Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr13
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55873576
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 1239791 characters in sequence are not A, C, G, or T
File 137 of 182
Found at i:42132931 original size:35 final size:34
Alignment explanation
Indices: 42132868--42132942 Score: 87
Period size: 35 Copynumber: 2.2 Consensus size: 34
42132858 GCGCCGAGCG
* * *
42132868 CTAGTCGGATAACCAACAATAGTTGTGCCCAGCA
1 CTAGTCGAATAACCAACAATAATTGTGCCCAACA
* * *
42132902 CTAGTCGAATAATCGACAAATAATTGTGCCCAACG
1 CTAGTCGAATAACCAAC-AATAATTGTGCCCAACA
42132937 CTAGTC
1 CTAGTC
42132943 AGATTACCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
34 14 0.41
35 20 0.59
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (34 bp):
CTAGTCGAATAACCAACAATAATTGTGCCCAACA
Found at i:42135643 original size:137 final size:137
Alignment explanation
Indices: 42135397--42135670 Score: 512
Period size: 137 Copynumber: 2.0 Consensus size: 137
42135387 GATTTTGTAC
*
42135397 ATCTTACCAATTATCTGATTCTAATATTTGTTTCCGTTATGGACTTAGGTCCGAATCTATATCTG
1 ATCTTACCAATTATCTGATTCCAATATTTGTTTCCGTTATGGACTTAGGTCCGAATCTATATCTG
*
42135462 ACTGTATATGAAATTCTGTGTATGTTGCATGGCTATCTCTGTTGGGTTACACACTGAGTTTACAA
66 ACTGTATATGAAATTCTGTGTATGTTCCATGGCTATCTCTGTTGGGTTACACACTGAGTTTACAA
42135527 AAACTCA
131 AAACTCA
* *
42135534 ATCTTACCAATTATCTGATTCCGATATTTGTTTCTGTTATGGACTTAGGTCCGAATCTATATCTG
1 ATCTTACCAATTATCTGATTCCAATATTTGTTTCCGTTATGGACTTAGGTCCGAATCTATATCTG
42135599 ACTGTATATGAAATTCTGTGTATGTTCCATGGCTATCTCTGTTGGGTTACACACTGAGTTTACAA
66 ACTGTATATGAAATTCTGTGTATGTTCCATGGCTATCTCTGTTGGGTTACACACTGAGTTTACAA
42135664 AAACTCA
131 AAACTCA
42135671 CATCGGTTTG
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 133 1.00
ACGTcount: A:0.26, C:0.18, G:0.17, T:0.39
Consensus pattern (137 bp):
ATCTTACCAATTATCTGATTCCAATATTTGTTTCCGTTATGGACTTAGGTCCGAATCTATATCTG
ACTGTATATGAAATTCTGTGTATGTTCCATGGCTATCTCTGTTGGGTTACACACTGAGTTTACAA
AAACTCA
Found at i:42138423 original size:25 final size:25
Alignment explanation
Indices: 42138389--42138459 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
42138379 CAGGCCTATT
42138389 TTCACAGCTCGTGTGAGCAT-TCTGA
1 TTCACAGCTCGTGTGAGCATAT-TGA
* *
42138414 TTCACAGCTCGTGTAAGAATATTGA
1 TTCACAGCTCGTGTGAGCATATTGA
*
42138439 TTCATAGCTCGTGTGAGCATA
1 TTCACAGCTCGTGTGAGCATA
42138460 CATGTACAGG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
25 39 0.98
26 1 0.03
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATATTGA
Found at i:42139608 original size:12 final size:12
Alignment explanation
Indices: 42139591--42139620 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
42139581 TCAGGCTGTT
42139591 ACACGGCCTAGC
1 ACACGGCCTAGC
*
42139603 ACACGGCCTGGC
1 ACACGGCCTAGC
42139615 ACACGG
1 ACACGG
42139621 GCATGTTCTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.23, C:0.40, G:0.30, T:0.07
Consensus pattern (12 bp):
ACACGGCCTAGC
Found at i:42141112 original size:104 final size:103
Alignment explanation
Indices: 42140947--42141174 Score: 366
Period size: 104 Copynumber: 2.2 Consensus size: 103
42140937 CCCGAGGGGT
***
42140947 TGCTAAGTGCGATATCCATTGTATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
1 TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* * *
42141012 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGG
66 AGGGGTTGCTAAGTGATGATTCCCCGATTCAGTGGTGG
* *
42141050 TGCTAAGTGCGATATCCACCATATCTTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCATATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
42141115 GAGGGGTTGCTAAGTGATGATTCCCCGATTCAGTGGTGG
65 GAGGGGTTGCTAAGTGATGATTCCCCGATTCAGTGGTGG
*
42141154 TGCTAAGTGCGAGATCCACCA
1 TGCTAAGTGCGATATCCACCA
42141175 ATAACGGTTA
Statistics
Matches: 115, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 30 0.26
104 85 0.74
ACGTcount: A:0.21, C:0.19, G:0.29, T:0.30
Consensus pattern (103 bp):
TGCTAAGTGCGATATCCACCATATATTTGAAATGAAAAGGGGGTTGCTATGTGCTGATTCCCCCG
AGGGGTTGCTAAGTGATGATTCCCCGATTCAGTGGTGG
Found at i:42149690 original size:21 final size:20
Alignment explanation
Indices: 42149649--42149690 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
42149639 ACCTCTACAG
*
42149649 TTTTGAAAATTTTCATTGTT
1 TTTTGAAAATTTTCATAGTT
42149669 TTTTGAAAAATTCTTCA-AGTT
1 TTTTG-AAAATT-TTCATAGTT
42149690 T
1 T
42149691 CTGATTTAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.55
Consensus pattern (20 bp):
TTTTGAAAATTTTCATAGTT
Found at i:42154532 original size:29 final size:29
Alignment explanation
Indices: 42154490--42154549 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
42154480 TTTAAACAAG
42154490 TCTGTACTCATATTATCCATTCCTATATC
1 TCTGTACTCATATTATCCATTCCTATATC
42154519 TCTGTACTCATATTATCCATTCCTATATC
1 TCTGTACTCATATTATCCATTCCTATATC
42154548 TC
1 TC
42154550 CATTTCAGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.23, C:0.28, G:0.03, T:0.45
Consensus pattern (29 bp):
TCTGTACTCATATTATCCATTCCTATATC
Found at i:42158115 original size:42 final size:43
Alignment explanation
Indices: 42158013--42158300 Score: 266
Period size: 43 Copynumber: 6.7 Consensus size: 43
42158003 AATGTGATAT
* * *
42158013 CGTGTAAGACCAC-GTCTGGGACGTTGGCATCGATTTGA-GATTTA
1 CGTGTAAGACC-CTATCTGGGACATTGGCATCGATAT-ATGA-TTA
* *
42158057 CGTGTAAGACCATATCTGGGACATTGGCGTC-ATATATGATTA
1 CGTGTAAGACCCTATCTGGGACATTGGCATCGATATATGATTA
* * * *
42158099 CGTGTAAGACCCTATCTGGGACAGTGGAATCGTTATTTGATTA
1 CGTGTAAGACCCTATCTGGGACATTGGCATCGATATATGATTA
* * * *
42158142 CATGTAAGACCAC-GTCTGGGACGTTGGCATCGATTTGA-GATTTA
1 CGTGTAAGACC-CTATCTGGGACATTGGCATCGATAT-ATGA-TTA
* *
42158186 CGTGTAAGACCATATCTGGGACATTGGCGTC-ATATATGATTA
1 CGTGTAAGACCCTATCTGGGACATTGGCATCGATATATGATTA
* * * *
42158228 CGTGTAAGACCCTATCTGGGACAGTGGAATCGTTATTTGATTA
1 CGTGTAAGACCCTATCTGGGACATTGGCATCGATATATGATTA
* * *
42158271 CATGTAAGACCAC-GTCTGGGACGTTGGCAT
1 CGTGTAAGACC-CTATCTGGGACATTGGCAT
42158301 TGTATGAGCT
Statistics
Matches: 198, Mismatches: 36, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
42 62 0.31
43 80 0.40
44 56 0.28
ACGTcount: A:0.26, C:0.18, G:0.26, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCCTATCTGGGACATTGGCATCGATATATGATTA
Found at i:42158331 original size:129 final size:129
Alignment explanation
Indices: 42158015--42158300 Score: 572
Period size: 129 Copynumber: 2.2 Consensus size: 129
42158005 TGTGATATCG
42158015 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATTTACGTGTAAGACCATATCTGGGACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATTTACGTGTAAGACCATATCTGGGACA
42158080 TTGGCGTCATATATGATTACGTGTAAGACCCTATCTGGGACAGTGGAATCGTTATTTGATTACA
66 TTGGCGTCATATATGATTACGTGTAAGACCCTATCTGGGACAGTGGAATCGTTATTTGATTACA
42158144 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATTTACGTGTAAGACCATATCTGGGACA
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATTTACGTGTAAGACCATATCTGGGACA
42158209 TTGGCGTCATATATGATTACGTGTAAGACCCTATCTGGGACAGTGGAATCGTTATTTGATTACA
66 TTGGCGTCATATATGATTACGTGTAAGACCCTATCTGGGACAGTGGAATCGTTATTTGATTACA
42158273 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
42158301 TGTATGAGCT
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 157 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (129 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATTTGAGATTTACGTGTAAGACCATATCTGGGACA
TTGGCGTCATATATGATTACGTGTAAGACCCTATCTGGGACAGTGGAATCGTTATTTGATTACA
Found at i:42165160 original size:51 final size:52
Alignment explanation
Indices: 42165083--42165211 Score: 181
Period size: 52 Copynumber: 2.5 Consensus size: 52
42165073 CGGATACCCG
* * *
42165083 GTGGCCTGCACATAGTACCACCCTTGT-AGCCAAAGCTA-CCTTCTTCATAAA
1 GTGGCCTTCACATAGTACCACACTTGTGA-CCAAAGCTATCCTTCTTCACAAA
* * *
42165134 GTGGCCTTCAAATAATACCACACTTGTGACCAAAGCTATCTTTCTTCACAAA
1 GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCCTTCTTCACAAA
42165186 GTGGCCTTCACATAGTACCACACTTG
1 GTGGCCTTCACATAGTACCACACTTG
42165212 AGTCACTAGT
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
51 32 0.47
52 36 0.53
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.27
Consensus pattern (52 bp):
GTGGCCTTCACATAGTACCACACTTGTGACCAAAGCTATCCTTCTTCACAAA
Found at i:42165552 original size:15 final size:16
Alignment explanation
Indices: 42165517--42165555 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
42165507 CAATTTAGCC
42165517 CAAAAATCATATTTTG
1 CAAAAATCATATTTTG
42165533 CAAAAATCATATTTTG
1 CAAAAATCATATTTTG
*
42165549 AAAAAAT
1 CAAAAAT
42165556 TACATTTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.33
Consensus pattern (16 bp):
CAAAAATCATATTTTG
Found at i:42165562 original size:16 final size:16
Alignment explanation
Indices: 42165518--42165563 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
42165508 AATTTAGCCC
* *
42165518 AAAAATCATATTTTGC
1 AAAAATCACATTTTGA
*
42165534 AAAAATCATATTTTGA
1 AAAAATCACATTTTGA
*
42165550 AAAAATTACATTTT
1 AAAAATCACATTTT
42165564 TGCCCTAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (16 bp):
AAAAATCACATTTTGA
Found at i:42168149 original size:39 final size:39
Alignment explanation
Indices: 42168025--42168142 Score: 150
Period size: 40 Copynumber: 3.0 Consensus size: 39
42168015 GGCGTTTGGA
* *
42168025 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGACGCTTT
1 TAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
* * * *
42168064 TAAAAAAATGCCACTAAAGATCGAGTATTAGCGGCGCTTCT
1 T-AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTT-T
42168105 TAAAAAACGCCGCTAAAAAT-GAGCATTAGCGGCG-TTT
1 TAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
42168142 T
1 T
42168143 CCAAAAAGTG
Statistics
Matches: 67, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
37 2 0.03
38 2 0.03
39 14 0.21
40 47 0.70
41 2 0.03
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (39 bp):
TAAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
Found at i:42168156 original size:39 final size:39
Alignment explanation
Indices: 42168025--42168162 Score: 145
Period size: 40 Copynumber: 3.5 Consensus size: 39
42168015 GGCGTTTGGA
* * *
42168025 TAAAAAACGCCGCTAAAAATCAAGCATTAGCGACGCTTT
1 TAAAAAATGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
* * *
42168064 TAAAAAAATGCCACTAAAGATCGAGTATTAGCGGCGCTTCT
1 T-AAAAAATGCCGCTAAAAATCGAGCATTAGCGGCGCTT-T
*
42168105 TAAAAAACGCCGCTAAAAAT-GAGCATTAGCGGCG-TTT
