Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 143 of 144
Found at i:38105226 original size:14 final size:14
Alignment explanation
Indices: 38105207--38105236 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
38105197 AACAATTATC
*
38105207 TTTAATTTTGGGTT
1 TTTAATTCTGGGTT
38105221 TTTAATTCTGGGTT
1 TTTAATTCTGGGTT
38105235 TT
1 TT
38105237 ATTTGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.13, C:0.03, G:0.20, T:0.63
Consensus pattern (14 bp):
TTTAATTCTGGGTT
Found at i:38108682 original size:117 final size:116
Alignment explanation
Indices: 38108554--38108786 Score: 306
Period size: 117 Copynumber: 2.0 Consensus size: 116
38108544 AAAATAATCA
* * * **
38108554 AAATAATTTAAAAATTCTTGAAATTTTATTGTTAACAAAAATATTTATG-AATTTTTTTTGAAAT
1 AAATAACTTAAAAATTCTTGAAATTTTATTCTT-ACAAAAATATCTATGAAATAATTTTT-AAAT
* *
38108618 TTTGTGAAATAACATTAAAAAATTATAAATCAAAAATTATTTTAGCAAAATAT
64 GTTGTGAAATAACATTAAAAAATTATAAAACAAAAATTATTTTAGCAAAATAT
**
38108671 AAATAACTTAAAAATTCTTGAAATTTTATTCTTTTAAAAATATCTATGAAAATAATTTTTAAATG
1 AAATAACTTAAAAATTCTTGAAATTTTATTCTTACAAAAATATCTATG-AAATAATTTTTAAATG
* * * * *
38108736 TTGTGAAATGATATTCAAAAGTTATAAAACAAAATTTATTTTAGCAAAATA
65 TTGTGAAATAACATTAAAAAATTATAAAACAAAAATTATTTTAGCAAAATA
38108787 AATCTCAAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
116 12 0.12
117 80 0.80
118 8 0.08
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.41
Consensus pattern (116 bp):
AAATAACTTAAAAATTCTTGAAATTTTATTCTTACAAAAATATCTATGAAATAATTTTTAAATGT
TGTGAAATAACATTAAAAAATTATAAAACAAAAATTATTTTAGCAAAATAT
Found at i:38122045 original size:9 final size:9
Alignment explanation
Indices: 38122024--38122056 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
38122014 AAGAAACAAA
38122024 AATTTGCCAT
1 AATTTG-CAT
38122034 AATTTGCAT
1 AATTTGCAT
38122043 AATTTGCAT
1 AATTTGCAT
38122052 AATTT
1 AATTT
38122057 CAAGATGGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.33, C:0.12, G:0.09, T:0.45
Consensus pattern (9 bp):
AATTTGCAT
Found at i:38122571 original size:39 final size:38
Alignment explanation
Indices: 38122490--38122581 Score: 107
Period size: 39 Copynumber: 2.4 Consensus size: 38
38122480 TTTTCGTTCC
* *
38122490 ATTATTATTGGAGTTTTTTTTTTTTTTTCTGAAACAAC
1 ATTATTGTTGGAGTTTTTTTTTTTTTTTCTGAAACAAA
**
38122528 ATTATTGTTGGAGTTTTTATTTTTTTATTT-T-TTACAAGA
1 ATTATTGTTGGAGTTTTT-TTTTTTT-TTTCTGAAACAA-A
38122567 ATTATTGTTGGAGTT
1 ATTATTGTTGGAGTT
38122582 ATATACTTAG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
38 21 0.45
39 23 0.49
40 3 0.06
ACGTcount: A:0.23, C:0.04, G:0.14, T:0.59
Consensus pattern (38 bp):
ATTATTGTTGGAGTTTTTTTTTTTTTTTCTGAAACAAA
Found at i:38123113 original size:13 final size:13
Alignment explanation
Indices: 38123095--38123135 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
38123085 TAACTTTTAT
*
38123095 TATATTTTATAAA
1 TATATTTTAAAAA
38123108 TATATTTTAAAAA
1 TATATTTTAAAAA
38123121 TATATTTTAAAAA
1 TATATTTTAAAAA
38123134 TA
1 TA
38123136 AAATTAAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TATATTTTAAAAA
Found at i:38123805 original size:30 final size:31
Alignment explanation
Indices: 38123770--38123828 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
38123760 TCTAGTGACT
*
38123770 TAAAAT-AAAACTTTTAAATAATTTAATGTC
1 TAAAATGAAAACTTTTAAATAATTCAATGTC
* *
38123800 TAAAATGAAAATTTTTGAATAATTCAATG
1 TAAAATGAAAACTTTTAAATAATTCAATG
38123829 ATCATTTTGT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 6 0.24
31 19 0.76
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.39
Consensus pattern (31 bp):
TAAAATGAAAACTTTTAAATAATTCAATGTC
Found at i:38131013 original size:21 final size:20
Alignment explanation
Indices: 38130990--38131029 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
38130980 TTTTTTATAT
38130990 TTTTA-TTTTCAAAATTTTAA
1 TTTTACTTTTC-AAATTTTAA
*
38131010 TTTTACTTTTCAGATTTTAA
1 TTTTACTTTTCAAATTTTAA
38131030 ATTCAAATCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.30, C:0.07, G:0.03, T:0.60
Consensus pattern (20 bp):
TTTTACTTTTCAAATTTTAA
Found at i:38133281 original size:2 final size:2
Alignment explanation
Indices: 38133274--38133307 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
38133264 AACAAACATT
38133274 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
38133308 AGATTCTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:38133712 original size:16 final size:15
Alignment explanation
Indices: 38133689--38133718 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
38133679 TTCAACTTGA
38133689 AAGTTTAACAGAGTG
1 AAGTTTAACAGAGTG
38133704 AAGTCTTAACAGAGT
1 AAGT-TTAACAGAGT
38133719 CAGGGCTATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.10, G:0.23, T:0.27
Consensus pattern (15 bp):
AAGTTTAACAGAGTG
Found at i:38140875 original size:2 final size:2
Alignment explanation
Indices: 38140870--38140898 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
38140860 AAATCTCTCT
38140870 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38140899 GTATCGTAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38141729 original size:31 final size:31
Alignment explanation
Indices: 38141691--38141754 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
38141681 AACCTTAAAA
*
38141691 TTCAAGCCCCAATGTAGCAACAATTGTCAAG
1 TTCAAGCCCCAATGTAGCAACAATTATCAAG
* * * *
38141722 TTCAAGCCTCAGTGTTGGAACAATTATCAAG
1 TTCAAGCCCCAATGTAGCAACAATTATCAAG
38141753 TT
1 TT
38141755 TTAAAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (31 bp):
TTCAAGCCCCAATGTAGCAACAATTATCAAG
Found at i:38144135 original size:12 final size:12
Alignment explanation
Indices: 38144118--38144142 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
38144108 AAACATAATA
38144118 TTATTAATAGTT
1 TTATTAATAGTT
38144130 TTATTAATAGTT
1 TTATTAATAGTT
38144142 T
1 T
38144143 AGTTGGTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TTATTAATAGTT
Found at i:38144456 original size:3 final size:3
Alignment explanation
Indices: 38144448--38144479 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
38144438 TGCTAAAAGT
38144448 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
38144480 TTATCTTAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:38146609 original size:13 final size:14
Alignment explanation
Indices: 38146575--38146610 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
38146565 GAAAATCAAT
38146575 TTATTTTTCAAAAA
1 TTATTTTTCAAAAA
* *
38146589 TTATTTTTCGAAAG
1 TTATTTTTCAAAAA
38146603 TTATTTTT
1 TTATTTTT
38146611 AATGAAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (14 bp):
TTATTTTTCAAAAA
Found at i:38146768 original size:14 final size:15
Alignment explanation
Indices: 38146749--38146778 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
38146739 TGAGGACGTG
38146749 TCATACAAT-TTAAC
1 TCATACAATGTTAAC
38146763 TCATACAATGTTAAC
1 TCATACAATGTTAAC
38146778 T
1 T
38146779 AATTTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (15 bp):
TCATACAATGTTAAC
Found at i:38147664 original size:30 final size:31
Alignment explanation
Indices: 38147611--38147683 Score: 112
Period size: 30 Copynumber: 2.4 Consensus size: 31
38147601 AAAAAAAGTT
* *
38147611 AATAACTCAATAGCTTAAGTAAATTTTTTTG
1 AATAATTCAATAGCTTAAATAAATTTTTTTG
38147642 AATAATTCAATA-CTTAAATAAATTTTTTTG
1 AATAATTCAATAGCTTAAATAAATTTTTTTG
*
38147672 AATAATTTAATA
1 AATAATTCAATA
38147684 ATTTTTGAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 28 0.72
31 11 0.28
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (31 bp):
AATAATTCAATAGCTTAAATAAATTTTTTTG
Found at i:38148916 original size:45 final size:45
Alignment explanation
Indices: 38148852--38148940 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 45
38148842 CTAATATTTA
*
38148852 TAATTCTGTACGAGATATATATGGCATGTTACATATAACTGTTTG
1 TAATTCAGTACGAGATATATATGGCATGTTACATATAACTGTTTG
* *
38148897 TAATTCAGTATGAGATATATATGGCATGTTACATATAATTGTTT
1 TAATTCAGTACGAGATATATATGGCATGTTACATATAACTGTTT
38148941 ATTTATTTCA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.33, C:0.09, G:0.17, T:0.42
Consensus pattern (45 bp):
TAATTCAGTACGAGATATATATGGCATGTTACATATAACTGTTTG
Found at i:38150418 original size:14 final size:15
Alignment explanation
Indices: 38150401--38150438 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
38150391 TAAAAAAATC
*
38150401 AAATCCAAAAT-TAA
1 AAATCCAAAATCCAA
38150415 AAATCCAAAATCCAA
1 AAATCCAAAATCCAA
38150430 AAAT-CAAAA
1 AAATCCAAAA
38150439 CATAATATCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 16 0.73
15 6 0.27
ACGTcount: A:0.66, C:0.18, G:0.00, T:0.16
Consensus pattern (15 bp):
AAATCCAAAATCCAA
Found at i:38152654 original size:131 final size:128
Alignment explanation
Indices: 38152424--38152747 Score: 409
Period size: 130 Copynumber: 2.5 Consensus size: 128
38152414 ATTCTAATGC
* * *
38152424 TATGTTTAAGAACATGAAATTGAAAATTTG-GATTTAGGTTTCAATTACTCTATAAATCGTGGGG
1 TATGATTAAGAACATGAAATTGAAAA-TTGAG-TTTAGATTTCAATTACTCTATAAATCGTGAGG
*
38152488 AAAATGAAATTTATACTTAAAATTAGTTGAATTTCAGTATGATTACTATATCTCGAATTCAATTA
64 AAAATGAAATTTATACTTAAAATTAGATGAATTTCAGTATGATTA-TATATCTCGAATTCAATTA
38152553 G
128 G
* *
38152554 TATGATTAAGAACGTGAATTTGAAATATTAGAGTTTAGATTTCAATTACTCTATAAATC-TCGAG
1 TATGATTAAGAACATGAAATTGAAA-ATT-GAGTTTAGATTTCAATTACTCTATAAATCGT-GAG
* * * * *
