Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 90 of 153
Found at i:28289216 original size:118 final size:118
Alignment explanation
Indices: 28289008--28289245 Score: 440
Period size: 118 Copynumber: 2.0 Consensus size: 118
28288998 CTAACAAATA
28289008 ATTGTTTGGTTTCAGCCATATGAATTTACAATTCAATTCATAATAACTAATTGAAATGAAACATT
1 ATTGTTTGGTTTCAGCCATATGAATTTACAATTCAATTCATAATAACTAATTGAAATGAAACATT
*
28289073 ATGTCATTTCTAATTCAACGTTTATCAAATATAATCGGGCATATGACCAATTT
66 ATGTCATTTCTAATTCAACGTTTATCAAATATAATCGGGAATATGACCAATTT
* *
28289126 ATTGTTTGGTTTCAGCCGTGTGAATTTACAATTCAATTCATAATAACTAATTGAAATGAAACATT
1 ATTGTTTGGTTTCAGCCATATGAATTTACAATTCAATTCATAATAACTAATTGAAATGAAACATT
*
28289191 ATGTCATTTCTAATTTAACGTTTATCAAATATAATCGGGAATATGACCAATTT
66 ATGTCATTTCTAATTCAACGTTTATCAAATATAATCGGGAATATGACCAATTT
28289244 AT
1 AT
28289246 ATACAAATCA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
118 116 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (118 bp):
ATTGTTTGGTTTCAGCCATATGAATTTACAATTCAATTCATAATAACTAATTGAAATGAAACATT
ATGTCATTTCTAATTCAACGTTTATCAAATATAATCGGGAATATGACCAATTT
Found at i:28289624 original size:193 final size:193
Alignment explanation
Indices: 28289290--28289669 Score: 670
Period size: 193 Copynumber: 2.0 Consensus size: 193
28289280 TCTCCACTCC
*
28289290 ATTCCACATCCTTAATGTACATAACACTCTTATAAATAACATTTTCTATAATTTTACTATTCACT
1 ATTCAACATCCTTAATGTACATAACACTCTTATAAATAACATTTTCTATAATTTTACTATTCACT
*
28289355 CACATGTATATTCAAAGCTGTCTATCCAAGTCAGAGTCACTAAATTATTTTTATCCGAAGCTATA
66 CACATGTATATTCAAAGCTGTCTATCCAAGTCAGAGTCACTAAATTATTTTTATCCGAAGCTACA
* *
28289420 GTTGTCCAAATTAAGATATGTTAATTTTCCCTGAAACTAGATTCACATATATTCTTAATGTAT
131 GTTGTCCAAATTAAGATACGTTAATTTTCCCTAAAACTAGATTCACATATATTCTTAATGTAT
28289483 ATTCAACATCCTTAATGTACATAACACTCTTATAAATAACATTTTCTATAATTTTACTATTCACT
1 ATTCAACATCCTTAATGTACATAACACTCTTATAAATAACATTTTCTATAATTTTACTATTCACT
* * *
28289548 CACATGTATATTCAAAGCTGTCTATCCGAGTCAGAGTCACTAAGTTATTTTTATCCGGAGCTACA
66 CACATGTATATTCAAAGCTGTCTATCCAAGTCAGAGTCACTAAATTATTTTTATCCGAAGCTACA
* * *
28289613 GTTGTCCAAATTAAGATCCGTTAATTTTTCCTAAAACTAGATTTACATATATTCTTA
131 GTTGTCCAAATTAAGATACGTTAATTTTCCCTAAAACTAGATTCACATATATTCTTA
28289670 CCATAAAATT
Statistics
Matches: 177, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
193 177 1.00
ACGTcount: A:0.34, C:0.19, G:0.09, T:0.39
Consensus pattern (193 bp):
ATTCAACATCCTTAATGTACATAACACTCTTATAAATAACATTTTCTATAATTTTACTATTCACT
CACATGTATATTCAAAGCTGTCTATCCAAGTCAGAGTCACTAAATTATTTTTATCCGAAGCTACA
GTTGTCCAAATTAAGATACGTTAATTTTCCCTAAAACTAGATTCACATATATTCTTAATGTAT
Found at i:28290332 original size:23 final size:23
Alignment explanation
Indices: 28290306--28290404 Score: 137
Period size: 23 Copynumber: 4.3 Consensus size: 23
28290296 ATAAGTGCAA
28290306 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
28290329 CACTGATACGTAGCCCTAA-CTAC
1 CACTGATATGTAG-CCGAAGCTAC
* *
28290352 CACTGAAATGCAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
28290375 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
28290398 CACTGAT
1 CACTGAT
28290405 CAATAACATT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
22 4 0.06
23 57 0.88
24 4 0.06
ACGTcount: A:0.30, C:0.29, G:0.19, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:28290373 original size:46 final size:46
Alignment explanation
Indices: 28290306--28290403 Score: 151
Period size: 46 Copynumber: 2.1 Consensus size: 46
28290296 ATAAGTGCAA
* *
28290306 CACTGATATGTAGCCGAAGCTACCACTGATACGTAGCCCTAACTAC
1 CACTGAAATGCAGCCGAAGCTACCACTGATACGTAGCCCTAACTAC
* * *
28290352 CACTGAAATGCAGCCGAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGCAGCCGAAGCTACCACTGATACGTAGCCCTAACTAC
28290398 CACTGA
1 CACTGA
28290404 TCAATAACAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.20
Consensus pattern (46 bp):
CACTGAAATGCAGCCGAAGCTACCACTGATACGTAGCCCTAACTAC
Found at i:28290656 original size:18 final size:17
Alignment explanation
Indices: 28290630--28290668 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28290620 ATTTTCCTTC
28290630 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
28290647 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
28290665 CACA
1 CACA
28290669 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:28294784 original size:16 final size:17
Alignment explanation
Indices: 28294754--28294786 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28294744 TTGTTTATTA
*
28294754 TTTAATAAATGTAATAT
1 TTTAATAAATATAATAT
28294771 TTTAAT-AATATAATAT
1 TTTAATAAATATAATAT
28294787 AATAATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (17 bp):
TTTAATAAATATAATAT
Found at i:28301806 original size:34 final size:35
Alignment explanation
Indices: 28301746--28301812 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
28301736 CAAACACCAG
*
28301746 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* * *
28301781 AAAACATTTTCCCG-AAATTATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
28301813 TATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28318710 original size:49 final size:49
Alignment explanation
Indices: 28318621--28318715 Score: 122
Period size: 49 Copynumber: 1.9 Consensus size: 49
28318611 CTATTTATAG
* * * *
28318621 GTTGAAAAACCTTATTCTAATCATTGTCAAATAGATGAAGTGTAGTAAA
1 GTTGAAAAACCTTATTCTAATCAATGTCAAATAAAAGAAGTATAGTAAA
28318670 GTTGAAAAA-CTTGATTCTAATCAATGT-AAAGTAAAAGAAGTATAGT
1 GTTGAAAAACCTT-ATTCTAATCAATGTCAAA-TAAAAGAAGTATAGT
28318716 TCTATATGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
48 6 0.15
49 34 0.85
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (49 bp):
GTTGAAAAACCTTATTCTAATCAATGTCAAATAAAAGAAGTATAGTAAA
Found at i:28324942 original size:28 final size:27
Alignment explanation
Indices: 28324901--28325003 Score: 88
Period size: 28 Copynumber: 3.9 Consensus size: 27
28324891 TTTTATTTTC
*
28324901 TTAAAAATACTTTTTAACATCAATAGTT
1 TTAAAAACACTTTTTAACATCAATA-TT
*** *
28324929 TTAAAAACA-TTTTTTTTATC--T-TC
1 TTAAAAACACTTTTTAACATCAATATT
*
28324952 TTAAAAATACTTTTTAACATCAATAATT
1 TTAAAAACACTTTTTAACATCAAT-ATT
* *
28324980 TTAAAAACATTTTTTAACCTCAAT
1 TTAAAAACACTTTTTAACATCAAT
28325004 GGTGTAATAG
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
23 9 0.16
24 8 0.14
25 1 0.02
26 1 0.02
27 8 0.14
28 30 0.53
ACGTcount: A:0.41, C:0.13, G:0.01, T:0.46
Consensus pattern (27 bp):
TTAAAAACACTTTTTAACATCAATATT
Found at i:28324953 original size:51 final size:51
Alignment explanation
Indices: 28324891--28324994 Score: 190
Period size: 51 Copynumber: 2.0 Consensus size: 51
28324881 AAAATAGAAA
* *
28324891 TTTTATTTTCTTAAAAATACTTTTTAACATCAATAGTTTTAAAAACATTTT
1 TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
28324942 TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
1 TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
28324993 TT
1 TT
28324995 AACCTCAATG
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.51
Consensus pattern (51 bp):
TTTTATCTTCTTAAAAATACTTTTTAACATCAATAATTTTAAAAACATTTT
Found at i:28325249 original size:3 final size:3
Alignment explanation
Indices: 28325241--28325291 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
28325231 AGTAGGTCTT
28325241 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28325289 TTA
1 TTA
28325292 ATTAAGTGAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28336032 original size:27 final size:27
Alignment explanation
Indices: 28335961--28336032 Score: 108
Period size: 27 Copynumber: 2.7 Consensus size: 27
28335951 ATATTGGGTG
* * * *
28335961 TGCCGCCTATCAAATAGACACCACCAG
1 TGCCGCCTATCAGATAGGCACAACCAA
28335988 TGCCGCCTATCAGATAGGCACAACCAA
1 TGCCGCCTATCAGATAGGCACAACCAA
28336015 TGCCGCCTATCAGATAGG
1 TGCCGCCTATCAGATAGG
28336033 GGTCGCTGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (27 bp):
TGCCGCCTATCAGATAGGCACAACCAA
Found at i:28345755 original size:16 final size:17
Alignment explanation
Indices: 28345716--28345757 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
28345706 TTTCAGTTTC
28345716 TGTTC-TTAGTAAATTT
1 TGTTCTTTAGTAAATTT
*
28345732 T-ATCTTTA-TAAATTT
1 TGTTCTTTAGTAAATTT
28345747 TGTTCTTTAGT
1 TGTTCTTTAGT
28345758 TTTAGTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 5
0.75 0.07 0.18
Matches are distributed among these distances:
15 10 0.48
16 10 0.48
17 1 0.05
ACGTcount: A:0.24, C:0.07, G:0.10, T:0.60
Consensus pattern (17 bp):
TGTTCTTTAGTAAATTT
Found at i:28347408 original size:15 final size:15
Alignment explanation
Indices: 28347390--28347439 Score: 64
Period size: 15 Copynumber: 3.2 Consensus size: 15
28347380 ATAGATACAA
28347390 ATTTTATTTTTAGTT
1 ATTTTATTTTTAGTT
* *
28347405 ATTTTCTTTTTACTT
1 ATTTTATTTTTAGTT
28347420 AATTTTATTTTTCAGTT
1 -ATTTTATTTTT-AGTT
28347437 ATT
1 ATT
28347440 AATTTTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 13 0.45
16 13 0.45
17 3 0.10
ACGTcount: A:0.20, C:0.06, G:0.04, T:0.70
Consensus pattern (15 bp):
ATTTTATTTTTAGTT
Found at i:28356337 original size:21 final size:22
Alignment explanation
Indices: 28356302--28356342 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
28356292 GCATCTACTC
* *
28356302 AGGGAAATTATAATCCACAATA
1 AGGGAAATTACAATCAACAATA
28356324 AGGG-AATTACAATCAACAA
1 AGGGAAATTACAATCAACAA
28356343 CAAAACTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.20
Consensus pattern (22 bp):
AGGGAAATTACAATCAACAATA
Found at i:28365793 original size:18 final size:19
Alignment explanation
Indices: 28365755--28365793 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
28365745 GGTTTATTGA
*
28365755 TTTCTTTCATTTGTTTATT
1 TTTCTTTCATTTATTTATT
*
28365774 TTTCTTT-ATTTATTTCTT
1 TTTCTTTCATTTATTTATT
28365792 TT
1 TT
28365794 AGTTATTTAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTCTTTCATTTATTTATT
Found at i:28388309 original size:30 final size:31
Alignment explanation
Indices: 28388235--28388324 Score: 80
Period size: 29 Copynumber: 2.9 Consensus size: 31
28388225 TCCAAACACA
* *
28388235 TAGATAGCCATAAAGGCATCCACATAATAGT
1 TAGATAGCCATAAAGGCATCCATATAACAGT
* *
28388266 T--ATAACCAAAAAGGC-TCTCATATAACA-T
1 TAGATAGCCATAAAGGCATC-CATATAACAGT
*
28388294 TAGATAGCCATAAAGGCGTCCACATATAACA
1 TAGATAGCCATAAAGGCAT-C-CATATAACA
28388325 AACTTCACCA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
28 4 0.09
29 19 0.40
30 12 0.26
31 2 0.04
32 10 0.21
ACGTcount: A:0.43, C:0.21, G:0.13, T:0.22
Consensus pattern (31 bp):
TAGATAGCCATAAAGGCATCCATATAACAGT
Found at i:28400180 original size:140 final size:141
Alignment explanation
Indices: 28399927--28400211 Score: 482
Period size: 140 Copynumber: 2.0 Consensus size: 141
28399917 CTAATTCCGT
* *
28399927 TAAAATCATAACGATTTTACCGTAAAAGAATCTATGAGAAATTATATTTAATATTTCTACATTAT
1 TAAAATCATAACGATTTTACCGTAAAAGAACCTATGAGAAAATATATTTAATATTTCTACATTAT
* *
28399992 AATATCTCGCCTAACGAAGCCCTAGTATTTGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
66 AAAATCTCGCCTAACGAAGCCCTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
28400057 CCCTAGATAAG
131 CCCTAGATAAG
*
28400068 TAAAATCATAACGATTTTACCGTAAAATAACCTATG-GAAAATATATTTAATATTTCTACATTAT
1 TAAAATCATAACGATTTTACCGTAAAAGAACCTATGAGAAAATATATTTAATATTTCTACATTAT
* *
28400132 AAAATCTCGCCTAGCGAAGCCTTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
66 AAAATCTCGCCTAACGAAGCCCTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
* *
28400197 CCTTGGATAAG
131 CCCTAGATAAG
28400208 TAAA
1 TAAA
28400212 GTGATGGATT
