Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008719.1 Hibiscus syriacus cultivar Beakdansim tig00111774_pilon, whole genome shotgun sequence
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: 4817204
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 18
Found at i:940021 original size:45 final size:45
Alignment explanation
Indices: 939970--940059 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
939960 ATTGAGTGTA
939970 CAAGTATTGAAGATAAAATATGTAATTATATTAATTTTGTTAATT
1 CAAGTATTGAAGATAAAATATGTAATTATATTAATTTTGTTAATT
940015 CAAGTATTGAAGATAAAATATGTAATTATATTAATTTTGTTAATT
1 CAAGTATTGAAGATAAAATATGTAATTATATTAATTTTGTTAATT
940060 GCCATGTAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.42, C:0.02, G:0.11, T:0.44
Consensus pattern (45 bp):
CAAGTATTGAAGATAAAATATGTAATTATATTAATTTTGTTAATT
Found at i:940549 original size:21 final size:19
Alignment explanation
Indices: 940507--940550 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
940497 TTTTTAAAAT
* *
940507 TTTAATATCTTAAAATTTA
1 TTTAATATATTAAAAATTA
940526 TTTAATATAATTAAATAATTA
1 TTTAATAT-ATTAAA-AATTA
940547 TTTA
1 TTTA
940551 TAAATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 5 0.24
21 8 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTAATATATTAAAAATTA
Found at i:940557 original size:29 final size:30
Alignment explanation
Indices: 940525--940581 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
940515 CTTAAAATTT
*
940525 ATTTAATATAATTA-AATA-ATTATTTATAA
1 ATTTAATAT-ATTAGAATATATAATTTATAA
*
940554 ATTTTATATATTAGAATATATAATTTAT
1 ATTTAATATATTAGAATATATAATTTAT
940582 TTAAGTGCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.17
29 12 0.50
30 8 0.33
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
ATTTAATATATTAGAATATATAATTTATAA
Found at i:942256 original size:117 final size:117
Alignment explanation
Indices: 942038--942257 Score: 255
Period size: 117 Copynumber: 1.9 Consensus size: 117
942028 AAAAGTTATG
* * **
942038 TAATTGGTGATAATTTTAATTATAATAAAAAATATTACATTACGACGAATTTTAACCTAAAATGT
1 TAATTGGTAATAATTTTAATTATAACAAAAAATATTACATTACGACGAATTTTAACCTAAAACAT
***
942103 TACTCTATCTACTCTAAAAACTTTGTAATCACATAATACTATTAAAAATGTA
66 TACTCTATCTACTCTAAAAACTTCACAATCACATAATACTATTAAAAATGTA
* * * * **
942155 TAATTGGTAATAATTTTAGTTATAACAACAAATGTTACATTACGATGGGTTTTAATCC-AAAACA
1 TAATTGGTAATAATTTTAATTATAACAAAAAATATTACATTACGACGAATTTTAA-CCTAAAACA
* * * *
942219 TTATTCTGTCTACTCTAAAAAGTTACACAATTA-ATAATA
65 TTACTCTATCTACTCTAAAAACTT-CACAATCACATAATA
942258 ATTTCAATTA
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
117 78 0.93
118 6 0.07
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (117 bp):
TAATTGGTAATAATTTTAATTATAACAAAAAATATTACATTACGACGAATTTTAACCTAAAACAT
TACTCTATCTACTCTAAAAACTTCACAATCACATAATACTATTAAAAATGTA
Found at i:942660 original size:12 final size:12
Alignment explanation
Indices: 942643--942679 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
942633 CTAGGAACAA
942643 ACACACATACCT
1 ACACACATACCT
942655 ACACACATACCT
1 ACACACATACCT
*
942667 ACACATATACCT
1 ACACACATACCT
942679 A
1 A
942680 ATTTACCACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.43, C:0.38, G:0.00, T:0.19
Consensus pattern (12 bp):
ACACACATACCT
Found at i:943062 original size:27 final size:27
Alignment explanation
Indices: 943029--943092 Score: 112
Period size: 27 Copynumber: 2.4 Consensus size: 27
943019 AATTTAGTTT
943029 TCATTTTAATTAAAT-TGGTTGATTTAA
1 TCATTTTAATT-AATCTGGTTGATTTAA
943056 TCATTTTAATTAATCTGGTTGATTTAA
1 TCATTTTAATTAATCTGGTTGATTTAA
943083 TCATTTTAAT
1 TCATTTTAAT
943093 ATATATTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 3 0.08
27 33 0.92
ACGTcount: A:0.31, C:0.06, G:0.09, T:0.53
Consensus pattern (27 bp):
TCATTTTAATTAATCTGGTTGATTTAA
Found at i:945165 original size:49 final size:49
Alignment explanation
Indices: 945093--945190 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
945083 AAAGAAGAAC
945093 CAATACTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTCAAGGG
1 CAATACTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTCAAGGG
945142 CAATACTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTCAAGGG
1 CAATACTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTCAAGGG
945191 GTGGTATTAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (49 bp):
CAATACTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTCAAGGG
Found at i:950209 original size:15 final size:15
Alignment explanation
Indices: 950169--950211 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
950159 AAAGGAAATA
*
950169 GAAATGTAAAGAATT
1 GAAATGAAAAGAATT
*
950184 GAAACGAAAAGAATT
1 GAAATGAAAAGAATT
*
950199 GAAATGGAAAGAA
1 GAAATGAAAAGAA
950212 ATGTTATCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.58, C:0.02, G:0.23, T:0.16
Consensus pattern (15 bp):
GAAATGAAAAGAATT
Found at i:950460 original size:36 final size:35
Alignment explanation
Indices: 950362--950471 Score: 116
Period size: 36 Copynumber: 3.1 Consensus size: 35
950352 TATGGTTATT
* * * *
950362 TAGGCGTGAAATGGTGATAGAAGATGGTAATGATA
1 TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
* *
950397 TAGGCGTGCAATGGTA-ATGAAAAGATGGTGATGTTA
1 TAGGCGTGAAATGG-AGATG-GAAGATGGTGATGTTA
*
950433 TAGGCGTGAAAATGGAGATGGATGATGGTGATGTT-
1 TAGGCGTG-AAATGGAGATGGAAGATGGTGATGTTA
950468 TAGG
1 TAGG
950472 TAGTATCTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
35 19 0.31
36 35 0.56
37 8 0.13
ACGTcount: A:0.33, C:0.04, G:0.36, T:0.27
Consensus pattern (35 bp):
TAGGCGTGAAATGGAGATGGAAGATGGTGATGTTA
Found at i:954189 original size:6 final size:6
Alignment explanation
Indices: 954175--954209 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
954165 TGTAGGAGTC
*
954175 TTTTCT TTTTGT TTTTCT TCTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT T-TTTCT TTTTCT TTTT
954210 GTTGCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (6 bp):
TTTTCT
Found at i:954204 original size:13 final size:12
Alignment explanation
Indices: 954175--954209 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
954165 TGTAGGAGTC
*
954175 TTTTCTTTTTGT
1 TTTTCTTTTTCT
954187 TTTTCTTCTTTCT
1 TTTTCTT-TTTCT
954200 TTTTCTTTTT
1 TTTTCTTTTT
954210 GTTGCTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.48
13 11 0.52
ACGTcount: A:0.00, C:0.14, G:0.03, T:0.83
Consensus pattern (12 bp):
TTTTCTTTTTCT
Found at i:954562 original size:36 final size:35
Alignment explanation
Indices: 954478--954579 Score: 118
Period size: 35 Copynumber: 2.9 Consensus size: 35
954468 ATTTAGGCAC
* * * * *
954478 GAAATGGTGATAGAAGATGGTAATGATATAAGCGT
1 GAAATGGAGATGGAAGATGGTGATGTTATAGGCGT
*
954513 GCAATGGTA-ATGGAAGATGGTGATGTTATAGGCGT
1 GAAATGG-AGATGGAAGATGGTGATGTTATAGGCGT
954548 GAAAATGGAGATGGAAGATGGTGATGTT-TAGG
1 G-AAATGGAGATGGAAGATGGTGATGTTATAGG
954580 TAGTATCTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
35 34 0.60
36 23 0.40
ACGTcount: A:0.34, C:0.03, G:0.36, T:0.26
Consensus pattern (35 bp):
GAAATGGAGATGGAAGATGGTGATGTTATAGGCGT
Found at i:959986 original size:21 final size:22
Alignment explanation
Indices: 959931--959986 Score: 55
Period size: 23 Copynumber: 2.5 Consensus size: 22
959921 CACTTATTAT
959931 TGTATCGATACACAGTCAAGGAA
1 TGTATCGATACACAGTCAAGG-A
*
959954 TGTATC-AGTACACATTCATA-G-
1 TGTATCGA-TACACAGTCA-AGGA
959975 TGTATCGATACA
1 TGTATCGATACA
959987 TAGCGAAGAG
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
21 10 0.34
22 2 0.07
23 16 0.55
24 1 0.03
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Consensus pattern (22 bp):
TGTATCGATACACAGTCAAGGA
Found at i:964259 original size:18 final size:18
Alignment explanation
Indices: 964218--964260 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
964208 AACTCCAATG
*
964218 TTCTTCTTTTTCTCTGTC
1 TTCTTCTTTGTCTCTGTC
*
964236 TCCTTCTTTGTCTC-GTCC
1 TTCTTCTTTGTCTCTGT-C
964254 TTCTTCT
1 TTCTTCT
964261 CGAGGTCTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.00, C:0.33, G:0.07, T:0.60
Consensus pattern (18 bp):
TTCTTCTTTGTCTCTGTC
Found at i:965992 original size:20 final size:20
Alignment explanation
Indices: 965950--965993 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
965940 CGAATATTTT
* * *
965950 AATTGAATATATAATTTTGA
1 AATTGAATATAAAATCTTAA
965970 AATTGAATATAAAATCTTAA
1 AATTGAATATAAAATCTTAA
965990 AATT
1 AATT
965994 TATTTACACT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (20 bp):
AATTGAATATAAAATCTTAA
Found at i:967081 original size:14 final size:14
Alignment explanation
Indices: 967062--967093 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
967052 ATTAAAATGA
967062 TTAAATCAACCAAT
1 TTAAATCAACCAAT
*
967076 TTAAATCAATCAAT
1 TTAAATCAACCAAT
967090 TTAA
1 TTAA
967094 TTAAAATGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (14 bp):
TTAAATCAACCAAT
Found at i:968074 original size:121 final size:120
Alignment explanation
Indices: 967901--968138 Score: 291
Period size: 121 Copynumber: 2.0 Consensus size: 120
967891 TGTAACCTTG
* *
967901 TAGAGTAGACAAAATAATATTTTAGATTAAAACCCATCGTAATGTAACATTTTTTTGTTATAACT
1 TAGAGTAGACAAAATAACATTTTAGATTAAAACCCATCGTAATGTAACA--TTTTTATTATAACT
* * *
967966 AAAATTATTATCAATTAT-ACAAC-CTTTTTAATAGTCTGAGGTGATTACAAAGTTTT
64 AAAATTATCACCAATT-TCACAACTCTTTTTAATAGTCTGAGGTGATTAAAAAGTTTT
** * * * * * *
968022 TAGAGTAGACGGAGTAACATTTTAGGTTAAAATCCGTCGTAATGTAATATTTTTATTATAATTAA
1 TAGAGTAGACAAAATAACATTTTAGATTAAAACCCATCGTAATGTAACATTTTTATTATAACTAA
* * *
968087 AATTATCACCAATTTCATAACTTTTTTTAATAGTCTGGGGTGATTAAAAAGT
66 AATTATCACCAATTTCACAACTCTTTTTAATAGTCTGAGGTGATTAAAAAGT
968139 AATATATGTT
Statistics
Matches: 99, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
118 1 0.01
119 30 0.30
120 27 0.27
121 41 0.41
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (120 bp):
TAGAGTAGACAAAATAACATTTTAGATTAAAACCCATCGTAATGTAACATTTTTATTATAACTAA