1 TAAAAAATGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
* *
42168142 TCCAAAAAGTGCCGCAAAAAA
1 T--AAAAAATGCCGCTAAAAA
42168163 CCTAAGTCCA
Statistics
Matches: 82, Mismatches: 13, Indels: 8
0.80 0.13 0.08
Matches are distributed among these distances:
37 2 0.02
38 2 0.02
39 29 0.35
40 47 0.57
41 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (39 bp):
TAAAAAATGCCGCTAAAAATCGAGCATTAGCGGCGCTTT
Found at i:42168259 original size:41 final size:41
Alignment explanation
Indices: 42168202--42168442 Score: 358
Period size: 41 Copynumber: 5.9 Consensus size: 41
42168192 TTTTTAGGCA
* * *
42168202 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGATCAGTGCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGGGCT
*
42168243 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCCCAGGGCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGGGCT
* * *
42168284 TTAGCGGTGTTTTTTAAGAAGCGCCGCTAATGCTAAGGGCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGGGCT
* *
42168325 TTAGCGGCGTTTTTGAAGAAGCGTCGCTAATGCTCAAGGCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGGGCT
* * *
42168366 TTAG-GGCATTTTTGAAGAAGCTCTGCTAATGCTCAGGGCT
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGGGCT
*
42168406 TTAGCGCCGTTTTTGAAGAAGCGCCGCTAATGCTCAG
1 TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAG
42168443 ATTTATCATA
Statistics
Matches: 177, Mismatches: 22, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 35 0.20
41 142 0.80
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (41 bp):
TTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCAGGGCT
Found at i:42168425 original size:122 final size:123
Alignment explanation
Indices: 42168202--42168439 Score: 363
Period size: 122 Copynumber: 1.9 Consensus size: 123
42168192 TTTTTAGGCA
*
42168202 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGATCAGTGCTTTAGCGGCGTTTTTGAAGAAGCGC
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGATCAGTGCTTTAGCGGCATTTTTGAAGAAGCGC
** *
42168267 CGCTAATGCCCAGGGCTTTAGCGGTGTTTTTTAAGAAGCGCCGCTAATGCTAAGGGCT
66 CGCTAATGCCCAGGGCTTTAGCGCCGTTTTTGAAGAAGCGCCGCTAATGCTAAGGGCT
* * * *
42168325 TTAGCGGCGTTTTTGAAGAAGCGTCGCTAATGCTCAAG-GCTTTAG-GGCATTTTTGAAGAAGCT
1 TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGATC-AGTGCTTTAGCGGCATTTTTGAAGAAGCG
* *
42168388 CTGCTAATGCTCAGGGCTTTAGCGCCGTTTTTGAAGAAGCGCCGCTAATGCT
65 CCGCTAATGCCCAGGGCTTTAGCGCCGTTTTTGAAGAAGCGCCGCTAATGCT
42168440 CAGATTTATC
Statistics
Matches: 104, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
122 63 0.61
123 39 0.38
124 2 0.02
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (123 bp):
TTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGATCAGTGCTTTAGCGGCATTTTTGAAGAAGCGC
CGCTAATGCCCAGGGCTTTAGCGCCGTTTTTGAAGAAGCGCCGCTAATGCTAAGGGCT
Found at i:42169416 original size:14 final size:15
Alignment explanation
Indices: 42169397--42169441 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
42169387 AGGACAATTA
42169397 TAAGGGTT-GGGGTT
1 TAAGGGTTAGGGGTT
42169411 TAAGGGTTAGGGG-T
1 TAAGGGTTAGGGGTT
* *
42169425 TAGGGGTTAAGGGTT
1 TAAGGGTTAGGGGTT
42169440 TA
1 TA
42169442 CGGTTTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
14 20 0.74
15 7 0.26
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (15 bp):
TAAGGGTTAGGGGTT
Found at i:42169424 original size:21 final size:21
Alignment explanation
Indices: 42169400--42169439 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
42169390 ACAATTATAA
42169400 GGGTT-GGGGTTTAAGGGTTAG
1 GGGTTAGGGG-TTAAGGGTTAG
42169421 GGGTTAGGGGTTAAGGGTT
1 GGGTTAGGGGTTAAGGGTT
42169440 TACGGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.15, C:0.00, G:0.53, T:0.33
Consensus pattern (21 bp):
GGGTTAGGGGTTAAGGGTTAG
Found at i:42169793 original size:15 final size:16
Alignment explanation
Indices: 42169765--42169794 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42169755 TATTATATTT
42169765 AACAAAAAACATTGAC
1 AACAAAAAACATTGAC
42169781 AACAAAAAA-ATTGA
1 AACAAAAAACATTGA
42169795 GAAATAAAAA
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:0.67, C:0.13, G:0.07, T:0.13
Consensus pattern (16 bp):
AACAAAAAACATTGAC
Found at i:42174027 original size:86 final size:87
Alignment explanation
Indices: 42173882--42174088 Score: 274
Period size: 87 Copynumber: 2.4 Consensus size: 87
42173872 AGATTATGTT
* ** * * *
42173882 TTTAGCGGCGTTTTTGCTAGAAGCGTCGTTAAAGGTCGTGGTTTGTAGCGGCGTTTGTGG-GAAA
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGTTAAAGGTCGTGGTTTGTAGCGGCGTTTGTGGAAAAA
* *
42173946 AGCGTCGCTAAAGGTCATGGTC
66 AACGCCGCTAAAGGTCATGGTC
42173968 TTTAGCGGCGTTTGTGGAAAAAGCGCCGTTAAAGGTCGTGGTCTT-TAGCGGCGTTTGTGGAAAA
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGTTAAAGGTCGTGGT-TTGTAGCGGCGTTTGTGGAAAA
*
42174032 AAACGCCGCTAAAGGTCGTGGTC
65 AAACGCCGCTAAAGGTCATGGTC
* * * *
42174055 TTTAGTGGCGTTTGTGGGAAAAGTGCCGCTAAAG
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGTTAAAG
42174089 TTAGCGACGC
Statistics
Matches: 106, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
86 52 0.49
87 54 0.51
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.29
Consensus pattern (87 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGTTAAAGGTCGTGGTTTGTAGCGGCGTTTGTGGAAAAA
AACGCCGCTAAAGGTCATGGTC
Found at i:42174048 original size:44 final size:43
Alignment explanation
Indices: 42173882--42174088 Score: 263
Period size: 43 Copynumber: 4.8 Consensus size: 43
42173872 AGATTATGTT
* ** * * *
42173882 TTTAGCGGCGTTTTTGCTAGAAGCGTCGTTAAAGGTCGTGGT-
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCGTGGTC
* * *
42173924 TTGTAGCGGCGTTTGTGGGAAAAGCGTCGCTAAAGGTCATGGTC
1 TT-TAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCGTGGTC
*
42173968 TTTAGCGGCGTTTGTGGAAAAAGCGCCGTTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCGTGGTC
*
42174011 TTTAGCGGCGTTTGTGGAAAAAAACGCCGCTAAAGGTCGTGGTC
1 TTTAGCGGCGTTTGTGG-AAAAAGCGCCGCTAAAGGTCGTGGTC
* * *
42174055 TTTAGTGGCGTTTGTGGGAAAAGTGCCGCTAAAG
1 TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAG
42174089 TTAGCGACGC
Statistics
Matches: 146, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
42 2 0.01
43 102 0.70
44 42 0.29
ACGTcount: A:0.21, C:0.15, G:0.34, T:0.29
Consensus pattern (43 bp):
TTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCGTGGTC
Found at i:42175304 original size:21 final size:22
Alignment explanation
Indices: 42175278--42175318 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
42175268 AATAAATACC
42175278 AAAAA-TTTATTTTAAAAATTA
1 AAAAATTTTATTTTAAAAATTA
42175299 AAAAATTTTATTTTAAAAAT
1 AAAAATTTTATTTTAAAAAT
42175319 ATTTTAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAAAATTTTATTTTAAAAATTA
Found at i:42175323 original size:11 final size:11
Alignment explanation
Indices: 42175307--42175409 Score: 55
Period size: 11 Copynumber: 9.9 Consensus size: 11
42175297 TAAAAAATTT
42175307 TATTTTAAAAA
1 TATTTTAAAAA
42175318 TATTTT--AAA
1 TATTTTAAAAA
42175327 -A--TTAAAAA
1 TATTTTAAAAA
* * *
42175335 AAATTAAAAAA
1 TATTTTAAAAA
42175346 GTATTTTAAAAA
1 -TATTTTAAAAA
42175358 TATTTT--AAA
1 TATTTTAAAAA
42175367 -A--TTAAAAA
1 TATTTTAAAAA
*
42175375 AATTTTAAAAAAA
1 TATTTT--AAAAA
*
42175388 GTATTTTAAAAG
1 -TATTTTAAAAA
42175400 TATTTTAAAA
1 TATTTTAAAA
42175410 TTAAAAAAAT
Statistics
Matches: 72, Mismatches: 6, Indels: 28
0.68 0.06 0.26
Matches are distributed among these distances:
6 4 0.06
8 8 0.11
9 8 0.11
11 30 0.42
12 12 0.17
13 5 0.07
14 5 0.07
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:42175351 original size:40 final size:40
Alignment explanation
Indices: 42175291--42175418 Score: 193
Period size: 42 Copynumber: 3.1 Consensus size: 40
42175281 AATTTATTTT
*
42175291 AAAAATTAAAAAATTTTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAA--GTATTTTAAAAATATTTTAAAATTAAA
42175333 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
1 AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
* *
42175373 AAAATTTTAAAAAAAGTATTTTAAAAGTATTTTAAAATTAAA
1 AAAA-ATT-AAAAAAGTATTTTAAAAATATTTTAAAATTAAA
42175415 AAAA
1 AAAA
42175419 TAAAAATAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
40 30 0.37
41 2 0.02
42 49 0.60
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (40 bp):
AAAAATTAAAAAAGTATTTTAAAAATATTTTAAAATTAAA
Found at i:42175387 original size:30 final size:30
Alignment explanation
Indices: 42175334--42175398 Score: 89
Period size: 30 Copynumber: 2.1 Consensus size: 30
42175324 AAAATTAAAA
42175334 AAAATTAAAAAAGTATTTTAAAAA-TATTTT
1 AAAATTAAAAAAG-ATTTTAAAAAGTATTTT
42175364 AAAATTAAAAAA-ATTTTAAAAAAAGTATTTT
1 AAAATTAAAAAAGATTTT--AAAAAGTATTTT
42175395 AAAA
1 AAAA
42175399 GTATTTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
28 5 0.16
30 17 0.53
31 10 0.31
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (30 bp):
AAAATTAAAAAAGATTTTAAAAAGTATTTT
Found at i:42175419 original size:42 final size:41
Alignment explanation
Indices: 42175307--42175420 Score: 194
Period size: 42 Copynumber: 2.8 Consensus size: 41
42175297 TAAAAAATTT
42175307 TATTTTAAAAATATTTTAAAATTAAAAAAA-ATTAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATATTAAAAAAG
*
42175347 TATTTTAAAAATATTTTAAAATTAAAAAAATTTTAAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATATT-AAAAAAG
*
42175389 TATTTTAAAAGTATTTTAAAATTAAAAAAATA
1 TATTTTAAAAATATTTTAAAATTAAAAAAATA
42175421 AAAATAAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
40 30 0.43
41 2 0.03
42 37 0.54
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (41 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAATATTAAAAAAG
Found at i:42175435 original size:42 final size:41
Alignment explanation
Indices: 42175307--42175435 Score: 188
Period size: 42 Copynumber: 3.1 Consensus size: 41
42175297 TAAAAAATTT
*
42175307 TATTTTAAAAATATTTTAAAATTAAAAAAA-ATTAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAATATAAAAAAAG
*
42175347 TATTTTAAAAATATTTTAAAATTAAAAAAATTTTAAAAAAAG
1 TATTTTAAAAATATTTTAAAATTAAAAAAA-TATAAAAAAAG
* * *
42175389 TATTTTAAAAGTATTTTAAAATTAAAAAAATAAAAATAAAAA
1 TATTTTAAAAATATTTTAAAATTAAAAAAATATAAA-AAAAG
42175431 TATTT
1 TATTT
42175436 ATTATATTCG
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 30 0.38
41 4 0.05
42 46 0.57
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (41 bp):
TATTTTAAAAATATTTTAAAATTAAAAAAATATAAAAAAAG