Statistics
Matches: 135, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
140 101 0.75
141 34 0.25
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (141 bp):
TAAAATCATAACGATTTTACCGTAAAAGAACCTATGAGAAAATATATTTAATATTTCTACATTAT
AAAATCTCGCCTAACGAAGCCCTAGTATTCGAGTGTTGTTTTAGAAGTAAGAATTTTGGAACGAG
CCCTAGATAAG
Found at i:28405180 original size:42 final size:41
Alignment explanation
Indices: 28405134--28405255 Score: 145
Period size: 43 Copynumber: 2.9 Consensus size: 41
28405124 GATATGTGAT
*
28405134 TTACGTGTAAGACCATGTCTGGGACATTGGCAACGTATATGA
1 TTACGTGTAAGACCATGTCTGGGA-ATTGGCATCGTATATGA
* * * *
28405176 TTACGTGTAAGACCCTGTCTGGCATAGTGGCATCGTTATTTGA
1 TTACGTGTAAGACCATGTCTGGGA-ATTGGCATCG-TATATGA
* *
28405219 TTACATGTAAGACCACGTCTGGGAAGTTGGCATCGTA
1 TTACGTGTAAGACCATGTCTGGGAA-TTGGCATCGTA
28405256 CGAGCTTTTT
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
42 33 0.49
43 34 0.51
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (41 bp):
TTACGTGTAAGACCATGTCTGGGAATTGGCATCGTATATGA
Found at i:28407160 original size:59 final size:57
Alignment explanation
Indices: 28407057--28407216 Score: 189
Period size: 59 Copynumber: 2.8 Consensus size: 57
28407047 ACTATCTCTA
* * * *
28407057 AAATG-AAGCCTTTGTGACTATCTCTGTTAAAGAAAGCCTTTGTGGTGATCTTTGTT
1 AAATGAAAGCTTTTGTGACAATCTCTATTAAAGAAAGCCTTTGTGGCGATCTTTGTT
* *
28407113 AAATGAAAGCTTTTGTGACAAATCTCTATTATAAGGAAGTCTTTGTGGCGATCTTTGTT
1 AAATGAAAGCTTTTGTGAC-AATCTCTATTA-AAGAAAGCCTTTGTGGCGATCTTTGTT
* * *
28407172 AAATGAAAG-TCTTTGTGGCGATCTCTATTAAATGAATGCCTTTGT
1 AAATGAAAGCT-TTTGTGACAATCTCTATTAAA-GAAAGCCTTTGT
28407217 TGTTGTTTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 8
0.82 0.10 0.07
Matches are distributed among these distances:
56 5 0.06
57 14 0.16
58 29 0.33
59 40 0.45
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.39
Consensus pattern (57 bp):
AAATGAAAGCTTTTGTGACAATCTCTATTAAAGAAAGCCTTTGTGGCGATCTTTGTT
Found at i:28407181 original size:29 final size:29
Alignment explanation
Indices: 28407057--28407289 Score: 170
Period size: 29 Copynumber: 8.1 Consensus size: 29
28407047 ACTATCTCTA
* * *
28407057 AAATG-AAGCCTTTGTGACTATCTCTGTT
1 AAATGAAAGCCTTTGTGGCGATCTTTGTT
*
28407085 AAA-GAAAGCCTTTGTGGTGATCTTTGTT
1 AAATGAAAGCCTTTGTGGCGATCTTTGTT
* * * * *
28407113 AAATGAAAGCTTTTGTGACAAATCTCTATT
1 AAATGAAAGCCTTTGTGGC-GATCTTTGTT
* *
28407143 ATAA-GGAAGTCTTTGTGGCGATCTTTGTT
1 A-AATGAAAGCCTTTGTGGCGATCTTTGTT
* * *
28407172 AAATGAAAGTCTTTGTGGCGATCTCTATT
1 AAATGAAAGCCTTTGTGGCGATCTTTGTT
* ** * *
28407201 AAATGAATGCCTTTGTTGTTG-TTTTTGTC
1 AAATGAAAGCCTTTG-TGGCGATCTTTGTT
* * *
28407230 AAA-GGAAGCCTTTGTGGCTATCTTTGTC
1 AAATGAAAGCCTTTGTGGCGATCTTTGTT
* * * *
28407258 AAAAGGATGCCTTTGTGGCTATCTTTGTT
1 AAATGAAAGCCTTTGTGGCGATCTTTGTT
28407287 AAA
1 AAA
28407290 GGAATGTCTT
Statistics
Matches: 161, Mismatches: 36, Indels: 15
0.76 0.17 0.07
Matches are distributed among these distances:
27 3 0.02
28 46 0.29
29 88 0.55
30 22 0.14
31 2 0.01
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.40
Consensus pattern (29 bp):
AAATGAAAGCCTTTGTGGCGATCTTTGTT
Found at i:28407285 original size:57 final size:57
Alignment explanation
Indices: 28407061--28407327 Score: 166
Period size: 57 Copynumber: 4.6 Consensus size: 57
28407051 TCTCTAAAAT
* * * * *
28407061 GAAGCCTTTGTGACTATCTCTGT-TAAAGAAAGCCTTTGTGG-TGATCTTTGTTAAATG
1 GAAGCCTTTGTGGCGATCTCTATCAAAAGAATGCCTTTGTGGCT-ATCTTTGTTAAA-G
* * * * * * * *
28407118 AAAGCTTTTGTGACAAATCTCTATTATAAGGAA-GTCTTTGTGGCGATCTTTGTTAAATG
1 GAAGCCTTTGTGGC-GATCTCTATCA-AAAGAATGCCTTTGTGGCTATCTTTGTTAAA-G
* * * * * * * * *
28407177 AAAGTCTTTGTGGCGATCTCTATTAAATGAATGCCTTTGTTGTTGTTTTTGTCAAAG
1 GAAGCCTTTGTGGCGATCTCTATCAAAAGAATGCCTTTGTGGCTATCTTTGTTAAAG
* * * *
28407234 GAAGCCTTTGTGGCTATCTTTGTCAAAAGGATGCCTTTGTGGCTATCTTTGTTAAAG
1 GAAGCCTTTGTGGCGATCTCTATCAAAAGAATGCCTTTGTGGCTATCTTTGTTAAAG
* * * *
28407291 GAATGTC-TTGTGGCAAAT-TCTATTAAAAGGATGCCTT
1 GAA-GCCTTTGTGGC-GATCTCTATCAAAAGAATGCCTT
28407328 GAAGACAACT
Statistics
Matches: 165, Mismatches: 38, Indels: 14
0.76 0.18 0.06
Matches are distributed among these distances:
57 88 0.53
58 38 0.23
59 34 0.21
60 5 0.03
ACGTcount: A:0.25, C:0.13, G:0.22, T:0.39
Consensus pattern (57 bp):
GAAGCCTTTGTGGCGATCTCTATCAAAAGAATGCCTTTGTGGCTATCTTTGTTAAAG
Found at i:28412154 original size:60 final size:60
Alignment explanation
Indices: 28412005--28412163 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 60
28411995 CTTTTTTTTT
* * * * * *
28412005 AATTTTTAAAATTAAAACTAAATTGATAAATTTTGTAGATGTTATAGACTAAATTTATTA
1 AATTTTTAGAATTAGAATTAAATTGATAAATTCTGTAAATATTATAGACTAAATTTATTA
* * * * *
28412065 AATTTTTAGAATTCGAATTAAAATAATAAATTCTGTAAATATTAT-GGCTAAATTTATTG
1 AATTTTTAGAATTAGAATTAAATTGATAAATTCTGTAAATATTATAGACTAAATTTATTA
* * * *
28412124 AATTTATTAGATTTAGGATTAAATTGATAAAATGTGTAAA
1 AATTT-TTAGAATTAGAATTAAATTGATAAATTCTGTAAA
28412164 CATTGAAATG
Statistics
Matches: 80, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
59 17 0.21
60 63 0.79
ACGTcount: A:0.44, C:0.03, G:0.11, T:0.42
Consensus pattern (60 bp):
AATTTTTAGAATTAGAATTAAATTGATAAATTCTGTAAATATTATAGACTAAATTTATTA
Found at i:28416133 original size:23 final size:24
Alignment explanation
Indices: 28416107--28416170 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 24
28416097 TAATTTTTAA
*
28416107 ATTTTA-AATTATTTAGTGATAAT
1 ATTTTAGAATTATTTAGTAATAAT
28416130 A-TTTAGAATTATTTAGTAATAAT
1 ATTTTAGAATTATTTAGTAATAAT
* **
28416153 ATTTAAGAAAAATTTAGT
1 ATTTTAGAATTATTTAGT
28416171 TAAATTTTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 4 0.11
23 18 0.51
24 13 0.37
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (24 bp):
ATTTTAGAATTATTTAGTAATAAT
Found at i:28417039 original size:22 final size:23
Alignment explanation
Indices: 28417014--28417071 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
28417004 TTATTTATCC
*
28417014 ATTTATTTTATTTTCTTAA-AT-T
1 ATTTATTTTATTTT-TGAATATAT
*
28417036 ATTTTTTTTATTTTTGAATATAT
1 ATTTATTTTATTTTTGAATATAT
*
28417059 TTTTATTTTATTT
1 ATTTATTTTATTT
28417072 ACTTTTCGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 3 0.10
22 15 0.50
23 12 0.40
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (23 bp):
ATTTATTTTATTTTTGAATATAT
Found at i:28417723 original size:17 final size:17
Alignment explanation
Indices: 28417701--28417734 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28417691 CTGAAAGAGT
28417701 TCCACATGGTTTGTCTA
1 TCCACATGGTTTGTCTA
28417718 TCCACATGGTTTGTCTA
1 TCCACATGGTTTGTCTA
28417735 AGCATGAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.41
Consensus pattern (17 bp):
TCCACATGGTTTGTCTA
Found at i:28424242 original size:23 final size:23
Alignment explanation
Indices: 28424216--28424267 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
28424206 TGATTTTTAA
*
28424216 ATTTTGAATCATTTAGTGATAAT
1 ATTTAGAATCATTTAGTGATAAT
*
28424239 ATTTAGAATTATTTAGTGATAAT
1 ATTTAGAATCATTTAGTGATAAT
28424262 ATTTAG
1 ATTTAG
28424268 GAAAAATCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.02, G:0.13, T:0.48
Consensus pattern (23 bp):
ATTTAGAATCATTTAGTGATAAT
Found at i:28424244 original size:13 final size:13
Alignment explanation
Indices: 28424226--28424267 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
28424216 ATTTTGAATC
28424226 ATTTAGTGATAAT
1 ATTTAGTGATAAT
*
28424239 ATTTA--GA-ATT
1 ATTTAGTGATAAT
28424249 ATTTAGTGATAAT
1 ATTTAGTGATAAT
28424262 ATTTAG
1 ATTTAG
28424268 GAAAAATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 7 0.29
11 2 0.08
12 2 0.08
13 13 0.54
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (13 bp):
ATTTAGTGATAAT
Found at i:28426089 original size:16 final size:16
Alignment explanation
Indices: 28426068--28426103 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
28426058 TTTGGTTCGT
28426068 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28426084 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28426100 TGTA
1 TGTA
28426104 ATAGTAAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:28426360 original size:18 final size:17
Alignment explanation
Indices: 28426339--28426373 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28426329 TTATTATTAA
*
28426339 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28426357 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28426374 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28426427 original size:157 final size:157
Alignment explanation
Indices: 28426226--28426542 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
28426216 TAGAATACCC
*
28426226 TTAGCATAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* *
28426291 ATATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
28426356 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
28426383 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
28426448 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
28426513 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
28426540 TTA
1 TTA
28426543 ATATTCTTAT
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGATAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:28426513 original size:16 final size:16
Alignment explanation
Indices: 28426476--28426517 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28426466 TTAATCATAT
*
28426476 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28426492 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28426507 TTAAAATATAT
1 TTAAAATATAT
28426518 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28426524 original size:14 final size:15
Alignment explanation
Indices: 28426485--28426526 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28426475 TTTAAACATA
*
28426485 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28426500 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28426514 A-TATAATTTAATA
1 ATTATAATTAAATA
28426527 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28426539 original size:82 final size:82
Alignment explanation
Indices: 28426296--28426545 Score: 215
Period size: 76 Copynumber: 3.1 Consensus size: 82
28426286 TATTAATATC
* *
28426296 AATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
28426361 AATTTAATAAAATTCTT
66 AATTTAATAAAATTCTT
* * * *
28426378 AATAATTAGCAGA-AATTT-GT--T-TTGGT-AA-ATTATTATTGTT--AT-TGTTAT--TTAAA
1 AATAA-TA--A-ATAATTTAATCATATT--TAAACATAATTATTATTAAATATATTATAATTAAA
* * * * *
28426431 TTTTAATAAGATTATTAATA-TC--
60 ATAT-ATAA-TTTAATAAAATTCTT
28426453 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
28426518 AATTTAATAAAATTCTT
66 AATTTAATAAAATTCTT
*
28426535 AATAATTAATA
1 AATAATAAATA
28426546 TTCTTATATG
Statistics
Matches: 124, Mismatches: 21, Indels: 46
0.65 0.11 0.24
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 3 0.02
75 8 0.06
76 19 0.15
77 6 0.05
78 13 0.10
79 14 0.11
80 6 0.05
81 19 0.15
82 18 0.15
83 3 0.02
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (82 bp):
AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATAT
AATTTAATAAAATTCTT
Found at i:28426614 original size:120 final size:121
Alignment explanation
Indices: 28426474--28426771 Score: 505
Period size: 120 Copynumber: 2.5 Consensus size: 121
28426464 ATTTAATCAT
*
28426474 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
28426539 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
