Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 5 of 259
Found at i:1256680 original size:22 final size:22
Alignment explanation
Indices: 1256652--1256696 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
1256642 AGGGGGAGTG
1256652 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
1256674 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
1256696 T
1 T
1256697 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:1258747 original size:191 final size:192
Alignment explanation
Indices: 1258419--1258782 Score: 579
Period size: 191 Copynumber: 1.9 Consensus size: 192
1258409 AAAAACTGAG
* * * * *
1258419 CAACAAAATTTATTCACACATGCAGAGGTAGCAAGTGTACAACCCAACCATTGGCATGCTCATAC
1 CAACAAAACTCATTCACACATGCAGAGGTAACAAATGTACAACCCAACCAATGGCATGCTCATAC
*
1258484 AAAAATAAACCCAAAAATACATTGAAAGAAATTTGCTGCAGTAGTGTGAGATAACTCTGGTTAAA
66 AAAAATAAACCCAAAAATACATAGAAAGAAATTTGCTGCAGTAGTGTGAGATAACTCTGGTTAAA
* * *
1258549 ACTCATTTAAAAATCATAGAAAGTTTGATAAATAAGAATCACTAGGAAAACAACCAGAAAGC
131 ACTCATTTAAAAATCATAGAAAGCTTGATAAAGAAGAACCACTAGGAAAACAACCAGAAAGC
*
1258611 CAACAAAACTCATTCACACATGCAGAGGTAACAAATGTAC-ACCCAACCACAT-GCCTGCTCATA
1 CAACAAAACTCATTCACACATGCAGAGGTAACAAATGTACAACCCAACCA-ATGGCATGCTCATA
* * *
1258674 CAAAAATAAGCCCAAAAATATATAGGAAGAAATTTGCTGCAGTAGTGTGAGATAACTCTGGTTAA
65 CAAAAATAAACCCAAAAATACATAGAAAGAAATTTGCTGCAGTAGTGTGAGATAACTCTGGTTAA
*
1258739 ATCTCATTTAAAAATCATAGAAAGCTTGATAAAGAAGAACCACT
130 AACTCATTTAAAAATCATAGAAAGCTTGATAAAGAAGAACCACT
1258783 GCGGAAACAG
Statistics
Matches: 157, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
191 120 0.76
192 37 0.24
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (192 bp):
CAACAAAACTCATTCACACATGCAGAGGTAACAAATGTACAACCCAACCAATGGCATGCTCATAC
AAAAATAAACCCAAAAATACATAGAAAGAAATTTGCTGCAGTAGTGTGAGATAACTCTGGTTAAA
ACTCATTTAAAAATCATAGAAAGCTTGATAAAGAAGAACCACTAGGAAAACAACCAGAAAGC
Found at i:1262130 original size:25 final size:24
Alignment explanation
Indices: 1262102--1262148 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1262092 AACAACCAAA
*
1262102 CTTTTTCCATTAACCGAAATTTACC
1 CTTTTT-CATTAACAGAAATTTACC
1262127 CTTTTTCATTAACAGAAATTTA
1 CTTTTTCATTAACAGAAATTTA
1262149 TATTTTTATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.32, C:0.21, G:0.04, T:0.43
Consensus pattern (24 bp):
CTTTTTCATTAACAGAAATTTACC
Found at i:1262155 original size:24 final size:24
Alignment explanation
Indices: 1262103--1262155 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
1262093 ACAACCAAAC
* *
1262103 TTTTTCCATTAACCGAAATTTACCC
1 TTTTTCCATTAACAGAAATTTA-CA
*
1262128 TTTTT-CATTAACAGAAATTTATA
1 TTTTTCCATTAACAGAAATTTACA
1262151 TTTTT
1 TTTTT
1262156 ATGTTAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 5 0.20
24 15 0.60
25 5 0.20
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.49
Consensus pattern (24 bp):
TTTTTCCATTAACAGAAATTTACA
Found at i:1262976 original size:30 final size:30
Alignment explanation
Indices: 1262908--1262981 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
1262898 GAATAAAATT
* *
1262908 TTATAAATTTATAAAAAATTATAAAAAATA
1 TTATAAATTTATAAAAAATCATAAAAAAAA
* **
1262938 TTAGAAATTTATTTAAAATCATAAAAAAAAA
1 TTATAAATTTATAAAAAATCAT-AAAAAAAA
1262969 TT-TAAATTTATAA
1 TTATAAATTTATAA
1262982 CAATTATTAG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
30 26 0.74
31 9 0.26
ACGTcount: A:0.59, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
TTATAAATTTATAAAAAATCATAAAAAAAA
Found at i:1262979 original size:108 final size:106
Alignment explanation
Indices: 1262845--1263051 Score: 272
Period size: 108 Copynumber: 1.9 Consensus size: 106
1262835 TAGAAGTATA
1262845 AAAAACATAAAAAAAAATAAATTTTATAAAAATTATTAGAAACTAATTAAAAAGAATAAAATTTT
1 AAAAACATAAAAAAAAATAAATTTTATAAAAATTATTAGAAACTAATTAAAAAGAATAAAATTTT
* *
1262910 ATAAATTTATAAAAAATTATAAAAAATATTAGAAATTTATTT
66 AGAAAATT-TAAAAAATTATAAAAAATATTAGAAATTTATTT
* * * * **
1262952 AAAATCATAAAAAAAAATTTAAA-TTTATAACAATTATTAGAAATTAATTTAAAATCATAAAATT
1 AAAAACATAAAAAAAAA--TAAATTTTATAAAAATTATTAGAAACTAATTAAAAAGAATAAAATT
* * * *
1263016 TTAGAAAATTTAGAAAATTTTATAAACTATTAGAAA
64 TTAGAAAATTTAAAAAATTATAAAAAATATTAGAAA
1263052 CTAATTGAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
107 38 0.44
108 44 0.51
109 4 0.05
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (106 bp):
AAAAACATAAAAAAAAATAAATTTTATAAAAATTATTAGAAACTAATTAAAAAGAATAAAATTTT
AGAAAATTTAAAAAATTATAAAAAATATTAGAAATTTATTT
Found at i:1263001 original size:30 final size:28
Alignment explanation
Indices: 1262967--1263022 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
1262957 CATAAAAAAA
* *
1262967 AATTTAAATTTATAACAATTATTAGAAATT
1 AATTTAAAATCATAA-AATT-TTAGAAATT
1262997 AATTTAAAATCATAAAATTTTAGAAA
1 AATTTAAAATCATAAAATTTTAGAAA
1263023 ATTTAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 4 0.17
30 13 0.54
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (28 bp):
AATTTAAAATCATAAAATTTTAGAAATT
Found at i:1263032 original size:19 final size:20
Alignment explanation
Indices: 1263010--1263051 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1263000 TTAAAATCAT
1263010 AAAATTTTAGAAAAT-TTAG
1 AAAATTTTAGAAAATATTAG
* *
1263029 AAAATTTTATAAACTATTAG
1 AAAATTTTAGAAAATATTAG
1263049 AAA
1 AAA
1263052 CTAATTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (20 bp):
AAAATTTTAGAAAATATTAG
Found at i:1264640 original size:59 final size:61
Alignment explanation
Indices: 1264571--1264688 Score: 168
Period size: 62 Copynumber: 2.0 Consensus size: 61
1264561 ATCACTTTAA
* *
1264571 TATTAAATTAATATAATATTTA-T-CAAGATAAATATTACATTAAATTTAAAATTAAATCT
1 TATTAAATTAATAGAATATTTACTACAAGATAAATATTAAATTAAATTTAAAATTAAATCT
* * *
1264630 TATTAAATTAATAGAATGTTTATCTACAAGATTAATATTAAATTAAATTTAATATTAAA
1 TATTAAATTAATAGAATATTTA-CTACAAGATAAATATTAAATTAAATTTAAAATTAAA
1264689 ATAATCACCT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
59 20 0.39
61 1 0.02
62 30 0.59
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.42
Consensus pattern (61 bp):
TATTAAATTAATAGAATATTTACTACAAGATAAATATTAAATTAAATTTAAAATTAAATCT
Found at i:1266380 original size:14 final size:15
Alignment explanation
Indices: 1266346--1266375 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1266336 TTGTTTATGC
*
1266346 AAAATATGAAAGACA
1 AAAATATAAAAGACA
1266361 AAAATATAAAAGACA
1 AAAATATAAAAGACA
1266376 TAATAGTGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.10, T:0.13
Consensus pattern (15 bp):
AAAATATAAAAGACA
Found at i:1267065 original size:25 final size:26
Alignment explanation
Indices: 1267025--1267074 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
1267015 TTGTAAATTA
1267025 AAAAAATATCTCTAGA-AATTTTCTG
1 AAAAAATATCTCTAGAGAATTTTCTG
* *
1267050 AAAAAATCTCTTTAGAGAATTTTCT
1 AAAAAATATCTCTAGAGAATTTTCT
1267075 CTCTACAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.38
Consensus pattern (26 bp):
AAAAAATATCTCTAGAGAATTTTCTG
Found at i:1267254 original size:59 final size:61
Alignment explanation
Indices: 1267183--1267299 Score: 166
Period size: 62 Copynumber: 1.9 Consensus size: 61
1267173 ATCACTTTAA
* * * * *
1267183 TATTAAATTAATATAATATTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAAAATATTTACTACAAAATAAACATTAAATTAAATTTAATATTAAATCT
1267242 TATTAAAATAATAAAATATTTATCTACAAAATAAACATTAAATTAAATTTAATATTAA
1 TATTAAAATAATAAAATATTTA-CTACAAAATAAACATTAAATTAAATTTAATATTAA
1267300 GATATCACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
59 20 0.40
61 1 0.02
62 29 0.58
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (61 bp):
TATTAAAATAATAAAATATTTACTACAAAATAAACATTAAATTAAATTTAATATTAAATCT
Found at i:1273292 original size:47 final size:46
Alignment explanation
Indices: 1273232--1273543 Score: 181
Period size: 47 Copynumber: 6.6 Consensus size: 46
1273222 GACAAGGGAT
* * *
1273232 AGTGTAATACATGTCTAGGACATGCATCAGCCACATTATCATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCACATGATCATAGCC
* * * * **
1273278 AGTGTAAGACCATGTCTAGGACATGGCATC-GGCATAGAGAGGAGT-GCC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCCACA-TGATCA-TAGCC
* ** *
1273326 AGTGTAAGACATGTCTGGGACATGGATTGGCCACGATGATGATAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATGATCATAGCC
** * * * *
1273373 AGTGTAAGATGTGTCTGGGACATGCAT-AG--ACTAAGCTTCGT-GCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC-ATG-ATCATAGCC
* * *
1273417 AGTGTAAGACATGTCTGGGACATGCATCAG-CACGTAT-ACACGAGAGCT
1 AGTGTAAGACATGTCTGGGACATGCATCAGCCAC--ATGA-TC-ATAGCC
* * **
1273465 AGTGTAAGACTATGTCTGGGACATGGCATCGGCCTCGATGAAGATAGCC
1 AGTGTAAGAC-ATGTCTGGGACAT-GCATCAGCCAC-ATGATCATAGCC
*
1273514 AGTGTAAGACCATGCCTGGGACATGGCATC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATC
1273544 GGCAACTTAA
Statistics
Matches: 209, Mismatches: 38, Indels: 35
0.74 0.13 0.12
Matches are distributed among these distances:
44 31 0.15
45 4 0.02
46 16 0.08
47 67 0.32
48 33 0.16
49 45 0.22
50 10 0.05
51 3 0.01
ACGTcount: A:0.29, C:0.20, G:0.29, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCAGCCACATGATCATAGCC
Found at i:1273301 original size:94 final size:95
Alignment explanation
Indices: 1273180--1273497 Score: 267
Period size: 94 Copynumber: 3.4 Consensus size: 95
1273170 GTTATGTGAG
* * * * *
1273180 AGCCAGTGTAAGATCATGTCTGGGACATGGCATCGGCATTGAGACAAGGGATAGTGTAATACATG
1 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATAGAGACAAGGGACAGTGTAAGACATG
*
1273245 TCTAGGACATGCATCAGCCAC-ATTATCAT
66 TCTAGGACATGCATCAGCCACGATGATCAT
** * *
1273274 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATAGAGAGGAGTGCCAGTGTAAGACATG
1 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATAGAGACAAGGGACAGTGTAAGACATG
* * ** *
1273339 TCTGGGACATGGATTGGCCACGATGATGAT
66 TCTAGGACATGCATCAGCCACGATGATCAT
** * * * ** *
1273369 AGCCAGTGTAAGA-TGTGTCTGGGACAT-GCATAGAC-TA-AG-CTTCGTG-CTAGTGTAAGACA
1 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATAGAGAC-AAGGGAC-AGTGTAAGACA
* * *
1273428 TGTCTGGGACATGCATCAG-CACGTAT-ACACGAG
64 TGTCTAGGACATGCATCAGCCACG-ATGA-TC-AT
* * *
1273461 AGCTAGTGTAAGACTATGTCTGGGACATGGCATCGGC
1 AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGC
1273498 CTCGATGAAG
Statistics
Matches: 183, Mismatches: 33, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
90 6 0.03
91 34 0.19
92 15 0.08
93 19 0.10
94 90 0.49
95 19 0.10
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (95 bp):
AGCCAGTGTAAGACCATGTCTAGGACATGGCATCGGCATAGAGACAAGGGACAGTGTAAGACATG
TCTAGGACATGCATCAGCCACGATGATCAT
Found at i:1277415 original size:16 final size:17
Alignment explanation
Indices: 1277386--1277420 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1277376 AAGATATTTA
1277386 ATAAAAATAATTTAATC
1 ATAAAAATAATTTAATC