Found at i:42176469 original size:79 final size:79
Alignment explanation
Indices: 42176338--42176495 Score: 271
Period size: 79 Copynumber: 2.0 Consensus size: 79
42176328 TCATTGTAAA
* *
42176338 ACACTTCAGTTTGGAGCAATAATAAATCTTAAGAGCATTCACTCAAATTTCTCATTCTCTTGCGT
1 ACACTTCAGTTTGGAGCAATAATAAATCTTAAGAACATTCACTCAAATTTCTCACTCTCTTGCGT
42176403 TCTTATTTTCTGTG
66 TCTTATTTTCTGTG
* * *
42176417 ACACTTGAGTTTGGAGCAATAATAATTCTTAAGAACATTCACTCAAATTTCTCCCTCTCTTGCGT
1 ACACTTCAGTTTGGAGCAATAATAAATCTTAAGAACATTCACTCAAATTTCTCACTCTCTTGCGT
42176482 TCTTATTTTCTGTG
66 TCTTATTTTCTGTG
42176496 GCTTGTTCTT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 74 1.00
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.41
Consensus pattern (79 bp):
ACACTTCAGTTTGGAGCAATAATAAATCTTAAGAACATTCACTCAAATTTCTCACTCTCTTGCGT
TCTTATTTTCTGTG
Found at i:42183364 original size:21 final size:21
Alignment explanation
Indices: 42183340--42183429 Score: 130
Period size: 21 Copynumber: 4.3 Consensus size: 21
42183330 CCATCACTGT
42183340 TGCCTCTGCCTCCCTCGCTAG-
1 TGCCTCTGCCTCCCTCGCT-GC
42183361 TGCCTCTGCCTCCCTCGCTGC
1 TGCCTCTGCCTCCCTCGCTGC
*
42183382 TGCCGCTGCCTCCCTCGCTGC
1 TGCCTCTGCCTCCCTCGCTGC
*
42183403 TG-CTGCTGCCTCCCTCTCTGC
1 TGCCT-CTGCCTCCCTCGCTGC
42183424 TGCCTC
1 TGCCTC
42183430 CGCTCTAAGT
Statistics
Matches: 63, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.03
21 59 0.94
22 2 0.03
ACGTcount: A:0.01, C:0.50, G:0.20, T:0.29
Consensus pattern (21 bp):
TGCCTCTGCCTCCCTCGCTGC
Found at i:42183870 original size:13 final size:14
Alignment explanation
Indices: 42183843--42183871 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
42183833 GGATGAATCG
42183843 AATTAAACAATTAT
1 AATTAAACAATTAT
42183857 AATTAAAC-ATTAT
1 AATTAAACAATTAT
42183870 AA
1 AA
42183872 ATATTTAGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACAATTAT
Found at i:42184060 original size:17 final size:16
Alignment explanation
Indices: 42184038--42184076 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
42184028 AAAATATTAT
42184038 TTAATAGTAGAAAGTAA
1 TTAATAGTAGAAAG-AA
* *
42184055 TTAATATTTGAAAGAA
1 TTAATAGTAGAAAGAA
42184071 TTAATA
1 TTAATA
42184077 AATTCATAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (16 bp):
TTAATAGTAGAAAGAA
Found at i:42184289 original size:9 final size:9
Alignment explanation
Indices: 42184263--42184375 Score: 51
Period size: 9 Copynumber: 12.8 Consensus size: 9
42184253 GTCTTACGTC
*
42184263 AGTTAAGTA
1 AGTTATGTA
42184272 AGCTT-TGTA
1 AG-TTATGTA
42184281 AGTTATGTA
1 AGTTATGTA
*
42184290 AGTTATGTT
1 AGTTATGTA
* *
42184299 A-TGATATA
1 AGTTATGTA
*
42184307 CATTTATGTAA
1 -AGTTATGT-A
42184318 AG-TATGTA
1 AGTTATGTA
42184326 AGTTATGATA
1 AGTTATG-TA
* * *
42184336 TGATATAT-
1 AGTTATGTA
42184344 A-TTGATGT-
1 AGTT-ATGTA
42184352 A-TTATGTA
1 AGTTATGTA
*
42184360 AGTTGTGTA
1 AGTTATGTA
42184369 AGTTATG
1 AGTTATG
42184376 ATATGATATA
Statistics
Matches: 78, Mismatches: 16, Indels: 20
0.68 0.14 0.18
Matches are distributed among these distances:
7 5 0.06
8 16 0.21
9 43 0.55
10 13 0.17
11 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.44
Consensus pattern (9 bp):
AGTTATGTA
Found at i:42184324 original size:36 final size:36
Alignment explanation
Indices: 42184284--42184352 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 36
42184274 CTTTGTAAGT
* *
42184284 TATGTAAGTTATGTTATGATATACATTTATGTAAAG
1 TATGTAAGTTATGATATGATATACATTGATGTAAAG
*
42184320 TATGTAAGTTATGATATGATATATATTGATGTA
1 TATGTAAGTTATGATATGATATACATTGATGTA
42184353 TTATGTAAGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.36, C:0.01, G:0.17, T:0.45
Consensus pattern (36 bp):
TATGTAAGTTATGATATGATATACATTGATGTAAAG
Found at i:42184369 original size:43 final size:43
Alignment explanation
Indices: 42184310--42184418 Score: 155
Period size: 43 Copynumber: 2.5 Consensus size: 43
42184300 TGATATACAT
* *
42184310 TTATGTAAAGTATGTAAGTTATGATATGATATATATTGATGTA
1 TTATGTAAGGTATGTAAGTTATGATATGATATATATTGATATA
* * *
42184353 TTATGTAAGTTGTGTAAGTTATGATATGATATATATTTATATA
1 TTATGTAAGGTATGTAAGTTATGATATGATATATATTGATATA
* *
42184396 TTTTGTAAGGTATATAAGTTATG
1 TTATGTAAGGTATGTAAGTTATG
42184419 TAAGTTATTA
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 57 1.00
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (43 bp):
TTATGTAAGGTATGTAAGTTATGATATGATATATATTGATATA
Found at i:42184414 original size:52 final size:55
Alignment explanation
Indices: 42184334--42184499 Score: 198
Period size: 56 Copynumber: 3.0 Consensus size: 55
42184324 TAAGTTATGA
* * * *
42184334 TATGATATATATTGATGTATTATGTAAGTTGTGTAAGTTATGATATGATATATATT
1 TATGATATATATTTAGGTATTA-GTAAGTTATGTAAGTTATTATATGATATATATT
42184390 TAT-ATAT-T-TTGTAAGGTA-TA-TAAGTTATGTAAGTTATTATATGATATATATT
1 TATGATATATATT-T-AGGTATTAGTAAGTTATGTAAGTTATTATATGATATATATT
* * *
42184442 TATGATATATATTTATGTATTATGTAAGTTTTGTAAGTTTTTATATGATATATATT
1 TATGATATATATTTAGGTATTA-GTAAGTTATGTAAGTTATTATATGATATATATT
42184498 TA
1 TA
42184500 ACATTAAGAT
Statistics
Matches: 95, Mismatches: 7, Indels: 16
0.81 0.06 0.14
Matches are distributed among these distances:
52 33 0.35
53 10 0.11
54 7 0.07
55 10 0.11
56 35 0.37
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (55 bp):
TATGATATATATTTAGGTATTAGTAAGTTATGTAAGTTATTATATGATATATATT
Found at i:42184431 original size:43 final size:44
Alignment explanation
Indices: 42184277--42184442 Score: 144
Period size: 43 Copynumber: 3.8 Consensus size: 44
42184267 AAGTAAGCTT
* * * *
42184277 TGTAAGTTATG-TAAGTTATGTTATGATATACATTTATGTAAAGTA
1 TGTAAGTTATGATAAGATAT-ATATGATATATATTT-TGTAAGGTA
* * * * *
42184322 TGTAAGTTATGATATGATATATAT--TGATGTATTATGTAAGTTG
1 TGTAAGTTATGATAAGATATATATGAT-ATATATTTTGTAAGGTA
* *
42184365 TGTAAGTTATGATATGATATATAT-TTATATATTTTGTAAGGTA
1 TGTAAGTTATGATAAGATATATATGATATATATTTTGTAAGGTA
* *
42184408 TATAAGTTATG-TAAGTTATTATATGATATATATTT
1 TGTAAGTTATGATAAGATA-TATATGATATATATTT
42184443 ATGATATATA
Statistics
Matches: 99, Mismatches: 17, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
42 5 0.05
43 59 0.60
44 15 0.15
45 14 0.14
46 6 0.06
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.48
Consensus pattern (44 bp):
TGTAAGTTATGATAAGATATATATGATATATATTTTGTAAGGTA
Found at i:42184447 original size:13 final size:13
Alignment explanation
Indices: 42184424--42184458 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
42184414 TTATGTAAGT
42184424 TATTATATGATATA
1 TATT-TATGATATA
42184438 TATTTATGATATA
1 TATTTATGATATA
42184451 TATTTATG
1 TATTTATG
42184459 TATTATGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (13 bp):
TATTTATGATATA
Found at i:42184568 original size:12 final size:12
Alignment explanation
Indices: 42184530--42184575 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 12
42184520 TCCCAAGCTA
42184530 AAAAAAATATTTT
1 AAAAAAA-ATTTT
42184543 AATTAAATAAATTTT
1 AA--AAA-AAATTTT
42184558 AAAAAAAATTTT
1 AAAAAAAATTTT
42184570 AAAAAA
1 AAAAAA
42184576 TCACATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
12 13 0.43
13 5 0.17
15 10 0.33
16 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
AAAAAAAATTTT
Found at i:42188522 original size:15 final size:15
Alignment explanation
Indices: 42188499--42188549 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
42188489 CTAACCTCCA
*
42188499 TTTTATATTCATTTT
1 TTTTGTATTCATTTT
*
42188514 TTTTGTATTTAATTTT
1 TTTTGTA-TTCATTTT
42188530 TATTTGT-TATCATTTT
1 T-TTTGTAT-TCATTTT
42188546 TTTT
1 TTTT
42188550 AAATCTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
15 10 0.33
16 15 0.50
17 5 0.17
ACGTcount: A:0.18, C:0.04, G:0.04, T:0.75
Consensus pattern (15 bp):
TTTTGTATTCATTTT
Found at i:42188626 original size:14 final size:14
Alignment explanation
Indices: 42188591--42188626 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
42188581 TATTATCTCT
42188591 TAAATAATTTAATC
1 TAAATAATTTAATC
42188605 TAAA-AATTTAATC
1 TAAATAATTTAATC
42188618 TAAATAATT
1 TAAATAATT
42188627 CCATTTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAATAATTTAATC
Found at i:42188868 original size:36 final size:36
Alignment explanation
Indices: 42188828--42188897 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
42188818 ACATGTAACC
42188828 ATTAACCATATAA-ACATAAACCCTAAACCATAATTT
1 ATTAACCATA-AACACATAAACCCTAAACCATAATTT
* * * *
42188864 ATTAACCCTAAACCCATAACCCCTAATCCATAAT
1 ATTAACCATAAACACATAAACCCTAAACCATAAT
42188898 CCATAAACCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 2 0.07
36 27 0.93
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.26
Consensus pattern (36 bp):
ATTAACCATAAACACATAAACCCTAAACCATAATTT
Found at i:42189290 original size:18 final size:18
Alignment explanation
Indices: 42189267--42189308 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
42189257 TCTGAAGAAT
42189267 ATAAATATATAATTAAAA
1 ATAAATATATAATTAAAA
* * *
42189285 ATAAAT-TATATTTTAAC
1 ATAAATATATAATTAAAA
42189302 ATAAATA
1 ATAAATA
42189309 AACCACTTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAAATATATAATTAAAA
Found at i:42189661 original size:39 final size:39
Alignment explanation
Indices: 42189558--42189661 Score: 97
Period size: 39 Copynumber: 2.6 Consensus size: 39
42189548 AAAATTTGCA
*
42189558 GCGTTTTTTAACAAACGCCGCT-ATATGCATACCTTTAGCG
1 GCGTTTTTT-ACAAACGCCGCTAATATGCATA-CTATAGCG
* * * *
42189598 GCGCTTCTTTAAAAATGCCACTAATACTG-AT-CTATAGCG
1 GCG-TTTTTTACAAACGCCGCTAATA-TGCATACTATAGCG
42189637 GCGTTTTTGTACAAACGCCGCTAAT
1 GCGTTTTT-TACAAACGCCGCTAAT
42189662 GCCATTGAAG
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
38 4 0.08
39 23 0.45
40 12 0.24
41 10 0.20
42 2 0.04
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.32
Consensus pattern (39 bp):
GCGTTTTTTACAAACGCCGCTAATATGCATACTATAGCG
Found at i:42197474 original size:13 final size:13
Alignment explanation
Indices: 42197454--42197486 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
42197444 TGTATATGGT
42197454 AAAAATTTATT-A
1 AAAAATTTATTCA
42197466 AACAAATTTATTCA
1 AA-AAATTTATTCA
42197480 AAAAATT
1 AAAAATT
42197487 ACAAGTAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 2 0.11
13 14 0.74
14 3 0.16
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAATTTATTCA
Found at i:42199709 original size:52 final size:53
Alignment explanation
Indices: 42199558--42199713 Score: 197
Period size: 54 Copynumber: 2.9 Consensus size: 53
