Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D13
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: 60343961
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 596159 characters in sequence are not A, C, G, or T
File 8 of 204
Found at i:2568403 original size:10 final size:10
Alignment explanation
Indices: 2568388--2568414 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2568378 ACATGACACA
2568388 ATAATATCTT
1 ATAATATCTT
2568398 ATAATATCTT
1 ATAATATCTT
2568408 ATAATAT
1 ATAATAT
2568415 AATAATATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATATCTT
Found at i:2582950 original size:34 final size:34
Alignment explanation
Indices: 2582907--2582972 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 34
2582897 AGTAAAATAT
2582907 TTTTCGTAAAATGATTT-CTGGAAAATATTTTAC
1 TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
2582940 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTC-GTAAAATGATTTACTGGAAAATATTTT
2582973 TTGGTGTTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 5 0.16
34 12 0.39
35 14 0.45
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.47
Consensus pattern (34 bp):
TTTTCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:2584476 original size:29 final size:29
Alignment explanation
Indices: 2584443--2584500 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
2584433 GATGTCCATT
2584443 GGTAAATAATGTGACTCATTAATACCTTA
1 GGTAAATAATGTGACTCATTAATACCTTA
*
2584472 GGTAAATAATGTGCCTCATTAATACCTTA
1 GGTAAATAATGTGACTCATTAATACCTTA
2584501 TTAGGAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (29 bp):
GGTAAATAATGTGACTCATTAATACCTTA
Found at i:2585288 original size:16 final size:15
Alignment explanation
Indices: 2585250--2585293 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 15
2585240 TTGATATGAA
*
2585250 TAAAATTATATTTTT
1 TAAATTTATATTTTT
2585265 TATTAATTTATATATTTT
1 TA--AATTTATAT-TTTT
2585283 TAAATTTATAT
1 TAAATTTATAT
2585294 CTACCACGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 2 0.08
16 9 0.36
17 8 0.32
18 6 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TAAATTTATATTTTT
Found at i:2594772 original size:16 final size:16
Alignment explanation
Indices: 2594751--2594802 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
2594741 TTTGGTTCAC
2594751 TGTATTGAATTAGAGG
1 TGTATTGAATTAGAGG
*
2594767 TGTATTGGATTAGAGG
1 TGTATTGAATTAGAGG
* *
2594783 TATAATGGAA-TAGAGG
1 TGT-ATTGAATTAGAGG
2594799 TGTA
1 TGTA
2594803 ATGGAATAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 1 0.03
16 25 0.83
17 4 0.13
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.35
Consensus pattern (16 bp):
TGTATTGAATTAGAGG
Found at i:2594804 original size:16 final size:16
Alignment explanation
Indices: 2594761--2594820 Score: 84
Period size: 16 Copynumber: 3.8 Consensus size: 16
2594751 TGTATTGAAT
* *
2594761 TAGAGGTGTATTGGAT
1 TAGAGGTGTAATGGAA
*
2594777 TAGAGGTATAATGGAA
1 TAGAGGTGTAATGGAA
2594793 TAGAGGTGTAATGGAA
1 TAGAGGTGTAATGGAA
*
2594809 TAGATGTGTAAT
1 TAGAGGTGTAAT
2594821 AGCAAATCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.35, C:0.00, G:0.33, T:0.32
Consensus pattern (16 bp):
TAGAGGTGTAATGGAA
Found at i:2595075 original size:18 final size:17
Alignment explanation
Indices: 2595054--2595088 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2595044 TTATTATTAA
*
2595054 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
2595072 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
2595089 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:2595135 original size:61 final size:61
Alignment explanation
Indices: 2595069--2595256 Score: 197
Period size: 61 Copynumber: 3.1 Consensus size: 61
2595059 TTTTAATTAA
*
2595069 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCAT
* * * * * * * * * * *
2595130 AATATATGATACT-ATAAAA-TATAAATTAA-C-ATAATTATTAT-TAAATATATTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAATCAAT-ATTCTTATATGAATTTACTAAAATCAT
*
2595189 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCAT
2595250 AATATAT
1 AATATAT
2595257 GATACTATAA
Statistics
Matches: 95, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
58 1 0.01
59 31 0.33
60 23 0.24
61 39 0.41
62 1 0.01
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATCAATATTCTTATATGAATTTACTAAAATCAT
Found at i:2595202 original size:14 final size:15
Alignment explanation
Indices: 2595153--2595204 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
2595143 ATAAAATATA
2595153 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
2595168 TATTAAATATATTAT
1 AATTAAATATATTAT
2595183 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
2595196 AATTTAATA
1 AATTAAATA
2595205 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:2595206 original size:59 final size:59
Alignment explanation
Indices: 2595037--2595333 Score: 180
Period size: 59 Copynumber: 5.0 Consensus size: 59
2595027 ATCATATTTA
* * * *
2595037 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAA-T
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAA-TATAAATT
* * * * * * *
2595096 AATCA-ATATTCTTATATGAATTTACTCA-AATCATAATATATGATACT-ATAAAATATAAATT
1 AA-CATA-ATTATTAT-TAAATATA-TTATAATTAAAATATATGAT-TTAATAAAATATAAATT
* *
2595157 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATT
1 AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAA-T-AT-A-AATT
* * * * * * * * * *
2595220 -A-AT-ATTCTTATATGAATTTACTAAAATCATAATATATGATACT-ATAAAAGATAATTT
1 AACATAATTATTAT-TAAATATATTATAATTAAAATATATGAT-TTAATAAAATATAAATT
* * *
2595277 GAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATTTAAA
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATATAAA
2595334 ATAATTATAA
Statistics
Matches: 174, Mismatches: 45, Indels: 38
0.68 0.18 0.15
Matches are distributed among these distances:
57 3 0.02
58 5 0.03
59 62 0.36
60 36 0.21
61 59 0.34
62 5 0.03
63 4 0.02
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (59 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATGATTTAATAAAATATAAATT
Found at i:2595250 original size:120 final size:121
Alignment explanation
Indices: 2595037--2595329 Score: 509
Period size: 120 Copynumber: 2.4 Consensus size: 121
2595027 ATCATATTTA
2595037 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
* *
2595102 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT-
66 TATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATAAATTG
* *
2595157 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
*