*
1277403 ATAAAAA-ATTTTAATC
1 ATAAAAATAATTTAATC
1277419 AT
1 AT
1277421 CCAAATATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAAAAATAATTTAATC
Found at i:1281215 original size:34 final size:34
Alignment explanation
Indices: 1281172--1281295 Score: 133
Period size: 34 Copynumber: 3.6 Consensus size: 34
1281162 TTCTGATATG
* * * *
1281172 ATATGACATTTTGATATGAAATATGCTTCTAAAA
1 ATATGACATTCTGATATGATATATGTTTCTAGAA
* * *
1281206 ATATGACATTCTAATCT-AGTATATGTTTCTGGAA
1 ATATGACATTCTGATATGA-TATATGTTTCTAGAA
* * *
1281240 ATATGACATTTTGATCTGATATATGTTTCTAGTA
1 ATATGACATTCTGATATGATATATGTTTCTAGAA
*
1281274 ATGTGACATTCTGATATGATAT
1 ATATGACATTCTGATATGATAT
1281296 TTGTATATGT
Statistics
Matches: 74, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
33 1 0.01
34 72 0.97
35 1 0.01
ACGTcount: A:0.34, C:0.10, G:0.15, T:0.42
Consensus pattern (34 bp):
ATATGACATTCTGATATGATATATGTTTCTAGAA
Found at i:1282145 original size:14 final size:15
Alignment explanation
Indices: 1282117--1282145 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1282107 CAGTTAACTG
1282117 TACTTTAGTTACTTT
1 TACTTTAGTTACTTT
1282132 TACTTTAG-TACTTT
1 TACTTTAGTTACTTT
1282146 AGTAAAACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.59
Consensus pattern (15 bp):
TACTTTAGTTACTTT
Found at i:1285751 original size:27 final size:27
Alignment explanation
Indices: 1285711--1285797 Score: 115
Period size: 27 Copynumber: 3.2 Consensus size: 27
1285701 AGGAAGCGTC
*
1285711 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
*
1285738 CTGGTGGCTCTGCCAC-ATATATCTGCT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
1285765 CTGGTGGCTCTGCCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
*
1285792 CCGGTG
1 CTGGTG
1285798 AGTTCGTCAC
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
26 8 0.15
27 44 0.83
28 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.32
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:1295898 original size:50 final size:50
Alignment explanation
Indices: 1295776--1296024 Score: 275
Period size: 50 Copynumber: 4.8 Consensus size: 50
1295766 GATAATAACA
* * ** * *
1295776 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGAT-GG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCAT-CTCGG
* *
1295827 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
1295877 TGCCAATGCCATGTCCCAGACATGGCCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
1295927 TGCCCATGCCATGTCCCAGACATGGTCTTACTGGGGACCTCTCATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTC---ATC-T-CGG
* *
1295982 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
1296025 TTACCCAAAT
Statistics
Matches: 168, Mismatches: 23, Indels: 9
0.84 0.12 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.54
51 33 0.20
53 2 0.01
54 1 0.01
55 2 0.01
56 38 0.23
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:1295953 original size:100 final size:104
Alignment explanation
Indices: 1295775--1296024 Score: 350
Period size: 100 Copynumber: 2.4 Consensus size: 104
1295765 TGATAATAAC
* **
1295775 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCGTGATGGTGCCCATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCGTGATGGTGCCCATGCCATG
*
1295840 TCCCAGACATGGTCTTA-TAGGGGACCTCTC-ATC-T-CGG
65 TCCCAGACATGGTCTTACT-GGGGACCTCTCAATCTTAAGG
* *
1295877 -TGCCAATGCCATGTCCCAGACATGGCCTTACATGGGACCTCTCGT-CTCGGTGCCCATGCCATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGAT-GGTGCCCATGCCATG
1295940 TCCCAGACATGGTCTTACTGGGGACCTCTCATGATCTTAAGG
65 TCCCAGACATGGTCTTACTGGGGACCTCTCA--ATCTTAAGG
*
1295982 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1296025 TTACCCAAAT
Statistics
Matches: 132, Mismatches: 8, Indels: 12
0.87 0.05 0.08
Matches are distributed among these distances:
99 1 0.01
100 49 0.37
101 36 0.27
103 3 0.02
104 1 0.01
105 2 0.02
106 40 0.30
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.26
Consensus pattern (104 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTGATGGTGCCCATGCCATGT
CCCAGACATGGTCTTACTGGGGACCTCTCAATCTTAAGG
Found at i:1296140 original size:13 final size:13
Alignment explanation
Indices: 1296119--1296150 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1296109 GCTTGGATCA
*
1296119 TCATCAAATAAAT
1 TCATAAAATAAAT
1296132 TCATAAAATAAAT
1 TCATAAAATAAAT
1296145 TCATAA
1 TCATAA
1296151 TTGCTGGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:1298657 original size:77 final size:77
Alignment explanation
Indices: 1298566--1298742 Score: 234
Period size: 77 Copynumber: 2.3 Consensus size: 77
1298556 GATGAACTAT
*
1298566 TATCATGGCCCGAAGCCAAATT-ATCCAATATGCATGG-CCTGAAGTCAAATCAATAATATACAC
1 TATCATGGCCCGAAGCC-AATTCATCCAATATGCATGGTCC-GAAGCCAAATCAATAATATACAC
* *
1298629 ACCCGAAGTGTTGA
64 ACCCGAAGTGCTAA
* ** *
1298643 TATCATGGCCCGAAGCCAATTCATCCGATATGCATGGTCCGAAGCCAAATCGGTAATATACGCAC
1 TATCATGGCCCGAAGCCAATTCATCCAATATGCATGGTCCGAAGCCAAATCAATAATATACACAC
1298708 CCGAAGTGCTAA
66 CCGAAGTGCTAA
*
1298720 TATCATGGCTCGATA-CCAATTCA
1 TATCATGGCCCGA-AGCCAATTCA
1298743 ACGTATCACT
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
76 4 0.04
77 82 0.92
78 3 0.03
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.23
Consensus pattern (77 bp):
TATCATGGCCCGAAGCCAATTCATCCAATATGCATGGTCCGAAGCCAAATCAATAATATACACAC
CCGAAGTGCTAA
Found at i:1299297 original size:13 final size:14
Alignment explanation
Indices: 1299262--1299300 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
1299252 GAAGATATTT
1299262 ATATATTATATATAA
1 ATATATTAT-TATAA
*
1299277 ATAAATTATTAT-A
1 ATATATTATTATAA
1299290 ATATATTATTA
1 ATATATTATTA
1299301 GTAACTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 3 0.14
15 8 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATTATTATAA
Found at i:1304906 original size:22 final size:21
Alignment explanation
Indices: 1304853--1304906 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1304843 TTTAATGTCT
* * *
1304853 ATTTATAATGTAATATATAAA
1 ATTTAAAATCTAATATAAAAA
*
1304874 ACTTAATAATCTAATAATAAAAA
1 ATTTAA-AATCTAAT-ATAAAAA
1304897 ATTTAAAATC
1 ATTTAAAATC
1304907 AACTATCCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
21 4 0.15
22 11 0.42
23 11 0.42
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.37
Consensus pattern (21 bp):
ATTTAAAATCTAATATAAAAA
Found at i:1315366 original size:20 final size:20
Alignment explanation
Indices: 1315341--1315380 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
1315331 ATATAAATGA
1315341 CTTTGAAATTA-ATTTAATTT
1 CTTTG-AATTATATTTAATTT
1315361 CTTTGAATTATTATTTAATT
1 CTTTGAATTA-TATTTAATT
1315381 GAATGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 5 0.28
21 8 0.44
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (20 bp):
CTTTGAATTATATTTAATTT
Found at i:1316144 original size:18 final size:19
Alignment explanation
Indices: 1316109--1316146 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1316099 TATTAATTTT
* *
1316109 AAATTTTATTTTTGAAATA
1 AAATTTTAATATTGAAATA
1316128 AAATTTTAATATT-AAATA
1 AAATTTTAATATTGAAATA
1316146 A
1 A
1316147 TAAATTATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AAATTTTAATATTGAAATA
Found at i:1317375 original size:169 final size:166
Alignment explanation
Indices: 1317089--1317429 Score: 450
Period size: 169 Copynumber: 2.0 Consensus size: 166
1317079 CACTTTCCAA
*
1317089 GAAAAACTATTGGTGACCGACGAAGTTTTAGCGAACAACAGCCGTCATCTGTCTATCACAACTTG
1 GAAAAACTATTGGTGACCGACGAAGTTTTAGCGAACAACAGCCGTCATCTGTCCATCACAACTTG
* * * *
1317154 TGAAGACAACAAAAATGCCTACAAAATAGATCTGCAAGATGAAAATAGAGAAGACGAGTAGTAAA
66 TGAAGACAACAAAAATACCCACAAAATAGATCTGCAAGATGAAAAGAGAGAAGACGAGCAGTAAA
*
1317219 TGAGAAGAAGAAAGCAAGAAATGGTTAATAGGAGGG
131 TGAGAAGAAGAAAGAAAGAAATGGTTAATAGGAGGG
** ** *
1317255 GAAAAACTATTGGTGACCGGTGAAGTTTTAGCGAATGACATGCACCGTCATCTGTCCATTACAAC
1 GAAAAACTATTGGTGACCGACGAAGTTTTAGCGAACAACA-G--CCGTCATCTGTCCATCACAAC
* * * * *
1317320 TTGTGAAGATAACAAAGATACCCACAATATAGATCTGTAA-ATTGAAAAGAGAGAAGACGTGCAG
63 TTGTGAAGACAACAAAAATACCCACAAAATAGATCTGCAAGA-TGAAAAGAGAGAAGACGAGCAG
* * * *
1317384 TGAATGAGAAGAAGAAATAAAGAAATGGTTGATGGGAGGG
127 TAAATGAGAAGAAGAAAGAAAGAAATGGTTAATAGGAGGG
*
1317424 AAAAAA
1 GAAAAA
1317430 TGCAGGCGAT
Statistics
Matches: 150, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
166 36 0.24
167 1 0.01
168 1 0.01
169 112 0.75
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (166 bp):
GAAAAACTATTGGTGACCGACGAAGTTTTAGCGAACAACAGCCGTCATCTGTCCATCACAACTTG
TGAAGACAACAAAAATACCCACAAAATAGATCTGCAAGATGAAAAGAGAGAAGACGAGCAGTAAA
TGAGAAGAAGAAAGAAAGAAATGGTTAATAGGAGGG
Found at i:1318278 original size:19 final size:20
Alignment explanation
Indices: 1318235--1318278 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
1318225 AAATACATTT
*
1318235 AAAAACATAAAAACAAATAT
1 AAAAACATAAAAACAAATAA
* *
1318255 TAAAACA-AGAAACAAATAA
1 AAAAACATAAAAACAAATAA
1318274 AAAAA
1 AAAAA
1318279 TGATACTAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.77, C:0.09, G:0.02, T:0.11
Consensus pattern (20 bp):
AAAAACATAAAAACAAATAA
Found at i:1320254 original size:24 final size:24
Alignment explanation
Indices: 1320226--1320274 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1320216 TGAAGAATGC
1320226 TGGTCCATAATTAAAGAACGAGCA
1 TGGTCCATAATTAAAGAACGAGCA
1320250 TGGTCCATAATTAAAGAACGAGCA
1 TGGTCCATAATTAAAGAACGAGCA
1320274 T
1 T
1320275 TGATGGCCTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.22
Consensus pattern (24 bp):
TGGTCCATAATTAAAGAACGAGCA
Found at i:1322279 original size:210 final size:210
Alignment explanation
Indices: 1321903--1322398 Score: 593
Period size: 210 Copynumber: 2.4 Consensus size: 210
1321893 TAACGGGGCA
* * * * * * * *
1321903 ATGTTCCTCTCTTAAAAAGCTTCGCGTTTCCAGGTG-TAAAACATTAAGCAAGATCAGAGACGGG
1 ATGTTCATCTCTTGAAAAGCTTAGCATTTCCAGTTGCGAAAA-ATTAAGCAAGATCGGAGACGGA
* * ** * * * * * **** *
1321967 CTGTCAACCTCCATTTATCTCAAGGAATTAGATTTAAAAGATTGTCCTAATTTAAGTTGGATTCC
65 TTATTTACCTCCACTTGTCTCAAAGAATTATATCTATGTCATTGTCCTAATTTAAGTTCGATTCC
* * **
1322032 GGATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAAGGAATTGGAAGTTC
130 AGATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATTAATAGCTGCAACAAATTGGAAGTTC
* * *
1322097 TTCCTATAACCGGAGG
195 TTCCGATAACAGGAAG
* * *** *
1322113 TTGTTCATCTCTTGAAAAGCTTAGGATTTTGGGTTGTGAAAAATTAAGCAAGATCGGAGACGGAT
1 ATGTTCATCTCTTGAAAAGCTTAGCATTTCCAGTTGCGAAAAATTAAGCAAGATCGGAGACGGAT
* *
1322178 TATTTAGCTCCACTTGTCTCAAAGAATTATATCTATGTCATTGTTCTAATTTAAGTTCGATTCCA
66 TATTTACCTCCACTTGTCTCAAAGAATTATATCTATGTCATTGTCCTAATTTAAGTTCGATTCCA
*
1322243 GATTTGGAAGGATGTTT-CTCTCTT-AAAATTCTGTCAATTAATAGCTGCAACAAATTTGAAGTT
131 GATTTGGAAGGAT-TTTCCTCTCTTCAAAA-TCTGTCAATTAATAGCTGCAACAAATTGGAAGTT