AATTATCACCAATTTCACAACTCTTTTTAATAGTCTGAGGTGATTAAAAAGTTTT
Found at i:969546 original size:60 final size:59
Alignment explanation
Indices: 969442--969557 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 59
969432 AGGTACATTA
* * *
969442 TTGGAATGTTCAAAAGTTTGGGGATCACTTTAAAATGAGGGTCATAATTTGAGGATGAAT
1 TTGGAATGTTCAAAAGTTTAGGGATCAATTTAAAATGA-GGTCATAATTTAAGGATGAAT
* * *
969502 TTGGAATGTTTAAAAGTTTATGGATTAATTTAAGATATGA-GTCATAATTTAAGGAT
1 TTGGAATGTTCAAAAGTTTAGGGATCAATTTAA-A-ATGAGGTCATAATTTAAGGAT
969558 AAAATCAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
60 43 0.90
61 1 0.02
62 4 0.08
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.37
Consensus pattern (59 bp):
TTGGAATGTTCAAAAGTTTAGGGATCAATTTAAAATGAGGTCATAATTTAAGGATGAAT
Found at i:970681 original size:21 final size:20
Alignment explanation
Indices: 970640--970681 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
970630 ATTGCTCAGA
* *
970640 GGGTATCGATTCCCCCCAAG
1 GGGTACCGATTCCCCCAAAG
970660 GGGTACCGATTCCCCCTAAAG
1 GGGTACCGATTCCCCC-AAAG
970681 G
1 G
970682 ATATGGCTCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.21, C:0.33, G:0.26, T:0.19
Consensus pattern (20 bp):
GGGTACCGATTCCCCCAAAG
Found at i:972672 original size:21 final size:19
Alignment explanation
Indices: 972641--972683 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
972631 TATGAGAAAT
972641 TGATTTTAAAATAT-AAAAA
1 TGATTTTAAAAT-TGAAAAA
972660 TGATGTTTCAAAATTGAAAAA
1 TGAT-TTT-AAAATTGAAAAA
972681 TGA
1 TGA
972684 AAATAAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 4 0.19
20 4 0.19
21 13 0.62
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.35
Consensus pattern (19 bp):
TGATTTTAAAATTGAAAAA
Found at i:978441 original size:19 final size:19
Alignment explanation
Indices: 978419--978456 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
978409 TTATTCGAAT
978419 ATCAAAATATTACTCCAAA
1 ATCAAAATATTACTCCAAA
978438 ATCAAAATATTACTCCAAA
1 ATCAAAATATTACTCCAAA
978457 TCTTTTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (19 bp):
ATCAAAATATTACTCCAAA
Found at i:979773 original size:52 final size:53
Alignment explanation
Indices: 979694--979800 Score: 164
Period size: 52 Copynumber: 2.0 Consensus size: 53
979684 ATTTATTTTT
979694 TAAAATATAAATATGAAAAAAATATTGAATTT-AGTTTAAGAATATAAAAATAA
1 TAAAATATAAATATGAAAAAAATATTGAATTTAAGTTTAA-AATATAAAAATAA
* * *
979747 TAAAAT-TTAATATGAAAAAAATATTGAATTTAATTTTAAAATGTAAAAATAA
1 TAAAATATAAATATGAAAAAAATATTGAATTTAAGTTTAAAATATAAAAATAA
979799 TA
1 TA
979801 TATTTATTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
52 38 0.76
53 12 0.24
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.35
Consensus pattern (53 bp):
TAAAATATAAATATGAAAAAAATATTGAATTTAAGTTTAAAATATAAAAATAA
Found at i:979785 original size:29 final size:28
Alignment explanation
Indices: 979701--979801 Score: 86
Period size: 24 Copynumber: 3.6 Consensus size: 28
979691 TTTTAAAATA
*
979701 TAAATATGAAAAAAATATTGAATTTAGTT
1 TAAA-ATGAAAAAAATATTGAATTTAATT
* *
979730 TAAGAAT-ATAAAAATAAT-AA---AATT
1 TAA-AATGAAAAAAATATTGAATTTAATT
*
979754 TAATATGAAAAAAATATTGAATTTAATTT
1 TAAAATGAAAAAAATATTGAATTTAA-TT
979783 TAAAATGTAAAAATAATAT
1 TAAAATG-AAAAA-AATAT
979802 ATTTATTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
23 2 0.04
24 15 0.27
25 2 0.04
27 2 0.04
28 11 0.20
29 13 0.23
30 6 0.11
31 5 0.09
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.36
Consensus pattern (28 bp):
TAAAATGAAAAAAATATTGAATTTAATT
Found at i:980520 original size:24 final size:22
Alignment explanation
Indices: 980488--980546 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 22
980478 ATTAAATTCA
980488 AAATTTTCTAATATTTCATATAAT
1 AAATTTTCTAATATTTC-TA-AAT
980512 AAATTTTCTAATATTTCTAAAT
1 AAATTTTCTAATATTTCTAAAT
*
980534 -ATTTTTCTAATAT
1 AAATTTTCTAATAT
980547 ATATTAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 12 0.35
22 3 0.09
23 2 0.06
24 17 0.50
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (22 bp):
AAATTTTCTAATATTTCTAAAT
Found at i:984778 original size:22 final size:22
Alignment explanation
Indices: 984746--984791 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
984736 CATCTTTCAA
*
984746 TTGAATAGTTTACTTTTTTAGAT
1 TTGAATAGTTTACTTGTTT-GAT
*
984769 TTGAA-AGTTTCCTTGTTTGAT
1 TTGAATAGTTTACTTGTTTGAT
984790 TT
1 TT
984792 ACCATAATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 5 0.24
22 11 0.52
23 5 0.24
ACGTcount: A:0.22, C:0.07, G:0.15, T:0.57
Consensus pattern (22 bp):
TTGAATAGTTTACTTGTTTGAT
Found at i:988752 original size:10 final size:10
Alignment explanation
Indices: 988725--988755 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
988715 TCACCCAGGT
*
988725 AGCTCAGCTC
1 AGCTCAGTTC
988735 AGCTCAGTTC
1 AGCTCAGTTC
988745 AGCTCAGTTC
1 AGCTCAGTTC
988755 A
1 A
988756 ACTATGCTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.23, C:0.32, G:0.19, T:0.26
Consensus pattern (10 bp):
AGCTCAGTTC
Found at i:995170 original size:21 final size:21
Alignment explanation
Indices: 995141--995188 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
995131 GGAAACCAAG
*
995141 GCTGTTGATAGAGGGGAAATA
1 GCTGCTGATAGAGGGGAAATA
995162 GCTGCTGATAGAGGGGAAATA
1 GCTGCTGATAGAGGGGAAATA
995183 GCTGCT
1 GCTGCT
995189 AAAGAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.10, G:0.38, T:0.23
Consensus pattern (21 bp):
GCTGCTGATAGAGGGGAAATA
Found at i:996685 original size:32 final size:33
Alignment explanation
Indices: 996648--996716 Score: 106
Period size: 33 Copynumber: 2.1 Consensus size: 33
996638 TACACCTATC
996648 TGAGTCAC-C-AAAGTCATACCATTACCTCTCTT
1 TGAGTCACTCAAAAG-CATACCATTACCTCTCTT
*
996680 TGAGTCACTCAAAAGCATACCCTTACCTCTCTT
1 TGAGTCACTCAAAAGCATACCATTACCTCTCTT
996713 TGAG
1 TGAG
996717 GCAATAAAGT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 8 0.24
33 22 0.65
34 4 0.12
ACGTcount: A:0.28, C:0.30, G:0.12, T:0.30
Consensus pattern (33 bp):
TGAGTCACTCAAAAGCATACCATTACCTCTCTT
Found at i:997489 original size:25 final size:25
Alignment explanation
Indices: 997410--997499 Score: 69
Period size: 25 Copynumber: 3.5 Consensus size: 25
997400 TTCATATTCT
*
997410 AAAAGAAAGAGATA-AAAAAAGGAAA
1 AAAAGAAAGAGA-AGAAAAAAAGAAA
* * *
997435 AATAGAATA-A-AATGAGATAAAACAACA
1 AAAAGAA-AGAGAA-GA-AAAAAAGAA-A
997462 AAAAGAAAGAGAAGAAAAAAAGAAA
1 AAAAGAAAGAGAAGAAAAAAAGAAA
*
997487 AAAATAAAGAGAA
1 AAAAGAAAGAGAA
997500 CAAATCAAGT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 21 0.42
26 15 0.30
27 10 0.20
28 2 0.04
ACGTcount: A:0.74, C:0.02, G:0.17, T:0.07
Consensus pattern (25 bp):
AAAAGAAAGAGAAGAAAAAAAGAAA
Found at i:999872 original size:2 final size:2
Alignment explanation
Indices: 999861--999889 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
999851 ATTGTTAGTG
999861 AT AT -T 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
999890 TATTTGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1002185 original size:19 final size:19
Alignment explanation
Indices: 1002163--1002204 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
1002153 TTATAAAGTT
1002163 TGATATCTGTTATGATCTC
1 TGATATCTGTTATGATCTC
*
1002182 TGATTTCTGTTATGATCTC
1 TGATATCTGTTATGATCTC
1002201 TGAT
1 TGAT
1002205 CTCTACTCTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.17, T:0.50
Consensus pattern (19 bp):
TGATATCTGTTATGATCTC
Found at i:1003932 original size:24 final size:26
Alignment explanation
Indices: 1003885--1003951 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
1003875 TCAAGTGTGA
1003885 TAAATAATATTATTTATTAGAAAATAAT
1 TAAATAATATTATTTATTA-AAAAT-AT
1003913 T-AATAATATTATTT-TT-AAAATAT
1 TAAATAATATTATTTATTAAAAATAT
1003936 TAGAATAAT-TTATTTA
1 TA-AATAATATTATTTA
1003952 ATATGATTTA
Statistics
Matches: 36, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
23 3 0.08
24 11 0.31
25 6 0.17
26 2 0.06
27 13 0.36
28 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (26 bp):
TAAATAATATTATTTATTAAAAATAT
Found at i:1004134 original size:17 final size:17
Alignment explanation
Indices: 1004078--1004138 Score: 52
Period size: 17 Copynumber: 3.4 Consensus size: 17
1004068 TTAAGATAAA
1004078 AATATTA-TATTATTAGT
1 AATATTATTATTATTA-T
* *
1004095 TATATTAATTACTTACTAGAT
1 AATATT-ATTA-TTA-T-TAT
1004116 AATATTATTATTATTAT
1 AATATTATTATTATTAT
1004133 AATATT
1 AATATT
1004139 GCAATAAGAA
Statistics
Matches: 35, Mismatches: 4, Indels: 10
0.71 0.08 0.20
Matches are distributed among these distances:
17 13 0.37
18 2 0.06
19 5 0.14
20 7 0.20
21 7 0.20
22 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (17 bp):
AATATTATTATTATTAT
Found at i:1004429 original size:22 final size:21
Alignment explanation
Indices: 1004404--1004449 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
1004394 AATAGTATAT
1004404 TATTATTAAATATATAAAATAA
1 TATTATTAAATATAT-AAATAA
* *
1004426 TATTATTAAATTTATGAATAA
1 TATTATTAAATATATAAATAA
1004447 TAT
1 TAT
1004450 ATTTTAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TATTATTAAATATATAAATAA
Found at i:1004496 original size:30 final size:29
Alignment explanation
Indices: 1004373--1004497 Score: 76
Period size: 30 Copynumber: 4.1 Consensus size: 29
1004363 ATAATTTATT
1004373 TTTTTATTAAAATGTTAATAAAATAGTATA
1 TTTTTATTAAAATGTT-ATAAAATAGTATA
* * *
1004403 TTATTATT-AAAT-ATATAAAATAATATTA
1 TTTTTATTAAAATGTTATAAAATAGTA-TA
* * * *
1004431 TTAAATTTATGAATAATATATTTTAATAAT-TTATA
1 TT---TTTAT---TAAAATGTTATAA-AATAGTATA
1004466 TTTTTATTAAAATGTTACTAAAATAGTATA
1 TTTTTATTAAAATGTTA-TAAAATAGTATA
1004496 TT
1 TT
1004498 AACATTTAAT
Statistics
Matches: 71, Mismatches: 12, Indels: 24
0.66 0.11 0.22
Matches are distributed among these distances:
27 10 0.14
28 5 0.07
29 14 0.20
30 16 0.23
31 4 0.06
32 5 0.07
34 1 0.01
35 7 0.10
36 6 0.08
37 3 0.04
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (29 bp):
TTTTTATTAAAATGTTATAAAATAGTATA