2595222 TATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATAATTTG
66 TATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATAAATTG
* *
2595278 AA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATT
2595330 TAAAATAATT
Statistics
Matches: 164, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
120 162 0.99
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (121 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATCAA
TATTCTTATATGAATTTACTAAAATCATAATATATGATACTATAAAAGATAAATTG
Found at i:2595377 original size:101 final size:93
Alignment explanation
Indices: 2595270--2595552 Score: 317
Period size: 91 Copynumber: 3.0 Consensus size: 93
2595260 ACTATAAAAG
* * * *
2595270 ATAATTTGAAATAATTAATATTAAATATATTTTAATTAA-AATATATGATTTAATAAAATTTAAA
1 ATAATTTAAAATAATTAATATTAAATATAATTTAA-TAATAATATATAATTTCATAAAATTT---
* *
2595334 ATAATTATAACTAATAAATTATCTTATATGAATTTGT
62 -T--CT-TAA-TAATAAATTATCTTATATGAATTTAT
* *
2595371 ATAATTTAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
* *
2595434 GATAATAAATTTTCTTATATGAATTTAT
66 AATAATAAATTATCTTATATGAATTTAT
* *
2595462 ACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCATAAAA--TTCTT
1 ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
2595525 AATAATAAAATGT-TCTTATATGAATTTA
66 AATAAT-AAAT-TATCTTATATGAATTTA
2595553 CTAAAATCAA
Statistics
Matches: 164, Mismatches: 15, Indels: 15
0.85 0.08 0.08
Matches are distributed among these distances:
91 88 0.54
92 21 0.13
93 2 0.01
95 1 0.01
99 1 0.01
100 3 0.02
101 48 0.29
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (93 bp):
ATAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCATAAAATTTTCTT
AATAATAAATTATCTTATATGAATTTAT
Found at i:2595399 original size:26 final size:28
Alignment explanation
Indices: 2595370--2595430 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
2595360 TATGAATTTG
*
2595370 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
2595396 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
2595424 TAAAATT
1 TATAATT
2595431 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:2595428 original size:47 final size:46
Alignment explanation
Indices: 2595377--2595520 Score: 113
Period size: 47 Copynumber: 3.1 Consensus size: 46
2595367 TTGTATAATT
2595377 TAAAATAATTATTATTACATATAATTTAATAATAATATATAATTTCA
1 TAAAATAATTATTATTA-ATATAATTTAATAATAATATATAATTTCA
* ** * *
2595424 TAAAAT--TCT-TGA-TAATA-AATTTTCTTATATGAATTTATACAATT--
1 TAAAATAAT-TATTATTAATATAA-TTTAATA-AT-AATATATA-ATTTCA
* *
2595468 TAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCA
1 TAAAATAATTATTATT-AATATAATTTAATAATAATATATAATTTCA
2595515 TAAAAT
1 TAAAAT
2595521 TCTTAATAAT
Statistics
Matches: 72, Mismatches: 12, Indels: 26
0.65 0.11 0.24
Matches are distributed among these distances:
42 2 0.03
43 8 0.11
44 10 0.14
45 14 0.19
46 12 0.17
47 15 0.21
48 9 0.12
49 2 0.03
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (46 bp):
TAAAATAATTATTATTAATATAATTTAATAATAATATATAATTTCA
Found at i:2595440 original size:91 final size:90
Alignment explanation
Indices: 2595345--2595552 Score: 326
Period size: 91 Copynumber: 2.3 Consensus size: 90
2595335 TAATTATAAC
* * * *
2595345 TAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAATTTAATAAT
1 TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
2595410 AATATATAATTTCATAAAATTCTTGA
65 AATATATAATTTCATAAAATTCTTAA
2595436 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
1 TAATAAA-TTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAAT
*
2595501 GATATATAATTTCATAAAATTCTTAA
65 AATATATAATTTCATAAAATTCTTAA
2595527 TAATAAAATGTTCTTATATGAATTTA
1 TAAT-AAAT-TTCTTATATGAATTTA
2595553 CTAAAATCAA
Statistics
Matches: 108, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
91 87 0.81
92 21 0.19
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (90 bp):
TAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATA
ATATATAATTTCATAAAATTCTTAA
Found at i:2595512 original size:44 final size:43
Alignment explanation
Indices: 2595370--2595512 Score: 119
Period size: 44 Copynumber: 3.2 Consensus size: 43
2595360 TATGAATTTG
* *
2595370 TATAATTTAAAATAATTATTATTACATATAATTTAATAATAATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
** * * * *
2595414 TATAATTTCATAAAATTCTTGATAATAAAT-T-TTCTTATATGAATTTA
1 TATAA-TT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
2595461 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
2595505 TATAATTT
1 TATAATTT
2595513 CATAAAATTC
Statistics
Matches: 74, Mismatches: 16, Indels: 18
0.69 0.15 0.17
Matches are distributed among these distances:
43 3 0.04
44 32 0.43
45 7 0.09
46 7 0.09
47 22 0.30
48 3 0.04
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.46
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:2595527 original size:47 final size:47
Alignment explanation
Indices: 2595395--2595533 Score: 137
Period size: 47 Copynumber: 3.0 Consensus size: 47
2595385 TTATTATTAC
* *
2595395 ATATAATTTAATAATAATATATAATTTCATAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
* * * ** *
2595442 AT-T--TTCTTAT-ATGAATTTATACAATT--TAAAATAATTAATATTAA
1 ATATAATT-TAATAATG-ATATATA-ATTTCATAAAATTCTTAATAATAA
2595486 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
2595533 A
1 A
2595534 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 14, Indels: 18
0.68 0.14 0.18
Matches are distributed among these distances:
44 20 0.29
45 13 0.19
46 13 0.19
47 23 0.33
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (47 bp):
ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
Found at i:2599160 original size:62 final size:59
Alignment explanation
Indices: 2599047--2599160 Score: 138
Period size: 62 Copynumber: 1.9 Consensus size: 59
2599037 ATTGAACCTA
* * **
2599047 AAAAAAACTTAGGTACCAAATTAGGAAAAAATGTCAGGTTCAGGTGCCAAATTGGGCCC
1 AAAAAAACTTAGGGACCAAATTAGGAAAAAATGTAAAATTCAGGTGCCAAATTGGGCCC
* * *
2599106 AAAAAAATTTAGGGACCAAATTAGGGAAAAAAAATGTAAAATTTAGGTTCCAAAT
1 AAAAAAACTTAGGGACCAAATTA-GG--AAAAAATGTAAAATTCAGGTGCCAAAT
2599161 GTTACATTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
59 21 0.47
60 2 0.04
62 22 0.49
ACGTcount: A:0.46, C:0.12, G:0.19, T:0.22
Consensus pattern (59 bp):
AAAAAAACTTAGGGACCAAATTAGGAAAAAATGTAAAATTCAGGTGCCAAATTGGGCCC
Found at i:2608822 original size:9 final size:9
Alignment explanation
Indices: 2608808--2608853 Score: 56
Period size: 9 Copynumber: 5.0 Consensus size: 9
2608798 TTTCATTTTC
2608808 TTATAATTT
1 TTATAATTT
2608817 TTATAATGTT
1 TTATAAT-TT
*
