Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D06
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: 62964862
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 132689 characters in sequence are not A, C, G, or T
File 10 of 207
Found at i:3371557 original size:20 final size:20
Alignment explanation
Indices: 3371534--3372005 Score: 82
Period size: 20 Copynumber: 23.6 Consensus size: 20
3371524 TTTATATCCT
3371534 CTCATAATTTTTGGTACTTC
1 CTCATAATTTTTGGTACTTC
** *
3371554 CTCAT-ATTTTTTTTATATTC
1 CTCATAATTTTTGGTA-CTTC
* **
3371574 CTCATAACTTTCCGTACATT-
1 CTCATAATTTTTGGTAC-TTC
* ** *
3371594 CTCGTGGTTTTTAGTA-TTC
1 CTCATAATTTTTGGTACTTC
* *
3371613 CATCATAAATTTTGATACTTC
1 C-TCATAATTTTTGGTACTTC
* *
3371634 CTCA-AGTTTTATAGTA-TTC
1 CTCATAATTTT-TGGTACTTC
** * *
3371653 TCTCGCAATTTTTTGTA-TAC
1 -CTCATAATTTTTGGTACTTC
* * *
3371673 ACTCATAACTTTTGTTACATC
1 -CTCATAATTTTTGGTACTTC
* * *
3371694 ATCAT--TTTTT-TTACATC
1 CTCATAATTTTTGGTACTTC
* *
3371711 CTCATATTTTTTTGTA-TTCC
1 CTCATAATTTTTGGTACTT-C
*
3371731 CTCATAATTTTTCGTACTTC
1 CTCATAATTTTTGGTACTTC
* * * *
3371751 ATCATACGTTTTGTGGCACATC
1 CTCATA-ATTTT-TGGTACTTC
* * * * *
3371773 TTTAAAAATTTTGGTACATC
1 CTCATAATTTTTGGTACTTC
** *
3371793 CTCATTTTTTTTTTGTA-TTC
1 CTCA-TAATTTTTGGTACTTC
*
3371813 CTTCATATTTTTTGGTACTTC
1 C-TCATAATTTTTGGTACTTC
* * *
3371834 CTCATATGTTTTATGGTGCATC
1 CTCATA-ATTTT-TGGTACTTC
* * * *
3371856 TTTAAAATTTTTGGTACATC
1 CTCATAATTTTTGGTACTTC
**
3371876 CTCAT--TTTTTTATACTTC
1 CTCATAATTTTTGGTACTTC
* *
3371894 CT--TAGGTATTATGGTA-TTC
1 CTCATA-AT-TTTTGGTACTTC
* * *
3371913 TCTCATAATTTTTGATATTTT
1 -CTCATAATTTTTGGTACTTC
** * *
3371934 CTTGT-ATTTTTAGT-TTTC
1 CTCATAATTTTTGGTACTTC
* *
3371952 TCTCATAATTTTTTGTGCTTC
1 -CTCATAATTTTTGGTACTTC
*
3371973 CTCA-AATTTTTTGGTAATTC
1 CTCATAA-TTTTTGGTACTTC
*
3371993 CTTATAATCTTTT
1 CTCATAAT-TTTT
3372006 ATATCCCCTC
Statistics
Matches: 318, Mismatches: 98, Indels: 71
0.65 0.20 0.15
Matches are distributed among these distances:
16 1 0.00
17 11 0.03
18 21 0.07
19 38 0.12
20 165 0.52
21 61 0.19
22 21 0.07
ACGTcount: A:0.21, C:0.18, G:0.09, T:0.53
Consensus pattern (20 bp):
CTCATAATTTTTGGTACTTC
Found at i:3371702 original size:17 final size:17
Alignment explanation
Indices: 3371662--3371720 Score: 55
Period size: 17 Copynumber: 3.3 Consensus size: 17
3371652 CTCTCGCAAT
*
3371662 TTTTTGTATACACTCATAA
1 TTTTTGT-TACA-TCATCA
*
3371681 CTTTTGTTACATCATCA
1 TTTTTGTTACATCATCA
* *
3371698 TTTTTTTTACATCCTCA
1 TTTTTGTTACATCATCA
3371715 TATTTT
1 T-TTTT
3371721 TTTGTATTCC
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 20 0.59
18 8 0.24
19 6 0.18
ACGTcount: A:0.24, C:0.19, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTTTGTTACATCATCA
Found at i:3371756 original size:40 final size:40
Alignment explanation
Indices: 3371521--3371845 Score: 112
Period size: 40 Copynumber: 8.1 Consensus size: 40
3371511 ATCCTCGTAA
*
3371521 TTTTT-TATATCCTCTCATAATTTTTGGTACTTCCTCATATT
1 TTTTTGTAT-TCC-CTCATAATTTTTCGTACTTCCTCATATT
* * * * **
3371562 TTTTT-TATATTCCTCATAACTTTCCGTACATT-CTCGTGGT
1 TTTTTGTAT-TCCCTCATAATTTTTCGTAC-TTCCTCATATT
* * *
3371602 TTTTAGTATTCCATCATAAATTTT-GATACTTCCTCA-AGTT
1 TTTTTGTATTCCCTCATAATTTTTCG-TACTTCCTCATA-TT
* * * ** * * *
3371642 TTATAGTATTCTCTCGCAATTTTTTGTA-TACACTCATA-A
1 TTTTTGTATTCCCTCATAATTTTTCGTACTTC-CTCATATT
* * * * ** *
3371681 CTTTTG--TTACATCATCATTTTTTTTACATCCTCATATT
1 TTTTTGTATTCCCTCATAATTTTTCGTACTTCCTCATATT
*
3371719 TTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATACGTT
1 TTTTTGTATTCCCTCATAATTTTTCGTACTTCCTCATA--TT
* * * * * * * * * * *
3371761 TTGTGGCACAT-CTTTAAAAATTTTGGTACATCCTCATTTTT
1 TTTTTGTA-TTCCCTCATAATTTTTCGTACTTCCTCA-TATT
* * * *
3371802 TTTTTGTATTCCTTCATATTTTTTGGTACTTCCTCATATG
1 TTTTTGTATTCCCTCATAATTTTTCGTACTTCCTCATATT
3371842 TTTT
1 TTTT
3371846 ATGGTGCATC
Statistics
Matches: 200, Mismatches: 67, Indels: 35
0.66 0.22 0.12
Matches are distributed among these distances:
37 19 0.09
38 6 0.03
39 8 0.04
40 95 0.47
41 45 0.22
42 25 0.12
43 2 0.01
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.52
Consensus pattern (40 bp):
TTTTTGTATTCCCTCATAATTTTTCGTACTTCCTCATATT
Found at i:3371812 original size:83 final size:83
Alignment explanation
Indices: 3371705--3371886 Score: 267
Period size: 83 Copynumber: 2.2 Consensus size: 83
3371695 TCATTTTTTT
* *
3371705 TACATCCTCA-TATTTTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATACGTTTTGTGGCA
1 TACATCCTCATTTTTTTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATACGTTTTATGGCA
3371769 CATCTTTAAAAATTTTGG
66 CATCTTTAAAAATTTTGG
* * * * * **
3371787 TACATCCTCATTTTTTTTTTGTATTCCTTCATATTTTTTGGTACTTCCTCATATGTTTTATGGTG
1 TACATCCTCATTTTTTTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATACGTTTTATGGCA
*
3371852 CATCTTTAAAATTTTTGG
66 CATCTTTAAAAATTTTGG
3371870 TACATCCTCATTTTTTT
1 TACATCCTCATTTTTTT
3371887 ATACTTCCTT
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 10 0.11
83 79 0.89
ACGTcount: A:0.20, C:0.18, G:0.09, T:0.52
Consensus pattern (83 bp):
TACATCCTCATTTTTTTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATACGTTTTATGGCA
CATCTTTAAAAATTTTGG
Found at i:3371871 original size:42 final size:41
Alignment explanation
Indices: 3371769--3371888 Score: 118
Period size: 41 Copynumber: 2.9 Consensus size: 41
3371759 TTTTGTGGCA
* **
3371769 CATCTTTAAAAATTTTGGTACATCCTCATT-TTTT-TTTTG
1 CATCTTTAAAATTTTTGGTACATCCTCATTGTTTTATGGTG
* * * * *
3371808 TATTCCTTCATATTTTTTGGTACTTCCTCATATGTTTTATGGTG
1 CA-T-CTTTAAAATTTTTGGTACATCCTCAT-TGTTTTATGGTG
*
3371852 CATCTTTAAAATTTTTGGTACATCCTCATTTTTTTAT
1 CATCTTTAAAATTTTTGGTACATCCTCATTGTTTTAT
3371889 ACTTCCTTAG
Statistics
Matches: 62, Mismatches: 14, Indels: 8
0.74 0.17 0.10
Matches are distributed among these distances:
39 1 0.02
40 1 0.02
41 28 0.45
42 23 0.37
43 5 0.08
44 4 0.06
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.54
Consensus pattern (41 bp):
CATCTTTAAAATTTTTGGTACATCCTCATTGTTTTATGGTG
Found at i:3371963 original size:19 final size:21
Alignment explanation
Indices: 3371910--3371963 Score: 51
Period size: 19 Copynumber: 2.7 Consensus size: 21
3371900 TATTATGGTA
*
3371910 TTCTCTCATAATTTTTGATAT
1 TTCTCTCATAATTTTAGATAT
** *
3371931 TT-TCTTGTATTTTTAG-T-T
1 TTCTCTCATAATTTTAGATAT
3371949 TTCTCTCATAATTTT
1 TTCTCTCATAATTTT
3371964 TTGTGCTTCC
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
18 3 0.12
19 10 0.40
20 10 0.40
21 2 0.08
ACGTcount: A:0.19, C:0.13, G:0.06, T:0.63
Consensus pattern (21 bp):
TTCTCTCATAATTTTAGATAT
Found at i:3374956 original size:29 final size:28
Alignment explanation
Indices: 3374921--3374975 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
3374911 TGATATCTGA
3374921 AAAAGTAAAAAGAATAAAATTTTAAATAT
1 AAAAGTAAAAAGAAT-AAATTTTAAATAT
* * *
3374950 AAAAGTATAGAGACTAAATTTTAAAT
1 AAAAGTAAAAAGAATAAATTTTAAAT
3374976 TTACAAAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.60, C:0.02, G:0.09, T:0.29
Consensus pattern (28 bp):
AAAAGTAAAAAGAATAAATTTTAAATAT
Found at i:3378096 original size:21 final size:21
Alignment explanation
Indices: 3378070--3378131 Score: 58
Period size: 21 Copynumber: 3.0 Consensus size: 21
3378060 TGAGTAATTT
3378070 TAAATATTATATCAAAATAAA
1 TAAATATTATATCAAAATAAA
3378091 TAAATA-TA-ATCAAAACTTATAA
1 TAAATATTATATCAAAA--TA-AA
* *
3378113 TAAA-ATTATTTAAAAATAA
1 TAAATATTATATCAAAATAA
3378132 TAATTTTATT
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
19 7 0.21
20 3 0.09
21 11 0.32
22 8 0.24
23 5 0.15
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (21 bp):
TAAATATTATATCAAAATAAA
Found at i:3386367 original size:3 final size:3
Alignment explanation
Indices: 3386359--3386387 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3386349 AATTCACCTT
3386359 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3386388 CTATTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3387011 original size:36 final size:36
Alignment explanation
Indices: 3386969--3387039 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
3386959 TTTTTATCAG
*
3386969 AGCTTGAATCTGGG-TTTTGGGGTTCTTTTCATTTGT
1 AGCTTGAATCTGGGTTTTTGGGGTAC-TTTCATTTGT
3387005 AGCTTGAATCTGGGTTTTTGGGGTACTTTCATTTG
1 AGCTTGAATCTGGGTTTTTGGGGTACTTTCATTTG
3387040 CAGGAGTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
36 23 0.70
37 10 0.30
ACGTcount: A:0.13, C:0.11, G:0.28, T:0.48
Consensus pattern (36 bp):
AGCTTGAATCTGGGTTTTTGGGGTACTTTCATTTGT
Found at i:3389387 original size:184 final size:184
Alignment explanation
Indices: 3389078--3389445 Score: 682
Period size: 184 Copynumber: 2.0 Consensus size: 184
3389068 CCTATATGTT
*
3389078 TGTTTCTCTTTTTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
1 TGTTTCTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
*
3389143 GTGTATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGT
66 GTGTATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGA
3389208 AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACTCTCTTGTATAAGTTTC
131 AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACTCTCTTGTATAAGTTTC
3389262 TGTTTCTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
1 TGTTTCTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
* *
3389327 GTGTATATCTACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTTTCTTTTATTTTGACTGA
66 GTGTATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGA
* *
3389392 AAGTGAGTGTTTCAAAATTTTTTTTATTGGAAATGACTCTCTTGTATAAGTTTC
131 AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACTCTCTTGTATAAGTTTC
3389446 CAGTAACAAG
Statistics
Matches: 178, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
184 178 1.00
ACGTcount: A:0.22, C:0.11, G:0.19, T:0.49
Consensus pattern (184 bp):
TGTTTCTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
GTGTATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGA
AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACTCTCTTGTATAAGTTTC
Found at i:3395711 original size:24 final size:24
Alignment explanation
Indices: 3395684--3395732 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3395674 CACTGAATTA
*
3395684 TTCAAAAGTTTTCATTTCAGTCAC
1 TTCAAAAGTCTTCATTTCAGTCAC
*
3395708 TTCAAAAGTCTTCATTTGAGTCAC