38152618 GAGAATGAAATTTCTACTTAAAATTAGATGAGTTTCAGTATGATTATATATTTCGAATTCCATTA
63 GAAAATGAAATTTATACTTAAAATTAGATGAATTTCAGTATGATTATATATCTCGAATTCAATTA
38152683 G
128 G
* * * * * *
38152684 CATGATTAAGAACATGAACTTGAAAGCTCTGAGTTTAAATTTCAAGTACTCTTTAAATCGTGAG
1 TATGATTAAGAACATGAAATTGAAA-AT-TGAGTTTAGATTTCAATTACTCTATAAATCGTGAG
38152748 AAGAGTAAAA
Statistics
Matches: 169, Mismatches: 19, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
130 95 0.56
131 73 0.43
132 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (128 bp):
TATGATTAAGAACATGAAATTGAAAATTGAGTTTAGATTTCAATTACTCTATAAATCGTGAGGAA
AATGAAATTTATACTTAAAATTAGATGAATTTCAGTATGATTATATATCTCGAATTCAATTAG
Found at i:38152949 original size:83 final size:83
Alignment explanation
Indices: 38152838--38152997 Score: 189
Period size: 83 Copynumber: 1.9 Consensus size: 83
38152828 ACAAGGAGAA
** ** ** *** *
38152838 TAAAATGTTTACTTAAATTATTCAAGTTTTTGTTTGATTATATATTTTGAATTTA-TATAGTATG
1 TAAAATGCATACTTAAATTATTCAAGTTTCAGCATGATTATATATTCCAAATTCAGT-TAGTATG
38152902 ATTAAGAACATGAGGGGAG
65 ATTAAGAACATGAGGGGAG
*
38152921 TAAAATGCATACTTAAATTAGTT-GAGTTTCAGCATGATTATATATTCCAAATTCAGTTAGTATG
1 TAAAATGCATACTTAAATTA-TTCAAGTTTCAGCATGATTATATATTCCAAATTCAGTTAGTATG
38152985 ATTAAGAACATGA
65 ATTAAGAACATGA
38152998 ATTTGAGACA
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
83 61 0.95
84 3 0.05
ACGTcount: A:0.37, C:0.07, G:0.16, T:0.41
Consensus pattern (83 bp):
TAAAATGCATACTTAAATTATTCAAGTTTCAGCATGATTATATATTCCAAATTCAGTTAGTATGA
TTAAGAACATGAGGGGAG
Found at i:38162052 original size:25 final size:25
Alignment explanation
Indices: 38162024--38162075 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
38162014 CATGATTCTC
* *
38162024 AAATCACAAATAATAATAGTATAAT
1 AAATCACAAAAAAAAATAGTATAAT
***
38162049 AAATTTGAAAAAAAAATAGTATAAT
1 AAATCACAAAAAAAAATAGTATAAT
38162074 AA
1 AA
38162076 TTACGTTCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (25 bp):
AAATCACAAAAAAAAATAGTATAAT
Found at i:38162115 original size:2 final size:2
Alignment explanation
Indices: 38162108--38162169 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
38162098 ACAAATCTGA
38162108 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
38162150 AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT
38162170 GTTTTTTGAG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38165927 original size:29 final size:29
Alignment explanation
Indices: 38165871--38165936 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
38165861 ATAGGGATTA
* * *
38165871 GATCAAATTAATTCTTTTACAATTAAATG
1 GATCAAATTAATCCTTATACAATAAAATG
* *
38165900 GATCAATTTAATCCTTATACTATAAAATAG
1 GATCAAATTAATCCTTATACAATAAAAT-G
*
38165930 AATCAAA
1 GATCAAA
38165937 CAAAATCAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
29 23 0.79
30 6 0.21
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (29 bp):
GATCAAATTAATCCTTATACAATAAAATG
Found at i:38183424 original size:3 final size:3
Alignment explanation
Indices: 38183418--38183443 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
38183408 AATGATGATG
38183418 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
38183444 GCTGGCCTTT
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:38184724 original size:15 final size:14
Alignment explanation
Indices: 38184690--38184724 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
38184680 TTTTAAAAGT
38184690 AAAAACTAAAAAAA
1 AAAAACTAAAAAAA
38184704 ATAAAACTAAAAAGAA
1 A-AAAACTAAAAA-AA
38184720 AAAAA
1 AAAAA
38184725 GAGAAAGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 15 0.79
16 3 0.16
ACGTcount: A:0.83, C:0.06, G:0.03, T:0.09
Consensus pattern (14 bp):
AAAAACTAAAAAAA
Found at i:38185149 original size:32 final size:32
Alignment explanation
Indices: 38185113--38185173 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
38185103 TACTAGGTCT
38185113 AATTAAAATTTTTAAAA-AATTTGAAGAAATAG
1 AATT-AAATTTTTAAAATAATTTGAAGAAATAG
* *
38185145 AATTAATTTTTTAAAATATTTTGAAGAAA
1 AATTAAATTTTTAAAATAATTTGAAGAAA
38185174 GTAACGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 11 0.42
32 15 0.58
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.39
Consensus pattern (32 bp):
AATTAAATTTTTAAAATAATTTGAAGAAATAG
Found at i:38193401 original size:187 final size:178
Alignment explanation
Indices: 38193087--38193419 Score: 452
Period size: 187 Copynumber: 1.8 Consensus size: 178
38193077 CTATAAATCA
* * *
38193087 GATTTGAATTGTCACTTAACACTAAGAATTTAATGGTTAAACTAATGGAAGGACATGATTGATAC
1 GATTTGAATTGTCACTTAACACTAAAAATTTAATGATTAAACTAATGAAAGGACATGATTGATAC
* * * * *
38193152 GCTACTTGTTATACTCTTAGGCATTACTTGCATCGCAAAGAAAGAACCTATATTGTTATTGACAT
66 ACTACTTGTTATACCCTTAGGCATTACTTGCACCACAAAGAAAGAACCTACATTGTTATTGACAT
38193217 TTAGTAGGCAACGCCATGATACCATTGTCACAAATCCACTGAGGACAT
131 TTAGTAGGCAACGCCATGATACCATTGTCACAAATCCACTGAGGACAT
*
38193265 GATTT-AAGTTGTCACTTAACACTAAAAATTTAATGATTAAACTAATGAAAGGATATGATTGATG
1 GATTTGAA-TTGTCACTTAACACTAAAAATTTAATGATTAAACTAATGAAAGGACATGA-T--T-
* * *
38193329 CGATACTTACTATACTTGTTATACCCTTAGGCATTACTTGCACCACAAAGAAAGAGCTTACGTTG
61 -GATAC--AC--TACTTGTTATACCCTTAGGCATTACTTGCACCACAAAGAAAGAACCTACATTG
*
38193394 TTATTGACATTTAGTAGGCAATGCCA
121 TTATTGACATTTAGTAGGCAACGCCA
38193420 CAATGCAATG
Statistics
Matches: 132, Mismatches: 13, Indels: 11
0.85 0.08 0.07
Matches are distributed among these distances:
177 2 0.02
178 51 0.39
179 1 0.01
181 1 0.01
183 5 0.04
185 1 0.01
187 71 0.54
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (178 bp):
GATTTGAATTGTCACTTAACACTAAAAATTTAATGATTAAACTAATGAAAGGACATGATTGATAC
ACTACTTGTTATACCCTTAGGCATTACTTGCACCACAAAGAAAGAACCTACATTGTTATTGACAT
TTAGTAGGCAACGCCATGATACCATTGTCACAAATCCACTGAGGACAT
Found at i:38198854 original size:29 final size:30
Alignment explanation
Indices: 38198817--38198875 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
38198807 TATAATTTAA
*
38198817 TGTGCAATTGTATACAT-AAACTTTGATTT
1 TGTGCAATTATATACATGAAACTTTGATTT
* *
38198846 TGTGTAATTATATACATGAAATTTTGATTT
1 TGTGCAATTATATACATGAAACTTTGATTT
38198876 GATCAAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (30 bp):
TGTGCAATTATATACATGAAACTTTGATTT
Found at i:38203633 original size:35 final size:35
Alignment explanation
Indices: 38203587--38203662 Score: 93
Period size: 35 Copynumber: 2.2 Consensus size: 35
38203577 CTCTATATAC
* * *
38203587 TAATAATTAAATT-ATATTTTATCTTTT-TATTCAAA
1 TAATAAATAAATTAAT-TTTTATATTTTGGA-TCAAA
38203622 TAATAAATAAATTAATTTTTATATTTTGGATCAAA
1 TAATAAATAAATTAATTTTTATATTTTGGATCAAA
38203657 TAATAA
1 TAATAA
38203663 GTTGGTCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 33 0.92
36 3 0.08
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (35 bp):
TAATAAATAAATTAATTTTTATATTTTGGATCAAA
Found at i:38224674 original size:19 final size:21
Alignment explanation
Indices: 38224638--38224676 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38224628 TCTAATGCAA
38224638 TTTTAACATATAAAAATTGAT
1 TTTTAACATATAAAAATTGAT
38224659 TTTTAACAT-T-AAAATTGA
1 TTTTAACATATAAAAATTGA
38224677 ATGAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.44
20 1 0.06
21 9 0.50
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (21 bp):
TTTTAACATATAAAAATTGAT
Found at i:38231876 original size:127 final size:123
Alignment explanation
Indices: 38231687--38231935 Score: 322
Period size: 130 Copynumber: 2.0 Consensus size: 123
38231677 TCACTTTAAC
* *
38231687 GGCAGCAATTACCTATGTTATCAATTTGGACATACACATTATAAAAGTAACAAGACCAAATTATG
1 GGCAGCAATTACCTATGTTATCAATTTGAACATAAACATTATAAAAGTAACAAGACCAAATTATG
* * * *
38231752 TCAAATT-AGGACTAAATTATAATTTTC-AGTATAGTAGAGGGACAAAAATCATGGGTA
66 CCAAATTAAGGACCAAATTACAAATTTCTA-TATAGTAGAGGGACAAAAATCATGGGTA
* *
38231809 GGCAGTAATTACCTATGTTATCAATTTGAACCTACTAATAACATTATAAAAGTAATAAGACCAAA
1 GGCAGCAATTACCTATGTTATCAATTTGAA-C-A-T-A-AACATTATAAAAGTAACAAGACCAAA
* *
38231874 TTATGCCAAATTAGAAGGACCAAATTACAAATTTCTATATAGTAGAGGGGCCAAAATCATGG
61 TTATGCCAAATT--AAGGACCAAATTACAAATTTCTATATAGTAGAGGGACAAAAATCATGG
38231936 CTAGACCGAC
Statistics
Matches: 108, Mismatches: 10, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
122 28 0.26
123 1 0.01
124 1 0.01
125 1 0.01
126 1 0.01
127 35 0.32
130 40 0.37
131 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (123 bp):
GGCAGCAATTACCTATGTTATCAATTTGAACATAAACATTATAAAAGTAACAAGACCAAATTATG
CCAAATTAAGGACCAAATTACAAATTTCTATATAGTAGAGGGACAAAAATCATGGGTA
Found at i:38245489 original size:24 final size:23
Alignment explanation
Indices: 38245444--38245489 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
38245434 AAGGTAGAAA
* *
38245444 TATGCCACAAGGCAAAGGAAAAG
1 TATGCCACAAAGCAAAGAAAAAG
*
38245467 TATGCCACAAAAGCAAATAAAAA
1 TATGCCAC-AAAGCAAAGAAAAA
38245490 CTAAAAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.54, C:0.17, G:0.17, T:0.11
Consensus pattern (23 bp):
TATGCCACAAAGCAAAGAAAAAG
Found at i:38247191 original size:16 final size:16
Alignment explanation
Indices: 38247170--38247202 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
38247160 TCTAATAACA
*
38247170 AAACTTTAATTTGTAT
1 AAACTTTAATTTCTAT
38247186 AAACTTTAATTTCTAT
1 AAACTTTAATTTCTAT
38247202 A
1 A
38247203 CCCATAAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.48
Consensus pattern (16 bp):
AAACTTTAATTTCTAT
Found at i:38248916 original size:24 final size:24