42199548 GGACCATGGC
* * *
42199558 AACAAGTGATAAGCGATATCTGTATAAGACCATAGCTAGGCTATGGCATCGGAA
1 AACAAGTGATAAGTGAT-TCTGTATAAGACCATAGCTGGGCTATGGCATCAGAA
* *
42199612 AACAAGTGATAAGTGATTCCCGTATAAGACCATAGCTGGGCTATGGCATCAGAG
1 AACAAGTGATAAGTGATT-CTGTATAAGACCATAGCTGGGCTATGGCATCAGAA
* * * * *
42199666 AA-AAGTGATAAGTGCTTCTGTGTAAGACCATATCCGGGATATGGCATC
1 AACAAGTGATAAGTGATTCTGTATAAGACCATAGCTGGGCTATGGCATC
42199714 GATATGATAT
Statistics
Matches: 90, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
52 26 0.29
53 15 0.17
54 49 0.54
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.24
Consensus pattern (53 bp):
AACAAGTGATAAGTGATTCTGTATAAGACCATAGCTGGGCTATGGCATCAGAA
Found at i:42201286 original size:64 final size:64
Alignment explanation
Indices: 42201092--42201297 Score: 238
Period size: 64 Copynumber: 3.2 Consensus size: 64
42201082 CATAATTTTG
* * * * *
42201092 GCTCTCTTGTAC-ACATGGTGAACACTTAATACCACCCATGTGACCTAGC--CAGTTTATCTCGT
1 GCTCTCTTGT-CTACATGGTGTACACATAGTACCACCCATGCGACCTAGCTACA-TATATCTCGT
42201154 A
64 A
* * * * * *
42201155 GCTCTCTTGTCTACATGGTGTCCTTCACCTGGAACCACGCATGCGACCTAGCTACATATATCCCG
1 GCTCTCTTGTCTACATGGTG---TACACATAGTACCACCCATGCGACCTAGCTACATATATCTCG
42201220 TA
63 TA
*
42201222 GCTCTCTTGTCTACATGGTGTACACATAGTATCACCCATGCGACCTAGCTACATATATCTCGTA
1 GCTCTCTTGTCTACATGGTGTACACATAGTACCACCCATGCGACCTAGCTACATATATCTCGTA
42201286 GCTCTCTTGTCT
1 GCTCTCTTGTCT
42201298 NNNNNNNNNN
Statistics
Matches: 120, Mismatches: 17, Indels: 11
0.81 0.11 0.07
Matches are distributed among these distances:
62 1 0.01
63 18 0.15
64 49 0.41
66 21 0.17
67 29 0.24
68 2 0.02
ACGTcount: A:0.22, C:0.30, G:0.17, T:0.31
Consensus pattern (64 bp):
GCTCTCTTGTCTACATGGTGTACACATAGTACCACCCATGCGACCTAGCTACATATATCTCGTA
Found at i:42201758 original size:20 final size:18
Alignment explanation
Indices: 42201733--42201769 Score: 56
Period size: 20 Copynumber: 1.9 Consensus size: 18
42201723 ATTGCTAAGT
42201733 TGTAAAATGAGTTGTAAATG
1 TGTAAAAT-AGTTG-AAATG
42201753 TGTAAAATAGTTGAAAT
1 TGTAAAATAGTTGAAAT
42201770 TATGAGTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 5 0.29
20 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (18 bp):
TGTAAAATAGTTGAAATG
Found at i:42216502 original size:82 final size:82
Alignment explanation
Indices: 42216365--42216528 Score: 328
Period size: 82 Copynumber: 2.0 Consensus size: 82
42216355 GTCGTTTGAC
42216365 GGTATCCGAATATGAACGTGAGTTTGTAAGGCTCAGTCGATATGTTCAAGAGTGTGTAGCTGATG
1 GGTATCCGAATATGAACGTGAGTTTGTAAGGCTCAGTCGATATGTTCAAGAGTGTGTAGCTGATG
42216430 AAGTTACCATGTGTAAA
66 AAGTTACCATGTGTAAA
42216447 GGTATCCGAATATGAACGTGAGTTTGTAAGGCTCAGTCGATATGTTCAAGAGTGTGTAGCTGATG
1 GGTATCCGAATATGAACGTGAGTTTGTAAGGCTCAGTCGATATGTTCAAGAGTGTGTAGCTGATG
42216512 AAGTTACCATGTGTAAA
66 AAGTTACCATGTGTAAA
42216529 AGATTTGAAG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 82 1.00
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.30
Consensus pattern (82 bp):
GGTATCCGAATATGAACGTGAGTTTGTAAGGCTCAGTCGATATGTTCAAGAGTGTGTAGCTGATG
AAGTTACCATGTGTAAA
Found at i:42221210 original size:17 final size:17
Alignment explanation
Indices: 42221188--42221225 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
42221178 ACTAAAGTTA
42221188 TCTTACATTTTCATCAT
1 TCTTACATTTTCATCAT
42221205 TCTTACATTTTCATCAT
1 TCTTACATTTTCATCAT
42221222 TCTT
1 TCTT
42221226 TCTTCCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (17 bp):
TCTTACATTTTCATCAT
Found at i:42222111 original size:37 final size:37
Alignment explanation
Indices: 42222061--42222131 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
42222051 CTTAAATTAC
42222061 AAGTATATGGTTATTTGATATGTGAACGAAAATGAAT
1 AAGTATATGGTTATTTGATATGTGAACGAAAATGAAT
*
42222098 AAGTATATGGTTATTTGATATGTGTACGAAAATG
1 AAGTATATGGTTATTTGATATGTGAACGAAAATG
42222132 TTCAAAAGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.37
Consensus pattern (37 bp):
AAGTATATGGTTATTTGATATGTGAACGAAAATGAAT
Found at i:42222525 original size:17 final size:17
Alignment explanation
Indices: 42222495--42222527 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
42222485 TTAAATAATT
42222495 ATTTAGTTTATATTTTC
1 ATTTAGTTTATATTTTC
42222512 ATTTA-TTTATTATTTT
1 ATTTAGTTTA-TATTTT
42222528 TTGACTTCTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTTAGTTTATATTTTC
Found at i:42232415 original size:3 final size:3
Alignment explanation
Indices: 42232407--42232435 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
42232397 TTTGCTTGAG
42232407 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
42232436 ATATGTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:42233347 original size:15 final size:15
Alignment explanation
Indices: 42233327--42233357 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42233317 ACTAATTATC
42233327 TTGTTTCAAATATTA
1 TTGTTTCAAATATTA
42233342 TTGTTTCAAATATTA
1 TTGTTTCAAATATTA
42233357 T
1 T
42233358 CTTAAGTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.55
Consensus pattern (15 bp):
TTGTTTCAAATATTA
Found at i:42234065 original size:17 final size:18
Alignment explanation
Indices: 42234043--42234090 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
42234033 CAAAATTATT
*
42234043 TTTTAAAATATT-TTTAA
1 TTTTAAAATATTAATTAA
*
42234060 TTTTAAAAAATTAATTAA
1 TTTTAAAATATTAATTAA
*
42234078 TTATTAATATATT
1 TT-TTAAAATATT
42234091 GTGTCAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 11 0.44
18 6 0.24
19 8 0.32
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTTTAAAATATTAATTAA
Found at i:42234077 original size:18 final size:17
Alignment explanation
Indices: 42234034--42234084 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
42234024 CAACTATAAC
42234034 AAAATTATT--TTTTAA
1 AAAATTATTAATTTTAA
* *
42234049 AATATTTTTAATTTTAA
1 AAAATTATTAATTTTAA
42234066 AAAATTAATTAATTATTAA
1 AAAATT-ATTAATT-TTAA
42234085 TATATTGTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 7 0.25
17 11 0.39
18 6 0.21
19 4 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AAAATTATTAATTTTAA
Found at i:42235616 original size:18 final size:18
Alignment explanation
Indices: 42235593--42235863 Score: 145
Period size: 18 Copynumber: 14.6 Consensus size: 18
42235583 GAATAATTAT
42235593 TTATTCAGTAACAGTCAG
1 TTATTCAGTAACAGTCAG
* * *
42235611 TTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAG
* * **
42235629 TTATTCAATAATAACCAG
1 TTATTCAGTAACAGTCAG
*
42235647 TTATTCAGTATCGATCAATTGATCGG
1 TTATTCAGTA---A-C-A--G-TCAG
* *
42235673 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAG
*
42235691 TTATTCAGTAA-AATCAG
1 TTATTCAGTAACAGTCAG
* * *
42235708 ATATTCAGTAACAATTAAG
1 TTATTCAGTAAC-AGTCAG
*
42235727 TTATTCAGTAGCAGTCA-
1 TTATTCAGTAACAGTCAG
* *
42235744 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAG
* *
42235763 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAG
* *
42235781 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAG
42235799 TTATTCAGTAACAGTCTA-
1 TTATTCAGTAACAGTC-AG
* * * *
42235817 ATATCCAGTAACAGTAAA
1 TTATTCAGTAACAGTCAG
* * * *
42235835 TTATCCGGTAATAGTCAA
1 TTATTCAGTAACAGTCAG
42235853 TTATTCAGTAA
1 TTATTCAGTAA
42235864 TAATAAGTTA
Statistics
Matches: 190, Mismatches: 47, Indels: 32
0.71 0.17 0.12
Matches are distributed among these distances:
17 17 0.09
18 139 0.73
19 18 0.09
21 2 0.01
22 1 0.01
23 2 0.01
26 11 0.06
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAG
Found at i:42235635 original size:36 final size:36
Alignment explanation
Indices: 42235593--42235863 Score: 172
Period size: 36 Copynumber: 7.3 Consensus size: 36
42235583 GAATAATTAT
*
42235593 TTATTCAGTAACAGTCAGTTATTCGGTAACAATCAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATCAA
* * ** * *
42235629 TTATTCAATAATAACCAGTTATTCAGTATCGATCAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATCAA
*
42235665 TTGATCGGTTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGA
1 TT-A-----T-T-CAGTAACAGTCAGTTATTCAGTAACAATCA-A
* * * *
42235709 -TATTCAGTAACAATTAAGTTATTCAGTAGCAGTC-A
1 TTATTCAGTAAC-AGTCAGTTATTCAGTAACAATCAA
* * **
42235744 TTCATTCAGTGACAATCAGTTATTCAGTAATGATCAA
1 TT-ATTCAGTAACAGTCAGTTATTCAGTAACAATCAA
* * *
42235781 TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATC-AA
* * * * * * *
42235818 -TATCCAGTAACAGTAAATTATCCGGTAATAGTCAA
1 TTATTCAGTAACAGTCAGTTATTCAGTAACAATCAA
42235853 TTATTCAGTAA
1 TTATTCAGTAA
42235864 TAATAAGTTA
Statistics
Matches: 178, Mismatches: 41, Indels: 32
0.71 0.16 0.13
Matches are distributed among these distances:
35 10 0.06
36 122 0.69
37 19 0.11
42 2 0.01
43 6 0.03
44 19 0.11
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (36 bp):
TTATTCAGTAACAGTCAGTTATTCAGTAACAATCAA
Found at i:42235736 original size:54 final size:54
Alignment explanation
Indices: 42235672--42235863 Score: 176
Period size: 54 Copynumber: 3.6 Consensus size: 54
42235662 CAATTGATCG
*
42235672 GTTATCCAGTAACAGTCAATTATTCAGTAA-AATCAGATATTCAGTAACAATTAA
1 GTTATTCAGTAACAGTCAATTATTCAGTAACAATCAGATATTCAGTAAC-ATTAA
* * * * *
42235726 GTTATTCAGTAGCAGTC-ATTCATTCAGTGACAATCAGTTATTCAGTAATGATCAA
1 GTTATTCAGTAACAGTCAATT-ATTCAGTAACAATCAGATATTCAGTAA-CATTAA
* * * * * *
42235781 -TTATTCAGTAATATTCAGTTATTCAGTAACAGTCTA-ATATCCAGTAACAGTAA
1 GTTATTCAGTAACAGTCAATTATTCAGTAACAATC-AGATATTCAGTAACATTAA
* * * *
42235834 ATTATCCGGTAATAGTCAATTATTCAGTAA
1 GTTATTCAGTAACAGTCAATTATTCAGTAA
42235864 TAATAAGTTA
Statistics
Matches: 111, Mismatches: 21, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
53 6 0.05
54 82 0.74
55 23 0.21
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (54 bp):
GTTATTCAGTAACAGTCAATTATTCAGTAACAATCAGATATTCAGTAACATTAA
Found at i:42235808 original size:72 final size:71
Alignment explanation
Indices: 42235674--42235875 Score: 210
Period size: 72 Copynumber: 2.8 Consensus size: 71
42235664 ATTGATCGGT
* * * * *
42235674 TATCCAGTAACAGTCAATTATTCAGTAAAATCAGA-TATTCAGTAACAATTAAGTTATTCAGTAG
1 TATCCAGTAACAATAAATTATTCAGTAATATCA-ATTATTCAGTAA-TATTAAGTTATTCAGTAA
*
42235738 CAGTC-AT
64 CAGTCTAA
* * * * *
42235745 TCATTCAGTGACAATCAGTTATTCAGTAATGATCAATTATTCAGTAATATTCAGTTATTCAGTAA
1 T-ATCCAGTAACAATAAATTATTCAGTAAT-ATCAATTATTCAGTAATATTAAGTTATTCAGTAA
42235810 CAGTCTAA
64 CAGTCTAA
* * * *
42235818 TATCCAGTAACAGTAAATTATCCGGTAATAGTCAATTATTCAGTAATAATAAGTTATT
1 TATCCAGTAACAATAAATTATTCAGTAATA-TCAATTATTCAGTAATATTAAGTTATT
42235876 TTATTCCTTT