1 TTCAAAAGTCTTCATTTCAGTCAC
3395732 T
1 T
3395733 CGGATGTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (24 bp):
TTCAAAAGTCTTCATTTCAGTCAC
Found at i:3396063 original size:31 final size:31
Alignment explanation
Indices: 3396027--3396088 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
3396017 GTCTAGTGGC
* *
3396027 TTAAAT-AGAAATTTTTAAATAGTTTAATGAT
1 TTAAATGA-AAATTTTTAAATAATTCAATGAT
*
3396058 TTAAATGAAAATTTTTGAATAATTCAATGAT
1 TTAAATGAAAATTTTTAAATAATTCAATGAT
3396089 CAAATTATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 26 0.96
32 1 0.04
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.44
Consensus pattern (31 bp):
TTAAATGAAAATTTTTAAATAATTCAATGAT
Found at i:3396347 original size:28 final size:28
Alignment explanation
Indices: 3396294--3396348 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
3396284 CTTAATTCAA
*
3396294 TAGTTGGTCCTTAAATTATGATTTTTTT
1 TAGTTGGTACTTAAATTATGATTTTTTT
*
3396322 TAGTTAGGTACTTAAATTATTATTTTT
1 TAGTT-GGTACTTAAATTATGATTTTT
3396349 GGTCAAATCA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.25, C:0.05, G:0.13, T:0.56
Consensus pattern (28 bp):
TAGTTGGTACTTAAATTATGATTTTTTT
Found at i:3396815 original size:16 final size:18
Alignment explanation
Indices: 3396794--3396839 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
3396784 GAAAATGAAG
3396794 AAAAAAATAATTAA-A-T
1 AAAAAAATAATTAATATT
*
3396810 AAAAAATTATATTAATATT
1 AAAAAAATA-ATTAATATT
3396829 AAATAAAATAA
1 AAA-AAAATAA
3396840 AAAATTCCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 8 0.33
17 5 0.21
18 1 0.04
19 5 0.21
20 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAAAATAATTAATATT
Found at i:3407863 original size:30 final size:29
Alignment explanation
Indices: 3407829--3407886 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
3407819 AATAATTGGA
* *
3407829 CTAAATCTGAAAAATAAAAAAATTAAATTC
1 CTAAAACT-AAAAATAAAAAAACTAAATTC
*
3407859 CTAAAAGTAAAAATAAAAAAACTAAATT
1 CTAAAACTAAAAATAAAAAAACTAAATT
3407887 ATAAATTTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 19 0.76
30 6 0.24
ACGTcount: A:0.64, C:0.09, G:0.03, T:0.24
Consensus pattern (29 bp):
CTAAAACTAAAAATAAAAAAACTAAATTC
Found at i:3411201 original size:102 final size:102
Alignment explanation
Indices: 3411021--3411212 Score: 260
Period size: 102 Copynumber: 1.9 Consensus size: 102
3411011 TGATTAATGT
* * ** *
3411021 TATCCGGTACACATAGTAACCTACACTTAGTACTACACATGTGACCAATACCATCTAATACACGT
1 TATCCAGTACACATAATAACCTACACTTAGTACTACACATGTGACCAATAAAATCTAATACACAT
* *
3411086 AGTAGCTTGCACATAGTACTACACACGTAACTAAAGC
66 AGTAGCCTACACATAGTACTACACACGTAACTAAAGC
* * * *
3411123 TATCCAGTACACATAATAGCCTACACTTAGTACTACACATGTTA-CAATAAAAATCTTATACTCA
1 TATCCAGTACACATAATAACCTACACTTAGTACTACACATGTGACCAAT-AAAATCTAATACACA
*
3411187 TATTAGCCTACACATAGTACTACACA
65 TAGTAGCCTACACATAGTACTACACA
3411213 TGAGTTCTCA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 4 0.05
102 73 0.95
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.27
Consensus pattern (102 bp):
TATCCAGTACACATAATAACCTACACTTAGTACTACACATGTGACCAATAAAATCTAATACACAT
AGTAGCCTACACATAGTACTACACACGTAACTAAAGC
Found at i:3414320 original size:33 final size:33
Alignment explanation
Indices: 3414277--3414341 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
3414267 CTAATTTATA
* * *
3414277 ACAAAGTTTGTTGCAATGAATCT-AACTTAAATT
1 ACAAAATTTGTTCCAATAAATCTCAA-TTAAATT
3414310 ACAAAATTTGTTCCAATAAATCTCAATTAAAT
1 ACAAAATTTGTTCCAATAAATCTCAATTAAAT
3414342 AAATACAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.43, C:0.14, G:0.08, T:0.35
Consensus pattern (33 bp):
ACAAAATTTGTTCCAATAAATCTCAATTAAATT
Found at i:3420545 original size:28 final size:28
Alignment explanation
Indices: 3420505--3420575 Score: 115
Period size: 28 Copynumber: 2.5 Consensus size: 28
3420495 AGCCCCGTGA
3420505 CAAGTGGTATCCGAGCCAAGTTTTGAAC
1 CAAGTGGTATCCGAGCCAAGTTTTGAAC
*
3420533 CAAGTGGTATCCGAGCCAAGTTTTGAGC
1 CAAGTGGTATCCGAGCCAAGTTTTGAAC
* *
3420561 CAAGTGCTATTCGAG
1 CAAGTGGTATCCGAG
3420576 TTGGTTCGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.27, C:0.21, G:0.27, T:0.25
Consensus pattern (28 bp):
CAAGTGGTATCCGAGCCAAGTTTTGAAC
Found at i:3420553 original size:16 final size:16
Alignment explanation
Indices: 3420505--3420553 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
3420495 AGCCCCGTGA
3420505 CAAGTGGTATCCGAGC
1 CAAGTGGTATCCGAGC
* *
3420521 CAAGT--T-T-TGAAC
1 CAAGTGGTATCCGAGC
3420533 CAAGTGGTATCCGAGC
1 CAAGTGGTATCCGAGC
3420549 CAAGT
1 CAAGT
3420554 TTTGAGCCAA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 8 0.32
13 1 0.04
14 2 0.08
15 1 0.04
16 13 0.52
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (16 bp):
CAAGTGGTATCCGAGC
Found at i:3424283 original size:88 final size:88
Alignment explanation
Indices: 3424134--3424311 Score: 320
Period size: 88 Copynumber: 2.0 Consensus size: 88
3424124 ATAGTTATGA
* * *
3424134 GTCATCTAAGGAATTATAAAAGATTAAAAAGGATAAGATGGTAATTAGTCAAGTAGATATTTTTA
1 GTCATCCAAGGAATTATAAAAGATGAAAAAGGATAAGATGATAATTAGTCAAGTAGATATTTTTA
3424199 GACATAATGATTAGGACTAAAGT
66 GACATAATGATTAGGACTAAAGT
*
3424222 GTCATCCAAGGAATTATAAAAGATGAAAAATGATAAGATGATAATTAGTCAAGTAGATATTTTTA
1 GTCATCCAAGGAATTATAAAAGATGAAAAAGGATAAGATGATAATTAGTCAAGTAGATATTTTTA
3424287 GACATAATGATTAGGACTAAAGT
66 GACATAATGATTAGGACTAAAGT
3424310 GT
1 GT
3424312 AAAGCTGGAT
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 86 1.00
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.30
Consensus pattern (88 bp):
GTCATCCAAGGAATTATAAAAGATGAAAAAGGATAAGATGATAATTAGTCAAGTAGATATTTTTA
GACATAATGATTAGGACTAAAGT
Found at i:3426162 original size:75 final size:75
Alignment explanation
Indices: 3426072--3426257 Score: 336
Period size: 75 Copynumber: 2.5 Consensus size: 75
3426062 CCGGATTACA
* *
3426072 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATT
1 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATT
3426137 CCACCGTATC
66 CCACCGTATC
*
3426147 TTAAGTGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATT
1 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATT
3426212 CCACCGTATC
66 CCACCGTATC
*
3426222 TTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCC
1 TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
3426258 CGAGGGTTGC
Statistics
Matches: 106, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
75 106 1.00
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.32
Consensus pattern (75 bp):
TTAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATT
CCACCGTATC
Found at i:3426178 original size:42 final size:41
Alignment explanation
Indices: 3426119--3426255 Score: 173
Period size: 42 Copynumber: 3.5 Consensus size: 41
3426109 ATTCATTGGT
3426119 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAGTGTGAAAGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAA-TGTGAAAGG
* *
3426161 GGTTGCTAAGTGCTGATTCC-CCG-A-C-TCAT-T---AGT
1 GGTTGCTAAGTGCTGATTCCACCGTATCTTAATGTGAAAGG
*
3426194 GGTTGCTAAGTGCTGATTCCACCGTATCTTAAATGTGAAGGG
1 GGTTGCTAAGTGCTGATTCCACCGTATCTT-AATGTGAAAGG
3426236 GGTTGCTAAGTGCTGATTCC
1 GGTTGCTAAGTGCTGATTCC
3426256 CCCGAGGGTT
Statistics
Matches: 81, Mismatches: 5, Indels: 18
0.78 0.05 0.17
Matches are distributed among these distances:
33 22 0.27
34 3 0.04
35 1 0.01
36 2 0.02
37 2 0.02
38 4 0.05
39 2 0.02
40 1 0.01
41 3 0.04
42 41 0.51
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (41 bp):
GGTTGCTAAGTGCTGATTCCACCGTATCTTAATGTGAAAGG
Found at i:3426298 original size:100 final size:101
Alignment explanation
Indices: 3426160--3426357 Score: 344
Period size: 100 Copynumber: 2.0 Consensus size: 101
3426150 AGTGTGAAAG
* *
3426160 GGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTCCACCGTATCTTA
1 GGGTTGCTAAGTGCTGATTCCCCGAATCATTAGTGGTTGCTAAGTGCTGATCCCACCGTATCTTA
*
3426225 AATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCGA
66 AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCGA
* *
3426261 GGGTTGCTAAGTGCTGATT-CCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTTTA
1 GGGTTGCTAAGTGCTGATTCCCCGAATCATTAGTGGTTGCTAAGTGCTGATCCCACCGTATCTTA
3426325 AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
3426358 GACTCATTGG
Statistics
Matches: 92, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
100 73 0.79
101 19 0.21
ACGTcount: A:0.20, C:0.21, G:0.28, T:0.31
Consensus pattern (101 bp):
GGGTTGCTAAGTGCTGATTCCCCGAATCATTAGTGGTTGCTAAGTGCTGATCCCACCGTATCTTA
AATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCGA
Found at i:3426377 original size:175 final size:177
Alignment explanation
Indices: 3426083--3426569 Score: 897
Period size: 175 Copynumber: 2.8 Consensus size: 177
3426073 TAAATGTGAA
* *
3426083 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
*
3426148 TAAGTGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTC
3426213 CACCGTATCTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
131 CACCGTATCTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
*
3426260 A-GGGTTGCTAAGTGCTGATT-CCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
*
3426323 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTC
3426388 CACCGTATCTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
131 CACCGTATCTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
3426435 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
* *
3426500 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTAGTTGCTAAGTGCTGAATC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTC
3426565 CACCG
131 CACCG
3426570 ATAACGAATA
Statistics
Matches: 299, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
175 151 0.51
176 38 0.13
177 110 0.37
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.31
Consensus pattern (177 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCGACTCATTAGTGGTTGCTAAGTGCTGATTC
CACCGTATCTTAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:3426383 original size:75 final size:75
Alignment explanation
Indices: 3426261--3426432 Score: 301
Period size: 75 Copynumber: 2.3 Consensus size: 75
3426251 ATTCCCCCGA
*
3426261 GGGTTGCTAAGTGCTGATT-CCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATTTTA
1 GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTTA
3426325 AATGTGAAAG
66 AATGTGAAAG
* *
3426335 GGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCTTA
1 GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTTA
*
3426400 AATGTGAAGG
66 AATGTGAAAG
3426410 GGGTTGCTAAGTGCTGATTCCCC
1 GGGTTGCTAAGTGCTGATTCCCC
3426433 CGAGGGGTTG
Statistics
Matches: 93, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
74 19 0.20
75 74 0.80
ACGTcount: A:0.20, C:0.20, G:0.28, T:0.32
Consensus pattern (75 bp):
GGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCTTA
AATGTGAAAG
Found at i:3426457 original size:102 final size:102
Alignment explanation
Indices: 3426333--3426534 Score: 377
Period size: 102 Copynumber: 2.0 Consensus size: 102
3426323 TAAATGTGAA
* *
3426333 AGGGGTTGCTAAGTGCTGATTCCCCGACTCATTGGTGGTTGCTAAGTGCTGATTCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
*
3426398 TAAATGTGAAGGGGGTTGCTAAGTGCTGATTCCCCCG
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
3426435 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
3426500 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
3426535 GACTCATTAG
Statistics
Matches: 97, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 97 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:3428274 original size:22 final size:22
Alignment explanation
Indices: 3428212--3428276 Score: 87
Period size: 22 Copynumber: 3.0 Consensus size: 22
3428202 CTCAGATTAT
* *
3428212 TAGCACATTAGTGCTCTTCGTT
1 TAGCACATTAGTGCTCTTTGTA
3428234 TAGCACATTCA-TGCTCTTTGTA
1 TAGCACATT-AGTGCTCTTTGTA
*
3428256 TAGCACCTTAGTGCTCTTTGT
1 TAGCACATTAGTGCTCTTTGT
3428277 TCATTAGTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 1 0.03
22 36 0.95
23 1 0.03
ACGTcount: A:0.18, C:0.23, G:0.17, T:0.42
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTTTGTA
Found at i:3433401 original size:23 final size:23
Alignment explanation
Indices: 3433375--3433495 Score: 179
Period size: 23 Copynumber: 5.3 Consensus size: 23
3433365 ATAAGTGCCA
*
3433375 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
* *
3433398 CACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
* *
3433421 AACTGAAATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
3433444 CACTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
3433467 CGCTGAAATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
3433490 CGCTGA
1 CACTGA
3433496 TCAATAACAC
Statistics
Matches: 92, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 92 1.00
ACGTcount: A:0.31, C:0.26, G:0.23, T:0.21
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:3435457 original size:18 final size:19
Alignment explanation
Indices: 3435434--3435484 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 19
3435424 AGGTAAATTG
3435434 TATTATTTATTAT-TTTTA
1 TATTATTTATTATATTTTA
3435452 TATTA-TTATT-TATTTTA
1 TATTATTTATTATATTTTA
*
3435469 TTTTATTTTATTATAT
1 TATTA-TTTATTATAT
3435485 ATACTTAACA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
16 1 0.04
17 14 0.50
18 5 0.18
19 5 0.18
20 3 0.11
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TATTATTTATTATATTTTA
Found at i:3435465 original size:10 final size:10
Alignment explanation
Indices: 3435434--3435480 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
3435424 AGGTAAATTG
3435434 TATTATTTAT
1 TATTATTTAT
*
3435444 TATTTTTATAT
1 TATTATT-TAT
3435455 TATTATTTAT
1 TATTATTTAT
3435465 T-TTATTTTAT
1 TATTA-TTTAT
3435475 T-TTATT
1 TATTATT
3435481 ATATATACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
9 5 0.15
10 19 0.58
11 9 0.27
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TATTATTTAT
Found at i:3435466 original size:25 final size:22
Alignment explanation
Indices: 3435434--3435482 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
3435424 AGGTAAATTG
*
3435434 TATTATTTATTAT-TTTTATAT
1 TATTATTTATTTTATTTTATAT
*
3435455 TATTATTTATTTTATTTTATTT
1 TATTATTTATTTTATTTTATAT
3435477 TATTAT
1 TATTAT
3435483 ATATACTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (22 bp):
TATTATTTATTTTATTTTATAT
Found at i:3437834 original size:6 final size:6
Alignment explanation
Indices: 3437825--3437875 Score: 68
Period size: 6 Copynumber: 8.7 Consensus size: 6
3437815 TATATATATC
* * *
3437825 AAATAA AAATAA AAATAA AAATAT ATAT-C AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA AAATAA
3437872 AAAT
1 AAAT
3437876 CACATTCTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
5 3 0.08
6 36 0.92
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (6 bp):
AAATAA
Found at i:3437858 original size:29 final size:29
Alignment explanation
Indices: 3437816--3437875 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
3437806 AATATAATAT
3437816 ATATATATCAAATAAAAATAAAAATAAAA
1 ATATATATCAAATAAAAATAAAAATAAAA
3437845 ATATATATCAAATAAAAATAAAAATAAAA
1 ATATATATCAAATAAAAATAAAAATAAAA
3437874 AT
1 AT
3437876 CACATTCTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (29 bp):
ATATATATCAAATAAAAATAAAAATAAAA
Found at i:3437859 original size:17 final size:17
Alignment explanation
Indices: 3437816--3437864 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 17
3437806 AATATAATAT
3437816 ATATATATCAAAT-AAA
1 ATATATATCAAATAAAA
3437832 A-ATA-A--AAATAAAA
1 ATATATATCAAATAAAA
3437845 ATATATATCAAATAAAA
1 ATATATATCAAATAAAA
3437862 ATA
1 ATA
3437865 AAAATAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
12 4 0.14
13 4 0.14
14 4 0.14
15 4 0.14
16 1 0.04
17 11 0.39
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (17 bp):
ATATATATCAAATAAAA
Found at i:3437877 original size:23 final size:23
Alignment explanation
Indices: 3437831--3437877 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
3437821 TATCAAATAA
* *
3437831 AAATAAAAATAAAAATATATATC
1 AAATAAAAATAAAAATAAAAATC
3437854 AAATAAAAATAAAAATAAAAATC
1 AAATAAAAATAAAAATAAAAATC
3437877 A
1 A
3437878 CATTCTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.21
Consensus pattern (23 bp):
AAATAAAAATAAAAATAAAAATC
Found at i:3441283 original size:22 final size:20
Alignment explanation
Indices: 3441224--3441284 Score: 50
Period size: 22 Copynumber: 2.9 Consensus size: 20
3441214 TTAAAATTGA
* *
3441224 AAAAATTTTGAAAAAATATTT
1 AAAAATTTTAAAAAAATA-AT
* *
3441245 AAAATTTTTCAATAAAATAAAT
1 AAAAATTTT-AAAAAAAT-AAT
3441267 AAAAATTTATAAAAAAAT
1 AAAAATTT-TAAAAAAAT
3441285 GAATTCATAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
21 8 0.26
22 21 0.68
23 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
AAAAATTTTAAAAAAATAAT
Found at i:3445944 original size:52 final size:55
Alignment explanation
Indices: 3445888--3446023 Score: 181
Period size: 55 Copynumber: 2.5 Consensus size: 55
3445878 TTTATTAATC
*
3445888 TTTGGTG-CTGCCTCCTTCAATGGAGG-ACCAGT-TAGGAATT-TTTTTAATATTT
1 TTTGGTGTC-GCCTCCTTCAATAGAGGCACCAGTGTAGGAATTCTTTTTAATATTT
* * * * *
3445940 TTTGGTGTCGCCTACTTCTATTGAGGCACCAGTGTAGGAGTTCTTTTTCATATTT
1 TTTGGTGTCGCCTCCTTCAATAGAGGCACCAGTGTAGGAATTCTTTTTAATATTT
3445995 TTTGGTGTCGCCTCCTTCAATAGAGGCAC
1 TTTGGTGTCGCCTCCTTCAATAGAGGCAC
3446024 TAAATTTTAG
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
52 21 0.29
53 7 0.10
54 7 0.10
55 37 0.51
ACGTcount: A:0.18, C:0.19, G:0.22, T:0.40
Consensus pattern (55 bp):
TTTGGTGTCGCCTCCTTCAATAGAGGCACCAGTGTAGGAATTCTTTTTAATATTT
Found at i:3455445 original size:70 final size:67
Alignment explanation
Indices: 3455320--3455452 Score: 158
Period size: 70 Copynumber: 1.9 Consensus size: 67
3455310 ATAAACAATA
* * * * * *
3455320 TAATAGTTTTGCCTTTTAACTTAATAGGTGAACATTTATTAAAATGACGTAGTTTTACCTTTTAA
1 TAATAGTTTTGACTTTTAACTTAAAAGGTAAACATTTATCAAAACGACATAGTTTTACCTTTTAA
3455385 CT
66 CT
* * *
3455387 TAATGGTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAACGATATAGTTTTGCCTTT
1 TAATAGTTTTGACTTTTAAC-TT--AAAAGGTAAACATTTATCAAAACGACATAGTTTTACCTTT
3455452 T
63 T
3455453 TTTATTCAAA
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
67 18 0.33
68 2 0.04
70 34 0.63
ACGTcount: A:0.32, C:0.11, G:0.13, T:0.44
Consensus pattern (67 bp):
TAATAGTTTTGACTTTTAACTTAAAAGGTAAACATTTATCAAAACGACATAGTTTTACCTTTTAA
CT
Found at i:3459738 original size:29 final size:29
Alignment explanation
Indices: 3459705--3459762 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
3459695 TTTTATCAAA
3459705 ATGGTCCTAATTGTATTTTTGAAAATTTT
1 ATGGTCCTAATTGTATTTTTGAAAATTTT
3459734 ATGGTCCTAATTGTATTTTTGAAAATTTT
1 ATGGTCCTAATTGTATTTTTGAAAATTTT
3459763 TCTATCATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.07, G:0.14, T:0.52
Consensus pattern (29 bp):
ATGGTCCTAATTGTATTTTTGAAAATTTT
Found at i:3461012 original size:17 final size:18
Alignment explanation
Indices: 3460982--3461017 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
3460972 AAAAAAGTAT
3460982 TTTAAAAGTATTTTAAAA
1 TTTAAAAGTATTTTAAAA
3461000 TTTAAAA-TATTTTAAAA
1 TTTAAAAGTATTTTAAAA
3461017 T
1 T
3461018 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
TTTAAAAGTATTTTAAAA
Found at i:3461015 original size:10 final size:10
Alignment explanation
Indices: 3460954--3461027 Score: 75
Period size: 10 Copynumber: 7.5 Consensus size: 10
3460944 ATAAATACCA
3460954 AAAATTATTTT
1 AAAA-TATTTT
**
3460965 AAAA-ATTAA
1 AAAATATTTT
3460974 AAAAGTATTTT
1 AAAA-TATTTT
3460985 AAAAGTATTTT
1 AAAA-TATTTT
3460996 -AAA-A-TTT
1 AAAATATTTT
3461003 AAAATATTTT
1 AAAATATTTT
3461013 AAAATATTTT
1 AAAATATTTT
3461023 AAAAT
1 AAAAT
3461028 TAAAAAATAA
Statistics
Matches: 54, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
7 3 0.06
8 4 0.07
9 8 0.15
10 21 0.39
11 18 0.33
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (10 bp):
AAAATATTTT
Found at i:3461070 original size:17 final size:17
Alignment explanation
Indices: 3461050--3461095 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
3461040 AAAAAGTATT
*
3461050 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
3461067 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
* *
3461083 ATAAATATATTTA
1 TTAAAAATATTTA
3461096 TTATATCGGG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:3461082 original size:40 final size:38
Alignment explanation
Indices: 3461003--3461095 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 38
3460993 TTTAAAATTT