*
1322306 CTTCCGGTAACAGGAAG
194 CTTCCGATAACAGGAAG
1322323 ATGTTCATCTCTTGAAAAGCTTAGCATTTCCAGTTGCGAAAAATTAAGCAAGATCGGAGACGGAT
1 ATGTTCATCTCTTGAAAAGCTTAGCATTTCCAGTTGCGAAAAATTAAGCAAGATCGGAGACGGAT
1322388 TATTTACCTCC
66 TATTTACCTCC
1322399 TCTCTTCAAA
Statistics
Matches: 238, Mismatches: 45, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
209 4 0.02
210 227 0.95
211 7 0.03
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.33
Consensus pattern (210 bp):
ATGTTCATCTCTTGAAAAGCTTAGCATTTCCAGTTGCGAAAAATTAAGCAAGATCGGAGACGGAT
TATTTACCTCCACTTGTCTCAAAGAATTATATCTATGTCATTGTCCTAATTTAAGTTCGATTCCA
GATTTGGAAGGATTTTCCTCTCTTCAAAATCTGTCAATTAATAGCTGCAACAAATTGGAAGTTCT
TCCGATAACAGGAAG
Found at i:1322476 original size:138 final size:138
Alignment explanation
Indices: 1322260--1322528 Score: 396
Period size: 138 Copynumber: 1.9 Consensus size: 138
1322250 AAGGATGTTT
* *
1322260 CTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTTGAAGTTCTTCCGGTAACAGGAAGAT
1 CTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTAGAAGTTCTTCCAGTAACAGGAAGAT
1322325 GTTCATCTCTTGAAAAGCTTAGCATTTCCAGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTA
66 GTTCATCTCTTGAAAAGCTTAGCATTTCCAGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTA
1322390 TTTACCTC
131 TTTACCTC
* * * * * * * *
1322398 CTCTCTTCAAAA-TCTGTCAATTGATAGTTGCAACGAATTAGAAGTTCTTTCATTACCTGGAAGG
1 CTCTCTT-AAAATTCTGTCAATTAATAGCTGCAACAAATTAGAAGTTCTTCCAGTAACAGGAAGA
*** *
1322462 TGTTCATCTCTTGAAAAGCTTAGCATTTTTGGTTGCGAAAAATTAAGCAAGATTGGAGACGGATT
65 TGTTCATCTCTTGAAAAGCTTAGCATTTCCAGTTGCGAAAAATTAAGCAAGATCGGAGACGGATT
1322527 AT
130 AT
1322529 CTGCCTGCGC
Statistics
Matches: 116, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
138 112 0.97
139 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (138 bp):
CTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTAGAAGTTCTTCCAGTAACAGGAAGAT
GTTCATCTCTTGAAAAGCTTAGCATTTCCAGTTGCGAAAAATTAAGCAAGATCGGAGACGGATTA
TTTACCTC
Found at i:1322688 original size:348 final size:348
Alignment explanation
Indices: 1322048--1322746 Score: 1021
Period size: 348 Copynumber: 2.0 Consensus size: 348
1322038 GGAAGGATTT
* *
1322048 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAAGGAATTGGAAGTTCTTCCTATAACCGGAGG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTAGAAGTTCTTCCTATAACCGGAGG
* *
1322113 TTGTTCATCTCTTGAAAAGCTTAGGATTTTGGGTTGTGAAAAATTAAGCAAGATCGGAGACGGAT
66 TTGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGGAGACGGAT
* * * * *
1322178 TATTTAGCTCCACTTGTCTCAAAGAATTATATCTATGTCATTGTTCTAATTTAAGTTCGATTCCA
131 TATCTAGCTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTCCA
* ** *
1322243 GATTTGGAAGGATGTTTCTCTCTTAAAATTCTGTCAATTAATAGCTGCAACAAATTTGAAGTTCT
196 AATTTGGAAGGATGTTTCTCTCTTAAAAGCCTGTCAATTAATAGCTGCAACAAATTGGAAGTTCT
** * *
1322308 TCCGGTAACAGGAAGATGTTCATCTCTTGAAAAGCTTAGCATTTCCAGTTGCGAAAAAT-TAAGC
261 TCCAATAACAGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGC-AAAAATATAAGC
*
1322372 AAGATCGGAGACGGATTATTTACC
325 AAGATCGGAGACGGATTATCTACC
* * *
1322396 TCCTCTCTTCAAAATCTGTCAATTGATAGTTGCAACGAATTAGAAGTTCTTTC-ATTACCTGGAA
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTAGAAGTTCTTCCTATAACC-GG-A
* *
1322460 GG-TGTTCATCTCTTGAAAAGCTTAGCATTTTTGGTTGCGAAAAATTAAGCAAGATTGGAGACGG
64 GGTTGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGGAGACGG
* * *
1322524 ATTATCT-GCCTGCGCTTGTCTCAAAGAATTAGGTCTATATAATTGTCCTAATTTAAGTTCGATT
129 ATTATCTAG-CTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATT
* * * **
1322588 CCAAATTTGGAAGGAT-TTTCCTCTCTTCAGAGCCTGTCAATTAATAGGTGCAATGAATTGGAAG
193 CCAAATTTGGAAGGATGTTT-CTCTCTTAAAAGCCTGTCAATTAATAGCTGCAACAAATTGGAAG
*
1322652 TTCTTCCAATAACTGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATA
257 TTCTTCCAATAACAGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATA
*
1322717 AGCAAGATCGGAGACGGGTTATCTACC
322 AGCAAGATCGGAGACGGATTATCTACC
1322744 TCC
1 TCC
1322747 ACTTGTCTCA
Statistics
Matches: 313, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
347 15 0.05
348 295 0.94
349 3 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (348 bp):
TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTAGAAGTTCTTCCTATAACCGGAGG
TTGTTCATCTCTTGAAAAGCTTAGCATTTTGGGTTGCGAAAAATTAAGCAAGATCGGAGACGGAT
TATCTAGCTCCACTTGTCTCAAAGAATTAGATCTATATAATTGTCCTAATTTAAGTTCGATTCCA
AATTTGGAAGGATGTTTCTCTCTTAAAAGCCTGTCAATTAATAGCTGCAACAAATTGGAAGTTCT
TCCAATAACAGGAAGATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAAGCA
AGATCGGAGACGGATTATCTACC
Found at i:1322758 original size:210 final size:210
Alignment explanation
Indices: 1322396--1323068 Score: 988
Period size: 210 Copynumber: 3.2 Consensus size: 210
1322386 ATTATTTACC
* * * * *
1322396 TCCTCTCTTCAAAATCTGTCAATTGATAGTTGCAACGAATTAGAAGTTCTTTCATTACCTGGAAG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACTGGAAG
* * *** *
1322461 GTGTTCATCTCTTGAAAAGCTTAGCATTTTTGGTTGCGAAAAAT-TAAGCAAGATTGGAGACGGA
66 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGC-AAAAATATAAGCAAGATCGGAGACGGA
* * * * ** *
1322525 TTATCTGCCTGCGCTTGTCTCAAAGAATTAGGTCTATATAATTGTCCTAATTTAAGTTCGATTCC
130 TTATCTACCTCCACTTGTCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTCGATTCC
*
1322590 AAATTTGGAAGGATTT
195 AGATTTGGAAGGATTT
* ** * * *
1322606 TCCTCTCTTCAGAGCCTGTCAATTAATAGGTGCAATGAATTGGAAGTTCTTCCAATAACTGGAAG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACTGGAAG
* *
1322671 ATGTTCATCTATTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAAGCAAGATCGGAGACGGGT
66 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAAGCAAGATCGGAGACGGAT
* *
1322736 TATCTACCTCCACTTGTCTCAAAGAATTATATCTATATCTTTGTTCTAATTTAAGTTTGATTCCA
131 TATCTACCTCCACTTGTCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTCGATTCCA
1322801 GATTTGGAAGGATTT
196 GATTTGGAAGGATTT
* * *
1322816 TCCTCTCTTCAAAATCTATCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCCATAACAGGAAG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACTGGAAG
*
1322881 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATGAGCAAGATCGGAGACGGAT
66 ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAAGCAAGATCGGAGACGGAT
* * * *
1322946 TATCTACCTCCACTTATCTTAAAGAATTAGATCAATATCTTTGTTCTAATTTAAGTTGGATTCCA
131 TATCTACCTCCACTTGTCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTCGATTCCA
1323011 GATTTGGAAGGATTT
196 GATTTGGAAGGATTT
*
1323026 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAAGGAATTGG
1 TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGG
1323069 CGAGTTTTCC
Statistics
Matches: 415, Mismatches: 47, Indels: 2
0.89 0.10 0.00
Matches are distributed among these distances:
209 6 0.01
210 409 0.99
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (210 bp):
TCCTCTCTTCAAAATCTGTCAATTGATAGCTGCAACGAATTGGAAGTTCTTCCAATAACTGGAAG
ATGTTCATCTCTTGAAAAGCTTAGAATTTCCAGTTGCAAAAATATAAGCAAGATCGGAGACGGAT
TATCTACCTCCACTTGTCTCAAAGAATTAGATCTATATCTTTGTTCTAATTTAAGTTCGATTCCA
GATTTGGAAGGATTT
Found at i:1323686 original size:144 final size:143
Alignment explanation
Indices: 1323436--1323699 Score: 341
Period size: 144 Copynumber: 1.8 Consensus size: 143
1323426 CTGGTTGGGA
* * * * *
1323436 AAAGCTTAAGAGTCTTCCCCCCAACTTCAATCCCTCTCTGCCCTTGAAGAATTGACGATATTAGA
1 AAAGCTAAAGAGTCTTCCCACCAACTCCAATCCCTCACTGCCCTTGAAGAATTGACGATATGAGA
* * * * ** *
1323501 GTTTCAAGGAATAGAAGCCTTTCCAGAGTGGTTGGGAAATCTCTCTTCTTTAAGGCATCTATATT
66 GTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGGCATCTATATT
1323566 TAAGTGGTTTTGG
131 TAAGTGGTTTTGG
* * * *
1323579 AAAGCTAAAGAGTCTTCCTCACCAACTCCAACTCCC-CACTGCCCTTGAAGATTTGACTATGTGG
1 AAAGCTAAAGAGTCTTCC-CACCAACTCCAA-TCCCTCACTGCCCTTGAAGAATTGACGATATGA
* *
1323643 GGGTTTCATGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGG
64 GAGTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGG
1323700 TGTCTGCGTA
Statistics
Matches: 101, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
143 17 0.17
144 80 0.79
145 4 0.04
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (143 bp):
AAAGCTAAAGAGTCTTCCCACCAACTCCAATCCCTCACTGCCCTTGAAGAATTGACGATATGAGA
GTTTCAAGAAATAGAAGCCTTGCCAGACTCGTTCAGAAATCTCTCTTCTCTAAGGCATCTATATT
TAAGTGGTTTTGG
Found at i:1327045 original size:25 final size:25
Alignment explanation
Indices: 1327017--1327065 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
1327007 TTATTTATTA
*
1327017 ATTTCTAATACTTTTTATAAATTTT
1 ATTTCTAATAATTTTTATAAATTTT
* *
1327042 ATTTTTTATAATTTTTATAAATTT
1 ATTTCTAATAATTTTTATAAATTT
1327066 ATAAATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (25 bp):
ATTTCTAATAATTTTTATAAATTTT
Found at i:1327055 original size:10 final size:10
Alignment explanation
Indices: 1327042--1327132 Score: 50
Period size: 9 Copynumber: 9.6 Consensus size: 10
1327032 TATAAATTTT
1327042 ATTTTTTATA
1 ATTTTTTATA
1327052 A-TTTTTATA
1 ATTTTTTATA
*
1327061 A--ATTTATA
1 ATTTTTTATA
*
1327069 A-ATTTTATA
1 ATTTTTTATA
** *
1327078 AAATTTTATG
1 ATTTTTTATA
*
1327088 ATTTTTAATTA
1 ATTTTTTA-TA
* *
1327099 ATTTCTAATA
1 ATTTTTTATA
1327109 A-TTTTTAT-
1 ATTTTTTATA
1327117 ATTTTTTATA
1 ATTTTTTATA
*
1327127 CTTTTT
1 ATTTTT
1327133 AGAATGAACC
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
8 8 0.12
9 28 0.43
10 21 0.32
11 8 0.12
ACGTcount: A:0.34, C:0.02, G:0.01, T:0.63
Consensus pattern (10 bp):
ATTTTTTATA
Found at i:1327066 original size:8 final size:9
Alignment explanation
Indices: 1326987--1327086 Score: 71
Period size: 9 Copynumber: 10.9 Consensus size: 9
1326977 GTTTACCCTT
1326987 AATTTTATAA
1 AATTTTAT-A
*
1326997 AATTTTATG
1 AATTTTATA
* *
1327006 ATTATTTATT
1 AAT-TTTATA
1327016 AATTTCTAATA
1 AATTT-T-ATA
**
1327027 CTTTTTATA
1 AATTTTATA
1327036 AATTTTAT-
1 AATTTTATA
*
1327044 -TTTTTATA
1 AATTTTATA
*
1327052 ATTTTTATA
1 AATTTTATA
1327061 AA-TTTATA
1 AATTTTATA
1327069 AATTTTATAA
1 AATTTTAT-A
1327079 AATTTTAT
1 AATTTTAT
1327087 GATTTTTAAT
Statistics
Matches: 72, Mismatches: 11, Indels: 14
0.74 0.11 0.14
Matches are distributed among these distances:
7 6 0.08
8 8 0.11
9 27 0.38
10 26 0.36
11 5 0.07
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (9 bp):
AATTTTATA
Found at i:1327066 original size:17 final size:17
Alignment explanation
Indices: 1327046--1327117 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 17
1327036 AATTTTATTT
1327046 TTTATAATTTTTATAAA
1 TTTATAATTTTTATAAA
*
1327063 TTTATAAATTTTATAAAA
1 TTTATAATTTTTAT-AAA
* *
1327081 TTTTATGATTTTTAATTAAT
1 -TTTATAATTTTT-A-TAAA
1327101 TTCTAATAATTTTTATA
1 TT-T-ATAATTTTTATA
1327118 TTTTTTATAC
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
17 13 0.30
18 3 0.07
19 14 0.32
20 5 0.11
21 9 0.20
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (17 bp):
