGCA
29822318 TTTTATAATTT
1 TTTTATAATTT
29822329 TTTTATAATTT
1 TTTTATAATTT
*
29822340 TTCTATAA
1 TTTTATAA
29822348 CTTCTATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTTATAATTT
Found at i:29822503 original size:10 final size:10
Alignment explanation
Indices: 29822490--29822541 Score: 52
Period size: 10 Copynumber: 5.2 Consensus size: 10
29822480 TTTTGATGTA
29822490 TTTTATAATT
1 TTTTATAATT
*
29822500 TTTTATGA-T
1 TTTTATAATT
**
29822509 TTTTATAAAA
1 TTTTATAATT
*
29822519 TTTTAGAATT
1 TTTTATAATT
29822529 TTTTATATATT
1 TTTTATA-ATT
29822540 TT
1 TT
29822542 ACAATTTATA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
9 8 0.24
10 20 0.61
11 5 0.15
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (10 bp):
TTTTATAATT
Found at i:29822521 original size:29 final size:28
Alignment explanation
Indices: 29822489--29822628 Score: 112
Period size: 29 Copynumber: 5.0 Consensus size: 28
29822479 TTTTTGATGT
29822489 ATTTTATAATTTTTTATGATTTTTATAAA
1 ATTTTATAATTTTTTAT-ATTTTTATAAA
* * *
29822518 ATTTTAGAATTTTTTATATATTT-TACA
1 ATTTTATAATTTTTTATATTTTTATAAA
29822545 A-TTTATATATTTTTCTA-ATTTTTAGT-AA
1 ATTTTATA-ATTTTT-TATATTTTTA-TAAA
* *
29822573 ATTTTAAATATTCTTTTATATTTTTGTTAAA
1 ATTTTATA-ATT-TTTTATATTTTT-ATAAA
* *
29822604 GTTTAATAA-TTTTTAT-TTTTTATAA
1 ATTTTATAATTTTTTATATTTTTATAA
29822629 TTTTTGTCAC
Statistics
Matches: 90, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
26 8 0.09
27 20 0.22
28 15 0.17
29 29 0.32
30 11 0.12
31 7 0.08
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (28 bp):
ATTTTATAATTTTTTATATTTTTATAAA
Found at i:29822529 original size:19 final size:20
Alignment explanation
Indices: 29822507--29822554 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
29822497 ATTTTTTATG
*
29822507 ATTTTTATA-AAATTTTAGA
1 ATTTTTATATAAATTTTACA
*
29822526 ATTTTT-TATATATTTTACA
1 ATTTTTATATAAATTTTACA
*
29822545 ATTTATATAT
1 ATTTTTATAT
29822555 TTTTCTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 2 0.08
19 19 0.79
20 3 0.12
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (20 bp):
ATTTTTATATAAATTTTACA
Found at i:29822575 original size:55 final size:55
Alignment explanation
Indices: 29822491--29822597 Score: 132
Period size: 55 Copynumber: 1.9 Consensus size: 55
29822481 TTTGATGTAT
*
29822491 TTTATAATTTTTTATGATTTTTATAAAATTTTAGA-ATT-TTTTATATATTTTACAA
1 TTTATAATTTTTTA-GATTTTTATAAAATTTTAAATATTCTTTTATAT-TTTTACAA
29822546 TTTATATATTTTTCTA-ATTTTTAGT-AAATTTTAAATATTCTTTTATATTTTT
1 TTTATA-ATTTTT-TAGATTTTTA-TAAAATTTTAAATATTCTTTTATATTTTT
29822598 GTTAAAGTTT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
55 22 0.48
56 14 0.30
57 10 0.22
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (55 bp):
TTTATAATTTTTTAGATTTTTATAAAATTTTAAATATTCTTTTATATTTTTACAA
Found at i:29822866 original size:89 final size:87
Alignment explanation
Indices: 29822755--29822997 Score: 238
Period size: 89 Copynumber: 2.7 Consensus size: 87
29822745 TGCATTTTTG
* * * * *
29822755 CCAATTGAGTACAAAAAGAGCAGGGGCTTAATTGCTTGTTTTGAAAAATTTTGAGGGTATTTTTG
1 CCAATTGACTGCAAAAAAAGCAGGGGCTTAATTGCTT-TTTTAAAAAATTTTGAGGGCATTTTTG
* *
29822820 ATGCATTTTGACAGTTCAAGTAC
65 ATGCATTTTGAAACTTCAAGTAC
**** * *
29822843 CCAATTGACTAAG-AAAAAAAGCAGGGGCTTAATTGCTTTTTTTTTTAATGTTTGAAGGCCTTTT
1 CCAATTGACT--GCAAAAAAAGCAGGGGCTTAATTGCTTTTTTAAAAAAT-TTTGAGGGCATTTT
*
29822907 TGATGCATTTTGAAACTTCAAGTGC
63 TGATGCATTTTGAAACTTCAAGTAC
* * * *
29822932 CTAATTGAGTGCAAAAAAAGGGAGGGGGGCTTAATTGCTTTTTTAAAAAAAGTTTGAGGGC-TTT
1 CCAATTGACTGCAAAAAAA-GCA--GGGGCTTAATTGCTTTTTT-AAAAAATTTTGAGGGCATTT
29822996 TT
62 TT
29822998 ACACTCTTAA
Statistics
Matches: 125, Mismatches: 22, Indels: 14
0.78 0.14 0.09
Matches are distributed among these distances:
87 1 0.01
88 23 0.18
89 67 0.54
90 5 0.04
91 27 0.22
92 2 0.02
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (87 bp):
CCAATTGACTGCAAAAAAAGCAGGGGCTTAATTGCTTTTTTAAAAAATTTTGAGGGCATTTTTGA
TGCATTTTGAAACTTCAAGTAC
Found at i:29823066 original size:18 final size:17
Alignment explanation
Indices: 29823021--29823066 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 17
29823011 TTTTAAAATA
29823021 ATTTTTAGAATTTTTTAT
1 ATTTTTA-AATTTTTTAT
*
29823039 TTTTTGTAAATTTTATTAT
1 ATTTT-TAAATTTT-TTAT
29823058 ATTTTTAAA
1 ATTTTTAAA
29823067 ATATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
ATTTTTAAATTTTTTAT
Found at i:29823068 original size:19 final size:18
Alignment explanation
Indices: 29823021--29823075 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 18
29823011 TTTTAAAATA
*
29823021 ATTTTTAGAATTTTTTAT
1 ATTTTTAAAATTTTTTAT
*
29823039 -TTTTTGTAAATTTTATTAT
1 ATTTTT-AAAATTTT-TTAT
29823058 ATTTTTAAAATATTTTTA
1 ATTTTTAAAAT-TTTTTA
29823076 ATGGTTTTTC
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
17 5 0.17
18 6 0.20
19 11 0.37
20 8 0.27
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (18 bp):
ATTTTTAAAATTTTTTAT
Found at i:29825133 original size:46 final size:46
Alignment explanation
Indices: 29824927--29825183 Score: 256
Period size: 46 Copynumber: 5.6 Consensus size: 46
29824917 GATCAGAGGG
* * * * * *
29824927 TGCCATGGTGTCTTTCAA-TCATGGTCTTATTTATTCT-CGACTTGA
1 TGCCATAGTGTCTTTCAACT-ATGGTCTTATTCATTTTCCGTCGTGT
* * * *
29824972 TGCCATAGTGTCTTTCTACCATGTTCTTATTCATTTTCCGTTGTGT
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCGTCGTGT
* * *
29825018 TTCCATAGTGCCTTTCAACTATGGTCTTATTCATTTTCCGTCATGT
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCGTCGTGT
* * *
29825064 TGCCATAGCGTCTTTCAACTATGGTTTTATTCATTTTCCGCCGTGT
1 TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCGTCGTGT
* * *
29825110 TGCCATAGTGTCTTTCAACTATGG-CATTATTTA-TTT-C-TAGTAT
1 TGCCATAGTGTCTTTCAACTATGGTC-TTATTCATTTTCCGTCGTGT
*
29825153 AGTGTCATAGTGTCTTTCAACTATGGTCTTA
1 --TGCCATAGTGTCTTTCAACTATGGTCTTA
29825184 ATAATTTCCT
Statistics
Matches: 176, Mismatches: 30, Indels: 12
0.81 0.14 0.06
Matches are distributed among these distances:
43 3 0.02
44 1 0.01
45 59 0.34
46 113 0.64
ACGTcount: A:0.18, C:0.21, G:0.16, T:0.46
Consensus pattern (46 bp):
TGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTTCCGTCGTGT
Found at i:29829973 original size:17 final size:17
Alignment explanation
Indices: 29829942--29829975 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
29829932 TAATTAATTG
*
29829942 AAATATTTCACATATAA
1 AAATATTTCAAATATAA
*
29829959 AAATATTTGAAATATAA
1 AAATATTTCAAATATAA
29829976 TACTCACAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (17 bp):
AAATATTTCAAATATAA
Found at i:29847743 original size:24 final size:24
Alignment explanation
Indices: 29847696--29847743 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
29847686 TCGTTCTGTG
* **
29847696 GCAAAGGATGAATTGACGGTAAAT
1 GCAAAGGATGAATTAACGACAAAT