2608827 TTACAATTT
1 TTATAATTT
* *
2608836 TTAAAAGTT
1 TTATAATTT
2608845 TTATAATTT
1 TTATAATTT
2608854 AAAAATTACA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
9 23 0.74
10 8 0.26
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (9 bp):
TTATAATTT
Found at i:2609467 original size:51 final size:51
Alignment explanation
Indices: 2609372--2609469 Score: 124
Period size: 51 Copynumber: 1.9 Consensus size: 51
2609362 ATTTTTTGAT
* * * *
2609372 TTTTTTAGAATTAGGATTAAATTGATATCATTTGCAAATCTTGAGGGTTAA
1 TTTTTTAAAATTAGGATTAAATTGATATAATATGCAAAACTTGAGGGTTAA
* * * *
2609423 TTTTTTAAAATTATGATTCAATTGATATAATATGTAAAAGTTGAGGG
1 TTTTTTAAAATTAGGATTAAATTGATATAATATGCAAAACTTGAGGG
2609470 CTAAATTTAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 39 1.00
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.43
Consensus pattern (51 bp):
TTTTTTAAAATTAGGATTAAATTGATATAATATGCAAAACTTGAGGGTTAA
Found at i:2609988 original size:13 final size:11
Alignment explanation
Indices: 2609923--2609981 Score: 58
Period size: 11 Copynumber: 5.9 Consensus size: 11
2609913 ATTTTTTTAA
2609923 TTTTAAAATAT
1 TTTTAAAATAT
2609934 TTTTAAAATAT
1 TTTTAAAATAT
2609945 TTTT--AAT-T
1 TTTTAAAATAT
* *
2609953 TTTT---TTAA
1 TTTTAAAATAT
2609961 TTTTAAAATAT
1 TTTTAAAATAT
2609972 TTTTAAAATA
1 TTTTAAAATA
2609982 AATTTTTGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
7 1 0.03
8 9 0.22
9 3 0.08
11 27 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:2610238 original size:2 final size:2
Alignment explanation
Indices: 2610231--2610258 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2610221 AGATCATTTA
2610231 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
2610259 CGATTTTCTA
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:2628140 original size:2 final size:2
Alignment explanation
Indices: 2628133--2628161 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2628123 TATTTATACT
2628133 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2628162 CCATTAGTTT
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):
TA
Found at i:2628278 original size:16 final size:14
Alignment explanation
Indices: 2628252--2628291 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
2628242 ACTATTATAA
2628252 TTATT-TATATATC
1 TTATTATATATATC
2628265 TTTATATATATATATC
1 -TTAT-TATATATATC
2628281 TTATTATATAT
1 TTATTATATAT
2628292 GTGTATACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 11 0.46
15 5 0.21
16 8 0.33
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTATATATATC
Found at i:2636885 original size:13 final size:13
Alignment explanation
Indices: 2636865--2636941 Score: 73
Period size: 13 Copynumber: 5.7 Consensus size: 13
2636855 TTTCAACATT
2636865 TATTTAAAACAAA
1 TATTTAAAACAAA
* **
2636878 TATCTAAAACATT
1 TATTTAAAACAAA
*
2636891 TATTTAAATATTTAAA
1 TATTTAAA-A--CAAA
2636907 TATTTAAAACAAA
1 TATTTAAAACAAA
**
2636920 TATTTAAAACATT
1 TATTTAAAACAAA
2636933 TATTTAAAA
1 TATTTAAAA
2636942 TTTCTTAGTT
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
13 40 0.78
14 1 0.02
15 1 0.02
16 9 0.18
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.40
Consensus pattern (13 bp):
TATTTAAAACAAA
Found at i:2636900 original size:21 final size:20
Alignment explanation
Indices: 2636875--2636940 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
2636865 TATTTAAAAC
2636875 AAATATCTAAAACATTTATTT
1 AAATAT-TAAAACATTTATTT
* * ***
2636896 AAATATTTAAATATTTAAAAC
1 AAATATTAAAACATTT-ATTT
2636917 AAATATTTAAAACATTTATTT
1 AAATA-TTAAAACATTTATTT
2636938 AAA
1 AAA
2636941 ATTTCTTAGT
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
20 8 0.24
21 16 0.48
22 9 0.27
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATATTAAAACATTTATTT
Found at i:2636912 original size:42 final size:41
Alignment explanation
Indices: 2636865--2636944 Score: 142
Period size: 42 Copynumber: 1.9 Consensus size: 41
2636855 TTTCAACATT
2636865 TATTTAAAACAAATATCTAAAACATTTATTTAAATATTTAAA
1 TATTTAAAACAAATATCTAAAACATTTATTTAAA-ATTTAAA
*
2636907 TATTTAAAACAAATATTTAAAACATTTATTTAAAATTT
1 TATTTAAAACAAATATCTAAAACATTTATTTAAAATTT
2636945 CTTAGTTTGT
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
41 4 0.11
42 33 0.89
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.42
Consensus pattern (41 bp):
TATTTAAAACAAATATCTAAAACATTTATTTAAAATTTAAA
Found at i:2637229 original size:22 final size:20
Alignment explanation
Indices: 2637198--2637260 Score: 58
Period size: 22 Copynumber: 3.1 Consensus size: 20
2637188 TTATATTTTT
*
2637198 AAAAAA-TAAAAAATTTTCAA
1 AAAAAATTAAAAAATTAT-AA
*
2637218 AAAAAATCTAAAATATATATAA
1 AAAAAAT-TAAAAAAT-TATAA
*
2637240 AGAAAATTAAAAAATTA-AA
1 AAAAAATTAAAAAATTATAA
2637259 AA
1 AA
2637261 TTTTCTAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
19 3 0.09
20 8 0.23
21 7 0.20
22 15 0.43
23 2 0.06
ACGTcount: A:0.71, C:0.03, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAAATTAAAAAATTATAA
Found at i:2644210 original size:13 final size:12
Alignment explanation
Indices: 2644192--2644230 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 12
2644182 AGAGTTATTG
2644192 ATATTTATTTATA
1 ATATTTA-TTATA
2644205 ATATTTATTATTA
1 ATATTTATTA-TA
2644218 ATATTTAATTATA
1 ATATTT-ATTATA
2644231 TTTAAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.12
13 17 0.71
14 4 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
ATATTTATTATA
Found at i:2653128 original size:20 final size:20
Alignment explanation
Indices: 2653092--2653129 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2653082 ACAACACACG
*
2653092 GCCATGAAGAAGGAAAAGAA
1 GCCATGAAGAAGAAAAAGAA
2653112 GCCAT-AAGAGAGAAAAAG
1 GCCATGAAGA-AGAAAAAG
2653130 GAATATGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.55, C:0.11, G:0.29, T:0.05
Consensus pattern (20 bp):
GCCATGAAGAAGAAAAAGAA
Found at i:2659878 original size:9 final size:9
Alignment explanation
Indices: 2659810--2659876 Score: 98
Period size: 9 Copynumber: 7.4 Consensus size: 9
2659800 GTAGTGATTC
*
2659810 AATTTGGTT
1 AATTCGGTT
*
2659819 AATTCGGGT
1 AATTCGGTT
2659828 AATTCGGTT
1 AATTCGGTT
*
2659837 AATTCGGGT
1 AATTCGGTT
2659846 AATTCGGTT
1 AATTCGGTT
2659855 AATTCGGTT
1 AATTCGGTT
*
2659864 AATTTGGTT
1 AATTCGGTT
2659873 AATT
1 AATT
2659877 TGATTAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 52 1.00
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:2659883 original size:18 final size:18
Alignment explanation
Indices: 2659810--2659886 Score: 100