TTTATAATTTTTATAAA
Found at i:1332079 original size:69 final size:69
Alignment explanation
Indices: 1331968--1332106 Score: 269
Period size: 69 Copynumber: 2.0 Consensus size: 69
1331958 GATAGGAAAA
*
1331968 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTTGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1332033 GCTG
66 GCTG
1332037 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1 ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
1332102 GCTG
66 GCTG
1332106 A
1 A
1332107 TAGAGTCTTG
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 69 1.00
ACGTcount: A:0.27, C:0.13, G:0.32, T:0.28
Consensus pattern (69 bp):
ACAGGTTCCAAAACAGGAATAACAGTGGCTGTAGGATTTTCAGCAGGTTTTGTAGTGGTGGTAGG
GCTG
Found at i:1342134 original size:10 final size:10
Alignment explanation
Indices: 1342066--1342165 Score: 60
Period size: 10 Copynumber: 9.4 Consensus size: 10
1342056 CATGTTCCAC
1342066 AAAAAAAAAG
1 AAAAAAAAAG
*
1342076 -ACAAAAAAG
1 AAAAAAAAAG
*
1342085 CAAAAAAAAAC
1 -AAAAAAAAAG
*
1342096 AACAAAAAAG
1 AAAAAAAAAG
1342106 AAGAAGAAATAATTCG
1 AA-AA-AAA-AA---G
1342122 AAAAAAAAAG
1 AAAAAAAAAG
*
1342132 -AAAAGAAAG
1 AAAAAAAAAG
1342141 AAAAAAAAAG
1 AAAAAAAAAG
* *
1342151 TTAAAAAAAAT
1 -AAAAAAAAAG
1342162 AAAA
1 AAAA
1342166 GTTTGATGAT
Statistics
Matches: 69, Mismatches: 11, Indels: 20
0.69 0.11 0.20
Matches are distributed among these distances:
9 16 0.23
10 22 0.32
11 16 0.23
12 3 0.04
13 4 0.06
14 3 0.04
15 2 0.03
16 3 0.04
ACGTcount: A:0.79, C:0.05, G:0.10, T:0.06
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:1342160 original size:16 final size:16
Alignment explanation
Indices: 1342122--1342168 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1342112 AAATAATTCG
1342122 AAAAAAAAAGAAAAG--
1 AAAAAAAAA-AAAAGTT
*
1342137 AAAGAAAAAAAAAGTT
1 AAAAAAAAAAAAAGTT
*
1342153 AAAAAAAATAAAAGTT
1 AAAAAAAAAAAAAGTT
1342169 TGATGATTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
16 14 0.52
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (16 bp):
AAAAAAAAAAAAAGTT
Found at i:1350632 original size:12 final size:12
Alignment explanation
Indices: 1350617--1350684 Score: 50
Period size: 12 Copynumber: 5.4 Consensus size: 12
1350607 GAAAAAAGAC
1350617 AAAAAGCAAAAA
1 AAAAAGCAAAAA
*
1350629 AAAAAACAACAAA
1 AAAAAGCAA-AAA
1350642 AAAAAG-AAGAAGA
1 AAAAAGCAA-AA-A
**
1350655 AATAATTCAAAAA
1 AA-AAAGCAAAAA
1350668 AAAAAG-AAAATA
1 AAAAAGCAAAA-A
1350680 AAAAA
1 AAAAA
1350685 AAGTTAAAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
11 4 0.09
12 20 0.45
13 14 0.32
14 4 0.09
15 2 0.05
ACGTcount: A:0.81, C:0.06, G:0.07, T:0.06
Consensus pattern (12 bp):
AAAAAGCAAAAA
Found at i:1350693 original size:16 final size:15
Alignment explanation
Indices: 1350663--1350705 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
1350653 GAAATAATTC
1350663 AAAAAAAAAAG--AA
1 AAAAAAAAAAGTTAA
1350676 AATAAAAAAAAGTTAA
1 AA-AAAAAAAAGTTAA
1350692 AAAAAATAAAAGTT
1 AAAAAA-AAAAGTT
1350706 TGATGATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.08
14 9 0.35
15 4 0.15
16 11 0.42
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (15 bp):
AAAAAAAAAAGTTAA
Found at i:1350699 original size:41 final size:39
Alignment explanation
Indices: 1350623--1350700 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 39
1350613 AGACAAAAAG
* *
1350623 CAAAAAAAAAAACAACAAAAAAAAGAAGAAGAAATAATT
1 CAAAAAAAAAAAAAACAAAAAAAAGAAGAAAAAATAATT
*
1350662 CAAAAAAAAAAGAAAATAAAAAAAAGTTAA-AAAAAATAA
1 CAAAAAAAAAA-AAAACAAAAAAAAG--AAGAAAAAATAA
1350701 AAGTTTGATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 11 0.33
40 12 0.36
41 8 0.24
42 2 0.06
ACGTcount: A:0.79, C:0.05, G:0.06, T:0.09
Consensus pattern (39 bp):
CAAAAAAAAAAAAAACAAAAAAAAGAAGAAAAAATAATT
Found at i:1354825 original size:24 final size:24
Alignment explanation
Indices: 1354798--1354849 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1354788 TTCGTAGGTC
*
1354798 AAATAAATTATACTAATAAATGTT
1 AAATAAATTATACTAATAAATATT
* *
1354822 AAATATATTATACTAATGAATATT
1 AAATAAATTATACTAATAAATATT
1354846 AAAT
1 AAAT
1354850 CTTCTAGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATATT
Found at i:1359625 original size:2 final size:2
Alignment explanation
Indices: 1359613--1359680 Score: 82
Period size: 2 Copynumber: 34.0 Consensus size: 2
1359603 ATAATTTTGG
* * *
1359613 GA GA AA GA GA GA GA GA GA GA AA GA GA AA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
* * *
1359655 GA GA GA GA AA AA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
1359681 TAGACGTGTT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1360290 original size:124 final size:124
Alignment explanation
Indices: 1360070--1360317 Score: 451
Period size: 124 Copynumber: 2.0 Consensus size: 124
1360060 TCGGCCACCA
*
1360070 ATCCGGTTTAAAAAACATTGAGATTAATATTTTATGCATTAATATTTTATATAGGATGGAAATTT
1 ATCCGGTTTAAAAAACATTGAGATTAATATTTTATGCATTAATATTTTATATAAGATGGAAATTT
1360135 GAAGTGTATAATTCTATGTACCATCAATCAATTTGATTATTCCCAATCACTAAGGCTTT
66 GAAGTGTATAATTCTATGTACCATCAATCAATTTGATTATTCCCAATCACTAAGGCTTT
1360194 ATCCGGTTTAAAAAACATTGAGATTAATATTTTATGCATTAATATTTTATATAAGATGGAAATTT
1 ATCCGGTTTAAAAAACATTGAGATTAATATTTTATGCATTAATATTTTATATAAGATGGAAATTT
* * * *
1360259 GAAGTGTATAATTCTATTTACCATTAATCAATTTGATTATTCTCAATCATTAAGGCTTT
66 GAAGTGTATAATTCTATGTACCATCAATCAATTTGATTATTCCCAATCACTAAGGCTTT
1360318 GCTTGGTAGA
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 119 1.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.41
Consensus pattern (124 bp):
ATCCGGTTTAAAAAACATTGAGATTAATATTTTATGCATTAATATTTTATATAAGATGGAAATTT
GAAGTGTATAATTCTATGTACCATCAATCAATTTGATTATTCCCAATCACTAAGGCTTT
Found at i:1364950 original size:22 final size:22
Alignment explanation
Indices: 1364907--1364946 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1364897 TTAATTTGAG
1364907 TTAAATTTAAATATTAATTAAA
1 TTAAATTTAAATATTAATTAAA
1364929 TTAAATTT-AAT-TTAATTA
1 TTAAATTTAAATATTAATTA
1364947 TAAAATAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAAATTTAAATATTAATTAAA
Found at i:1367832 original size:77 final size:77
Alignment explanation
Indices: 1367705--1367858 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
1367695 TAGACGGTTT
1367705 GAAATTGGGGTTGTTCTGTTGGCTAGGTCTAAGGATTCAATCTGCCATCCATGCTTGAGTTCAAG
1 GAAATTGGGGTTGTTCTGTTGGCTAGGTCTAAGGATTCAATCTGCCATCCATGCTTGAGTTCAAG
1367770 ATTATTAGCTTC
66 ATTATTAGCTTC
1367782 GAAATTGGGGTTGTTCTGTTGGCTAGGTCTAAGGATTCAATCTGCCATCCATGCTTGAGTTCAAG
1 GAAATTGGGGTTGTTCTGTTGGCTAGGTCTAAGGATTCAATCTGCCATCCATGCTTGAGTTCAAG
1367847 ATTATTAGCTTC
66 ATTATTAGCTTC
1367859 AACCATGCTG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (77 bp):
GAAATTGGGGTTGTTCTGTTGGCTAGGTCTAAGGATTCAATCTGCCATCCATGCTTGAGTTCAAG
ATTATTAGCTTC
Found at i:1369213 original size:21 final size:21
Alignment explanation
Indices: 1369189--1369231 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1369179 TGTGGATGCA
1369189 TTTG-AGTATGCTGATTGTAAT
1 TTTGTAGT-TGCTGATTGTAAT
* *
1369210 TTTGTTGTTGTTGATTGTAAT
1 TTTGTAGTTGCTGATTGTAAT
1369231 T
1 T
1369232 CCCTTATCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.19, C:0.02, G:0.23, T:0.56
Consensus pattern (21 bp):
TTTGTAGTTGCTGATTGTAAT
Found at i:1371168 original size:21 final size:21
Alignment explanation
Indices: 1371127--1371168 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1371117 CATCTGAGTG
* *
1371127 TGTTAATTGTAATTTCGTTGT
1 TGTTAATTGTAATTCCCTTGT
*
1371148 TGTTGATTGTAATTCCCTTGT
1 TGTTAATTGTAATTCCCTTGT
1371169 CTGGGATTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.10, G:0.19, T:0.55
Consensus pattern (21 bp):
TGTTAATTGTAATTCCCTTGT
Found at i:1379784 original size:13 final size:13
Alignment explanation
Indices: 1379766--1379829 Score: 92
Period size: 13 Copynumber: 4.9 Consensus size: 13
1379756 AGTTTGGCAA
1379766 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
1379779 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
* *
1379792 TGCTGTGGAAAAG
1 TGCTTTTGAAAAG
*
1379805 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
1379818 TGCTTTTGAAAA
1 TGCTTTTGAAAA
1379830 ATTTGGTTTA
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 43 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:1379795 original size:26 final size:26
Alignment explanation
Indices: 1379766--1379829 Score: 110
Period size: 26 Copynumber: 2.5 Consensus size: 26
1379756 AGTTTGGCAA
1379766 TGCTTTTGAAAAGTGCTTTTGAGAAG
1 TGCTTTTGAAAAGTGCTTTTGAGAAG
* *
1379792 TGCTGTGGAAAAGTGCTTTTGAGAAG
1 TGCTTTTGAAAAGTGCTTTTGAGAAG
1379818 TGCTTTTGAAAA
1 TGCTTTTGAAAA
1379830 ATTTGGTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.28, C:0.08, G:0.28, T:0.36
Consensus pattern (26 bp):
TGCTTTTGAAAAGTGCTTTTGAGAAG
Found at i:1380303 original size:13 final size:13
Alignment explanation
Indices: 1380285--1380309 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1380275 TTCAGAAGTG
1380285 CTTTTGAAAAGCA
1 CTTTTGAAAAGCA
1380298 CTTTTGAAAAGC
1 CTTTTGAAAAGC
1380310 TAAAAATTTC
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
CTTTTGAAAAGCA
Found at i:1394959 original size:21 final size:21
Alignment explanation
Indices: 1394934--1394986 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
1394924 CAGTGGAGAT
*
1394934 AGGAACAACAGGTTCCAAAAC
1 AGGAAAAACAGGTTCCAAAAC
1394955 AGGAAAAACAGGTTCCAAAAC
1 AGGAAAAACAGGTTCCAAAAC
*
1394976 AGGAATAACAG
1 AGGAAAAACAG
1394987 TGGCTGTAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.51, C:0.19, G:0.21, T:0.09
Consensus pattern (21 bp):
AGGAAAAACAGGTTCCAAAAC
Found at i:1406802 original size:9 final size:9
Alignment explanation
Indices: 1406783--1406828 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
1406773 ATCACGTCAA
1406783 TAAATAATTT
1 TAAA-AATTT
1406793 TAAAAATTT
1 TAAAAATTT
*
1406802 TAAAAATAT
1 TAAAAATTT
1406811 TAGAAAATTT
1 TA-AAAATTT
*
1406821 TCAAAATT
1 TAAAAATT
1406829 CAAAAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
9 21 0.66
10 11 0.34
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (9 bp):
TAAAAATTT
Found at i:1408555 original size:29 final size:29
Alignment explanation
Indices: 1408485--1408556 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
1408475 GTTACAATTC
* * *
1408485 GGACTTATTTGATTCATTTTAATAATATAG
1 GGACTGATTTGA-TCATTTTAATAATAGAA
*
1408515 GGACTGAATTGATCATTTTAATAATAGAA
1 GGACTGATTTGATCATTTTAATAATAGAA
*
1408544 TGACT-AGTTTGAT
1 GGACTGA-TTTGAT
1408557 ACGGTCCCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
28 1 0.03
29 24 0.69
30 10 0.29
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (29 bp):
GGACTGATTTGATCATTTTAATAATAGAA