Statistics
Matches: 108, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
71 2 0.02
72 90 0.83
73 16 0.15
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.35
Consensus pattern (71 bp):
TATCCAGTAACAATAAATTATTCAGTAATATCAATTATTCAGTAATATTAAGTTATTCAGTAACA
GTCTAA
Found at i:42235865 original size:18 final size:18
Alignment explanation
Indices: 42235673--42235863 Score: 149
Period size: 18 Copynumber: 10.6 Consensus size: 18
42235663 AATTGATCGG
*
42235673 TTATCCAGTAACAGTCAA
1 TTATTCAGTAACAGTCAA
*
42235691 TTATTCAGTAA-AATCAGA
1 TTATTCAGTAACAGTCA-A
* *
42235709 -TATTCAGTAACAATTAA
1 TTATTCAGTAACAGTCAA
*
42235726 GTTATTCAGTAGCAGTC-A
1 -TTATTCAGTAACAGTCAA
* * *
42235744 TTCATTCAGTGACAATCAG
1 TT-ATTCAGTAACAGTCAA
*
42235763 TTATTCAGTAA-TGATCAA
1 TTATTCAGTAACAG-TCAA
* * *
42235781 TTATTCAGTAATATTCAG
1 TTATTCAGTAACAGTCAA
42235799 TTATTCAGTAACAGTCTAA
1 TTATTCAGTAACAGTC-AA
* *
42235818 -TATCCAGTAACAGTAAA
1 TTATTCAGTAACAGTCAA
* * *
42235835 TTATCCGGTAATAGTCAA
1 TTATTCAGTAACAGTCAA
42235853 TTATTCAGTAA
1 TTATTCAGTAA
42235864 TAATAAGTTA
Statistics
Matches: 136, Mismatches: 27, Indels: 20
0.74 0.15 0.11
Matches are distributed among these distances:
17 19 0.14
18 102 0.75
19 15 0.11
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.35
Consensus pattern (18 bp):
TTATTCAGTAACAGTCAA
Found at i:42236099 original size:45 final size:45
Alignment explanation
Indices: 42236051--42236290 Score: 345
Period size: 45 Copynumber: 5.3 Consensus size: 45
42236041 ATCTGGAATA
* * * * *
42236051 GTAACAGTAACAATAACAGTATTCAACACACAAAGTGCTGAATCA
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* *
42236096 GTAACGGTAACAGTAACAATATTCGACACACACAGTGCCGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* * *
42236141 ATAACGGTAACAGTAACAATACTCGACACACAAAGTGCCGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* *
42236186 GTAACAGTAGCAGTAACAATATTCGACACACAAAGTACCGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
* *
42236231 GTAACAGTAGCAGTAACAATATTCGACACACAAAGTACCGAATCG
1 GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
*
42236276 GTAACAGTAGCAGTA
1 GTAACAGTAACAGTA
42236291 GCGTTAACAA
Statistics
Matches: 180, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 180 1.00
ACGTcount: A:0.42, C:0.22, G:0.18, T:0.18
Consensus pattern (45 bp):
GTAACAGTAACAGTAACAATATTCGACACACAAAGTGCCGAATCG
Found at i:42236710 original size:5 final size:5
Alignment explanation
Indices: 42236699--42236740 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
42236689 AATTAATCAT
* *
42236699 AATTC CATTC CATTC AATTC AATTC AATTC AATTC AAATTC A
1 AATTC AATTC AATTC AATTC AATTC AATTC AATTC -AATTC A
42236741 CTTTTCCACT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
5 29 0.85
6 5 0.15
ACGTcount: A:0.38, C:0.24, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTC
Found at i:42240616 original size:30 final size:32
Alignment explanation
Indices: 42240582--42240651 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 32
42240572 TGGCCCAAGA
* *
42240582 GTAAATATTCAAAA-TTTGAAGGATTAA-AGT
1 GTAAATATTCAAAATTTTAAAGGACTAATAGT
*
42240612 GTAAATA-TGAAAATTTTAAAGGACTAATAGT
1 GTAAATATTCAAAATTTTAAAGGACTAATAGT
*
42240643 GCAAATATT
1 GTAAATATT
42240652 TTAAGGACAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 5 0.15
30 18 0.55
31 9 0.27
32 1 0.03
ACGTcount: A:0.47, C:0.04, G:0.16, T:0.33
Consensus pattern (32 bp):
GTAAATATTCAAAATTTTAAAGGACTAATAGT
Found at i:42240898 original size:8 final size:8
Alignment explanation
Indices: 42240887--42240911 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
42240877 TTTAATAAGA
42240887 TATTTTAT
1 TATTTTAT
42240895 TATTTTAT
1 TATTTTAT
42240903 TATTTTAT
1 TATTTTAT
42240911 T
1 T
42240912 TAGTCTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTTTAT
Found at i:42242193 original size:43 final size:43
Alignment explanation
Indices: 42242145--42242317 Score: 205
Period size: 43 Copynumber: 4.0 Consensus size: 43
42242135 AGCTCGTACA
* *
42242145 ATGCCAACGTCCTAGACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCG
*
42242188 ATGCC-ACTGTCCCAG--GTAAGGTCTTACACGAAATCAAATA-CG
1 ATGCCAAC-GTCCCAGACGT--GGTCTTACACGTAATCAAATATCG
*
42242230 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATACCAA-ATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGT-AAT-CAAATATCG
*
42242274 ATGCCAACGTCCCAGACGTGGTCTTACACG-ATATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTA-ATCAAATATCG
42242317 A
1 A
42242318 AAATCCTATG
Statistics
Matches: 112, Mismatches: 7, Indels: 22
0.79 0.05 0.16
Matches are distributed among these distances:
41 2 0.02
42 30 0.27
43 43 0.38
44 37 0.33
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAATCAAATATCG
Found at i:42242286 original size:44 final size:43
Alignment explanation
Indices: 42242145--42242303 Score: 195
Period size: 44 Copynumber: 3.7 Consensus size: 43
42242135 AGCTCGTACA
* * *
42242145 ATGCCAACGTCCTAGACGTGGTCTTACATGT-AATCAAATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCCAA-ATCG
42242188 ATGCC-ACTGTCCCAG--GTAAGGTCTTACACG-AAAT-CAAATACG
1 ATGCCAAC-GTCCCAGACGT--GGTCTTACACGTAAATCCAAAT-CG
42242230 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATACCAAATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAAT-CCAAATCG
42242274 ATGCCAACGTCCCAGACGTGGTCTTACACG
1 ATGCCAACGTCCCAGACGTGGTCTTACACG
42242304 ATATCACATA
Statistics
Matches: 102, Mismatches: 3, Indels: 21
0.81 0.02 0.17
Matches are distributed among these distances:
41 4 0.04
42 29 0.28
43 30 0.29
44 34 0.33
45 5 0.05
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAATCCAAATCG
Found at i:42247276 original size:15 final size:15
Alignment explanation
Indices: 42247258--42247308 Score: 63
Period size: 15 Copynumber: 3.6 Consensus size: 15
42247248 CCGTTGTTGG
42247258 TGTGGTAGGAGTCCC
1 TGTGGTAGGAGTCCC
* *
42247273 TGTGGTTGGTGT---
1 TGTGGTAGGAGTCCC
42247285 TGTGGTAGGAGTCCC
1 TGTGGTAGGAGTCCC
42247300 TGTGGTAGG
1 TGTGGTAGG
42247309 TGTTGTTGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
12 10 0.34
15 19 0.66
ACGTcount: A:0.10, C:0.12, G:0.45, T:0.33
Consensus pattern (15 bp):
TGTGGTAGGAGTCCC
Found at i:42247288 original size:27 final size:27
Alignment explanation
Indices: 42247258--42247338 Score: 114
Period size: 27 Copynumber: 3.1 Consensus size: 27
42247248 CCGTTGTTGG
*
42247258 TGTGGTAGGAGTCCCTGTGGTTGGTGT
1 TGTGGTAGGAGTCCCTGTGGTAGGTGT
42247285 TGTGGTAGGAGTCCCTGTGGTAGGTGT
1 TGTGGTAGGAGTCCCTGTGGTAGGTGT
* *
42247312 TGT--T-GGAGTCCCTGTAGTAGGAGT
1 TGTGGTAGGAGTCCCTGTGGTAGGTGT
42247336 TGT
1 TGT
42247339 CGGAGTCCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
24 21 0.41
25 1 0.02
27 29 0.57
ACGTcount: A:0.11, C:0.11, G:0.42, T:0.36
Consensus pattern (27 bp):
TGTGGTAGGAGTCCCTGTGGTAGGTGT
Found at i:42247385 original size:24 final size:24
Alignment explanation
Indices: 42247234--42247386 Score: 128
Period size: 24 Copynumber: 6.2 Consensus size: 24
42247224 TGCTTGTCCC
* * * *
42247234 TGTTGTCGGTGTCCCCGTTGTTGG
1 TGTTGTCGGAGTCCCTGTGGTAGG
* * *
42247258 TGTGGTAGGAGTCCCTGTGGTTGG
1 TGTTGTCGGAGTCCCTGTGGTAGG
*
42247282 TGTTGTGGTAGGAGTCCCTGTGGTAGG
1 TG-T-T-GTCGGAGTCCCTGTGGTAGG
* *
42247309 TGTTGTTGGAGTCCCTGTAGTAGG
1 TGTTGTCGGAGTCCCTGTGGTAGG
* ** *
42247333 AGTTGTCGGAGTCCCTGTACTCGG
1 TGTTGTCGGAGTCCCTGTGGTAGG
*
42247357 AGTTGTCGGAGTCCCTGTGG-ATGG
1 TGTTGTCGGAGTCCCTGTGGTA-GG
42247381 TGTTGT
1 TGTTGT
42247387 GCTTGTGCCA
Statistics
Matches: 108, Mismatches: 17, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
24 84 0.78
25 2 0.02
26 1 0.01
27 21 0.19
ACGTcount: A:0.09, C:0.16, G:0.40, T:0.35
Consensus pattern (24 bp):
TGTTGTCGGAGTCCCTGTGGTAGG
Found at i:42249512 original size:23 final size:20
Alignment explanation
Indices: 42249450--42249515 Score: 60
Period size: 20 Copynumber: 3.0 Consensus size: 20
42249440 AACACAATAT
42249450 AAATATATTTGTGATAAAAA
1 AAATATATTTGTGATAAAAA
* * *
42249470 AATTATAGTAGTGTATTAAATTAA
1 AAATATATTTGTG-A-TAAA--AA
42249494 ATAATATATTTGTGATAAAAA
1 A-AATATATTTGTGATAAAAA
42249515 A
1 A
42249516 TTATAGTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 9
0.70 0.12 0.18
Matches are distributed among these distances:
20 10 0.29
21 4 0.11
22 4 0.11
23 4 0.11
24 4 0.11
25 9 0.26
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.38
Consensus pattern (20 bp):
AAATATATTTGTGATAAAAA
Found at i:42249776 original size:16 final size:18
Alignment explanation
Indices: 42249754--42249795 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 18
42249744 TTTATAATTG
*
42249754 TAATATATAT-TTTTTAA
1 TAATATATATATTTTCAA
*
42249771 -AATATAAATATTTTCAA
1 TAATATATATATTTTCAA
42249788 TAATATAT
1 TAATATAT
42249796 TAAGAATATT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
16 8 0.40
17 6 0.30
18 6 0.30
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATATATATATTTTCAA
Found at i:42251712 original size:30 final size:30
Alignment explanation
Indices: 42251664--42251722 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
42251654 AACTTTTTAT
* *
42251664 TTTCCCCCTAAATTTTTAC-TCCCTCCCAC
1 TTTCCCCCAAAACTTTTACTTCCCTCCCAC
*
42251693 TTTCCCTCCAAAACTTTTACTTCCTTCCCA
1 TTTCCC-CCAAAACTTTTACTTCCCTCCCA
42251723 TCCCAGCCCT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
30 11 0.44
31 8 0.32
ACGTcount: A:0.19, C:0.42, G:0.00, T:0.39
Consensus pattern (30 bp):
TTTCCCCCAAAACTTTTACTTCCCTCCCAC
Found at i:42256916 original size:47 final size:48
Alignment explanation
Indices: 42256858--42256949 Score: 150
Period size: 47 Copynumber: 1.9 Consensus size: 48
42256848 CAATGTATAA
*
42256858 AGCTTGATTAGGTGGGCTGAATCAGGT-AGAGATATTGTATGTAACAG
1 AGCTTGATTAGGTGGGCTGAATCAGGTAAAAGATATTGTATGTAACAG
**
42256905 AGCTTGATTAGGTGGTTTGAATCAGGTAAAAGATATTGTATGTAA
1 AGCTTGATTAGGTGGGCTGAATCAGGTAAAAGATATTGTATGTAA
42256950 TTATATTGAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
47 25 0.61
48 16 0.39
ACGTcount: A:0.32, C:0.07, G:0.29, T:0.33
Consensus pattern (48 bp):
AGCTTGATTAGGTGGGCTGAATCAGGTAAAAGATATTGTATGTAACAG
Found at i:42258821 original size:89 final size:87
Alignment explanation
Indices: 42258609--42258808 Score: 221
Period size: 89 Copynumber: 2.3 Consensus size: 87
42258599 ATAAACTACT
* *
42258609 ATTTAAAATATT--TGTATT-ATTTCTTTAGAATGTTTGTATTTTTTATATCTGTAAATTTAATT