Found at i:1009722 original size:106 final size:106
Alignment explanation
Indices: 1009543--1009961 Score: 544
Period size: 106 Copynumber: 4.0 Consensus size: 106
1009533 TTACGTGTCG
1009543 CAATCATTCAGGTCGTTTTTGCTTTCCTTTTA--TTTTATATTGTTTTGCATTTGATTGAGATTT
1 CAATCATTCAGGTCGTTTTTGCTTTCCTTTTATTTTTTATATTGTTTTGCATTTGATTGAGATTT
* * *
1009606 CAAAGCATATATTTCTTTGACTGAATTACATCATATGTCTG
66 CAAAGCATATATTTCTTTGAGTTAATTACATCATATGTCTA
* * * *
1009647 CAATCATTCAGGTCGTTTTTGCCATT-CTTTTATTTTTGATATTGTTTTGCGTTTTATTGAGATT
1 CAATCATTCAGGTCGTTTTTG-CTTTCCTTTTATTTTTTATATTGTTTTGCATTTGATTGAGATT
* *
1009711 TCAAAGCATATATTTCTTTGAGTTAACTACGA-CATATAT-TCA
65 TCAAAGCATATATTTCTTTGAGTTAATTAC-ATCATATGTCT-A
* * * *
1009753 CAATCATTCATGTCGTTTTTGCTTTCCTTTTATTTTTTATATTGTTTTACATTGGATTAAGATTT
1 CAATCATTCAGGTCGTTTTTGCTTTCCTTTTATTTTTTATATTGTTTTGCATTTGATTGAGATTT
* *
1009818 CAAAACATATATTTCTTTGAGTTAATTGCATCATATGTCTA
66 CAAAGCATATATTTCTTTGAGTTAATTACATCATATGTCTA
* * * * * *
1009859 CAATCATTTAGGTCATTTTCGCTTTCCCTGTATTTTTTATATTTGTTTTGC-TTTGGATTGACAT
1 CAATCATTCAGGTCGTTTTTGCTTTCCTTTTATTTTTTATA-TTGTTTTGCATTT-GATTGAGAT
* *
1009923 TTCAAATCATATATTTCTTTGAGTTAATTGCATCATATG
64 TTCAAAGCATATATTTCTTTGAGTTAATTACATCATATG
1009962 CTCCTAAACT
Statistics
Matches: 273, Mismatches: 32, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
104 27 0.10
105 8 0.03
106 183 0.67
107 55 0.20
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (106 bp):
CAATCATTCAGGTCGTTTTTGCTTTCCTTTTATTTTTTATATTGTTTTGCATTTGATTGAGATTT
CAAAGCATATATTTCTTTGAGTTAATTACATCATATGTCTA
Found at i:1011131 original size:27 final size:27
Alignment explanation
Indices: 1011093--1011146 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1011083 GTAGTCTACC
1011093 CTGAATAAAAATATGTATGAATTATGT
1 CTGAATAAAAATATGTATGAATTATGT
1011120 CTGAATAAAAATATGTATGAATTATGT
1 CTGAATAAAAATATGTATGAATTATGT
1011147 TAAGAAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.37
Consensus pattern (27 bp):
CTGAATAAAAATATGTATGAATTATGT
Found at i:1011140 original size:16 final size:16
Alignment explanation
Indices: 1011094--1011141 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
1011084 TAGTCTACCC
1011094 TGAATAAAAATATGTA
1 TGAATAAAAATATGTA
*
1011110 TGAAT-----TATGTC
1 TGAATAAAAATATGTA
1011121 TGAATAAAAATATGTA
1 TGAATAAAAATATGTA
1011137 TGAAT
1 TGAAT
1011142 TATGTTAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 10
0.68 0.05 0.27
Matches are distributed among these distances:
11 10 0.40
16 15 0.60
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (16 bp):
TGAATAAAAATATGTA
Found at i:1011160 original size:27 final size:27
Alignment explanation
Indices: 1011093--1011154 Score: 92
Period size: 27 Copynumber: 2.4 Consensus size: 27
1011083 GTAGTCTACC
*
1011093 CTGAATAAAAATATGTATGAATTATGT
1 CTGAAGAAAAATATGTATGAATTATGT
*
1011120 CTGAATAAAAATATGTATGAATTATGT
1 CTGAAGAAAAATATGTATGAATTATGT
1011147 -T-AAGAAAA
1 CTGAAGAAAA
1011155 TTATATTGAT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
25 6 0.18
26 1 0.03
27 27 0.79
ACGTcount: A:0.48, C:0.03, G:0.15, T:0.34
Consensus pattern (27 bp):
CTGAAGAAAAATATGTATGAATTATGT
Found at i:1023085 original size:139 final size:147
Alignment explanation
Indices: 1022886--1023175 Score: 506
Period size: 139 Copynumber: 2.0 Consensus size: 147
1022876 TGTATGAGTT
1022886 TATTATATTTTCAATGCTTGTAATATGTGATTTTTACATTGTGTGTTGTGTTATTTATTTATTTT
1 TATTATATTTTCAA--CTTGTAATATGTGATTTTTACATTGTGTGTTGTGTTATTTATTTATTTT
1022951 GCTTTTGAGACATTAAA-TTCCAGTTTTAA-TATTT-GTCTCTCGTGTAGTATTCTA-TGTGATT
64 GCTTTTGAGACATTAAATTTCCAGTTTTAATTATTTAGTCTCTCGTGTAGTATTCTATTGTGATT
1023012 TCATCACTTGCTTTTATGC
129 TCATCACTTGCTTTTATGC
1023031 TATTATATTTTCAA-TTGTAATATGTGA-TTTTACATTGTGTG-T-TGTTATTTATTTATTTTGC
1 TATTATATTTTCAACTTGTAATATGTGATTTTTACATTGTGTGTTGTGTTATTTATTTATTTTGC
1023092 TTTTGAGACATTAAATTTCCAGTTTTAATTATTTAGTCTCTCGTGTAGTATTCTATTGTGATTTC
66 TTTTGAGACATTAAATTTCCAGTTTTAATTATTTAGTCTCTCGTGTAGTATTCTATTGTGATTTC
1023157 ATCACTTGCTTTTATGC
131 ATCACTTGCTTTTATGC
1023174 TA
1 TA
1023176 GTTGAATATT
Statistics
Matches: 141, Mismatches: 0, Indels: 10
0.93 0.00 0.07
Matches are distributed among these distances:
139 34 0.24
140 13 0.09
141 19 0.13
142 33 0.23
143 28 0.20
145 14 0.10
ACGTcount: A:0.22, C:0.11, G:0.14, T:0.53
Consensus pattern (147 bp):
TATTATATTTTCAACTTGTAATATGTGATTTTTACATTGTGTGTTGTGTTATTTATTTATTTTGC
TTTTGAGACATTAAATTTCCAGTTTTAATTATTTAGTCTCTCGTGTAGTATTCTATTGTGATTTC
ATCACTTGCTTTTATGC
Found at i:1027559 original size:75 final size:76
Alignment explanation
Indices: 1027465--1027702 Score: 317
Period size: 76 Copynumber: 3.1 Consensus size: 76
1027455 ATCTCACCTG
1027465 AGATTGTTTTTCTTAAAACAA-ACTTTGTCTCACTTGAGA-ATGTTTTACTCGAAAGAAGAGATT
1 AGATTGTTTTTCTTAAAACAAGA-TTTGTCTCACTTGAGACATGTTTTACTCGAAAGAAGAGATT
* *
1027528 TCATTTAACTTA
65 TCATTTCACTCA
* *
1027540 AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACA-GTTTTTACTTGAAACAAGAAGAT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACATG-TTTTACTCGAAAGAAG-AGAT
1027604 TT-ATTTCACTCA
64 TTCATTTCACTCA
* * * *
1027616 AGATTGTTTTTCTTAAAACAAGATTTGTCTCGCTTTAGACTAT-TTTTAGTCAAAAGAAG-GCAT
1 AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGAC-ATGTTTTACTCGAAAGAAGAG-AT
1027679 TTCATTTCACTCA
64 TTCATTTCACTCA
1027692 AGATTGTTTTT
1 AGATTGTTTTT
1027703 AAAGAAGATT
Statistics
Matches: 145, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
74 1 0.01
75 42 0.29
76 95 0.66
77 7 0.05
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (76 bp):
AGATTGTTTTTCTTAAAACAAGATTTGTCTCACTTGAGACATGTTTTACTCGAAAGAAGAGATTT
CATTTCACTCA
Found at i:1027625 original size:40 final size:39
Alignment explanation
Indices: 1027450--1027638 Score: 122
Period size: 36 Copynumber: 5.0 Consensus size: 39
1027440 TAATACAGAG
* * * *
1027450 GATTTATCTCACCTGAGATTGTTTTTCTTAAAAC-A-AA
1 GATTTATTTCACTTAAGATTGTTTTTCTTGAAACAAGAA
* * * * * * * *
1027487 -CTTTGTCTCACTTGAGAATGTTTTACTCGAAAGAAG-A
1 GATTTATTTCACTTAAGATTGTTTTTCTTGAAACAAGAA
* *
1027524 GATTTCATTTAACTTAAGATTGTTTTTCTT--AA-AACAA
1 GATTT-ATTTCACTTAAGATTGTTTTTCTTGAAACAAGAA
* * * **
1027561 GATTTGTCTCACTTGAGACAGTTTTTACTTGAAACAAGAA
1 GATTTATTTCACTTAAGATTGTTTTT-CTTGAAACAAGAA
* *
1027601 GATTTATTTCACTCAAGATTGTTTTTCTTAAAACAAGA
1 GATTTATTTCACTTAAGATTGTTTTTCTTGAAACAAGA
1027639 TTTGTCTCGC
Statistics
Matches: 112, Mismatches: 31, Indels: 16
0.70 0.19 0.10
Matches are distributed among these distances:
36 42 0.38
37 13 0.12
38 3 0.03
39 30 0.27
40 24 0.21
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (39 bp):
GATTTATTTCACTTAAGATTGTTTTTCTTGAAACAAGAA
Found at i:1027662 original size:36 final size:36
Alignment explanation
Indices: 1027535--1027662 Score: 105
Period size: 36 Copynumber: 3.4 Consensus size: 36
1027525 ATTTCATTTA
* *
1027535 ACTTAAGATTGTTTTTCTTAAAACAAGATTTGTCTC
1 ACTTAAGACTATTTTTCTTAAAACAAGATTTGTCTC
* * * *
1027571 ACTTGAGAC-AGTTTTTACTTGAAACAAGAAGATTTATTTC
1 ACTTAAGACTA-TTTTT-CTT--AA-AACAAGATTTGTCTC
* * *
1027611 ACTCAAGATTGTTTTTCTTAAAACAAGATTTGTCTC
1 ACTTAAGACTATTTTTCTTAAAACAAGATTTGTCTC
* *
1027647 GCTTTAGACTATTTTT
1 ACTTAAGACTATTTTT
1027663 AGTCAAAAGA
Statistics
Matches: 68, Mismatches: 18, Indels: 12
0.69 0.18 0.12
Matches are distributed among these distances:
36 35 0.51
37 5 0.07
39 5 0.07
40 23 0.34
ACGTcount: A:0.30, C:0.14, G:0.12, T:0.43
Consensus pattern (36 bp):
ACTTAAGACTATTTTTCTTAAAACAAGATTTGTCTC
Found at i:1027763 original size:39 final size:39
Alignment explanation
Indices: 1027707--1027987 Score: 400
Period size: 39 Copynumber: 7.2 Consensus size: 39
1027697 GTTTTTAAAG
* * *
1027707 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCAAAATAA
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAA
* *
1027746 AAGATTTTGTCTTGCTTGAGATAGTTTCCCACGAAACAA
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAA
*
1027785 AAGATTTTGGCTCGCTTGAGATAGTTTCCCTCGAAACAA
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * * *
1027824 AAGATTTTGTCTCGCTTTAGATAGTATCCCTCTAAACAG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAA
* *
1027863 AAGATTTTGTCTCGCTTGAGATATTTTCCCTCGAAACAG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * *
1027902 AAGATTTTGTATCGTTTGAGATAGTTTCCCTCGAAACAG
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAA
* *
1027941 AAGATTTTATCTCGCTTGAGATAGTTTCTCTCGAAACAA
1 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAA
*
1027980 AGGATTTT
1 AAGATTTT
1027988 ATAAGAAACT
Statistics
Matches: 216, Mismatches: 26, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 216 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (39 bp):
AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAA
Found at i:1028606 original size:22 final size:22
Alignment explanation
Indices: 1028580--1028621 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1028570 ATTTTCAAAT
*
1028580 TTTCAACACCCACCATCCCATA
1 TTTCAACACACACCATCCCATA
*
1028602 TTTCAACACATACCATCCCA
1 TTTCAACACACACCATCCCA
1028622 CCATCTCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.43, G:0.00, T:0.24
Consensus pattern (22 bp):
TTTCAACACACACCATCCCATA
Found at i:1029091 original size:2 final size:2
Alignment explanation
Indices: 1029086--1029191 Score: 73
Period size: 2 Copynumber: 55.0 Consensus size: 2
1029076 TAATTTACGC
* *
1029086 AT AT AT AT AT AT AT AT AT AT AT GAT TT A- AT AT -T AT -T AT TT
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT
* * * * *
1029126 TT AT -T AA AC AT CAT AT TT GA- AT -T AT AT AT AT A- AT AT CT AT
1 AT AT AT AT AT AT -AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT
1029166 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
1029192 TTATGAGATT
Statistics
Matches: 83, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
1 7 0.08
2 72 0.87
3 4 0.05
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1029366 original size:2 final size:2