Found at i:1408769 original size:12 final size:12
Alignment explanation
Indices: 1408752--1408793 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
1408742 TTTTAATCAT
*
1408752 CACATGGCAGCC
1 CACATGGCAACC
1408764 CACATGGCAACC
1 CACATGGCAACC
*
1408776 CACATGGCAATC
1 CACATGGCAACC
1408788 CACATG
1 CACATG
1408794 TATTTTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.31, C:0.38, G:0.19, T:0.12
Consensus pattern (12 bp):
CACATGGCAACC
Found at i:1408911 original size:17 final size:17
Alignment explanation
Indices: 1408865--1408912 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
1408855 AGATTAAAAT
*
1408865 AAAAATATTTAAAATTC
1 AAAAAAATTTAAAATTC
** *
1408882 AAAAAAAAATAAAGTTC
1 AAAAAAATTTAAAATTC
*
1408899 ATAAAAATTTAAAA
1 AAAAAAATTTAAAA
1408913 AGATTAGCAT
Statistics
Matches: 23, Mismatches: 8, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAAAAATTTAAAATTC
Found at i:1411596 original size:59 final size:60
Alignment explanation
Indices: 1411483--1411606 Score: 142
Period size: 59 Copynumber: 2.1 Consensus size: 60
1411473 ATATTGTCTC
* * ** ** ** * * *
1411483 AATTTAGTACCTAAACTTGATGCTTTTTCTTAATTTGGTATTTAAGCTTTTTTTA-TTTT
1 AATTTAATACCTAAAATTGACACTTTTTCTTAATTTAATACCTAAACTTGTTTTACGTTT
1411542 AATTTAATACCTAAAATTGACACTTTTTCTTAATTTAATACCTAAACTTGTTTTACGTTT
1 AATTTAATACCTAAAATTGACACTTTTTCTTAATTTAATACCTAAACTTGTTTTACGTTT
1411602 AATTT
1 AATTT
1411607 CGTATCTAAC
Statistics
Matches: 53, Mismatches: 11, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
59 45 0.85
60 8 0.15
ACGTcount: A:0.29, C:0.12, G:0.07, T:0.52
Consensus pattern (60 bp):
AATTTAATACCTAAAATTGACACTTTTTCTTAATTTAATACCTAAACTTGTTTTACGTTT
Found at i:1412484 original size:46 final size:46
Alignment explanation
Indices: 1412432--1412527 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
1412422 AAAGCTAGAT
*
1412432 TAAAATGTTGATTAAGCTCAAAGAATTTATGCAAACCCCTACACAA
1 TAAAATGTTGATTAAGCTCAAAGAACTTATGCAAACCCCTACACAA
* * * *
1412478 TAAAATGTTGATTCAGCTCAAAGAACTTATGCTATCCCCTACTCAA
1 TAAAATGTTGATTAAGCTCAAAGAACTTATGCAAACCCCTACACAA
1412524 TAAA
1 TAAA
1412528 GCCAAGACCC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.41, C:0.21, G:0.10, T:0.28
Consensus pattern (46 bp):
TAAAATGTTGATTAAGCTCAAAGAACTTATGCAAACCCCTACACAA
Found at i:1413266 original size:3 final size:3
Alignment explanation
Indices: 1413258--1413290 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1413248 TGCTTGGCCA
1413258 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1413291 CTAGTATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1416435 original size:17 final size:16
Alignment explanation
Indices: 1416395--1416438 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
1416385 TTTTTCGGTT
1416395 TTTCTTCTTCCCTGCC
1 TTTCTTCTTCCCTGCC
* *
1416411 TTTCCTTCTTCCATTGTC
1 TTT-CTTCTTCC-CTGCC
1416429 TTTCTTCTTC
1 TTTCTTCTTC
1416439 TTTTTTCGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 15 0.62
18 6 0.25
ACGTcount: A:0.02, C:0.36, G:0.05, T:0.57
Consensus pattern (16 bp):
TTTCTTCTTCCCTGCC
Found at i:1432587 original size:17 final size:18
Alignment explanation
Indices: 1432550--1432593 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
1432540 AATCAAAATT
*
1432550 TATTTTATAATAAGATAA
1 TATTTTATAACAAGATAA
*
1432568 TATTTTATAACAA-TTAA
1 TATTTTATAACAAGATAA
*
1432585 TATCTTATA
1 TATTTTATA
1432594 TAAACTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
17 11 0.48
18 12 0.52
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (18 bp):
TATTTTATAACAAGATAA
Found at i:1433015 original size:13 final size:13
Alignment explanation
Indices: 1432997--1433021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1432987 TGTGTCTTTT
1432997 TTTTAAATATTTA
1 TTTTAAATATTTA
1433010 TTTTAAATATTT
1 TTTTAAATATTT
1433022 TACTATACCC
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTAAATATTTA
Found at i:1433213 original size:20 final size:20
Alignment explanation
Indices: 1433190--1433227 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1433180 ATTTTTTAAA
1433190 ATTAAAATTAA-AATTTTATT
1 ATTAAAA-TAATAATTTTATT
*
1433210 ATTAATATAATAATTTTA
1 ATTAAAATAATAATTTTA
1433228 AACTTGATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAAAATAATAATTTTATT
Found at i:1435512 original size:28 final size:30
Alignment explanation
Indices: 1435480--1435536 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 30
1435470 TTATTTTTAT
*
1435480 ATATTATATAAT-TTATAA-ATATATATTA
1 ATATTATATAATATTATAATATAAATATTA
*
1435508 ATATTATATATTATTATAATATAAATATT
1 ATATTATATAATATTATAATATAAATATT
1435537 TAAAAAATTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 11 0.44
29 6 0.24
30 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (30 bp):
ATATTATATAATATTATAATATAAATATTA
Found at i:1436168 original size:21 final size:22
Alignment explanation
Indices: 1436121--1436174 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
1436111 CCCTGTACCT
* *
1436121 GCAAAA-ACATACAAACGTACA
1 GCAAAATACAAACAAACGAACA
1436142 GC-AAATACAAACAAAC-AACA
1 GCAAAATACAAACAAACGAACA
1436162 GCAAAATAGCAAA
1 GCAAAATA-CAAA
1436175 GGGAAAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 8 0.29
21 16 0.57
22 4 0.14
ACGTcount: A:0.61, C:0.22, G:0.09, T:0.07
Consensus pattern (22 bp):
GCAAAATACAAACAAACGAACA
Found at i:1438499 original size:130 final size:130
Alignment explanation
Indices: 1438248--1438732 Score: 402
Period size: 130 Copynumber: 3.7 Consensus size: 130
1438238 AAAATTCTTC
* * * *
1438248 AAAACGAAGGCGAAATTTGATGTTCGGCGATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * * * *
1438313 TTTCGTATTTGCTCAAAATAATCGAATTTCCCTTCGAAATTTCATTCATATTTTTTAAAAT-TCC
66 TTTCGCATTTGTTCAAAATAATCGAATATCACTTCAAAATTTCACTCATATCTTTTAAAATCT-C
1438377 T
130 T
* * * * * *
1438378 TAAATGAAGATGAGATTTGATGTTTGGCAATTCGTGGAATTGTGTCCTAACGTGTTGGGTTGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * ** * *
1438443 TTTCGCATTTGTTCAAAATAATCGAATATCATTTTAAAATTTTGCTCGTGTCTTTTAAAATCTCT
66 TTTCGCATTTGTTCAAAATAATCGAATATCACTTCAAAATTTCACTCATATCTTTTAAAATCTCT
* * * * * * * *
1438508 AAAACGAAGGCGATATGTAATATTTGGCAATTCGCGGGATCATGCCCTAACGTGTTGGGTAGCAA
1 AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
* * * * *** *
1438573 TTTCCCGA-TTGTTTAAAATAATCAAATATCCCTTCAAAATTTCACTCGGCTCTTCTAAAAATCC
66 TTTCGC-ATTTGTTCAAAATAATCGAATATCACTTCAAAATTTCACTCATATCTT-TTAAAAT-C
*
1438637 TTT
128 TCT
* * * ** * * * * * **
1438640 AAAACGAA-AGCAATATTCGGCGTTTGACAATTCG-AGAATCATGCCCTATCGTGCTGGGTTGTG
1 AAAACGAAGA-CGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCA
* **
1438703 ATTTCTCATTTGTTCAAAACGATCGAATAT
65 ATTTCGCATTTGTTCAAAATAATCGAATAT
1438733 TCTTTTGTAG
Statistics
Matches: 279, Mismatches: 70, Indels: 11
0.77 0.19 0.03
Matches are distributed among these distances:
130 199 0.71
131 53 0.19
132 27 0.10
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (130 bp):
AAAACGAAGACGAGATTTGATGTTTGGCAATTCGCGGAATCGTGCCCTAACGTGTTGGGTTGCAA
TTTCGCATTTGTTCAAAATAATCGAATATCACTTCAAAATTTCACTCATATCTTTTAAAATCTCT
Found at i:1442615 original size:17 final size:17
Alignment explanation
Indices: 1442576--1442618 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1442566 ACTATCAATA
1442576 TAAATAATAAATTTAAT
1 TAAATAATAAATTTAAT
* *
1442593 TTAATATTAAATTT-AT
1 TAAATAATAAATTTAAT
1442609 TAAAATAATA
1 T-AAATAATA
1442619 TTGTTTTTAG
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TAAATAATAAATTTAAT
Found at i:1442860 original size:25 final size:25
Alignment explanation
Indices: 1442832--1442885 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
1442822 TTGCTGGTTA
* *
1442832 GGTTCAGGCCTGTGACAACCCAATC
1 GGTTCAGGCCAGTGACAACCCAACC
**
1442857 GGTTCAGGCCAGTGATGACCCAACC
1 GGTTCAGGCCAGTGACAACCCAACC
1442882 GGTT
1 GGTT
1442886 TGGTCCAGCC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.22, C:0.30, G:0.28, T:0.20
Consensus pattern (25 bp):
GGTTCAGGCCAGTGACAACCCAACC
Found at i:1449187 original size:2 final size:2
Alignment explanation
Indices: 1449180--1449204 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1449170 GTAACCACCA
1449180 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1449205 ACAGCTGGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1457406 original size:26 final size:24
Alignment explanation
Indices: 1457377--1457425 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
1457367 ATAAAAAAAG
*
1457377 TTTAAAAATATAATAAATCAAATATA
1 TTTAAAAACATAA-AAA-CAAATATA
1457403 TTTAAAAACATAAAAACAAATAT
1 TTTAAAAACATAAAAACAAATAT
1457426 TAAAACAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.63, C:0.06, G:0.00, T:0.31
Consensus pattern (24 bp):
TTTAAAAACATAAAAACAAATATA
Found at i:1457445 original size:21 final size:21
Alignment explanation
Indices: 1457396--1457454 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1457386 ATAATAAATC
*
1457396 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
1457416 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
1457438 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
1457455 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:1457531 original size:15 final size:16
Alignment explanation
Indices: 1457501--1457533 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1457491 AAATGGTTAT
1457501 ATTAAAAATTTAAAATA
1 ATTAAAAA-TTAAAATA
1457518 ATTAAAAA-TAAAATA
1 ATTAAAAATTAAAATA
1457533 A
1 A
1457534 ATATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.50
17 8 0.50
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
ATTAAAAATTAAAATA
Found at i:1459213 original size:27 final size:27
Alignment explanation
Indices: 1459183--1459235 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1459173 AGGATAATGT
1459183 AAGGATATTAGGGATTGAATCAAAGTC
1 AAGGATATTAGGGATTGAATCAAAGTC
1459210 AAGGATATTAGGGATTGAATCAAAGT
1 AAGGATATTAGGGATTGAATCAAAGT
1459236 TCTTTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.42, C:0.06, G:0.26, T:0.26
Consensus pattern (27 bp):
AAGGATATTAGGGATTGAATCAAAGTC
Found at i:1459692 original size:18 final size:18
Alignment explanation
Indices: 1459671--1459708 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1459661 AAAAAGTAAC
* *
1459671 AAAATAATAAAATTATTA
1 AAAAAAATAAAAATATTA
1459689 AAAAAAATAAAAATATTA
1 AAAAAAATAAAAATATTA
1459707 AA
1 AA
1459709 TTTTATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAAAAATAAAAATATTA
Found at i:1460074 original size:10 final size:10
Alignment explanation
Indices: 1460059--1460105 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
1460049 TATTTTATTA
1460059 TTTTTATAAC
1 TTTTTATAAC
1460069 TTTTTA-ATAC
1 TTTTTATA-AC
1460079 -TTTTATTAAC
1 TTTTTA-TAAC