Alignment explanation
Indices: 38248885--38248953 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
38248875 AGTTTGACTC
38248885 AAACAAATAAACATG-GTTTAATTG
1 AAACAAATAAACA-GAGTTTAATTG
*
38248909 AAATAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
*
38248933 AAACAATTAAACAGAGTTTAA
1 AAACAAATAAACAGAGTTTAA
38248954 CTAAAATATT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.54, C:0.07, G:0.12, T:0.28
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:38262150 original size:31 final size:30
Alignment explanation
Indices: 38262105--38262184 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 30
38262095 TTGTAACTTG
* *
38262105 ATACAT-AAATTTTAATTTGGTACAATTA-T
1 ATACATGAAACTTTAATTTGGTACAA-AAGT
*
38262134 ATACATGAAAACTTTAATTGTGGTTCAAAAGT
1 ATACATG-AAACTTTAATT-TGGTACAAAAGT
*
38262166 GTACATGAAACTTTAATTT
1 ATACATGAAACTTTAATTT
38262185 TAAGTTAACT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
29 6 0.14
30 1 0.02
31 22 0.51
32 14 0.33
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (30 bp):
ATACATGAAACTTTAATTTGGTACAAAAGT
Found at i:38262692 original size:73 final size:73
Alignment explanation
Indices: 38262601--38262743 Score: 286
Period size: 73 Copynumber: 2.0 Consensus size: 73
38262591 CTTGAATGAA
38262601 AAATAGTGAGTAAAAGGATAGAAGGAACAAAGAATTTCATGAATTACATGTTGATTAAGGAATCA
1 AAATAGTGAGTAAAAGGATAGAAGGAACAAAGAATTTCATGAATTACATGTTGATTAAGGAATCA
38262666 AATCATTC
66 AATCATTC
38262674 AAATAGTGAGTAAAAGGATAGAAGGAACAAAGAATTTCATGAATTACATGTTGATTAAGGAATCA
1 AAATAGTGAGTAAAAGGATAGAAGGAACAAAGAATTTCATGAATTACATGTTGATTAAGGAATCA
38262739 AATCA
66 AATCA
38262744 AATGAATGAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 70 1.00
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.25
Consensus pattern (73 bp):
AAATAGTGAGTAAAAGGATAGAAGGAACAAAGAATTTCATGAATTACATGTTGATTAAGGAATCA
AATCATTC
Found at i:38262754 original size:37 final size:37
Alignment explanation
Indices: 38262712--38262791 Score: 160
Period size: 37 Copynumber: 2.2 Consensus size: 37
38262702 AAAGAATTTC
38262712 ATGAATTACATGTTGATTAAGGAATCAAATCAAATGA
1 ATGAATTACATGTTGATTAAGGAATCAAATCAAATGA
38262749 ATGAATTACATGTTGATTAAGGAATCAAATCAAATGA
1 ATGAATTACATGTTGATTAAGGAATCAAATCAAATGA
38262786 ATGAAT
1 ATGAAT
38262792 GAAGGAACAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.30
Consensus pattern (37 bp):
ATGAATTACATGTTGATTAAGGAATCAAATCAAATGA
Found at i:38268528 original size:2 final size:2
Alignment explanation
Indices: 38268521--38268545 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38268511 AATCTAATGC
38268521 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
38268546 GTATGAACTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38270697 original size:27 final size:27
Alignment explanation
Indices: 38270667--38270730 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
38270657 AGGTCCAACA
38270667 CCAGGAGCTCCAGGTGGAGGTGGAGGT
1 CCAGGAGCTCCAGGTGGAGGTGGAGGT
38270694 CCAGGAGCTCCAGGTGGAGGTGGAGGT
1 CCAGGAGCTCCAGGTGGAGGTGGAGGT
*
38270721 CCCGGAGCTC
1 CCAGGAGCTC
38270731 GACCTCCAGG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.17, C:0.23, G:0.45, T:0.14
Consensus pattern (27 bp):
CCAGGAGCTCCAGGTGGAGGTGGAGGT
Found at i:38270827 original size:33 final size:33
Alignment explanation
Indices: 38270783--38270867 Score: 98
Period size: 33 Copynumber: 2.6 Consensus size: 33
38270773 CTCCAGGAAT
* *
38270783 AGGAGGCGGTGGTGGTGGTCCTCCAAGTGCGGG
1 AGGAGGTGGTGGTGGTGGTCCTCCAAATGCGGG
* * ** *
38270816 TGGAGGTGGTGGGGGTGGGGCTCCAAATGGGGG
1 AGGAGGTGGTGGTGGTGGTCCTCCAAATGCGGG
*
38270849 AGGAGGTGGAGGTGGTGGT
1 AGGAGGTGGTGGTGGTGGT
38270868 GAAGTAGAAG
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.13, C:0.11, G:0.58, T:0.19
Consensus pattern (33 bp):
AGGAGGTGGTGGTGGTGGTCCTCCAAATGCGGG
Found at i:38317121 original size:42 final size:42
Alignment explanation
Indices: 38317062--38317145 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
38317052 TAGATCTATG
*
38317062 CAGTGTCGATGGTGTATTTGTGTTTTTCATGCAACAAATTCT
1 CAGTGTCGATGCTGTATTTGTGTTTTTCATGCAACAAATTCT
* ** *
38317104 CAGTGTTGATGCTGTATTTGTGTTTTTGGTGGAACAAATTCT
1 CAGTGTCGATGCTGTATTTGTGTTTTTCATGCAACAAATTCT
38317146 ACGAAACTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.20, C:0.12, G:0.24, T:0.44
Consensus pattern (42 bp):
CAGTGTCGATGCTGTATTTGTGTTTTTCATGCAACAAATTCT
Found at i:38317818 original size:48 final size:48
Alignment explanation
Indices: 38317763--38317860 Score: 153
Period size: 48 Copynumber: 2.0 Consensus size: 48
38317753 TAATAATCAT
*
38317763 TTTCATTTTAGTCC-CTCAACTTTAATAAGCTTTCATTTTGGTCACTCA
1 TTTCATTTTAG-CCACTCAACTTTAACAAGCTTTCATTTTGGTCACTCA
* *
38317811 TTTCATTTTAGCCATTCAACTTTAACATGCTTTCATTTTGGTCACTCA
1 TTTCATTTTAGCCACTCAACTTTAACAAGCTTTCATTTTGGTCACTCA
38317859 TT
1 TT
38317861 AATTCAATGT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 2 0.04
48 44 0.96
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.47
Consensus pattern (48 bp):
TTTCATTTTAGCCACTCAACTTTAACAAGCTTTCATTTTGGTCACTCA
Found at i:38319136 original size:18 final size:17
Alignment explanation
Indices: 38319089--38319128 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
38319079 GGATGAGAAT
38319089 AATTTT-TTAATTGAGTA
1 AATTTTATTAATTGAG-A
38319106 AATTTTATTAATTGA-A
1 AATTTTATTAATTGAGA
38319122 AATTTTA
1 AATTTTA
38319129 AATTAATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.36
17 6 0.27
18 8 0.36
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (17 bp):
AATTTTATTAATTGAGA
Found at i:38321255 original size:50 final size:50
Alignment explanation
Indices: 38321190--38321298 Score: 173
Period size: 50 Copynumber: 2.2 Consensus size: 50
38321180 AAACATTGAG
* * *
38321190 GAGTTAGAAGTGATTTTATAGATAAAAGTAAGATGGATTTGAAAAAATTAA
1 GAGTT-GAAGTGATTTTATAGATAAAAATAAAATGGATTTGAAAAAATGAA
*
38321241 GAGTTGAAGTGATTTTATAGATAAAAATAAAATGGATTTGGAAAAATGAA
1 GAGTTGAAGTGATTTTATAGATAAAAATAAAATGGATTTGAAAAAATGAA
38321291 GAGTTGAA
1 GAGTTGAA
38321299 TTGCTTAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
50 49 0.91
51 5 0.09
ACGTcount: A:0.47, C:0.00, G:0.23, T:0.30
Consensus pattern (50 bp):
GAGTTGAAGTGATTTTATAGATAAAAATAAAATGGATTTGAAAAAATGAA
Found at i:38323310 original size:31 final size:31
Alignment explanation
Indices: 38323217--38323320 Score: 115
Period size: 31 Copynumber: 3.4 Consensus size: 31
38323207 AGTAGTTGAA
*
38323217 CAGGTACCAAAGTGGATCT-ATTTC-AAGTT
1 CAGGTACCAAAATGGATCTAATTTCAAAGTT
* * *
38323246 CGAGG-ACCAAAATGAAACTAGTTTCAAAGTT
1 C-AGGTACCAAAATGGATCTAATTTCAAAGTT
* * *
38323277 CAGGTACCAAACTGGATCTAATTGCAAAATT
1 CAGGTACCAAAATGGATCTAATTTCAAAGTT
38323308 CAGGTACCAAAAT
1 CAGGTACCAAAAT
38323321 AGACCTAGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 12 0.20
30 10 0.17
31 38 0.63
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.25
Consensus pattern (31 bp):
CAGGTACCAAAATGGATCTAATTTCAAAGTT
Found at i:38323338 original size:62 final size:60
Alignment explanation
Indices: 38323217--38323338 Score: 140
Period size: 62 Copynumber: 2.0 Consensus size: 60
38323207 AGTAGTTGAA
* * * *
38323217 CAGGTACCAAAGTGGATCTATTTCAAGTTCGAGGACCAAAATGAAACTAGTTTCAAAGTT
1 CAGGTACCAAACTGGATCTATTGCAAATTCGAGGACCAAAATGAAACTAGTTGCAAAGTT
* *
38323277 CAGGTACCAAACTGGATCTAATTGCAAAATTC-AGGTACCAAAAT-AGACCTAGTTGCCAAGTT
1 CAGGTACCAAACTGGATCT-ATTGC-AAATTCGAGG-ACCAAAATGA-AACTAGTTGCAAAGTT
38323339 AGGGGCAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
60 18 0.35
61 8 0.15
62 26 0.50
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (60 bp):
CAGGTACCAAACTGGATCTATTGCAAATTCGAGGACCAAAATGAAACTAGTTGCAAAGTT
Found at i:38333873 original size:30 final size:32
Alignment explanation
Indices: 38333814--38333877 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 32
38333804 TCTATGAAAG
38333814 TTGACAAATTATTTCCATAATAAAACTTAAAC
1 TTGACAAATTATTTCCATAATAAAACTTAAAC
* **
38333846 TTGAC-AATTATTTTCAT-ATCGAACTTAAAC
1 TTGACAAATTATTTCCATAATAAAACTTAAAC
38333876 TT
1 TT
38333878 TAAGATTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 13 0.45
31 11 0.38
32 5 0.17
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.39
Consensus pattern (32 bp):
TTGACAAATTATTTCCATAATAAAACTTAAAC
Found at i:38334463 original size:31 final size:32
Alignment explanation
Indices: 38334420--38334481 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
38334410 AGTGTTTTTA
*
38334420 TATTAAGATTTGA-ATTTTTTATTCAAATTAAT
1 TATTAAGATTTGACATTTATT-TTCAAATTAAT
*
38334452 TATTAA-ATTTGACATTTATTTTCATATTAA
1 TATTAAGATTTGACATTTATTTTCAAATTAA
38334482 AGATTGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (32 bp):
TATTAAGATTTGACATTTATTTTCAAATTAAT
Found at i:38334465 original size:56 final size:54
Alignment explanation
Indices: 38334399--38334509 Score: 125
Period size: 56 Copynumber: 2.0 Consensus size: 54
38334389 AGTTAGTTCA
* * **
38334399 TAAACTTGACAAGTGTTTTTATATT-AAGATTTGAATTTTTTATTCAAATTAATTAT
1 TAAACTTGACAAGTATTTTCATATTAAAGA-TTG-ATTTTTT-TAAAAATTAATTAT
* **
38334455 TAAATTTGACATTTATTTTCATATTAAAGATTGATTTTTTTAAAAATTAATTAT
1 TAAACTTGACAAGTATTTTCATATTAAAGATTGATTTTTTTAAAAATTAATTAT
38334509 T
1 T
38334510 TAAAAATACT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
54 13 0.28
55 7 0.15
56 23 0.49
57 4 0.09