28426596 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
28426659 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* * *
28426715 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
28426772 TAAAATAATT
Statistics
Matches: 169, Mismatches: 4, Indels: 8
0.93 0.02 0.04
Matches are distributed among these distances:
119 7 0.04
120 157 0.93
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:28426644 original size:14 final size:15
Alignment explanation
Indices: 28426595--28426646 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28426585 GTAAAATATA
28426595 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
28426610 TATTAAATATATTAT
1 AATTAAATATATTAT
28426625 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
28426638 AATTTAATA
1 AATTAAATA
28426647 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:28426858 original size:24 final size:25
Alignment explanation
Indices: 28426812--28426859 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
28426802 TATGAATTTG
28426812 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
28426838 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
28426860 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:28426863 original size:92 final size:92
Alignment explanation
Indices: 28426767--28426995 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
28426757 TGATTTAATA
* * *
28426767 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
28426829 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
28426859 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
28426924 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
28426949 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
28426996 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:28430520 original size:25 final size:25
Alignment explanation
Indices: 28430492--28430662 Score: 189
Period size: 25 Copynumber: 7.1 Consensus size: 25
28430482 TTAATAAAAT
28430492 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
* *
28430517 ATT--AGTCCTTATTTTAATAAAAT-
1 ATTAAAGTCCTTATTTTAAT-TATTG
28430540 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
* *
28430565 ATT--AGTCCTTATTTTAATAAAAT-
1 ATTAAAGTCCTTATTTTAAT-TATTG
28430588 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
* * *
28430613 A-T-GAGTCCTTATTTTAATAAAAT-
1 ATTAAAGTCCTTATTTTAAT-TATTG
28430636 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAATTATTG
28430661 AT
1 AT
28430663 GTAATTTTTA
Statistics
Matches: 120, Mismatches: 14, Indels: 24
0.76 0.09 0.15
Matches are distributed among these distances:
23 52 0.43
24 14 0.12
25 54 0.45
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (25 bp):
ATTAAAGTCCTTATTTTAATTATTG
Found at i:28430527 original size:23 final size:24
Alignment explanation
Indices: 28430496--28430662 Score: 175
Period size: 23 Copynumber: 7.0 Consensus size: 24
28430486 TAAAATATTA
28430496 AAGTCCTTATTTTAATTATTGATT
1 AAGTCCTTATTTTAATTATTGATT
* *
28430520 -AGTCCTTATTTTAATAAAAT-ATT
1 AAGTCCTTATTTTAAT-TATTGATT
28430543 AAAGTCCTTATTTTAATTATTGATT
1 -AAGTCCTTATTTTAATTATTGATT
* *
28430568 -AGTCCTTATTTTAATAAAAT-ATT
1 AAGTCCTTATTTTAAT-TATTGATT
28430591 AAAGTCCTTATTTTAATTATTGA-T
1 -AAGTCCTTATTTTAATTATTGATT
* * *
28430615 GAGTCCTTATTTTAATAAAAT-ATT
1 AAGTCCTTATTTTAAT-TATTGATT
28430639 AAAGTCCTTATTTTAATTATTGAT
1 -AAGTCCTTATTTTAATTATTGAT
28430663 GTAATTTTTA
Statistics
Matches: 117, Mismatches: 14, Indels: 23
0.76 0.09 0.15
Matches are distributed among these distances:
23 52 0.44
24 14 0.12
25 51 0.44
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (24 bp):
AAGTCCTTATTTTAATTATTGATT
Found at i:28430532 original size:48 final size:48
Alignment explanation
Indices: 28430480--28430662 Score: 357
Period size: 48 Copynumber: 3.8 Consensus size: 48
28430470 ATTTCTTGAT
28430480 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
28430528 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
*
28430576 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATGAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
28430624 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGAT
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGAT
28430663 GTAATTTTTA
Statistics
Matches: 134, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 134 1.00
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.50
Consensus pattern (48 bp):
TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
Found at i:28435172 original size:13 final size:13
Alignment explanation
Indices: 28435154--28435204 Score: 68
Period size: 13 Copynumber: 3.9 Consensus size: 13
28435144 TTTGACAATA
28435154 CTTTTGAAAAGTG
1 CTTTTGAAAAGTG
*
28435167 CTTTTGAGAAGTG
1 CTTTTGAAAAGTG
*
28435180 -TTGTGGAAAAGTG
1 CTT-TTGAAAAGTG
28435193 CTTTTGAAAAGT
1 CTTTTGAAAAGT
28435205 TTGGTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
12 2 0.06
13 28 0.88
14 2 0.06
ACGTcount: A:0.29, C:0.06, G:0.27, T:0.37
Consensus pattern (13 bp):
CTTTTGAAAAGTG
Found at i:28436901 original size:32 final size:32
Alignment explanation
Indices: 28436865--28436933 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
28436855 TGATATTGCG
*
28436865 ATGTCTTTGATATGTGAGGATGGGTGATTGTA
1 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
28436897 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
1 ATGTCTTTGATATGTGAGGATAGGTGATTGTA
28436929 ATGTC
1 ATGTC
28436934 AGTTTGGTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.23, C:0.04, G:0.32, T:0.41
Consensus pattern (32 bp):
ATGTCTTTGATATGTGAGGATAGGTGATTGTA
Found at i:28444360 original size:18 final size:18
Alignment explanation
Indices: 28444337--28444386 Score: 82
Period size: 18 Copynumber: 2.7 Consensus size: 18
28444327 CTAAGCAAAG
*
28444337 GAAACAATCAATTTTTAT
1 GAAACAATCAATTTTCAT
28444355 GAAACAATCAATTTTCAT
1 GAAACAATCAATTTTCAT
28444373 GAAACAATCTAATT
1 GAAACAATC-AATT
28444387 ACAATATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
18 26 0.87
19 4 0.13
ACGTcount: A:0.46, C:0.14, G:0.06, T:0.34
Consensus pattern (18 bp):
GAAACAATCAATTTTCAT
Found at i:28447673 original size:17 final size:17
Alignment explanation
Indices: 28447629--28447685 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
28447619 TGAGATAACA
28447629 TAAA-TAAACAATTAAA-
1 TAAATTAAA-AATTAAAT
*
28447645 TAAATCAAAAATTAAAT
1 TAAATTAAAAATTAAAT
*
28447662 TAAATTAGAAATTAAAT
1 TAAATTAAAAATTAAAT
28447679 TCAAATT
1 T-AAATT
28447686 TTATAAACAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
16 11 0.31
17 19 0.54
18 5 0.14
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (17 bp):
TAAATTAAAAATTAAAT
Found at i:28449680 original size:12 final size:13
Alignment explanation
Indices: 28449655--28449685 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
28449645 TGCAAATGAA
28449655 TCATTTCTCATTT
1 TCATTTCTCATTT
28449668 TCATTTC-CATTT
1 TCATTTCTCATTT
28449680 TCATTT
1 TCATTT
28449686 TGAGAAAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.16, C:0.23, G:0.00, T:0.61
Consensus pattern (13 bp):
TCATTTCTCATTT
Found at i:28457400 original size:18 final size:19
Alignment explanation
Indices: 28457369--28457404 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28457359 ACCCATTAGG
28457369 TTAATTTAGGTTAATTAAT
1 TTAATTTAGGTTAATTAAT
*
28457388 TTAA-TTAGTTTAATTAA
1 TTAATTTAGGTTAATTAA
28457405 AATATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TTAATTTAGGTTAATTAAT
Found at i:28462339 original size:6 final size:6
Alignment explanation
Indices: 28462321--28462358 Score: 67
Period size: 6 Copynumber: 6.2 Consensus size: 6
28462311 TATATCCCAA
28462321 TTTTAT CTTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT -TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
28462359 CGCATTTCCA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:28467845 original size:21 final size:22
Alignment explanation
Indices: 28467800--28467845 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
28467790 TAGATTTTTT
*
28467800 AATTTTAAATAGTTTTATTATA
1 AATTTTAAATAGTTTTATTAGA
* *
28467822 AATTTT-AATATTTTTATTGGA
1 AATTTTAAATAGTTTTATTAGA
28467843 AAT
1 AAT
28467846 AGAATAACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (22 bp):
AATTTTAAATAGTTTTATTAGA
Found at i:28477993 original size:34 final size:34
Alignment explanation
Indices: 28477955--28478024 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
28477945 AAACATGAAA
28477955 TATTTGTT-AATCATTGGATAACCTAAGGAAGTGG
1 TATTT-TTCAATCATTGGATAACCTAAGGAAGTGG
* *
28477989 TATTTTTCTATCATTGGATAACCTAAGGTAGTGG
1 TATTTTTCAATCATTGGATAACCTAAGGAAGTGG
28478023 TA
1 TA
28478025 GTACCTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 2 0.06
34 31 0.94
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (34 bp):
TATTTTTCAATCATTGGATAACCTAAGGAAGTGG
Found at i:28480775 original size:29 final size:29
Alignment explanation
Indices: 28480742--28480797 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
28480732 AAGGCCGGTT
28480742 TTTTTTCAA-AATTTACCGAAATGGGCCGG
1 TTTTTT-AATAATTTACCGAAATGGGCCGG
* *
28480771 TTTTTTAATTATTTACCGGAATGGGCC
1 TTTTTTAATAATTTACCGAAATGGGCC
28480798 ATTTTCCGCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCGG
Found at i:28492240 original size:13 final size:14
Alignment explanation
Indices: 28492217--28492247 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
28492207 CCTTTCTCTC
28492217 TTTTTATTTTTATT
1 TTTTTATTTTTATT
28492231 TTTTTA-TTTTATT
1 TTTTTATTTTTATT
28492244 TTTT
1 TTTT
28492248 AAATCCAGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:28505177 original size:25 final size:24
Alignment explanation
Indices: 28505148--28505213 Score: 96
Period size: 24 Copynumber: 2.7 Consensus size: 24
28505138 TCCTATACAT
28505148 GTATGCTCATACGAGCTATGAATCG
1 GTATGCTCATACGAGCTAT-AATCG
* *
28505173 GTATGCTCTTACGAGCTGTAATCG
1 GTATGCTCATACGAGCTATAATCG
*
28505197 GTAAGCTCATACGAGCT
1 GTATGCTCATACGAGCT
28505214 GAGTAACAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
24 20 0.54
25 17 0.46
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (24 bp):
GTATGCTCATACGAGCTATAATCG
Found at i:28505204 original size:24 final size:24
Alignment explanation
Indices: 28505152--28505240 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 24
28505142 ATACATGTAT
* *
28505152 GCTCATACGAGCTATGAATCGGTAT
1 GCTCATACGAGCTGT-AATCGGTAA
*
28505177 GCTCTTACGAGCTGTAATCGGTAA
1 GCTCATACGAGCTGTAATCGGTAA
*
28505201 GCTCATACGAGCTGAGTAA-CAGTAA
1 GCTCATACGAGCT--GTAATCGGTAA
*
28505226 GCTCATTCGAGCTGT
1 GCTCATACGAGCTGT
28505241 GTTGTGTCCT
Statistics
Matches: 56, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
23 2 0.04
24 20 0.36
25 30 0.54
26 4 0.07
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (24 bp):
GCTCATACGAGCTGTAATCGGTAA
Found at i:28509276 original size:19 final size:20
Alignment explanation
Indices: 28509252--28509289 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28509242 TAATTTTTGA
28509252 AGTTTATT-CAATTTAGTCT
1 AGTTTATTGCAATTTAGTCT
28509271 AGTTTATTGCAATTTAGTC
1 AGTTTATTGCAATTTAGTC
28509290 GCTGACCCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (20 bp):
AGTTTATTGCAATTTAGTCT
Found at i:28509742 original size:20 final size:21
Alignment explanation
Indices: 28509717--28509755 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
28509707 ATGAAAGAAA
28509717 AACCT-AAACTAAAGCTTTCT