1 ATTTAAAATTTTCGTGTATTAATTTC-TTACAATGTTTGTATTTTTTATATCTGTAAATTTAATT
* *
42258671 TATTCGTTTAAGGTTTAGGGTTTCA
65 TATCCATTTAA-GTTTA-GGTTTCA
* * * * *
42258696 TTTTTATATTTTCGTGTATTAATTTCTTAGAATGTTTGTATTTTTTGTATCTGTAAATTTAATTT
1 ATTTAAAATTTTCGTGTATTAATTTCTTACAATGTTTGTATTTTTTATATCTGTAAATTTAATTT
*
42258761 AGTCCATATTATA-TTTA-GTTTGA
66 A-TCCAT-TTA-AGTTTAGGTTTCA
42258784 ATTTAAAATTTTCGTGTATTAATTT
1 ATTTAAAATTTTCGTGTATTAATTT
42258809 TACCCATCTG
Statistics
Matches: 96, Mismatches: 11, Indels: 11
0.81 0.09 0.09
Matches are distributed among these distances:
87 8 0.08
88 27 0.28
89 45 0.47
90 12 0.12
91 3 0.03
92 1 0.01
ACGTcount: A:0.27, C:0.05, G:0.12, T:0.56
Consensus pattern (87 bp):
ATTTAAAATTTTCGTGTATTAATTTCTTACAATGTTTGTATTTTTTATATCTGTAAATTTAATTT
ATCCATTTAAGTTTAGGTTTCA
Found at i:42261474 original size:18 final size:20
Alignment explanation
Indices: 42261451--42261514 Score: 60
Period size: 22 Copynumber: 3.1 Consensus size: 20
42261441 ACCCATATTG
42261451 TCAAA-TTATTTT-TTCATT
1 TCAAATTTATTTTATTCATT
42261469 TCAAATTTATTTTAACTTCATT
1 TCAAATTTATTTT-A-TTCATT
* *
42261491 TCAAACTTCATTTCATTCCATT
1 TCAAA-TTTATTTTATT-CATT
42261513 TC
1 TC
42261515 CTTTTAACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 5 0.13
19 7 0.18
21 2 0.05
22 18 0.47
23 6 0.16
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (20 bp):
TCAAATTTATTTTATTCATT
Found at i:42261499 original size:12 final size:12
Alignment explanation
Indices: 42261463--42261505 Score: 54
Period size: 11 Copynumber: 3.8 Consensus size: 12
42261453 AAATTATTTT
42261463 TTCATTTCAAA-
1 TTCATTTCAAAC
* *
42261474 TTTATTT-TAAC
1 TTCATTTCAAAC
42261485 TTCATTTCAAAC
1 TTCATTTCAAAC
42261497 TTCATTTCA
1 TTCATTTCA
42261506 TTCCATTTCC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 2 0.08
11 12 0.46
12 12 0.46
ACGTcount: A:0.30, C:0.19, G:0.00, T:0.51
Consensus pattern (12 bp):
TTCATTTCAAAC
Found at i:42261554 original size:20 final size:19
Alignment explanation
Indices: 42261529--42261588 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 19
42261519 TAACATTCCA
42261529 TTTCATTTAAATTTTCTTTT
1 TTTCATTTAAATTTT-TTTT
42261549 TTTCATTTAAATTTAATTTTT
1 TTTCATTTAAATTT--TTTTT
* *
42261570 TCTCATTTCAATTTTTTTT
1 TTTCATTTAAATTTTTTTT
42261589 CATATTAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 5 0.14
20 14 0.39
21 16 0.44
22 1 0.03
ACGTcount: A:0.22, C:0.10, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCATTTAAATTTTTTTT
Found at i:42261575 original size:21 final size:20
Alignment explanation
Indices: 42261529--42261583 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
42261519 TAACATTCCA
**
42261529 TTTCATTTAAATTTTCTTTT
1 TTTCATTTAAATTTAATTTT
42261549 TTTCATTTAAATTTAATTTT
1 TTTCATTTAAATTTAATTTT
*
42261569 TTCTCATTTCAATTT
1 TT-TCATTTAAATTT
42261584 TTTTTCATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 20 0.65
21 11 0.35
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTCATTTAAATTTAATTTT
Found at i:42261584 original size:16 final size:15
Alignment explanation
Indices: 42261559--42261597 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
42261549 TTTCATTTAA
42261559 ATTTAATTTTTTCTC
1 ATTTAATTTTTTCTC
*
42261574 ATTTCAATTTTTTTTC
1 ATTT-AATTTTTTCTC
42261590 ATATTAAT
1 AT-TTAAT
42261598 AACAAGTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 15 0.71
17 2 0.10
ACGTcount: A:0.26, C:0.10, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTAATTTTTTCTC
Found at i:42261633 original size:19 final size:18
Alignment explanation
Indices: 42261609--42261652 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 18
42261599 ACAAGTAGTC
*
42261609 TCATTTGAATTTTGTTTTT
1 TCATTTCAATTTT-TTTTT
42261628 TCATTTCAA--TTTTTTT
1 TCATTTCAATTTTTTTTT
42261644 TCATTTCAA
1 TCATTTCAA
42261653 ATTATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 14 0.58
17 2 0.08
19 8 0.33
ACGTcount: A:0.20, C:0.11, G:0.05, T:0.64
Consensus pattern (18 bp):
TCATTTCAATTTTTTTTT
Found at i:42261675 original size:5 final size:5
Alignment explanation
Indices: 42261665--42261704 Score: 53
Period size: 5 Copynumber: 7.4 Consensus size: 5
42261655 TATAATTTTT
42261665 TTTCA TTTCA TTTCA TATTCA TTTAACA TTTCA TTTCA TT
1 TTTCA TTTCA TTTCA T-TTCA TTT--CA TTTCA TTTCA TT
42261705 AAAATTTTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 22 0.69
6 5 0.16
7 5 0.16
ACGTcount: A:0.25, C:0.17, G:0.00, T:0.57
Consensus pattern (5 bp):
TTTCA
Found at i:42261722 original size:16 final size:16
Alignment explanation
Indices: 42261682--42261730 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
42261672 TCATTTCATA
* *
42261682 TTCATTTAACATTTCAT
1 TTCATTTAAAATTT-TT
42261699 TTCA-TTAAAATTTTT
1 TTCATTTAAAATTTTT
42261714 TTCATTT-AAATTTTT
1 TTCATTTAAAATTTTT
42261729 TT
1 TT
42261731 TTTTCTAGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 15 0.52
16 10 0.34
17 4 0.14
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (16 bp):
TTCATTTAAAATTTTT
Found at i:42261731 original size:16 final size:16
Alignment explanation
Indices: 42261658--42261731 Score: 62
Period size: 16 Copynumber: 4.6 Consensus size: 16
42261648 TTCAAATTAT
42261658 AATTTTTTTTCATTT-
1 AATTTTTTTTCATTTA
* * *
42261673 CATTTCATATTCATTTA
1 AATTT-TTTTTCATTTA
**
42261690 ACATTTCATTTCA-TTA
1 A-ATTTTTTTTCATTTA
*
42261706 AAATTTTTTTCATTTA
1 AATTTTTTTTCATTTA
42261722 AATTTTTTTT
1 AATTTTTTTT
42261732 TTTCTAGTAT
Statistics
Matches: 44, Mismatches: 11, Indels: 7
0.71 0.18 0.11
Matches are distributed among these distances:
15 12 0.27
16 24 0.55
17 4 0.09
18 4 0.09
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (16 bp):
AATTTTTTTTCATTTA
Found at i:42261761 original size:19 final size:19
Alignment explanation
Indices: 42261709--42261763 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 19
42261699 TTCATTAAAA
42261709 TTTTTTTCAT-TTAAATTTT
1 TTTTTTTCATATTAAA-TTT
42261728 TTTTTTTCTAGTATTCAAA-TT
1 TTTTTTTC-A-TATT-AAATTT
42261749 TTTTTTTCATATTAA
1 TTTTTTTCATATTAA
42261764 TCACAAGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 9
0.78 0.00 0.22
Matches are distributed among these distances:
18 2 0.06
19 12 0.38
20 2 0.06
21 11 0.34
22 2 0.06
23 3 0.09
ACGTcount: A:0.24, C:0.07, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTTTTCATATTAAATTT
Found at i:42261933 original size:25 final size:26
Alignment explanation
Indices: 42261900--42261953 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
42261890 TTTTTCTCAA
* *
42261900 TTTAAATTTCATTT-CATTTCAAAAT
1 TTTAAATTTCATTTAAATTTAAAAAT
*
42261925 TTTAAATTTTATTTAAATTTAAAAAT
1 TTTAAATTTCATTTAAATTTAAAAAT
42261951 TTT
1 TTT
42261954 CTCATTTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
25 13 0.52
26 12 0.48
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (26 bp):
TTTAAATTTCATTTAAATTTAAAAAT
Found at i:42262133 original size:19 final size:19
Alignment explanation
Indices: 42262109--42262146 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
42262099 ACATGTTTTG
*
42262109 CCAATTTTTTTTTCTCATT
1 CCAATTTTTATTTCTCATT
42262128 CCAATTTTTATTTCTCATT
1 CCAATTTTTATTTCTCATT
42262147 TTTTTTCATT
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:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (19 bp):
CCAATTTTTATTTCTCATT
Found at i:42262148 original size:29 final size:29
Alignment explanation
Indices: 42262116--42262176 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
42262106 TTGCCAATTT
*
42262116 TTTTTTCTCA-TTCCAATTTTTATTTCTCA
1 TTTTTTCTCATTTCC-ATTTTCATTTCTCA
* *
42262145 TTTTTTTTCATTTTCATTTTCATTTCTCA
1 TTTTTTCTCATTTCCATTTTCATTTCTCA
42262174 TTT
1 TTT
42262177 AATTTCATTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.15, C:0.18, G:0.00, T:0.67
Consensus pattern (29 bp):
TTTTTTCTCATTTCCATTTTCATTTCTCA
Found at i:42262151 original size:16 final size:16
Alignment explanation
Indices: 42262132--42262164 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42262122 CTCATTCCAA
42262132 TTTTT-ATTTCTCATTT
1 TTTTTCATTT-TCATTT
42262148 TTTTTCATTTTCATTT
1 TTTTTCATTTTCATTT
42262164 T
1 T
42262165 CATTTCTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTTTCATTTTCATTT
Found at i:42262158 original size:6 final size:6
Alignment explanation
Indices: 42262131--42262176 Score: 51
Period size: 6 Copynumber: 7.7 Consensus size: 6
42262121 TCTCATTCCA
*
42262131 ATTTTT ATTTCTC ATTTT- -TTTTC ATTTTC ATTTTC ATTTCTC ATTT
1 ATTTTC ATTT-TC ATTTTC ATTTTC ATTTTC ATTTTC ATTT-TC ATTT
42262177 AATTTCATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
4 4 0.11
6 20 0.57
7 11 0.31
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (6 bp):
ATTTTC
Found at i:42262164 original size:12 final size:12
Alignment explanation
Indices: 42262131--42262176 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
42262121 TCTCATTCCA
*
42262131 ATTTTTATTTCTC
1 ATTTTCATTT-TC
42262144 ATTTT--TTTTC
1 ATTTTCATTTTC
42262154 ATTTTCATTTTC
1 ATTTTCATTTTC
42262166 ATTTCTCATTT
1 ATTT-TCATTT
42262177 AATTTCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 7 0.23
11 3 0.10
12 9 0.30
13 11 0.37
ACGTcount: A:0.15, C:0.15, G:0.00, T:0.70
Consensus pattern (12 bp):
ATTTTCATTTTC
Found at i:42262182 original size:29 final size:29
Alignment explanation
Indices: 42262131--42262186 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
42262121 TCTCATTCCA
* **
42262131 ATTTTTATTTCTCATTTTTTTTCATTTTC
1 ATTTTCATTTCTCATTTAATTTCATTTTC
42262160 ATTTTCATTTCTCATTTAATTTCATTT
1 ATTTTCATTTCTCATTTAATTTCATTT
42262187 AAATTTATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.68
Consensus pattern (29 bp):
ATTTTCATTTCTCATTTAATTTCATTTTC
Found at i:42262192 original size:29 final size:29
Alignment explanation
Indices: 42262130--42262192 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
42262120 TTCTCATTCC
* ** *
42262130 AATTTTTATTTCTCATTTTTTTTCATTTT
1 AATTTTCATTTCTCATTTAATTTCATTTA
*
42262159 CATTTTCATTTCTCATTTAATTTCATTTA
1 AATTTTCATTTCTCATTTAATTTCATTTA
42262188 AATTT
1 AATTT
42262193 ATTTTTAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.22, C:0.13, G:0.00, T:0.65
Consensus pattern (29 bp):
AATTTTCATTTCTCATTTAATTTCATTTA
Found at i:42262227 original size:23 final size:21
Alignment explanation
Indices: 42262189--42262278 Score: 90
Period size: 22 Copynumber: 4.1 Consensus size: 21
42262179 TTTCATTTAA