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (54 bp):
TAAACTTGACAAGTATTTTCATATTAAAGATTGATTTTTTTAAAAATTAATTAT
Found at i:38340917 original size:22 final size:22
Alignment explanation
Indices: 38340889--38340934 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
38340879 ATAATAAATA
*
38340889 ATCTTTTAGGAATATATTGTAT
1 ATCTTTTACGAATATATTGTAT
* *
38340911 ATCTTTTACGCATATATTTTAT
1 ATCTTTTACGAATATATTGTAT
38340933 AT
1 AT
38340935 ATCTTTTCTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (22 bp):
ATCTTTTACGAATATATTGTAT
Found at i:38348784 original size:16 final size:15
Alignment explanation
Indices: 38348763--38348796 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
38348753 AATTAACAGT
38348763 TTAAAATCAATAAAAA
1 TTAAAATCAA-AAAAA
*
38348779 TTAAAATTAAAAAAA
1 TTAAAATCAAAAAAA
38348794 TTA
1 TTA
38348797 GATCTAACAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (15 bp):
TTAAAATCAAAAAAA
Found at i:38353040 original size:17 final size:17
Alignment explanation
Indices: 38353009--38353042 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38352999 TATTTTATTT
**
38353009 TATTTTTATTTTTTAAA
1 TATTTTTATAATTTAAA
38353026 TATTTTTATAATTTAAA
1 TATTTTTATAATTTAAA
38353043 ACGGTTTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTTTATAATTTAAA
Found at i:38355013 original size:4 final size:4
Alignment explanation
Indices: 38355004--38355040 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
38354994 GACCCTTTTG
* *
38355004 TGTA TGTA TGTA CGTA TGCA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA T
38355041 AATTGATTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.24, C:0.05, G:0.24, T:0.46
Consensus pattern (4 bp):
TGTA
Found at i:38356611 original size:13 final size:13
Alignment explanation
Indices: 38356593--38356617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38356583 AGTTCGATGA
38356593 TTTAAATAATTTT
1 TTTAAATAATTTT
38356606 TTTAAATAATTT
1 TTTAAATAATTT
38356618 AATAATAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTAAATAATTTT
Found at i:38367523 original size:6 final size:7
Alignment explanation
Indices: 38367498--38367531 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
38367488 TAATATATAA
38367498 AAAAATTT
1 AAAAA-TT
38367506 AAAAATT
1 AAAAATT
38367513 AAAAATT
1 AAAAATT
38367520 AAAAATT
1 AAAAATT
38367527 AAAAA
1 AAAAA
38367532 AATCTAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.81
8 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:38367530 original size:31 final size:31
Alignment explanation
Indices: 38367495--38367573 Score: 90
Period size: 31 Copynumber: 2.6 Consensus size: 31
38367485 ATATAATATA
*
38367495 TAAAAAAATTTAAAA-ATTAAAAATTAAAAAT
1 TAAAAAAATCTAAAATA-TAAAAATTAAAAAT
* * *
38367526 TAAAAAAATCTAAAATATATAATTTTAAAAT
1 TAAAAAAATCTAAAATATAAAAATTAAAAAT
*
38367557 TAAAAAAAT-AAAAATAT
1 TAAAAAAATCTAAAATAT
38367574 TATAGAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
30 7 0.17
31 34 0.81
32 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.30
Consensus pattern (31 bp):
TAAAAAAATCTAAAATATAAAAATTAAAAAT
Found at i:38367600 original size:8 final size:8
Alignment explanation
Indices: 38367498--38367620 Score: 58
Period size: 8 Copynumber: 15.0 Consensus size: 8
38367488 TAATATATAA
*
38367498 AAAAATTT
1 AAAAATAT
38367506 AAAAAT-T
1 AAAAATAT
38367513 AAAAAT-T
1 AAAAATAT
38367520 AAAAAT-T
1 AAAAATAT
*
38367527 AAAAAAAT
1 AAAAATAT
*
38367535 CTAAAATAT
1 -AAAAATAT
* * *
38367544 ATAATTTT
1 AAAAATAT
* *
38367552 AAAATTAA
1 AAAAATAT
38367560 AAAAATA-
1 AAAAATAT
38367567 AAAATATTAT
1 AAAA-A-TAT
*
38367577 AGAAAAATAG
1 --AAAAATAT
38367587 AAAAATAT
1 AAAAATAT
38367595 AAAAATA-
1 AAAAATAT
38367602 AATAAATAAAT
1 AA-AAAT--AT
38367613 AAAAATAT
1 AAAAATAT
38367621 TATATAAAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 22
0.72 0.10 0.17
Matches are distributed among these distances:
7 26 0.29
8 43 0.47
9 8 0.09
10 7 0.08
11 3 0.03
12 4 0.04
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.28
Consensus pattern (8 bp):
AAAAATAT
Found at i:38367631 original size:19 final size:17
Alignment explanation
Indices: 38367560--38367619 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 17
38367550 TTAAAATTAA
*
38367560 AAAAATAAAAATATTATAG
1 AAAAATAAAAATA--ATAT
*
38367579 AAAAATAGAAA-AATAT
1 AAAAATAAAAATAATAT
38367595 AAAAATAAATAAATAA-AT
1 AAAAAT-AA-AAATAATAT
38367613 AAAAATA
1 AAAAATA
38367620 TTATATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
16 9 0.26
17 2 0.06
18 12 0.34
19 12 0.34
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (17 bp):
AAAAATAAAAATAATAT
Found at i:38368609 original size:22 final size:22
Alignment explanation
Indices: 38368581--38368638 Score: 82
Period size: 22 Copynumber: 2.7 Consensus size: 22
38368571 CAGAAATAAG
38368581 AAAGATATATAATATATTCCTA
1 AAAGATATATAATATATTCCTA
* **
38368603 AAAGATATACAATATATTTGTA
1 AAAGATATATAATATATTCCTA
38368625 AAAGATA-ATAATAT
1 AAAGATATATAATAT
38368639 CGTACCAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 6 0.19
22 26 0.81
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.34
Consensus pattern (22 bp):
AAAGATATATAATATATTCCTA
Found at i:38385932 original size:21 final size:20
Alignment explanation
Indices: 38385894--38385933 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
38385884 TTGATTCTCT
38385894 TTAATAATGTAAAAATTAAG
1 TTAATAATGTAAAAATTAAG
* *
38385914 TTAATCAATTTAATAATTAA
1 TTAAT-AATGTAAAAATTAA
38385934 AGCATGTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.40
Consensus pattern (20 bp):
TTAATAATGTAAAAATTAAG
Found at i:38388073 original size:17 final size:16
Alignment explanation
Indices: 38388047--38388080 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
38388037 TTTTTTTTAC
38388047 TATTACAAATAAAATA
1 TATTACAAATAAAATA
*
38388063 TATTCACAAATATAATA
1 TATT-ACAAATAAAATA
38388080 T
1 T
38388081 TAATACAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.56, C:0.09, G:0.00, T:0.35
Consensus pattern (16 bp):
TATTACAAATAAAATA
Found at i:38397175 original size:14 final size:15
Alignment explanation
Indices: 38397143--38397176 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
38397133 TATTTTCAGT
38397143 TATTTTATTTTTCTA
1 TATTTTATTTTTCTA
38397158 -ATTTTATTTTT-TA
1 TATTTTATTTTTCTA
38397171 TATTTT
1 TATTTT
38397177 TTATAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (15 bp):
TATTTTATTTTTCTA
Found at i:38397185 original size:10 final size:9
Alignment explanation
Indices: 38397162--38397213 Score: 52
Period size: 9 Copynumber: 5.6 Consensus size: 9
38397152 TTTCTAATTT
38397162 TATTTTTTA
1 TATTTTTTA
38397171 TATTTTTTA
1 TATTTTTTA
* *
38397180 TAATTTATA
1 TATTTTTTA
38397189 TATTTTTCTGA
1 TATTTTT-T-A
38397200 -ATTTTTATA
1 TATTTTT-TA
38397209 TATTT
1 TATTT
38397214 ATTTTCGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 22 0.63
10 12 0.34
11 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (9 bp):
TATTTTTTA
Found at i:38400650 original size:20 final size:21
Alignment explanation
Indices: 38400625--38400670 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
38400615 TCACTCTATC
* *
38400625 ATATATTTACA-ATAAAGCAT
1 ATATATTAACATAGAAAGCAT
38400645 ATATATTAACATTAGAAAGCAT
1 ATATATTAACA-TAGAAAGCAT
38400667 ATAT
1 ATAT
38400671 GTTATACAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
22 12 0.55
ACGTcount: A:0.50, C:0.09, G:0.07, T:0.35
Consensus pattern (21 bp):
ATATATTAACATAGAAAGCAT
Found at i:38401287 original size:22 final size:21
Alignment explanation
Indices: 38401261--38401315 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
38401251 GAATTTTTTT
*
38401261 AAATTTAATTAGATTATTTCAA
1 AAATTTAATTAGAATATTT-AA
* *
38401283 AAATTTTATTA-AATGTTTAA
1 AAATTTAATTAGAATATTTAA
38401303 AAATTTTAATTAG
1 AAA-TTTAATTAG
38401316 GCCTTTCAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
20 5 0.19
21 12 0.44
22 10 0.37
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (21 bp):
AAATTTAATTAGAATATTTAA
Found at i:38402013 original size:21 final size:21
Alignment explanation
Indices: 38401964--38402019 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
38401954 TTAATATATT
38401964 ATTTGATATTT-AAA-TTTAA
1 ATTTGATATTTAAAATTTTAA
* *
38401983 ATTTAATATTTAAAATTTTTA
1 ATTTGATATTTAAAATTTTAA
*
38402004 ATTTGCTATTTAAAAT
1 ATTTGATATTTAAAAT
38402020 AATTTTTTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.32
20 3 0.10
21 18 0.58
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.54
Consensus pattern (21 bp):
ATTTGATATTTAAAATTTTAA
Found at i:38405501 original size:17 final size:18
Alignment explanation
Indices: 38405470--38405507 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
38405460 ACTCTCTAAA
38405470 AATTTAAAATAAAAT-CT
1 AATTTAAAATAAAATACT
38405487 AATTTAAAA-ATAAATACT
1 AATTTAAAATA-AAATACT
38405505 AAT
1 AAT
38405508 ATTACAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.05
17 13 0.68
18 5 0.26
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
AATTTAAAATAAAATACT
Found at i:38408602 original size:31 final size:30
Alignment explanation
Indices: 38408510--38408606 Score: 106
Period size: 31 Copynumber: 3.2 Consensus size: 30
38408500 AAGTAATTTG
38408510 ATACATAAATTTTGA-TTTGATTCAATTAT
1 ATACATAAATTTTGATTTTGATTCAATTAT
* * * ** *