3461003 AAAATATTTTAAAATATTTTAAAATTAAAAAATAAAAA
1 AAAATATTTTAAAATATTTTAAAATTAAAAAATAAAAA
3461041 AAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTTAAAAA
1 AAAA-TATTTT-AAAATATTTTAAAATTAAAAAA--TAAAAA
3461083 ATAAATATATTTA
1 A-AAATAT-TTTA
3461096 TTATATCGGG
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
38 4 0.08
39 6 0.12
40 22 0.45
42 11 0.22
43 6 0.12
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (38 bp):
AAAATATTTTAAAATATTTTAAAATTAAAAAATAAAAA
Found at i:3466031 original size:31 final size:29
Alignment explanation
Indices: 3465989--3466069 Score: 83
Period size: 31 Copynumber: 2.7 Consensus size: 29
3465979 TACTTTGTAA
3465989 AAATTATAAATTTAAT-CTCCATACTATTC
1 AAATTATAAATTTAATCCT-CATACTATTC
* *
3466018 AAATTGATCAAATTTAATCCTTATACTTTTC
1 AAATT-AT-AAATTTAATCCTCATACTATTC
*
3466049 AAATTTTAAAATTTTAATCCT
1 AAATTAT-AAA-TTTAATCCT
3466070 AACTCAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
29 5 0.11
30 6 0.14
31 31 0.70
32 2 0.05
ACGTcount: A:0.40, C:0.15, G:0.01, T:0.44
Consensus pattern (29 bp):
AAATTATAAATTTAATCCTCATACTATTC
Found at i:3473137 original size:10 final size:10
Alignment explanation
Indices: 3473124--3473191 Score: 57
Period size: 10 Copynumber: 6.4 Consensus size: 10
3473114 AATAACAAAT
3473124 AAAGAAAGAA
1 AAAGAAAGAA
3473134 AAAGAAATAGAA
1 AAAG-AA-AGAA
*
3473146 AGAACAAACGAA
1 A-AAGAAA-GAA
3473158 AAAGAAAGAA
1 AAAGAAAGAA
* *
3473168 ACAGAAAG-G
1 AAAGAAAGAA
3473177 AAAGAAAAGAA
1 AAAG-AAAGAA
3473188 AAAG
1 AAAG
3473192 GGAAGGAAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 11
0.73 0.10 0.17
Matches are distributed among these distances:
9 3 0.07
10 18 0.39
11 12 0.26
12 11 0.24
13 2 0.04
ACGTcount: A:0.74, C:0.04, G:0.21, T:0.01
Consensus pattern (10 bp):
AAAGAAAGAA
Found at i:3473158 original size:18 final size:16
Alignment explanation
Indices: 3473124--3473191 Score: 77
Period size: 15 Copynumber: 4.2 Consensus size: 16
3473114 AATAACAAAT
3473124 AAAGAAAGAAAAAGAA
1 AAAGAAAGAAAAAGAA
*
3473140 ATAGAAAGAACAAACGAA
1 AAAGAAAGAA-AAA-GAA
*
3473158 AAAGAAAGAAACAG-A
1 AAAGAAAGAAAAAGAA
*
3473173 AAGGAAAG-AAAAGAA
1 AAAGAAAGAAAAAGAA
3473188 AAAG
1 AAAG
3473192 GGAAGGAAAG
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
14 4 0.09
15 12 0.28
16 10 0.23
17 5 0.12
18 12 0.28
ACGTcount: A:0.74, C:0.04, G:0.21, T:0.01
Consensus pattern (16 bp):
AAAGAAAGAAAAAGAA
Found at i:3474209 original size:39 final size:39
Alignment explanation
Indices: 3474080--3474220 Score: 153
Period size: 39 Copynumber: 3.6 Consensus size: 39
3474070 GACTTCGAGT
* * * *
3474080 CGATGAGACACTGGGTGTCAATTTACTACTTTGGATTAATT
1 CGATGAGACACTGGGTGTCAAATTATTAC-TTCGATT-ATC
* * *
3474121 CGATGAGACACTAGGTGTC-AA-T-TTACTTCGGTTTAGC
1 CGATGAGACACTGGGTGTCAAATTATTACTTC-GATTATC
*
3474158 CGATGAGACACTGGGTGTCAAATTATTACTTCAATTATC
1 CGATGAGACACTGGGTGTCAAATTATTACTTCGATTATC
*
3474197 CGATGAGGCACTGGGTGTCAAATT
1 CGATGAGACACTGGGTGTCAAATT
3474221 GGTGTGTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 10
0.79 0.11 0.09
Matches are distributed among these distances:
37 21 0.25
38 8 0.10
39 29 0.35
40 8 0.10
41 18 0.21
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (39 bp):
CGATGAGACACTGGGTGTCAAATTATTACTTCGATTATC
Found at i:3474914 original size:22 final size:22
Alignment explanation
Indices: 3474889--3474935 Score: 76
Period size: 22 Copynumber: 2.1 Consensus size: 22
3474879 GGTATCAATG
*
3474889 AGGGTACATTGGTTAGACACCT
1 AGGGTACATTGCTTAGACACCT
*
3474911 AGGGTACATTGCTTAGGCACCT
1 AGGGTACATTGCTTAGACACCT
3474933 AGG
1 AGG
3474936 ATGTATGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.26
Consensus pattern (22 bp):
AGGGTACATTGCTTAGACACCT
Found at i:3477213 original size:49 final size:49
Alignment explanation
Indices: 3477141--3477237 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
3477131 AGAACATACA
* *
3477141 AAATGAAATCTAACGTCTAATATAATGATCTTCATGGTACTTTTACCGC
1 AAATGAAATCTAACGTCAAATATAATGATCTCCATGGTACTTTTACCGC
*
3477190 AAATGAAATCTACCGTCAAATATAATGATCTCCATGGTACTTTTACCG
1 AAATGAAATCTAACGTCAAATATAATGATCTCCATGGTACTTTTACCG
3477238 TGATAAATCT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.35, C:0.20, G:0.12, T:0.33
Consensus pattern (49 bp):
AAATGAAATCTAACGTCAAATATAATGATCTCCATGGTACTTTTACCGC
Found at i:3481550 original size:6 final size:6
Alignment explanation
Indices: 3481539--3481563 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3481529 CCTTTGAGGT
3481539 TTCATC TTCATC TTCATC TTCATC T
1 TTCATC TTCATC TTCATC TTCATC T
3481564 ATGCAATCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCATC
Found at i:3499104 original size:28 final size:29
Alignment explanation
Indices: 3499073--3499128 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
3499063 TATTATTATT
*
3499073 TATATAAATATATAAATTA-ATTATAAAG
1 TATATAAATAAATAAATTACATTATAAAG
* * *
3499101 TATATTATTAAATTAATTACATTATAAA
1 TATATAAATAAATAAATTACATTATAAA
3499129 TATTATATTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TATATAAATAAATAAATTACATTATAAAG
Found at i:3499897 original size:3 final size:3
Alignment explanation
Indices: 3499889--3499933 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
3499879 GTGAGGTAAG
3499889 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
3499934 GAGTGGGAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3500346 original size:37 final size:39
Alignment explanation
Indices: 3500287--3500382 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
3500277 CGGATAGATT
* * * *
3500287 CGATGAGGTACTGGGTACCAACT-TT-CTTCG-GCTTTGC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTAT-C
* *
3500324 CGATGAGACACTGGGTGTCAACTATTGCTTCGAACTATC
1 CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
3500363 CGATGAGGCACTGGGTGCCA
1 CGATGAGGCACTGGGTGCCA
3500383 TTCTGGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
37 19 0.40
38 2 0.04
39 24 0.50
40 3 0.06
ACGTcount: A:0.21, C:0.24, G:0.28, T:0.27
Consensus pattern (39 bp):
CGATGAGGCACTGGGTGCCAACTATTGCTTCGAACTATC
Found at i:3502643 original size:74 final size:73
Alignment explanation
Indices: 3502547--3502689 Score: 214
Period size: 74 Copynumber: 1.9 Consensus size: 73
3502537 TAACAAAAAT
* * * *
3502547 CCAACCAAACTCAATCCCTAAAATCCCTAGTAATCAACTTCGCTACCACCAAGTCTACCAAGATG
1 CCAACCAAACCCAATCCCTAAAACCCCTAGTAATCAACTT-GCTACCACCAAGTCAACCAAGAAG
3502612 AGGGACAAC
65 AGGGACAAC
* * *
3502621 CCAATCAAACCCAATCCTTAAAACCCCTAGTAATCAACTTGCTACCACCAAGTCAACGAAGAAGA
1 CCAACCAAACCCAATCCCTAAAACCCCTAGTAATCAACTTGCTACCACCAAGTCAACCAAGAAGA
3502686 GGGA
66 GGGA
3502690 GAAAATAGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
73 26 0.42
74 36 0.58
ACGTcount: A:0.39, C:0.32, G:0.12, T:0.17
Consensus pattern (73 bp):
CCAACCAAACCCAATCCCTAAAACCCCTAGTAATCAACTTGCTACCACCAAGTCAACCAAGAAGA
GGGACAAC
Found at i:3512711 original size:23 final size:23
Alignment explanation
Indices: 3512662--3512726 Score: 60
Period size: 22 Copynumber: 2.8 Consensus size: 23
3512652 GGTAGTGTCT
*
3512662 TTTAATATAAATATTTTTAATGT
1 TTTAATATAAATATTTTTAATGA
* *
3512685 TTTAAT-TTAATATTTTTAGTGCA
1 TTTAATATAAATATTTTTAATG-A
* *
3512708 TTTAGTATATTATATTTTT
1 TTTAATATA-AATATTTTT
3512727 TAAAAGTTAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 13 0.39
23 11 0.33
24 1 0.03
25 8 0.24
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
TTTAATATAAATATTTTTAATGA
Found at i:3525255 original size:24 final size:21
Alignment explanation
Indices: 3525228--3525270 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 21
3525218 TATAGGGTAC
3525228 AATATAGGTATTTCACAATATTAA
1 AATATA-GTATTT-A-AATATTAA
3525252 AATATAGTATTTAAATATT
1 AATATAGTATTTAAATATT
3525271 TACAACAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 6 0.32
24 6 0.32
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
AATATAGTATTTAAATATTAA
Found at i:3526668 original size:115 final size:116
Alignment explanation
Indices: 3526465--3526699 Score: 436
Period size: 115 Copynumber: 2.0 Consensus size: 116
3526455 TTAAGTTTGC
3526465 TTAATGAAATGTTCCTTTTTTCGACAAATCATAAGTGTTTTCATCCGTTTTACGACCTGAAATTA
1 TTAATGAAATGTTCCTTTTTTCGACAAATCATAAGTGTTTTCATCCGTTTTACGACCTGAAATTA
* *
3526530 ATCCTATTTAAACTAGAAGAATATTCAAGTGATGCACTCCCGATATCAAAA
66 ATCCTATTCAAACCAGAAGAATATTCAAGTGATGCACTCCCGATATCAAAA
3526581 TTAATGAAATGTT-CTTTTTTCGACAAATCATAAGTGTTTTCATCCGTTTTACGACCTGAAATTA
1 TTAATGAAATGTTCCTTTTTTCGACAAATCATAAGTGTTTTCATCCGTTTTACGACCTGAAATTA
*
3526645 ATCCTATTCAAACCAGAAGAATATTCAAGTGATGCACTCCCGATATCAGAA
66 ATCCTATTCAAACCAGAAGAATATTCAAGTGATGCACTCCCGATATCAAAA
3526696 TTAA
1 TTAA
3526700 AACAACTTTG
Statistics
Matches: 116, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
115 103 0.89
116 13 0.11
ACGTcount: A:0.34, C:0.18, G:0.12, T:0.35
Consensus pattern (116 bp):
TTAATGAAATGTTCCTTTTTTCGACAAATCATAAGTGTTTTCATCCGTTTTACGACCTGAAATTA
ATCCTATTCAAACCAGAAGAATATTCAAGTGATGCACTCCCGATATCAAAA
Found at i:3535988 original size:20 final size:19
Alignment explanation
Indices: 3535952--3536007 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 19
3535942 TTGATCTCAA
* *
3535952 GAAATTAAAAACAAAAATT
1 GAAAATAAAATCAAAAATT
3535971 GAAAATAAAATCATAAAATT
1 GAAAATAAAATCA-AAAATT
*
3535991 AAAAATAAAAT-AAAAAT
1 GAAAATAAAATCAAAAAT
3536008 AAAAAAGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.15
19 12 0.36
20 16 0.48
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.21
Consensus pattern (19 bp):
GAAAATAAAATCAAAAATT
Found at i:3535999 original size:6 final size:6
Alignment explanation
Indices: 3535957--3536012 Score: 51
Period size: 6 Copynumber: 9.0 Consensus size: 6
3535947 CTCAAGAAAT
* * *
3535957 TAAAAA CAAAAA TTGAAAA TAAAATCA TAAAAT TAAAAA T-AAAA TAAAAA
1 TAAAAA TAAAAA -TAAAAA TAAAA--A TAAAAA TAAAAA TAAAAA TAAAAA
3536007 TAAAAA
1 TAAAAA
3536013 AGGAAACTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
5 5 0.12
6 25 0.62
7 4 0.10
8 6 0.15
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:3536012 original size:12 final size:12
Alignment explanation
Indices: 3535957--3536012 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 12
3535947 CTCAAGAAAT
*
3535957 TAAAAACAAAAA
1 TAAAAATAAAAA
*
3535969 TTGAAAATAAAATCA
1 -TAAAAATAAAA--A