1 AACCTAAAACTAAAGCTTTCT
*
28509737 AACCTAAAACTACAGCTTT
1 AACCTAAAACTAAAGCTTT
28509756 TTTTTTCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.41, C:0.26, G:0.05, T:0.28
Consensus pattern (21 bp):
AACCTAAAACTAAAGCTTTCT
Found at i:28511718 original size:19 final size:19
Alignment explanation
Indices: 28511694--28511732 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
28511684 TTTTTTAACT
28511694 ATTTTAAAATTTCATTAGA
1 ATTTTAAAATTTCATTAGA
* *
28511713 ATTTTATAATTTTATTAGA
1 ATTTTAAAATTTCATTAGA
28511732 A
1 A
28511733 GAGGCAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
ATTTTAAAATTTCATTAGA
Found at i:28512729 original size:17 final size:18
Alignment explanation
Indices: 28512702--28512736 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
28512692 AATTCAGTTT
*
28512702 GAAATTAAATAATTAATA
1 GAAATTAAATAATAAATA
28512720 GAAA-TAAATAATAAATA
1 GAAATTAAATAATAAATA
28512737 TTATATATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.66, C:0.00, G:0.06, T:0.29
Consensus pattern (18 bp):
GAAATTAAATAATAAATA
Found at i:28515878 original size:42 final size:42
Alignment explanation
Indices: 28515819--28515903 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
28515809 CTTGATTAAT
28515819 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
1 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
28515861 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
1 TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
28515903 T
1 T
28515904 CAGTTATTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.16, C:0.12, G:0.33, T:0.39
Consensus pattern (42 bp):
TAGTGGAAGTGTCTTCTTGAAGGCACGTTGTTTGGTATTGGC
Found at i:28523651 original size:42 final size:40
Alignment explanation
Indices: 28523604--28523686 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 40
28523594 TTTCGAGATG
* * *
28523604 TGATTTCACGTAAGACCATGTTTGGGACATTGGCATCGTATA
1 TGATTTCACGTAAGACC-TGTCTGAGACAGTGGCATCG-ATA
**
28523646 TGATTTCGTGTAAGACCTGTCTGAGACAGTGGCATCGATA
1 TGATTTCACGTAAGACCTGTCTGAGACAGTGGCATCGATA
28523686 T
1 T
28523687 CTTATAACAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
40 4 0.11
41 17 0.47
42 15 0.42
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TGATTTCACGTAAGACCTGTCTGAGACAGTGGCATCGATA
Found at i:28524318 original size:25 final size:25
Alignment explanation
Indices: 28524282--28524368 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
28524272 AAATTGGGGC
28524282 TTAATTGCTGTCCATTTTTTAGCATA
1 TTAA-TGCTGTCCATTTTTTAGCATA
* **
28524308 TTAATGCTGTCCAAATTAGT-GC-T-
1 TTAATGCTGTCC-ATTTTTTAGCATA
* *
28524331 TAAATGCTTTCCATTTTTTAGCATA
1 TTAATGCTGTCCATTTTTTAGCATA
*
28524356 TTAGTGCTGTCCA
1 TTAATGCTGTCCA
28524369 AATTAGTGCT
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
22 4 0.09
23 12 0.26
24 2 0.04
25 20 0.43
26 8 0.17
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (25 bp):
TTAATGCTGTCCATTTTTTAGCATA
Found at i:28524336 original size:23 final size:23
Alignment explanation
Indices: 28524310--28524391 Score: 76
Period size: 23 Copynumber: 3.5 Consensus size: 23
28524300 TTAGCATATT
28524310 AATGCTGTCCAAATTAGTGCTTA
1 AATGCTGTCCAAATTAGTGCTTA
* * ** *
28524333 AATGCTTTCC-ATTTTTTAGCATATT
1 AATGCTGTCCAAATTAGT-GC-T-TA
*
28524358 AGTGCTGTCCAAATTAGTGCTTA
1 AATGCTGTCCAAATTAGTGCTTA
28524381 AATGCTGTCCA
1 AATGCTGTCCA
28524392 TTTTTTTTGA
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
22 4 0.09
23 22 0.51
24 2 0.05
25 11 0.26
26 4 0.09
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (23 bp):
AATGCTGTCCAAATTAGTGCTTA
Found at i:28524344 original size:48 final size:49
Alignment explanation
Indices: 28524263--28524491 Score: 300
Period size: 48 Copynumber: 4.7 Consensus size: 49
28524253 TGATGATAAG
* * *
28524263 ATGCTGTCCAAATTGGGGCTTAATTGCTGTCCATTTTTT-AGCATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
*
28524311 ATGCTGTCCAAATTAGTGCTTAAATGCTTTCCATTTTTT-AGCATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
* *
28524359 GTGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTTTGAGCACATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCA--TTTTTTGAGCATATTA
* * * * *
28524410 ATGCTATCCAAATTAATGCTTAATTGCTATCCATTTTTTGAGTATATTA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
* * *
28524459 ATGCTGTCCAAATTGGTACTTAAATGTTGTCCA
1 ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCA
28524492 AATATTTGTG
Statistics
Matches: 157, Mismatches: 21, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
48 75 0.48
49 40 0.25
50 6 0.04
51 36 0.23
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (49 bp):
ATGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTGAGCATATTA
Found at i:28524443 original size:99 final size:97
Alignment explanation
Indices: 28524263--28524491 Score: 316
Period size: 99 Copynumber: 2.3 Consensus size: 97
28524253 TGATGATAAG
* * * * *
28524263 ATGCTGTCCAAATTGGGGCTTAATTGCTGTCCATTTTTTAGCATATTAATGCTGTCCAAATTAGT
1 ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCATTTTTTAGCACATTAATGCTATCCAAATTAAT
*
28524328 GCTTAAATGCTTTCCATTTTTT-AGCATATTA
66 GCTTAAATGCTATCCATTTTTTGAGCATATTA
* *
28524359 GTGCTGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTTTGAGCACATTAATGCTATCCAAATT
1 ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCA--TTTTTT-AGCACATTAATGCTATCCAAATT
* *
28524424 AATGCTTAATTGCTATCCATTTTTTGAGTATATTA
63 AATGCTTAAATGCTATCCATTTTTTGAGCATATTA
* *
28524459 ATGCTGTCCAAATTGGTACTTAAATGTTGTCCA
1 ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCA
28524492 AATATTTGTG
Statistics
Matches: 115, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
96 29 0.25
98 6 0.05
99 43 0.37
100 37 0.32
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (97 bp):
ATGCTGTCCAAATTGGTGCTTAAATGCTGTCCATTTTTTAGCACATTAATGCTATCCAAATTAAT
GCTTAAATGCTATCCATTTTTTGAGCATATTA
Found at i:28531576 original size:42 final size:42
Alignment explanation
Indices: 28531466--28531577 Score: 118
Period size: 42 Copynumber: 2.7 Consensus size: 42
28531456 TGTGATCTAG
* ** *
28531466 TGTAAGACCATGTCTGGGACATTGGCATCGTATATGATTTCG
1 TGTAAGACCATGTCTGGGACAGTGGCATCGTATATGATAACA
* * * *
28531508 TGGAAGACCCTGTCTGAGACAGTGGCATCGATATATTATAACA
1 TGTAAGACCATGTCTGGGACAGTGGCATCG-TATATGATAACA
* *
28531551 TGTAAGACCATATCTGGGATA-TGGCAT
1 TGTAAGACCATGTCTGGGACAGTGGCAT
28531578 TGTACGAGCT
Statistics
Matches: 56, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 32 0.57
43 24 0.43
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (42 bp):
TGTAAGACCATGTCTGGGACAGTGGCATCGTATATGATAACA
Found at i:28532173 original size:25 final size:25
Alignment explanation
Indices: 28532138--28532224 Score: 81
Period size: 25 Copynumber: 3.5 Consensus size: 25
28532128 AAATTGGTGC
28532138 TTAATTGCTGTCCATTTTTTAGCATA
1 TTAA-TGCTGTCCATTTTTTAGCATA
* **
28532164 TTAATGCTGTCCAAATTAGT-GC-T-
1 TTAATGCTGTCC-ATTTTTTAGCATA
* *
28532187 TAAATGCTTTCCATTTTTTAGCATA
1 TTAATGCTGTCCATTTTTTAGCATA
*
28532212 TTAGTGCTGTCCA
1 TTAATGCTGTCCA
28532225 AATTAGTGCT
Statistics
Matches: 46, Mismatches: 11, Indels: 9
0.70 0.17 0.14
Matches are distributed among these distances:
22 4 0.09
23 12 0.26
24 2 0.04
25 20 0.43
26 8 0.17
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (25 bp):
TTAATGCTGTCCATTTTTTAGCATA
Found at i:28532192 original size:23 final size:23
Alignment explanation
Indices: 28532166--28532247 Score: 67
Period size: 23 Copynumber: 3.5 Consensus size: 23
28532156 TTAGCATATT
28532166 AATGCTGTCCAAATTAGTGCTTA
1 AATGCTGTCCAAATTAGTGCTTA
* * ** *
28532189 AATGCTTTCC-ATTTTTTAGCATATT
1 AATGCTGTCCAAATTAGT-GC-T-TA
*
28532214 AGTGCTGTCCAAATTAGTGCTTA
1 AATGCTGTCCAAATTAGTGCTTA
*
28532237 AATGTTGTCCA
1 AATGCTGTCCA
28532248 TTTTTTTTGA
Statistics
Matches: 42, Mismatches: 13, Indels: 8
0.67 0.21 0.13
Matches are distributed among these distances:
22 4 0.10
23 21 0.50
24 2 0.05
25 11 0.26
26 4 0.10
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.40
Consensus pattern (23 bp):
AATGCTGTCCAAATTAGTGCTTA
Found at i:28532200 original size:48 final size:48
Alignment explanation
Indices: 28532123--28532346 Score: 288
Period size: 48 Copynumber: 4.6 Consensus size: 48
28532113 GATAAGATGT
* *
28532123 TGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTAATGC
1 TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
* *
28532171 TGTCCAAATTAGTGCTTAAATGCTTTCCATTTTTTAGCATATTAGTGC
1 TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
*
28532219 TGTCCAAATTAGTGCTTAAATGTTGTCCATTTTTTTTGAGCATATTAATGC
1 TGTCCAAATTAGTGCTTAAATGCTGTCCA--TTTTTT-AGCATATTAATGC
* * * *
28532270 TATCCAAATT-GATGCTTAATTGCTGTCCATTTTTGAGTATATTAATGC
1 TGTCCAAATTAG-TGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
* * * *
28532318 TGTCCAAATTGGTACGTAAATGTTGTCCA
1 TGTCCAAATTAGTGCTTAAATGCTGTCCA
28532347 AATATTTGTG
Statistics
Matches: 154, Mismatches: 17, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
48 105 0.68
49 6 0.04
50 7 0.05
51 36 0.23
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (48 bp):
TGTCCAAATTAGTGCTTAAATGCTGTCCATTTTTTAGCATATTAATGC
Found at i:28532299 original size:99 final size:96
Alignment explanation
Indices: 28532123--28532346 Score: 306
Period size: 99 Copynumber: 2.3 Consensus size: 96
28532113 GATAAGATGT
* * *
28532123 TGTCCAAATTGGTGCTTAATTGCTGTCCATTTTTTAGCATATTAATGCTGTCCAAATTAGTGCTT
1 TGTCCAAATTGGTGCTTAAATGTTGTCCATTTTTTAGCATATTAATGCTATCCAAATTAGTGCTT
* * *
28532188 AAATGCTTTCCATTTTTTAGCATATTAGTGC
66 AAATGCTGTCCATTTTTGAGCATATTAATGC
*
28532219 TGTCCAAATTAGTGCTTAAATGTTGTCCATTTTTTTTGAGCATATTAATGCTATCCAAATT-GAT
1 TGTCCAAATTGGTGCTTAAATGTTGTCCA--TTTTTT-AGCATATTAATGCTATCCAAATTAG-T
* *
28532283 GCTTAATTGCTGTCCATTTTTGAGTATATTAATGC
62 GCTTAAATGCTGTCCATTTTTGAGCATATTAATGC
* *
28532318 TGTCCAAATTGGTACGTAAATGTTGTCCA
1 TGTCCAAATTGGTGCTTAAATGTTGTCCA
28532347 AATATTTGTG
Statistics
Matches: 112, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
96 26 0.23
98 7 0.06
99 79 0.71
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.43
Consensus pattern (96 bp):
TGTCCAAATTGGTGCTTAAATGTTGTCCATTTTTTAGCATATTAATGCTATCCAAATTAGTGCTT
AAATGCTGTCCATTTTTGAGCATATTAATGC
Found at i:28533467 original size:27 final size:27
Alignment explanation
Indices: 28533406--28533468 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
28533396 CTGAAAAATG
* *
28533406 AATCAA-TCCAAAAATAATAGAGACTC
1 AATCAATTCCAAAAAGAATAGAAACTC
* *
28533432 AATTC-ATTCGAAAAAGAATAGAAACTT
1 AA-TCAATTCCAAAAAGAATAGAAACTC
28533459 AATCAATTCC
1 AATCAATTCC
28533469 CAATGATTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
26 5 0.17
27 24 0.83
ACGTcount: A:0.51, C:0.17, G:0.08, T:0.24
Consensus pattern (27 bp):
AATCAATTCCAAAAAGAATAGAAACTC
Found at i:28535243 original size:157 final size:157
Alignment explanation
Indices: 28534957--28535270 Score: 610
Period size: 157 Copynumber: 2.0 Consensus size: 157
28534947 GTCCATGAAG
28534957 GGACAAGAGGCAAACTACAAGGGCCATGGTGATGGAAATAGCAGCTGAAGTCACAGCATTAAAAG
1 GGACAAGAGGCAAACTACAAGGGCCATGGTGATGGAAATAGCAGCTGAAGTCACAGCATTAAAAG
28535022 TTGCAGAGAATCGCCTCTCTTGCAGATCCCACAGCGTCCTAACAAACAATCCCAAGCCATCAATC
66 TTGCAGAGAATCGCCTCTCTTGCAGATCCCACAGCGTCCTAACAAACAATCCCAAGCCATCAATC
28535087 ACCACCGCCAGCACCACCGCCATCTTC
131 ACCACCGCCAGCACCACCGCCATCTTC
28535114 GGACAAGAGGCAAACTACAAGGGCCATGGTGATGGAAATAGCAGCTGAAGTCACAGCATTAAAAG
1 GGACAAGAGGCAAACTACAAGGGCCATGGTGATGGAAATAGCAGCTGAAGTCACAGCATTAAAAG