Alignment explanation
Indices: 1029359--1029440 Score: 150
Period size: 2 Copynumber: 42.0 Consensus size: 2
1029349 TGCATGGCTA
1029359 AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T 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
1029399 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
1029441 GTTAATGTTT
Statistics
Matches: 78, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
1 2 0.03
2 76 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1034618 original size:30 final size:30
Alignment explanation
Indices: 1034582--1034655 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 30
1034572 TTTGGTCAAA
*
1034582 GTCAAAGTCAACGATCAAC-GAGTTGATTCG
1 GTCAAAGTCAACGATCAACTG-GTTGACTCG
* *
1034612 GTCAAAGTTAACGGTCAACTGGTTGACTCG
1 GTCAAAGTCAACGATCAACTGGTTGACTCG
*
1034642 ATCAAAGTCAACGA
1 GTCAAAGTCAACGA
1034656 GTTGACCCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
30 36 0.97
31 1 0.03
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (30 bp):
GTCAAAGTCAACGATCAACTGGTTGACTCG
Found at i:1039068 original size:29 final size:26
Alignment explanation
Indices: 1039014--1039064 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
1039004 ACCTATTTTC
*
1039014 AATTTTGTAAAAAAATATATGAATTT
1 AATTTTGTAAAAAAATATATAAATTT
*
1039040 AATTTTTTAAAGAAAATATATAAAT
1 AATTTTGTAAA-AAAATATATAAAT
1039065 ATTTTCCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (26 bp):
AATTTTGTAAAAAAATATATAAATTT
Found at i:1056225 original size:22 final size:24
Alignment explanation
Indices: 1056200--1056244 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
1056190 TATTATTGAA
1056200 TTATTAA-AAATTT-AAAATATAT
1 TTATTAATAAATTTCAAAATATAT
*
1056222 TTATTAATAAATTTCAAAGTATA
1 TTATTAATAAATTTCAAAATATA
1056245 ATATAATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
23 6 0.30
24 7 0.35
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
TTATTAATAAATTTCAAAATATAT
Found at i:1056352 original size:31 final size:32
Alignment explanation
Indices: 1056309--1056384 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 32
1056299 CTATTATTTT
1056309 AATAGTATAATATAATTTAT-T-TTATTTTAATA
1 AATA-TATAATATAATTTATATATT-TTTTAATA
1056341 AATATATAATATAATTTATAATAATTTTTTAATA
1 AATATATAATATAATTTAT-AT-ATTTTTTAATA
1056375 AA-ATATAATA
1 AATATATAATA
1056385 GTATGAATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
31 15 0.38
32 4 0.10
33 9 0.22
34 10 0.25
35 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (32 bp):
AATATATAATATAATTTATATATTTTTTAATA
Found at i:1056404 original size:33 final size:35
Alignment explanation
Indices: 1056328--1056405 Score: 83
Period size: 33 Copynumber: 2.3 Consensus size: 35
1056318 ATATAATTTA
**
1056328 TTTTATTTTAATAAATATATAATATAATTTATAAT
1 TTTTATTTTAATAAATATATAATATAATGAATAAT
**
1056363 AATT-TTTTAATAAA-ATATAATAGT-ATGAAT-AT
1 TTTTATTTTAATAAATATATAATA-TAATGAATAAT
1056395 TTTTATTTTAA
1 TTTTATTTTAA
1056406 AATTTGTAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
32 4 0.11
33 18 0.51
34 11 0.31
35 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (35 bp):
TTTTATTTTAATAAATATATAATATAATGAATAAT
Found at i:1057282 original size:29 final size:29
Alignment explanation
Indices: 1057204--1057430 Score: 215
Period size: 29 Copynumber: 7.7 Consensus size: 29
1057194 TTTTTTTTGA
* *
1057204 ATATTTTTAAATTAAGATAATAAT-AAAT
1 ATATTTTTAAATTAAAATAAAAATAAAAT
* *
1057232 ATATTTTTAAAAGTTAATATAATAATAAAAT
1 ATATTTTT-AAA-TTAAAATAAAAATAAAAT
* *
1057263 ATATTTTTAATTTAAAATAAGAATAAAAT
1 ATATTTTTAAATTAAAATAAAAATAAAAT
*
1057292 ATA-TTTTAAAATAAACATAAAAATAAAAT
1 ATATTTTTAAATTAAA-ATAAAAATAAAAT
*
1057321 ATATATTTTAAAATAAAATAAAAATAAAAT
1 ATAT-TTTTAAATTAAAATAAAAATAAAAT
* ** *
1057351 CTATTTTTAAATTAAGTTAAGAATAAAAT
1 ATATTTTTAAATTAAAATAAAAATAAAAT
* * * * *
1057380 ATATTTAATAAGTCAAGATAAAAATAGAAT
1 ATATTT-TTAAATTAAAATAAAAATAAAAT
*
1057410 ATATCTTCTAAAGTTAAAATA
1 ATAT-TTTTAAA-TTAAAATA
1057431 TATAAAATGT
Statistics
Matches: 167, Mismatches: 23, Indels: 15
0.81 0.11 0.07
Matches are distributed among these distances:
28 18 0.11
29 63 0.38
30 54 0.32
31 32 0.19
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.37
Consensus pattern (29 bp):
ATATTTTTAAATTAAAATAAAAATAAAAT
Found at i:1057288 original size:59 final size:58
Alignment explanation
Indices: 1057204--1057413 Score: 210
Period size: 59 Copynumber: 3.6 Consensus size: 58
1057194 TTTTTTTTGA
* * *
1057204 ATATTTTTAAATTAAGATAATAATAAATATATTTTTAAAAGTTAATATAATAATAAAAT
1 ATATTTTTAAATTAAAATAAAAATAAATATATTTTTAAAA-TTAATATAAAAATAAAAT
* * * *
1057263 ATATTTTTAATTTAAAATAAGAATAAA-ATATATTTTAAAATAAACATAAAAATAAAAT
1 ATATTTTTAAATTAAAATAAAAATAAATATAT-TTTTAAAATTAATATAAAAATAAAAT
* * *
1057321 ATATATTTTAAAATAAAATAAAAATAAAATCTATTTTT-AAATTAAGT-TAAGAATAAAAT
1 ATAT-TTTTAAATTAAAATAAAAAT-AAATATATTTTTAAAATTAA-TATAAAAATAAAAT
* * * *
1057380 ATATTTAATAAGTCAAGATAAAAATAGAATATAT
1 ATATTT-TTAAATTAAAATAAAAATA-AATATAT
1057414 CTTCTAAAGT
Statistics
Matches: 125, Mismatches: 19, Indels: 14
0.79 0.12 0.09
Matches are distributed among these distances:
58 26 0.21
59 89 0.71
60 7 0.06
61 3 0.02
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.38
Consensus pattern (58 bp):
ATATTTTTAAATTAAAATAAAAATAAATATATTTTTAAAATTAATATAAAAATAAAAT
Found at i:1057306 original size:17 final size:17
Alignment explanation
Indices: 1057284--1057340 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 17
1057274 TTAAAATAAG
1057284 AATAAAATATATTTTAA
1 AATAAAATATATTTTAA
*
1057301 AAT-AAACATA----AA
1 AATAAAATATATTTTAA
1057313 AATAAAATATATATTTTAA
1 AAT-AAA-ATATATTTTAA
1057332 AATAAAATA
1 AATAAAATA
1057341 AAAATAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
12 5 0.16
14 2 0.06
15 4 0.13
16 6 0.19
17 6 0.19
18 3 0.10
19 5 0.16
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AATAAAATATATTTTAA
Found at i:1057317 original size:88 final size:89
Alignment explanation
Indices: 1057204--1057438 Score: 268
Period size: 88 Copynumber: 2.7 Consensus size: 89
1057194 TTTTTTTTGA
* * * *
1057204 ATATTTTTAAATTAAGATAATAATAAATATAT-TTTTAAAAGTTAATATAATAATAAAATATATT
1 ATATTTTAAAATAAAGATAAAAATAAATATATATTTTAAAAGTTAAAATAATAATAAAATATATT
*
1057268 TTTAATTTAAAATAAGAATAAAAT
66 TTTAAATTAAAATAAGAATAAAAT
* * *
1057292 ATATTTTAAAATAAACATAAAAATAAAATATATATTTTAAAA--TAAAATAAAAATAAAATCTAT
1 ATATTTTAAAATAAAGATAAAAAT-AAATATATATTTTAAAAGTTAAAATAATAATAAAATATAT
**
1057355 TTTTAAATTAAGTTAAGAATAAAAT
65 TTTTAAATTAAAATAAGAATAAAAT
* * *
1057380 ATA-TTTAATAAGTCAAGATAAAAATAGAATATATCTTCT-AAAGTTAAAAT-AT-ATAAAAT
1 ATATTTTAA-AA-TAAAGATAAAAATA-AATATATATTTTAAAAGTTAAAATAATAATAAAAT
1057439 GTTATGAATT
Statistics
Matches: 125, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
87 5 0.04
88 76 0.61
89 30 0.24
90 14 0.11
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (89 bp):
ATATTTTAAAATAAAGATAAAAATAAATATATATTTTAAAAGTTAAAATAATAATAAAATATATT
TTTAAATTAAAATAAGAATAAAAT
Found at i:1061308 original size:2 final size:2
Alignment explanation
Indices: 1061297--1061354 Score: 93
Period size: 2 Copynumber: 30.0 Consensus size: 2
1061287 TTTATTTTAT
*
1061297 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA -A TC TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1061337 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1061355 ATCTATATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
1 2 0.04
2 50 0.96
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:1061328 original size:27 final size:27
Alignment explanation
Indices: 1061297--1061362 Score: 123
Period size: 27 Copynumber: 2.4 Consensus size: 27
1061287 TTTATTTTAT
*
1061297 TATAATATATATATATATATATATATA
1 TATAATCTATATATATATATATATATA
1061324 TATAATCTATATATATATATATATATA
1 TATAATCTATATATATATATATATATA
1061351 TATAATCTATAT
1 TATAATCTATAT
1061363 TGATGAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (27 bp):
TATAATCTATATATATATATATATATA
Found at i:1070604 original size:29 final size:29
Alignment explanation
Indices: 1070544--1070606 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
1070534 AATGCATACT
* * * *
1070544 TGTTTCTGCATGGGATTATATCTCTGTCC
1 TGTTTCTGCATGGGATTAAATCCCCGTAC
*
1070573 TGTTTCTGTATGGGATTAAATCCCCGTAC
1 TGTTTCTGCATGGGATTAAATCCCCGTAC
1070602 TGTTT
1 TGTTT
1070607 TTGTTTGAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (29 bp):
TGTTTCTGCATGGGATTAAATCCCCGTAC
Found at i:1077445 original size:98 final size:98
Alignment explanation
Indices: 1077326--1077520 Score: 381
Period size: 98 Copynumber: 2.0 Consensus size: 98
1077316 CAAGAAGAAC
*
1077326 ATTTTTGGTTTATGCTTCAAAGCAACTACAAAATCATGAAAGAAATTATCTGACGCATGATCTTG
1 ATTTTTGGTTTATGCTTCAAAGCAACTACAAAATCATGAAAGAAATTATCTGACGCACGATCTTG
1077391 AGTTGGCAATAGTTGTGTTTACTTTGTTGATAA
66 AGTTGGCAATAGTTGTGTTTACTTTGTTGATAA
1077424 ATTTTTGGTTTATGCTTCAAAGCAACTACAAAATCATGAAAGAAATTATCTGACGCACGATCTTG
1 ATTTTTGGTTTATGCTTCAAAGCAACTACAAAATCATGAAAGAAATTATCTGACGCACGATCTTG
1077489 AGTTGGCAATAGTTGTGTTTACTTTGTTGATA
66 AGTTGGCAATAGTTGTGTTTACTTTGTTGATA
1077521 TAACACCATT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
98 96 1.00
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.37
Consensus pattern (98 bp):
ATTTTTGGTTTATGCTTCAAAGCAACTACAAAATCATGAAAGAAATTATCTGACGCACGATCTTG
AGTTGGCAATAGTTGTGTTTACTTTGTTGATAA
Found at i:1081567 original size:21 final size:21
Alignment explanation
Indices: 1081543--1081582 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1081533 CATTAAGGCC
* *
1081543 TTTGTTGAAGCCATGAAATAT
1 TTTGTCGAAGCCATAAAATAT
*
1081564 TTTGTCGAGGCCATAAAAT
1 TTTGTCGAAGCCATAAAAT
1081583 CTTGCAGTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (21 bp):
TTTGTCGAAGCCATAAAATAT
Found at i:1084832 original size:45 final size:45
Alignment explanation
Indices: 1084768--1084861 Score: 170
Period size: 45 Copynumber: 2.1 Consensus size: 45
1084758 AACAGATGAA