*
3535984 TAAAATTAAAAA
1 TAAAAATAAAAA
3535996 T-AAAATAAAAA
1 TAAAAATAAAAA
3536007 TAAAAA
1 TAAAAA
3536013 AGGAAACTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 10 0.29
12 6 0.17
13 9 0.26
14 9 0.26
15 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.20
Consensus pattern (12 bp):
TAAAAATAAAAA
Found at i:3539442 original size:11 final size:11
Alignment explanation
Indices: 3539426--3539450 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3539416 TTGAGTTAGC
3539426 TAAAAATAGTT
1 TAAAAATAGTT
3539437 TAAAAATAGTT
1 TAAAAATAGTT
3539448 TAA
1 TAA
3539451 TGAATCTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
TAAAAATAGTT
Found at i:3543337 original size:173 final size:173
Alignment explanation
Indices: 3543028--3543369 Score: 521
Period size: 173 Copynumber: 2.0 Consensus size: 173
3543018 TTCGAAATTG
* *
3543028 CTATTATGTTGATGATGCCATAAAGCAGTGTTAATGTTGCTTGAAGGAAAAGCGAGTCTCTCCCC
1 CTATTATGTTGATGATGCCATAAAGCAGTGTTAATGTGGCTTGAAGGAAAAGAGAGTCTCTCCCC
* * *
3543093 TGAGATGTATCTATTCTGCTGGAAGGAGCAGTCATATACTAAAATATGAGGTCATAGTGGAATCA
66 TGAGATGTATCTAATCTGCTGCAAGGAGCAGTCAAATACTAAAATATGAGGTCATAGTGGAATCA
3543158 AATGTCATCCTATAGCGTTCATGAGATGTTTCTATTGTAATCA
131 AATGTCATCCTATAGCGTTCATGAGATGTTTCTATTGTAATCA
*
3543201 CTATTATGTTGATGATGCCATAAATTG-A-TGTTTATGTGGCTTGAACGGAAAA-AGAGTCTCTC
1 CTATTATGTTGATGATGCCATAAA--GCAGTGTTAATGTGGCTTGAA-GGAAAAGAGAGTCTCTC
* *
3543263 TCCTGAGATGTCTCTAATCTGCTGCAAGGAGCAGTCAAATACTAAAATATGAGGGTCATAGT-GA
63 CCCTGAGATGTATCTAATCTGCTGCAAGGAGCAGTCAAATACTAAAATATGA-GGTCATAGTGGA
* * *
3543327 ATCGAATGTCATCCTATAGTGTTCATGAGGTGTTTCTATTGTA
127 ATCAAATGTCATCCTATAGCGTTCATGAGATGTTTCTATTGTA
3543370 TATATTTAAA
Statistics
Matches: 154, Mismatches: 11, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
173 137 0.89
174 16 0.10
175 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (173 bp):
CTATTATGTTGATGATGCCATAAAGCAGTGTTAATGTGGCTTGAAGGAAAAGAGAGTCTCTCCCC
TGAGATGTATCTAATCTGCTGCAAGGAGCAGTCAAATACTAAAATATGAGGTCATAGTGGAATCA
AATGTCATCCTATAGCGTTCATGAGATGTTTCTATTGTAATCA
Found at i:3559287 original size:30 final size:29
Alignment explanation
Indices: 3559252--3559309 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
3559242 GTAATTTTTG
3559252 AAAATTGAA-ACAAATAAATAATTTATGTAT
1 AAAATTGAACA-AAATAAA-AATTTATGTAT
* *
3559282 AAAATTGCACAAAATCAAAATTTATGTA
1 AAAATTGAACAAAATAAAAATTTATGTA
3559310 AAACTGTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.40
30 14 0.56
31 1 0.04
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (29 bp):
AAAATTGAACAAAATAAAAATTTATGTAT
Found at i:3567417 original size:5 final size:5
Alignment explanation
Indices: 3567395--3567428 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
3567385 ATAATAAATG
*
3567395 TTAAT TTTAT TCTAAT TTAAT TTAAT TTAAT TTA
1 TTAAT TTAAT T-TAAT TTAAT TTAAT TTAAT TTA
3567429 TTCTAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 22 0.85
6 4 0.15
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (5 bp):
TTAAT
Found at i:3567425 original size:15 final size:16
Alignment explanation
Indices: 3567395--3567428 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3567385 ATAATAAATG
*
3567395 TTAATTTTATTCTAAT
1 TTAATTTAATTCTAAT
3567411 TTAATTTAATT-TAAT
1 TTAATTTAATTCTAAT
3567426 TTA
1 TTA
3567429 TTCTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TTAATTTAATTCTAAT
Found at i:3567845 original size:18 final size:17
Alignment explanation
Indices: 3567814--3567847 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3567804 GGCGAGACTC
*
3567814 TAAATTAAATATTAAAT
1 TAAATTAAAAATTAAAT
3567831 TAAATTTAAAAATTAAA
1 TAAA-TTAAAAATTAAA
3567848 AAACAGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTAAAAATTAAAT
Found at i:3574062 original size:6 final size:6
Alignment explanation
Indices: 3574051--3574075 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3574041 ATCATATTAC
3574051 TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT T
3574076 AATATTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:3575366 original size:13 final size:14
Alignment explanation
Indices: 3575342--3575378 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3575332 ATGTTAATGA
3575342 TTAAATTAAAATTT
1 TTAAATTAAAATTT
3575356 TTAAA-TAAAA-TT
1 TTAAATTAAAATTT
*
3575368 TTAATTTAAAA
1 TTAAATTAAAA
3575379 AATATAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAATTAAAATTT
Found at i:3580638 original size:31 final size:31
Alignment explanation
Indices: 3580599--3580674 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
3580589 TTAATATAAC
*
3580599 ATTTGGTACCTAAACTTGACATTTATTTC-TA
1 ATTTGGTACCTAAACTTGACACTT-TTTCTTA
* * * *
3580630 TTTTGGTACTTGATCTTGACACTTTTTCTTA
1 ATTTGGTACCTAAACTTGACACTTTTTCTTA
*
3580661 ATTTGGAACCTAAA
1 ATTTGGTACCTAAA
3580675 AGTTTTTGGC
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.46
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCTTA
Found at i:3584248 original size:3 final size:3
Alignment explanation
Indices: 3584240--3584266 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3584230 TCACAGTTGA
3584240 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
3584267 TCAATTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3588959 original size:3 final size:3
Alignment explanation
Indices: 3588951--3588976 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3588941 TTCATTTTGT
3588951 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3588977 TAGGATATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3590939 original size:89 final size:84
Alignment explanation
Indices: 3590778--3590976 Score: 195
Period size: 89 Copynumber: 2.3 Consensus size: 84
3590768 GTTTATCTGC
* * ** * *
3590778 AAACACTGGTGATTTATCCACAAACTTACTGGCAGCTTTTATCTGCAAATTCGTTGCGCATTAAC
1 AAACATTGGTGGTTTATCCAC-AACTTACTGGCAGCTTTTATCTGCAAACCCATTGCG-ATTAAA
* *
3590843 CTGCTGGCAGCGTATTAACCTGT
64 CTACTGGCAACGTATTAACC--T
* *
3590866 AAACATTGGTGGTTTATCCACAACTTTTATTGGCAGCTTTTATCTGCAAACCCATTGTG-TTCAC
1 AAACATTGGTGGTTTATCCACAAC--TTACTGGCAGCTTTTATCTGCAAACCCATTGCGATT-A-
3590930 AACTACTGGCAACGTATTAACCT
62 AACTACTGGCAACGTATTAACCT
*
3590953 ACAACACTT-GTGGTTCATCCACAA
1 A-AACA-TTGGTGGTTTATCCACAA
3590977 TCTAGAGTGT
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
87 7 0.07
88 38 0.40
89 49 0.52
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (84 bp):
AAACATTGGTGGTTTATCCACAACTTACTGGCAGCTTTTATCTGCAAACCCATTGCGATTAAACT
ACTGGCAACGTATTAACCT
Found at i:3592664 original size:22 final size:22
Alignment explanation
Indices: 3592639--3592682 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3592629 ACAAGTATTG
3592639 TATTGAAATTTAAAAT-AAAATA
1 TATTGAAATTT-AAATCAAAATA
* *
3592661 TATTTAGATTTAAATCAAAATA
1 TATTGAAATTTAAATCAAAATA
3592683 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (22 bp):
TATTGAAATTTAAATCAAAATA
Found at i:3595225 original size:27 final size:26
Alignment explanation
Indices: 3595128--3595225 Score: 85
Period size: 27 Copynumber: 3.7 Consensus size: 26
3595118 TTTTAACTTG
* *
3595128 ATTTTATTTTATTTTTAGCTTTTAAAA
1 ATTTTA-TTTATTTTTAGATTTTTAAA
3595155 ATTTTATTTTATTTTT--ATTTTT-AA
1 ATTTTA-TTTATTTTTAGATTTTTAAA
* **
3595179 GTATTTATAGATTTTATAGATTTTTAAA
1 AT-TTTATTTATTTT-TAGATTTTTAAA
3595207 ATTTCTATTTATTTTTAGA
1 ATTT-TATTTATTTTTAGA
3595226 ATCTTCTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
24 9 0.16
25 9 0.16
27 28 0.49
28 11 0.19
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (26 bp):
ATTTTATTTATTTTTAGATTTTTAAA
Found at i:3595993 original size:29 final size:29
Alignment explanation
Indices: 3595923--3595987 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
3595913 GTATTTTTAT
* *
3595923 AAAATATCCAATACGGTACTTGTACTTTG
1 AAAATGTCCAATGCGGTACTTGTACTTTG
3595952 AAAATGTCCAATGCGGTACTTGTACTTTG
1 AAAATGTCCAATGCGGTACTTGTACTTTG
3595981 AAAATGT
1 AAAATGT
3595988 TTAATGTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (29 bp):
AAAATGTCCAATGCGGTACTTGTACTTTG
Found at i:3595999 original size:29 final size:29
Alignment explanation
Indices: 3595923--3596001 Score: 95
Period size: 29 Copynumber: 2.7 Consensus size: 29
3595913 GTATTTTTAT
* * *
3595923 AAAATATCCAATACGGTACTTGTACTTTG
1 AAAATGTCCAATGCAGTACTTGTACTTTG
*
3595952 AAAATGTCCAATGCGGTACTTGTACTTTG
1 AAAATGTCCAATGCAGTACTTGTACTTTG
** *
3595981 AAAATGTTTAATGTAGTACTT
1 AAAATGTCCAATGCAGTACTT
3596002 ATGTTTTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (29 bp):
AAAATGTCCAATGCAGTACTTGTACTTTG
Found at i:3596886 original size:20 final size:20
Alignment explanation
Indices: 3596827--3596891 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
3596817 TAAAAAAAAT
3596827 AAAAAGTTATAAAATTTATTAA
1 AAAAAG-TATAAAA-TTATTAA
* *
3596849 ATAAA-TATTAACATTATTAA
1 AAAAAGTA-TAAAATTATTAA
*
3596869 AAAAAGTATAAAAATATTAA
1 AAAAAGTATAAAATTATTAA
3596889 AAA
1 AAA
3596892 TATAATTTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
20 26 0.72
21 6 0.17
22 4 0.11
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAAAGTATAAAATTATTAA
Found at i:3600782 original size:3 final size:3
Alignment explanation
Indices: 3600776--3600813 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3600766 AGTGTTGTTT
3600776 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
3600814 CTACTCTAAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:3617434 original size:89 final size:89
Alignment explanation
Indices: 3617246--3617452 Score: 274
Period size: 90 Copynumber: 2.3 Consensus size: 89
3617236 CTCTAGCCCT
* * *
3617246 CAAACTTTTTCAAAAACAGCAATTAAGCCCCTGCTTTTTTTTGCACTCACTTGGGCACTTGAACT
1 CAAACTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCAATTGGGCACTTGAACT
* *
3617311 TTCAAAATGCATAAAAAAGGCCTT
66 TTCAAAAGGCATAAAAAAGGCCTC
* * * *
3617335 TAAACTTTTTCAAAAAAATCAATTAAGCCCCTACTTTTCTTTTTG-ACTTAATTGGGTACTTGAA
1 CAAACTTTTTCAAAAAAAGCAATTAAGCCCCTAC-TTT-TTTTTGCACTCAATTGGGCACTTGAA
*
3617399 CTTTCAAAAGGCATCAAAAAGGTCC-C
64 CTTTCAAAAGGCATAAAAAAGG-CCTC
*
3617425 CAAACTTTTCCAAAAAAAGCAATTAAGC
1 CAAACTTTTTCAAAAAAAGCAATTAAGC
3617453 TCCTGTTTTT
Statistics
Matches: 102, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
89 30 0.29
90 64 0.63
91 8 0.08