28535179 TTGCAGAGAATCGCCTCTCTTGCAGATCCCACAGCGTCCTAACAAACAATCCCAAGCCATCAATC
66 TTGCAGAGAATCGCCTCTCTTGCAGATCCCACAGCGTCCTAACAAACAATCCCAAGCCATCAATC
* *
28535244 CCCCCCGCCAGCACCACCGCCATCTTC
131 ACCACCGCCAGCACCACCGCCATCTTC
28535271 TAAAACAAAA
Statistics
Matches: 155, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.32, C:0.32, G:0.20, T:0.16
Consensus pattern (157 bp):
GGACAAGAGGCAAACTACAAGGGCCATGGTGATGGAAATAGCAGCTGAAGTCACAGCATTAAAAG
TTGCAGAGAATCGCCTCTCTTGCAGATCCCACAGCGTCCTAACAAACAATCCCAAGCCATCAATC
ACCACCGCCAGCACCACCGCCATCTTC
Found at i:28542661 original size:25 final size:27
Alignment explanation
Indices: 28542615--28542666 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
28542605 TCGCATATTT
* *
28542615 AAAATTTAATCTATTTTTTATTTTAAA
1 AAAATTTAATCTATTATATATTTTAAA
28542642 AAAATTTAAT-T-TTATATATTTTAAA
1 AAAATTTAATCTATTATATATTTTAAA
28542667 TTTAGAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 12 0.52
26 1 0.04
27 10 0.43
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
AAAATTTAATCTATTATATATTTTAAA
Found at i:28547258 original size:25 final size:24
Alignment explanation
Indices: 28547230--28547287 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
28547220 TATTATCAAT
* *
28547230 AATTTTATGAAATTATATATTATTA
1 AATTATATGAAATAATA-ATTATTA
*
28547255 AATTATATGTAATAATAATTATTTTA
1 AATTATATGAAATAATAATTA--TTA
28547281 AATTATA
1 AATTATA
28547288 CAAATTCATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 4 0.14
25 14 0.50
26 10 0.36
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (24 bp):
AATTATATGAAATAATAATTATTA
Found at i:28547354 original size:47 final size:49
Alignment explanation
Indices: 28547230--28547355 Score: 123
Period size: 47 Copynumber: 2.6 Consensus size: 49
28547220 TATTATCAAT
* *
28547230 AATTTTATGAAATTATATATTATTAAATTATATGTAATAATAATTATTTTA
1 AATTTTATCAAATCATATATT-TT-AATTATATGTAATAATAATTATTTTA
* *** * *
28547281 AATTATA-CAAATTCATATAAGATAATT-TAT-TAGTTATAATTATTTTA
1 AATTTTATCAAA-TCATATATTTTAATTATATGTAATAATAATTATTTTA
*
28547328 AATTTTATTAAATCATATATTTTAATTA
1 AATTTTATCAAATCATATATTTTAATTA
28547356 AAATATATTT
Statistics
Matches: 59, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
47 33 0.56
48 6 0.10
49 4 0.07
50 4 0.07
51 12 0.20
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.50
Consensus pattern (49 bp):
AATTTTATCAAATCATATATTTTAATTATATGTAATAATAATTATTTTA
Found at i:28547494 original size:25 final size:26
Alignment explanation
Indices: 28547462--28547516 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
28547452 TTATTAAATT
*
28547462 ATATATTTTAATTATAA-TATATTTA
1 ATATATTTTAATAATAATTATATTTA
*
28547487 ATATA-TTTAATAATAATTATGTTTA
1 ATATATTTTAATAATAATTATATTTA
28547512 A-ATAT
1 ATATAT
28547517 GATTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (26 bp):
ATATATTTTAATAATAATTATATTTA
Found at i:28547684 original size:39 final size:41
Alignment explanation
Indices: 28547641--28547740 Score: 105
Period size: 44 Copynumber: 2.4 Consensus size: 41
28547631 TCTATTATGT
28547641 TATTACACCTCTATTC-CATTCAACCAAACACAAGA-TTAC
1 TATTACACCTCTATTCACATTCAACCAAACACAAGATTTAC
* *** *
28547680 TATTACGCCTCTATTTCATTACATTCAACCAAACAGTTGATTTGC
1 TATTACACCTCTA-TTC---ACATTCAACCAAACACAAGATTTAC
28547725 TATTACACCTCTATTC
1 TATTACACCTCTATTC
28547741 TATTACACCT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
39 12 0.24
40 3 0.06
44 19 0.39
45 15 0.31
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (41 bp):
TATTACACCTCTATTCACATTCAACCAAACACAAGATTTAC
Found at i:28547738 original size:45 final size:44
Alignment explanation
Indices: 28547650--28547747 Score: 117
Period size: 45 Copynumber: 2.2 Consensus size: 44
28547640 TTATTACACC
* *
28547650 TCTATTCCATTCAACCAAACACAAGATTACTATTACGCCTCTAT
1 TCTATTACATTCAACCAAACACAAGATTACTATTACACCTCTAT
*** *
28547694 T-TCATTACATTCAACCAAACAGTTGATTTGCTATTACACCTCTAT
1 TCT-ATTACATTCAACCAAACACAAGA-TTACTATTACACCTCTAT
28547739 TCTATTACA
1 TCTATTACA
28547748 CCTCTAATCC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
43 1 0.02
44 20 0.44
45 23 0.51
46 1 0.02
ACGTcount: A:0.33, C:0.27, G:0.05, T:0.36
Consensus pattern (44 bp):
TCTATTACATTCAACCAAACACAAGATTACTATTACACCTCTAT
Found at i:28547773 original size:16 final size:16
Alignment explanation
Indices: 28547728--28547779 Score: 77
Period size: 16 Copynumber: 3.2 Consensus size: 16
28547718 GATTTGCTAT
* * *
28547728 TACACCTCTATTCTAT
1 TACACCTCTAATCCAA
28547744 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28547760 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28547776 TACA
1 TACA
28547780 GCGAACCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.35, C:0.35, G:0.00, T:0.31
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28552627 original size:18 final size:19
Alignment explanation
Indices: 28552604--28552645 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
28552594 AAAAACTCAA
28552604 TTAAAACATT-TTTGA-AAT
1 TTAAAA-ATTATTTGAGAAT
28552622 TTAAAAATTATTTGAGAAT
1 TTAAAAATTATTTGAGAAT
28552641 TTAAA
1 TTAAA
28552646 TCATAATTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 11 0.50
19 8 0.36
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (19 bp):
TTAAAAATTATTTGAGAAT
Found at i:28552656 original size:20 final size:18
Alignment explanation
Indices: 28552614--28552656 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
28552604 TTAAAACATT
*
28552614 TTTGAAATTTAAAAATTA
1 TTTGAAATTTAAAAATAA
*
28552632 TTTGAGAATTTAAATCATAA
1 TTTGA-AATTTAAA-AATAA
28552652 TTTGA
1 TTTGA
28552657 TGATTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 8 0.38
20 8 0.38
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.44
Consensus pattern (18 bp):
TTTGAAATTTAAAAATAA
Found at i:28561237 original size:17 final size:17
Alignment explanation
Indices: 28561215--28561248 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
28561205 AGAAAATACA
28561215 TGGGGTTGATTTGATCC
1 TGGGGTTGATTTGATCC
28561232 TGGGGTTGATTTGATCC
1 TGGGGTTGATTTGATCC
28561249 GGGAAACAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.35, T:0.41
Consensus pattern (17 bp):
TGGGGTTGATTTGATCC
Found at i:28575377 original size:9 final size:9
Alignment explanation
Indices: 28575360--28575396 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28575350 TGAGTTTTAG
28575360 AATTCGAAT
1 AATTCGAAT
*
28575369 AACTCGAAT
1 AATTCGAAT
28575378 AATTCGAAT
1 AATTCGAAT
28575387 AATTCGAAT
1 AATTCGAAT
28575396 A
1 A
28575397 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:28583105 original size:27 final size:27
Alignment explanation
Indices: 28583075--28583133 Score: 109
Period size: 27 Copynumber: 2.2 Consensus size: 27
28583065 TATCAAAGAA
*
28583075 ACCAAATCTCAAACATTAATAAACCAC
1 ACCAAACCTCAAACATTAATAAACCAC
28583102 ACCAAACCTCAAACATTAATAAACCAC
1 ACCAAACCTCAAACATTAATAAACCAC
28583129 ACCAA
1 ACCAA
28583134 CTTTATTTCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (27 bp):
ACCAAACCTCAAACATTAATAAACCAC
Found at i:28591367 original size:617 final size:617
Alignment explanation
Indices: 28590194--28591430 Score: 2339
Period size: 617 Copynumber: 2.0 Consensus size: 617
28590184 TGTATTTCTA
* *
28590194 AACATTTTACACACTAGGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAACCCGTTAGGGTT
1 AACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAAACCGTTAGGGTT
*
28590259 AAACGAAAACTCATATGAGTTAACAAAAGCTCGTGAGAGCTAAACGGAAAGTAAATACGAAAGTT
66 AAACGAAAACTCATATGAGTTAACAAAAGCTCGTGAGAGCTAAACGGAAAGTAAATACAAAAGTT
*
28590324 CGCAACAAATGCCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAAT
131 CGCAACAAATACCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAAT
*
28590389 GACTGTACTCAATCCCGCGTTCCGTTTACTTCGAACGTTCAATTCAATTTCATAGCTTTAACAAT
196 GACTGTACTCAATCCCGCGTTCCGTTTACTTCGAACGTTCAATTCAATTTCATAGCTGTAACAAT
28590454 AATTTTATTTTCAACAAACGATATGAATAAATACATAATACTATTCATCAATTTAACATATAATA
261 AATTTTATTTTCAACAAACGATATGAATAAATACATAATACTATTCATCAATTTAACATATAATA
*
28590519 TTAAATTTCAACTATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTAT
326 TTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTAT
* * *
28590584 TCTGTTAATTTCCCTTTTTTATGATTATCTACGGGATCTTGATTTAAAATGTTTATGACTTGATT
391 TCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGATT
28590649 TATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCTTAATAATTTCTTACGACACA
456 TATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCTTAATAATTTCTTACGACACA
28590714 CAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAATT
521 CAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAATT
*
28590779 CACAAGCTCACTTGTCAGATTTGGTGGTCTCG
586 CACAAGCTCACTTGTCAAATTTGGTGGTCTCG
28590811 AACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAAACCGTTAGGGTT
1 AACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAAACCGTTAGGGTT
**
28590876 AAACGAAAACTCATATGAGTTAACGGAAGCTCGTGAGAGCTAAACGGAAAGTAAATACAAAAGTT
66 AAACGAAAACTCATATGAGTTAACAAAAGCTCGTGAGAGCTAAACGGAAAGTAAATACAAAAGTT
*
28590941 CGCAACAAATACCGAACCTTGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAAT
131 CGCAACAAATACCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAAT
*
28591006 GACTGTACTCAATCCCGCGTTCCGTTTGCTTCGAACGTTCAATTCAATTTCATAGCTGTAACAAT
196 GACTGTACTCAATCCCGCGTTCCGTTTACTTCGAACGTTCAATTCAATTTCATAGCTGTAACAAT
*
28591071 AATTTTATTTTCAACAAATGATATGAATAAATACATAATACTATTCATCAATTTAACATATAATA
261 AATTTTATTTTCAACAAACGATATGAATAAATACATAATACTATTCATCAATTTAACATATAATA
28591136 TTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTAT
326 TTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTAT
28591201 TCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGATT
391 TCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGATT
28591266 TATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCTTAATAATTTCTTACGACACA
456 TATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCTTAATAATTTCTTACGACACA
28591331 CAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAATT
521 CAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAATT
28591396 CACAAGCTCACTTGTCAAATTTGGTGGTCTCG
586 CACAAGCTCACTTGTCAAATTTGGTGGTCTCG
28591428 AAC
1 AAC
28591431 CACTATTTCT
Statistics
Matches: 605, Mismatches: 15, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
617 605 1.00
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.34
Consensus pattern (617 bp):
AACATTTTACACACTACGTTTGTTCTGAGAAGCTCAAAAGAGCTTAACGGAAAACCGTTAGGGTT
AAACGAAAACTCATATGAGTTAACAAAAGCTCGTGAGAGCTAAACGGAAAGTAAATACAAAAGTT
CGCAACAAATACCGAACCTCGATTTACTTGGGTAATTTGTCGTCAATTCCTCGTTTGCACTGAAT
GACTGTACTCAATCCCGCGTTCCGTTTACTTCGAACGTTCAATTCAATTTCATAGCTGTAACAAT
AATTTTATTTTCAACAAACGATATGAATAAATACATAATACTATTCATCAATTTAACATATAATA
TTAAATTTCAACCATTCAAAATTACCTGGATTAAATTGTAGAATTTGTAGTAGTTCAGGGACTAT
TCTGTTAATTTCCCTTTTTTATGATTATCTACAGGATCTTGATTTAAAATGTTTACGACTCGATT
TATAAAATTGAGGTCTCGATACCTCATTTTGTAAACCACTTAGCTTAATAATTTCTTACGACACA
CAAATTAATACTTCAAAAATTCTCCTAAAATCACATTTAGATCGTAAGTACTAAATAATAAAATT
CACAAGCTCACTTGTCAAATTTGGTGGTCTCG
Found at i:28604523 original size:73 final size:73
Alignment explanation
Indices: 28604404--28604572 Score: 254
Period size: 73 Copynumber: 2.3 Consensus size: 73
28604394 TTCACAAGCC
* *
28604404 AAAATAGTCGTAGAAAATAACAAAACTAAGCATAAGGAACAATTAAAGAGAAGAATAGAAGAAGA
1 AAAATAGTCGTAGAAAACAACAAAACTAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAG-