1084768 AAACGTTTCGCAGAGGCAAGAAAAATTGAAAAGTGAAGTGAGCAG
1 AAACGTTTCGCAGAGGCAAGAAAAATTGAAAAGTGAAGTGAGCAG
* *
1084813 AAACGTTTGGCCGAGGCAAGAAAAATTGAAAAGTGAAGTGAGCAG
1 AAACGTTTCGCAGAGGCAAGAAAAATTGAAAAGTGAAGTGAGCAG
1084858 AAAC
1 AAAC
1084862 ATTTTTCGTG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.45, C:0.12, G:0.29, T:0.15
Consensus pattern (45 bp):
AAACGTTTCGCAGAGGCAAGAAAAATTGAAAAGTGAAGTGAGCAG
Found at i:1093030 original size:44 final size:44
Alignment explanation
Indices: 1092944--1093038 Score: 136
Period size: 44 Copynumber: 2.2 Consensus size: 44
1092934 TGCTCTTGAA
**
1092944 AAGATCAGATATAGAAAAAGAGATATGCTTCACTACTTTTTAGG
1 AAGATCAGATATAGAAAAAGAGATATGCTTCACTACGCTTTAGG
* * * *
1092988 AATATCAGATATGGAAAAAGGGATATGCTTCACTGCGCTTTAGG
1 AAGATCAGATATAGAAAAAGAGATATGCTTCACTACGCTTTAGG
1093032 AAGATCA
1 AAGATCA
1093039 TATCTTGAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.27
Consensus pattern (44 bp):
AAGATCAGATATAGAAAAAGAGATATGCTTCACTACGCTTTAGG
Found at i:1099427 original size:24 final size:24
Alignment explanation
Indices: 1099381--1099427 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1099371 ATGTCTTGCA
* *
1099381 TTTTAATCTTCAAATTTAATATTT
1 TTTTAATCTTAAAAATTAATATTT
* *
1099405 TTTTAATTTTAAAAATTACTATT
1 TTTTAATCTTAAAAATTAATATT
1099428 GGTTTATTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.57
Consensus pattern (24 bp):
TTTTAATCTTAAAAATTAATATTT
Found at i:1109573 original size:15 final size:15
Alignment explanation
Indices: 1109550--1109581 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1109540 CTAGGAAGAT
*
1109550 AGTATCGATACCATA
1 AGTACCGATACCATA
1109565 AGTACCGATACCATA
1 AGTACCGATACCATA
1109580 AG
1 AG
1109582 GGAGGTATCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (15 bp):
AGTACCGATACCATA
Found at i:1110049 original size:2 final size:2
Alignment explanation
Indices: 1110044--1110077 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1110034 ATGAAATAAG
1110044 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
1110078 GGATACATGA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1110407 original size:18 final size:17
Alignment explanation
Indices: 1110379--1110417 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
1110369 GGACTTATGT
1110379 GATATGTGGTCCTTCGG
1 GATATGTGGTCCTTCGG
1110396 GATATAGTGGTCCTTCGG
1 GATAT-GTGGTCCTTCGG
1110414 GATA
1 GATA
1110418 AATTCTATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.18, C:0.15, G:0.33, T:0.33
Consensus pattern (17 bp):
GATATGTGGTCCTTCGG
Found at i:1114504 original size:18 final size:19
Alignment explanation
Indices: 1114477--1114516 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
1114467 AGGGTTCTAC
*
1114477 GTGGTCCTTCAGGACAT-T
1 GTGGTACTTCAGGACATAT
*
1114495 GTGGTACTTCGGGACATAT
1 GTGGTACTTCAGGACATAT
1114514 GTG
1 GTG
1114517 ATATGTGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (19 bp):
GTGGTACTTCAGGACATAT
Found at i:1118229 original size:14 final size:14
Alignment explanation
Indices: 1118212--1118238 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1118202 ATTTTAGATG
1118212 AATTATTTTTTAAC
1 AATTATTTTTTAAC
1118226 AATTATTTTTTAA
1 AATTATTTTTTAA
1118239 AATGAAGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
AATTATTTTTTAAC
Found at i:1118454 original size:9 final size:8
Alignment explanation
Indices: 1118423--1118454 Score: 55
Period size: 8 Copynumber: 3.9 Consensus size: 8
1118413 ACCATAATTA
1118423 TTTTAAAT
1 TTTTAAAT
1118431 TTTTAAAT
1 TTTTAAAT
1118439 TTTTAAAT
1 TTTTAAAT
1118447 TTTATAAA
1 TTT-TAAA
1118455 AAATATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 19 0.83
9 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (8 bp):
TTTTAAAT
Found at i:1118500 original size:13 final size:15
Alignment explanation
Indices: 1118482--1118514 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
1118472 ATTTGTTTGA
1118482 ATATTTTTAA-AA-T
1 ATATTTTTAATAACT
1118495 ATATTTTTAATAACT
1 ATATTTTTAATAACT
1118510 ATATT
1 ATATT
1118515 AATAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
14 2 0.11
15 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTTTTAATAACT
Found at i:1119714 original size:111 final size:111
Alignment explanation
Indices: 1119517--1119719 Score: 261
Period size: 111 Copynumber: 1.8 Consensus size: 111
1119507 ATTAAAAAAG
* *
1119517 TAAATTTTAAGAGTATGCTCACAATAACAAATATTGAAAAAAGATGGACCTCTAATAAAAGTAGT
1 TAAATTTTAAAAGTATGCTCACAATAACAAATATTGAAAAAAGATGGACCACTAATAAAAGTAGT
*
1119582 GAACAAAATTGGACTCATAATAACAAAAAACTATTAGAAAAGAAAT
66 GAACAAAATTGGACCCATAATAACAAAAAACTATTAGAAAAGAAAT
* *
1119628 TAAATTTTAAAAGTATG-TCCCTAATAACATATATTGAAAAAA-ATTAGG-CCACTAATAATAAG
1 TAAATTTTAAAAGTATGCTCAC-AATAACAAATATTGAAAAAAGA-T-GGACCACTAATAA-AAG
* * * *
1119690 TATTGAA-AAATTTGGGCCCTTAATAACAAA
62 TAGTGAACAAAATTGGACCCATAATAACAAA
1119720 TGTTAGAAAA
Statistics
Matches: 79, Mismatches: 9, Indels: 8
0.82 0.09 0.08
Matches are distributed among these distances:
110 4 0.05
111 64 0.81
112 11 0.14
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (111 bp):
TAAATTTTAAAAGTATGCTCACAATAACAAATATTGAAAAAAGATGGACCACTAATAAAAGTAGT
GAACAAAATTGGACCCATAATAACAAAAAACTATTAGAAAAGAAAT
Found at i:1130222 original size:2 final size:2
Alignment explanation
Indices: 1130215--1130242 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1130205 ACAAAGAAGA
1130215 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
1130243 GGATAAGATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1131508 original size:18 final size:20
Alignment explanation
Indices: 1131485--1131534 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 20
1131475 TTTGGTAAAA
*
1131485 GTCAACAGTCAATG-GTC-G
1 GTCAACAGTCAACGAGTCAG
*
1131503 GTCAACGGTCAACGAGTCAG
1 GTCAACAGTCAACGAGTCAG
1131523 GTCAACGAGTCA
1 GTCAAC-AGTCA
1131535 GGTCGGGTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 12 0.46
19 3 0.12
20 7 0.27
21 4 0.15
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (20 bp):
GTCAACAGTCAACGAGTCAG
Found at i:1131527 original size:13 final size:13
Alignment explanation
Indices: 1131509--1131538 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1131499 GTCGGTCAAC
1131509 GGTCAACGAGTCA
1 GGTCAACGAGTCA
1131522 GGTCAACGAGTCA
1 GGTCAACGAGTCA
1131535 GGTC
1 GGTC
1131539 GGGTCGGGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.27, C:0.23, G:0.33, T:0.17
Consensus pattern (13 bp):
GGTCAACGAGTCA
Found at i:1144301 original size:26 final size:26
Alignment explanation
Indices: 1144245--1144301 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
1144235 AAATGGCCTA
*
1144245 AAATACCCTCAAGCCCTAGAATGATT
1 AAATACCCTCAAGCCCTAGAATGAAT
* * *
1144271 GAATACCCTTAAGCTCTAGAATGAAT
1 AAATACCCTCAAGCCCTAGAATGAAT
1144297 AAATA
1 AAATA
1144302 TACCCCAGAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.25
Consensus pattern (26 bp):
AAATACCCTCAAGCCCTAGAATGAAT
Found at i:1145381 original size:32 final size:32
Alignment explanation
Indices: 1145342--1145468 Score: 164
Period size: 32 Copynumber: 4.0 Consensus size: 32
1145332 CCTAAGGTGA
* * *
1145342 CCTTGGGTAGGCTCTAAGGCCCTAAGGTATTT
1 CCTTGGATAGGCTCTAAGGCCCTAAGGTACTC
* * *
1145374 CCTTGGGTAGGCTCTAAGGCCCCAAGGTACCC
1 CCTTGGATAGGCTCTAAGGCCCTAAGGTACTC
*
1145406 CCTTGGATAGGCTCTTAGGCCCTAAGGTACTC
1 CCTTGGATAGGCTCTAAGGCCCTAAGGTACTC
* * *
1145438 CCTTGGATAGGCTCTCAGGCCCCAAGATACT
1 CCTTGGATAGGCTCTAAGGCCCTAAGGTACT
1145469 TCTTTAAGTT
Statistics
Matches: 84, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 84 1.00
ACGTcount: A:0.20, C:0.29, G:0.26, T:0.25
Consensus pattern (32 bp):
CCTTGGATAGGCTCTAAGGCCCTAAGGTACTC
Found at i:1145443 original size:64 final size:64
Alignment explanation
Indices: 1145342--1145463 Score: 190
Period size: 64 Copynumber: 1.9 Consensus size: 64
1145332 CCTAAGGTGA
* * * *
1145342 CCTTGGGTAGGCTCTAAGGCCCTAAGGTATTTCCTTGGGTAGGCTCTAAGGCCCCAAGGTACCC
1 CCTTGGATAGGCTCTAAGGCCCTAAGGTACTCCCTTGGATAGGCTCTAAGGCCCCAAGGTACCC
* *
1145406 CCTTGGATAGGCTCTTAGGCCCTAAGGTACTCCCTTGGATAGGCTCTCAGGCCCCAAG
1 CCTTGGATAGGCTCTAAGGCCCTAAGGTACTCCCTTGGATAGGCTCTAAGGCCCCAAG
1145464 ATACTTCTTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.19, C:0.30, G:0.27, T:0.25
Consensus pattern (64 bp):
CCTTGGATAGGCTCTAAGGCCCTAAGGTACTCCCTTGGATAGGCTCTAAGGCCCCAAGGTACCC
Found at i:1150429 original size:14 final size:13
Alignment explanation
Indices: 1150401--1150428 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1150391 ATTTTGGTTG
1150401 TTGTATTTTTTTT
1 TTGTATTTTTTTT
1150414 TTGTATTTTTTTT
1 TTGTATTTTTTTT
1150427 TT
1 TT
1150429 TTGCTTGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.07, C:0.00, G:0.07, T:0.86
Consensus pattern (13 bp):
TTGTATTTTTTTT
Found at i:1150629 original size:20 final size:20
Alignment explanation
Indices: 1150604--1150655 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1150594 GCTGATGAAA
1150604 GGTGACGGTCGAAGGTAAAG
1 GGTGACGGTCGAAGGTAAAG
1150624 GGTGACGGTCGAAGGTAAAG
1 GGTGACGGTCGAAGGTAAAG
*
1150644 GGTGAAGGTCGA
1 GGTGACGGTCGA
1150656 GTAGCTGGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.29, C:0.10, G:0.46, T:0.15
Consensus pattern (20 bp):
GGTGACGGTCGAAGGTAAAG
Found at i:1151264 original size:24 final size:26
Alignment explanation
Indices: 1151226--1151273 Score: 73
Period size: 24 Copynumber: 1.9 Consensus size: 26
1151216 ATTAATCAGT
*
1151226 ATTTAATATTACTATTTAT-ATATAA
1 ATTTAATAATACTATTTATCATATAA
1151251 ATTTAA-AATACTATTTATCATAT
1 ATTTAATAATACTATTTATCATAT
1151274 TTAATATTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (26 bp):
ATTTAATAATACTATTTATCATATAA
Found at i:1151289 original size:24 final size:24
Alignment explanation
Indices: 1151220--1151290 Score: 62
Period size: 24 Copynumber: 3.0 Consensus size: 24
1151210 AAATAAATTA
1151220 ATCAGTATTTAATATTACTAT-TTAT