38408539 ACATATAAAACTTTGATTTTGGCTCAAATAT
1 ATACAT-AAATTTTGATTTTGATTCAATTAT
*
38408570 ATACATGAAATTTTAATTTTGATTCAATTAT
1 ATACAT-AAATTTTGATTTTGATTCAATTAT
38408601 ATACAT
1 ATACAT
38408607 TTAAATAAAT
Statistics
Matches: 52, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 4 0.08
30 8 0.15
31 40 0.77
ACGTcount: A:0.39, C:0.09, G:0.07, T:0.44
Consensus pattern (30 bp):
ATACATAAATTTTGATTTTGATTCAATTAT
Found at i:38408603 original size:33 final size:32
Alignment explanation
Indices: 38408492--38408603 Score: 97
Period size: 31 Copynumber: 3.5 Consensus size: 32
38408482 ATATAGAAAC
* *
38408492 TTTGATTCAAGTAATTTGATACATAAATTTTGA-
1 TTTGATTCAA-TTATAT-ATACATAAATTTTGAT
* * *
38408525 TTTGATTCAATTATACATATA-AAACTTTGAT
1 TTTGATTCAATTATATATACATAAATTTTGAT
** *
38408556 TTTGGCTCAA--ATATATACATGAAATTTTAAT
1 TTTGATTCAATTATATATACAT-AAATTTTGAT
38408587 TTTGATTCAATTATATA
1 TTTGATTCAATTATATA
38408604 CATTTAAATA
Statistics
Matches: 61, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
29 7 0.11
30 8 0.13
31 28 0.46
32 3 0.05
33 15 0.25
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.46
Consensus pattern (32 bp):
TTTGATTCAATTATATATACATAAATTTTGAT
Found at i:38409247 original size:15 final size:16
Alignment explanation
Indices: 38409216--38409253 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
38409206 ATATACAACT
38409216 TTAAAAGTCAAATTATA
1 TTAAAAGTC-AATTATA
38409233 TTAAAAGTC-ATTATA
1 TTAAAAGTCAATTATA
38409248 TTAAAA
1 TTAAAA
38409254 ATAATGCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 12 0.57
17 9 0.43
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (16 bp):
TTAAAAGTCAATTATA
Found at i:38418094 original size:252 final size:247
Alignment explanation
Indices: 38417749--38418430 Score: 722
Period size: 252 Copynumber: 2.8 Consensus size: 247
38417739 AAGTATTTAG
* *
38417749 TATTTACTACCAAATGAATAAAAATTGAAAAAAAAAAAGATTATC--A-A-ACAATCAGACATAT
1 TATTTACTACCAAATGAATAAAAATTG----AAAAAATGATTATCAAACAGACAATAAGACATAT
* * * * * * *
38417810 TTACCACTCAACTAAACAAAATTAAAAACACTGAATCCTTTAGGAAATGAATAACCATGTTCATA
62 TTACAACTCAGCTAAACAAGATTAAAAACACTGAATTCTTTAGAAAATGAAGAACAATGTTCATA
* *
38417875 AAAAATGAATATAAAATTCTTCTGCAAACAAAATAGTTCCTGAAACTGAATACATTTCACCTTAA
127 AAAAATGAATATAAAATCCTTCTGCAAACAAAATAGTTCCTGAAACTGAATTCATTTCACCTT--
* *
38417940 AGCAGTGTCACCATTATCATCAT-C-AA-AAC-CCATTTCTTTTTTTCA-GGATTCTCGACACAG
190 ---AGTGTCACCATTATCAT-ATGCAAATAACACCACTTC-TTTTTTCATGG-TTCTC-A-ACAA
38418000 C
247 C
* * *
38418001 TATTTACTACCGAATGAATAAAAATTGAAAATATGATTATCAAACAGACAATAAGACACATTTAC
1 TATTTACTACCAAATGAATAAAAATTGAAAAAATGATTATCAAACAGACAATAAGACATATTTAC
* * *
38418066 TACTCAGTTAAACAAGATTTAAAACACTGAATTCTTTAGAAAATGAAGAACAATGTT--TGAAAA
66 AACTCAGCTAAACAAGATTAAAAACACTGAATTCTTTAGAAAATGAAGAACAATGTTCAT-AAAA
* * * * * *
38418129 AATGGATATAAAATCCTTTTGCTAACAACATAGTTCCTGAAACTTAATTCATTTCACATTAGTGT
130 AATGAATATAAAATCCTTCTGCAAACAAAATAGTTCCTGAAACTGAATTCATTTCACCTTAGTGT
38418194 CACCATTATCATATGCAAATAACACCACTTCTTTTTTCATGGTTCTCAACAAC
195 CACCATTATCATATGCAAATAACACCACTTCTTTTTTCATGGTTCTCAACAAC
* *
38418247 TATTTCCTACCAAATGAAT-AAAATATGAAACTAAAT-ATGATCAAAC-G---ATCAAG-CATA-
1 TATTTACTACCAAATGAATAAAAAT-TGAAA--AAATGATTATCAAACAGACAAT-AAGACATAT
* * *
38418304 TTA-AACTCAGCTGAACAAGATTAAAAACACTG-TTTCTATAGAAAATGAAGAACAATGTTCATA
62 TTACAACTCAGCTAAACAAGATTAAAAACACTGAATTCTTTAGAAAATGAAGAACAATGTTCATA
* * * * *
38418367 AAAAATGTATATAACATCCTGCTGCGAACAAAATAGATCCTGAGAACTGAATTCATTTCACCTT
127 AAAAATGAATATAAAATCCTTCTGCAAACAAAATAGTTCCTGA-AACTGAATTCATTTCACCTT
38418431 GAATTAGTGT
Statistics
Matches: 369, Mismatches: 44, Indels: 44
0.81 0.10 0.10
Matches are distributed among these distances:
240 25 0.07
241 62 0.17
242 22 0.06
243 5 0.01
244 3 0.01
245 7 0.02
246 45 0.12
247 12 0.03
248 31 0.08
249 8 0.02
250 2 0.01
251 57 0.15
252 90 0.24
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (247 bp):
TATTTACTACCAAATGAATAAAAATTGAAAAAATGATTATCAAACAGACAATAAGACATATTTAC
AACTCAGCTAAACAAGATTAAAAACACTGAATTCTTTAGAAAATGAAGAACAATGTTCATAAAAA
ATGAATATAAAATCCTTCTGCAAACAAAATAGTTCCTGAAACTGAATTCATTTCACCTTAGTGTC
ACCATTATCATATGCAAATAACACCACTTCTTTTTTCATGGTTCTCAACAAC
Found at i:38437126 original size:13 final size:13
Alignment explanation
Indices: 38437110--38437143 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
38437100 AAAATTTATA
38437110 TAATTTTATTTTT
1 TAATTTTATTTTT
*
38437123 TAATATTATTTTT
1 TAATTTTATTTTT
38437136 TGAATTTT
1 T-AATTTT
38437144 TAATTTATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (13 bp):
TAATTTTATTTTT
Found at i:38437814 original size:26 final size:28
Alignment explanation
Indices: 38437771--38437822 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 28
38437761 GAACCTAATA
*
38437771 CATCAATTGTTATTTAAAAAA-AAATTT
1 CATCAATTGTTATATAAAAAATAAATTT
*
38437798 CATC-ATTTTTATATAAAAAATAAAT
1 CATCAATTGTTATATAAAAAATAAAT
38437823 AAATATACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (28 bp):
CATCAATTGTTATATAAAAAATAAATTT
Found at i:38442198 original size:25 final size:25
Alignment explanation
Indices: 38442153--38442203 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
38442143 TTTGACAAAA
*
38442153 TTTTAAAGTATTTTTCATAAATATT
1 TTTTAAAGTATTTTTCATAAAAATT
* *
38442178 TTTTAAATTTATTTTT-TTAAAAATT
1 TTTTAAA-GTATTTTTCATAAAAATT
38442203 T
1 T
38442204 CAACTTTCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 15 0.68
26 7 0.32
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (25 bp):
TTTTAAAGTATTTTTCATAAAAATT
Found at i:38442544 original size:16 final size:16
Alignment explanation
Indices: 38442520--38442550 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38442510 TATTTGAATT
38442520 ATTTATATTTTATATG
1 ATTTATATTTTATATG
*
38442536 ATTTTTATTTTATAT
1 ATTTATATTTTATAT
38442551 AATTAATCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTATATTTTATATG
Found at i:38442650 original size:15 final size:16
Alignment explanation
Indices: 38442623--38442668 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
38442613 TTGAATTTTT
*
38442623 AAATTTATATATATTC
1 AAATTTATATATAATC
38442639 AAATTT-TATATAATC
1 AAATTTATATATAATC
38442654 AATATATTATA-ATAA
1 AA-AT-TTATATATAA
38442669 AATAAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 10 0.38
16 8 0.31
17 6 0.23
18 2 0.08
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (16 bp):
AAATTTATATATAATC
Found at i:38451067 original size:30 final size:30
Alignment explanation
Indices: 38451023--38451109 Score: 120
Period size: 30 Copynumber: 2.9 Consensus size: 30
38451013 ATCGACCGCA
* *
38451023 GGGAGAAACCAAGGAAAAGCACCGATGCCC
1 GGGAAAAACCAAGGAAAAGCACCGATACCC
* * *
38451053 GGGACAAGCCAAGGAAATGCACCGATACCC
1 GGGAAAAACCAAGGAAAAGCACCGATACCC
*
38451083 GGGAAAAACCAAGGAAAAGCATCGATA
1 GGGAAAAACCAAGGAAAAGCACCGATA
38451110 GGCCTGAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.43, C:0.24, G:0.28, T:0.06
Consensus pattern (30 bp):
GGGAAAAACCAAGGAAAAGCACCGATACCC
Found at i:38467788 original size:4 final size:4
Alignment explanation
Indices: 38467781--38467816 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
38467771 GTATGTATGT
38467781 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG ATGG
38467817 TAGCCTTTCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.25, C:0.00, G:0.50, T:0.25
Consensus pattern (4 bp):
ATGG
Found at i:38473607 original size:16 final size:16
Alignment explanation
Indices: 38473580--38473664 Score: 57
Period size: 18 Copynumber: 4.8 Consensus size: 16
38473570 ATTTGATTAA
38473580 ATAAATAATTAAAATTC
1 ATAAA-AATTAAAATTC
*
38473597 ATAAAAATTAAAAAATTA
1 ATAAAAATT--AAAATTC
38473615 ATAAAAATCT--AATTCAAC
1 ATAAAAAT-TAAAATT---C
38473633 AAGTAAATAATTAAAATTC
1 -A-TAAA-AATTAAAATTC
38473652 ATAAAAATTAAAA
1 ATAAAAATTAAAA
38473665 AATTAATAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 23
0.69 0.03 0.29
Matches are distributed among these distances:
15 4 0.07
16 12 0.22
17 9 0.16
18 15 0.27
19 3 0.05
20 5 0.09
21 3 0.05
22 4 0.07
ACGTcount: A:0.64, C:0.06, G:0.01, T:0.29
Consensus pattern (16 bp):
ATAAAAATTAAAATTC
Found at i:38473613 original size:18 final size:18
Alignment explanation
Indices: 38473590--38473677 Score: 74
Period size: 18 Copynumber: 4.8 Consensus size: 18
38473580 ATAAATAATT
*
38473590 AAAATTCATAAAAATTAA
1 AAAATTAATAAAAATTAA
38473608 AAAATTAATAAAAATCTAA
1 AAAATTAATAAAAAT-TAA
** *
38473627 TTCAA-CAAGTAAATAATT--
1 -AAAATTAA-TAAA-AATTAA
*
38473645 AAAATTCATAAAAATTAA
1 AAAATTAATAAAAATTAA
38473663 AAAATTAATAAAAAT
1 AAAATTAATAAAAAT
38473678 CTAATTCAAC
Statistics
Matches: 54, Mismatches: 9, Indels: 14
0.70 0.12 0.18
Matches are distributed among these distances:
16 4 0.07
17 6 0.11
18 29 0.54
19 5 0.09
20 7 0.13
21 3 0.06
ACGTcount: A:0.65, C:0.06, G:0.01, T:0.28
Consensus pattern (18 bp):
AAAATTAATAAAAATTAA
Found at i:38473613 original size:24 final size:24
Alignment explanation
Indices: 38473581--38473670 Score: 72
Period size: 24 Copynumber: 3.5 Consensus size: 24
38473571 TTTGATTAAA
*
38473581 TAAATAATTAAAATTCATAAAAAT
1 TAAAAAATTAAAATTCATAAAAAT
* * *
38473605 TAAAAAATTAATAAAAATCTAATTCAACAAG
1 TAAAAAA-T--T-AAAAT-TCA-T-AAAAAT
*
38473636 TAAATAATTAAAATTCATAAAAAT
1 TAAAAAATTAAAATTCATAAAAAT
38473660 TAAAAAATTAA
1 TAAAAAATTAA
38473671 TAAAAATCTA