29847720 GCAAAGGATGAATTAACGACAAAT
1 GCAAAGGATGAATTAACGACAAAT
29847744 CACCCAAGTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.25, T:0.19
Consensus pattern (24 bp):
GCAAAGGATGAATTAACGACAAAT
Found at i:29852309 original size:50 final size:50
Alignment explanation
Indices: 29852191--29852354 Score: 211
Period size: 50 Copynumber: 3.3 Consensus size: 50
29852181 GATAATAACA
* * ** *
29852191 TGCCAAAGTCATGTCCCAGACATGGTCTTACATGGGATTTTCTCATGTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * ** **
29852242 TGCCCATGCCAAATCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
29852292 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTTTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
29852342 TGCCAACGCCATG
1 TGCCAACGCCATG
29852355 NNNNNNNNNN
Statistics
Matches: 96, Mismatches: 17, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
50 66 0.69
51 30 0.31
ACGTcount: A:0.21, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:29852636 original size:13 final size:13
Alignment explanation
Indices: 29852615--29852644 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
29852605 GCTTGGACCA
29852615 TCATCAAATAAAT
1 TCATCAAATAAAT
*
29852628 TCATGAAATAAAT
1 TCATCAAATAAAT
29852641 TCAT
1 TCAT
29852645 AGTTGCTGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.50, C:0.13, G:0.03, T:0.33
Consensus pattern (13 bp):
TCATCAAATAAAT
Found at i:29852893 original size:30 final size:30
Alignment explanation
Indices: 29852858--29852915 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
29852848 CCTCGACTCT
*
29852858 AACTTTTTCAAAATTACAATTTTGCCCCTA
1 AACTTTTGCAAAATTACAATTTTGCCCCTA
* *
29852888 AACTTTTGCATAATTACATTTTTGCCCC
1 AACTTTTGCAAAATTACAATTTTGCCCC
29852916 AAGACCCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.41
Consensus pattern (30 bp):
AACTTTTGCAAAATTACAATTTTGCCCCTA
Found at i:29854452 original size:14 final size:15
Alignment explanation
Indices: 29854433--29854483 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 15
29854423 AGGTAGTGGG
29854433 ATTTTTTTTC-TTCT
1 ATTTTTTTTCGTTCT
*
29854447 A-TTTTTTTCTTTCT
1 ATTTTTTTTCGTTCT
*
29854461 -TTTTCTTTCGTTCTT
1 ATTTTTTTTCGTTC-T
29854476 ATTTTTTT
1 ATTTTTTT
29854484 AGAAGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
13 8 0.27
14 15 0.50
15 1 0.03
16 6 0.20
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (15 bp):
ATTTTTTTTCGTTCT
Found at i:29866045 original size:19 final size:19
Alignment explanation
Indices: 29866021--29866067 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
29866011 TGTTATGGGA
29866021 AAGAATATTAAAAATTAGG
1 AAGAATATTAAAAATTAGG
*
29866040 AAGAATATTAAAAATTGGG
1 AAGAATATTAAAAATTAGG
29866059 AAGAATATT
1 AAGAATATT
29866068 TGCCATTTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.17, T:0.28
Consensus pattern (19 bp):
AAGAATATTAAAAATTAGG
Found at i:29867495 original size:13 final size:13
Alignment explanation
Indices: 29867477--29867501 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29867467 GAATTTACTT
29867477 GTGTGAAAATTTC
1 GTGTGAAAATTTC
29867490 GTGTGAAAATTT
1 GTGTGAAAATTT
29867502 TATCGTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:29868680 original size:85 final size:85
Alignment explanation
Indices: 29868591--29868760 Score: 340
Period size: 85 Copynumber: 2.0 Consensus size: 85
29868581 AATTGCAGAA
29868591 ATTCTATATATATTTAGCCGAATATATATGCTGGGTTTTGTAAGTTGAATGAAATTTAATGAATT
1 ATTCTATATATATTTAGCCGAATATATATGCTGGGTTTTGTAAGTTGAATGAAATTTAATGAATT
29868656 ACATATATGTTAGCCGAATG
66 ACATATATGTTAGCCGAATG
29868676 ATTCTATATATATTTAGCCGAATATATATGCTGGGTTTTGTAAGTTGAATGAAATTTAATGAATT
1 ATTCTATATATATTTAGCCGAATATATATGCTGGGTTTTGTAAGTTGAATGAAATTTAATGAATT
29868741 ACATATATGTTAGCCGAATG
66 ACATATATGTTAGCCGAATG
29868761 TATATATATG
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.34, C:0.08, G:0.18, T:0.40
Consensus pattern (85 bp):
ATTCTATATATATTTAGCCGAATATATATGCTGGGTTTTGTAAGTTGAATGAAATTTAATGAATT
ACATATATGTTAGCCGAATG
Found at i:29869330 original size:41 final size:40
Alignment explanation
Indices: 29869272--29869390 Score: 168
Period size: 41 Copynumber: 2.9 Consensus size: 40
29869262 TATCCGCGGT
*
29869272 ATTCAGACTTTATGTCTAGCAGGCTTAATGCCGGTGAATT
1 ATTCAGACTTTATGTCTAGCAGGCTTAATGCCGGTGAATG
*
29869312 ATTTCAGACTTTATGTCTAGCAGGCTTAAGGCCGGTGAAATG
1 A-TTCAGACTTTATGTCTAGCAGGCTTAATGCCGGTG-AATG
* *
29869354 ATTCGGACTTTAAGTCTAGCAGGC-TAAGTGCCGGTGA
1 ATTCAGACTTTATGTCTAGCAGGCTTAA-TGCCGGTGA
29869391 TCTGAATCAG
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
40 5 0.07
41 62 0.87
42 4 0.06
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (40 bp):
ATTCAGACTTTATGTCTAGCAGGCTTAATGCCGGTGAATG
Found at i:29869414 original size:41 final size:41
Alignment explanation
Indices: 29869369--29869472 Score: 190
Period size: 41 Copynumber: 2.5 Consensus size: 41
29869359 GACTTTAAGT
*
29869369 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
*
29869410 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGC
1 CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
29869451 CTAGCAGGCTAAGTGCCGGTGA
1 CTAGCAGGCTAAGTGCCGGTGA
29869473 ATATGTTAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (41 bp):
CTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAAC
Found at i:29869621 original size:36 final size:36
Alignment explanation
Indices: 29869581--29869652 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
29869571 TGTATTTGAT
29869581 GAGCATATAAATGTTTGGATCTATGTGTTTAGTGAA
1 GAGCATATAAATGTTTGGATCTATGTGTTTAGTGAA
29869617 GAGCATATAAATGTTTGGATCTATGTGTTTAGTGAA
1 GAGCATATAAATGTTTGGATCTATGTGTTTAGTGAA
29869653 TAGGCACATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.31, C:0.06, G:0.25, T:0.39
Consensus pattern (36 bp):
GAGCATATAAATGTTTGGATCTATGTGTTTAGTGAA
Found at i:29871674 original size:14 final size:14
Alignment explanation
Indices: 29871655--29871682 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
29871645 GAGACCATTG
29871655 ATTTAAGTATTTAA
1 ATTTAAGTATTTAA
29871669 ATTTAAGTATTTAA
1 ATTTAAGTATTTAA
29871683 TGATTTGATA
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
ATTTAAGTATTTAA
Found at i:29875105 original size:2 final size:2
Alignment explanation
Indices: 29875098--29875128 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29875088 ATAATACTCA
29875098 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29875129 ATGGTTGAAT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29879381 original size:21 final size:21
Alignment explanation
Indices: 29879357--29879401 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
29879347 TTAAACAGAT
29879357 TTTTATATATTTTAA-AATATA
1 TTTTATAT-TTTTAATAATATA
* *
29879378 TTTTTTATTTTTAATAATTTA
1 TTTTATATTTTTAATAATATA
29879399 TTT
1 TTT