*
1460089 TTTTTATAAA
1 TTTTTATAAC
1460099 TTTTTAT
1 TTTTTAT
1460106 GTACAACTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
9 6 0.19
10 20 0.62
11 6 0.19
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTATAAC
Found at i:1460221 original size:10 final size:10
Alignment explanation
Indices: 1460177--1460266 Score: 73
Period size: 10 Copynumber: 9.3 Consensus size: 10
1460167 TCTAAATTTA
*
1460177 TTTATAGTAT
1 TTTATAATAT
1460187 TTATATAATAT
1 TT-TATAATAT
1460198 TTTCAT-AT-T
1 TTT-ATAATAT
*
1460207 TTTATAACAT
1 TTTATAATAT
1460217 TTTATAATAT
1 TTTATAATAT
* *
1460227 TTAAAAATAT
1 TTTATAATAT
*
1460237 CTTATAATAT
1 TTTATAATAT
*
1460247 TGTAT-A-AT
1 TTTATAATAT
1460255 TTTATAA-AT
1 TTTATAATAT
1460264 TTT
1 TTT
1460267 CTTTGTAATG
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
8 8 0.12
9 12 0.19
10 33 0.52
11 11 0.17
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (10 bp):
TTTATAATAT
Found at i:1462982 original size:16 final size:16
Alignment explanation
Indices: 1462960--1463030 Score: 108
Period size: 16 Copynumber: 4.4 Consensus size: 16
1462950 GTTTGGTTCA
1462960 CTGTAATGGAATA-AGG
1 CTGTAATGGAATAGA-G
* *
1462976 TTGTAATTGAATAGAG
1 CTGTAATGGAATAGAG
1462992 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
1463008 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAG
1463024 CTGTAAT
1 CTGTAAT
1463031 CAGTAATTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
16 49 0.98
17 1 0.02
ACGTcount: A:0.37, C:0.06, G:0.28, T:0.30
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:1463098 original size:44 final size:46
Alignment explanation
Indices: 1463012--1463105 Score: 120
Period size: 44 Copynumber: 2.1 Consensus size: 46
1463002 ATAGAGCTGT
*
1463012 AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTAGTTGAATGG
1 AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTAGTTGAATGA
* *** *
1463058 AATGGAGTAGAGCTGTAAT-AG-AATTCTTGTGTTTGGTTGAATGA
1 AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTAGTTGAATGA
1463102 AATG
1 AATG
1463106 ATGTTGTAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
44 22 0.52
45 2 0.05
46 18 0.43
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATCAGTAATTCAACTGTTTAGTTGAATGA
Found at i:1463220 original size:25 final size:25
Alignment explanation
Indices: 1463176--1463226 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 25
1463166 ATTGATAGAT
1463176 GATTATTGTTATTAAA-TTTTAATAA
1 GATTATTGTTA-TAAATTTTTAATAA
1463201 GATTATTGTTA-AATATTTTTTAATAA
1 GATTATTGTTATAA-A-TTTTTAATAA
1463227 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 2 0.09
24 1 0.04
25 11 0.48
26 9 0.39
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (25 bp):
GATTATTGTTATAAATTTTTAATAA
Found at i:1463287 original size:24 final size:21
Alignment explanation
Indices: 1463266--1463324 Score: 75
Period size: 20 Copynumber: 2.8 Consensus size: 21
1463256 TAACATAATT
1463266 ATTATTAAATATAATTTAATAA
1 ATTATT-AATATAATTTAATAA
* *
1463288 AATAAT-ATATAATTTAATAA
1 ATTATTAATATAATTTAATAA
1463308 CATTATTAATATAATTT
1 -ATTATTAATATAATTT
1463325 TTAATAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
20 14 0.45
21 4 0.13
22 13 0.42
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTATTAATATAATTTAATAA
Found at i:1463288 original size:55 final size:54
Alignment explanation
Indices: 1463228--1463348 Score: 127
Period size: 57 Copynumber: 2.2 Consensus size: 54
1463218 TTTTAATAAA
* * *
1463228 AATAAAAATAAATAATTTAATCATATT-TTAACATAATTATTATTAAATATAATTT
1 AATAAAAATAAATAATTTAATAACATTATTAACATAATTATTAAT-AATA-AATTT
* * * *
1463283 AATAAAATAATATATAATTTAATAACATTATTAATATAATTTTTAATAATAATTTT
1 AAT-AAA-AATAAATAATTTAATAACATTATTAACATAATTATTAATAATAAATTT
1463339 AATATAAAAT
1 AATA-AAAAT
1463349 TATTATTATG
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
55 7 0.13
56 12 0.22
57 22 0.40
58 14 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (54 bp):
AATAAAAATAAATAATTTAATAACATTATTAACATAATTATTAATAATAAATTT
Found at i:1463327 original size:24 final size:24
Alignment explanation
Indices: 1463300--1463345 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1463290 TAATATATAA
*
1463300 TTTAATAA-CATTATTAATATAATT
1 TTTAATAATAATT-TTAATATAATT
1463324 TTTAATAATAATTTTAATATAA
1 TTTAATAATAATTTTAATATAA
1463346 AATTATTATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAATAATAATTTTAATATAATT
Found at i:1465431 original size:25 final size:25
Alignment explanation
Indices: 1465397--1465449 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
1465387 CAATCATTCG
1465397 CCTTAGAAGATCAAATTCTGAAGCA
1 CCTTAGAAGATCAAATTCTGAAGCA
1465422 CCTTAGAAGATCAAATTCTGAAGCA
1 CCTTAGAAGATCAAATTCTGAAGCA
1465447 CCT
1 CCT
1465450 GGGAATAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (25 bp):
CCTTAGAAGATCAAATTCTGAAGCA
Found at i:1465858 original size:40 final size:40
Alignment explanation
Indices: 1465814--1465891 Score: 156
Period size: 40 Copynumber: 1.9 Consensus size: 40
1465804 GTTATACTGT
1465814 AGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGATGC
1 AGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGATGC
1465854 AGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGAT
1 AGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGAT
1465892 AGAGTTCCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (40 bp):
AGATACTCAAGCAAATAAGTTATTTTGCCAATTTAGATGC
Found at i:1467322 original size:69 final size:69
Alignment explanation
Indices: 1467240--1467386 Score: 208
Period size: 69 Copynumber: 2.1 Consensus size: 69
1467230 AAATCTTTTA
* * * *
1467240 TTTTTATTGTAATGACTATGTCTTTTAATTTT-AA-AAATTTATTTTTTTAATGGCTCATTCATA
1 TTTTTTTTTTAATGACTAAGTCTATTAATTTTCAACAAA-TTATTTTTTT-ATGGCTCATTCATA
1467303 TGCATG
64 TGCATG
*
1467309 TTTTTTTTTTAATGATTAAGTCTATTAATTTTCAACAAATTATTTTTTTATGGCTCATTCATATG
1 TTTTTTTTTTAATGACTAAGTCTATTAATTTTCAACAAATTATTTTTTTATGGCTCATTCATATG
1467374 CATG
66 CATG
*
1467378 TTGTTTTTT
1 TTTTTTTTT
1467387 GATTTTAGGA
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
69 55 0.79
70 12 0.17
71 3 0.04
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.56
Consensus pattern (69 bp):
TTTTTTTTTTAATGACTAAGTCTATTAATTTTCAACAAATTATTTTTTTATGGCTCATTCATATG
CATG
Found at i:1468126 original size:21 final size:20
Alignment explanation
Indices: 1468093--1468131 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
1468083 GATATAATGC
*
1468093 ATTTTAAACATATAATTTACT
1 ATTTGAAACATAT-ATTTACT
*
1468114 ATTTGAAATATATATTTA
1 ATTTGAAACATATATTTA
1468132 ATTTAGTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (20 bp):
ATTTGAAACATATATTTACT
Found at i:1472636 original size:10 final size:9
Alignment explanation
Indices: 1472563--1472637 Score: 53
Period size: 9 Copynumber: 7.8 Consensus size: 9
1472553 TAAAATTTTG
1472563 TAAAAAATT
1 TAAAAAATT
*
1472572 AAAAAAATT
1 TAAAAAATT
1472581 ATAAAAAATATT
1 -T-AAAAA-ATT
**
1472593 TAAATTATT
1 TAAAAAATT
1472602 T-AAAAATT
1 TAAAAAATT
*
1472610 CAAAAATCATT
1 TAAAAA--ATT
1472621 TAAAAAATT
1 TAAAAAATT
1472630 TAGAAAAA
1 TA-AAAAA
1472638 AAATTAAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
8 5 0.10
9 21 0.41
10 8 0.16
11 14 0.27
12 3 0.06
ACGTcount: A:0.64, C:0.03, G:0.01, T:0.32
Consensus pattern (9 bp):
TAAAAAATT
Found at i:1480032 original size:136 final size:136
Alignment explanation
Indices: 1479775--1480042 Score: 455
Period size: 136 Copynumber: 2.0 Consensus size: 136
1479765 CCCAAAAATT
1479775 CCCCTTACTCATGACTTTCAAAAGAATAGTGATATAAATGCTTAGCAAATACATTCAAATAGTCA
1 CCCCTTACTCATGACTTTCAAAAGAATAGTGATATAAATGCTTAGCAAATACATTCAAATAGTCA
* *
1479840 TTTGAAAGACTAGTGTTCAAGATTGAATACGTAGAATATGAGAAAGTATGTAATGTTTTCATGAG
66 TTTGAAAGACTAGTATTCAAGATTGAATACGTAGAATATGAGAAAGCATGTAATGTTTTCATGAG
1479905 GGGGAG
131 GGGGAG
* *
1479911 CCCCTTCCTCATGACTTTCAAAAGAATGGTGATATAAATGCTTAGCAAATACATTCAAATAGTCA
1 CCCCTTACTCATGACTTTCAAAAGAATAGTGATATAAATGCTTAGCAAATACATTCAAATAGTCA
* * * * *
1479976 TTTGAAATATTAGTATTCAAGATTGAATATGTAGAATATGAGGAAGCATGTGATGTTTTCATGAG
66 TTTGAAAGACTAGTATTCAAGATTGAATACGTAGAATATGAGAAAGCATGTAATGTTTTCATGAG
1480041 GG
131 GG
1480043 AGAGTAAATA
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
136 123 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (136 bp):
CCCCTTACTCATGACTTTCAAAAGAATAGTGATATAAATGCTTAGCAAATACATTCAAATAGTCA
TTTGAAAGACTAGTATTCAAGATTGAATACGTAGAATATGAGAAAGCATGTAATGTTTTCATGAG
GGGGAG
Found at i:1481104 original size:24 final size:26
Alignment explanation
Indices: 1481077--1481127 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1481067 TACTGTTTAA
* *
1481077 TATAGTT-AATAATTATAA-AATTTT
1 TATAGTTCAATAAATAAAATAATTTT
1481101 TATAGTTCAATAAATAAAATAATTTT
1 TATAGTTCAATAAATAAAATAATTTT
1481127 T
1 T
1481128 TGAAATTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 9 0.39
26 7 0.30
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (26 bp):
TATAGTTCAATAAATAAAATAATTTT
Found at i:1498202 original size:40 final size:40
Alignment explanation
Indices: 1498156--1498384 Score: 250
Period size: 40 Copynumber: 5.8 Consensus size: 40
1498146 TACATATGTA
* * *
1498156 ATTGTCGGTTTATCCCACTACTGCTGGGCACATATTTGAT
1 ATTGTCGGTTTATCCAACTAGTGCTGGGCACACATTTGAT
* * ** *
1498196 GTTGTCGGCTTATCTGACTAGTGATGGGCACACATTTGAT
1 ATTGTCGGTTTATCCAACTAGTGCTGGGCACACATTTGAT
* *
1498236 ATTGTAGGTTTATCCAACTAGTGCTGGGCCCACATTTGAT
1 ATTGTCGGTTTATCCAACTAGTGCTGGGCACACATTTGAT
*
1498276 ATTGTCGGTTTATCCAACTAGTGCTGGGCCCACATTTGAT
1 ATTGTCGGTTTATCCAACTAGTGCTGGGCACACATTTGAT
** * * * * *
1498316 ATTGTCGGTTTATCGGATTAGCGCTGGGCGCA-A---AAC
1 ATTGTCGGTTTATCCAACTAGTGCTGGGCACACATTTGAT
* *
1498352 ATTATCGGTTTATCCAACTAGTGCAGGGCACAC
1 ATTGTCGGTTTATCCAACTAGTGCTGGGCACAC
1498385 CTATCATTGG
Statistics
Matches: 159, Mismatches: 29, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
36 26 0.16
39 1 0.01
40 132 0.83
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (40 bp):
ATTGTCGGTTTATCCAACTAGTGCTGGGCACACATTTGAT
Found at i:1510573 original size:23 final size:25
Alignment explanation
Indices: 1510515--1510577 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
1510505 AATCTAAAAT
1510515 TAAATATTAATAATT-TTAGTTAAAC
1 TAAATATTAATAATTATTAG-TAAAC
1510540 -ATAAT-TT-ATAATTATTA-T-AAC
1 TA-AATATTAATAATTATTAGTAAAC
1510561 TAAATATTAATAATTAT
1 TAAATATTAATAATTAT
1510578 CGGATTTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
21 6 0.18
22 4 0.12
23 14 0.42
24 6 0.18
25 3 0.09
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (25 bp):
TAAATATTAATAATTATTAGTAAAC
Found at i:1510641 original size:21 final size:21
Alignment explanation
Indices: 1510615--1510656 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1510605 TAGGATTTAA