28604469 T-AACAACT
65 TGAACAACT
*
28604477 AAAATAGTCATAGAAAACAACTAAAA-TAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAG
1 AAAATAGTCGTAGAAAACAAC-AAAACTAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAG
28604541 TGAACAACT
65 TGAACAACT
*
28604550 AAAACAGTCGTAGAAGAA-AACAA
1 AAAATAGTCGTAGAA-AACAACAA
28604573 GCTCACCAGT
Statistics
Matches: 88, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
72 3 0.03
73 79 0.90
74 6 0.07
ACGTcount: A:0.59, C:0.10, G:0.17, T:0.14
Consensus pattern (73 bp):
AAAATAGTCGTAGAAAACAACAAAACTAAGCATAAGGAACAATTAAAGAGAAGAAGAGAAGAAGT
GAACAACT
Found at i:28607264 original size:27 final size:27
Alignment explanation
Indices: 28607220--28607277 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
28607210 AGTTTGCCAG
28607220 AAAGACATTCCTTTCATATTCTACCAC
1 AAAGACATTCCTTTCATATTCTACCAC
* * *
28607247 AAAGGCATT-CTTTCCATATTGTGCCAC
1 AAAGACATTCCTTT-CATATTCTACCAC
28607274 AAAG
1 AAAG
28607278 CTGTTCCTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 4 0.15
27 23 0.85
ACGTcount: A:0.33, C:0.26, G:0.10, T:0.31
Consensus pattern (27 bp):
AAAGACATTCCTTTCATATTCTACCAC
Found at i:28611886 original size:28 final size:28
Alignment explanation
Indices: 28611822--28611887 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
28611812 TGGTTTATTG
* *
28611822 ATTTATTTTGTTTTTTTTATTTTTCCTT
1 ATTTATTTTATTTTTTTTATTTTTCCTA
28611850 ATTTA-TTTATTTATTTTTATTTCTT-C-A
1 ATTTATTTTATTT-TTTTTATTT-TTCCTA
28611877 ATTTATTTTAT
1 ATTTATTTTAT
28611888 GGTTTTTCGT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 11 0.33
28 20 0.61
29 2 0.06
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (28 bp):
ATTTATTTTATTTTTTTTATTTTTCCTA
Found at i:28615891 original size:20 final size:19
Alignment explanation
Indices: 28615866--28615920 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
28615856 ACCAAGCAGG
*
28615866 GGTATCGATAATTTTTGAAA
1 GGTATCGATACTTTTT-AAA
*
28615886 GGTATCGATACTTTGTTAAG
1 GGTATCGATACTTT-TTAAA
28615906 GGTATCGATACTTTT
1 GGTATCGATACTTTT
28615921 ATTTTTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 1 0.03
20 29 0.91
21 2 0.06
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.42
Consensus pattern (19 bp):
GGTATCGATACTTTTTAAA
Found at i:28616063 original size:93 final size:92
Alignment explanation
Indices: 28615886--28616064 Score: 231
Period size: 93 Copynumber: 1.9 Consensus size: 92
28615876 ATTTTTGAAA
*
28615886 GGTATCGATACTTTGTTAAGGGTATCGATACTTTTATTTTTGTTTAATTTTCCAAAATATCGAAG
1 GGTATCGATACTTTGTTAAGGATATCGATACTTTTATTTTTGTTTAATTTTCCAAAATATCGAAG
*
28615951 CTCAAATTGGTATTGATACCAGGTCAT
66 CTCAAATTGGTATCGATACCAGGTCAT
*
28615978 GGTATCGATACTTT-TATAAGGATATCGATACTTTTGATTTTT-TCTATAGTTTT-CAAAACT-T
1 GGTATCGATACTTTGT-TAAGGATATCGATACTTTT-ATTTTTGT-T-TAATTTTCCAAAA-TAT
* **
28616039 TGAAGCTCATTTTGGTATCGATACCA
61 CGAAGCTCAAATTGGTATCGATACCA
28616065 ATCATAGGTA
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
91 1 0.01
92 33 0.43
93 35 0.46
94 7 0.09
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.42
Consensus pattern (92 bp):
GGTATCGATACTTTGTTAAGGATATCGATACTTTTATTTTTGTTTAATTTTCCAAAATATCGAAG
CTCAAATTGGTATCGATACCAGGTCAT
Found at i:28623496 original size:27 final size:27
Alignment explanation
Indices: 28623454--28623653 Score: 172
Period size: 27 Copynumber: 7.4 Consensus size: 27
28623444 GTAATGGGCC
* *
28623454 TAAAATGACCGAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* *
28623481 TAAAATGACTGGAATACCCCCGAGGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
* * **
28623508 TAAAATAACTTAAATACCGTCGAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
** * **
28623535 TAAAATGACCAAAATATCCCTAAAGGG
1 TAAAATGACTGAAATACCCCCGAAGGG
*
28623562 TAAAATGA-TAGAAATACCCCCGAGGGG
1 TAAAATGACT-GAAATACCCCCGAAGGG
* * * *
28623589 TATAATGA-TAGAAATACACTCGAAGGT
1 TAAAATGACT-GAAATACCCCCGAAGGG
* *
28623616 TAAAATGACCGAAATACTCCC-ATAGGG
1 TAAAATGACTGAAATACCCCCGA-AGGG
28623643 TAAAATGACTG
1 TAAAATGACTG
28623654 TTATGCCCCT
Statistics
Matches: 135, Mismatches: 35, Indels: 6
0.77 0.20 0.03
Matches are distributed among these distances:
26 1 0.01
27 134 0.99
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.18
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCCCGAAGGG
Found at i:28623589 original size:81 final size:80
Alignment explanation
Indices: 28623454--28623653 Score: 253
Period size: 81 Copynumber: 2.5 Consensus size: 80
28623444 GTAATGGGCC
* *
28623454 TAAAATGACCGAAATACCCCCAAAGGGTAAAATGACTGGAATACCCCCGAGGGGTAAAATAACT-
1 TAAAATGACCGAAATA-TCCCAAAGGGTAAAATGACTGAAATACCCCCGAGGGGTAAAATAA-TA
*
28623518 TAAATAC-CGTCGAAGGG
64 GAAATACAC-TCGAAGGG
* * *
28623535 TAAAATGACCAAAATATCCCTAAAGGGTAAAATGA-TAGAAATACCCCCGAGGGGTATAATGATA
1 TAAAATGACCGAAATATCCC-AAAGGGTAAAATGACT-GAAATACCCCCGAGGGGTAAAATAATA
*
28623599 GAAATACACTCGAAGGT
64 GAAATACACTCGAAGGG
*
28623616 TAAAATGACCGAAATACTCCCATAGGGTAAAATGACTG
1 TAAAATGACCGAAATA-TCCCAAAGGGTAAAATGACTG
28623654 TTATGCCCCT
Statistics
Matches: 104, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
80 5 0.05
81 93 0.89
82 6 0.06
ACGTcount: A:0.42, C:0.18, G:0.20, T:0.18
Consensus pattern (80 bp):
TAAAATGACCGAAATATCCCAAAGGGTAAAATGACTGAAATACCCCCGAGGGGTAAAATAATAGA
AATACACTCGAAGGG
Found at i:28623855 original size:26 final size:26
Alignment explanation
Indices: 28623826--28623902 Score: 109
Period size: 26 Copynumber: 3.0 Consensus size: 26
28623816 TTGCCACATA
*
28623826 TACTGTTACTGGCAGCTTTACTGCGT
1 TACTGTTACTGGCAGCTTTACTGCAT
* *
28623852 TACTGTTACTAGCAGCTTTGCTGCAT
1 TACTGTTACTGGCAGCTTTACTGCAT
* *
28623878 CACTATTACTGGCAGCTTTACTGCA
1 TACTGTTACTGGCAGCTTTACTGCA
28623903 ATATTGGTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 44 1.00
ACGTcount: A:0.19, C:0.25, G:0.19, T:0.36
Consensus pattern (26 bp):
TACTGTTACTGGCAGCTTTACTGCAT
Found at i:28631001 original size:27 final size:27
Alignment explanation
Indices: 28630961--28631074 Score: 140
Period size: 27 Copynumber: 4.2 Consensus size: 27
28630951 GTAATGGGCC
*
28630961 TAAAATGACTGAAATACCCCCGAAGGG
1 TAAAATGACTGAAATACCCCCAAAGGG
* *
28630988 TAAAATGA-TCGAAATACCCCTAAAAGG
1 TAAAATGACT-GAAATACCCCCAAAGGG
** *
28631015 TAAAATGACTGAAATACCCTTAAAGGA
1 TAAAATGACTGAAATACCCCCAAAGGG
**
28631042 TAAAATGACCAAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCCCAAAGGG
28631069 TAAAAT
1 TAAAAT
28631075 AACTATTATA
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
26 1 0.01
27 72 0.97
28 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (27 bp):
TAAAATGACTGAAATACCCCCAAAGGG
Found at i:28631046 original size:54 final size:54
Alignment explanation
Indices: 28630961--28631074 Score: 156
Period size: 54 Copynumber: 2.1 Consensus size: 54
28630951 GTAATGGGCC
* * * * *
28630961 TAAAATGACTGAAATACCCCCGAAGGGTAAAATGATCGAAATACCCCTAAAAGG
1 TAAAATGACTGAAATACCCCCAAAGGATAAAATGACCAAAATACCCCCAAAAGG
** *
28631015 TAAAATGACTGAAATACCCTTAAAGGATAAAATGACCAAAATACCCCCAAAGGG
1 TAAAATGACTGAAATACCCCCAAAGGATAAAATGACCAAAATACCCCCAAAAGG
28631069 TAAAAT
1 TAAAAT
28631075 AACTATTATA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (54 bp):
TAAAATGACTGAAATACCCCCAAAGGATAAAATGACCAAAATACCCCCAAAAGG
Found at i:28648886 original size:167 final size:171
Alignment explanation
Indices: 28648303--28649034 Score: 654
Period size: 167 Copynumber: 4.4 Consensus size: 171
28648293 CTAAACGAAT
* * * * * **
28648303 ATTAAAATTAAATAAAATCTGTTTCAAGATTTACTCCCATCATTTAACAGA----TTTT-ATTCG
1 ATTAAAATTAAATAAAATCTATTTCGAGATTTATTCCCGTCATTTAACAAATTTTTTTTGATTTT
* * * * * *
28648363 ATTTTGTTTCTAAATT---A--AAAGTGAATAAAATTTGTTTCGGGATTTATTCCGGCCGTTCAA
66 ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTCAA
** * * * * *
28648423 TGA-ATTTTATTCCAATTTTGATTTTATTTCCAAAATGAGT
131 CAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAGA
* * ** * **
28648463 ATTAAAATTAAAATAAAATCCATTTTGAGATTTATTCCTATCATTCAACGGATTTTATCCTTT--
1 ATTAAAATT-AAATAAAATCTATTTCGAGATTTATTCCCGTCATTTAACAAATTTT-T--TTTGA
* * * ** *
28648526 TTTTATTTTATTTCCAAATGAGAAATTAAAGTTAAATAAAATCTGTTTCGGGATTTATTCCCACT
62 TTTTATTTTGTTTCCAAATTAG-AATTAAA-TTAAATAAAATCTGTTTCAGGATTTATTCCTGCC
* * *
28648591 GTTCAAC-GGATTTTATTAC-ATTTTGATTTTGTTGCCAAAACAAGAA
125 GTTCAACAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAG-A
* * * * *
28648637 ATTAAAATTAAATAAAATCTA-TTCTG-GATTTATTCCGGCCATTTAGCAAGATTTTATTCGATT
1 ATTAAAATTAAATAAAATCTATTTC-GAGATTTATTCCCGTCATTTAACAA-ATTTTTTTTGATT
* *
28648700 TTATTTTGTTTCTAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTT
64 TTATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTC
*
28648765 AACAAGATTTTATT-CGATTTT-ATTTTGTTTCC-AAATTAGA
129 AACAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAGA
* * *
28648805 ATT-AAATTAAATAAAATTTGTTTCGAGATTTATTCCCGTCGTTTAACAAATTTTTTTTGATTTT
1 ATTAAAATTAAATAAAATCTATTTCGAGATTTATTCCCGTCATTTAACAAATTTTTTTTGATTTT
* * * *
28648869 ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATTTGTTTCAGGATTTATTACTGTCGTTTAA
66 ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTCAA
*
28648934 CAAGATTTTATT-CGATATTG-TTTTGTTTCCAAACA-AAGA
131 CAAGATTTTATTACGATTTTGATTTTGTTTCCAAA-ATAAGA
* * * * * *
28648973 CTT--AATCAAAT-AATTCTATTTCGGGATTTATTCCCGTCATTTAACAGATTCTATTTTGATTT
1 ATTAAAATTAAATAAAATCTATTTCGAGATTTATTCCCGTCATTTAACAAATT-TTTTTTGATTT
28649035 AATTATATAA
Statistics
Matches: 470, Mismatches: 73, Indels: 51
0.79 0.12 0.09
Matches are distributed among these distances:
160 9 0.02
161 34 0.07
166 34 0.07
167 150 0.32
168 36 0.08
169 6 0.01
170 49 0.10
171 22 0.05
172 37 0.08
173 41 0.09
174 52 0.11
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (171 bp):
ATTAAAATTAAATAAAATCTATTTCGAGATTTATTCCCGTCATTTAACAAATTTTTTTTGATTTT
ATTTTGTTTCCAAATTAGAATTAAATTAAATAAAATCTGTTTCAGGATTTATTCCTGCCGTTCAA
CAAGATTTTATTACGATTTTGATTTTGTTTCCAAAATAAGA
Found at i:28648905 original size:83 final size:84
Alignment explanation
Indices: 28648307--28649027 Score: 545
Period size: 84 Copynumber: 8.7 Consensus size: 84
28648297 ACGAATATTA
* * * *
28648307 AAATTAAATAAAATCTGTTTCAAGATTTACTCCCATCATTTAAC-AGATTTTATTCG-----ATT
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTATT
*
28648366 TTGTTTCTAAATT---A--
66 TTGTTTCCAAATTAGAATT
* * * * * * * ** *
28648380 AAAGTGAATAAAATTTGTTTCGGGATTTATTCCGGCCGTTCAATGA-ATTTTATTCCAATTTTGA
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATT-CGATTTT-A
* * *
28648444 TTTTATTTCCAAAATGAGTATT
64 TTTTGTTTCC-AAATTAGAATT
** * ** * * * * **
28648466 AAAATTAAAATAAAATCCATTTTGAGATTTATTCCTATCATTCAAC-GGATTTTATCCTTTTTTT
1 -AAATT-AAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTC-GATTTT
* *
28648530 ATTTTATTTCCAAATGAGAAATT
63 ATTTTGTTTCCAAATTAG-AATT
* * * *
28648553 AAAGTTAAATAAAATCTGTTTCGGGATTTATTCCC-ACTGTTCAAC-GGATTTTATTAC-ATTTT
1 AAA-TTAAATAAAATCTGTTTCGAGATTTATTCCCGTC-GTTTAACAAGATTTTATT-CGATTTT
* **
28648615 GATTTTGTTGCCAAAACAAGAAATT
63 -ATTTTGTTTCC-AAATTAG-AATT
* * * * *
28648640 AAAATTAAATAAAATCT-ATTCTG-GATTTATTCCGGCCATTTAGCAAGATTTTATTCGATTTTA
1 -AAATTAAATAAAATCTGTTTC-GAGATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTA
*
28648703 TTTTGTTTCTAAATTAGAATT
64 TTTTGTTTCCAAATTAGAATT
* *
28648724 AAATTAAATAAAATCTGTTTC-AGGATTTATTCCTGCCGTTTAACAAGATTTTATTCGATTTTAT
1 AAATTAAATAAAATCTGTTTCGA-GATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTAT
28648788 TTTGTTTCCAAATTAGAATT
65 TTTGTTTCCAAATTAGAATT
* * *