29879402 ACTCGAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATATTTTTAATAATATA
Found at i:29881204 original size:15 final size:15
Alignment explanation
Indices: 29881157--29881220 Score: 65
Period size: 15 Copynumber: 4.1 Consensus size: 15
29881147 AAGTTATATT
* *
29881157 TATAAATTTTTATAA
1 TATATATTTTAATAA
* *
29881172 CATATATTTTTATAA
1 TATATATTTTAATAA
29881187 TATATATTTGTAATATA
1 TATATATTT-TAATA-A
*
29881204 TATAAATTTTAATAA
1 TATATATTTTAATAA
29881219 TA
1 TA
29881221 CTTTTTACGT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
15 24 0.57
16 9 0.21
17 9 0.21
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
TATATATTTTAATAA
Found at i:29881205 original size:13 final size:13
Alignment explanation
Indices: 29881151--29881206 Score: 55
Period size: 13 Copynumber: 4.4 Consensus size: 13
29881141 ATAAAAAAGT
29881151 TATATTTATAA-A
1 TATATTTATAATA
29881163 T-T-TTTATAACATA
1 TATATTTAT-A-ATA
*
29881176 TATTTTTATAATA
1 TATATTTATAATA
*
29881189 TATATTTGTAATA
1 TATATTTATAATA
29881202 TATAT
1 TATAT
29881207 AAATTTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 5 0.14
11 2 0.05
12 2 0.05
13 21 0.57
14 2 0.05
15 5 0.14
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (13 bp):
TATATTTATAATA
Found at i:29886760 original size:23 final size:23
Alignment explanation
Indices: 29886734--29886778 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
29886724 GAGAAATCTG
29886734 TATGTATAGGTATAAAATGTGCT
1 TATGTATAGGTATAAAATGTGCT
*
29886757 TATGTATATGTATAAAATGTGC
1 TATGTATAGGTATAAAATGTGC
29886779 AGACTTCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.04, G:0.20, T:0.40
Consensus pattern (23 bp):
TATGTATAGGTATAAAATGTGCT
Found at i:29891603 original size:46 final size:45
Alignment explanation
Indices: 29891547--29891652 Score: 149
Period size: 46 Copynumber: 2.3 Consensus size: 45
29891537 CTCACTTCCG
* * *
29891547 TCATGATGCCATAGCATATTTCAGCTATGGTTTTACTCGTTTTAA
1 TCATGTTGCCATAGCATATTTCAACTATGGTCTTACTCGTTTTAA
** *
29891592 TTCATGTTGCCATAGTGTCTTTCAACTATGGTCTTACTCGTTTTAA
1 -TCATGTTGCCATAGCATATTTCAACTATGGTCTTACTCGTTTTAA
29891638 TCATGTTGCCATAGC
1 TCATGTTGCCATAGC
29891653 GTCTTCTAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 14 0.26
46 39 0.74
ACGTcount: A:0.22, C:0.20, G:0.16, T:0.42
Consensus pattern (45 bp):
TCATGTTGCCATAGCATATTTCAACTATGGTCTTACTCGTTTTAA
Found at i:29891657 original size:45 final size:45
Alignment explanation
Indices: 29891547--29891686 Score: 174
Period size: 45 Copynumber: 3.1 Consensus size: 45
29891537 CTCACTTCCG
* * * *
29891547 TCATGATGCCATAGCATATTTCAGCTATGGTTTTACTCGTTTTAA
1 TCATGTTGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTTAA
* *
29891592 TTCATGTTGCCATAGTGTCTTTCAACTATGGTCTTACTCGTTTTAA
1 -TCATGTTGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTTAA
* * *
29891638 TCATGTTGCCATAGCGTC-TTCTAGTTATGGTCTTACTTGTGTTAA
1 TCATGTTGCCATAGCGTCTTTC-AGCTATGGTCTTACTCGTTTTAA
29891683 TCAT
1 TCAT
29891687 ATTTACGGTA
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
44 3 0.04
45 40 0.49
46 39 0.48
ACGTcount: A:0.21, C:0.19, G:0.16, T:0.44
Consensus pattern (45 bp):
TCATGTTGCCATAGCGTCTTTCAGCTATGGTCTTACTCGTTTTAA
Found at i:29895449 original size:25 final size:25
Alignment explanation
Indices: 29895417--29895480 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
29895407 AGGTCATTTT
29895417 ACAACTCGTGTGAGCATTTACAATC
1 ACAACTCGTGTGAGCATTTACAATC
* * **
29895442 ACAGCTCGTCTGAGCATTTACCGTC
1 ACAACTCGTGTGAGCATTTACAATC
*
29895467 ACAACTTGTGTGAG
1 ACAACTCGTGTGAG
29895481 TATTGTTCCA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.27, C:0.25, G:0.20, T:0.28
Consensus pattern (25 bp):
ACAACTCGTGTGAGCATTTACAATC
Found at i:29895583 original size:26 final size:26
Alignment explanation
Indices: 29895554--29895611 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 26
29895544 ATGGTTATTC
*
29895554 GAAATGGATA-TATGAAAT-AAACATTT
1 GAAATGGATACT-TGAAATGAAA-ATGT
29895580 GAAATGGATACTTGAAATGAAAATGT
1 GAAATGGATACTTGAAATGAAAATGT
29895606 GAAATG
1 GAAATG
29895612 TGAAATGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 25 0.86
27 4 0.14
ACGTcount: A:0.48, C:0.03, G:0.21, T:0.28
Consensus pattern (26 bp):
GAAATGGATACTTGAAATGAAAATGT
Found at i:29901179 original size:25 final size:25
Alignment explanation
Indices: 29901098--29901179 Score: 58
Period size: 25 Copynumber: 3.3 Consensus size: 25
29901088 GGTATGTCCA
*
29901098 TACGAGCATGTA-ATTGGAAAGCTCT
1 TACGAGC-TGTATAATGGAAAGCTCT
* ** * * **
29901123 TTCGAGCCATGTAATGGGAAGCTAA
1 TACGAGCTGTATAATGGAAAGCTCT
**
29901148 TGTGAGCTGTATAATGGAAAGCTCT
1 TACGAGCTGTATAATGGAAAGCTCT
29901173 TACGAGC
1 TACGAGC
29901180 CAATTATCAG
Statistics
Matches: 38, Mismatches: 18, Indels: 2
0.66 0.31 0.03
Matches are distributed among these distances:
24 1 0.03
25 37 0.97
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.27
Consensus pattern (25 bp):
TACGAGCTGTATAATGGAAAGCTCT
Found at i:29901204 original size:25 final size:25
Alignment explanation
Indices: 29901176--29901357 Score: 163
Period size: 25 Copynumber: 7.3 Consensus size: 25
29901166 AAGCTCTTAC
* * *
29901176 GAGCCAATTATCAGGAAGCTCATGT
1 GAGCCAATTATCGGGAAGCTCGTGA
*
29901201 GAGCC-ATATATCGAGAAGCTCGTGA
1 GAGCCAAT-TATCGGGAAGCTCGTGA
* **
29901226 GAGCCATATAAT-GGGAAGCTCAAGA
1 GAGCCA-ATTATCGGGAAGCTCGTGA
* *
29901251 GAG-CTATTAATCGGGAAGCTCATGA
1 GAGCCAATT-ATCGGGAAGCTCGTGA
* * * * *
29901276 GAGCTAAATAACGGCAAGCTTGTGA
1 GAGCCAATTATCGGGAAGCTCGTGA
*
29901301 GAGCCAAGTATCGGGAAGCTCGTGA
1 GAGCCAATTATCGGGAAGCTCGTGA
* *
29901326 GAGCCAAGTATCAGGAAGCTCGTGA
1 GAGCCAATTATCGGGAAGCTCGTGA
29901351 GAGCCAA
1 GAGCCAA
29901358 ACACCCGGAT
Statistics
Matches: 127, Mismatches: 24, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.02
24 5 0.04
25 114 0.90
26 4 0.03
27 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.19
Consensus pattern (25 bp):
GAGCCAATTATCGGGAAGCTCGTGA
Found at i:29901371 original size:25 final size:25
Alignment explanation
Indices: 29901264--29901371 Score: 74
Period size: 25 Copynumber: 4.3 Consensus size: 25
29901254 CTATTAATCG
* * * *
29901264 GGAAGCTCATGAGAGCTAAATAAC-
1 GGAAGCTCGTGAGAGCCAAACACCA
* ** * *
29901288 GGCAAGCTTGTGAGAGCCAAGTATCG
1 GG-AAGCTCGTGAGAGCCAAACACCA
** *
29901314 GGAAGCTCGTGAGAGCCAAGTATCA
1 GGAAGCTCGTGAGAGCCAAACACCA
*
29901339 GGAAGCTCGTGAGAGCCAAACACCC
1 GGAAGCTCGTGAGAGCCAAACACCA
*
29901364 GGATGCTC
1 GGAAGCTC
29901372 ATAAGAGCTA
Statistics
Matches: 70, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
24 2 0.03
25 66 0.94
26 2 0.03
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (25 bp):
GGAAGCTCGTGAGAGCCAAACACCA
Found at i:29916738 original size:27 final size:27
Alignment explanation
Indices: 29916708--29916801 Score: 116