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
24 20 0.40
25 2 0.04
26 2 0.04
27 6 0.12
28 6 0.12
29 2 0.04
30 2 0.04
31 10 0.20
ACGTcount: A:0.63, C:0.06, G:0.01, T:0.30
Consensus pattern (24 bp):
TAAAAAATTAAAATTCATAAAAAT
Found at i:38473627 original size:11 final size:10
Alignment explanation
Indices: 38473585--38473682 Score: 51
Period size: 10 Copynumber: 9.4 Consensus size: 10
38473575 ATTAAATAAA
*
38473585 TAATTAAAAT
1 TAATAAAAAT
*
38473595 TCATAAAAAT
1 TAATAAAAAT
38473605 T-A-AAAAAT
1 TAATAAAAAT
38473613 TAATAAAAAT
1 TAATAAAAAT
*
38473623 CTAATTCAACAAGTAAA
1 -TAA-T--A-AA--AAT
*
38473640 TAATTAAAAT
1 TAATAAAAAT
*
38473650 TCATAAAAAT
1 TAATAAAAAT
38473660 T-A-AAAAAT
1 TAATAAAAAT
38473668 TAATAAAAAT
1 TAATAAAAAT
38473678 CTAAT
1 -TAAT
38473683 TCAACAAGTA
Statistics
Matches: 69, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
8 14 0.20
9 4 0.06
10 32 0.46
11 7 0.10
12 3 0.04
14 1 0.01
15 3 0.04
16 3 0.04
17 2 0.03
ACGTcount: A:0.62, C:0.06, G:0.01, T:0.31
Consensus pattern (10 bp):
TAATAAAAAT
Found at i:38473642 original size:55 final size:55
Alignment explanation
Indices: 38473581--38473692 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
38473571 TTTGATTAAA
38473581 TAAATAATTAAAATTCATAAAAATTAAAAAATTAATAAAAATCTAATTCAACAAG
1 TAAATAATTAAAATTCATAAAAATTAAAAAATTAATAAAAATCTAATTCAACAAG
38473636 TAAATAATTAAAATTCATAAAAATTAAAAAATTAATAAAAATCTAATTCAACAAG
1 TAAATAATTAAAATTCATAAAAATTAAAAAATTAATAAAAATCTAATTCAACAAG
38473691 TA
1 TA
38473693 TTTTGCTTGG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (55 bp):
TAAATAATTAAAATTCATAAAAATTAAAAAATTAATAAAAATCTAATTCAACAAG
Found at i:38477248 original size:33 final size:33
Alignment explanation
Indices: 38477211--38477285 Score: 150
Period size: 33 Copynumber: 2.3 Consensus size: 33
38477201 CCAACCTAGT
38477211 TGCGAGCTCCACATCTGCAAACTCACCTAAAGC
1 TGCGAGCTCCACATCTGCAAACTCACCTAAAGC
38477244 TGCGAGCTCCACATCTGCAAACTCACCTAAAGC
1 TGCGAGCTCCACATCTGCAAACTCACCTAAAGC
38477277 TGCGAGCTC
1 TGCGAGCTC
38477286 ACTCAAGGAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.28, C:0.36, G:0.17, T:0.19
Consensus pattern (33 bp):
TGCGAGCTCCACATCTGCAAACTCACCTAAAGC
Found at i:38477286 original size:18 final size:18
Alignment explanation
Indices: 38477232--38477287 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
38477222 CATCTGCAAA
38477232 CTCACCTAAAGCTGCGAG
1 CTCACCTAAAGCTGCGAG
* * * *
38477250 CT--CC-ACATCTGCAAA
1 CTCACCTAAAGCTGCGAG
38477265 CTCACCTAAAGCTGCGAG
1 CTCACCTAAAGCTGCGAG
38477283 CTCAC
1 CTCAC
38477288 TCAAGGACGC
Statistics
Matches: 27, Mismatches: 8, Indels: 6
0.66 0.20 0.15
Matches are distributed among these distances:
15 9 0.33
16 2 0.07
17 2 0.07
18 14 0.52
ACGTcount: A:0.29, C:0.38, G:0.16, T:0.18
Consensus pattern (18 bp):
CTCACCTAAAGCTGCGAG
Found at i:38477586 original size:32 final size:30
Alignment explanation
Indices: 38477525--38477600 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 30
38477515 ATTTTACGTA
* *
38477525 TTTAATATTTAATTAATTTTTAAATATATT
1 TTTAATATTTAATTAATTATAAAATATATT
38477555 TTTAATTATATTAATTAA-TATAAAATAATATT
1 TTTAA-TAT-TTAATTAATTATAAAAT-ATATT
*
38477587 TTTTAT-TTTAATTA
1 TTTAATATTTAATTA
38477601 TTAAATATAA
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 7 0.17
30 6 0.15
31 10 0.25
32 17 0.43
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTTAATATTTAATTAATTATAAAATATATT
Found at i:38477604 original size:32 final size:34
Alignment explanation
Indices: 38477546--38477633 Score: 85
Period size: 34 Copynumber: 2.7 Consensus size: 34
38477536 ATTAATTTTT
* *
38477546 AAAT-ATATTTTTAATTAT-ATTAATT-AATATA
1 AAATAATATTTTTTATTTTAATTAATTAAATATA
38477577 AAATAATATTTTTTATTTTAATT-ATTAAATATA
1 AAATAATATTTTTTATTTTAATTAATTAAATATA
* * * *
38477610 ATTAGAATATATTTTATTTCAATT
1 A-AATAATATTTTTTATTTTAATT
38477634 GAAATGTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
31 4 0.09
32 15 0.32
33 10 0.21
34 18 0.38
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (34 bp):
AAATAATATTTTTTATTTTAATTAATTAAATATA
Found at i:38484521 original size:2 final size:2
Alignment explanation
Indices: 38484514--38484573 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
38484504 TACAAGGTCC
38484514 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
38484556 CT CT CT CT CT CT GT CT CT
1 CT CT CT CT CT CT CT CT CT
38484574 TATATACATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.00, C:0.48, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:38485808 original size:44 final size:43
Alignment explanation
Indices: 38485728--38485810 Score: 103
Period size: 44 Copynumber: 1.9 Consensus size: 43
38485718 GAGGCGATAA
** * *
38485728 GAATGATGTTGTTGTTAAGGTAAGTCCTCTTGAAGATGATTTT
1 GAATGATGTTACTGTTAAAGTAAGTCCTCTTAAAGATGATTTT
* *
38485771 GAATGATGTTACTGTTTAAAGTAAGTCTTGTTAAAGATGA
1 GAATGATGTTACTG-TTAAAGTAAGTCCTCTTAAAGATGA
38485811 CTTTAAAGCC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
43 12 0.36
44 21 0.64
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (43 bp):
GAATGATGTTACTGTTAAAGTAAGTCCTCTTAAAGATGATTTT
Found at i:38492782 original size:57 final size:58
Alignment explanation
Indices: 38492694--38492824 Score: 201
Period size: 57 Copynumber: 2.3 Consensus size: 58
38492684 TAATTATTAG
* * *
38492694 TATTTTTTTTGTCATTCGATTTTAAAAAATTA-CAAAATATTCTTTTAACCATTCAAT
1 TATTTTTTTTGTCATTCAATTTTAAAAAATTATAAAAATACTCTTTTAACCATTCAAT
*
38492751 TATTTTTTTTGTCATTCAATTTTAAAAAATTATAAAAATACTCTTTTAACCATTTAAT
1 TATTTTTTTTGTCATTCAATTTTAAAAAATTATAAAAATACTCTTTTAACCATTCAAT
*
38492809 TGTCTTTTTTTGTCAT
1 TAT-TTTTTTTGTCAT
38492825 CATAGTCATA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
57 31 0.46
58 24 0.36
59 12 0.18
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.52
Consensus pattern (58 bp):
TATTTTTTTTGTCATTCAATTTTAAAAAATTATAAAAATACTCTTTTAACCATTCAAT
Found at i:38495102 original size:22 final size:20
Alignment explanation
Indices: 38495077--38495117 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
38495067 AATTAGCTAA
*
38495077 AACATGATACAAAATACAAAAC
1 AACATGA-A-AAAAAACAAAAC
38495099 AACATGAAAAAAAACAAAA
1 AACATGAAAAAAAACAAAA
38495118 ATACGACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 1 0.06
22 7 0.39
ACGTcount: A:0.71, C:0.15, G:0.05, T:0.10
Consensus pattern (20 bp):
AACATGAAAAAAAACAAAAC
Found at i:38500916 original size:15 final size:15
Alignment explanation
Indices: 38500893--38500932 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
38500883 GACTAAATTT
*
38500893 TAAATTTAAAAAATA
1 TAAAATTAAAAAATA
*
38500908 TAAAATTAAAAACTA
1 TAAAATTAAAAAATA
*
38500923 TCAAATTAAA
1 TAAAATTAAA
38500933 TTAGAAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAATTAAAAAATA
Found at i:38529711 original size:24 final size:25
Alignment explanation
Indices: 38529670--38529716 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
38529660 TTAATCTAAT
* *
38529670 AATTCTTTAAGTTGA-TTTAATTGA
1 AATTCTTTAAATTCATTTTAATTGA
*
38529694 AATTTTTTAAATTCATTTTAATT
1 AATTCTTTAAATTCATTTTAATT
38529717 TTTTGAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (25 bp):
AATTCTTTAAATTCATTTTAATTGA
Found at i:38549906 original size:2 final size:2
Alignment explanation
Indices: 38549899--38549925 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
38549889 TTATTAATTA
38549899 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
38549926 AGATATAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38550424 original size:17 final size:18
Alignment explanation
Indices: 38550402--38550437 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
38550392 TAAATGAGTT
38550402 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
38550419 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
38550437 A
1 A
38550438 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:38561126 original size:19 final size:19
Alignment explanation
Indices: 38561085--38561126 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
38561075 TAATGTGGAT
**
38561085 AATTTTAATATTTTTTATG
1 AATTTTAATATTTTTTAAA
38561104 AATTTGTAA-ATTTTTTAAA
1 AATTT-TAATATTTTTTAAA
38561123 AATT
1 AATT
38561127 ATGAATATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 17 0.85
20 3 0.15
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
AATTTTAATATTTTTTAAA
Found at i:38563939 original size:14 final size:14
Alignment explanation
Indices: 38563920--38563948 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
38563910 ATTTTTTTGT
38563920 TAAATTTATTGATG
1 TAAATTTATTGATG
38563934 TAAATTTATTGATG
1 TAAATTTATTGATG
38563948 T
1 T
38563949 GATATTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TAAATTTATTGATG
Found at i:38574361 original size:30 final size:31
Alignment explanation
Indices: 38574322--38574387 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
38574312 CTTAACATCC
*
38574322 CAGTAATTTAAAT-AAAAATTTCAAATAGTT
1 CAGTGATTTAAATGAAAAATTTCAAATAGTT
* *
38574352 CAGTGATTTAAATGAAAACTTTTAAATAGTT
1 CAGTGATTTAAATGAAAAATTTCAAATAGTT
*
38574383 TAGTG
1 CAGTG
38574388 GTGACAGTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (31 bp):
CAGTGATTTAAATGAAAAATTTCAAATAGTT
Found at i:38610238 original size:16 final size:17
Alignment explanation
Indices: 38610217--38610249 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