1 ATCA-TATTTAATATTACTATATT-T
*
1151245 AT-ATAAATTTAA-AATAC--TATTT
1 ATCAT--ATTTAATATTACTATATTT
1151267 ATCATATTTAATATTACTATATTT
1 ATCATATTTAATATTACTATATTT
1151291 TAAAAGTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
21 6 0.16
22 8 0.22
23 5 0.14
24 10 0.27
25 8 0.22
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (24 bp):
ATCATATTTAATATTACTATATTT
Found at i:1151292 original size:25 final size:25
Alignment explanation
Indices: 1151220--1151292 Score: 59
Period size: 25 Copynumber: 3.0 Consensus size: 25
1151210 AAATAAATTA
1151220 ATCAGTATTTAATATTACTAT-TTATAT
1 ATCA-TATTTAATATTACTATATT-T-T
* *
1151247 AT-AAATTTAA-AATAC--TA-TTT
1 ATCATATTTAATATTACTATATTTT
1151267 ATCATATTTAATATTACTATATTTT
1 ATCATATTTAATATTACTATATTTT
1151292 A
1 A
1151293 AAAGTATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 14
0.67 0.07 0.26
Matches are distributed among these distances:
20 3 0.08
21 8 0.22
22 6 0.17
24 6 0.17
25 10 0.28
26 1 0.03
27 2 0.06
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (25 bp):
ATCATATTTAATATTACTATATTTT
Found at i:1153697 original size:29 final size:29
Alignment explanation
Indices: 1153629--1153697 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 29
1153619 AATTACATTT
* * * * * *
1153629 TTAGTTCCTAAACTTTTATAATTTATACT
1 TTAGTCCCTAAACTTTAAAAACTTACACC
1153658 TTAG-CCACTAAACTTTAAAAACTTACACC
1 TTAGTCC-CTAAACTTTAAAAACTTACACC
1153687 TTAGTCCCTAA
1 TTAGTCCCTAA
1153698 TCCAAAATTT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
28 1 0.03
29 29 0.91
30 2 0.06
ACGTcount: A:0.35, C:0.22, G:0.04, T:0.39
Consensus pattern (29 bp):
TTAGTCCCTAAACTTTAAAAACTTACACC
Found at i:1157048 original size:54 final size:54
Alignment explanation
Indices: 1156961--1157065 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
1156951 TAATTATATC
1156961 ACTCAAAATATTTTATAGGGAAATACCTCTTTCTCTAACAAATTTTGTACCAAT
1 ACTCAAAATATTTTATAGGGAAATACCTCTTTCTCTAACAAATTTTGTACCAAT
* * * * *
1157015 ACTCGAAATATTTTCTAGGGATATACCTCTTTCTCTGACCAATTTTGTACC
1 ACTCAAAATATTTTATAGGGAAATACCTCTTTCTCTAACAAATTTTGTACC
1157066 TATATATGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (54 bp):
ACTCAAAATATTTTATAGGGAAATACCTCTTTCTCTAACAAATTTTGTACCAAT
Found at i:1163340 original size:72 final size:71
Alignment explanation
Indices: 1163209--1163349 Score: 185
Period size: 72 Copynumber: 2.0 Consensus size: 71
1163199 TAATTGGTTG
* * *
1163209 GAAATTGATTTCAAGCATGACTGTTCTGTGATATGATTGCATTAAAAATAATTCAGATAAGTATG
1 GAAATTGATTTCAAGCATGAATGTTCTGTGATATGATTGCATTAAAAACAATTCAGATAAATATG
1163274 TTATTT
66 TTATTT
* ** * *
1163280 GAAAGTTGATTTCAAGCATGAATGTTCTGTGATACTG-TTGTATTAATTACAGTTCGGATAAATA
1 GAAA-TTGATTTCAAGCATGAATGTTCTGTGATA-TGATTGCATTAAAAACAATTCAGATAAATA
1163344 TGTTAT
64 TGTTAT
1163350 GTGATTTATT
Statistics
Matches: 60, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
71 4 0.07
72 54 0.90
73 2 0.03
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (71 bp):
GAAATTGATTTCAAGCATGAATGTTCTGTGATATGATTGCATTAAAAACAATTCAGATAAATATG
TTATTT
Found at i:1163924 original size:21 final size:21
Alignment explanation
Indices: 1163868--1163924 Score: 53
Period size: 23 Copynumber: 2.5 Consensus size: 21
1163858 TTTTAATCAA
1163868 ATTTATTATTTCAGATTTTATAT
1 ATTT-TTATTT-AGATTTTATAT
*
1163891 GTATTTTATTTTAGATTATTAT-T
1 AT-TTTTA-TTTAGATT-TTATAT
1163914 ATTTTTATTTA
1 ATTTTTATTTA
1163925 TGTATTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
21 4 0.14
22 5 0.17
23 11 0.38
24 9 0.31
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (21 bp):
ATTTTTATTTAGATTTTATAT
Found at i:1167146 original size:19 final size:19
Alignment explanation
Indices: 1167118--1167154 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1167108 TTTATTAACA
*
1167118 AGTGTGAAAAATAAAATGC
1 AGTGTAAAAAATAAAATGC
*
1167137 AGTGTAAAAAGTAAAATG
1 AGTGTAAAAAATAAAATG
1167155 TTGATGCAAA
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:0.54, C:0.03, G:0.22, T:0.22
Consensus pattern (19 bp):
AGTGTAAAAAATAAAATGC
Found at i:1169637 original size:221 final size:219
Alignment explanation
Indices: 1169274--1169759 Score: 713
Period size: 221 Copynumber: 2.2 Consensus size: 219
1169264 TCATTTAATC
* * * * * *
1169274 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCACTAAATCCCTAAGCTTGTAAGCTTATT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA-TAATTTCATAAGCTTGTAAACTTATG
* * * *
1169339 TTACCAATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTA
65 TTACCAATATACTTACCATAATTCCATAAACTCGTAAGCTTATGTTACCAATATACTTACCATAA
* *
1169404 TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTAATCT-ATATGCTCGTAAGTTT
130 TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA-TAAT-TAATAAGCTCGTAAGCTT
1169468 ATTTTACCAATATACTTACTATAATTT
193 ATTTTACCAATATACTTACTATAATTT
1169495 CATAAGCTCGTAAGCTTATTTTTACCAATATACTTACTATAATTTCATAAGCTTGTAAACTTATG
1 CATAAGCTCGTAAGCTTA-TTTTACCAATATACTTACTATAATTTCATAAGCTTGTAAACTTATG
* * * * * * *
1169560 TTATCAATCTACTTACTATAATTTCATAAACTCGTAAGCTTATGTTATCAATCTACTTACTATAA
65 TTACCAATATACTTACCATAATTCCATAAACTCGTAAGCTTATGTTACCAATATACTTACCATAA
* *
1169625 TTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTACATAAGCTCGTAAGCTTA
130 TTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATAATTA-ATAAGCTCGTAAGCTTA
*
1169690 TTTTATCAATATACTTACTATAATTT
194 TTTTACCAATATACTTACTATAATTT
*
1169716 CATAAGCTCATAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1169760 ACATCACTGA
Statistics
Matches: 239, Mismatches: 23, Indels: 7
0.89 0.09 0.03
Matches are distributed among these distances:
219 1 0.00
220 30 0.13
221 189 0.79
222 19 0.08
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.41
Consensus pattern (219 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTTCATAAGCTTGTAAACTTATGT
TACCAATATACTTACCATAATTCCATAAACTCGTAAGCTTATGTTACCAATATACTTACCATAAT
TCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATAATTAATAAGCTCGTAAGCTTATT
TTACCAATATACTTACTATAATTT
Found at i:1169759 original size:44 final size:44
Alignment explanation
Indices: 1169274--1169759 Score: 695
Period size: 44 Copynumber: 11.0 Consensus size: 44
1169264 TCATTTAATC
* * *
1169274 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCACTAAATC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA-TAATTT
* * * * *
1169319 CCTAAGCTTGTAAGCTTATTTTACCAATATACTTACCATTATTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* * *
1169363 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTATTC
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* *
1169407 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTAATCT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTA-TAATTT
* *
1169452 -ATATGCTCGTAAGTTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1169495 CATAAGCTCGTAAGCTTATTTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTA-TTTTACCAATATACTTACTATAATTT
* * * * *
1169540 CATAAGCTTGTAAACTTATGTTATCAATCTACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
* * * *
1169584 CATAAACTCGTAAGCTTATGTTATCAATCTACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
1169628 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTA
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
1169672 CATAAGCTCGTAAGCTTATTTTATCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
*
1169716 CATAAGCTCATAAGCTTATTTTACCAATATACTTACTATAATTT
1 CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
1169760 ACATCACTGA
Statistics
Matches: 406, Mismatches: 32, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
43 5 0.01
44 320 0.79
45 81 0.20
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.41
Consensus pattern (44 bp):
CATAAGCTCGTAAGCTTATTTTACCAATATACTTACTATAATTT
Found at i:1169959 original size:59 final size:60
Alignment explanation
Indices: 1169896--1170022 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
1169886 ATATACTTAA
* * * *
1169896 TATGATTTCCTCCT-CATTT-TAGCACACGAAGTTCCCTATGCGAGAATCCATACCATTAG
1 TATGATTTCCT-CTACATTTGTAGCACACAAAGTGCCCTATACGAAAATCCATACCATTAG
* * * *
1169955 TATGA-TTCCTTTACCATTTGTAGCACATAAAGTGCCCTATATGAAAATCCATACTATTAG
1 TATGATTTCCTCTA-CATTTGTAGCACACAAAGTGCCCTATACGAAAATCCATACCATTAG
1170015 TATGATTT
1 TATGATTT
1170023 ACCCTTAGTA
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
57 1 0.02
58 5 0.09
59 10 0.18
60 38 0.68
61 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (60 bp):
TATGATTTCCTCTACATTTGTAGCACACAAAGTGCCCTATACGAAAATCCATACCATTAG
Found at i:1169993 original size:60 final size:59
Alignment explanation
Indices: 1169910--1170021 Score: 152
Period size: 60 Copynumber: 1.9 Consensus size: 59
1169900 ATTTCCTCCT
* * * *
1169910 CATTTTAGCACACGAAGTTCCCTATGCGAGAATCCATACCATTAGTATGATTCCTTTAC
1 CATTTTAGCACACAAAGTGCCCTATACGAAAATCCATACCATTAGTATGATTCCTTTAC
* * *
1169969 CATTTGTAGCACATAAAGTGCCCTATATGAAAATCCATACTATTAGTATGATT
1 CATTT-TAGCACACAAAGTGCCCTATACGAAAATCCATACCATTAGTATGATT
1170022 TACCCTTAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
59 5 0.11
60 40 0.89
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.33
Consensus pattern (59 bp):
CATTTTAGCACACAAAGTGCCCTATACGAAAATCCATACCATTAGTATGATTCCTTTAC
Found at i:1170179 original size:59 final size:59
Alignment explanation
Indices: 1170087--1170255 Score: 268
Period size: 59 Copynumber: 2.9 Consensus size: 59
1170077 ATGCCCTATC
* * *
1170087 TGGAAATCCATATATTCAATATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATA
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATA
* *
1170146 TGGAAATCCATACACTCAGTATGATTTCCTTATCTTTTTAGCACACT-AGGTTCTCCATA
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCA-GTGCTCCATA
*
1170205 TGGAAATTCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGT
1 TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGT
1170256 ATGATTTCCT
Statistics
Matches: 101, Mismatches: 7, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