Period size: 27 Copynumber: 3.5 Consensus size: 27
29916698 CCTTGTAAGT
* * * *
29916708 TAAAATGACCGTAATACCCTCAAAGGA
1 TAAAATTACCGAAATACCCTCGAAGGG
* *
29916735 TAAAATTACCGAAATACCTTCGATGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
*
29916762 TAAAATTACCGAAATACCCCCGAAGGG
1 TAAAATTACCGAAATACCCTCGAAGGG
*
29916789 TAAAATTATCGAA
1 TAAAATTACCGAA
29916802 GTACTCCATA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.21
Consensus pattern (27 bp):
TAAAATTACCGAAATACCCTCGAAGGG
Found at i:29921479 original size:10 final size:10
Alignment explanation
Indices: 29921464--29921493 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
29921454 TTTTTAATCC
29921464 TTCATTACCA
1 TTCATTACCA
29921474 TTCATTACCA
1 TTCATTACCA
29921484 TTCATTACCA
1 TTCATTACCA
29921494 AAAGTCCCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.40
Consensus pattern (10 bp):
TTCATTACCA
Found at i:29929403 original size:14 final size:15
Alignment explanation
Indices: 29929376--29929409 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
29929366 ACCCGAATCT
*
29929376 ATTTTTAGGTAAGAA
1 ATTTTGAGGTAAGAA
29929391 ATTTTGAGG-AAGAA
1 ATTTTGAGGTAAGAA
29929405 ATTTT
1 ATTTT
29929410 CTAAGGGGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (15 bp):
ATTTTGAGGTAAGAA
Found at i:29933989 original size:92 final size:92
Alignment explanation
Indices: 29933832--29933999 Score: 336
Period size: 92 Copynumber: 1.8 Consensus size: 92
29933822 ATCCAAAAAG
29933832 TTTTATTGATCTTCCTAAGTAGAAAGCCTTTATCCAAAAAGTTCTTTACCATAATAATGATAATC
1 TTTTATTGATCTTCCTAAGTAGAAAGCCTTTATCCAAAAAGTTCTTTACCATAATAATGATAATC
29933897 GAACCAATTATCCATAGCTTTTTGACA
66 GAACCAATTATCCATAGCTTTTTGACA
29933924 TTTTATTGATCTTCCTAAGTAGAAAGCCTTTATCCAAAAAGTTCTTTACCATAATAATGATAATC
1 TTTTATTGATCTTCCTAAGTAGAAAGCCTTTATCCAAAAAGTTCTTTACCATAATAATGATAATC
29933989 GAACCAATTAT
66 GAACCAATTAT
29934000 GCCCCAGTTA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 76 1.00
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (92 bp):
TTTTATTGATCTTCCTAAGTAGAAAGCCTTTATCCAAAAAGTTCTTTACCATAATAATGATAATC
GAACCAATTATCCATAGCTTTTTGACA
Found at i:29937313 original size:29 final size:29
Alignment explanation
Indices: 29937271--29937333 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
29937261 GGCTTATACT
* *
29937271 GTGTGTCCCACACGACCTAGCACACGATC
1 GTGTGTCCCACACGACCTACCACACGACC
* *
29937300 GTGTGTCGCACACGGCCTACCACACGACC
1 GTGTGTCCCACACGACCTACCACACGACC
29937329 GTGTG
1 GTGTG
29937334 GCGTTGATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.17
Consensus pattern (29 bp):
GTGTGTCCCACACGACCTACCACACGACC
Found at i:29938201 original size:20 final size:19
Alignment explanation
Indices: 29938172--29938223 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
29938162 ACAAAAACTT
29938172 AAAAA-ATATAAAATTATAA
1 AAAAATATATAAAATTAT-A
*
29938191 AAAAATTTATAAAATTATA
1 AAAAATATATAAAATTATA
*
29938210 AGAAATATATAAAA
1 AAAAATATATAAAA
29938224 AATCAATACC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATATATAAAATTATA
Found at i:29938224 original size:20 final size:19
Alignment explanation
Indices: 29938172--29938224 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
29938162 ACAAAAACTT
29938172 AAAAAATAT-AAAATTATA
1 AAAAAATATAAAAATTATA
*
29938190 AAAAAATTTATAAAATTATA
1 AAAAAATATA-AAAATTATA
*
29938210 AGAAATATATAAAAA
1 A-AAAAATATAAAAA
29938225 ATCAATACCT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 8 0.28
20 14 0.48
21 7 0.24
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAAAATATAAAAATTATA
Found at i:29946781 original size:19 final size:18
Alignment explanation
Indices: 29946738--29946792 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
29946728 CATATTTCAA
*
29946738 ATAGGTTCACACATGC--
1 ATAGGTTCGCACATGCAT
* *
29946754 ATCGGTTCGCATATAGCAT
1 ATAGGTTCGCACAT-GCAT
29946773 ATAGGTTCGCACATGCAT
1 ATAGGTTCGCACATGCAT
29946791 AT
1 AT
29946793 TGGATCTTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 11 0.35
17 2 0.06
18 6 0.19
19 12 0.39
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (18 bp):
ATAGGTTCGCACATGCAT
Found at i:29947007 original size:18 final size:19
Alignment explanation
Indices: 29946984--29947028 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
29946974 GCTTATATAC
29946984 ATAGGCTCGA-ATAAATGA
1 ATAGGCTCGACATAAATGA
29947002 ATAGGCTC-ACATAAATGA
1 ATAGGCTCGACATAAATGA
*
29947020 ATATGCTCG
1 ATAGGCTCG
29947029 CATGCATAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (19 bp):
ATAGGCTCGACATAAATGA
Found at i:29948736 original size:23 final size:23
Alignment explanation
Indices: 29948701--29948812 Score: 107
Period size: 23 Copynumber: 4.9 Consensus size: 23
29948691 CGGTTTTGGG
* * *
29948701 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACAAAATGGTAATGCGA
* *
29948724 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACAAAATGGTAATGCGA
* * * *
29948747 TTTGGTACGAATTGGTAAGGTGA
1 TTTGGTACAAAATGGTAATGCGA
* * *
29948770 TTTGGTTCGAAATGGTAATACGA
1 TTTGGTACAAAATGGTAATGCGA
*
29948793 TTTGGTACAAAATGTTAATG
1 TTTGGTACAAAATGGTAATG
29948813 GTTCAAAAAG
Statistics
Matches: 69, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 69 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (23 bp):
TTTGGTACAAAATGGTAATGCGA
Found at i:29948763 original size:46 final size:46
Alignment explanation
Indices: 29948701--29948806 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
29948691 CGGTTTTGGG
* *
29948701 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
* *
29948747 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAAATGGTAATACGA
1 TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
*
29948793 TTTGGTACAAAATG
1 TTTGGTACGAAATG
29948807 TTAATGGTTC
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 54 1.00
ACGTcount: A:0.31, C:0.07, G:0.26, T:0.36
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
Found at i:29955298 original size:13 final size:13
Alignment explanation
Indices: 29955268--29955309 Score: 52
Period size: 12 Copynumber: 3.3 Consensus size: 13
29955258 GTATGCAATT
29955268 TTTTTTCTTTTC-A
1 TTTTTT-TTTTCGA
*
29955281 ATTTTTTTTT-GA
1 TTTTTTTTTTCGA
29955293 TTTTTTTTTTCGA
1 TTTTTTTTTTCGA
29955306 TTTT
1 TTTT
29955310 GAATTTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
12 14 0.56
13 11 0.44
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.79
Consensus pattern (13 bp):
TTTTTTTTTTCGA
Found at i:29955309 original size:20 final size:19
Alignment explanation
Indices: 29955287--29955324 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
29955277 TTCAATTTTT
*
29955287 TTTTGATTTTTTTTTTCGA
1 TTTTGAATTTTTTTTTCGA
29955306 TTTTGAATTTTTTTTTCGA
1 TTTTGAATTTTTTTTTCGA