38610207 ATCCTAATTT
38610217 AATTAA-TAAAATTTTA
1 AATTAATTAAAATTTTA
*
38610233 AATTAATTAATATTTTA
1 AATTAATTAAAATTTTA
38610250 TTTTGATATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTAATTAAAATTTTA
Found at i:38622038 original size:60 final size:61
Alignment explanation
Indices: 38621968--38622084 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 61
38621958 GAAACTAATA
* *
38621968 TATATCACAAAAATAGTATACATATTTCCACCAAG-TTTTTCAGTGTGTAGACTTAAAATG
1 TATATCACAAAAACAGTATACATATTTCCACCAAGTTTTTTCAGTGTGTAAACTTAAAATG
* * * *
38622028 TATATCACAAACACAGTATACATATTTTCTCCGAGTTTTTTCAGTGTGTAAACTTAA
1 TATATCACAAAAACAGTATACATATTTCCACCAAGTTTTTTCAGTGTGTAAACTTAA
38622085 CTATTTAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
60 30 0.60
61 20 0.40
ACGTcount: A:0.36, C:0.16, G:0.11, T:0.37
Consensus pattern (61 bp):
TATATCACAAAAACAGTATACATATTTCCACCAAGTTTTTTCAGTGTGTAAACTTAAAATG
Found at i:38628440 original size:116 final size:115
Alignment explanation
Indices: 38628200--38628764 Score: 442
Period size: 116 Copynumber: 4.9 Consensus size: 115
38628190 TTCTATATCG
* ** * ** * *
38628200 ATGCTAATACCTAACAATGTTTCATCG-CAGAATTATATTCCTTTTAAGTCATTGAACTAGGTCC
1 ATGCTAATACCTATCAATGGCTCATCGCCA-AATT-CATT-CTCATAAGTCATTGAACCAAGTCC
* * ** **
38628264 TACAAGCCTATTTCCCATGAGTCATGGGTGTTATGCCATATTTTGCAAAATTG
63 TACAAGCCTATTTCCCATGAGCCATGGGTGTTATGCCATATTGTGCAAGGTCA
* **
38628317 ATGCTAATACCTAACAATGGCTCATCGCCAAATGTCATTCTTGTAAGTCATTGAACCAAGTCCTA
1 ATGCTAATACCTATCAATGGCTCATCGCCAAAT-TCATTCTCATAAGTCATTGAACCAAGTCCTA
* * * *
38628382 CAAGCCAATTTCCCATGAGCCATTGGTGCTAAGCCATATTGTGCAAGGTCA
65 CAAGCCTATTTCCCATGAGCCATGGGTGTTATGCCATATTGTGCAAGGTCA
* * * ** * * * *
38628433 ATACTAATGCCCATTGAT-GTTCATTGCCAACATGT-ATTC-CCTAACTCATTGAACCAAGTCCT
1 ATGCTAATACCTATCAATGGCTCATCGCCAA-AT-TCATTCTCATAAGTCATTGAACCAAGTCCT
* * * * * * ** *
38628495 ATAAGCCCATTTCCAATGAGTCACGGGTGTTATCCCATACCGTTCAAGGTCA
64 ACAAGCCTATTTCCCATGAGCCATGGGTGTTATGCCATATTGTGCAAGGTCA
* * * * * * *
38628547 ATGCTAATAGCTATCAATGGCTCATTGCCAGAATACATTCCCAT-AGTTATTGTACTTAAGTCCT
1 ATGCTAATACCTATCAATGGCTCATCGCCA-AATTCATTCTCATAAGTCATTGAAC-CAAGTCCT
** *
38628611 ATGAGCCTATTTCCCATAAGCCATGGGTGTTATGCCATATTGTGCAAGGTCA
64 ACAAGCCTATTTCCCATGAGCCATGGGTGTTATGCCATATTGTGCAAGGTCA
* * * * * * *
38628663 ATGCTAATACCTATCAATGCCTCATCACCAAATTATATTC-CTATGAGTTATTGAACTAAAT-CT
1 ATGCTAATACCTATCAATGGCTCATCGCCAAATT-CATTCTC-ATAAGTCATTGAACCAAGTCCT
* * ** *
38628726 ACAAGCTTATTTCCAATGAGTAATGGGTGTAATGCCATA
64 ACAAGCCTATTTCCCATGAGCCATGGGTGTTATGCCATA
38628765 CTGGCTTGAT
Statistics
Matches: 359, Mismatches: 78, Indels: 24
0.78 0.17 0.05
Matches are distributed among these distances:
114 72 0.20
115 75 0.21
116 168 0.47
117 41 0.11
118 3 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.32
Consensus pattern (115 bp):
ATGCTAATACCTATCAATGGCTCATCGCCAAATTCATTCTCATAAGTCATTGAACCAAGTCCTAC
AAGCCTATTTCCCATGAGCCATGGGTGTTATGCCATATTGTGCAAGGTCA
Found at i:38631833 original size:28 final size:29
Alignment explanation
Indices: 38631764--38631833 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 29
38631754 ATAAAAGTGG
* *
38631764 AAATTTTATAAAAA-TGAAAAAAAGTATTT
1 AAATTTTA-AAAAATTGAAAAAAAGAATTA
*
38631793 AAATTTT-AGAAATTG-AAAAAAGAATTA
1 AAATTTTAAAAAATTGAAAAAAAGAATTA
38631820 AAATTTTAAAAAAT
1 AAATTTTAAAAAAT
38631834 ATATATTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 21 0.60
28 7 0.20
29 7 0.20
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (29 bp):
AAATTTTAAAAAATTGAAAAAAAGAATTA
Found at i:38644116 original size:28 final size:28
Alignment explanation
Indices: 38644080--38644159 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 28
38644070 CAAAAACCAT
*
38644080 GAATCTAAAATCTCGAACCTTAAACCCTA
1 GAATATAAAA-CTCGAACCTTAAACCCTA
* *
38644109 -AATATAAAACCCAAAACC-TAAACCCTA
1 GAATATAAAACTC-GAACCTTAAACCCTA
* *
38644136 GACTATTAAACTCGAACCTTAAAC
1 GAATATAAAACTCGAACCTTAAAC
38644160 TCATACCTCA
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
27 15 0.37
28 26 0.63
ACGTcount: A:0.46, C:0.28, G:0.05, T:0.21
Consensus pattern (28 bp):
GAATATAAAACTCGAACCTTAAACCCTA
Found at i:38646249 original size:30 final size:30
Alignment explanation
Indices: 38646183--38646254 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 30
38646173 AATATTTTAT
* * *
38646183 ATTTTTATAATTTTTAAAGGATTAAATTAA
1 ATTTTTATCATTTTTAAAGGATAAAAGTAA
38646213 ATTTTTATCATTTTTAGAAGGATAAAACGT-A
1 ATTTTTATCATTTTTA-AAGGATAAAA-GTAA
38646244 A-TTTTATCATT
1 ATTTTTATCATT
38646255 AAAATTTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 25 0.68
31 11 0.30
32 1 0.03
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.49
Consensus pattern (30 bp):
ATTTTTATCATTTTTAAAGGATAAAAGTAA
Found at i:38663602 original size:26 final size:26
Alignment explanation
Indices: 38663534--38663605 Score: 135
Period size: 26 Copynumber: 2.8 Consensus size: 26
38663524 AACTCTTTAA
*
38663534 CAAAAAATTAAATGTTCTGATTTCAC
1 CAAAAAATTAAATGTTTTGATTTCAC
38663560 CAAAAAATTAAATGTTTTGATTTCAC
1 CAAAAAATTAAATGTTTTGATTTCAC
38663586 CAAAAAATTAAATGTTTTGA
1 CAAAAAATTAAATGTTTTGA
38663606 ATCAAGCTAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 45 1.00
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.36
Consensus pattern (26 bp):
CAAAAAATTAAATGTTTTGATTTCAC
Found at i:38664094 original size:61 final size:61
Alignment explanation
Indices: 38663934--38664315 Score: 415
Period size: 60 Copynumber: 6.3 Consensus size: 61
38663924 AAAAATTGCA
** * *
38663934 TTTTTGGTGTTGGCCATTAAATGGCTGACACCCCCTATT-TC-A-AAAAAAAATTGC--A-T
1 TTTTTGGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAAATT-CAAATT
* * ** *
38663990 TTTTGGGTGTTGGCTATTGCATAACCGACACCCCCTATTTCTCGAGAAAAAAAATTCAATTT
1 TTTTTGGTGTTGGCCATTGCATGGCCGACACCCCCT-TTTCTCGAGAAAAAAAATTCAAATT
*
38664052 TTTTTAGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAG-AAAAAAATTCAAATT
1 TTTTTGGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAAATTCAAATT
* * * *
38664112 TTTTCGGTGTTGGTCATTGCATGGCCGACACCCACCTTTTTTCTCGAG-AAAAAAATTTAAAAT
1 TTTTTGGTGTTGGCCATTGCATGGCCGACACCC-CC--TTTTCTCGAGAAAAAAAATTCAAATT
* * ** *
38664175 TTTTTGATGTTGGCCATTGCATGGCCGACACCCCTTTTTCTCGAGAAAAAATTTTTAAATT
1 TTTTTGGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAAATTCAAATT
* * *
38664236 TTTTTGGTGTTGGCCATCAG-ATGGCCGACACCCCCCTTTTCTCAAGAAAAAAAAATTCACA-T
1 TTTTTGGTGTTGGCCAT-TGCATGGCCGACA-CCCCCTTTTCTCGAG-AAAAAAAATTCAAATT
*
38664298 TTTTGGGTGTTGGCCATT
1 TTTTTGGTGTTGGCCATT
38664316 TTCCTCGGAT
Statistics
Matches: 275, Mismatches: 37, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
56 29 0.11
57 2 0.01
58 2 0.01
59 2 0.01
60 64 0.23
61 49 0.18
62 64 0.23
63 63 0.23
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (61 bp):
TTTTTGGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAAATTCAAATT
Found at i:38664207 original size:123 final size:120
Alignment explanation
Indices: 38663934--38664315 Score: 416
Period size: 123 Copynumber: 3.1 Consensus size: 120
38663924 AAAAATTGCA
* ** * * *
38663934 TTTTTGGTGTTGGCCATTAAATGGCTGACACCCCCTATT-TC-AAAAAAAAATTGC--A-TTTTT
1 TTTTTGATGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAATT-CAAATTTTTT
* ** * *
38663994 GGGTGTTGGCTATTGCATAACCGACACCCCCTATTTCTCGAGAAAAAAAATTCAATT
65 CGGTGTTGGC-ATTGCATGGCCGACACCCCCTTTTTCTCGAGAAAAAAAATTCAAAT
*
38664051 TTTTTTAGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAATTCAAATTTTTT
1 TTTTTGA-TGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAATTCAAATTTTTT
* *
38664116 CGGTGTTGGTCATTGCATGGCCGACACCCACCTTTTTTCTCGAGAAAAAAATTTAAAAT
65 CGGTGTTGG-CATTGCATGGCCGACACCC-CC-TTTTTCTCGAGAAAAAAAATTCAAAT
* * *
38664175 TTTTTGATGTTGGCCATTGCATGGCCGACACCCCTTTTTCTCGAGAAAAAATTTTTAAATTTTTT
1 TTTTTGATGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAA-ATTCAAATTTTTT
* * * * *
38664240 TGGTGTTGGCCATCAG-ATGGCCGACACCCCCCTTTTCTCAAGAAAAAAAAATTCACAT
65 CGGTGTTGG-CAT-TGCATGGCCGACACCCCCTTTTTCTCGAG-AAAAAAAATTCAAAT
* *
38664298 TTTTGGGTGTTGGCCATT
1 TTTTTGATGTTGGCCATT
38664316 TTCCTCGGAT
Statistics
Matches: 225, Mismatches: 28, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
117 5 0.02
118 28 0.12
119 3 0.01
120 10 0.04
121 1 0.00
122 38 0.17
123 76 0.34
124 63 0.28
125 1 0.00
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (120 bp):
TTTTTGATGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAATTCAAATTTTTTC
GGTGTTGGCATTGCATGGCCGACACCCCCTTTTTCTCGAGAAAAAAAATTCAAAT
Found at i:38664307 original size:62 final size:60
Alignment explanation
Indices: 38663880--38664315 Score: 401
Period size: 60 Copynumber: 7.3 Consensus size: 60
38663870 AAAAAAAAAA
*** * * **
38663880 TTGGGTGTTGGCCATCAAATGACCGACA-TCCCTTTT-TCTTGAAAAAAAATTGC--ATTT
1 TTGGGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAAATT-CAAATTT
** * *
38663937 TT-GGTGTTGGCCATTAAATGGCTGACACCCCCTATT-TC-A-AAAAAAAATTGC--ATTT
1 TTGGGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAAATT-CAAATTT
* ** *
38663992 TTGGGTGTTGGCTATTGCATAACCGACACCCCCTATTTCTCGAGAAAAAAAATTCAATTTTT
1 TTGGGTGTTGGCCATTGCATGGCCGACACCCCCT-TTTCTCGAGAAAAAAAATTCAA-ATTT
**
38664054 TTTAGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAG-AAAAAAATTCAAATTTT
1 TTGGGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAAATTCAAA-TTT
* * * *