Period size: 18 Copynumber: 4.3 Consensus size: 18
2659800 GTAGTGATTC
*
2659810 AATTTGGTTAATTCGGGT
1 AATTTGGTTAATTCGGTT
* *
2659828 AATTCGGTTAATTCGGGT
1 AATTTGGTTAATTCGGTT
*
2659846 AATTCGGTTAATTCGGTT
1 AATTTGGTTAATTCGGTT
* *
2659864 AATTTGGTTAATTTGATT
1 AATTTGGTTAATTCGGTT
2659882 AATTT
1 AATTT
2659887 TTAACCAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 54 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (18 bp):
AATTTGGTTAATTCGGTT
Found at i:2659883 original size:27 final size:27
Alignment explanation
Indices: 2659810--2659885 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
2659800 GTAGTGATTC
*
2659810 AATTTGGTTAATTCGGGTAATTCGGTT
1 AATTTGGTTAATTCGGTTAATTCGGTT
* *
2659837 AATTCGGGTAATTCGGTTAATTCGGTT
1 AATTTGGTTAATTCGGTTAATTCGGTT
* *
2659864 AATTTGGTTAATTTGATTAATT
1 AATTTGGTTAATTCGGTTAATT
2659886 TTTAACCAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.25, C:0.07, G:0.22, T:0.46
Consensus pattern (27 bp):
AATTTGGTTAATTCGGTTAATTCGGTT
Found at i:2660037 original size:12 final size:12
Alignment explanation
Indices: 2660020--2660044 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2660010 TGTTATTTCA
2660020 GGTCGGTTAACC
1 GGTCGGTTAACC
2660032 GGTCGGTTAACC
1 GGTCGGTTAACC
2660044 G
1 G
2660045 AATAAACACC
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:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:2663686 original size:3 final size:3
Alignment explanation
Indices: 2663678--2663706 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2663668 ACGTCAGCTC
2663678 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2663707 CGTCCTCGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:2674078 original size:13 final size:13
Alignment explanation
Indices: 2674060--2674090 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2674050 ATTATTTTTC
2674060 TAATTTTGATATG
1 TAATTTTGATATG
2674073 TAATTTTGATATG
1 TAATTTTGATATG
*
2674086 CAATT
1 TAATT
2674091 ATATCATCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.03, G:0.13, T:0.52
Consensus pattern (13 bp):
TAATTTTGATATG
Found at i:2683076 original size:19 final size:19
Alignment explanation
Indices: 2683034--2683084 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 19
2683024 AAAAATTACA
2683034 AAAAATTCAAAATAATTTT
1 AAAAATTCAAAATAATTTT
*
2683053 TAAAATTCAAAAT-ATTTAT
1 AAAAATTCAAAATAATTT-T
2683072 AAAAATTCTAAAA
1 AAAAATTC-AAAA
2683085 CATATAGAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 4 0.14
19 20 0.71
20 4 0.14
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (19 bp):
AAAAATTCAAAATAATTTT
Found at i:2689063 original size:22 final size:22
Alignment explanation
Indices: 2689038--2689086 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2689028 TGGTGTAAAA
*
2689038 TATATAAACAAATTAATGAAAT
1 TATATAAACAAATAAATGAAAT
* * *
2689060 TATAAAAATAAATAAATTAAAT
1 TATATAAACAAATAAATGAAAT
2689082 TATAT
1 TATAT
2689087 CAAAATTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TATATAAACAAATAAATGAAAT
Found at i:2690448 original size:21 final size:23
Alignment explanation
Indices: 2690422--2690464 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
2690412 TATTTAGATT
2690422 ATATTTTCAATTA-AT-TAAAAA
1 ATATTTTCAATTATATGTAAAAA
*
2690443 ATATTTTTAATTATATGTAAAA
1 ATATTTTCAATTATATGTAAAA
2690465 GTTAAAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATTTTCAATTATATGTAAAAA
Found at i:2696213 original size:3 final size:3
Alignment explanation
Indices: 2696205--2696238 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
2696195 AAACAATGTG
2696205 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2696239 ACACATTAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2697046 original size:18 final size:17
Alignment explanation
Indices: 2697025--2697058 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2697015 GATTTAAAAA
2697025 AGAAAAAAAATACATAAG
1 AGAAAAAAAATA-ATAAG
*
2697043 AGAATAAAAATAATAA
1 AGAAAAAAAATAATAA
2697059 ATCGAAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.74, C:0.03, G:0.09, T:0.15
Consensus pattern (17 bp):
AGAAAAAAAATAATAAG
Found at i:2701913 original size:40 final size:40
Alignment explanation
Indices: 2701853--2701980 Score: 136
Period size: 40 Copynumber: 3.2 Consensus size: 40
2701843 AACACACCAG
* * * *
2701853 TTTGGCACCCAGTGCCTCATCGGATAATTTGAAATAATAA
1 TTTGACACCCAATGCCTCATCGGATAATCTGAAGTAATAA
* * *
2701893 TTTGACACCCAATGTCTCATCGGCTAAACTGAAGT-A-AA
1 TTTGACACCCAATGCCTCATCGGATAATCTGAAGTAATAA
* * *
2701931 -TTGGCACCCAATGCCTCATCGAATATATCCGAAGTAATAA
1 TTTGACACCCAATGCCTCATCGGATA-ATCTGAAGTAATAA
2701971 TTTGACACCC
1 TTTGACACCC
2701981 TGTGTCTCAT
Statistics
Matches: 70, Mismatches: 14, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
37 21 0.30
38 9 0.13
39 2 0.03
40 30 0.43
41 8 0.11
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (40 bp):
TTTGACACCCAATGCCTCATCGGATAATCTGAAGTAATAA
Found at i:2702138 original size:13 final size:13
Alignment explanation
Indices: 2702122--2702146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2702112 ATTCAAATAA
2702122 TCAATATATATAT
1 TCAATATATATAT
2702135 TCAATATATATA
1 TCAATATATATA
2702147 CCAATTCAAT
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:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (13 bp):
TCAATATATATAT
Found at i:2702169 original size:15 final size:16
Alignment explanation
Indices: 2702125--2702171 Score: 53
Period size: 15 Copynumber: 2.9 Consensus size: 16
2702115 CAAATAATCA
*
2702125 ATATATATATTCAA-T
1 ATATATAAATTCAATT
2702140 ATATATACCAATTCAATT
1 ATATATA--AATTCAATT
2702158 A-ATATAAATTCAAT
1 ATATATAAATTCAAT
2702172 AAATTCATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 15 0.54
17 11 0.39
18 2 0.07
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATATAAATTCAATT
Found at i:2702963 original size:5 final size:5
Alignment explanation
Indices: 2702955--2703045 Score: 86
Period size: 5 Copynumber: 18.8 Consensus size: 5
2702945 ATTTATTTAT
2702955 TATAA TATAA TATAA TATAA TATAA TATAA TATAATA TATAA TATAA TAT-A
1 TATAA TATAA TATAA TATAA TATAA TATAA TAT-A-A TATAA TATAA TATAA
* * *
2703006 TATAC T-TAA TA-AT TA-AGA TATAA TAT-- TATAT TATAA TATA
1 TATAA TATAA TATAA TATA-A TATAA TATAA TATAA TATAA TATA
2703046 TTTTAACTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
3 3 0.04
4 11 0.15
5 52 0.71
6 3 0.04
7 4 0.05
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (5 bp):
TATAA
Found at i:2702980 original size:20 final size:20