29955325 ACTCTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.13, C:0.05, G:0.11, T:0.71
Consensus pattern (19 bp):
TTTTGAATTTTTTTTTCGA
Found at i:29955639 original size:23 final size:23
Alignment explanation
Indices: 29955604--29955714 Score: 116
Period size: 23 Copynumber: 4.9 Consensus size: 23
29955594 CGGTTTTGGG
* *
29955604 TTTGTTACGAAATGGTAATGTGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
29955627 TTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
* * *
29955650 TTTGGTACGAATTGGTAAGGTGA
1 TTTGGTACGAAATGGTAATGCGA
* *
29955673 TTTGGTTCG-AATGGTAATACGA
1 TTTGGTACGAAATGGTAATGCGA
*
29955695 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
29955715 GTTCAAAAAG
Statistics
Matches: 68, Mismatches: 19, Indels: 2
0.76 0.21 0.02
Matches are distributed among these distances:
22 17 0.25
23 51 0.75
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (23 bp):
TTTGGTACGAAATGGTAATGCGA
Found at i:29955666 original size:46 final size:45
Alignment explanation
Indices: 29955604--29955714 Score: 168
Period size: 45 Copynumber: 2.4 Consensus size: 45
29955594 CGGTTTTGGG
*
29955604 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTC-AAATGGTAATACGA
* * *
29955650 TTTGGTACGAATTGGTAAGGTGATTTGGTTCGAATGGTAATACGA
1 TTTGGTACGAAATGGTAATGTGATTTGGTTCAAATGGTAATACGA
*
29955695 TTTGGTACGAAATGTTAATG
1 TTTGGTACGAAATGGTAATG
29955715 GTTCAAAAAG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
45 30 0.52
46 28 0.48
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (45 bp):
TTTGGTACGAAATGGTAATGTGATTTGGTTCAAATGGTAATACGA
Found at i:29955701 original size:45 final size:46
Alignment explanation
Indices: 29955604--29955708 Score: 167
Period size: 46 Copynumber: 2.3 Consensus size: 46
29955594 CGGTTTTGGG
* *
29955604 TTTGTTACGAAATGGTAATGTGATTTGGTTCAAAATGGTAATACGA
1 TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
* *
29955650 TTTGGTACGAATTGGTAAGGTGATTTGGTTC-GAATGGTAATACGA
1 TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
29955695 TTTGGTACGAAATG
1 TTTGGTACGAAATG
29955709 TTAATGGTTC
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 26 0.48
46 28 0.52
ACGTcount: A:0.30, C:0.07, G:0.28, T:0.36
Consensus pattern (46 bp):
TTTGGTACGAAATGGTAAGGTGATTTGGTTCAAAATGGTAATACGA
Found at i:29962416 original size:21 final size:21
Alignment explanation
Indices: 29962371--29962433 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
29962361 ATCTTCAAGG
29962371 ATATGCAATCTTAGATATG--
1 ATATGCAATCTTAGATATGAT
29962390 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
* *
29962411 ATATGCAATCTTGGACATGAT
1 ATATGCAATCTTAGATATGAT
29962432 AT
1 AT
29962434 GCAATATTGG
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
19 19 0.47
21 21 0.52
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:29962444 original size:19 final size:19
Alignment explanation
Indices: 29962370--29962438 Score: 102
Period size: 19 Copynumber: 3.5 Consensus size: 19
29962360 AATCTTCAAG
29962370 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
29962389 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
* *
29962408 GATATATGCAATCTTGGACAT
1 G--ATATGCAATCTTAGATAT
29962429 GATATGCAAT
1 GATATGCAAT
29962439 ATTGGAAGAT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
19 29 0.63
21 17 0.37
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:29969501 original size:88 final size:86
Alignment explanation
Indices: 29969335--29969553 Score: 260
Period size: 88 Copynumber: 2.5 Consensus size: 86
29969325 GAAATCACAA
* * * * * *
29969335 AGCCTTGCCTTCCTGGTTTGCAGCGGAGCAGGTTGAAAATAACAGATCTTACCTTCCCGCACTAA
1 AGCCTTGCCTCCCTGG-TTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTACCTTCCCGCACGAA
* * *
29969400 TGGCGAAGTAGATCGAAGATGCC
65 -GGCGAAGCAGATCAAAGATACC
* * *
29969423 GGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGA
1 AGCCTTGCCTCCCT-GGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTACCTTCCCGCA-CGA
*
29969488 CA-GTGAAGCAGATCAAAGATACC
64 -AGGCGAAGCAGATCAAAGATACC
29969511 AGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTTGAAGATAGC
1 AGCCTTGCCTCCCT-GGTTGTAGTGGAGCAGGTTGAAGATAGC
29969554 TGATAGAGGG
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
88 108 0.96
89 4 0.04
90 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (86 bp):
AGCCTTGCCTCCCTGGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTACCTTCCCGCACGAAG
GCGAAGCAGATCAAAGATACC
Found at i:29969550 original size:43 final size:43
Alignment explanation
Indices: 29969414--29969551 Score: 132
Period size: 44 Copynumber: 3.2 Consensus size: 43
29969404 GAAGTAGATC
* * *
29969414 GAAGATGCCGGCCTTGCCTCCCTAGGTTGTAGTGGAGCAGGTT
1 GAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTT
* * * ** * * * * *
29969457 GAAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATC
1 GAAGATACCAG-CCTTGCCTCCCTGGGTTG-TAGTGGAGCAGGTT
*
29969502 AAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTT
1 GAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTT
29969545 GAAGATA
1 GAAGATA
29969552 GCTGATAGAG
Statistics
Matches: 68, Mismatches: 25, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
43 24 0.35
44 25 0.37
45 19 0.28
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (43 bp):
GAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGCAGGTT
Found at i:29975196 original size:44 final size:43
Alignment explanation
Indices: 29975127--29975546 Score: 244
Period size: 44 Copynumber: 9.6 Consensus size: 43
29975117 TCGACAGCGA
* * *
29975127 AGCAGATCGAAGATAACAG-CCTTGCCTCCCTAGGTTGTAGTGG
1 AGCAGATTGAAGATAGCAGATCTTGCCTCCCT-GGTTGTAGTGG
* * * * * *
29975170 AGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGA
1 AGCAGATTGAAGATAGCAGATCTTGCCTCCCTG-GTTG-TAGTGG
* * * *
29975215 AGCAGATCGAAGATACCAG-CCTTGCCTCACTGGGTTGTAGTGG
1 AGCAGATTGAAGATAGCAGATCTTGCCTCCCT-GGTTGTAGTGG
* * *
29975258 AGCAGATTGAAGATAGCAGATCTTGCCTTCCT-GTACCGATAGTGA
1 AGCAGATTGAAGATAGCAGATCTTGCCTCCCTGGT--TG-TAGTGG
* * *
29975303 AGCAGATCGAAGATACCAG-CCTTGCCTCCCTGGGTTGTAGTGG
1 AGCAGATTGAAGATAGCAGATCTTGCCTCCCT-GGTTGTAGTGG
* * * * * * *
29975346 AGTAGGTTGAAGATAGCAGATCTTGCCTTCCT-GTACCGACAATGA
1 AGCAGATTGAAGATAGCAGATCTTGCCTCCCTGGT--TG-TAGTGG
* * * * *
29975391 AGCAGATCGAAGATACCA-ACCTTGCCTCTCTGGGCTGTAGTGG
1 AGCAGATTGAAGATAGCAGATCTTGCCTCCCT-GGTTGTAGTGG
* * * * *
29975434 AACAGGTTGAAGATAGCAGATCTTGCCTTCCT-GTACCGATAGTGA
1 AGCAGATTGAAGATAGCAGATCTTGCCTCCCTGGT--TG-TAGTGG
** * * *
29975479 AGCAGATCAAAGATACCAG-TCTTGCCTCCCTGGGTTGTCGTGA
1 AGCAGATTGAAGATAGCAGATCTTGCCTCCCT-GGTTGTAGTGG
* * *
29975522 AGTAGATCGAAGAAAGCAGATCTTG
1 AGCAGATTGAAGATAGCAGATCTTG
29975547 TATTCATGTA
Statistics
Matches: 278, Mismatches: 76, Indels: 45
0.70 0.19 0.11
Matches are distributed among these distances:
42 5 0.02
43 94 0.34
44 96 0.35