1510615 GAGTTTAGAATCTTAG-GTTTT
1 GAGTTTAGAAT-TTAGAGTTTT
1510636 GAGTTTAGAATTTAGAGTTTT
1 GAGTTTAGAATTTAGAGTTTT
1510657 AGCATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (21 bp):
GAGTTTAGAATTTAGAGTTTT
Found at i:1514286 original size:101 final size:100
Alignment explanation
Indices: 1514113--1514371 Score: 317
Period size: 101 Copynumber: 2.6 Consensus size: 100
1514103 ATTTTTCTTG
* ** * * ** *
1514113 TGCCATAGTCCAACTATGGTCTTACACGT-G-TATTGCCATGGCCCTGCCGTGGTCTTACATTCG
1 TGCCATAGCCCAACTATGGTCTTACATATAGATACTGCCATGGTCCAACCATGGTCTTACATTC-
* *
1514176 TAGTGCCATAACCCAATTATGGTCTTGTCATCAGAA
65 TAGTGCCATAACCCAATTACGGTCTTGTCATCAAAA
*
1514212 TGCCATAGCCCAACTATGGTCTTACATATAGATACTGCCATGGTCCAACCATGGTCTTACGTT-T
1 TGCCATAGCCCAACTATGGTCTTACATATAGATACTGCCATGGTCCAACCATGGTCTTACATTCT
** * *
1514276 AAGGTGCCATAACCCGGTTACGGTCTTTTCATTAAAA
66 -A-GTGCCATAACCCAATTACGGTCTTGTCATCAAAA
* *
1514313 TGCCATAGCCCAGCTATGGTCTTACATATAAATACTGCCATGGTCCAACCATGGTCTTA
1 TGCCATAGCCCAACTATGGTCTTACATATAGATACTGCCATGGTCCAACCATGGTCTTA
1514372 AGCTCAATTC
Statistics
Matches: 139, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
99 27 0.19
100 2 0.01
101 110 0.79
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.31
Consensus pattern (100 bp):
TGCCATAGCCCAACTATGGTCTTACATATAGATACTGCCATGGTCCAACCATGGTCTTACATTCT
AGTGCCATAACCCAATTACGGTCTTGTCATCAAAA
Found at i:1514353 original size:35 final size:33
Alignment explanation
Indices: 1514179--1514371 Score: 111
Period size: 33 Copynumber: 5.7 Consensus size: 33
1514169 ACATTCGTAG
* * * * *
1514179 TGCCATAACCCAATTATGGTCTTGTCATCAGAA-
1 TGCCATAGCCCAACTATGGTCTT-ACATTAAAAC
*
1514212 TGCCATAGCCCAACTATGGTCTTACATATAGATAC
1 TGCCATAGCCCAACTATGGTCTTACAT-TA-AAAC
* * * * * **
1514247 TGCCATGGTCCAACCATGGTCTTACGTTTAAGG
1 TGCCATAGCCCAACTATGGTCTTACATTAAAAC
* *** * *
1514280 TGCCATAACCCGGTTACGGTCTTTTCATTAAAA-
1 TGCCATAGCCCAACTATGGTC-TTACATTAAAAC
*
1514313 TGCCATAGCCCAGCTATGGTCTTACATATAAATAC
1 TGCCATAGCCCAACTATGGTCTTACAT-TAAA-AC
* * *
1514348 TGCCATGGTCCAACCATGGTCTTA
1 TGCCATAGCCCAACTATGGTCTTA
1514372 AGCTCAATTC
Statistics
Matches: 118, Mismatches: 35, Indels: 12
0.72 0.21 0.07
Matches are distributed among these distances:
32 8 0.07
33 57 0.48
34 10 0.08
35 43 0.36
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.30
Consensus pattern (33 bp):
TGCCATAGCCCAACTATGGTCTTACATTAAAAC
Found at i:1517325 original size:33 final size:33
Alignment explanation
Indices: 1517288--1517350 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
1517278 TGGCCCTGCC
1517288 ATGGTCTTA-CATTC-GTAATGCCATAACCCAATT
1 ATGGTCTTATCA-TCAG-AATGCCATAACCCAATT
*
1517321 ATGGTCTTATCATCAGAATGCCATAGCCCA
1 ATGGTCTTATCATCAGAATGCCATAACCCA
1517351 GCTACGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 24 0.89
34 3 0.11
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.30
Consensus pattern (33 bp):
ATGGTCTTATCATCAGAATGCCATAACCCAATT
Found at i:1517448 original size:101 final size:101
Alignment explanation
Indices: 1517306--1517493 Score: 286
Period size: 101 Copynumber: 1.9 Consensus size: 101
1517296 ACATTCGTAA
* * *
1517306 TGCCATAACCCAATTATGGTCTTATCATCAGAATGCCATAGCCCAGCTACGGTTTTACATATAGA
1 TGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAGCTACGGTCTTACATATAAA
* *
1517371 TACTGCCATGGTCTAACCATGGTTTTACGTTTAAGG
66 TACTACCATGGTCCAACCATGGTTTTACGTTTAAGG
* * * * *
1517407 TGCCATAACCTAGTTATGGTCTTTTCATTAAAATGCCATAGCCCAGCTATGGTCTTACATATAAA
1 TGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAGCTACGGTCTTACATATAAA
1517472 TACTACCATGGTCCAACCATGG
66 TACTACCATGGTCCAACCATGG
1517494 CCTTACACTC
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
101 77 1.00
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.31
Consensus pattern (101 bp):
TGCCATAACCCAATTATGGTCTTATCATCAAAATGCCATAGCCCAGCTACGGTCTTACATATAAA
TACTACCATGGTCCAACCATGGTTTTACGTTTAAGG
Found at i:1517603 original size:18 final size:19
Alignment explanation
Indices: 1517572--1517608 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1517562 ATTTAATTTG
1517572 ATTTCATATTTCAACAATA
1 ATTTCATATTTCAACAATA
1517591 ATTTCAT-TTTCAACAATA
1 ATTTCATATTTCAACAATA
1517609 GATACGAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (19 bp):
ATTTCATATTTCAACAATA
Found at i:1524351 original size:46 final size:46
Alignment explanation
Indices: 1524278--1524637 Score: 506
Period size: 46 Copynumber: 7.8 Consensus size: 46
1524268 TGATGTCATA
* * * *
1524278 GTATCTTTCAACTATGGTTTTACTCATTTTC-TGTCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGTTGCCATG
* ** *
1524324 GTATCTTTCAACCATGGTCTTATTCATTTTCCCATCATGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCA-TTTCATATCAGGTTGCCATG
* *
1524371 GTACCTTTCAACCATGGTCTTACTCATTTCATGTCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
1524417 GTATCTTTCAACCATGGTCTTATTCATTTCATATCACGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* **
1524463 GTATCTTTCAACCATGGTCTTACACATTTCATATCACATTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* *
1524509 GTATCTTTCAACCATGGTCTTACACATTTCATATTAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
*
1524555 GTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
* * *
1524601 GTATCTTTCAACCATTGTCTTACACATTCCATATCAG
1 GTATCTTTCAACCATGGTCTTACTCATTTCATATCAG
1524638 AGAGCACACT
Statistics
Matches: 289, Mismatches: 24, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
46 252 0.87
47 37 0.13
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (46 bp):
GTATCTTTCAACCATGGTCTTACTCATTTCATATCAGGTTGCCATG
Found at i:1527293 original size:21 final size:21
Alignment explanation
Indices: 1527269--1527311 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1527259 GCCCAGTTCC
*
1527269 AAAGAAGACTTGGGTTAAGTT
1 AAAGAAGACTTAGGTTAAGTT
*
1527290 AAAGAATACTTAGGTTAAGTT
1 AAAGAAGACTTAGGTTAAGTT
1527311 A
1 A
1527312 GGAAAGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.23, T:0.30
Consensus pattern (21 bp):
AAAGAAGACTTAGGTTAAGTT
Found at i:1527661 original size:104 final size:104
Alignment explanation
Indices: 1527481--1527692 Score: 298
Period size: 104 Copynumber: 2.0 Consensus size: 104
1527471 GCTATGTCTG
*
1527481 GGTTAAAAGTGATGGCAAGGATTACCCGAATGAGTTTTAATGAAATGTATCTATCTATCAAGGGA
1 GGTTAAAAGTGATGACAAGGATTACCCGAATGAGTTTTAATGAAATGTATCTATCTATCAAGGGA
* * *
1527546 AAAAGGAGGCTGTAGTGTTTGGTTAGGCAAAGAATCTAA
66 AAAAGGAGGCTGCAGTGTCTGGCTAGGCAAAGAATCTAA
* * ** * * * *
1527585 GGTTAAAAGTGATGATAATGATTACTTGAATGAGTTTTAATGAAATTTTTCTGTCTATCGAGGGA
1 GGTTAAAAGTGATGACAAGGATTACCCGAATGAGTTTTAATGAAATGTATCTATCTATCAAGGGA
* *
1527650 AAAAGGAGGCTGCAGTGTCTGGCTAGGTAAAGAATCTGA
66 AAAAGGAGGCTGCAGTGTCTGGCTAGGCAAAGAATCTAA
1527689 GGTT
1 GGTT
1527693 TAAACTGCCC
Statistics
Matches: 94, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
104 94 1.00
ACGTcount: A:0.33, C:0.09, G:0.27, T:0.30
Consensus pattern (104 bp):
GGTTAAAAGTGATGACAAGGATTACCCGAATGAGTTTTAATGAAATGTATCTATCTATCAAGGGA
AAAAGGAGGCTGCAGTGTCTGGCTAGGCAAAGAATCTAA
Found at i:1528045 original size:53 final size:54
Alignment explanation
Indices: 1527952--1528081 Score: 147
Period size: 53 Copynumber: 2.4 Consensus size: 54
1527942 CATGGTAAGT
* * *
1527952 AGACCATATTGTGTAAGGCCTAGCCATTTGCTATGGCATCATA-AGGAAAATGA
1 AGACCATATAGTGTAAGGCCTAGCCATTTGCTATGACATCATATAGGAAAACGA
* ** * *
1528005 ATACCATATAGTGTAAGGCCTAGCTGTTTGGC-ATGACATCATATGGGAATACGA
1 AGACCATATAGTGTAAGGCCTAGCCATTT-GCTATGACATCATATAGGAAAACGA
* *
1528059 AGACCACATAGTGTAAGACCTAG
1 AGACCATATAGTGTAAGGCCTAG
1528082 TCAGGGACTA
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
53 35 0.55
54 29 0.45
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.25
Consensus pattern (54 bp):
AGACCATATAGTGTAAGGCCTAGCCATTTGCTATGACATCATATAGGAAAACGA
Found at i:1535481 original size:443 final size:445
Alignment explanation
Indices: 1534646--1535521 Score: 1567
Period size: 443 Copynumber: 2.0 Consensus size: 445
1534636 CGTAACATAC
* *
1534646 GGTTTTTGTTCCTACACATCAGTAACCTAACAATCTCGAGAAGACAAAAGAAAAATTATAATGTA
1 GGTTGTTGTTCCTACACATCAATAACCTAACAATCTCGAGAAGACAAAAGAAAAATTATAATGTA
*
1534711 AAAATTAAACTAAAAACAAAAATATAAAAATAAAATAAAAAAGGCTAAATTGATAAAAATCAAAT
66 AAAATTAAACT-AAAACAAAAATATAAAAATAAAATAAAAAAGGCTAAATTAATAAAAATCAAAT
1534776 GTTCCTAATATTTTAGTCCCCGACAACGGTGCCAAAAACTTGATGGTCACTAAACTAACTATAAA
130 GTTCCTAATATTTTAGTCCCCGACAACGGTGCCAAAAACTTGATGGTCACTAAACTAACTATAAA
* *
1534841 TACGAAAAAGGCAAGTGCACCTATCGAACAATAGTATAGCTATGGTGAGTAGAGAATATTGTATG
195 TACGAAAAAGGCAAGTGCACCTATCGAACAATAGTATAGCTATGGTGAGTAGAGAATATCGTATC
* *
1534906 CACGAGGACTAAAAGTATTAGTAATTACCGTTTTTCTATTATTTAGCCGACAATTTGGAGTGATG
260 CACGAGGACTAAAAGTATTAGTAATTACCCTTTTTCCATTATTTAGCCGACAATTTGGAGTGATG
1534971 TGTTTTAATCTAAATTTACTAAACTAATTTAACTAAGAATGCAACTGAGAATGAATCAAAGAAAT
325 TGTTTTAATCTAAATTTACTAAACTAATTTAACTAAGAATGCAACTGAGAATGAATCAAAGAAAT
**
1535036 AATCGAATATTAACCAATGGGATAGACGATATCCAGGAAAGAAATAATCAACGTAA
390 AATCGAATATTAACCAATAAGATAGACGATATCCAGGAAAGAAATAATCAACGTAA
*
1535092 GGTTGTTGTTCCTAGACATCAATAACCTAACAATCTCGAGAAGACAAAAGAAAAATTATAATGTA
1 GGTTGTTGTTCCTACACATCAATAACCTAACAATCTCGAGAAGACAAAAGAAAAATTATAATGTA
* *
1535157 AAAATTAAACT-AAA-AAATATATAAAAATAAAATAAAAAAGGCTAAATTAATAAAAATCAAGTG
66 AAAATTAAACTAAAACAAAAATATAAAAATAAAATAAAAAAGGCTAAATTAATAAAAATCAAATG
1535220 TTCCTAATATTTTAGTCCCCGACAACGGTGCCAAAAACTTGATGGTCACTAAACTAACTATAAAT
131 TTCCTAATATTTTAGTCCCCGACAACGGTGCCAAAAACTTGATGGTCACTAAACTAACTATAAAT
1535285 ACGAAAAAGGCAAGTGCACCTATCGAACAATAGTATAGCTATGGTGAGTAGAGAATATCGTATCC
196 ACGAAAAAGGCAAGTGCACCTATCGAACAATAGTATAGCTATGGTGAGTAGAGAATATCGTATCC
* *
1535350 ACGAGGACTAAGAGTATTAGTAATTACCCTTTTTCCATTATTTAGCTGACAATTTGGAGTGATGT
261 ACGAGGACTAAAAGTATTAGTAATTACCCTTTTTCCATTATTTAGCCGACAATTTGGAGTGATGT
* * *
1535415 GTTTTAATCTAAGTTTACTAAACTGATTTAACTAAGAATGCAACTGAGAATGAATCAAATAAATA
326 GTTTTAATCTAAATTTACTAAACTAATTTAACTAAGAATGCAACTGAGAATGAATCAAAGAAATA
*
1535480 ATCGAATATTAACCAATAAGATAGACGATTTCCAGGAAAGAA
391 ATCGAATATTAACCAATAAGATAGACGATATCCAGGAAAGAA
1535522 TCCACAATAT
Statistics
Matches: 412, Mismatches: 18, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
443 336 0.82
444 3 0.01
446 73 0.18
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.27
Consensus pattern (445 bp):
GGTTGTTGTTCCTACACATCAATAACCTAACAATCTCGAGAAGACAAAAGAAAAATTATAATGTA
AAAATTAAACTAAAACAAAAATATAAAAATAAAATAAAAAAGGCTAAATTAATAAAAATCAAATG
TTCCTAATATTTTAGTCCCCGACAACGGTGCCAAAAACTTGATGGTCACTAAACTAACTATAAAT
ACGAAAAAGGCAAGTGCACCTATCGAACAATAGTATAGCTATGGTGAGTAGAGAATATCGTATCC
ACGAGGACTAAAAGTATTAGTAATTACCCTTTTTCCATTATTTAGCCGACAATTTGGAGTGATGT
GTTTTAATCTAAATTTACTAAACTAATTTAACTAAGAATGCAACTGAGAATGAATCAAAGAAATA