Alignment explanation
Indices: 2702955--2703045 Score: 86
Period size: 18 Copynumber: 4.7 Consensus size: 20
2702945 ATTTATTTAT
2702955 TATAATATAATATAATATAA
1 TATAATATAATATAATATAA
2702975 TATAATATAATATAATATATAA
1 TATAATATAATAT-A-ATATAA
*
2702997 TATAATAT-ATATACT-TAA
1 TATAATATAATATAATATAA
*
2703015 TA-ATTA-AGATATAATAT--
1 TATAATATA-ATATAATATAA
*
2703032 TATATTATAATATA
1 TATAATATAATATA
2703046 TTTTAACTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 16
0.76 0.04 0.20
Matches are distributed among these distances:
17 5 0.08
18 20 0.33
19 3 0.05
20 14 0.23
21 5 0.08
22 14 0.23
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (20 bp):
TATAATATAATATAATATAA
Found at i:2702999 original size:32 final size:34
Alignment explanation
Indices: 2702959--2703045 Score: 105
Period size: 32 Copynumber: 2.7 Consensus size: 34
2702949 ATTTATTATA
*
2702959 ATATAATATAATATAATATAATATAAT-A-TAAT
1 ATATAATATAATATAATATAATATAATAATTAAG
*
2702991 ATATAATATAATAT-ATATACT-TAATAATTAAG
1 ATATAATATAATATAATATAATATAATAATTAAG
*
2703023 ATATAATAT--TATATTATAATATA
1 ATATAATATAATATAATATAATATA
2703046 TTTTAACTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
30 7 0.15
31 12 0.26
32 28 0.60
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (34 bp):
ATATAATATAATATAATATAATATAATAATTAAG
Found at i:2706617 original size:30 final size:30
Alignment explanation
Indices: 2706554--2706655 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 30
2706544 TAAAAAATAA
* * *
2706554 AAATTGCATTTTGACACCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAAC-TTTCATT
* * * *
2706584 AAATTTTATTTTTACCCTTAAACTTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
* *
2706614 AAATTTCACTTAGACCCCTAAACTTTCATT
1 AAATTTCATTTTGACCCCTAAACTTTCATT
2706644 AAATTTCATTTT
1 AAATTTCATTTT
2706656 AATCCTAAAT
Statistics
Matches: 57, Mismatches: 14, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 4 0.07
30 53 0.93
ACGTcount: A:0.30, C:0.21, G:0.03, T:0.46
Consensus pattern (30 bp):
AAATTTCATTTTGACCCCTAAACTTTCATT
Found at i:2706938 original size:10 final size:10
Alignment explanation
Indices: 2706919--2706968 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
2706909 TTTTTCGAAG
*
2706919 GAAAAAAGAA
1 GAAAAGAGAA
2706929 GAAAAGAGAA
1 GAAAAGAGAA
2706939 GAAAAGAGAA
1 GAAAAGAGAA
* *
2706949 -AGAGGAGAA
1 GAAAAGAGAA
2706958 GAAAAGA-AA
1 GAAAAGAGAA
2706967 GA
1 GA
2706969 GTACCGGCGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
9 11 0.32
10 23 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (10 bp):
GAAAAGAGAA
Found at i:2706969 original size:17 final size:19
Alignment explanation
Indices: 2706922--2706964 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
2706912 TTCGAAGGAA
2706922 AAAAGAAGAAA-A-GAGAAG
1 AAAAG-AGAAAGAGGAGAAG
2706940 AAAAGAGAAAGAGGAGAAG
1 AAAAGAGAAAGAGGAGAAG
2706959 AAAAGA
1 AAAAGA
2706965 AAGAGTACCG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 5 0.22
18 6 0.26
19 12 0.52
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (19 bp):
AAAAGAGAAAGAGGAGAAG
Found at i:2707040 original size:3 final size:3
Alignment explanation
Indices: 2707034--2707068 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
2707024 GTGTAGGAGG
*
2707034 AGA AGA AGA AGA AGA AGA AGA AGAA AGA ATA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA A
2707069 AGAAAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:2707067 original size:10 final size:10
Alignment explanation
Indices: 2707034--2707082 Score: 57
Period size: 10 Copynumber: 5.1 Consensus size: 10
2707024 GTGTAGGAGG
2707034 AGAAG-AAGA
1 AGAAGAAAGA
2707043 AGAAG-AAGA
1 AGAAGAAAGA
2707052 AGAAGAAAGA
1 AGAAGAAAGA
*
2707062 ATAAGAAAGA
1 AGAAGAAAGA
* *
2707072 AAAAAAAAGA
1 AGAAGAAAGA
2707082 A
1 A
2707083 AAAAAATTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
9 14 0.39
10 22 0.61
ACGTcount: A:0.73, C:0.00, G:0.24, T:0.02
Consensus pattern (10 bp):
AGAAGAAAGA
Found at i:2707248 original size:14 final size:14
Alignment explanation
Indices: 2707202--2707268 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
2707192 CAACACAAAA
2707202 AAAAACAAATCAGCCC
1 AAAAA-AAA-CAGCCC
* ***
2707218 AAAAAAACCAAAGC
1 AAAAAAAACAGCCC
2707232 AAAAAAAACAGCCC
1 AAAAAAAACAGCCC
2707246 AAAAAGAAA-AGGCCC
1 AAAAA-AAACA-GCCC
2707261 AAAAAAAA
1 AAAAAAAA
2707269 GAAAAAACAG
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
14 22 0.54
15 14 0.34
16 5 0.12
ACGTcount: A:0.67, C:0.22, G:0.09, T:0.01
Consensus pattern (14 bp):
AAAAAAAACAGCCC
Found at i:2707407 original size:7 final size:7
Alignment explanation
Indices: 2707384--2707478 Score: 95
Period size: 7 Copynumber: 13.1 Consensus size: 7
2707374 CAGGCCAGGA
2707384 AAAAAAG
1 AAAAAAG
*
2707391 AGAGAAAG
1 A-AAAAAG
2707399 AAAAAAG
1 AAAAAAG
2707406 AAAAAAG
1 AAAAAAG
*
2707413 AAAGAAG
1 AAAAAAG
2707420 AAAAAAG
1 AAAAAAG
*
2707427 AAAAGAG
1 AAAAAAG
2707434 AAAAAAAGG
1 -AAAAAA-G
2707443 AAAAAAGG
1 AAAAAA-G
2707451 AAAAAAG
1 AAAAAAG
2707458 AAGAAAA-
1 AA-AAAAG
*
2707465 AAGAAA-
1 AAAAAAG
2707471 AAAAAAG
1 AAAAAAG
2707478 A
1 A
2707479 GTTTCAATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
6 8 0.11
7 37 0.49
8 29 0.39
9 1 0.01
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:2707428 original size:10 final size:10
Alignment explanation
Indices: 2707396--2707478 Score: 82
Period size: 10 Copynumber: 8.1 Consensus size: 10
2707386 AAAAGAGAGA
2707396 AAGAAAAAAG
1 AAGAAAAAAG
*
2707406 AAAAAAGAAAG
1 AAGAAA-AAAG
2707417 AAGAAAAAAG
1 AAGAAAAAAG
2707427 AAAAGAGAAAAA-
1 --AAGA-AAAAAG
2707439 AAGGAAAAAAG
1 AA-GAAAAAAG
2707450 --GAAAAAAG
1 AAGAAAAAAG
2707458 AAGAAAAAAG
1 AAGAAAAAAG
*
2707468 AAAAAAAAAG
1 AAGAAAAAAG
2707478 A
1 A
2707479 GTTTCAATTC
Statistics
Matches: 62, Mismatches: 3, Indels: 16
0.77 0.04 0.20
Matches are distributed among these distances:
8 8 0.13
10 34 0.55
11 11 0.18
12 4 0.06
13 5 0.08
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAG
Found at i:2707430 original size:26 final size:25
Alignment explanation
Indices: 2707383--2707478 Score: 90
Period size: 26 Copynumber: 3.8 Consensus size: 25
2707373 GCAGGCCAGG
*
2707383 AAAAAAAGAGAGAAAGAA-AAAAGAA
1 AAAAAAAGA-AGAAAAAAGAAAAGAA
*
2707408 AAAAGAAAGAAGAAAAAAGAAAAGAG
1 AAAA-AAAGAAGAAAAAAGAAAAGAA
2707434 AAAAAAAG--GAAAAAAGGAAAAAAGAA
1 AAAAAAAGAAGAAAAAA-G--AAAAGAA
* *
2707460 GAAAAAAGAAAAAAAAAGA
1 AAAAAAAGAAGAAAAAAGA
2707479 GTTTCAATTC
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
23 7 0.12