** *
42262189 ATTTATTTTTAATTTAAATTT
1 ATTTATTTTCCATTTTAATTT
42262210 ATTTCATTTTCCATTTTAATTT
1 ATTT-ATTTTCCATTTTAATTT
*
42262232 ATTTTTTTATCTCATTTTAATTT
1 ATTTATTT-TC-CATTTTAATTT
* *
42262255 ATTTAATTTTTCATTTCAATTT
1 ATTT-ATTTTCCATTTTAATTT
42262277 AT
1 AT
42262279 AATTTATTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
21 7 0.12
22 32 0.55
23 16 0.28
24 3 0.05
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.66
Consensus pattern (21 bp):
ATTTATTTTCCATTTTAATTT
Found at i:42262292 original size:23 final size:21
Alignment explanation
Indices: 42262190--42262418 Score: 125
Period size: 21 Copynumber: 10.4 Consensus size: 21
42262180 TTCATTTAAA
* *
42262190 TTTATTTTTAATTTAAATTTAT
1 TTTA-TTTTCATTTCAATTTAT
* *
42262212 TTCATTTTCCATTTTAATTTAT
1 TTTATTTT-CATTTCAATTTAT
* *
42262234 TTTTTTATCTCATTTTAATTTAT
1 TTTATT-T-TCATTTCAATTTAT
*
42262257 TTAATTTTTCATTTCAATTTAT
1 TTTA-TTTTCATTTCAATTTAT
*
42262279 AATTTATTTTCATTTCATATTCAT
1 --TTTATTTTCATTTCA-ATTTAT
*
42262303 TTAATACTTCGTTTCATTTCATATTCAT
1 TT--TA--T--TTTCATTTCA-ATTTAT
*
42262331 TTT-TTTATCATCTCAATTTAT
1 TTTATTT-TCATTTCAATTTAT
42262352 TTT-TTTCTCATTTCAATTTAT
1 TTTATTT-TCATTTCAATTTAT
*
42262373 TCTT-TTTTCA----AATTCAT
1 T-TTATTTTCATTTCAATTTAT
42262390 TTT-TTTCTCATTTCAATTTAT
1 TTTATTT-TCATTTCAATTTAT
42262411 TTT-TTTTC
1 TTTATTTTC
42262419 TTTTTAGTTT
Statistics
Matches: 171, Mismatches: 16, Indels: 42
0.75 0.07 0.18
Matches are distributed among these distances:
16 5 0.03
17 10 0.06
20 2 0.01
21 46 0.27
22 45 0.26
23 29 0.17
24 13 0.08
26 2 0.01
28 19 0.11
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTATTTTCATTTCAATTTAT
Found at i:42262292 original size:45 final size:46
Alignment explanation
Indices: 42262178--42262372 Score: 138
Period size: 45 Copynumber: 4.3 Consensus size: 46
42262168 TTCTCATTTA
* * * * *
42262178 ATTTC-ATTTA-AATTTATTTTTAATTTAAATTTATTTCATTTTCC
1 ATTTCAATTTATAATTTATTTATCATTTCAATTTATTTAATTTTTC
* *
42262222 ATTTTAATTTAT--TTT-TTTATCTCATTTTAATTTATTTAATTTTTC
1 ATTTCAATTTATAATTTATTTA--TCATTTCAATTTATTTAATTTTTC
* **
42262267 ATTTCAATTTATAATTTATTT-TCATTTCATATTCATTTAATACTTC
1 ATTTCAATTTATAATTTATTTATCATTTCA-ATTTATTTAATTTTTC
* * *
42262313 GTTTC-ATTTCATATTCATTTTTTTATCATCTCAATTTATTT--TTTTCTC
1 ATTTCAATTT-ATA---ATTTATTTATCATTTCAATTTATTTAATTTT-TC
42262361 ATTTCAATTTAT
1 ATTTCAATTTAT
42262373 TCTTTTTTCA
Statistics
Matches: 118, Mismatches: 18, Indels: 26
0.73 0.11 0.16
Matches are distributed among these distances:
43 3 0.03
44 7 0.06
45 47 0.40
46 20 0.17
47 5 0.04
48 11 0.09
49 18 0.15
50 7 0.06
ACGTcount: A:0.26, C:0.11, G:0.01, T:0.62
Consensus pattern (46 bp):
ATTTCAATTTATAATTTATTTATCATTTCAATTTATTTAATTTTTC
Found at i:42262392 original size:38 final size:37
Alignment explanation
Indices: 42262345--42262418 Score: 130
Period size: 38 Copynumber: 2.0 Consensus size: 37
42262335 TTATCATCTC
*
42262345 AATTTATTTTTTTCTCATTTCAATTTATTCTTTTTTCA
1 AATTCATTTTTTTCTCATTTCAATTTATT-TTTTTTCA
42262383 AATTCATTTTTTTCTCATTTCAATTTATTTTTTTTC
1 AATTCATTTTTTTCTCATTTCAATTTATTTTTTTTC
42262419 TTTTTAGTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
37 7 0.20
38 28 0.80
ACGTcount: A:0.20, C:0.14, G:0.00, T:0.66
Consensus pattern (37 bp):
AATTCATTTTTTTCTCATTTCAATTTATTTTTTTTCA
Found at i:42262435 original size:21 final size:22
Alignment explanation
Indices: 42262388--42262435 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 22
42262378 TTTCAAATTC
42262388 ATTTTTTTCTCATTTCAATTTAT
1 ATTTTTTTCT-ATTTCAATTTAT
* *
42262411 -TTTTTTTCT-TTTTAGTTTAT
1 ATTTTTTTCTATTTCAATTTAT
42262431 ATTTT
1 ATTTT
42262436 AATTTCATCC
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 9 0.41
21 4 0.18
22 9 0.41
ACGTcount: A:0.17, C:0.08, G:0.02, T:0.73
Consensus pattern (22 bp):
ATTTTTTTCTATTTCAATTTAT
Found at i:42262468 original size:17 final size:18
Alignment explanation
Indices: 42262429--42262471 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
42262419 TTTTTAGTTT
*
42262429 ATATTTTAATTTCATCCC
1 ATATTTTAAATTCATCCC
*
42262447 ATATTTTAAATTCAT-TC
1 ATATTTTAAATTCATCCC
42262464 ATATTTTA
1 ATATTTTA
42262472 TTCACTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 9 0.39
18 14 0.61
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (18 bp):
ATATTTTAAATTCATCCC
Found at i:42262976 original size:43 final size:44
Alignment explanation
Indices: 42262889--42262979 Score: 166
Period size: 44 Copynumber: 2.1 Consensus size: 44
42262879 GAATTAATAT
42262889 ATTTAATGTGTTTTAAATTAAATATATATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAATTAAATATATATGTATATTGTATTATA
*
42262933 ATTTAATGTGTTTTAAATTAAATA-GTATGTATATTGTATTATA
1 ATTTAATGTGTTTTAAATTAAATATATATGTATATTGTATTATA
42262976 ATTT
1 ATTT
42262980 GTATATCATT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 22 0.48
44 24 0.52
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (44 bp):
ATTTAATGTGTTTTAAATTAAATATATATGTATATTGTATTATA
Found at i:42266279 original size:21 final size:21
Alignment explanation
Indices: 42266233--42266294 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
42266223 CGAATACACC
42266233 AATAGAAGCTCG-AA-AGCTG
1 AATAGAAGCTCGTAAGAGCTG
* *
42266252 AACAGAAGCTCGTAAGAGCTT
1 AATAGAAGCTCGTAAGAGCTG
* *
42266273 AATAGAAACTCATAAGAGCTG
1 AATAGAAGCTCGTAAGAGCTG
42266294 A
1 A
42266295 TCCATCCATT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 11 0.31
20 2 0.06
21 22 0.63
ACGTcount: A:0.44, C:0.16, G:0.23, T:0.18
Consensus pattern (21 bp):
AATAGAAGCTCGTAAGAGCTG
Found at i:42268540 original size:54 final size:54
Alignment explanation
Indices: 42268473--42268685 Score: 277
Period size: 54 Copynumber: 3.9 Consensus size: 54
42268463 CATTATATAT
*
42268473 ATCTGATAAATTTGGTGTCTGCCATCAATATCCCAAAACCAAAAAAAAATAATA
1 ATCTGATAAAGTTGGTGTCTGCCATCAATATCCCAAAACCAAAAAAAAATAATA
*
42268527 ATCTGATAAATTTGGTGTCTGCCATCAATATCCCAAAACCAAAAAAAAATAATA
1 ATCTGATAAAGTTGGTGTCTGCCATCAATATCCCAAAACCAAAAAAAAATAATA
* ****
42268581 ATCTGATAAAGTTGGTGTCGGCCATCGGCGTCCCAAAACCAAAAAAAAA-AATA
1 ATCTGATAAAGTTGGTGTCTGCCATCAATATCCCAAAACCAAAAAAAAATAATA
* * ** *
42268634 ATCTGAGAAAGTTAGTG-CTAGCCATCTGTGTCCCAAAACCCAAAACAAAAAT
1 ATCTGATAAAGTTGGTGTCT-GCCATCAATATCCCAAAA-CCAAAA-AAAAAT
42268686 TTTAGGACCC
Statistics
Matches: 144, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
52 1 0.01
53 35 0.24
54 103 0.72
55 5 0.03
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.23
Consensus pattern (54 bp):
ATCTGATAAAGTTGGTGTCTGCCATCAATATCCCAAAACCAAAAAAAAATAATA
Found at i:42268747 original size:53 final size:54
Alignment explanation
Indices: 42268680--42268790 Score: 143
Period size: 53 Copynumber: 2.1 Consensus size: 54
42268670 AACCCAAAAC
* * * *
42268680 AAAAATTTTAGGACCCGAAAAAGGTGGTGTCGGCCATCAATGTCCCAGA-TAAA
1 AAAAATTTTAGGACCCAAAAAAGGTGGTGCCGACCATCAATGTCCCAAAGTAAA
* * * *
42268733 AAAAATTTTGGGACCTAAAAAAGGTGGTGCCGATCATCAGTGTCCCAAAGTAAA
1 AAAAATTTTAGGACCCAAAAAAGGTGGTGCCGACCATCAATGTCCCAAAGTAAA
42268787 AAAA
1 AAAA
42268791 GTTTGCTTTG
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
53 41 0.84
54 8 0.16
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.21
Consensus pattern (54 bp):
AAAAATTTTAGGACCCAAAAAAGGTGGTGCCGACCATCAATGTCCCAAAGTAAA
Found at i:42270259 original size:13 final size:13
Alignment explanation
Indices: 42270241--42270283 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
42270231 TTTAATAATA
42270241 AAATAAAGAAATG
1 AAATAAAGAAATG
42270254 AAATAAAGAAAT-
1 AAATAAAGAAATG
* *
42270266 AAATGAAATAAAAG
1 AAAT-AAAGAAATG
42270280 AAAT
1 AAAT
42270284 GAAAAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 4 0.15
13 18 0.69
14 4 0.15
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (13 bp):
AAATAAAGAAATG
Found at i:42270271 original size:17 final size:18
Alignment explanation
Indices: 42270237--42270283 Score: 69
Period size: 17 Copynumber: 2.7 Consensus size: 18
42270227 ATAGTTTAAT
* *
42270237 AATAAAATAAAGAAATGA
1 AATAAAAGAAATAAATGA
42270255 AAT-AAAGAAATAAATGA
1 AATAAAAGAAATAAATGA
42270272 AATAAAAGAAAT
1 AATAAAAGAAAT
42270284 GAAAAAGGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (18 bp):
AATAAAAGAAATAAATGA
Found at i:42270275 original size:9 final size:9
Alignment explanation
Indices: 42270249--42270283 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
42270239 TAAAATAAAG
42270249 AAATGAAAT
1 AAATGAAAT
42270258 AAA-GAAAT
1 AAATGAAAT
42270266 AAATGAAAT
1 AAATGAAAT
*
42270275 AAAAGAAAT
1 AAATGAAAT
42270284 GAAAAAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
8 8 0.33
9 16 0.67
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.17
Consensus pattern (9 bp):
AAATGAAAT
Found at i:42272909 original size:46 final size:46
Alignment explanation
Indices: 42272859--42273034 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
42272849 TGGTTGAGCA
42272859 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42272905 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
42272950 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
42272998 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42273035 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:42273015 original size:93 final size:93
Alignment explanation
Indices: 42272856--42273027 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
42272846 GGATGGTTGA
* *
42272856 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42272921 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
42272949 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
42273014 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
42273028 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42277919 original size:15 final size:15
Alignment explanation
Indices: 42277896--42277933 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
42277886 GGTAGTACGA
*
42277896 AAATGTATTATTTGT
1 AAATATATTATTTGT
42277911 AAATATATTATTTGT
1 AAATATATTATTTGT
42277926 AAATATAT
1 AAATATAT
42277934 GACCTTTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (15 bp):
AAATATATTATTTGT
Found at i:42278221 original size:27 final size:27
Alignment explanation
Indices: 42278183--42278266 Score: 105
Period size: 27 Copynumber: 3.1 Consensus size: 27
42278173 ATGGTATATA
* * *
42278183 GGTTGCGCTTATCTGATAGACGCGACT
1 GGTTGAGCTTATCTGACAGGCGCGACT
*
42278210 GGTTGTGCTTATCTGACAGGCGCGACT