58 1 0.01
59 99 0.98
60 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.11, T:0.37
Consensus pattern (59 bp):
TGGAAATCCATACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATA
Found at i:1170254 original size:31 final size:31
Alignment explanation
Indices: 1170216--1170404 Score: 128
Period size: 31 Copynumber: 6.3 Consensus size: 31
1170206 GGAAATTCAT
1170216 ACACTCAGTATGATTTCCTTATCATTTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTTAGC
*
1170247 ACACTCAGTATGATTTCCTTATCTTTTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTTAGC
* * * * * * * *
1170278 ACATTAAG--TG--CTCCATATGGAAATTCA-T
1 ACACTCAGTATGATTTCCTTAT--CATTTTAGC
*
1170306 ACACTCAGTATGATTGCCTTATCATTTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTTAGC
* * * * * *
1170337 ACACTCAG--TG--CTCCATATGGAAATTCA-T
1 ACACTCAGTATGATTTCCTTAT--CATTTTAGC
1170365 ACACTCAGTATGATTTCCTTATCATTTTAGC
1 ACACTCAGTATGATTTCCTTATCATTTTAGC
1170396 ACACTCAGT
1 ACACTCAGT
1170405 GCTCCATATG
Statistics
Matches: 112, Mismatches: 32, Indels: 28
0.65 0.19 0.16
Matches are distributed among these distances:
27 11 0.10
28 14 0.12
29 11 0.10
30 12 0.11
31 53 0.47
32 11 0.10
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (31 bp):
ACACTCAGTATGATTTCCTTATCATTTTAGC
Found at i:1170288 original size:149 final size:149
Alignment explanation
Indices: 1170106--1170404 Score: 519
Period size: 149 Copynumber: 2.0 Consensus size: 149
1170096 ATATATTCAA
*
1170106 TATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATCCATACACTCAGTATGAT
1 TATGATTTCCTTATCATTTTAGCACACTAAGTGCTCCATATGGAAATCCATACACTCAGTATGAT
* * *
1170171 TTCCTTATCTTTTTAGCACACT-AGGTTCTCCATATGGAAATTCATACACTCAGTATGATTTCCT
66 TGCCTTATCATTTTAGCACACTCA-GTGCTCCATATGGAAATTCATACACTCAGTATGATTTCCT
1170235 TATCATTTTAGCACACTCAG
130 TATCATTTTAGCACACTCAG
* * *
1170255 TATGATTTCCTTATCTTTTTAGCACATTAAGTGCTCCATATGGAAATTCATACACTCAGTATGAT
1 TATGATTTCCTTATCATTTTAGCACACTAAGTGCTCCATATGGAAATCCATACACTCAGTATGAT
1170320 TGCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCATACACTCAGTATGATTTCCTT
66 TGCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCATACACTCAGTATGATTTCCTT
1170385 ATCATTTTAGCACACTCAG
131 ATCATTTTAGCACACTCAG
1170404 T
1 T
1170405 GCTCCATATG
Statistics
Matches: 142, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
149 141 0.99
150 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.12, T:0.38
Consensus pattern (149 bp):
TATGATTTCCTTATCATTTTAGCACACTAAGTGCTCCATATGGAAATCCATACACTCAGTATGAT
TGCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCATACACTCAGTATGATTTCCTT
ATCATTTTAGCACACTCAG
Found at i:1170310 original size:90 final size:90
Alignment explanation
Indices: 1170157--1170345 Score: 342
Period size: 90 Copynumber: 2.1 Consensus size: 90
1170147 GGAAATCCAT
* *
1170157 ACACTCAGTATGATTTCCTTATCTTTTTAGCACACTAGGTTCTCCATATGGAAATTCATACACTC
1 ACACTCAGTATGATTTCCTTATCTTTTTAGCACACTAAGTGCTCCATATGGAAATTCATACACTC
*
1170222 AGTATGATTTCCTTATCATTTTAGC
66 AGTATGATTGCCTTATCATTTTAGC
*
1170247 ACACTCAGTATGATTTCCTTATCTTTTTAGCACATTAAGTGCTCCATATGGAAATTCATACACTC
1 ACACTCAGTATGATTTCCTTATCTTTTTAGCACACTAAGTGCTCCATATGGAAATTCATACACTC
1170312 AGTATGATTGCCTTATCATTTTAGC
66 AGTATGATTGCCTTATCATTTTAGC
1170337 ACACTCAGT
1 ACACTCAGT
1170346 GCTCCATATG
Statistics
Matches: 95, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
90 95 1.00
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.39
Consensus pattern (90 bp):
ACACTCAGTATGATTTCCTTATCTTTTTAGCACACTAAGTGCTCCATATGGAAATTCATACACTC
AGTATGATTGCCTTATCATTTTAGC
Found at i:1170373 original size:28 final size:28
Alignment explanation
Indices: 1170337--1170430 Score: 75
Period size: 28 Copynumber: 3.2 Consensus size: 28
1170327 TCATTTTAGC
1170337 ACACTCAGTGCTCCATATGGAAATTCAT
1 ACACTCAGTGCTCCATATGGAAATTCAT
* * * * * *
1170365 ACACTCAGTATGATTTCCTTAT--CATTTTAGC
1 ACACTCAG--TG--CTCCATATGGAAATTCA-T
1170396 ACACTCAGTGCTCCATATGGAAATTCAT
1 ACACTCAGTGCTCCATATGGAAATTCAT
1170424 ACACTCA
1 ACACTCA
1170431 ATATGATTTC
Statistics
Matches: 47, Mismatches: 12, Indels: 14
0.64 0.16 0.19
Matches are distributed among these distances:
27 6 0.13
28 15 0.32
29 6 0.13
30 6 0.13
31 8 0.17
32 6 0.13
ACGTcount: A:0.31, C:0.26, G:0.12, T:0.32
Consensus pattern (28 bp):
ACACTCAGTGCTCCATATGGAAATTCAT
Found at i:1170465 original size:59 final size:59
Alignment explanation
Indices: 1170247--1170457 Score: 377
Period size: 59 Copynumber: 3.6 Consensus size: 59
1170237 TCATTTTAGC
* * *
1170247 ACACTCAGTATGATTTCCTTATCTTTTTAGCACATTAAGTGCTCCATATGGAAATTCAT
1 ACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCAT
*
1170306 ACACTCAGTATGATTGCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCAT
1 ACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCAT
1170365 ACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCAT
1 ACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCAT
*
1170424 ACACTCAATATGATTTCCTTATCATTTTAGCACA
1 ACACTCAGTATGATTTCCTTATCATTTTAGCACA
1170458 TATAGTGCCA
Statistics
Matches: 146, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 146 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.36
Consensus pattern (59 bp):
ACACTCAGTATGATTTCCTTATCATTTTAGCACACTCAGTGCTCCATATGGAAATTCAT
Found at i:1171718 original size:59 final size:59
Alignment explanation
Indices: 1171598--1171718 Score: 165
Period size: 59 Copynumber: 2.1 Consensus size: 59
1171588 GGAGGGTTGG
* *
1171598 TTAGAGCCATATTATCGAGTTTGCTTTTTCATTGCAACTAAGAGGGTTTGATAAGACAC
1 TTAGAGCCATATTAACGAGTTTGCTTTTTCATTGCAACTAAGAGGGTTTGATAAGAAAC
* * *
1171657 TTAGAGCCATATTAACGAGTTTGCCTTTTT-ATTGCGACTAGGAGGGTTCT-ATAGGAAAC
1 TTAGAGCCATATTAACGAGTTTG-CTTTTTCATTGCAACTAAGAGGGTT-TGATAAGAAAC
1171716 TTA
1 TTA
1171719 TCCATCTATT
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 48 0.87
60 7 0.13
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (59 bp):
TTAGAGCCATATTAACGAGTTTGCTTTTTCATTGCAACTAAGAGGGTTTGATAAGAAAC
Found at i:1175642 original size:23 final size:23
Alignment explanation
Indices: 1175598--1175644 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
1175588 AATTTAATAT
1175598 ATTATGATTCATTATCTTTTAGG
1 ATTATGATTCATTATCTTTTAGG
* *
1175621 ATTAT-ATTTATTATTTTATTAGG
1 ATTATGATTCATTATCTT-TTAGG
1175644 A
1 A
1175645 ATTCAGGTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (23 bp):
ATTATGATTCATTATCTTTTAGG
Found at i:1184268 original size:14 final size:15
Alignment explanation
Indices: 1184235--1184271 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1184225 ATTTTCAATA
1184235 GGAAACAAATAGAGG
1 GGAAACAAATAGAGG
1184250 GGAAACAAATAGAGG
1 GGAAACAAATAGAGG
*
1184265 GAAAACA
1 GGAAACA
1184272 GGAAGGTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.57, C:0.08, G:0.30, T:0.05
Consensus pattern (15 bp):
GGAAACAAATAGAGG
Found at i:1184584 original size:13 final size:13
Alignment explanation
Indices: 1184566--1184590 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1184556 GCTATTTAAT
1184566 ATATATAATATAC
1 ATATATAATATAC
1184579 ATATATAATATA
1 ATATATAATATA
1184591 TAGTTTTTTG
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
ATATATAATATAC
Found at i:1184708 original size:35 final size:37
Alignment explanation
Indices: 1184579--1184720 Score: 119
Period size: 35 Copynumber: 3.7 Consensus size: 37
1184569 TATAATATAC
** *
1184579 ATATATAATATATAGTTTTTTGAAA-ATGTTTCGAAAACAT
1 ATATATAATATATAGTTTTTAAAAACAT-TTT-G--AATAT
* *
1184619 ATATATAATATAGAGTTTTTTTAAAAAAAATATTTTGAATAT
1 ATATATAATATATAG--TTTTT---AAAAACATTTTGAATAT
*
1184661 ATATATAATATATAGTTTTTGAAAACATTTTGAA-A-
1 ATATATAATATATAGTTTTTAAAAACATTTTGAATAT
*
1184696 ATATATATTATATAGTTTTTAAAAA
1 ATATATAATATATAGTTTTTAAAAA
1184721 ATATATATTT
Statistics
Matches: 87, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
35 23 0.26
36 1 0.01
37 12 0.14
40 19 0.22
42 23 0.26
44 1 0.01
45 6 0.07
46 2 0.02
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (37 bp):
ATATATAATATATAGTTTTTAAAAACATTTTGAATAT
Found at i:1184754 original size:7 final size:7
Alignment explanation
Indices: 1184726--1184802 Score: 88
Period size: 7 Copynumber: 10.7 Consensus size: 7
1184716 AAAAAATATA
1184726 TATTTAT
1 TATTTAT
1184733 GTATTATAT
1 -TATT-TAT
1184742 TATATTATT
1 TAT-TTA-T
1184751 TATTGTAT
1 TATT-TAT
1184759 TATTTAT
1 TATTTAT
1184766 TA--TAT
1 TATTTAT
1184771 TA-TTAT
1 TATTTAT
1184777 TATTTAT
1 TATTTAT
1184784 TATTTAT
1 TATTTAT
1184791 TATTTAT
1 TATTTAT
1184798 TATTT
1 TATTT
1184803 TCATTTTCAT
Statistics
Matches: 63, Mismatches: 0, Indels: 13
0.83 0.00 0.17
Matches are distributed among these distances:
5 5 0.08
6 5 0.08
7 28 0.44
8 15 0.24
9 10 0.16
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (7 bp):
TATTTAT
Found at i:1184759 original size:9 final size:8
Alignment explanation
Indices: 1184726--1184827 Score: 58
Period size: 7 Copynumber: 12.6 Consensus size: 8
1184716 AAAAAATATA
*
1184726 TATTTATG
1 TATTTATT
1184734 TA-TTATAT
1 TATTTAT-T
1184742 TATATTATT
1 TAT-TTATT
1184751 TATTGTA-T
1 TATT-TATT
1184759 TATTTA-T
1 TATTTATT
1184766 TATATTA-T
1 TAT-TTATT
1184774 TA-TTATT
1 TATTTATT
1184781 TA-TTATT
1 TATTTATT
1184788 TA-TTATT
1 TATTTATT
1184795 TA-TTATTT
1 TATTTA-TT
1184803 TCATTTTCATTT
1 T-A-TTT-A-TT
1184815 TATTTATT
1 TATTTATT
1184823 TATTT
1 TATTT
1184828 TGTTTTTATT
Statistics
Matches: 82, Mismatches: 1, Indels: 22
0.78 0.01 0.21
Matches are distributed among these distances:
6 3 0.04
7 30 0.37
8 26 0.32
9 8 0.10
10 7 0.09
11 3 0.04
12 5 0.06
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (8 bp):
TATTTATT
Found at i:1184762 original size:3 final size:3
Alignment explanation
Indices: 1184729--1184801 Score: 55
Period size: 3 Copynumber: 23.7 Consensus size: 3
1184719 AAATATATAT
*
1184729 TTA TGTA TTA -TA TTA -TA TTA TTTA TT- GTA TTA TTTA TTA -TA TTA