24 1 0.02
25 16 0.27
26 28 0.47
27 1 0.02
28 6 0.10
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (25 bp):
AAAAAAAGAAGAAAAAAGAAAAGAA
Found at i:2707468 original size:51 final size:51
Alignment explanation
Indices: 2707382--2707478 Score: 135
Period size: 51 Copynumber: 1.9 Consensus size: 51
2707372 AGCAGGCCAG
* *
2707382 GAAAAAAAGAGAGAAAGAAAAAAGAAAAAAGAAAGAAGAAAAAAGAAAAGA
1 GAAAAAAAGAGAAAAAGAAAAAAGAAAAAAGAAAGAAAAAAAAAGAAAAGA
*
2707433 GAAAAAAAG-GAAAAAAGGAAAAAAGAAGAAA-AAAGAAAAAAAAAGA
1 GAAAAAAAGAG-AAAAA-GAAAAAAGAAAAAAGAAAGAAAAAAAAAGA
2707479 GTTTCAATTC
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
50 1 0.02
51 27 0.66
52 13 0.32
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (51 bp):
GAAAAAAAGAGAAAAAGAAAAAAGAAAAAAGAAAGAAAAAAAAAGAAAAGA
Found at i:2708060 original size:19 final size:21
Alignment explanation
Indices: 2708020--2708061 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
2708010 AATTTTGTGT
*
2708020 AAAAAAATCCAGTGTTTTCAA
1 AAAAAAATCCAGTGTTTCCAA
2708041 AAAAAAATCCA-T-TTTCCAA
1 AAAAAAATCCAGTGTTTCCAA
2708060 AA
1 AA
2708062 TTTTTAGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 8 0.40
20 1 0.05
21 11 0.55
ACGTcount: A:0.52, C:0.17, G:0.05, T:0.26
Consensus pattern (21 bp):
AAAAAAATCCAGTGTTTCCAA
Found at i:2708131 original size:18 final size:17
Alignment explanation
Indices: 2708057--2708219 Score: 159
Period size: 17 Copynumber: 9.4 Consensus size: 17
2708047 ATCCATTTTC
* *
2708057 CAAAATTTTTAGTGTCTT
1 CAAAAATTTTCGTGT-TT
*
2708075 CTAAAAATTTTTGTGTTT
1 C-AAAAATTTTCGTGTTT
2708093 CAAAAATTTTCGT-TTT
1 CAAAAATTTTCGTGTTT
*
2708109 CAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTT
2708126 CAAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
* *
2708144 CAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTT
** *
2708161 CAAAAATCATCTTGTTTT
1 CAAAAATTTTCGTG-TTT
2708179 CAAAAA-TTTCGATGTTT
1 CAAAAATTTTCG-TGTTT
**
2708196 TGAAAATTTTCGTGTTTT
1 CAAAAATTTTCGTG-TTT
2708214 CAAAAA
1 CAAAAA
2708220 AAAAATCTCG
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
16 15 0.13
17 50 0.42
18 42 0.35
19 12 0.10
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
CAAAAATTTTCGTGTTT
Found at i:2708219 original size:35 final size:34
Alignment explanation
Indices: 2708057--2708219 Score: 168
Period size: 35 Copynumber: 4.7 Consensus size: 34
2708047 ATCCATTTTC
* * * *
2708057 CAAAATTTTTAGTGTCTTCTAAAAATTTTTGTGTTT
1 CAAAAATTTTCGTGTTTTC-AAAAA-TTTCGTGTTT
2708093 CAAAAATTTTC--GTTTTCAAAAATTTCCGTGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTT-CGTGTTT
* *
2708126 CAAAAATTTTCGTGTTTTCAAAATTTTTCGTATTT
1 CAAAAATTTTCGTGTTTTCAAAA-ATTTCGTGTTT
** *
2708161 CAAAAATCATCTTGTTTTCAAAAATTTCGATGTTT
1 CAAAAATTTTCGTGTTTTCAAAAATTTCG-TGTTT
**
2708196 TGAAAATTTTCGTGTTTTCAAAAA
1 CAAAAATTTTCGTGTTTTCAAAAA
2708220 AAAAATCTCG
Statistics
Matches: 106, Mismatches: 16, Indels: 11
0.80 0.12 0.08
Matches are distributed among these distances:
32 3 0.03
33 22 0.21
34 10 0.09
35 59 0.56
36 12 0.11
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (34 bp):
CAAAAATTTTCGTGTTTTCAAAAATTTCGTGTTT
Found at i:2723143 original size:46 final size:44
Alignment explanation
Indices: 2723076--2723443 Score: 212
Period size: 44 Copynumber: 8.5 Consensus size: 44
2723066 TTATTACAGG
*
2723076 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* *
2723122 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-T-AGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAG--A
* * * * * *
2723166 TCCTATCTCCTTGAGATTACAATGGAGCGGATTAAAG-----GA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * *
2723205 TCTTATCTCTCTGA-AGTTACAGTAGAGA-AGATC--ACA-TCAGG
1 TCTTATCTCCCTGAGA-TTACAGTGGA-ACAGATCAAAGATTCAGA
*
2723246 TCTTAT-TCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAG-A-TTCAGA
* * ** ****
2723291 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
* * * *
2723335 TCTTATCTCCCTGAGATTACAGCGGATCAGATCGAAGA--CACTA
1 TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCA-GA
* * * * **
2723378 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAA-ATAAAGGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAACAGATCAAAGATTCA-GA
* *
2723422 TCTTATCTCTCTGAGGTTACAG
1 TCTTATCTCCCTGAGATTACAG
2723444 CAGAGTAGAT
Statistics
Matches: 249, Mismatches: 52, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
37 1 0.00
38 1 0.00
39 24 0.10
40 19 0.08
41 9 0.04
42 6 0.02
43 31 0.12
44 88 0.35
45 11 0.04
46 59 0.24
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGTGGAACAGATCAAAGATTCAGA
Found at i:2723454 original size:87 final size:87
Alignment explanation
Indices: 2723294--2723455 Score: 211
Period size: 87 Copynumber: 1.9 Consensus size: 87
2723284 TTTCAGATCT
* * ** *
2723294 TATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGATCTTATCTCCCTGAGATTACAGCG
1 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGAAAGAGATCTTATCTCCCTGAGATTACAGCA
2723359 GATCAGATCGAAGACACTATCC
66 GATCAGATCGAAGACACTATCC
* * * *
2723381 TATCTCCCTGAAGTTACAGTGGAGCGGATTAAAATAAAG-GATCTTATCTCTCTGAGGTTACAGC
1 TATCTCCCTGAAGTTACAGTGGAGCAGATT-AAAGAAAGAGATCTTATCTCCCTGAGATTACAGC
2723445 AGAGT-AGATCG
65 AGA-TCAGATCG
2723456 CATTAAGTCT
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
87 59 0.92
88 5 0.08
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (87 bp):
TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGAAAGAGATCTTATCTCCCTGAGATTACAGCA
GATCAGATCGAAGACACTATCC
Found at i:2725458 original size:16 final size:16
Alignment explanation
Indices: 2725430--2725462 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2725420 TACACTCATG
2725430 TATATGTTTTATATTT
1 TATATGTTTTATATTT
2725446 TATA-GTTTATATATTT
1 TATATGTTT-TATATTT
2725462 T
1 T
2725463 CTTTGTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (16 bp):
TATATGTTTTATATTT
Found at i:2726774 original size:12 final size:12
Alignment explanation
Indices: 2726742--2726801 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
2726732 TTTGAACCAT
*
2726742 CTGCTTCTATCG
1 CTGCTTCTCTCG
2726754 CTGCTTCTCTCG
1 CTGCTTCTCTCG
* *
2726766 TTGCTTCTCTCA
1 CTGCTTCTCTCG
**
2726778 CTGCAGC-CT--
1 CTGCTTCTCTCG
2726787 CTGCTTCTCTCG
1 CTGCTTCTCTCG
2726799 CTG
1 CTG
2726802 TAGCCTCTGA
Statistics
Matches: 37, Mismatches: 8, Indels: 6
0.73 0.16 0.12
Matches are distributed among these distances:
9 5 0.14
10 2 0.05
11 2 0.05
12 28 0.76
ACGTcount: A:0.05, C:0.38, G:0.17, T:0.40
Consensus pattern (12 bp):
CTGCTTCTCTCG