38664114 TTCGGTGTTGGTCATTGCATGGCCGACACCCACCTTTTTTCTCGAGAAAAAAATTTAAAATTT
1 TTGGGTGTTGGCCATTGCATGGCCGACACCC-CC--TTTTCTCGAGAAAAAAAATTCAAATTT
* * * ** *
38664177 TTTGATGTTGGCCATTGCATGGCCGACACCCCTTTTTCTCGAGAAAAAATTTTTAAATTTT
1 TTGGGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAAATTCAAA-TTT
* * * *
38664238 TTTGGTGTTGGCCATCAG-ATGGCCGACACCCCCCTTTTCTCAAGAAAAAAAAATTCACATTT
1 TTGGGTGTTGGCCAT-TGCATGGCCGACA-CCCCCTTTTCTCGAG-AAAAAAAATTCAAATTT
38664300 TTGGGTGTTGGCCATT
1 TTGGGTGTTGGCCATT
38664316 TTCCTCGGAT
Statistics
Matches: 320, Mismatches: 41, Indels: 32
0.81 0.10 0.08
Matches are distributed among these distances:
55 18 0.06
56 47 0.15
57 12 0.04
58 2 0.01
59 2 0.01
60 75 0.23
61 38 0.12
62 64 0.20
63 51 0.16
64 11 0.03
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.34
Consensus pattern (60 bp):
TTGGGTGTTGGCCATTGCATGGCCGACACCCCCTTTTCTCGAGAAAAAAAATTCAAATTT
Found at i:38665237 original size:30 final size:30
Alignment explanation
Indices: 38665183--38665252 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
38665173 AAAAAATAAT
** *
38665183 AATTAAAATATACAGGAAATTAGAAAGAAA
1 AATTAAAATATACAAAAAAATAGAAAGAAA
**
38665213 AATTAAAATATACAAAAAAATAGAAATTAA
1 AATTAAAATATACAAAAAAATAGAAAGAAA
*
38665243 ATTTAAAATA
1 AATTAAAATA
38665253 AAAACAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (30 bp):
AATTAAAATATACAAAAAAATAGAAAGAAA
Found at i:38665820 original size:55 final size:59
Alignment explanation
Indices: 38665680--38665874 Score: 168
Period size: 62 Copynumber: 3.3 Consensus size: 59
38665670 TTATAAAGAA
*** *
38665680 AAAAAGGGGTGTCGGCCATGCAATGACCAACACCAAAAAAATTTAAAATTTTTTTCTCGAG
1 AAAAAGGGGTGTCGGCCATTTGATGACCAACACC-AAAAAATGT-AAATTTTTTTCTCGAG
* *
38665741 AAATAAGGGGTGCCGGCCATTTGATGGCCAACACC-AAAAATGT-AATTTTTTT-T-GAG
1 AAA-AAGGGGTGTCGGCCATTTGATGACCAACACCAAAAAATGTAAATTTTTTTCTCGAG
* * * * * *
38665797 -AAAAGGGGATGTCGGCCATTTGATGACTAACACTTAAAAATTTTGAATTTTTTT-TCCTGACA
1 AAAAAGGGG-TGTCGGCCATTTGATGACCAACAC-CAAAAAATGTAAATTTTTTTCT-C-GA-G
38665859 AAAAAGGGGTGTCGGC
1 AAAAAGGGGTGTCGGC
38665875 TATGCAATTT
Statistics
Matches: 111, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
54 6 0.05
55 23 0.21
56 3 0.03
57 7 0.06
58 19 0.17
60 7 0.06
61 5 0.05
62 33 0.30
63 8 0.07
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (59 bp):
AAAAAGGGGTGTCGGCCATTTGATGACCAACACCAAAAAATGTAAATTTTTTTCTCGAG
Found at i:38699439 original size:41 final size:40
Alignment explanation
Indices: 38699391--38699491 Score: 100
Period size: 38 Copynumber: 2.6 Consensus size: 40
38699381 TCGACCTCGA
** *
38699391 GTCGATGAGACACTGGGTGTCATTATTTTACTTCGGATAG
1 GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
* ** *
38699431 ATTCGATGAGGTACT-GG-GT-ACCACTTTACTTCGGCTAG
1 -GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
*
38699469 GCCGATGAGACACTGGGTGTCAC
1 GTCGATGAGACACTGGGTGTCAC
38699492 TTTATTGCTT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
37 10 0.22
38 17 0.37
39 4 0.09
40 4 0.09
41 11 0.24
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (40 bp):
GTCGATGAGACACTGGGTGTCACCACTTTACTTCGGATAG
Found at i:38723528 original size:40 final size:40
Alignment explanation
Indices: 38723483--38723566 Score: 150
Period size: 40 Copynumber: 2.1 Consensus size: 40
38723473 TGAACACAGT
*
38723483 AAAATTACAGTTACTTTAAAATATTTGATATATGTATATA
1 AAAATTACAATTACTTTAAAATATTTGATATATGTATATA
*
38723523 AAAATTACAATTATTTTAAAATATTTGATATATGTATATA
1 AAAATTACAATTACTTTAAAATATTTGATATATGTATATA
38723563 AAAA
1 AAAA
38723567 ATATTTATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (40 bp):
AAAATTACAATTACTTTAAAATATTTGATATATGTATATA
Found at i:38724244 original size:24 final size:24
Alignment explanation
Indices: 38724212--38724259 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
38724202 TACGCTATTT
38724212 ATTTTTATTTTCAATCACCAGTCA
1 ATTTTTATTTTCAATCACCAGTCA
38724236 ATTTTTATTTTCAATCACCAGTCA
1 ATTTTTATTTTCAATCACCAGTCA
38724260 CCACTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.04, T:0.46
Consensus pattern (24 bp):
ATTTTTATTTTCAATCACCAGTCA
Found at i:38725139 original size:21 final size:22
Alignment explanation
Indices: 38725094--38725140 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
38725084 AAAATATGTA
*
38725094 TTTTGGGGTTTGAGGTTTGATG
1 TTTTGGGGTTTGAGGTTTGAGG
* *
38725116 TTTTGGGTTTTGA-GTTTGGGG
1 TTTTGGGGTTTGAGGTTTGAGG
38725137 TTTT
1 TTTT
38725141 AGATATTAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.06, C:0.00, G:0.38, T:0.55
Consensus pattern (22 bp):
TTTTGGGGTTTGAGGTTTGAGG
Found at i:38725182 original size:7 final size:7
Alignment explanation
Indices: 38725162--38725433 Score: 100
Period size: 7 Copynumber: 37.7 Consensus size: 7
38725152 GTTGGGATTC
38725162 GGGTTTA
1 GGGTTTA
* *
38725169 AGATTTA
1 GGGTTTA
38725176 GGGTTTA
1 GGGTTTA
* * *
38725183 GAGTATG
1 GGGTTTA
38725190 GGGTTTGA
1 GGGTTT-A
*
38725198 GGTTTTA
1 GGGTTTA
38725205 GGGTTTTAA
1 GGG-TTT-A
* *
38725214 TGGTTAA
1 GGGTTTA
* *
38725221 TGGTTAA
1 GGGTTTA
*
38725228 TGGTTTA
1 GGGTTTA
38725235 GGGTTTA
1 GGGTTTA
38725242 GGGTTTA
1 GGGTTTA
*
38725249 GGGTTTG
1 GGGTTTA
*
38725256 GGGTTTG
1 GGGTTTA
*
38725263 GGGTTTG
1 GGGTTTA
*
38725270 GGGTTTG
1 GGGTTTA
*
38725277 GGGTTCA
1 GGGTTTA
* *
38725284 GGGGGTTG
1 -GGGTTTA
38725292 GGGTGTGT-
1 GGGT-T-TA
*
38725300 GGTTTTA
1 GGGTTTA
*
38725307 AGGTTT-
1 GGGTTTA
38725313 GAGGTTT-
1 G-GGTTTA
*
38725320 GAGGTTTT
1 G-GGTTTA
* *
38725328 GAGTTTG
1 GGGTTTA
*
38725335 GGGTTTG
1 GGGTTTA
38725342 GGGTTTTA
1 GGG-TTTA
38725350 GGGTTTA
1 GGGTTTA
**
38725357 TAGTTTA
1 GGGTTTA
*
38725364 GAGTTTA
1 GGGTTTA
*
38725371 GAGTTTA
1 GGGTTTA
38725378 GGGTTTTA
1 GGG-TTTA
38725386 GGGTTTAA
1 GGGTTT-A
* **
38725394 GGGCTCG
1 GGGTTTA
* **
38725401 GGGCTCG
1 GGGTTTA
*
38725408 GGGCTTA
1 GGGTTTA
*
38725415 GGGCTTA
1 GGGTTTA
38725422 GGGTTTA
1 GGGTTTA
38725429 GGGTT
1 GGGTT
38725434 CGGGGCTCGG
Statistics
Matches: 212, Mismatches: 41, Indels: 24
0.77 0.15 0.09
Matches are distributed among these distances:
6 1 0.00
7 170 0.80
8 37 0.17
9 4 0.02
ACGTcount: A:0.14, C:0.03, G:0.42, T:0.41
Consensus pattern (7 bp):
GGGTTTA
Found at i:38725355 original size:36 final size:36
Alignment explanation
Indices: 38725323--38725392 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
38725313 GAGGTTTGAG
* * * *
38725323 GTTTTGAGTTTGGGGTTTGGGGTTTTAGGGTTTATA
1 GTTTAGAGTTTAGAGTTTAGGGTTTTAGGGTTTATA
38725359 GTTTAGAGTTTAGAGTTTAGGGTTTTAGGGTTTA
1 GTTTAGAGTTTAGAGTTTAGGGTTTTAGGGTTTA
38725393 AGGGCTCGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.49
Consensus pattern (36 bp):
GTTTAGAGTTTAGAGTTTAGGGTTTTAGGGTTTATA
Found at i:38725375 original size:43 final size:43
Alignment explanation
Indices: 38725236--38725383 Score: 104
Period size: 43 Copynumber: 3.4 Consensus size: 43
38725226 AATGGTTTAG
* * ** ** *
38725236 GGTTTAGGGTTTAGGGTTTGGGG-TTTGGGGTTTGGGGTTTGG
1 GGTTTAGAGTTTGGGGTTTGGGGTTTTAAGGTTTGAAGTTTGA
* * * * * *
38725278 GGTTCAGGGGGTTGGGGTGTGTGGTTTTAAGGTTTGAGGTTTGA
1 GGTTTA-GAGTTTGGGGTTTGGGGTTTTAAGGTTTGAAGTTTGA
* *
38725322 GGTTTTGAGTTTGGGGTTTGGGGTTTTAGGGTTT-ATAGTTT-A
1 GGTTTAGAGTTTGGGGTTTGGGGTTTTAAGGTTTGA-AGTTTGA
*
38725364 GAGTTTAGAGTTTAGGGTTT
1 G-GTTTAGAGTTTGGGGTTT
38725384 TAGGGTTTAA
Statistics
Matches: 83, Mismatches: 19, Indels: 7
0.76 0.17 0.06
Matches are distributed among these distances:
42 8 0.10
43 56 0.67
44 19 0.23
ACGTcount: A:0.11, C:0.01, G:0.45, T:0.44
Consensus pattern (43 bp):
GGTTTAGAGTTTGGGGTTTGGGGTTTTAAGGTTTGAAGTTTGA
Found at i:38725423 original size:36 final size:36
Alignment explanation
Indices: 38725374--38725453 Score: 117
Period size: 35 Copynumber: 2.2 Consensus size: 36
38725364 GAGTTTAGAG
*
38725374 TTTAGGGTTTTAGGGTTTAAGGGCTCGGGGCTCGGGGC
1 TTTAGGG-CTTAGGGTTT-AGGGCTCGGGGCTCGGGGC
*
38725412 -TTAGGGCTTAGGGTTTAGGGTTCGGGGCTCGGGGC
1 TTTAGGGCTTAGGGTTTAGGGCTCGGGGCTCGGGGC
38725447 TTTAGGG
1 TTTAGGG
38725454 TTTTGGGGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
35 18 0.46
36 15 0.38
37 6 0.15
ACGTcount: A:0.10, C:0.12, G:0.46, T:0.31
Consensus pattern (36 bp):
TTTAGGGCTTAGGGTTTAGGGCTCGGGGCTCGGGGC
Found at i:38725436 original size:28 final size:30
Alignment explanation
Indices: 38725405--38725468 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
38725395 GGCTCGGGGC
*
38725405 TCGGGGCTTAGGGC-TTAGGG-TTTAGGGT
1 TCGGGGCTCAGGGCTTTAGGGTTTTAGGGT
* *
38725433 TCGGGGCTCGGGGCTTTAGGGTTTTGGGGT
1 TCGGGGCTCAGGGCTTTAGGGTTTTAGGGT
38725463 TCGGGG
1 TCGGGG
38725469 TTCGGGGTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
28 12 0.39
29 6 0.19
30 13 0.42
ACGTcount: A:0.06, C:0.12, G:0.50, T:0.31
Consensus pattern (30 bp):
TCGGGGCTCAGGGCTTTAGGGTTTTAGGGT
Found at i:38725470 original size:7 final size:7
Alignment explanation
Indices: 38725429--38725484 Score: 58
Period size: 7 Copynumber: 7.7 Consensus size: 7
38725419 TTAGGGTTTA
38725429 GGGTTCG
1 GGGTTCG
*
38725436 GGGCTCG
1 GGGTTCG
*
38725443 GGGCTTTAG
1 GGG--TTCG
* *
38725452 GGTTTTG
1 GGGTTCG
38725459 GGGTTCG
1 GGGTTCG
38725466 GGGTTCG
1 GGGTTCG
38725473 GGGTTCG
1 GGGTTCG
38725480 GGGTT
1 GGGTT
38725485 TAGTTGATCT
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
7 36 0.90
9 4 0.10
ACGTcount: A:0.02, C:0.12, G:0.54, T:0.32
Consensus pattern (7 bp):
GGGTTCG
Done.