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (89 bp):
CAAACTTTTTCAAAAAAAGCAATTAAGCCCCTACTTTTTTTTGCACTCAATTGGGCACTTGAACT
TTCAAAAGGCATAAAAAAGGCCTC
Found at i:3617630 original size:20 final size:20
Alignment explanation
Indices: 3617603--3617651 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3617593 TTTAATATTT
3617603 ATTA-AAAATTAGGAAAAAA
1 ATTATAAAATTAGGAAAAAA
* * *
3617622 ATTATAAAAATCGTAAAAAA
1 ATTATAAAATTAGGAAAAAA
3617642 ATTATAAAAT
1 ATTATAAAAT
3617652 ATATTTTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
ATTATAAAATTAGGAAAAAA
Found at i:3617900 original size:21 final size:19
Alignment explanation
Indices: 3617850--3617914 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
3617840 TTTTTGATGC
*
3617850 ATTTTATAATTTTTATAAA
1 ATTTTATAATTTTTTTAAA
* *
3617869 ATTTTACAATTTTTTTACA
1 ATTTTATAATTTTTTTAAA
3617888 ATTTCTAATAATTTTTTTAATA
1 ATTT-T-ATAATTTTTTTAA-A
3617910 ATTTT
1 ATTTT
3617915 TATTATAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
19 20 0.53
20 1 0.03
21 12 0.32
22 5 0.13
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTATAATTTTTTTAAA
Found at i:3617910 original size:12 final size:13
Alignment explanation
Indices: 3617893--3617925 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
3617883 TTACAATTTC
3617893 TAATAATTTTT-T
1 TAATAATTTTTAT
3617905 TAATAATTTTTAT
1 TAATAATTTTTAT
3617918 T-ATAATTT
1 TAATAATTT
3617926 AATAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 18 0.90
13 2 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TAATAATTTTTAT
Found at i:3618173 original size:22 final size:22
Alignment explanation
Indices: 3618127--3618173 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3618117 CTTAATTGTC
**
3618127 TTTTTTTGAAAAAGTTTGAGGG
1 TTTTTTTGAAAAAGTTTGAAAG
* *
3618149 TTTTTTTGATAAATTTTGAAAG
1 TTTTTTTGAAAAAGTTTGAAAG
3618171 TTT
1 TTT
3618174 AAGTACCCAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (22 bp):
TTTTTTTGAAAAAGTTTGAAAG
Found at i:3618255 original size:90 final size:88
Alignment explanation
Indices: 3618059--3618334 Score: 317
Period size: 90 Copynumber: 3.1 Consensus size: 88
3618049 TAACAGCTAA
* ** * * *
3618059 AGGGTTTTTTTGATGCA-TTTGACAGTTTAAGTACCCAATTCAGT-GAAAAAAA-TAAGGGCTTA
1 AGGGCTTTTTTGATAAATTTTGAAAGTTTAAGTACCCAATTGAGTGGAAAAAAAGTAAAGGCTTA
3618121 ATTGTCTTTTTTTGAAAAAGTTTG
66 ATTG-CTTTTTTTGAAAAAGTTTG
* * **
3618145 AGGGTTTTTTTGATAAATTTTGAAAGTTTAAGTACCCAATTGAGTGAGAAAAGAAAGTAATGATT
1 AGGGCTTTTTTGATAAATTTTGAAAGTTTAAGTACCCAATTGAGTG-GAAAA-AAAGTAAAGGCT
*
3618210 TAATTGCTTTTTTCTG-AAAGGTTTG
64 TAATTGCTTTTTT-TGAAAAAGTTTG
* * * * *
3618235 AGGGCTTTTTTGATATATTTTGAAAGTTTAAGTACTCAATCGATTGCGAAAATAAAGCAAAGGCT
1 AGGGCTTTTTTGATAAATTTTGAAAGTTTAAGTACCCAATTGAGTG-GAAAA-AAAGTAAAGGCT
*
3618300 TAATTACTTTTTTTGAAAAAGTTTG
64 TAATTGCTTTTTTTGAAAAAGTTTG
3618325 AGGGCTTTTT
1 AGGGCTTTTT
3618335 ACACCCTTAA
Statistics
Matches: 162, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
86 15 0.09
87 25 0.15
89 7 0.04
90 102 0.63
91 13 0.08
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (88 bp):
AGGGCTTTTTTGATAAATTTTGAAAGTTTAAGTACCCAATTGAGTGGAAAAAAAGTAAAGGCTTA
ATTGCTTTTTTTGAAAAAGTTTG
Found at i:3626674 original size:18 final size:17
Alignment explanation
Indices: 3626643--3626677 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3626633 TTTAAATTGA
*
3626643 TTAAAAATCGAAATTAT
1 TTAAAAATCAAAATTAT
3626660 TTAAAAATCCAAAATTAT
1 TTAAAAAT-CAAAATTAT
3626678 CTGATCCGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.54, C:0.09, G:0.03, T:0.34
Consensus pattern (17 bp):
TTAAAAATCAAAATTAT
Found at i:3628378 original size:15 final size:15
Alignment explanation
Indices: 3628344--3628393 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
3628334 AAATATAAGA
* *
3628344 AAATTAATAAATA-A
1 AAATTATTAAATATT
3628358 AAATTATTAAATATT
1 AAATTATTAAATATT
3628373 AAATTATTAAATATT
1 AAATTATTAAATATT
*
3628388 AGATTA
1 AAATTA
3628394 AATTTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
14 12 0.38
15 20 0.62
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (15 bp):
AAATTATTAAATATT
Found at i:3629611 original size:19 final size:19
Alignment explanation
Indices: 3629567--3629612 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
3629557 TTTTACCAAT
*
3629567 TTTTAAAATAAAAAAATTA
1 TTTTAATATAAAAAAATTA
3629586 TTTTAATATAAAAAAGA-TA
1 TTTTAATATAAAAAA-ATTA
3629605 TTTTAATA
1 TTTTAATA
3629613 GTTTTTCGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 24 0.96
20 1 0.04
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
TTTTAATATAAAAAAATTA
Found at i:3629944 original size:26 final size:27
Alignment explanation
Indices: 3629895--3629954 Score: 104
Period size: 26 Copynumber: 2.3 Consensus size: 27
3629885 AAAAATAACT
3629895 AAAATATTATAACTTTTTTTATTTACC
1 AAAATATTATAACTTTTTTTATTTACC
*
3629922 AAAATATTATAA-TTTTTTTATTTACT
1 AAAATATTATAACTTTTTTTATTTACC
3629948 AAAATAT
1 AAAATAT
3629955 ACAAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 20 0.62
27 12 0.38
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.52
Consensus pattern (27 bp):
AAAATATTATAACTTTTTTTATTTACC
Found at i:3630358 original size:19 final size:19
Alignment explanation
Indices: 3630334--3630397 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
3630324 ATTAAAATAG
3630334 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
3630353 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
3630371 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
3630390 TTTAATTT
1 TTTAATTT
3630398 TAAAAAAATT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 14 0.39
19 22 0.61
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:3630665 original size:18 final size:19
Alignment explanation
Indices: 3630626--3630684 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
3630616 ATTTTATATT
3630626 TTAAATGAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
* *
3630645 TTAAATGAGAATAG-TTTA
1 TTAAATGAAAATAGAGTTA
*
3630663 TTAAATTAAAATAGAGTTA
1 TTAAATGAAAATAGAGTTA
3630682 TTA
1 TTA
3630685 CTTAATTAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 15 0.44
19 19 0.56
ACGTcount: A:0.49, C:0.00, G:0.14, T:0.37
Consensus pattern (19 bp):
TTAAATGAAAATAGAGTTA
Found at i:3634649 original size:44 final size:43
Alignment explanation
Indices: 3634600--3634692 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 43
3634590 AACTTTTGTG
3634600 GCGCTTACATAAAAAAACACCGCTAAAGATCA-TGTTCTTTAGCA
1 GCGCTTA-ATAAAAAAACACCGCTAAA-ATCAGTGTTCTTTAGCA
* ** * * *
3634644 GCGCTT-GTTCAAAAACGCCGCTAAAATTAGTGTTCTTTAGCG
1 GCGCTTAATAAAAAAACACCGCTAAAATCAGTGTTCTTTAGCA
3634686 GCGCTTA
1 GCGCTTA
3634693 TTTCACAAAC
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
41 3 0.07
42 32 0.78
44 6 0.15
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (43 bp):
GCGCTTAATAAAAAAACACCGCTAAAATCAGTGTTCTTTAGCA
Found at i:3634665 original size:42 final size:43
Alignment explanation
Indices: 3634612--3634705 Score: 120
Period size: 42 Copynumber: 2.2 Consensus size: 43
3634602 GCTTACATAA
*
3634612 AAAAACACCGCTAAAGATCA-TGTTCTTTAGCAGCGCTT-GTTC
1 AAAAACGCCGCTAAA-ATCAGTGTTCTTTAGCAGCGCTTAGTTC
* * *
3634654 AAAAACGCCGCTAAAATTAGTGTTCTTTAGCGGCGCTTATTTC
1 AAAAACGCCGCTAAAATCAGTGTTCTTTAGCAGCGCTTAGTTC
*
3634697 ACAAACGCC
1 AAAAACGCC
3634706 ACTGTTTTGA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 3 0.07
42 31 0.69
43 11 0.24
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (43 bp):
AAAAACGCCGCTAAAATCAGTGTTCTTTAGCAGCGCTTAGTTC
Found at i:3635952 original size:18 final size:17
Alignment explanation
Indices: 3635919--3635957 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
3635909 TTGTATAAAT
3635919 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
3635937 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
3635954 TGTG
1 TGTG
3635958 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:3636210 original size:23 final size:23
Alignment explanation
Indices: 3636183--3636279 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
3636173 AGTGTTATTG
3636183 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
3636206 TTCAGTGGTAGCTTTGGCTAC--
1 ATCAGTGGTAGCTTCGGCTACAT
3636227 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
3636250 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
3636273 ATCAGTG
1 ATCAGTG
3636280 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
21 19 0.28
23 49 0.72
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:3636246 original size:44 final size:44
Alignment explanation
Indices: 3636183--3636272 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
3636173 AGTGTTATTG
* *
3636183 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTAC
1 ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
3636227 ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
1 ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
3636271 AT
1 AT
3636273 ATCAGTGTGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (44 bp):
ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
Found at i:3643285 original size:18 final size:17
Alignment explanation
Indices: 3643252--3643290 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
3643242 TTGTATAAAT
3643252 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
3643270 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
3643287 TGTG
1 TGTG
3643291 GAAGGAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:3643543 original size:23 final size:23
Alignment explanation
Indices: 3643516--3643612 Score: 162
Period size: 23 Copynumber: 4.3 Consensus size: 23
3643506 AGTGTTATTG
3643516 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
3643539 TTCAGTGGTAGCTTTGGCTAC--
1 ATCAGTGGTAGCTTCGGCTACAT
3643560 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
3643583 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
3643606 ATCAGTG
1 ATCAGTG
3643613 TGGCACTTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
21 19 0.28
23 49 0.72
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:3643579 original size:44 final size:44
Alignment explanation
Indices: 3643516--3643605 Score: 162
Period size: 44 Copynumber: 2.0 Consensus size: 44