28648808 AAATTAAATAAAATTTGTTTCGAGATTTATTCCCGTCGTTTAACAA-ATTTTTTTTGATTTTATT
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTATT
28648872 TTGTTTCCAAATTAGAATT
66 TTGTTTCCAAATTAGAATT
* * * * *
28648891 AAATTAAATAAAATTTGTTTC-AGGATTTATTACTGTCGTTTAACAAGATTTTATTCGATATTGT
1 AAATTAAATAAAATCTGTTTCGA-GATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTAT
** *
28648955 TTTGTTTCCAAACAAAGACTT
65 TTTGTTTCCAAA-TTAGAATT
* * * * * *
28648976 -AATCAAAT-AATTCTATTTCGGGATTTATTCCCGTCATTTAAC-AGATTCTATT
1 AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATT
28649028 TTGATTTAAT
Statistics
Matches: 526, Mismatches: 85, Indels: 65
0.78 0.13 0.10
Matches are distributed among these distances:
73 40 0.08
74 2 0.00
80 9 0.02
81 4 0.01
82 10 0.02
83 119 0.23
84 138 0.26
85 16 0.03
86 85 0.16
87 61 0.12
88 42 0.08
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (84 bp):
AAATTAAATAAAATCTGTTTCGAGATTTATTCCCGTCGTTTAACAAGATTTTATTCGATTTTATT
TTGTTTCCAAATTAGAATT
Found at i:28649045 original size:59 final size:59
Alignment explanation
Indices: 28648982--28649093 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
28648972 ACTTAATCAA
* *
28648982 ATAATTCTATTTCGGGATTTATTCCCGTCATTTAACAGATTCT-ATTTTGATTTAATTAT
1 ATAATTCTATTTCGGGATTTAATCCCGTCATTTAACAAATT-TGATTTTGATTTAATTAT
* * * * *
28649041 ATAATTTTGTTTCGTGATTTAATCCTGTCGTTTAACAAATTTGATTTTGATTT
1 ATAATTCTATTTCGGGATTTAATCCCGTCATTTAACAAATTTGATTTTGATTT
28649094 TGTTTTAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 1 0.02
59 44 0.98
ACGTcount: A:0.26, C:0.12, G:0.12, T:0.51
Consensus pattern (59 bp):
ATAATTCTATTTCGGGATTTAATCCCGTCATTTAACAAATTTGATTTTGATTTAATTAT
Found at i:28649106 original size:59 final size:59
Alignment explanation
Indices: 28648991--28649107 Score: 137
Period size: 59 Copynumber: 2.0 Consensus size: 59
28648981 AATAATTCTA
* * *
28648991 TTTCGGGATTTATTCCCGTCATTTAACAGATTCTATTTTGATTTAATTATATAATTTTG
1 TTTCGGGATTTAATCCCGTCATTTAACAAATTCTATTTTGATTTAATTATAGAATTTTG
* * * ** *
28649050 TTTCGTGATTTAATCCTGTCGTTTAACAAATT-TGATTTTGATTTTGTTTTAGAATTTT
1 TTTCGGGATTTAATCCCGTCATTTAACAAATTCT-ATTTTGATTTAATTATAGAATTTT
28649108 AATTCTACCG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
58 1 0.02
59 47 0.98
ACGTcount: A:0.24, C:0.10, G:0.13, T:0.53
Consensus pattern (59 bp):
TTTCGGGATTTAATCCCGTCATTTAACAAATTCTATTTTGATTTAATTATAGAATTTTG
Found at i:28652134 original size:27 final size:26
Alignment explanation
Indices: 28652103--28652280 Score: 169
Period size: 27 Copynumber: 6.6 Consensus size: 26
28652093 TAAATTGTAC
28652103 AGCACTAAGTGTGCGATTCGACTATGT
1 AGCACTAAGTGTGCGATT-GACTATGT
* * *
28652130 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCG-ATTGACTATGT
* *
28652156 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCG-ATTGACTATGT
*
28652184 GGCACTAAGTGTGCGAGTCTGACTATGT
1 AGCACTAAGTGTGCGA-T-TGACTATGT
* *
28652212 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGA-TTGACTATGT
* * *
28652239 GGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGA-TTGACTATGT
*
28652266 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
28652281 GGCTCAATAT
Statistics
Matches: 126, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 100 0.79
28 25 0.20
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (26 bp):
AGCACTAAGTGTGCGATTGACTATGT
Found at i:28652219 original size:82 final size:81
Alignment explanation
Indices: 28652104--28652259 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
28652094 AAATTGTACA
* * *
28652104 GCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGAT-GCACTAAGTG
1 GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACG-TGGCACTAAGTG
28652168 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
28652185 GCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTGGCACTAAGTG
1 GCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTG
*
28652250 TGCGAGTTGA
65 TGCGAATTGA
28652260 TTATATAGCA
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (81 bp):
GCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGTGGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:28652271 original size:82 final size:81
Alignment explanation
Indices: 28652100--28652280 Score: 220
Period size: 82 Copynumber: 2.2 Consensus size: 81
28652090 GATTAAATTG
* * *
28652100 TACAGCACTAAGTGTGCGATTCGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
28652165 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
28652181 TGCGGCACTAAGTGTGCGAGTCTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TGGCACT
1 TACAGCACTAAGTGTGCGAGTC-GACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
28652245 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
28652263 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
28652281 GGCTCAATAT
Statistics
Matches: 83, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
81 20 0.24
82 63 0.76
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.29
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGAGTCGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:28659273 original size:777 final size:777
Alignment explanation
Indices: 28657775--28659328 Score: 3036
Period size: 777 Copynumber: 2.0 Consensus size: 777
28657765 AGTTAGTTTG
28657775 GTCATCTTTACTAAGGATTGTGTTTATCCTTCTGGTTCTTCACAGGCTGCGAACATCCTAAATAT
1 GTCATCTTTACTAAGGATTGTGTTTATCCTTCTGGTTCTTCACAGGCTGCGAACATCCTAAATAT
28657840 TCATTATGTTCCCAACATTTGGCATATTCCTCTCTTACTTAGAGTATGTTCTATAGCAGTTCTTC
66 TCATTATGTTCCCAACATTTGGCATATTCCTCTCTTACTTAGAGTATGTTCTATAGCAGTTCTTC
28657905 CATTTGTCTGGAACTTAAAGATTCCTAGTCTCATTCTTTTATTTTCTTTTTGATGATGTTACATA
131 CATTTGTCTGGAACTTAAAGATTCCTAGTCTCATTCTTTTATTTTCTTTTTGATGATGTTACATA
28657970 TTGTATATTGCTTCAGAACCAAAATGCGCATCATTCAATTCTGAAACAGCTCAATTTGCTTAATT
196 TTGTATATTGCTTCAGAACCAAAATGCGCATCATTCAATTCTGAAACAGCTCAATTTGCTTAATT
28658035 TAGTTTTTGGTTCAACATTTCATCATCCCTCTTTCTCTAAGTATCATCAGATAACTAAGTTTGTT
261 TAGTTTTTGGTTCAACATTTCATCATCCCTCTTTCTCTAAGTATCATCAGATAACTAAGTTTGTT
28658100 ATAAATTTTACTTTGTTATGGCTTAACTCTTTACTGCACAATGCGGCTGGCCTAGGCAATCAATT
326 ATAAATTTTACTTTGTTATGGCTTAACTCTTTACTGCACAATGCGGCTGGCCTAGGCAATCAATT
28658165 TGGATTGAGGTACTAATTGTAGGAAGTTTTGATCAGTTTTACTAAGAGCTATAAAGTTCTGTTTC
391 TGGATTGAGGTACTAATTGTAGGAAGTTTTGATCAGTTTTACTAAGAGCTATAAAGTTCTGTTTC
28658230 AGCATTGCCACACCTCCAGATTTAGAAGCTTGGACCAGGAGAGCAGAAATAATGAAGTGTTGTGA
456 AGCATTGCCACACCTCCAGATTTAGAAGCTTGGACCAGGAGAGCAGAAATAATGAAGTGTTGTGA
*
28658295 TAAGGTTAGGAAATATGATAAGGTTAATAACTCATGGAGTGTTGTGAAGAGACTACCTGTGAGGG
521 TAAGGTTAAGAAATATGATAAGGTTAATAACTCATGGAGTGTTGTGAAGAGACTACCTGTGAGGG
*
28658360 CGGACTCTTCCTACGGTTGGGGGCTGGCATTTAAAGCATGCGGAAACAGTTTACTAGTAATAGGA
586 CGGACTCTTCCTACGGTTGGGGGCTGGCATTTAAAGCATGCAGAAACAGTTTACTAGTAATAGGA
28658425 GCTGGAGGTCATGGAGGGCATGATGATGGAGTAATTGTTCTGCATTCTTGGAATCAAGATGAGGA
651 GCTGGAGGTCATGGAGGGCATGATGATGGAGTAATTGTTCTGCATTCTTGGAATCAAGATGAGGA
28658490 AAACAGGGATGGACAAGAGTGGAATGTGCTTGCTGTCAAGGCACGGGCAGGTACTTTTGTGT
716 AAACAGGGATGGACAAGAGTGGAATGTGCTTGCTGTCAAGGCACGGGCAGGTACTTTTGTGT
28658552 GTCATCTTTACTAAGGATTGTGTTTATCCTTCTGGTTCTTCACAGGCTGCGAACATCCTAAATAT
1 GTCATCTTTACTAAGGATTGTGTTTATCCTTCTGGTTCTTCACAGGCTGCGAACATCCTAAATAT
**
28658617 TCATTATGTTCTGAACATTTGGCATATTCCTCTCTTACTTAGAGTATGTTCTATAGCAGTTCTTC
66 TCATTATGTTCCCAACATTTGGCATATTCCTCTCTTACTTAGAGTATGTTCTATAGCAGTTCTTC
28658682 CATTTGTCTGGAACTTAAAGATTCCTAGTCTCATTCTTTTATTTTCTTTTTGATGATGTTACATA
131 CATTTGTCTGGAACTTAAAGATTCCTAGTCTCATTCTTTTATTTTCTTTTTGATGATGTTACATA
28658747 TTGTATATTGCTTCAGAACCAAAATGCGCATCATTCAATTCTGAAACAGCTCAATTTGCTTAATT
196 TTGTATATTGCTTCAGAACCAAAATGCGCATCATTCAATTCTGAAACAGCTCAATTTGCTTAATT
28658812 TAGTTTTTGGTTCAACATTTCATCATCCCTCTTTCTCTAAGTATCATCAGATAACTAAGTTTGTT
261 TAGTTTTTGGTTCAACATTTCATCATCCCTCTTTCTCTAAGTATCATCAGATAACTAAGTTTGTT
28658877 ATAAATTTTACTTTGTTATGGCTTAACTCTTTACTGCACAATGCGGCTGGCCTAGGCAATCAATT
326 ATAAATTTTACTTTGTTATGGCTTAACTCTTTACTGCACAATGCGGCTGGCCTAGGCAATCAATT
28658942 TGGATTGAGGTACTAATTGTAGGAAGTTTTGATCAGTTTTACTAAGAGCTATAAAGTTCTGTTTC
391 TGGATTGAGGTACTAATTGTAGGAAGTTTTGATCAGTTTTACTAAGAGCTATAAAGTTCTGTTTC
* *
28659007 TGCATTGCCACACCTCCAGATTTAGAAGCTTGGACCAGGAGGGCAGAAATAATGAAGTGTTGTGA
456 AGCATTGCCACACCTCCAGATTTAGAAGCTTGGACCAGGAGAGCAGAAATAATGAAGTGTTGTGA
28659072 TAAGGTTAAGAAATATGATAAGGTTAATAACTCATGGAGTGTTGTGAAGAGACTACCTGTGAGGG
521 TAAGGTTAAGAAATATGATAAGGTTAATAACTCATGGAGTGTTGTGAAGAGACTACCTGTGAGGG
28659137 CGGACTCTTCCTACGGTTGGGGGCTGGCATTTAAAGCATGCAGAAACAGTTTACTAGTAATAGGA
586 CGGACTCTTCCTACGGTTGGGGGCTGGCATTTAAAGCATGCAGAAACAGTTTACTAGTAATAGGA
* *
28659202 GCTGGAGGTCATGGAGGGCATGATGATGGAGTAATTGTTCTGCATTCTTGGAATCCAGATGAGGG
651 GCTGGAGGTCATGGAGGGCATGATGATGGAGTAATTGTTCTGCATTCTTGGAATCAAGATGAGGA
28659267 AAACAGGGATGGACAAGAGTGGAATGTGCTTGCTGTCAAGGCACGGGCAGGTACTTTTGTGT
716 AAACAGGGATGGACAAGAGTGGAATGTGCTTGCTGTCAAGGCACGGGCAGGTACTTTTGTGT
28659329 ATAATTGTGC
Statistics
Matches: 769, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
777 769 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (777 bp):
GTCATCTTTACTAAGGATTGTGTTTATCCTTCTGGTTCTTCACAGGCTGCGAACATCCTAAATAT
TCATTATGTTCCCAACATTTGGCATATTCCTCTCTTACTTAGAGTATGTTCTATAGCAGTTCTTC
CATTTGTCTGGAACTTAAAGATTCCTAGTCTCATTCTTTTATTTTCTTTTTGATGATGTTACATA
TTGTATATTGCTTCAGAACCAAAATGCGCATCATTCAATTCTGAAACAGCTCAATTTGCTTAATT
TAGTTTTTGGTTCAACATTTCATCATCCCTCTTTCTCTAAGTATCATCAGATAACTAAGTTTGTT
ATAAATTTTACTTTGTTATGGCTTAACTCTTTACTGCACAATGCGGCTGGCCTAGGCAATCAATT
TGGATTGAGGTACTAATTGTAGGAAGTTTTGATCAGTTTTACTAAGAGCTATAAAGTTCTGTTTC
AGCATTGCCACACCTCCAGATTTAGAAGCTTGGACCAGGAGAGCAGAAATAATGAAGTGTTGTGA
TAAGGTTAAGAAATATGATAAGGTTAATAACTCATGGAGTGTTGTGAAGAGACTACCTGTGAGGG
CGGACTCTTCCTACGGTTGGGGGCTGGCATTTAAAGCATGCAGAAACAGTTTACTAGTAATAGGA
GCTGGAGGTCATGGAGGGCATGATGATGGAGTAATTGTTCTGCATTCTTGGAATCAAGATGAGGA
AAACAGGGATGGACAAGAGTGGAATGTGCTTGCTGTCAAGGCACGGGCAGGTACTTTTGTGT
Found at i:28659637 original size:34 final size:35
Alignment explanation
Indices: 28659571--28659637 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
28659561 CAAACACCAG
*
28659571 AAAATATTTTCTAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCTAGTAAATCATTTTACAGAAAAGT
* *
28659606 AAAACATTTTCTAG-AAATTATTTTACGGAAAA
1 AAAACATTTTCTAGTAAATCATTTTACAGAAAA
28659638 TATTTTACTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.36
Consensus pattern (35 bp):
AAAACATTTTCTAGTAAATCATTTTACAGAAAAGT
Found at i:28660593 original size:13 final size:13
Alignment explanation
Indices: 28660577--28660655 Score: 115
Period size: 13 Copynumber: 6.1 Consensus size: 13
28660567 TTTAAACTAA
28660577 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
28660590 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
*
28660603 ACTTTTCCATAA-C
1 ACTTTT-CAAAAGC
*
28660616 ACTTTTTAAAAGC
1 ACTTTTCAAAAGC
28660629 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
28660642 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
28660655 A
1 A
28660656 ATGAAGAACT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
12 3 0.05
13 51 0.88
14 4 0.07
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:28662731 original size:234 final size:234
Alignment explanation
Indices: 28662322--28662773 Score: 877
Period size: 234 Copynumber: 1.9 Consensus size: 234
28662312 AATCTGAACT
*
28662322 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGT
1 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
*