1 GGTTGAGCTTATCTGACAGGCGCGACT
* * *
42278237 TGTTGAACCTATCTGACAGGCGCGACT
1 GGTTGAGCTTATCTGACAGGCGCGACT
42278264 GGT
1 GGT
42278267 AGGTCCACAG
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.18, C:0.23, G:0.31, T:0.29
Consensus pattern (27 bp):
GGTTGAGCTTATCTGACAGGCGCGACT
Found at i:42279108 original size:94 final size:94
Alignment explanation
Indices: 42278947--42279133 Score: 338
Period size: 94 Copynumber: 2.0 Consensus size: 94
42278937 CGGAGATTTC
*
42278947 GATACATCGTACAATGAGTTACAGGGATAGATAGCCACTATGAGAGAGTACGTGTCGGGGACTAT
1 GATACATCGTACAATGAGTTACAGGAATAGATAGCCACTATGAGAGAGTACGTGTCGGGGACTAT
*
42279012 AATTGAGTTGCAGACACGATCTTATTACA
66 AATTGAGTCGCAGACACGATCTTATTACA
*
42279041 GATACATCGTACAATGAGTTACAGGAATAGATAGCCGCTATGAGAGAGTACGTGTCGGGGACTAT
1 GATACATCGTACAATGAGTTACAGGAATAGATAGCCACTATGAGAGAGTACGTGTCGGGGACTAT
*
42279106 AATTGAGTCGTAGACACGATCTTATTAC
66 AATTGAGTCGCAGACACGATCTTATTAC
42279134 GGCTTGAATG
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
94 89 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.26
Consensus pattern (94 bp):
GATACATCGTACAATGAGTTACAGGAATAGATAGCCACTATGAGAGAGTACGTGTCGGGGACTAT
AATTGAGTCGCAGACACGATCTTATTACA
Found at i:42287996 original size:27 final size:28
Alignment explanation
Indices: 42287966--42288027 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 28
42287956 TATGGGCCCT
*
42287966 ACCAGTCACGCCTCTG-AGATAGGCTCA
1 ACCAGTCACGCCCCTGCAGATAGGCTCA
*
42287993 ACCAGTCGCGCCCCTGTCAGATAGGCTCA
1 ACCAGTCACGCCCCTG-CAGATAGGCTCA
42288022 ACCAGT
1 ACCAGT
42288028 TGCACTTGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 14 0.45
29 17 0.55
ACGTcount: A:0.24, C:0.35, G:0.23, T:0.18
Consensus pattern (28 bp):
ACCAGTCACGCCCCTGCAGATAGGCTCA
Found at i:42288045 original size:27 final size:28
Alignment explanation
Indices: 42287982--42288050 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 28
42287972 CACGCCTCTG
*
42287982 AGATAGGCTCAACCAGTCGCGCCCCTGTC
1 AGATAGGCTCAACCAGTC-CGCACCTGTC
* *
42288011 AGATAGGCTCAACCAGT-TGCACTTGTC
1 AGATAGGCTCAACCAGTCCGCACCTGTC
*
42288038 AGATAGGCGCAAC
1 AGATAGGCTCAAC
42288051 TTCTTTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
27 19 0.53
29 17 0.47
ACGTcount: A:0.26, C:0.30, G:0.25, T:0.19
Consensus pattern (28 bp):
AGATAGGCTCAACCAGTCCGCACCTGTC
Found at i:42288785 original size:22 final size:22
Alignment explanation
Indices: 42288760--42288815 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
42288750 GATACCAAAT
*
42288760 TATTATTTCTTTAA-ATTTTAAA
1 TATTATTT-TTTAATATTTAAAA
42288782 TATTATTTTTTAATATTTAAAATA
1 TATTATTTTTTAATATTT-AAA-A
42288806 TATTATTTTT
1 TATTATTTTT
42288816 AAAGATACGA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 5 0.17
22 12 0.40
23 2 0.07
24 11 0.37
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTATTTTTTAATATTTAAAA
Found at i:42289029 original size:23 final size:23
Alignment explanation
Indices: 42288999--42289058 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
42288989 TAAAAAATAA
42288999 TTTAAAAAATTATATTTAAAAAT
1 TTTAAAAAATTATATTTAAAAAT
*
42289022 TTTAAAAAA-TAGTATTTGAAAAT
1 TTTAAAAAATTA-TATTTAAAAAT
*
42289045 TTTAAAATATTATA
1 TTTAAAAAATTATA
42289059 AAAAATTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
22 2 0.06
23 29 0.88
24 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (23 bp):
TTTAAAAAATTATATTTAAAAAT
Found at i:42289102 original size:19 final size:19
Alignment explanation
Indices: 42289056--42289095 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42289046 TTAAAATATT
* *
42289056 ATAAAAAATTGAAAAAGTAA
1 ATAAAAAA-GGAAAAAGGAA
42289076 ATAAAAAAGGAAAAAGGAA
1 ATAAAAAAGGAAAAAGGAA
42289095 A
1 A
42289096 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.12
Consensus pattern (19 bp):
ATAAAAAAGGAAAAAGGAA
Found at i:42290911 original size:125 final size:127
Alignment explanation
Indices: 42290710--42290971 Score: 323
Period size: 125 Copynumber: 2.1 Consensus size: 127
42290700 GAGTATGAGC
* * ***
42290710 TTGCCTTCTATTTCATTTAAAACTCATGTATTTAAATTTTAGAAATGAGATTCGGATGTTTAGAT
1 TTGCCTT-TATTTCATTTAAAACTCATGTATTTAAATTTTAGAAAGGAGAATCGGATACATAGAT
* * *
42290775 CAAACGGAAAATCAAAACCCAGTACGTTACGG-CACGACTACTCGAATTTCTAAATACGGAATA
65 CAAACGAAAAATCAAAACCCAGTACGTTA-GGACACGACTACTCGAATTTCCAAATACCGAATA
* * * * *
42290838 TTGCCTTTGTTTTATTTAAAACTCATGTATTTTAA-TTTA-AAAGGATAATCGGTTACATAGATC
1 TTGCCTTTATTTCATTTAAAACTCATGTATTTAAATTTTAGAAAGGAGAATCGGATACATAGATC
* * * * *
42290901 AAACGAAAAATCGAAACCCAGTACGTTAGGACACGATTTCTCGAATTTCCAAGTACCGAATT
66 AAACGAAAAATCAAAACCCAGTACGTTAGGACACGACTACTCGAATTTCCAAATACCGAATA
42290963 TTGCCTTTA
1 TTGCCTTTA
42290972 CTTGAAAAAT
Statistics
Matches: 114, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
124 2 0.02
125 76 0.67
126 4 0.04
127 25 0.22
128 7 0.06
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.34
Consensus pattern (127 bp):
TTGCCTTTATTTCATTTAAAACTCATGTATTTAAATTTTAGAAAGGAGAATCGGATACATAGATC
AAACGAAAAATCAAAACCCAGTACGTTAGGACACGACTACTCGAATTTCCAAATACCGAATA
Found at i:42291148 original size:3 final size:3
Alignment explanation
Indices: 42291134--42291604 Score: 67
Period size: 3 Copynumber: 153.3 Consensus size: 3
42291124 AATAGGATGG
* * * * *
42291134 ATA ATA AAA ATA ATA GTA ATA ATA AT- ATA ATG GTA ATA ATA TTA A-A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
42291180 AAA AGTAA ATA TATA ATG ATG ATA ATA GTG TTA AAA ATA ATA ATA ATA
1 ATA A-T-A ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
42291228 ATGA ATAA ATGGC ATA TTA ATG GTA ATA GAAA ATG ATG ATA ATA ATA
1 AT-A AT-A AT--A ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
* *
42291275 ATGGA AGTA ATGA A-A ATA ATA ATA ATA ATA GA-A ACA ATA GTA ATA
1 AT--A A-TA AT-A ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA
* *
42291320 A-A AGTA ATA ATA A-A ATA GAAA ATA ATA ATG ATA CATTA ATA ATA AT-
1 ATA A-TA ATA ATA ATA ATA -ATA ATA ATA ATA ATA -A-TA ATA ATA ATA
* * * * * * **
42291366 ATA CGTG CTA ACA ATA ATA ACA AT- ATA A-A AAA AGG A-A ATA ATA
1 ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
42291409 CT- ATA TTA ATA AAA ATA ATT ATA GTA GGTTA ATA ATA ATA GTA ATGA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA --ATA ATA ATA ATA ATA AT-A
* * * * * * *
42291456 A-A AGGTA AAA ATA ATA ATA A-A AAA ATA AAA ATA CTA TTA CGTA CTA
1 ATA A--TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* * * *
42291502 CTA ATA ATA ATA A-A A-A AGA A-A ACA ATA ATA GCATA TAGA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA --ATA -ATA ATA ATA
* * * * * * *
42291547 GTA A-A AGTA ATA AAA ATA ATA ATA GTA GTA GTA GTA GTA ATA ATA
1 ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
42291592 ATA ATA ATA ATA A
1 ATA ATA ATA ATA A
42291605 CACTCTCCCC
Statistics
Matches: 341, Mismatches: 86, Indels: 82
0.67 0.17 0.16
Matches are distributed among these distances:
2 31 0.09
3 262 0.77
4 32 0.09
5 15 0.04
6 1 0.00
ACGTcount: A:0.59, C:0.03, G:0.10, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:42291187 original size:35 final size:38
Alignment explanation
Indices: 42291138--42291229 Score: 90
Period size: 35 Copynumber: 2.5 Consensus size: 38
42291128 GGATGGATAA
42291138 TAAAAATAATAGTAATAATAATATAATG-G-TAATAATAT
1 TAAAAAT-A-AGTAATAATAATATAATGAGATAATAATAT
* *
42291176 TAAAAA-AAGT-A-AAT-ATATAATGATGATAATAGTGT
1 TAAAAATAAGTAATAATAATATAATGA-GATAATAATAT
42291211 TAAAAATAA-TAATAATAAT
1 TAAAAATAAGTAATAATAAT
42291230 GAATAAATGG
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
32 8 0.18
33 3 0.07
34 2 0.04
35 17 0.38
36 4 0.09
37 3 0.07
38 8 0.18
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.33
Consensus pattern (38 bp):
TAAAAATAAGTAATAATAATATAATGAGATAATAATAT
Found at i:42292405 original size:45 final size:45
Alignment explanation
Indices: 42292367--42292590 Score: 138
Period size: 45 Copynumber: 5.0 Consensus size: 45
42292357 TTCAAGAAGG
*
42292367 TAAGAGTTGGTAATTTCAACGTGCTCCACTGCAACTTCAGGGAGA
1 TAAGAGTTGGTAATTTCAACCTGCTCCACTGCAACTTCAGGGAGA
* * *** * *
42292412 TAAG-GTTTGTGATCTTCAGTTTTCTCCACTGCAACTTTAGGGAGA
1 TAAGAGTTGGTAAT-TTCAACCTGCTCCACTGCAACTTCAGGGAGA
* * * **
42292457 TAAGACTTGTTAA-TTCAACCTGCTCTACTGCAACTTCAGATAGA
1 TAAGAGTTGGTAATTTCAACCTGCTCCACTGCAACTTCAGGGAGA
** * * * *
42292501 TAA-AGTT--TACTATCTTTGATCTGCTTCGCTACAACTTCAGGGAGA
1 TAAGAGTTGGTA--AT-TTCAACCTGCTCCACTGCAACTTCAGGGAGA
* * * * *
42292546 TAAGA-TCTGCT-ATTTCAATCTCCTCCACTGTAACTTTAGGGAGA
1 TAAGAGT-TGGTAATTTCAACCTGCTCCACTGCAACTTCAGGGAGA
42292590 T
1 T
42292591 GACACCTGTA
Statistics
Matches: 132, Mismatches: 37, Indels: 21
0.69 0.19 0.11
Matches are distributed among these distances:
41 2 0.02
43 4 0.03
44 57 0.43
45 62 0.47
46 6 0.05
48 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (45 bp):
TAAGAGTTGGTAATTTCAACCTGCTCCACTGCAACTTCAGGGAGA
Found at i:42292474 original size:89 final size:88
Alignment explanation
Indices: 42292216--42292590 Score: 271
Period size: 89 Copynumber: 4.2 Consensus size: 88
42292206 AATCCACTCT
*
42292216 ACTGCAACTTCAGGGAGAT-AGGATTAGATG-TCTTCAGTCTACTCCGCTGCAACTTCAGGGAGA
1 ACTGCAACTTCAGGGAGATAAGG-TTTG-TGATCTTCAGTCTACTCCGCTGCAACTTCAGGGAGA
*** *
42292279 TAAGACTTGTGGCTTCAATCAGCTCC
64 TAAGACTTGTTAATTCAA-CTGCTCC
* * * * * * * * * *
42292305 AATGTAATTTCAGGGAGA-AGAGATTTGT-AGCTTC-GATCTACTTCGCTGGAACTTCAAGAAGG
1 ACTGCAACTTCAGGGAGATA-AGGTTTGTGATCTTCAG-TCTACTCCGCTGCAACTTCAGGGAGA
* *
42292367 TAAGAGTTGGTAATTTCAACGTGCTCC
64 TAAGACTTGTTAA-TTCAAC-TGCTCC
* * * *
42292394 ACTGCAACTTCAGGGAGATAAGGTTTGTGATCTTCAGTTTTCTCCACTGCAACTTTAGGGAGATA
1 ACTGCAACTTCAGGGAGATAAGGTTTGTGATCTTCAGTCTACTCCGCTGCAACTTCAGGGAGATA
*
42292459 AGACTTGTTAATTCAACCTGCTCT
66 AGACTTGTTAATTCAA-CTGCTCC
** * * * * * *
42292483 ACTGCAACTTCAGATAGATAAAGTTTACT-ATCTT-TGATCTGCTTCGCTACAACTTCAGGGAGA
1 ACTGCAACTTCAGGGAGATAAGGTTT-GTGATCTTCAG-TCTACTCCGCTGCAACTTCAGGGAGA
* * *
42292546 TAAGA-TCTGCTATTTCAATCTCCTCC
64 TAAGACT-TGTTAATTCAA-CTGCTCC
* *
42292572 ACTGTAACTTTAGGGAGAT
1 ACTGCAACTTCAGGGAGAT
42292591 GACACCTGTA
Statistics
Matches: 219, Mismatches: 54, Indels: 26
0.73 0.18 0.09
Matches are distributed among these distances:
87 1 0.00
88 37 0.17
89 142 0.65
90 38 0.17
91 1 0.00
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (88 bp):
ACTGCAACTTCAGGGAGATAAGGTTTGTGATCTTCAGTCTACTCCGCTGCAACTTCAGGGAGATA
AGACTTGTTAATTCAACTGCTCC
Done.