Found at i:2726793 original size:21 final size:21
Alignment explanation
Indices: 2726767--2726834 Score: 82
Period size: 21 Copynumber: 3.2 Consensus size: 21
2726757 CTTCTCTCGT
*
2726767 TGCTTCTCTCACTGCAGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
*
2726788 TGCTTCTCTCGCTGTAGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
* * * *
2726809 TGATTCCCTCGTTGCCGCCTC
1 TGCTTCTCTCGCTGCAGCCTC
2726830 TGCTT
1 TGCTT
2726835 TAAGTTGTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.06, C:0.40, G:0.18, T:0.37
Consensus pattern (21 bp):
TGCTTCTCTCGCTGCAGCCTC
Found at i:2728690 original size:39 final size:38
Alignment explanation
Indices: 2728563--2728690 Score: 112
Period size: 39 Copynumber: 3.2 Consensus size: 38
2728553 AAACAAACTT
**
2728563 TTAGCGGCGATTGGACAACAAACGCCGCTAAAAATTAAGCA
1 TTAGCGGCGATTCTACAA-AAACGCCGCT-AAAA-TAAGCA
* * * * *
2728604 GTAGCGGCGATTTTAAAAAAACGCCGCTAAATATCAGTA
1 TTAGCGGCGATTCTACAAAAACGCCGCTAAA-ATAAGCA
* * * *
2728643 TTACCGGCGCTTCTACAAAAACGCCGTTAACAATGAGCA
1 TTAGCGGCGATTCTACAAAAACGCCGCTAA-AATAAGCA
2728682 TTAGCGGCG
1 TTAGCGGCG
2728691 TTTTTTAAAA
Statistics
Matches: 70, Mismatches: 15, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
39 44 0.63
40 12 0.17
41 14 0.20
ACGTcount: A:0.35, C:0.23, G:0.22, T:0.20
Consensus pattern (38 bp):
TTAGCGGCGATTCTACAAAAACGCCGCTAAAATAAGCA
Found at i:2728811 original size:114 final size:114
Alignment explanation
Indices: 2728682--2729005 Score: 497
Period size: 113 Copynumber: 2.9 Consensus size: 114
2728672 ACAATGAGCA
*
2728682 TTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAAACTTAAGCCAAACGACGTCGTTTTTCTTAGTTT
1 TTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAAACCTAAGCCAAACGACGTCGTTTTTCTTAGTTT
* *
2728747 TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGCAGGTAATTCTCAGGGCT
66 TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGCAGCTAATGCTCAGGGCT
* * *
2728796 TTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAGACCTAAGCCCAACGACATCG-TTTTCTTAGTTT
1 TTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAAACCTAAGCCAAACGACGTCGTTTTTCTTAGTTT
* * * * *
2728860 TCGAGTCTTTGGTGGCTTTTTTGGGAAAGCGCCGCTAATGCTCAGGGTT
66 TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGCAGCTAATGCTCAGGGCT
* *
2728909 TTAGCGGCGTTTTTTAAAAATCGCCGCAAAAAACCTAAGCCTAACGACGTCGTTTTTCTTAGTTT
1 TTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAAACCTAAGCCAAACGACGTCGTTTTTCTTAGTTT
* * *
2728974 TGGAGGCTTTGGTGGTGTTTTTGTAAAAGCGC
66 TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGC
2729006 CGCAAAAAAC
Statistics
Matches: 188, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
113 102 0.54
114 86 0.46
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.33
Consensus pattern (114 bp):
TTAGCGGCGTTTTTTAAAAAGCGCCGCAAAAAACCTAAGCCAAACGACGTCGTTTTTCTTAGTTT
TCGAGGCTTTGGTGGCGTTTTTGGAAAAGCGCAGCTAATGCTCAGGGCT
Found at i:2729056 original size:72 final size:73
Alignment explanation
Indices: 2728917--2729058 Score: 216
Period size: 73 Copynumber: 2.0 Consensus size: 73
2728907 TTTTAGCGGC
* * * *
2728917 GTTTTTTAAAAATCGCCGCAAAAAACCTAAGCCTAACGACGTCGTTTTTCTTAGTTTTGGAGGCT
1 GTTTTTTAAAAAGCGCCGCAAAAAACCTAAGCCCAACGACATCGTTTTTCTTAGTTTTCGAGGCT
2728982 TTGGTGGT
66 TTGGTGGT
*
2728990 GTTTTTGT-AAAAGCGCCGCAAAAAACCTAAGCCCAACGACATCG-TTTTCTTAGTTTTCGAGTC
1 GTTTTT-TAAAAAGCGCCGCAAAAAACCTAAGCCCAACGACATCGTTTTTCTTAGTTTTCGAGGC
2729053 TTTGGT
65 TTTGGT
2729059 TGGGGATTTA
Statistics
Matches: 63, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
72 23 0.37
73 39 0.62
74 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (73 bp):
GTTTTTTAAAAAGCGCCGCAAAAAACCTAAGCCCAACGACATCGTTTTTCTTAGTTTTCGAGGCT
TTGGTGGT
Found at i:2729503 original size:15 final size:16
Alignment explanation
Indices: 2729466--2729508 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2729456 TTTAGGGTTT
*
2729466 AATTAAGGTTTATGTG
1 AATTATGGTTTATGTG
2729482 AATTATGGGTTTA-GTG
1 AATTAT-GGTTTATGTG
2729498 -ATTATGGTTTA
1 AATTATGGTTTA
2729509 CAGTTTAGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 8 0.32
17 6 0.24
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (16 bp):
AATTATGGTTTATGTG
Found at i:2729550 original size:21 final size:21
Alignment explanation
Indices: 2729511--2729555 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
2729501 ATGGTTTACA
* *
2729511 GTTTAGGGTTTACGGGTTGAG
1 GTTTAAGGTTTACGAGTTGAG
* *
2729532 GTTTAAGGTTTATGAGTTGGG
1 GTTTAAGGTTTACGAGTTGAG
2729553 GTT
1 GTT
2729556 CTAGGCTAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.02, G:0.40, T:0.42
Consensus pattern (21 bp):
GTTTAAGGTTTACGAGTTGAG
Found at i:2729578 original size:33 final size:32
Alignment explanation
Indices: 2729530--2729592 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
2729520 TTACGGGTTG
*
2729530 AGGTTTAAGGTTTATGAGTTGGGGTTCTAGGCT
1 AGGTTTAAGGATTATGAGTTGGGGTT-TAGGCT
* * *
2729563 AGGTTTAATGATTATGATTTTGGGTTTAGG
1 AGGTTTAAGGATTATGAGTTGGGGTTTAGG
2729593 GTTTAAAGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 4 0.15
33 22 0.85
ACGTcount: A:0.21, C:0.03, G:0.33, T:0.43
Consensus pattern (32 bp):
AGGTTTAAGGATTATGAGTTGGGGTTTAGGCT
Found at i:2730280 original size:115 final size:114
Alignment explanation
Indices: 2730076--2730531 Score: 454
Period size: 115 Copynumber: 4.0 Consensus size: 114
2730066 ATTTAAAGGA
* * * * * *
2730076 ATTTTGTTTCAATAAAAACGGTGGCGTTCTATAGGATATATTAGTGGCGTTTTGGGTAAAACGCC
1 ATTTTGTTTCAATAAAAACGTTGCCGTTCTGTAGGATTTATTACTGGCGTTTTTGGTAAAACGCC
* ** * * * * *
2730141 GTAAAAGTTTGGGCTTT-CCTGGCGCTAAGCTGAAAACGCCGTAAAATGTG
66 GCAAAAG-TCAGCCTTTAGC-GGCGCTAAGTTAAAAACGCCGCAAAATGTG
* *
2730191 ATTTTGTTTCAATAAAAACGTTGCCGTTCTGTAAGATTTCTTACTGGCGTTTTTGGTAAAACGCC
1 ATTTTGTTTCAATAAAAACGTTGCCGTTCTGTAGGATTTATTACTGGCGTTTTTGGTAAAACGCC
* * *
2730256 GCAAAAGATCATCCTTTAGCGGCGCTATGTCAAAAACGCCGCAAAATGTG
66 GCAAAAG-TCAGCCTTTAGCGGCGCTAAGTTAAAAACGCCGCAAAATGTG
* * * ** *
2730306 ATTTTGTTTCAATAAAAATC-TTGCCGTTTTGTGGGATTTCTTACTGGCGTTTTTGCCAAAATGC
1 ATTTTGTTTCAATAAAAA-CGTTGCCGTTCTGTAGGATTTATTACTGGCGTTTTTGGTAAAACGC
* *
2730370 CGCAAAAGGTCAGCCTTTAGTGGCGCT-AGATTAAAAACGCAGCAAAATGTG
65 CGCAAAA-GTCAGCCTTTAGCGGCGCTAAG-TTAAAAACGCCGCAAAATGTG
* * ** * * *
2730421 ATTCTGTTTTAAT-AAAACGCTT-CCGTGGTGTAGGATTTATTAGTGGCGTTTTTTGTAAAATGC
1 ATTTTGTTTCAATAAAAACG-TTGCCGTTCTGTAGGATTTATTACTGGCGTTTTTGGTAAAACGC
* * ** *
2730484 CGAAAAATGTCAGCCTTTAGCGTCGCTGCGTTGAAAACGCCGCAAAAT
65 CGCAAAA-GTCAGCCTTTAGCGGCGCTAAGTTAAAAACGCCGCAAAAT