ATCGAATATTAACCAATAAGATAGACGATATCCAGGAAAGAAATAATCAACGTAA
Found at i:1548754 original size:31 final size:31
Alignment explanation
Indices: 1548719--1548780 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
1548709 GTAAGTTTGA
1548719 GTATGTTGGTAAGGCATCGTAAACTGTTGGG
1 GTATGTTGGTAAGGCATCGTAAACTGTTGGG
1548750 GTATGTTGGTAAGGCATCGTAAACTGTTGGG
1 GTATGTTGGTAAGGCATCGTAAACTGTTGGG
1548781 TTAAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.10, G:0.35, T:0.32
Consensus pattern (31 bp):
GTATGTTGGTAAGGCATCGTAAACTGTTGGG
Found at i:1554327 original size:30 final size:30
Alignment explanation
Indices: 1554264--1554329 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 30
1554254 AGAGAGCACA
* *
1554264 GCCGGAGAAGCCGTTCATCCTCTCCACGTC
1 GCCGCAGAAGCCGTTCATCCTCTCCACGAC
1554294 GCCGCAGAAGCCGTTCA-CCATCT-CATCGAC
1 GCCGCAGAAGCCGTTCATCC-TCTCCA-CGAC
1554324 GCCGCA
1 GCCGCA
1554330 AAAGTCGATC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 4 0.12
30 28 0.88
ACGTcount: A:0.20, C:0.41, G:0.23, T:0.17
Consensus pattern (30 bp):
GCCGCAGAAGCCGTTCATCCTCTCCACGAC
Found at i:1556118 original size:37 final size:37
Alignment explanation
Indices: 1556063--1556141 Score: 124
Period size: 37 Copynumber: 2.1 Consensus size: 37
1556053 TTTGCTAGAG
*
1556063 ATAAAACACACCATGAACATTGTAAGTGAATTTATTT
1 ATAAAACACACCAGGAACATTGTAAGTGAATTTATTT
1556100 ATAAAA-AGCACCAGGAACATTGTAAGTGAATTTATTT
1 ATAAAACA-CACCAGGAACATTGTAAGTGAATTTATTT
*
1556137 TTAAA
1 ATAAA
1556142 CAGATTTAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
36 1 0.03
37 38 0.97
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.32
Consensus pattern (37 bp):
ATAAAACACACCAGGAACATTGTAAGTGAATTTATTT
Found at i:1558417 original size:51 final size:53
Alignment explanation
Indices: 1558317--1558465 Score: 141
Period size: 51 Copynumber: 2.9 Consensus size: 53
1558307 AAGTATATAT
* * * *
1558317 ATAATATAGACAAAAATATATGCATAATGTAGTATTGAAAGTATTTACATGGG
1 ATAATATAGACAAAAATATATGAATAATGTAGTATTAAAAATATATACATGGG
***
1558370 ATAATATA-A-AAAAATATATGAATAATGT-GATATTAAAAATATATACATAAA
1 ATAATATAGACAAAAATATATGAATAATGTAG-TATTAAAAATATATACATGGG
* *
1558421 ATATATATATATC--AAATATAT--ATAATATAGTATTAAAAATATATA
1 ATA-ATATAGA-CAAAAATATATGAATAATGTAGTATTAAAAATATATA
1558466 TAATACATAC
Statistics
Matches: 82, Mismatches: 8, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
50 1 0.01
51 57 0.70
52 7 0.09
53 17 0.21
ACGTcount: A:0.54, C:0.03, G:0.09, T:0.34
Consensus pattern (53 bp):
ATAATATAGACAAAAATATATGAATAATGTAGTATTAAAAATATATACATGGG
Found at i:1558428 original size:15 final size:15
Alignment explanation
Indices: 1558403--1558444 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
1558393 AATGTGATAT
1558403 TAAAA-ATATATACA
1 TAAAATATATATACA
*
1558417 TAAAATATATATATA
1 TAAAATATATATACA
*
1558432 TCAAATATATATA
1 TAAAATATATATA
1558445 ATATAGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (15 bp):
TAAAATATATATACA
Found at i:1558464 original size:21 final size:20
Alignment explanation
Indices: 1558407--1558465 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 20
1558397 TGATATTAAA
*
1558407 AATATATA-CATAAA-ATAT
1 AATATATATCAAAAATATAT
*
1558425 -ATATATATCAAATATATAT
1 AATATATATCAAAAATATAT
*
1558444 AATATAGTATTAAAAATATAT
1 AATATA-TATCAAAAATATAT
1558465 A
1 A
1558466 TAATACATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 7 0.21
18 4 0.12
19 4 0.12
20 5 0.15
21 13 0.39
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.37
Consensus pattern (20 bp):
AATATATATCAAAAATATAT
Found at i:1558571 original size:23 final size:23
Alignment explanation
Indices: 1558526--1558571 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1558516 AATACTTCAT
* *
1558526 AAATATATACATATATATGTTAA
1 AAATAAATACATATATATATTAA
1558549 AAATAAATACATAT-TAATATTAA
1 AAATAAATACATATAT-ATATTAA
1558572 GATGATGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 1 0.05
23 19 0.95
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (23 bp):
AAATAAATACATATATATATTAA
Found at i:1559824 original size:14 final size:12
Alignment explanation
Indices: 1559774--1559819 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1559764 ATATACATAC
1559774 TTATATATATTT
1 TTATATATATTT
*
1559786 TATATTTTATAATTT
1 T-TA-TATAT-ATTT
1559801 TTATATATATTT
1 TTATATATATTT
1559813 TTATATA
1 TTATATA
1559820 CATATACGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 12 0.41
13 6 0.21
14 6 0.21
15 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATATATATTT
Found at i:1562177 original size:19 final size:20
Alignment explanation
Indices: 1562137--1562180 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1562127 GTCTCTTTAG
* *
1562137 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
1562156 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
1562175 GCATTA
1 GCATTA
1562181 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:1567024 original size:85 final size:85
Alignment explanation
Indices: 1566873--1567533 Score: 1088
Period size: 85 Copynumber: 7.7 Consensus size: 85
1566863 CAGATCAGTG
1566873 AAGACAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCAT
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCAT
1566938 TGGTTGCAGTGGAGCTGGTTA
65 TGGTTGCAGTGGAGCTGGTTA
* * * *
1566959 AAGAAGTAGATCTTGTCTTCCTGTGTTAACAGCGAAGCAGATCGAAAACAAGCATTGCCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
*
1567024 GGTTACAGTGGAGCTGGTTA
66 GGTTGCAGTGGAGCTGGTTA
1567044 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
1567109 GGTTGCAGTGGAGCTGGTTA
66 GGTTGCAGTGGAGCTGGTTA
* * *
1567129 AAGAAGTAGATCTTGTCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCATTGCCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
*
1567194 GGTTACAGTGGAGCTGGTTA
66 GGTTGCAGTGGAGCTGGTTA
*
1567214 AAGAAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
1567279 GGTTGCAGTGGAGCTGGTTA
66 GGTTGCAGTGGAGCTGGTTA
* *
1567299 AAGAAGTAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCTTTGCCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
* *
1567364 GGTTACAGTGGAGCTGGTTG
66 GGTTGCAGTGGAGCTGGTTA
* * *
1567384 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAGCCTTGCCTCC
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG-AAAAC-AAGCCTTGCCTTC
* *
1567449 ATCGGTTGCAGTGGAGCTGGTTG
63 ATTGGTTGCAGTGGAGCTGGTTA
*
1567472 AAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAC-AAGCCTTGCCT
1567534 CTCTCGAGTG
Statistics
Matches: 538, Mismatches: 34, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
85 401 0.75
86 41 0.08
87 22 0.04
88 74 0.14
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (85 bp):
AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
GGTTGCAGTGGAGCTGGTTA
Found at i:1569395 original size:27 final size:26
Alignment explanation
Indices: 1569365--1569427 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 26
1569355 TATTTCCTCA
1569365 TTTATATATATACATACTTATATATAT
1 TTTATATATATA-ATACTTATATATAT
* **
1569392 TTTATATTTTATAATTTTTATATATAT
1 TTTATA-TATATAATACTTATATATAT
1569419 TTT-TATATA
1 TTTATATATA
1569428 CATATACGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
25 3 0.10
26 2 0.06
27 21 0.68
28 5 0.16
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (26 bp):
TTTATATATATAATACTTATATATAT
Found at i:1569432 original size:14 final size:12
Alignment explanation
Indices: 1569382--1569427 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1569372 ATATACATAC
1569382 TTATATATATTT
1 TTATATATATTT
*
1569394 TATATTTTATAATTT
1 T-TA-TATAT-ATTT
1569409 TTATATATATTT
1 TTATATATATTT
1569421 TTATATA
1 TTATATA
1569428 CATATACGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 12 0.41
13 6 0.21
14 6 0.21
15 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATATATATTT
Found at i:1571773 original size:19 final size:20
Alignment explanation
Indices: 1571733--1571776 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
1571723 GTCTCTTTAG
* *
1571733 GCATT-CATTTCATGCATTT
1 GCATTACATTGCATGCATAT
1571752 GCATTACATTGCAT-CATAT
1 GCATTACATTGCATGCATAT
1571771 GCATTA
1 GCATTA
1571777 GATTTTCACG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (20 bp):
GCATTACATTGCATGCATAT
Found at i:1576621 original size:85 final size:85
Alignment explanation
Indices: 1576470--1577130 Score: 1088
Period size: 85 Copynumber: 7.7 Consensus size: 85
1576460 CAGATCAGTG
1576470 AAGACAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCAT
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCAT
1576535 TGGTTGCAGTGGAGCTGGTTA
65 TGGTTGCAGTGGAGCTGGTTA
* * * *
1576556 AAGAAGTAGATCTTGTCTTCCTGTGTTAACAGCGAAGCAGATCGAAAACAAGCATTGCCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
*
1576621 GGTTACAGTGGAGCTGGTTA
66 GGTTGCAGTGGAGCTGGTTA
1576641 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
1576706 GGTTGCAGTGGAGCTGGTTA
66 GGTTGCAGTGGAGCTGGTTA
* * *
1576726 AAGAAGTAGATCTTGTCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCATTGCCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
*
1576791 GGTTACAGTGGAGCTGGTTA
66 GGTTGCAGTGGAGCTGGTTA
*
1576811 AAGAAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
1576876 GGTTGCAGTGGAGCTGGTTA
66 GGTTGCAGTGGAGCTGGTTA
* *
1576896 AAGAAGTAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCTTTGCCTTCATT
1 AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
* *
1576961 GGTTACAGTGGAGCTGGTTG
66 GGTTGCAGTGGAGCTGGTTA
* * *
1576981 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGTAGATCGAAAAACAAAGCCTTGCCTCC
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCG-AAAAC-AAGCCTTGCCTTC
* *
1577046 ATCGGTTGCAGTGGAGCTGGTTG
63 ATTGGTTGCAGTGGAGCTGGTTA
*
1577069 AAGATAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCT
1 AAGA-AGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAAC-AAGCCTTGCCT
1577131 CTCTCGAGTG
Statistics
Matches: 538, Mismatches: 34, Indels: 5
0.93 0.06 0.01
Matches are distributed among these distances:
85 401 0.75
86 41 0.08
87 22 0.04
88 74 0.14
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (85 bp):
AAGAAGCAGATCTTGCCTTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAGCCTTGCCTTCATT
GGTTGCAGTGGAGCTGGTTA
Found at i:1579056 original size:14 final size:12
Alignment explanation
Indices: 1579006--1579051 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
1578996 ATATACATAC
1579006 TTATATATATTT
1 TTATATATATTT
*
1579018 TATATTTTATAATTT
1 T-TA-TATAT-ATTT
1579033 TTATATATATTT
1 TTATATATATTT
1579045 TTATATA
1 TTATATA
1579052 CATATACGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 12 0.41
13 6 0.21
14 6 0.21
15 5 0.17
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TTATATATATTT
Done.