3643506 AGTGTTATTG
* *
3643516 ATCAGTGGTAGCTTCGGCTACATTTCAGTGGTAGCTTTGGCTAC
1 ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
3643560 ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
1 ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
3643604 AT
1 AT
3643606 ATCAGTGTGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.32
Consensus pattern (44 bp):
ATCAGTGGTAGCTTCGGCTACATATCAGTGGTAGCTTCGGCTAC
Found at i:3645037 original size:12 final size:12
Alignment explanation
Indices: 3645020--3645059 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
3645010 TTTTGAACCT
*
3645020 CTGCTTCTATTG
1 CTGCTTCTATCG
*
3645032 CTGCTTCTCTCG
1 CTGCTTCTATCG
*
3645044 CTGCTTCTCTCG
1 CTGCTTCTATCG
3645056 CTGC
1 CTGC
3645060 GGCCTCTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.03, C:0.38, G:0.17, T:0.42
Consensus pattern (12 bp):
CTGCTTCTATCG
Found at i:3645070 original size:21 final size:21
Alignment explanation
Indices: 3645044--3645112 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
3645034 GCTTCTCTCG
*
3645044 CTGCTTCTCTCGCTGCGGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
3645065 CTGCTTGTCTCGCTGTAGCCT
1 CTGCTTCTCTCGCTGCAGCCT
* *
3645086 CTGCTTCCCTCGCTGCCGCCT
1 CTGCTTCTCTCGCTGCAGCCT
3645107 CTGCTT
1 CTGCTT
3645113 TAAGTTGCTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.01, C:0.42, G:0.22, T:0.35
Consensus pattern (21 bp):
CTGCTTCTCTCGCTGCAGCCT
Found at i:3650689 original size:18 final size:18
Alignment explanation
Indices: 3650668--3650728 Score: 77
Period size: 18 Copynumber: 3.4 Consensus size: 18
3650658 TGTATGCCCC
*
3650668 ATGTAAGTAATGTAAGCT
1 ATGTAAGTAATGTAAGAT
3650686 ATGTAAGTAATGTAAGAT
1 ATGTAAGTAATGTAAGAT
* * * *
3650704 ATTTAATTTATGTAAGTT
1 ATGTAAGTAATGTAAGAT
3650722 ATGTAAG
1 ATGTAAG
3650729 ATATTTAATT
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.39
Consensus pattern (18 bp):
ATGTAAGTAATGTAAGAT
Found at i:3650698 original size:27 final size:27
Alignment explanation
Indices: 3650668--3650759 Score: 78
Period size: 27 Copynumber: 3.4 Consensus size: 27
3650658 TGTATGCCCC
3650668 ATGTAAG-TAATGTAAGCTATGTAAGTA
1 ATGTAAGAT-ATGTAAGCTATGTAAGTA
* ** *
3650695 ATGTAAGATATTTAATTTATGTAAGTT
1 ATGTAAGATATGTAAGCTATGTAAGTA
* ** * *
3650722 ATGTAAGATATTTAATTTATGTAAATT
1 ATGTAAGATATGTAAGCTATGTAAGTA
*
3650749 ATGCAAGATAT
1 ATGTAAGATAT
3650760 TTAATTTACT
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
27 57 0.98
28 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.16, T:0.41
Consensus pattern (27 bp):
ATGTAAGATATGTAAGCTATGTAAGTA
Found at i:3650717 original size:36 final size:36
Alignment explanation
Indices: 3650678--3651494 Score: 435
Period size: 36 Copynumber: 22.7 Consensus size: 36
3650668 ATGTAAGTAA
* * * ** * *
3650678 TGTAAGCTATGTAAGTAATGTAAGATATTTAATTTA
1 TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* *
3650714 TGTAAGTTATGTAAGATATTTAATTTATGTAAATTA
1 TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* * * * * *
3650750 TGCAAGATATTTAATTTACTTAATTTATGTAAATTA
1 TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* * * * * *
3650786 TGCAA-TATATTTAATTTATGTAAGTTATGTAAATTA
1 TGTAAGT-TATGTAAGTTATTTAATTTATGTAAGTTA
* * * * *
3650822 CT-TAATTTATGTAAGTTATGTAAGTTATTTAATTTA
1 -TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* * ** *
3650858 CT-TAATTTATGTAAGTTATTCAAGATATTTAAGTTA
1 -TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* *
3650894 TGTAAGTTATGTAAATTACTTAATTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* * *
3650930 TGTAAGTTATTTAATTTACTTAATTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* * * * *
3650966 T-TCAAGATATTTAAGTTATGTAAGTTAT-TCAAGATA
1 TGT-AAGTTATGTAAGTTATTTAATTTATGT-AAGTTA
* * * ** * *
3651002 TTTAATTTATGTAAGTTATGTAAGATATTTAATTTA
1 TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* * * *
3651038 TGTAAATTATGCAAGATATTTAATTTACT-TAATTTA
1 TGTAAGTTATGTAAGTTATTTAATTTA-TGTAAGTTA
* *
3651074 TGTAAGTTATTTAA-TTAACTTAATTTATGTAAGTTA
1 TGTAAGTTATGTAAGTT-ATTTAATTTATGTAAGTTA
* * * * * *
3651110 TGCAAGATAT-TAATTTATGTAAGTTATGTAAATTA
1 TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* * ** * *
3651145 CT-TAATTTATGTAAGTTATGTAAGATATTTAATTTA
1 -TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* * ** * * *
3651181 CT-TAATTTATGTAAGTTATTCAAGATATTTAATTTT
1 -TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* *
3651217 TGTAAGTTATGTAAATTACTTAATTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* * * *
3651253 TGTAAGATATTTAATTTACTTAATTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* * * *
3651289 T-TCAAGATATTTAAGTTATGTAAGTTATGTGAA-TTA
1 TGT-AAGTTATGTAAGTTATTTAATTTATGT-AAGTTA
* * * * *
3651325 CT-TAATTTATGTAAGTTATGTAAGTTATTTAATTTA
1 -TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
* * *
3651361 CT-TAATTTATGTAAGTTATTTAATTAACT-TAATTTA
1 -TGTAAGTTATGTAAGTTATTTAATTTA-TGTAAGTTA
* * *
3651397 TGTAAGTTCTGCAAGATATTTAATTTATGTAAGTTA
1 TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
** * * *
3651433 -CCAAGAATTACT-TAATTTATGTAAGTTATGTAAGTTA
1 TGTAAG--TTA-TGTAAGTTATTTAATTTATGTAAGTTA
* * * *
3651470 TTTAATTTCTGTAAGTTATGTAATT
1 TGTAAGTTATGTAAGTTATTTAATT
3651495 AACCAAATGT
Statistics
Matches: 634, Mismatches: 120, Indels: 54
0.78 0.15 0.07
Matches are distributed among these distances:
35 38 0.06
36 561 0.88
37 32 0.05
38 3 0.00
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (36 bp):
TGTAAGTTATGTAAGTTATTTAATTTATGTAAGTTA
Found at i:3650760 original size:27 final size:27
Alignment explanation
Indices: 3650685--3651492 Score: 566
Period size: 27 Copynumber: 27.6 Consensus size: 27
3650675 TAATGTAAGC
*
3650685 TATGTAAGTAATGTAAGATATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
3650712 TATGTAAGTTATGTAAGATATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
* *
3650739 TATGTAAATTATGCAAGATATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
*
3650766 TACT-TAATTTATGTAAATTATGCAATATATTTAATT
1 TA-TGTAAGTTATGT--A--A-G----ATATTTAATT
*
3650802 TATGTAAGTTATGTAA-ATTACTTAATT
1 TATGTAAGTTATGTAAGA-TATTTAATT
3650829 TATGTAAGTTATGTAAGTTATTTAATTTACTTAATT
1 TATGTAAGTTATGTAAG--A--T-A--T--TTAATT
*
3650865 TATGTAAGTTAT-TCAAGATATTTAAGT
1 TATGTAAGTTATGT-AAGATATTTAATT
*
3650892 TATGTAAGTTATGTAA-ATTACTTAATT
1 TATGTAAGTTATGTAAGA-TATTTAATT
3650919 TATGTAAGTTATGTAAGTTATTTAATTTACTTAATT
1 TATGTAAGTTATGTAAG--A--T-A--T--TTAATT
*
3650955 TATGTAAGTTAT-TCAAGATATTTAAGT
1 TATGTAAGTTATGT-AAGATATTTAATT
3650982 TATGTAAGTTAT-TCAAGATATTTAATT
1 TATGTAAGTTATGT-AAGATATTTAATT
3651009 TATGTAAGTTATGTAAGATATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
* *
3651036 TATGTAAATTATGCAAGATATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
*
3651063 TACT-TAATTTATGTAAGTTATTTAATTAACTTAATT
1 TA-TGTAAGTTATGTAAG--A--T-A-T---TTAATT
*
3651099 TATGTAAGTTATGCAAGATA-TTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
*
3651125 TATGTAAGTTATGTAA-ATTACTTAATT
1 TATGTAAGTTATGTAAGA-TATTTAATT
3651152 TATGTAAGTTATGTAAGATATTTAATTTACTTAATT
1 TATGTAAGTTATGTAAG--A--T-A--T--TTAATT
3651188 TATGTAAGTTAT-TCAAGATATTTAATT
1 TATGTAAGTTATGT-AAGATATTTAATT
* *
3651215 TTTGTAAGTTATGTAA-ATTACTTAATT
1 TATGTAAGTTATGTAAGA-TATTTAATT
3651242 TATGTAAGTTATGTAAGATATTTAATTTACTTAATT
1 TATGTAAGTTATGTAAG--A--T-A--T--TTAATT
*
3651278 TATGTAAGTTAT-TCAAGATATTTAAGT
1 TATGTAAGTTATGT-AAGATATTTAATT
* *
3651305 TATGTAAGTTATGTGA-ATTACTTAATT
1 TATGTAAGTTATGTAAGA-TATTTAATT
*
3651332 TATGTAAGTTATGTAAGTTATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
*
3651359 TACT-TAATTTATGTAAGTTATTTAATTAACTTAATT
1 TA-TGTAAGTTATGTAAG--A--T-A-T---TTAATT
* *
3651395 TATGTAAGTTCTGCAAGATATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
** *
3651422 TATGTAAGTTA-CCAAGAATTACTTAATT
1 TATGTAAGTTATGTAAG-A-TATTTAATT
*
3651450 TATGTAAGTTATGTAAGTTATTTAATT
1 TATGTAAGTTATGTAAGATATTTAATT
*
3651477 TCTGTAAGTTATGTAA
1 TATGTAAGTTATGTAA
3651493 TTAACCAAAT
Statistics
Matches: 648, Mismatches: 46, Indels: 174
0.75 0.05 0.20
Matches are distributed among these distances:
25 1 0.00
26 31 0.05
27 387 0.60
28 26 0.04
29 9 0.01
30 5 0.01
31 17 0.03
32 14 0.02
33 2 0.00
34 7 0.01
35 7 0.01
36 142 0.22
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (27 bp):
TATGTAAGTTATGTAAGATATTTAATT
Found at i:3650800 original size:90 final size:90
Alignment explanation
Indices: 3650685--3651492 Score: 888
Period size: 90 Copynumber: 9.1 Consensus size: 90
3650675 TAATGTAAGC
* * *
3650685 TATGTAAGTAATGTAAGATATTTAATTTATGTAAGTTATGTAAGATATTTAATTTATGTAAATTA
1 TATGTAAGTTATGCAAGATATTTAATTTATGTAAGTTATGTAAGATATTTAATTTATGTAAGTTA
* *
3650750 TGCAAGATATTTAATTTACTTAATT
66 TGTAAGTTATTTAATTTACTTAATT
* * *
3650775 TATGTAAATTATGCAATATATTTAATTTATGTAAGTTATGTAA-ATTACTTAATTTATGTAAGTT
1 TATGTAAGTTATGCAAGATATTTAATTTATGTAAGTTATGTAAGA-TATTTAATTTATGTAAGTT
3650839 ATGTAAGTTATTTAATTTACTTAATT
65 ATGTAAGTTATTTAATTTACTTAATT
* * *
3650865 TATGTAAGTTATTCAAGATATTTAAGTTATGTAAGTTATGTAA-ATTACTTAATTTATGTAAGTT
1 TATGTAAGTTATGCAAGATATTTAATTTATGTAAGTTATGTAAGA-TATTTAATTTATGTAAGTT
3650929 ATGTAAGTTATTTAATTTACTTAATT
65 ATGTAAGTTATTTAATTTACTTAATT
* *
3650955 TATGTAAGTTATTCAAGATATTTAAGTTATGTAAGTTAT-TCAAGATATTTAATTTATGTAAGTT
1 TATGTAAGTTATGCAAGATATTTAATTTATGTAAGTTATGT-AAGATATTTAATTTATGTAAGTT
3651019 ATGTAAG--A--T-A--T--TTAATT
65 ATGTAAGTTATTTAATTTACTTAATT
* * * * *
3651036 TATGTAAATTATGCAAGATATTTAATTTACT-TAATTTATGTAAGTTATTTAATTAACT-TAATT
1 TATGTAAGTTATGCAAGATATTTAATTTA-TGTAAGTTATGTAAGATATTTAATTTA-TGTAAGT
** **
3651099 TATGTAAGTTATGCAAGATA-TTAATT
64 TATGTAAGTTATTTAATTTACTTAATT
* * *
3651125 TATGTAAGTTATGTAA-ATTACTTAATTTATGTAAGTTATGTAAGATATTTAATTTACT-TAATT
1 TATGTAAGTTATGCAAGA-TATTTAATTTATGTAAGTTATGTAAGATATTTAATTTA-TGTAAGT
* ** *
3651188 TATGTAAGTTATTCAAGATATTTAATT
64 TATGTAAGTTATTTAATTTACTTAATT
* * * *
3651215 TTTGTAAGTTATGTAA-ATTACTTAATTTATGTAAGTTATGTAAGATATTTAATTTACT-TAATT
1 TATGTAAGTTATGCAAGA-TATTTAATTTATGTAAGTTATGTAAGATATTTAATTTA-TGTAAGT
* ** * *
3651278 TATGTAAGTTATTCAAGATATTTAAGT
64 TATGTAAGTTATTTAATTTACTTAATT
* * * * *
3651305 TATGTAAGTTATGTGAA-TTACTTAATTTATGTAAGTTATGTAAGTTATTTAATTTACT-TAATT
1 TATGTAAGTTATG-CAAGATATTTAATTTATGTAAGTTATGTAAGATATTTAATTTA-TGTAAGT