45 78 0.28
46 5 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (43 bp):
AGCAGATTGAAGATAGCAGATCTTGCCTCCCTGGTTGTAGTGG
Found at i:29975251 original size:88 final size:88
Alignment explanation
Indices: 29975094--29975546 Score: 654
Period size: 88 Copynumber: 5.1 Consensus size: 88
29975084 ACTAGTATCA
* * * * * *
29975094 ATAGCAGATATTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATAACAGCCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTG
29975159 GGTTGTAGTGGAGCAGGTTGAAG
66 GGTTGTAGTGGAGCAGGTTGAAG
* ** * *
29975182 ATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCGAAGATACCAGCCTTGCCTCACTG
1 ATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTG
*
29975247 GGTTGTAGTGGAGCAGATTGAAG
66 GGTTGTAGTGGAGCAGGTTGAAG
*
29975270 ATAGCAGATCTTGCCTTCCTGTACCGATAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTG
*
29975335 GGTTGTAGTGGAGTAGGTTGAAG
66 GGTTGTAGTGGAGCAGGTTGAAG
* * *
29975358 ATAGCAGATCTTGCCTTCCTGTACCGACAATGAAGCAGATCGAAGATACCAACCTTGCCTCTCTG
1 ATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTG
* *
29975423 GGCTGTAGTGGAACAGGTTGAAG
66 GGTTGTAGTGGAGCAGGTTGAAG
* * *
29975446 ATAGCAGATCTTGCCTTCCTGTACCGATAGTGAAGCAGATCAAAGATACCAGTCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTG
* * * * *
29975511 GGTTGTCGTGAAGTAGATCGAAG
66 GGTTGTAGTGGAGCAGGTTGAAG
*
29975534 AAAGCAGATCTTG
1 ATAGCAGATCTTG
29975547 TATTCATGTA
Statistics
Matches: 330, Mismatches: 35, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
88 330 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (88 bp):
ATAGCAGATCTTGCCTTCCTGTACCGACAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTG
GGTTGTAGTGGAGCAGGTTGAAG
Found at i:29975566 original size:44 final size:44
Alignment explanation
Indices: 29975517--29975816 Score: 384
Period size: 44 Copynumber: 6.8 Consensus size: 44
29975507 CCTGGGTTGT
* * *
29975517 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTATTCATGTATTAG
1 CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGG
* * *
29975561 CGTGAAGTAGATCAAAGATAGTAGATCTTGTCTTCATATATTGG
1 CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGG
*** *
29975605 CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGG
1 CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGG
* * * *
29975649 TGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGG
1 -CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGG
* * *
29975694 CGTGAAGTAGATCAAAGATAGTAGATATTGTCTTCATGTATTGG
1 CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGG
* *
29975738 CGTGAAGTAGATCGAAGATAGCAGATATTGTCTTCATGTATCGG
1 CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGG
* * * *
29975782 CATGAAATAGATCAAAGGTAGCAGATCTTGTCTTC
1 CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTC
29975817 CCATACTGGT
Statistics
Matches: 221, Mismatches: 34, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
44 185 0.84
45 36 0.16
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (44 bp):
CGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTGG
Found at i:29975624 original size:176 final size:175
Alignment explanation
Indices: 29975094--29975817 Score: 560
Period size: 176 Copynumber: 4.1 Consensus size: 175
29975084 ACTAGTATCA
* * * * * * * *
29975094 ATAGCAGATATTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATAACAGCCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGTACCGATAGTGAAGCAGATCGAAGATACCAGTCTTGCCTCCCTG
* * * * * * * * * *
29975159 GGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATT-GACAGCGAAGCAGATC
66 GGTTGTCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTAG-C-GTGAAGTAGATC
* * * ** ** ** *
29975223 GAAGATACCAG-CCTTG-CCTCACTGGGTTGTAGTGGAGCAGATTGAAG
129 GAAGATAGCAGATCTTGTCTTCA-TGTATTGGCGT-GAATAGATCGAAG
*
29975270 ATAGCAGATCTTGCCTTCCTGTACCGATAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGTACCGATAGTGAAGCAGATCGAAGATACCAGTCTTGCCTCCCTG
* * * * * * ** * *
29975335 GGTTGTAGTGGAGTAGGTTGAAGATAGCAGATCTTGCCTTCCTGTA-CCGACAATGAAGCAGATC
66 GGTTGTCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTAG-C-GTGAAGTAGATC
* * * *** ** * * *
29975399 GAAGATACCA-ACCTTGCCTCTC-TGGGCTGTAGTGGAACAGGTTGAAG
129 GAAGATAGCAGATCTTGTCT-TCATGTATTGGCGT-GAATAGATCGAAG
*
29975446 ATAGCAGATCTTGCCTTCCTGTACCGATAGTGAAGCAGATCAAAGATACCAGTCTTGCCTCCCTG
1 ATAGCAGATCTTGCCTTCCTGTACCGATAGTGAAGCAGATCGAAGATACCAGTCTTGCCTCCCTG
* * *
29975511 GGTTGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTATTCATGTATTAGCGTGAAGTAGATCAA
66 GGTTGTCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGA
* *
29975576 AGATAGTAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAG
131 AGATAGCAGATCTTGTCTTCATGTATTGGCGTGAA-TAGATCGAAG
* ** * * * * * * * ** * *
29975622 ATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCAT
1 ATAGCAGATCTTGCCTTCCTGTACCGATAGTGAAGCAGATCGAAGATACCAG-TCTTGCCTCCCT
** * * * * *
29975687 GTATTGGCGTGAAGTAGATCAAAGATAGTAGATATTGTCTTCATGTATTGGCGTGAAGTAGATCG
65 GGGTTGTCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCG
* * * *
29975752 AAGATAGCAGATATTGTCTTCATGTATCGGCATGAAATAGATCAAAG
130 AAGATAGCAGATCTTGTCTTCATGTATTGGCGTG-AATAGATCGAAG
* *
29975799 GTAGCAGATCTTGTCTTCC
1 ATAGCAGATCTTGCCTTCC
29975818 CATACTGGTG
Statistics
Matches: 462, Mismatches: 76, Indels: 19
0.83 0.14 0.03
Matches are distributed among these distances:
175 22 0.05
176 315 0.68
177 121 0.26
178 4 0.01
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (175 bp):
ATAGCAGATCTTGCCTTCCTGTACCGATAGTGAAGCAGATCGAAGATACCAGTCTTGCCTCCCTG
GGTTGTCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCATGTATTAGCGTGAAGTAGATCGA
AGATAGCAGATCTTGTCTTCATGTATTGGCGTGAATAGATCGAAG
Found at i:29975624 original size:264 final size:264
Alignment explanation
Indices: 29975094--29975640 Score: 646
Period size: 264 Copynumber: 2.1 Consensus size: 264
29975084 ACTAGTATCA
* * * *
29975094 ATAGCAGATATTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGATAACAGCCTTGCCTCCCTA
1 ATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGATAACAACCTTGCCTCCCTA
* * ** *
29975159 GGTTGTAGTGGAGCAGGTTGAAGATAGCAGATCTTGCCTTCCTGCATTGACAGCGAAGCAGATCG
66 GGCTGTAGTGGAACAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCA
* * * * *
29975224 AAGATACCAGCCTTGCCTCACTGGGTTGTAGTGGAGCAGATTGAAGATAGCAGATCTTGCCTTCC
131 AAGATACCAGCCTTGCCTCACTGGGTTGTAGTGAAGCAGATCGAAGAAAGCAGATCTTGCATTCA
* * * * * * * * *
29975289 TGTACCGATAGTGAAGCAGATCGAAGATACCAGCCTTGCCTCCCTGGGTTGTAGTGGAGTAGGTT
196 TGTACCGAGAGTGAAGCAGATCAAAGATACCAGCCTTGCCTCCATAGATTGGAGTGAAGTAGATC
29975354 GAAG
261 GAAG
* * * * *
29975358 ATAGCAGATCTTGCCTTCCTGTACCGACAATGAAGCAGATCGAAGATACCAACCTTGCCTCTCTG
1 ATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGATAACAACCTTGCCTCCCTA
* * *
29975423 GGCTGTAGTGGAACAGGTTGAAGATAGCAGATCTTGCCTTCCTGTACCGATAGTGAAGCAGATCA
66 GGCTGTAGTGGAACAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCA
* * * * *
29975488 AAGATACCAGTCTTGCCTCCCTGGGTTGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTATTCA
131 AAGATACCAGCCTTGCCTCACTGGGTTGTAGTGAAGCAGATCGAAGAAAGCAGATCTTGCATTCA
** * * ** * * * * *
29975553 TGTA-TTAGCGTGAAGTAGATCAAAGATAGTAGATCTTGTCTTCATATATTGGCGTGAAGTAGAT
196 TGTACCGAGAGTGAAGCAGATCAAAGATACCAG-CCTTGCCTCCATAGATTGGAGTGAAGTAGAT
29975617 CGAAG
260 CGAAG
*
29975622 ATAGCAGATCTTGTCTTCC
1 ATAGCAGATCTTGCCTTCC
29975641 CATACTGGTG
Statistics
Matches: 234, Mismatches: 48, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
263 20 0.09
264 214 0.91
ACGTcount: A:0.27, C:0.21, G:0.26, T:0.26
Consensus pattern (264 bp):
ATAGCAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAAGATAACAACCTTGCCTCCCTA
GGCTGTAGTGGAACAGGTTGAAGATAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCA
AAGATACCAGCCTTGCCTCACTGGGTTGTAGTGAAGCAGATCGAAGAAAGCAGATCTTGCATTCA
TGTACCGAGAGTGAAGCAGATCAAAGATACCAGCCTTGCCTCCATAGATTGGAGTGAAGTAGATC
GAAG
Found at i:29975686 original size:133 final size:133
Alignment explanation
Indices: 29975520--29975772 Score: 452
Period size: 133 Copynumber: 1.9 Consensus size: 133
29975510 GGGTTGTCGT
*
29975520 GAAGTAGATCGAAGAAAGCAGATCTTGTATTCATGTATTAGCGTGAAGTAGATCAAAGATAGTAG
1 GAAGTAGATCGAAGAAAGCAGATCTTATATTCATGTATTAGCGTGAAGTAGATCAAAGATAGTAG
* *
29975585 ATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGT
66 ATATTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATATTGTCTTCCCATACTGGT
29975650 GGC
131 GGC
* *
29975653 GAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGTAG
1 GAAGTAGATCGAAGAAAGCAGATCTTATATTCATGTATTAGCGTGAAGTAGATCAAAGATAGTAG
*
29975718 ATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATATTGTCTTC
66 ATATTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATATTGTCTTC
29975773 ATGTATCGGC
Statistics
Matches: 114, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
133 114 1.00
ACGTcount: A:0.32, C:0.13, G:0.25, T:0.30
Consensus pattern (133 bp):
GAAGTAGATCGAAGAAAGCAGATCTTATATTCATGTATTAGCGTGAAGTAGATCAAAGATAGTAG
ATATTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATATTGTCTTCCCATACTGGT
GGC
Found at i:29975745 original size:177 final size:177
Alignment explanation
Indices: 29975517--29975844 Score: 512
Period size: 177 Copynumber: 1.9 Consensus size: 177
29975507 CCTGGGTTGT
* *
29975517 CGTGAAGTAGATCGAAGAAAGCAGATCTTGTATTCATGTATTAGCGTGAAGTAGATCAAAGATAG
1 CGTGAAGTAGATCAAAGAAAGCAGATATTGTATTCATGTATTAGCGTGAAGTAGATCAAAGATAG
* * * * * *
29975582 TAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACT
66 CAGATATTGTCTTCATATATCGGCATGAAATAGATCAAAGATAGCAGATCTTGTCTTCCCATACT
*
29975647 GGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGG
131 GGTGGCGAAGTAGACCGAAGAAAGCAGATCTTATCTTCATGTATTGG
* * * * *
29975694 CGTGAAGTAGATCAAAGATAGTAGATATTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAG
1 CGTGAAGTAGATCAAAGAAAGCAGATATTGTATTCATGTATTAGCGTGAAGTAGATCAAAGATAG
* *
29975759 CAGATATTGTCTTCATGTATCGGCATGAAATAGATCAAAGGTAGCAGATCTTGTCTTCCCATACT
66 CAGATATTGTCTTCATATATCGGCATGAAATAGATCAAAGATAGCAGATCTTGTCTTCCCATACT
29975824 GGTGGCGAAGTAGACCGAAGA
131 GGTGGCGAAGTAGACCGAAGA
29975845 TACAAGTCTT
Statistics
Matches: 135, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
177 135 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.29
Consensus pattern (177 bp):
CGTGAAGTAGATCAAAGAAAGCAGATATTGTATTCATGTATTAGCGTGAAGTAGATCAAAGATAG
CAGATATTGTCTTCATATATCGGCATGAAATAGATCAAAGATAGCAGATCTTGTCTTCCCATACT
GGTGGCGAAGTAGACCGAAGAAAGCAGATCTTATCTTCATGTATTGG
Found at i:29975834 original size:133 final size:132
Alignment explanation
Indices: 29975524--29975846 Score: 346
Period size: 133 Copynumber: 2.4 Consensus size: 132
29975514 TGTCGTGAAG
* * * ** * * * *
29975524 TAGATCGAAGAAAGCAGATCTTGTATTCATGTATTAGCGTGAAGTAGATCAAAGATAGTAGATCT
1 TAGATCAAAGAAAGCAGATCTTATCTTCACATACTGGCGCGAAGTAGATCAAAGATAGTAGATAT
* *
29975589 TGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATCTTGTCTTCCCATACTGGTGGCG
66 TGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATATTGTCTT-CCATACTGATGGCG
*
29975654 AAG
130 AAA
* ** * *
29975657 TAGATCGAAGAAAGCAGATCTTATCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGTAGATAT
1 TAGATCAAAGAAAGCAGATCTTATCTTCACATACTGGCGCGAAGTAGATCAAAGATAGTAGATAT
* *
29975722 TGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATATTGTCTT-CAT-GT-ATCGGCA
66 TGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATATTGTCTTCCATACTGAT-GGC-
29975784 TGAAA
129 -GAAA
** * * * * *
29975789 TAGATCAAAGGTAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGACCGAAGATA
1 TAGATCAAAGAAAGCAGATCTTATCTTCACATACTGG-CGCGAAGTAGATCAAAGATA
29975847 CAAGTCTTAT
Statistics
Matches: 165, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
129 1 0.01
130 4 0.02
131 3 0.02
132 32 0.19
133 125 0.76
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.29
Consensus pattern (132 bp):
TAGATCAAAGAAAGCAGATCTTATCTTCACATACTGGCGCGAAGTAGATCAAAGATAGTAGATAT
TGTCTTCATATATTGGCGTGAAGTAGATCGAAGATAGCAGATATTGTCTTCCATACTGATGGCGA
AA
Found at i:29975882 original size:177 final size:174
Alignment explanation
Indices: 29975443--29975882 Score: 495
Period size: 177 Copynumber: 2.5 Consensus size: 174
29975433 GAACAGGTTG
* ** * * * * * * * **
29975443 AAGATAGCAGATCTTGCCTTCCTGTACCGATAGTGAAGCAGATCAAAGATACCAGTCTTGCCTCC
1 AAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGACCGAAGATA-CAGTCTTATCTCC
* * *
29975508 CTGGGTTGTCGTGAAGTAGATCGAAGAAAGCAGATCTTGTATTCATGTATTAGCGTGAAGTAGAT
65 CTGAGTTG-CGTGAAGTAGATCAAAGAAAGCAGATATTGTATTCATGTATTAGCGTGAAGTAGAT
* * * * * *
29975573 CAAAGATAGTAGATCTTGTCTTCATATATTGGCGTGAAGTAGATCG
129 CAAAGATAGCAGATATTGTCTTCATATATCGGCATGAAATAGATCA
* * *
29975619 AAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTATCTT
1 AAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGACCGAAGATA-CAG-TCTTATCTC
* * * * *
29975684 CATGTA-TTGGCGTGAAGTAGATCAAAGATAGTAGATATTGTCTTCATGTATTGGCGTGAAGTAG
64 CCTG-AGTT-GCGTGAAGTAGATCAAAGAAAGCAGATATTGTATTCATGTATTAGCGTGAAGTAG
* *
29975748 ATCGAAGATAGCAGATATTGTCTTCATGTATCGGCATGAAATAGATCA
127 ATCAAAGATAGCAGATATTGTCTTCATATATCGGCATGAAATAGATCA
*
29975796 AAGGTAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGACCGAAGATACAAGTCTTATCTCC
1 AAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGACCGAAGATAC-AGTCTTATCTCC
*
29975861 CTGAAGTTGCAGTGGAGTAGAT
65 CTG-AGTTGC-GTGAAGTAGAT
29975883 TGAATCACTA
Statistics
Matches: 221, Mismatches: 37, Indels: 11
0.82 0.14 0.04
Matches are distributed among these distances:
176 59 0.27
177 161 0.73
178 1 0.00
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (174 bp):
AAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGACCGAAGATACAGTCTTATCTCCC