1 TTA T-TA TTA TTA TTA TTA TTA -TTA TTA TTA TTA -TTA TTA TTA TTA
1184773 TTA TTA TTTA TTA TTTA TTA TTTA TTA TT
1 TTA TTA -TTA TTA -TTA TTA -TTA TTA TT
1184802 TTCATTTTCA
Statistics
Matches: 58, Mismatches: 2, Indels: 20
0.73 0.03 0.25
Matches are distributed among these distances:
2 7 0.12
3 33 0.57
4 18 0.31
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1184802 original size:21 final size:21
Alignment explanation
Indices: 1184726--1184802 Score: 88
Period size: 18 Copynumber: 3.6 Consensus size: 21
1184716 AAAAAATATA
1184726 TATTTATGTATTATATTATATTATT
1 TATTTAT-TATT-TATTAT-TTA-T
1184751 TATTGTATTATTTATTA--TAT
1 TATT-TATTATTTATTATTTAT
1184771 TA-TTATTATTTATTATTTAT
1 TATTTATTATTTATTATTTAT
1184791 TATTTATTATTT
1 TATTTATTATTT
1184803 TCATTTTCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
18 12 0.25
19 1 0.02
20 8 0.17
21 11 0.23
24 5 0.10
25 8 0.17
26 3 0.06
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (21 bp):
TATTTATTATTTATTATTTAT
Found at i:1191441 original size:19 final size:20
Alignment explanation
Indices: 1191419--1191456 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1191409 AATTAAATCA
*
1191419 AATATATAAT-TTAAAATTG
1 AATATAAAATCTTAAAATTG
1191438 AATATAAAATCTTAAAATT
1 AATATAAAATCTTAAAATT
1191457 TAATTGTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTG
Found at i:1191583 original size:13 final size:13
Alignment explanation
Indices: 1191567--1191602 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
1191557 TAAGATTTTC
1191567 TTTTTGAAAATCA
1 TTTTTGAAAATCA
1191580 TTTTTG-AAATCA
1 TTTTTGAAAATCA
*
1191592 ATTTTGAAAAT
1 TTTTTGAAAAT
1191603 TACTCTGCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (13 bp):
TTTTTGAAAATCA
Found at i:1193900 original size:21 final size:22
Alignment explanation
Indices: 1193852--1193906 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
1193842 CCCATAGGGG
1193852 GTATCGATACACATTCAAGGAAT
1 GTATCGATACACATTCAAGG-AT
* *
1193875 GTATCGGTACACATTCATGG-T
1 GTATCGATACACATTCAAGGAT
1193896 GTATCGATACA
1 GTATCGATACA
1193907 AGTATCGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 11 0.38
23 18 0.62
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (22 bp):
GTATCGATACACATTCAAGGAT
Found at i:1197003 original size:20 final size:22
Alignment explanation
Indices: 1196978--1197034 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 22
1196968 TCAACGTAAG
1196978 AGGTATCGGTACCT-TTGGC-T
1 AGGTATCGGTACCTCTTGGCAT
* *
1196998 AGGTATCGATACCTCTTTGCAT
1 AGGTATCGGTACCTCTTGGCAT
1197020 AGGGGTATCGGTACC
1 A--GGTATCGGTACC
1197035 CCATGGGGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 13 0.43
21 4 0.13
22 2 0.07
24 11 0.37
ACGTcount: A:0.19, C:0.21, G:0.28, T:0.32
Consensus pattern (22 bp):
AGGTATCGGTACCTCTTGGCAT
Found at i:1197420 original size:12 final size:12
Alignment explanation
Indices: 1197405--1197450 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
1197395 TTTAAGATTT
1197405 TTTTTAAAATCA
1 TTTTTAAAATCA
*
1197417 TTTTTTAAATCA
1 TTTTTAAAATCA
*
1197429 TTTTTTAAATCA
1 TTTTTAAAATCA
1197441 TTTTTTAAAA
1 -TTTTTAAAA
1197451 ATTGCTCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 23 0.74
13 8 0.26
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTTTAAAATCA
Found at i:1199734 original size:23 final size:23
Alignment explanation
Indices: 1199706--1199750 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1199696 ACCCATGGAG
1199706 GGGTATCAATACACATTCAAGGA
1 GGGTATCAATACACATTCAAGGA
**
1199729 GGGTATCCGTACACATTCAAGG
1 GGGTATCAATACACATTCAAGG
1199751 TGTATCGATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (23 bp):
GGGTATCAATACACATTCAAGGA
Found at i:1208759 original size:26 final size:26
Alignment explanation
Indices: 1208725--1208782 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
1208715 ATGATTAGAG
*
1208725 GATGATTAGAGTTATAAATCTCTCTA
1 GATGATTAGAGTTATAAACCTCTCTA
1208751 GATGATTAGAGTTATAAACCTCTCTA
1 GATGATTAGAGTTATAAACCTCTCTA
1208777 GATGAT
1 GATGAT
1208783 CCCACAGATG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.36
Consensus pattern (26 bp):
GATGATTAGAGTTATAAACCTCTCTA
Found at i:1213520 original size:25 final size:25
Alignment explanation
Indices: 1213483--1213532 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
1213473 ACCCAAAATT
*
1213483 AAATTTGTACAAACATATAAAAACAA
1 AAATTAGTACAAACA-ATAAAAACAA
*
1213509 AAATTAGT-CAAATAATAAAAACAA
1 AAATTAGTACAAACAATAAAAACAA
1213533 TTATAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 5 0.23
26 7 0.32
ACGTcount: A:0.64, C:0.10, G:0.04, T:0.22
Consensus pattern (25 bp):
AAATTAGTACAAACAATAAAAACAA
Found at i:1220212 original size:22 final size:22
Alignment explanation
Indices: 1220167--1220212 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
1220157 ATAATAATTA
* **
1220167 TTCTTTTATTTTTATTTTTTAT
1 TTCTTTTATTTTTATCTTAAAT
1220189 TTCTTTTATTTTTATCTTAAAT
1 TTCTTTTATTTTTATCTTAAAT
1220211 TT
1 TT
1220213 AGTAATATTT
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:0.17, C:0.07, G:0.00, T:0.76
Consensus pattern (22 bp):
TTCTTTTATTTTTATCTTAAAT
Found at i:1226743 original size:36 final size:36
Alignment explanation
Indices: 1226702--1226925 Score: 277
Period size: 36 Copynumber: 6.2 Consensus size: 36
1226692 CTTCTCCAAG
* *
1226702 CCAATCTTAGCCTTAACAGAAGAGAAGTGAAGCAAA
1 CCAATCTTAGCCTTCACAGAAGAGTAGTGAAGCAAA
* *
1226738 CCAATCTTAGCCTTCACAGAAGAGTAGTTAAACAAA
1 CCAATCTTAGCCTTCACAGAAGAGTAGTGAAGCAAA
* *
1226774 CCAATCTTAGCCTTCACAGAAAAGTAGTGAAGTAAA
1 CCAATCTTAGCCTTCACAGAAGAGTAGTGAAGCAAA
* * *
1226810 CAAATCTTAGCCTTCACATAAGAGTAGTGAAGCATA
1 CCAATCTTAGCCTTCACAGAAGAGTAGTGAAGCAAA
* *
1226846 TCAATCTTAAGCCTTCACGGAAGAGTAGTGAAGCAAA
1 CCAATCTT-AGCCTTCACAGAAGAGTAGTGAAGCAAA
* * *** *
1226883 TCAATCTTGGCCTTCTTGGATGAGTAGTGAAGCAAA
1 CCAATCTTAGCCTTCACAGAAGAGTAGTGAAGCAAA
*
1226919 TCAATCT
1 CCAATCT
1226926 CAAGTCTTAT
Statistics
Matches: 165, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
36 132 0.80
37 33 0.20
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (36 bp):
CCAATCTTAGCCTTCACAGAAGAGTAGTGAAGCAAA
Found at i:1227099 original size:46 final size:46
Alignment explanation
Indices: 1227032--1227222 Score: 184
Period size: 46 Copynumber: 3.9 Consensus size: 46
1227022 ATTTCTCGAG
*
1227032 TCTTATCTCCCTGAAACAAGAGTGGAGCAGATTCGTCTTCCTTGGA
1 TCTTATCTCCCTGAAACAAGAGTGGAGCAGATTCATCTTCCTTGGA
* * * * *
1227078 TCTTATCTCCCTGAAACAAGAGTGGAGCATATCCATTTTACAAAGATTTCTCGA
1 TCTTATCTCCCTGAAACAAGAGTGGAGCAGATTCATCTT-C------CT-TGGA
* * * *
1227132 GTCTTATCTCCCTAAAATAAGAGCGGAGCAAATTCATCTTTCCTTGGA
1 -TCTTATCTCCCTGAAACAAGAGTGGAGCAGATTCATC-TTCCTTGGA
* *
1227180 TCTTATCTCCCTGAAACAAGAGTGGAGCAGACTCATCATCCTT
1 TCTTATCTCCCTGAAACAAGAGTGGAGCAGATTCATCTTCCTT
1227223 AGATAGCTAG
Statistics
Matches: 115, Mismatches: 20, Indels: 20
0.74 0.13 0.13
Matches are distributed among these distances:
46 40 0.35
47 33 0.29
48 3 0.03
49 1 0.01
53 1 0.01
54 3 0.03
55 32 0.28
56 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (46 bp):
TCTTATCTCCCTGAAACAAGAGTGGAGCAGATTCATCTTCCTTGGA
Found at i:1227110 original size:101 final size:102
Alignment explanation
Indices: 1226923--1227208 Score: 493
Period size: 101 Copynumber: 2.8 Consensus size: 102
1226913 AGCAAATCAA
* *
1226923 TCTCAAGTCTTATCTCCCTGAAATAAGAGTGGAGCAGATTCGTCTTTCCTTGGATCTTATCTCCA
1 TCTCGAGTCTTATCTCCCTGAAATAAGAGTGGAGCAGATTCGTCTTTCCTTGGATCTTATCTCCC
*
1226988 TGAAACAATAGTGGAGCATATCCATTTTACAAAGATT
66 TGAAACAAGAGTGGAGCATATCCATTTTACAAAGATT
*
1227025 TCTCGAGTCTTATCTCCCTGAAACAAGAGTGGAGCAGATTCGTC-TTCCTTGGATCTTATCTCCC
1 TCTCGAGTCTTATCTCCCTGAAATAAGAGTGGAGCAGATTCGTCTTTCCTTGGATCTTATCTCCC
1227089 TGAAACAAGAGTGGAGCATATCCATTTTACAAAGATT
66 TGAAACAAGAGTGGAGCATATCCATTTTACAAAGATT
* * * *
1227126 TCTCGAGTCTTATCTCCCTAAAATAAGAGCGGAGCAAATTCATCTTTCCTTGGATCTTATCTCCC
1 TCTCGAGTCTTATCTCCCTGAAATAAGAGTGGAGCAGATTCGTCTTTCCTTGGATCTTATCTCCC
1227191 TGAAACAAGAGTGGAGCA
66 TGAAACAAGAGTGGAGCA
1227209 GACTCATCAT
Statistics
Matches: 174, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
101 94 0.54
102 80 0.46
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (102 bp):
TCTCGAGTCTTATCTCCCTGAAATAAGAGTGGAGCAGATTCGTCTTTCCTTGGATCTTATCTCCC
TGAAACAAGAGTGGAGCATATCCATTTTACAAAGATT
Found at i:1227618 original size:137 final size:137
Alignment explanation
Indices: 1227213--1227620 Score: 503
Period size: 137 Copynumber: 3.0 Consensus size: 137
1227203 GGAGCAGACT
* * * *
1227213 CATCATCCTTAGATAGCTAGACTTCCTCATCTTATAAGAACCATGTTATCTCAATTACCCCTACA
1 CATCATCCTTAGATAGCTAGACTTCCTCATCGTGTAAGAACCATGTTATCTCAATTAACCCTAAA
* ** * * *
1227278 GATGGCCAAATATCCTCATCTTGAAGGAACAATGTCATCCACAGACTAGATCTCTTCATCACGTA
66 GATGGCCAGATATCCTCATCAAGAAGGAACAATGTCATCCACTGACCATATCTCTTCATCACGTA
*
1227343 AGAGTCG
131 GGAGTCG
* * * * *
1227350 CGTCATCCTTAGATAGCTAGACTTCCTCATCGCGTATGAACCGTATTATCTCAATTAACCCTAAA
1 CATCATCCTTAGATAGCTAGACTTCCTCATCGTGTAAGAACCATGTTATCTCAATTAACCCTAAA
** * * * * *
1227415 GATTACCAGACATCCTCATCACGAAGGAACAATGTCATCCACTGACCATATCTCTTTACCATGTA
66 GATGGCCAGATATCCTCATCAAGAAGGAACAATGTCATCCACTGACCATATCTCTTCATCACGTA
1227480 GGAGTCG
131 GGAGTCG
* * * *
1227487 CATCATCCTTAGATAGAC-AGACTTCCTCATCGTGTAGGAACCTTGTTATCTCAATTATCCTTAA
1 CATCATCCTTAGATAG-CTAGACTTCCTCATCGTGTAAGAACCATGTTATCTCAATTAACCCTAA
* * * * * *
1227551 AGATGGTCAGATGTCCTCATCAAGAAAGAACAATATAATCCACTGACCATATCTCCTCATCACGT
65 AGATGGCCAGATATCCTCATCAAGAAGGAACAATGTCATCCACTGACCATATCTCTTCATCACGT
1227616 AGGAG
130 AGGAG
1227621 CAAGCATGTC
Statistics
Matches: 228, Mismatches: 42, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
137 227 1.00
138 1 0.00
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.28
Consensus pattern (137 bp):
CATCATCCTTAGATAGCTAGACTTCCTCATCGTGTAAGAACCATGTTATCTCAATTAACCCTAAA
GATGGCCAGATATCCTCATCAAGAAGGAACAATGTCATCCACTGACCATATCTCTTCATCACGTA
GGAGTCG
Done.