28662387 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTT
66 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
*
28662452 GCATTAACTTGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
131 GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
28662517 TATTTCCAGGATTGCACGCAACTCCACCTATTATTATGA
196 TATTTCCAGGATTGCACGCAACTCCACCTATTATTATGA
28662556 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
1 AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
28662621 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
66 GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
28662686 GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
131 GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
28662751 TATTTCCAGGATTGCACGCAACT
196 TATTTCCAGGATTGCACGCAACT
28662774 TCACTCAATT
Statistics
Matches: 215, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
234 215 1.00
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (234 bp):
AAACGATTTATTCACTTGTGTCTTGATCCGTAGAAATCCCTAAATTATGTTAATATCTCTTTCGA
GAGTAAGAACAACTGACTCTAGGTTGATTAATTGAAATCTCTTTCTAGTTAAAACATCTATCGTC
GCATTAACTCGATCTATGGATTCCCCTATTAGATTTGACTCTAATCCGGTAGATTTATGTCGTCC
TATTTCCAGGATTGCACGCAACTCCACCTATTATTATGA
Found at i:28668762 original size:15 final size:15
Alignment explanation
Indices: 28668744--28668774 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
28668734 TGGTTTAAAT
28668744 TTATATATTATCATC
1 TTATATATTATCATC
*
28668759 TTATATATTATTATC
1 TTATATATTATCATC
28668774 T
1 T
28668775 ATGTTAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.32, C:0.10, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATATATTATCATC
Found at i:28669778 original size:107 final size:107
Alignment explanation
Indices: 28669500--28669906 Score: 556
Period size: 103 Copynumber: 3.9 Consensus size: 107
28669490 GGGTTTTTCT
*
28669500 AAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
1 AAATAAGGCAATATTTCGCATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
*
28669565 TCTCGTTCGACCAAATAGCCAAATATCATTTTTAAACTTTTA
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
*
28669607 AAAT----CAATATTTCGCATTTGAAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
1 AAATAAGGCAATATTTCGCATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
*
28669668 TCTCCTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
* * * * * * *
28669710 AAATAAGGCAATATTTAGCGTTTGGAAAATCAAGGAAACGTACCCTAACGTGTTGGGTTTCGACT
1 AAATAAGGCAATATTTCGCATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
* **
28669775 TCTCGTTTGACCAAATAGCCAAATATCC-TTTTAAACTTTCG
66 TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
* * * * * * * *
28669816 AAGTGAGGCAATATTT-GCATTTGGAAATTTGAGAGAACGTGCTCTAACGTGCTGGGTCTCAATT
1 AAATAAGGCAATATTTCGCATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
* *
28669880 TCTCATTTGACCAAATAGCCAAATATC
66 TCTCGTTCGACCAAATAGCCAAATATC
28669907 TTCTTAACTT
Statistics
Matches: 265, Mismatches: 31, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
103 99 0.37
105 62 0.23
106 25 0.09
107 79 0.30
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Consensus pattern (107 bp):
AAATAAGGCAATATTTCGCATTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGATT
TCTCGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTTTA
Found at i:28674623 original size:41 final size:40
Alignment explanation
Indices: 28674518--28674625 Score: 99
Period size: 41 Copynumber: 2.6 Consensus size: 40
28674508 ACCGGCACGT
* ** * *
28674518 AGCCTACTAGGCCTGAAGCCTGATTTAGTTCACCGGCATAA
1 AGCCTACTAGGCATG-AGCCTGAAATAATTCACCAGCATAA
* * * * *
28674559 AGCCTGCTAGACATAAAGTCTGAAATAATTCACCAGCATTA
1 AGCCTACTAGGCAT-GAGCCTGAAATAATTCACCAGCATAA
28674600 AGCCTACTAGGCATCGAGCCTGAAAT
1 AGCCTACTAGGCAT-GAGCCTGAAAT
28674626 CACAGATACG
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.23
Consensus pattern (40 bp):
AGCCTACTAGGCATGAGCCTGAAATAATTCACCAGCATAA
Found at i:28703114 original size:46 final size:46
Alignment explanation
Indices: 28703052--28703228 Score: 284
Period size: 46 Copynumber: 3.8 Consensus size: 46
28703042 ATGAATTGAC
28703052 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
* * *
28703098 GTAGATATGGTGTTTCAGTGAAGAAAACTATACTGAGTTGTGAAAA
1 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
* *
28703144 GTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGTTGTAAAAA
1 GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
*
28703190 GTAGGTATGATATTTCCA-TGAAGAAAACCATACTGAGTT
1 GTAGGTATGGTATTT-CAGTGAAGAAAACCATACTGAGTT
28703229 ATAGCAATGT
Statistics
Matches: 122, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
46 120 0.98
47 2 0.02
ACGTcount: A:0.37, C:0.09, G:0.25, T:0.29
Consensus pattern (46 bp):
GTAGGTATGGTATTTCAGTGAAGAAAACCATACTGAGTTGTGAAAA
Found at i:28706482 original size:27 final size:26
Alignment explanation
Indices: 28706453--28706514 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
28706443 ACCCCCATAA
*
28706453 AAAATTTTGACGATTTTACCCCTGAT
1 AAAATTTTGACAATTTTACCCCTGAT
* *
28706479 AAAATTTTGACAAATTTACCCCTGGT
1 AAAATTTTGACAATTTTACCCCTGAT
28706505 AAAATTTTGA
1 AAAATTTTGA
28706515 GAAAATATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37
Consensus pattern (26 bp):
AAAATTTTGACAATTTTACCCCTGAT
Found at i:28716912 original size:19 final size:19
Alignment explanation
Indices: 28716884--28716920 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
28716874 TACTCTTCCT
*
28716884 ATCAATTAAAAAAAATTTG
1 ATCAACTAAAAAAAATTTG
*
28716903 ATCAACTAAAAATAATTT
1 ATCAACTAAAAAAAATTT
28716921 CACAAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (19 bp):
ATCAACTAAAAAAAATTTG
Found at i:28717399 original size:110 final size:111
Alignment explanation
Indices: 28717235--28717667 Score: 500
Period size: 113 Copynumber: 3.9 Consensus size: 111
28717225 TAAATTAATC
* *
28717235 AAACCTAATAAAACACAACAACAAAAATAATTTTTCCTTCAATACGAAAAACTAATATAAGATAC
1 AAACCTAATAAAACACAACAACAAAAAT-ATTTTTCCTTAAATACAAAAAACTAATATAAGATAC
* * *
28717300 CACAAAAATATTAATAAAACAAATTAATAAAACCTTAATACAAACTT
65 CACAAAAACATTAATAAAACAAATTAATCATACCTTAATACAAACTT
28717347 AAACCTAATAAAACACAACAA-AAATAAT-TTTTTCCTTAAATACAAAAAACTAATATAAGATAC
1 AAACCTAATAAAACACAACAACAAA-AATATTTTTCCTTAAATACAAAAAACTAATATAAGATAC
*
28717410 CACAAAAATATTAATAAAACAAATTAATCATACCTTTAATACAAA-TCT
65 CACAAAAACATTAATAAAACAAATTAATCATACC-TTAATACAAACT-T
** * ** * *
28717458 AAAATTAGTAAAACACAACAA-AAAAAT-TCCTTCCCCTTAAATACAAAAAAGTTGATATAAGAT
1 AAACCTAATAAAACACAACAACAAAAATAT--TTTTCCTTAAATACAAAAAA-CTAATATAAGAT
* * * *
28717521 ACAACAAAAGCATTAATAAAACAAACTAATCATACATTTAATACAAACTT
63 ACCACAAAAACATTAATAAAACAAATTAATCATAC-CTTAATACAAACTT
* * * ** *
28717571 AAATCTAATAAAACACAACAACAAAAA-ATCTTTCTTTTAAATACAAAAAACTGTTATAAGATAT
1 AAACCTAATAAAACACAACAACAAAAATATTTTTC-CTTAAATACAAAAAACTAATATAAGATAC
* * * *
28717635 CATAAAAACAATAGTAAAACAAATAAATCATAC
65 CACAAAAACATTAATAAAACAAATTAATCATAC
28717668 TTTTTTTTGT
Statistics
Matches: 277, Mismatches: 33, Indels: 22
0.83 0.10 0.07
Matches are distributed among these distances:
110 70 0.25
111 35 0.13
112 81 0.29
113 84 0.30
114 7 0.03
ACGTcount: A:0.56, C:0.16, G:0.03, T:0.25
Consensus pattern (111 bp):
AAACCTAATAAAACACAACAACAAAAATATTTTTCCTTAAATACAAAAAACTAATATAAGATACC
ACAAAAACATTAATAAAACAAATTAATCATACCTTAATACAAACTT
Found at i:28727249 original size:30 final size:30
Alignment explanation
Indices: 28727213--28727270 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
28727203 GCATTTGTAC
28727213 AAGACCATAAGTACCAATTTGCTATGACAT
1 AAGACCATAAGTACCAATTTGCTATGACAT
28727243 AAGACCATAAGTACCAATTTGCTATGAC
1 AAGACCATAAGTACCAATTTGCTATGAC
28727271 TGGCATGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.14, T:0.26
Consensus pattern (30 bp):
AAGACCATAAGTACCAATTTGCTATGACAT
Found at i:28728365 original size:32 final size:32
Alignment explanation
Indices: 28728327--28728413 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
28728317 AACTTTTCCG
** *
28728327 GAAAATATTTTCAAGAAATCTGTCAAACAGCA
1 GAAAATATTTTCAAGAAATCAATCAAACACCA
*
28728359 GAAAATATTTTACACAG-ATTCAATCAAACACCA
1 GAAAATATTTT-CA-AGAAATCAATCAAACACCA
*
28728392 GAAAATATTTTCCAGTAAATCA
1 GAAAATATTTTCAAG-AAATCA
28728414 TTTTACAGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
31 2 0.04
32 12 0.27
33 29 0.64
34 2 0.04
ACGTcount: A:0.47, C:0.17, G:0.09, T:0.26
Consensus pattern (32 bp):
GAAAATATTTTCAAGAAATCAATCAAACACCA
Found at i:28728451 original size:34 final size:35
Alignment explanation
Indices: 28728393--28728459 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
28728383 CAAACACCAG
28728393 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
*
28728428 AAAATATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAATATTTTCCAGTAAATCATTTTACAGAAAA
28728460 TATTTTACGG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 17 0.55
35 14 0.45
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.33
Consensus pattern (35 bp):
AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:28728458 original size:14 final size:14
Alignment explanation
Indices: 28728441--28728481 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
28728431 ATATTTTCCA
28728441 GAAATCATTTTACG
1 GAAATCATTTTACG
28728455 GAAAAT-ATTTTACG
1 G-AAATCATTTTACG
*
28728469 GAAAACATTTTAC
1 GAAATCATTTTAC
28728482 TGGCAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.12
14 17 0.71
15 4 0.17
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (14 bp):
GAAATCATTTTACG
Found at i:28728472 original size:28 final size:28
Alignment explanation
Indices: 28728428--28728481 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
28728418 ACAGAAAAGT
* *
28728428 AAAATATTTTCCAGAAATCATTTTACGG
1 AAAATATTTTACAGAAAACATTTTACGG
*
28728456 AAAATATTTTACGGAAAACATTTTAC
1 AAAATATTTTACAGAAAACATTTTAC
28728482 TGGCAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.43, C:0.13, G:0.09, T:0.35
Consensus pattern (28 bp):
AAAATATTTTACAGAAAACATTTTACGG
Found at i:28730644 original size:27 final size:27
Alignment explanation
Indices: 28730613--28730670 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
28730603 TAAAATTATT
* *
28730613 ATTTAAAAGAAATACATTTTTAATAAA
1 ATTTAAAAGAAATACAATTCTAATAAA
* **
28730640 ATTTAAAATAAATTTAATTCTAATAAA
1 ATTTAAAAGAAATACAATTCTAATAAA
28730667 ATTT
1 ATTT
28730671 CTACTAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (27 bp):
ATTTAAAAGAAATACAATTCTAATAAA
Found at i:28737240 original size:17 final size:17
Alignment explanation
Indices: 28737218--28737253 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28737208 GTTATTCGAG
28737218 ATGTAAAATTCAATTCA
1 ATGTAAAATTCAATTCA
28737235 ATGTAAAATTCAATTCA
1 ATGTAAAATTCAATTCA
28737252 AT
1 AT
28737254 TCAAACTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (17 bp):
ATGTAAAATTCAATTCA
Found at i:28738946 original size:33 final size:32
Alignment explanation
Indices: 28738874--28738949 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 32
28738864 ATGTTTAAAT
* *
28738874 GTAAGACCATAACTGGGCTATGACATTTTAAT
1 GTAAGACCATAACTGGGCTATGACATTTGAAC
* * *
28738906 GAAAAGACCATAACTGGGTTATGGCACTTTGAAC
1 G-TAAGACCATAACTGGGCTATGACA-TTTGAAC
28738940 GTAAGACCAT
1 GTAAGACCAT
28738950 GGTTGGACCA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 1 0.03
33 29 0.81
34 6 0.17
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (32 bp):
GTAAGACCATAACTGGGCTATGACATTTGAAC
Done.