*
3651368 TATGTAAGTTATTTAATTAACTTAATT
64 TATGTAAGTTATTTAATTTACTTAATT
* ** *
3651395 TATGTAAGTTCTGCAAGATATTTAATTTATGTAAGTTA-CCAAGAATTACTTAATTTATGTAAGT
1 TATGTAAGTTATGCAAGATATTTAATTTATGTAAGTTATGTAAG-A-TATTTAATTTATGTAAGT
*
3651459 TATGTAAGTTATTTAATTT-CTGTAAGT
64 TATGTAAGTTATTTAATTTACT-TAATT
3651486 TATGTAA
1 TATGTAA
3651493 TTAACCAAAT
Statistics
Matches: 644, Mismatches: 51, Indels: 45
0.87 0.07 0.06
Matches are distributed among these distances:
81 64 0.10
82 3 0.00
83 2 0.00
85 1 0.00
86 2 0.00
88 4 0.01
89 85 0.13
90 437 0.68
91 46 0.07
ACGTcount: A:0.36, C:0.04, G:0.12, T:0.48
Consensus pattern (90 bp):
TATGTAAGTTATGCAAGATATTTAATTTATGTAAGTTATGTAAGATATTTAATTTATGTAAGTTA
TGTAAGTTATTTAATTTACTTAATT
Found at i:3651458 original size:55 final size:56
Alignment explanation
Indices: 3651382--3651487 Score: 169
Period size: 55 Copynumber: 1.9 Consensus size: 56
3651372 TAAGTTATTT
*
3651382 AATTAACTTAATTTATGTAAGTTCTGCAAGATATTTAATTTATGTAAGTTACCAAG
1 AATTAACTTAATTTATGTAAGTTATGCAAGATATTTAATTTATGTAAGTTACCAAG
* * *
3651438 AATT-ACTTAATTTATGTAAGTTATGTAAGTTATTTAATTTCTGTAAGTTA
1 AATTAACTTAATTTATGTAAGTTATGCAAGATATTTAATTTATGTAAGTTA
3651488 TGTAATTAAC
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
55 42 0.91
56 4 0.09
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (56 bp):
AATTAACTTAATTTATGTAAGTTATGCAAGATATTTAATTTATGTAAGTTACCAAG
Found at i:3652138 original size:14 final size:14
Alignment explanation
Indices: 3652119--3652152 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3652109 CTCCATGGAA
*
3652119 ATATTTTTAATTAG
1 ATATTTTTAATTAC
3652133 ATA-TTTTAATTAC
1 ATATTTTTAATTAC
3652146 ATATTTT
1 ATATTTT
3652153 AATAAACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (14 bp):
ATATTTTTAATTAC
Found at i:3652141 original size:13 final size:13
Alignment explanation
Indices: 3652123--3652155 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
3652113 ATGGAAATAT
*
3652123 TTTTAATTAGATA
1 TTTTAATTACATA
3652136 TTTTAATTACATA
1 TTTTAATTACATA
3652149 TTTTAAT
1 TTTTAAT
3652156 AAACATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.58
Consensus pattern (13 bp):
TTTTAATTACATA
Found at i:3655109 original size:115 final size:114
Alignment explanation
Indices: 3654904--3655191 Score: 278
Period size: 115 Copynumber: 2.5 Consensus size: 114
3654894 GGTTAAGACC
* * * * *
3654904 AAAACTCTGCGTTTTGGTTAATA-CATTTTCCGGCGCTTATCAAAAAGCGCCGCTAATACAATGC
1 AAAACGCTGCGTTTTGGTGAATATC-TTTTGCGGCGCTTATAAAAAAGCGCCGCTAATACAATAC
* *** *
3654968 TATAGCGGCGATTTCTCGTGAACGCCACTAATTCCAGTATACATCAAG-A
65 TATAGCGGCGATATCTCAAAAACGCCACTAATTCCAATATACATCAAGTA
* * *
3655017 CTTAAACGCTGCGTTTTTGTGAATATCTTTTGCGGCGCTTATAAAAAAGCGCCGCTAATA-ATCT
1 --AAAACGCTGCGTTTTGGTGAATATCTTTTGCGGCGCTTATAAAAAAGCGCCGCTAATACA-AT
* * * * *
3655081 ACTTTAGTGGCGATATC-CAAAAAGCGCCACTAATTCTAATATACCTCATGTA
63 ACTATAGCGGCGATATCTCAAAAA-CGCCACTAATTCCAATATACATCAAGTA
* * * * ** *
3655133 AAAACGCAGCGTTTTGGTGAGTATATTTTGCGGCGCTTCTGCACAAGCGCCGCTAATAC
1 AAAACGCTGCGTTTTGGTGAATATCTTTTGCGGCGCTTATAAAAAAGCGCCGCTAATAC
3655192 TATGATTTAG
Statistics
Matches: 141, Mismatches: 27, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
114 53 0.38
115 86 0.61
116 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (114 bp):
AAAACGCTGCGTTTTGGTGAATATCTTTTGCGGCGCTTATAAAAAAGCGCCGCTAATACAATACT
ATAGCGGCGATATCTCAAAAACGCCACTAATTCCAATATACATCAAGTA
Found at i:3667876 original size:25 final size:24
Alignment explanation
Indices: 3667848--3667896 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3667838 ATTTTTACTA
*
3667848 TTTACCAAAAAAAGGTAAATAAATT
1 TTTAACAAAAAAA-GTAAATAAATT
* *
3667873 TTTAATAGAAAAAGTAAATAAATT
1 TTTAACAAAAAAAGTAAATAAATT
3667897 GATTGAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.31
Consensus pattern (24 bp):
TTTAACAAAAAAAGTAAATAAATT
Found at i:3668097 original size:21 final size:23
Alignment explanation
Indices: 3668073--3668119 Score: 62
Period size: 21 Copynumber: 2.1 Consensus size: 23
3668063 ACCAAACAAT
3668073 AAATAAACATA-TAA-TCTAGAA
1 AAATAAACATACTAAGTCTAGAA
* *
3668094 AAATAAATATACTAAGTTTAGAA
1 AAATAAACATACTAAGTCTAGAA
3668117 AAA
1 AAA
3668120 ACCACATCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 10 0.45
22 3 0.14
23 9 0.41
ACGTcount: A:0.62, C:0.06, G:0.06, T:0.26
Consensus pattern (23 bp):
AAATAAACATACTAAGTCTAGAA
Found at i:3670163 original size:21 final size:19
Alignment explanation
Indices: 3670119--3670155 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
3670109 GAAATAAATA
*
3670119 ATATACAATATATTTTTTT
1 ATATTCAATATATTTTTTT
*
3670138 ATATTCAATGTATTTTTT
1 ATATTCAATATATTTTTT
3670156 GTACTATTAT
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:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (19 bp):
ATATTCAATATATTTTTTT
Found at i:3673467 original size:31 final size:31
Alignment explanation
Indices: 3673419--3673498 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
3673409 TTAACTAGAA
* *
3673419 AATTTTACAATTT-AGTCATTAAACTGTTTAA-
1 AATTTT-C-ATTTAAGTCATTAAACTATTCAAT
3673450 AAGTTTTCATTTAAGTCATTAAACTATTCAAT
1 AA-TTTTCATTTAAGTCATTAAACTATTCAAT
*
3673482 AATTTTTATTTAAGTCA
1 AATTTTCATTTAAGTCA
3673499 CTGGATTGTT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
30 4 0.09
31 33 0.77
32 6 0.14
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (31 bp):
AATTTTCATTTAAGTCATTAAACTATTCAAT
Found at i:3674164 original size:16 final size:16
Alignment explanation
Indices: 3674145--3674176 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
3674135 CATTTAAGCT
*
3674145 ATTTTAAATTTATAAA
1 ATTTTAAATTAATAAA
3674161 ATTTTAAATTAATAAA
1 ATTTTAAATTAATAAA
3674177 GGTAGAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTTAAATTAATAAA
Found at i:3688502 original size:51 final size:51
Alignment explanation
Indices: 3688442--3688555 Score: 142
Period size: 51 Copynumber: 2.2 Consensus size: 51
3688432 AAATGTTGCA
* * * *
3688442 GACTGAATTTGTTAAA-CTAAAACTAAATTGACAGAATGTATAAA-TGTTATG
1 GACTAAATTTGTTAAATC-AAAACCAAATTGAAAGAATGTATAAACT-TTAAG
* *
3688493 GACTAAATTTGTTAAATCAAGACCAAATTGAAAGAATGTGTAAACTTTAAG
1 GACTAAATTTGTTAAATCAAAACCAAATTGAAAGAATGTATAAACTTTAAG
3688544 GACTAAATTTGT
1 GACTAAATTTGT
3688556 CAGTATATCA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
51 53 0.96
52 2 0.04
ACGTcount: A:0.43, C:0.09, G:0.16, T:0.32
Consensus pattern (51 bp):
GACTAAATTTGTTAAATCAAAACCAAATTGAAAGAATGTATAAACTTTAAG
Found at i:3711362 original size:208 final size:210
Alignment explanation
Indices: 3710996--3711414 Score: 644
Period size: 208 Copynumber: 2.0 Consensus size: 210
3710986 TTTGGTCTCT
* * *
3710996 ACCTCTTCCTTCGTGCATGCGTGCAATGGATTTGAAGACAACCTCAAAGTTATGATGTTTCCATA
1 ACCTCTTCCTTCGTGCACGCGTGCAATGGATTCGAAGACAACCTC-AAGTTATGATGTTCCCATA
*
3711061 TTTGATAAACAGTGGGACCATATAAACTTAACTCTAGGTCTCCAAATATTTGGATAGTGAGTTGC
65 TTTGATAAACAGTGGGACCATATAAACTTAACTCTAGGTCTCCAAATATTTGGATAGTGAGTTAC
* * *
3711126 AAGATAATAAACAAAGCAACAATTTAAAAGATTCGATAGAAAGGGAAGGTAATATTCTTCAAAGT
130 AAGATAATAAACAAAGCAACAATTTAAAAGATTCGATAAAAAGGAAAGGCAATATTCTTCAAAGT
*
3711191 AGGTTGAATATATTCA
195 AGGTTGAAGATATTCA
* *
3711207 ACCTC-TCCTTCGTGCACGTGTGCAATGGATTCGAAGACAATCTC-AGTTATGATGTTCCCATAT
1 ACCTCTTCCTTCGTGCACGCGTGCAATGGATTCGAAGACAACCTCAAGTTATGATGTTCCCATAT
* *
3711270 TTGATAAACAGTGGGACCATATAAACTTAACTCTAGGTCTCCAAGTATTTGGATAGTGAGTTACG
66 TTGATAAACAGTGGGACCATATAAACTTAACTCTAGGTCTCCAAATATTTGGATAGTGAGTTACA
* * * * * * *
3711335 AGATAATAACCAATGCGACAATTTAAAAGGTTTGATAAAAAGGAAAGGCAATATTTTTCGAAGTA
131 AGATAATAAACAAAGCAACAATTTAAAAGATTCGATAAAAAGGAAAGGCAATATTCTTCAAAGTA
3711400 GGTTGAAGATATTCA
196 GGTTGAAGATATTCA
3711415 CCATTGGAGA
Statistics
Matches: 189, Mismatches: 19, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
208 149 0.79
210 35 0.19
211 5 0.03
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (210 bp):
ACCTCTTCCTTCGTGCACGCGTGCAATGGATTCGAAGACAACCTCAAGTTATGATGTTCCCATAT
TTGATAAACAGTGGGACCATATAAACTTAACTCTAGGTCTCCAAATATTTGGATAGTGAGTTACA
AGATAATAAACAAAGCAACAATTTAAAAGATTCGATAAAAAGGAAAGGCAATATTCTTCAAAGTA
GGTTGAAGATATTCA
Found at i:3729463 original size:16 final size:16
Alignment explanation
Indices: 3729441--3729480 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
3729431 AACTTGAAAG
3729441 ACTTGAACCCAAAACA
1 ACTTGAACCCAAAACA
*
3729457 GCTTGAA-CCAAAACA
1 ACTTGAACCCAAAACA
3729472 ACTTGAACC
1 ACTTGAACC
3729481 TGGAATTGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.45, C:0.30, G:0.10, T:0.15
Consensus pattern (16 bp):
ACTTGAACCCAAAACA
Found at i:3731151 original size:3 final size:3
Alignment explanation
Indices: 3731143--3731168 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3731133 GGAAGAGCTA
3731143 GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GC
3731169 AGGAGCCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.35, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:3731540 original size:120 final size:119
Alignment explanation
Indices: 3731387--3731692 Score: 416
Period size: 123 Copynumber: 2.5 Consensus size: 119
3731377 AGAGGCAAGC
* **
3731387 TACCAGGTGAT-AGTTTTGGTGGTGGTGAGTATGAAGGTGATGAAGATTTTGGTGGTTTTGCTGC
1 TACCTGGTGATGA-TTTTGGTGGTGG-GAGTATGAAGGTGATGAAGATTTTGGTGGTTTTGCCCC
*
3731451 TCCTGGTGGTGTTTTACTAATGTATGGTCCTGGTGCAGCAGCTGGCGGTGGTACTT
64 TCCTGGTGGTGTGTTACTAATGTATGGTCCTGGTGCAGCAGCTGGCGGTGGTACTT
* *
3731507 TACCTGGTGGTGATTTTGGTGGTGGCGAGTATGAAGGTGACGACGAAGATTTTGGTGGTTTTGCC
1 TACCTGGTGATGATTTTGGTGGTGG-GAGTATGAAGGT---GATGAAGATTTTGGTGGTTTTGCC
* * *
3731572 CCTGCTGGTGGTGTGTTGCTACTGTATGGTCCTGGTGCAGCAGCTGGCGGTGGTACTT
62 CCTCCTGGTGGTGTGTTACTAATGTATGGTCCTGGTGCAGCAGCTGGCGGTGGTACTT
* *
3731630 TACCTGGTGATGATTTTGGTGGTGAAGGAAAGTGTGGAGGTGATGAAGATTTTGGTGGTTTTG
1 TACCTGGTGATGATTTTGGTGGTG--GG--AGTATGAAGGTGATGAAGATTTTGGTGGTTTTG
3731693 TTGGTGGTGA
Statistics
Matches: 164, Mismatches: 14, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
120 33 0.20
121 1 0.01
123 119 0.73
124 1 0.01
125 1 0.01
126 9 0.05
ACGTcount: A:0.16, C:0.11, G:0.38, T:0.35
Consensus pattern (119 bp):
TACCTGGTGATGATTTTGGTGGTGGGAGTATGAAGGTGATGAAGATTTTGGTGGTTTTGCCCCTC
CTGGTGGTGTGTTACTAATGTATGGTCCTGGTGCAGCAGCTGGCGGTGGTACTT
Done.