TGAGTTGCGTGAAGTAGATCAAAGAAAGCAGATATTGTATTCATGTATTAGCGTGAAGTAGATCA
AAGATAGCAGATATTGTCTTCATATATCGGCATGAAATAGATCA
Found at i:29983778 original size:22 final size:22
Alignment explanation
Indices: 29983746--29983789 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 22
29983736 AAAATTTAAA
29983746 ATTTTTAAAAAATTATAAAAATT
1 ATTTTTAAAAAATT-TAAAAATT
29983769 ATTTTTAAAAAATTTAAAAAT
1 ATTTTTAAAAAATTTAAAAAT
29983790 CATTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.33
23 14 0.67
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTTTAAAAAATTTAAAAATT
Found at i:29990697 original size:14 final size:14
Alignment explanation
Indices: 29990678--29990706 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
29990668 GTGGGAGATC
29990678 GGGTTTTCCTTAAG
1 GGGTTTTCCTTAAG
29990692 GGGTTTTCCTTAAG
1 GGGTTTTCCTTAAG
29990706 G
1 G
29990707 TATCTCCGTG
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:0.14, C:0.14, G:0.31, T:0.41
Consensus pattern (14 bp):
GGGTTTTCCTTAAG
Found at i:29997686 original size:24 final size:24
Alignment explanation
Indices: 29997658--29997714 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
29997648 TTCAACAGCT
*
29997658 TTGTAATAGCACAAGTTCATAGTC
1 TTGTAATAGCACAAGTTAATAGTC
* *
29997682 TTGTAACAACACAAGTTAATAGTC
1 TTGTAATAGCACAAGTTAATAGTC
*
29997706 ATGTAATAG
1 TTGTAATAG
29997715 TTTTGTAACA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (24 bp):
TTGTAATAGCACAAGTTAATAGTC
Found at i:30000377 original size:43 final size:45
Alignment explanation
Indices: 30000258--30000407 Score: 178
Period size: 45 Copynumber: 3.4 Consensus size: 45
30000248 AGGAGGAAGA
* * *
30000258 ATTGGTGGCTTCATCCACAACCTACATGACAACTTGTCTACAAAT
1 ATTGGTGGCTTCATCCACAACCTACATGGCAGCTTGTCTACGAAT
** * **
30000303 ATTGGTGGCTTTGTCCACAACCTACAAGGCAGCTTGTCTTTGAAT
1 ATTGGTGGCTTCATCCACAACCTACATGGCAGCTTGTCTACGAAT
* * * *
30000348 -TTGGTGG-TTTATCCACAACCCACATGGCAGTTTGTCTGCGAAT
1 ATTGGTGGCTTCATCCACAACCTACATGGCAGCTTGTCTACGAAT
30000391 ATTGGTGGCTTCATCCA
1 ATTGGTGGCTTCATCCA
30000408 TATATGTTAG
Statistics
Matches: 88, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
43 30 0.34
44 14 0.16
45 44 0.50
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.32
Consensus pattern (45 bp):
ATTGGTGGCTTCATCCACAACCTACATGGCAGCTTGTCTACGAAT
Found at i:30003926 original size:3 final size:3
Alignment explanation
Indices: 30003860--30003914 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
30003850 TTCAACAAAC
30003860 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
30003908 ATA ATA A
1 ATA ATA A
30003915 ATTTTTAATA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:30004656 original size:31 final size:31
Alignment explanation
Indices: 30004611--30004678 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
30004601 TTACAAAATG
* * *
30004611 GTCACTGAATTATTCAGAAGTTTTTATTCAA
1 GTCACTGAACTATTCAAAAGTTTTTATGCAA
*
30004642 GTCATTGAACTATTCAAAAGTTTTTATGCAA
1 GTCACTGAACTATTCAAAAGTTTTTATGCAA
30004673 GTCACT
1 GTCACT
30004679 AGGCAATTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAGTTTTTATGCAA
Found at i:30008076 original size:14 final size:17
Alignment explanation
Indices: 30008042--30008077 Score: 51
Period size: 14 Copynumber: 2.3 Consensus size: 17
30008032 TCTTTTTCCA
30008042 CTTCCACTTATTCCTTT
1 CTTCCACTTATTCCTTT
30008059 CTTCC-CTT-TTCC-TT
1 CTTCCACTTATTCCTTT
30008073 CTTCC
1 CTTCC
30008078 TTACTAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 7 0.37
15 4 0.21
16 3 0.16
17 5 0.26
ACGTcount: A:0.06, C:0.42, G:0.00, T:0.53
Consensus pattern (17 bp):
CTTCCACTTATTCCTTT
Found at i:30014957 original size:57 final size:57
Alignment explanation
Indices: 30014889--30015178 Score: 422
Period size: 57 Copynumber: 5.1 Consensus size: 57
30014879 ATTTTTTAGG
* * * * *
30014889 TCATTTACATTTTAGAGAAAACCACATTCATTTTCAAATGATTACATTTCTCCATTT
1 TCATTTTCATTTTAGAGAAAACCATATTAATTTCCAAATGATTCCATTTCTCCATTT
* *
30014946 TCATTTTCA-TTTAGGAGAAAACCTTATTTATTTCCAAATGATTCCATTTCTCCATTT
1 TCATTTTCATTTTA-GAGAAAACCATATTAATTTCCAAATGATTCCATTTCTCCATTT
*
30015003 TCATTTTCA-TTTAGGAGAAAACCATATTAATTTCCAAATGATTTCATTTCTCCATTT
1 TCATTTTCATTTTA-GAGAAAACCATATTAATTTCCAAATGATTCCATTTCTCCATTT
*
30015060 TCATTTTCATTTTGGAGAAAACCATATTAATTTCCAAATGATTCCATTTCTCCATTT
1 TCATTTTCATTTTAGAGAAAACCATATTAATTTCCAAATGATTCCATTTCTCCATTT
* * *
30015117 TCATTTTCATTTTGGAGAAAAGCATAATAATTTCCAAATGATTTCTCATTTCTCCATTT
1 TCATTTTCATTTTAGAGAAAACCATATTAATTTCCAAATGA-TTC-CATTTCTCCATTT
30015176 TCA
1 TCA
30015179 CCCTTTCTAT
Statistics
Matches: 216, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
56 4 0.02
57 190 0.88
58 6 0.03
59 16 0.07
ACGTcount: A:0.31, C:0.19, G:0.07, T:0.44
Consensus pattern (57 bp):
TCATTTTCATTTTAGAGAAAACCATATTAATTTCCAAATGATTCCATTTCTCCATTT
Found at i:30022125 original size:33 final size:33
Alignment explanation
Indices: 30022059--30022144 Score: 85
Period size: 33 Copynumber: 2.7 Consensus size: 33
30022049 ATACAACAAG
* * *
30022059 CAGTGACAGTCTGGGCCTGAGCCCTATTCAGTAA
1 CAGT-ACAGTGTGGGCCTTAGCCCAATTCAGTAA
30022093 CAGTACAGTGTGGGCCTTAGCCCAATAT-AGTAA
1 CAGTACAGTGTGGGCCTTAGCCCAAT-TCAGTAA
30022126 C-G----GTGTGGGCCTTAGCCCA
1 CAGTACAGTGTGGGCCTTAGCCCA
30022145 GTACAATATC
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
28 17 0.35
32 1 0.02
33 25 0.52
34 5 0.10
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (33 bp):
CAGTACAGTGTGGGCCTTAGCCCAATTCAGTAA
Found at i:30022305 original size:26 final size:26
Alignment explanation
Indices: 30022266--30022366 Score: 112
Period size: 26 Copynumber: 3.9 Consensus size: 26
30022256 CCAATATTAA
* * * **
30022266 AGCAAAACTGCCAGTAATATTATCGT
1 AGCAAAGCTGCCAGTAACAGTATCAC
*
30022292 AGCTAAGCTGCCAGTAACAGTATCAC
1 AGCAAAGCTGCCAGTAACAGTATCAC
30022318 AGCAAAGCTGCCAGTAACAGTATCAC
1 AGCAAAGCTGCCAGTAACAGTATCAC
* * * *
30022344 AGTAAAGATGGCAGTAATAGTAT
1 AGCAAAGCTGCCAGTAACAGTAT
30022367 ACTTCCTCCA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 64 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.22
Consensus pattern (26 bp):
AGCAAAGCTGCCAGTAACAGTATCAC
Found at i:30022610 original size:26 final size:27
Alignment explanation
Indices: 30022523--30022609 Score: 115
Period size: 27 Copynumber: 3.3 Consensus size: 27
30022513 GGGTATAACA
*
30022523 GTCATTTTACCCTAT-GAGGGTATTTCG
1 GTCATTTTACCCTATAG-GGGTATTTTG
* * *
30022550 ATCATTTTATCCTATA-GGGTATTTTA
1 GTCATTTTACCCTATAGGGGTATTTTG
30022576 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATAGGGGTATTTTG
30022603 GTCATTT
1 GTCATTT
30022610 ATTAACCTCT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
26 22 0.43
27 29 0.57
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.46
Consensus pattern (27 bp):
GTCATTTTACCCTATAGGGGTATTTTG
Done.