2730532 TTCAATGGGT
Statistics
Matches: 286, Mismatches: 48, Indels: 15
0.82 0.14 0.04
Matches are distributed among these distances:
113 1 0.00
114 77 0.27
115 205 0.72
116 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (114 bp):
ATTTTGTTTCAATAAAAACGTTGCCGTTCTGTAGGATTTATTACTGGCGTTTTTGGTAAAACGCC
GCAAAAGTCAGCCTTTAGCGGCGCTAAGTTAAAAACGCCGCAAAATGTG
Found at i:2730770 original size:115 final size:114
Alignment explanation
Indices: 2730570--2730880 Score: 534
Period size: 115 Copynumber: 2.7 Consensus size: 114
2730560 GTTTTGTTGG
* * ** * *
2730570 ATTTTGTGTTGACCGAAACGAAACCG-TTTTTATGTTTTTAGTGGTGTTTTTGTTAAAACGCCGC
1 ATTTTGTGTTTACCAAAACGTGACCGTTTTTTATGTATTTAGTGGCGTTTTTGTTAAAACGCCGC
* *
2730634 AAAAGATCTTGCTTTAGCGGCGCTTCTCTTAAAACGCCGCAAAAATGTT
66 AAAAGATGTTACTTTAGCGGCGCTTCTCTTAAAACGCCGCAAAAATGTT
2730683 ATTTTGTGTTTACCAAAACGTGACCGTTTTTTTATGTATTTAGTGGCGTTTTTGTTAAAACGCCG
1 ATTTTGTGTTTACCAAAACGTGACCG-TTTTTTATGTATTTAGTGGCGTTTTTGTTAAAACGCCG
2730748 CAAAAGATGTTACTTTAGCGGCGCTTCTCTTAAAACGCCGCAAAAATGTT
65 CAAAAGATGTTACTTTAGCGGCGCTTCTCTTAAAACGCCGCAAAAATGTT
2730798 ATTTTGTGTTTACCAAAACGTGACCGTTTTTTATGTATTTAGTGGCGTTTTTGTTAAAACGCCGC
1 ATTTTGTGTTTACCAAAACGTGACCGTTTTTTATGTATTTAGTGGCGTTTTTGTTAAAACGCCGC
2730863 AAAAGATGTTACTTTAGC
66 AAAAGATGTTACTTTAGC
2730881 TAGGGGTGAG
Statistics
Matches: 188, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
113 22 0.12
114 57 0.30
115 109 0.58
ACGTcount: A:0.26, C:0.17, G:0.20, T:0.38
Consensus pattern (114 bp):
ATTTTGTGTTTACCAAAACGTGACCGTTTTTTATGTATTTAGTGGCGTTTTTGTTAAAACGCCGC
AAAAGATGTTACTTTAGCGGCGCTTCTCTTAAAACGCCGCAAAAATGTT
Found at i:2731572 original size:16 final size:16
Alignment explanation
Indices: 2731551--2731581 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2731541 GGGAAAAATA
*
2731551 AAAAGTTTTAGGGAAT
1 AAAAGTTTGAGGGAAT
2731567 AAAAGTTTGAGGGAA
1 AAAAGTTTGAGGGAA
2731582 AGTAAATAGG
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:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (16 bp):
AAAAGTTTGAGGGAAT
Found at i:2731951 original size:9 final size:9
Alignment explanation
Indices: 2731937--2731973 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2731927 TATAGTTTGA
2731937 TATTCGAAT
1 TATTCGAAT
2731946 TATTCGAAT
1 TATTCGAAT
*
2731955 TATTCGAGT
1 TATTCGAAT
2731964 TATTCGAAT
1 TATTCGAAT
2731973 T
1 T
2731974 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:2732044 original size:9 final size:9
Alignment explanation
Indices: 2732027--2732057 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2732017 TCGAGTTGAT
2732027 TCGAATAAC
1 TCGAATAAC
*
2732036 TCGATTAAC
1 TCGAATAAC
2732045 TCGAATAAC
1 TCGAATAAC
2732054 TCGA
1 TCGA
2732058 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:2735764 original size:21 final size:21
Alignment explanation
Indices: 2735738--2735777 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2735728 GAACAACTTA
2735738 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCGGCAGCGAGGG
*
2735759 AAGCAGAGGCTGCAGCGAG
1 AAGCAGAGGCGGCAGCGAG
2735778 AAGCAGCGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.20, G:0.47, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCGGCAGCGAGGG
Found at i:2736287 original size:42 final size:41
Alignment explanation
Indices: 2736235--2736396 Score: 191
Period size: 42 Copynumber: 3.9 Consensus size: 41
2736225 GTGAAATAAC
* *
2736235 CGCCGCTAAAGAACACTA-CTTTTAGCGGCGTTTTTAACCAAG
1 CGCCGCTAAAGAACA-TATC-TTTAGCGACGTTTTTTACCAAG
* **
2736277 CGCCGCTAAAGAACATGATCTTTAGCGACGTTTTTTTCCTGG
1 CGCCGCTAAAGAACAT-ATCTTTAGCGACGTTTTTTACCAAG
* *
2736319 CGCCGCTAAAGAACATGTTCTTTAGCGACGTTTTTTACTAAG
1 CGCCGCTAAAGAACAT-ATCTTTAGCGACGTTTTTTACCAAG
* *
2736361 CGCCGCTAAAGAACATGATCTTTAGCGGCTTTTTTT
1 CGCCGCTAAAGAACAT-ATCTTTAGCGACGTTTTTT
2736397 TTCTGTAAGT
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.01
42 103 0.98
43 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (41 bp):
CGCCGCTAAAGAACATATCTTTAGCGACGTTTTTTACCAAG
Found at i:2736344 original size:84 final size:84
Alignment explanation
Indices: 2736235--2736397 Score: 247
Period size: 84 Copynumber: 1.9 Consensus size: 84
2736225 GTGAAATAAC
*
2736235 CGCCGCTAAAGAACACTACTTTTAGCGGCGTTTTTAACCAAGCGCCGCTAAAGAACATGATCTTT
1 CGCCGCTAAAGAACACTACTTTTAGCGACGTTTTTAACCAAGCGCCGCTAAAGAACATGATCTTT
2736300 AGCGACGTTTTTTTCCTGG
66 AGCGACGTTTTTTTCCTGG
** * *
2736319 CGCCGCTAAAGAACA-TGTTCTTTAGCGACGTTTTTTACTAAGCGCCGCTAAAGAACATGATCTT
1 CGCCGCTAAAGAACACTACT-TTTAGCGACGTTTTTAACCAAGCGCCGCTAAAGAACATGATCTT
* *
2736383 TAGCGGCTTTTTTTT
65 TAGCGACGTTTTTTT
2736398 TCTGTAAGTG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
83 2 0.03
84 69 0.97
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.33
Consensus pattern (84 bp):
CGCCGCTAAAGAACACTACTTTTAGCGACGTTTTTAACCAAGCGCCGCTAAAGAACATGATCTTT
AGCGACGTTTTTTTCCTGG
Found at i:2737669 original size:18 final size:18
Alignment explanation
Indices: 2737645--2738267 Score: 256
Period size: 17 Copynumber: 32.7 Consensus size: 18
2737635 ACAAAATAAT
2737645 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
*
2737663 GATTTTTTG-AAACACGAA
1 -AATTTTTGAAAACACGAA
*
2737681 AATTTTTTGAACACACGAGA
1 AA-TTTTTGAAAACACGA-A
* *
2737701 ATTTTTTGAAAACCCGAAA
1 AATTTTTGAAAACACG-AA
2737720 ACATGAAAATTTTGAAAACACGAA
1 A-AT-----TTTTGAAAACACGAA
*
2737744 AATTTTTG-AAACACGAG
1 AATTTTTGAAAACACGAA
**
2737761 AATTTTT-ATGACACGAA
1 AATTTTTGAAAACACGAA
*
2737778 AAATTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
* * *
2737796 AA-TTTCGAAAACATGTA
1 AATTTTTGAAAACACGAA
** *
2737813 TTTTTTTTAAAACAC-AA
1 AATTTTTGAAAACACGAA
*
2737830 AATTTTTTTACAAACAC-AA
1 AA-TTTTTGA-AAACACGAA
*
2737849 GAATTTTTTTTGAAAACACAAAA
1 -AA---TTTTTGAAAACAC-GAA
2737872 ACATGAAAATTTTGAAAACACGAA
1 A-AT-----TTTTGAAAACACGAA
*
2737896 AATTTTTG-AAACACGAG
1 AATTTTTGAAAACACGAA
**
2737913 AATTTTT-ATGACACGAA
1 AATTTTTGAAAACACGAA
*
2737930 AAATTTT-AAAACACGAA
1 AATTTTTGAAAACACGAA
* *
2737947 AA-TTTCGAAAACATG-A
1 AATTTTTGAAAACACGAA
* *
2737963 ATTTTTTTAAAACACGAA
1 AATTTTTGAAAACACGAA
* *
2737981 ATTTTTTTTAAAAACACGAGA
1 A--ATTTTTGAAAACACGA-A
* *
2738002 ATTTTTTTTTGAAAGCACGAA
1 A---ATTTTTGAAAACACGAA
2738023 GACATGAAAATTTTGAAAACACGAA
1 -A-AT-----TTTTGAAAACACGAA
2738048 AATTTTTG-AAACACGCAA
1 AATTTTTGAAAACACG-AA
* * *
2738066 ATTTTTTTTAAAACAGGAGA
1 A-ATTTTTGAAAACACGA-A
*
2738086 ATTTTTTGAAAACACGAAA
1 AATTTTTGAAAACACG-AA
2738105 ACATGAAAATTTTGAAAACACGAA
1 A-AT-----TTTTGAAAACACGAA
2738129 AATTTTTG-AAACACGAGA
1 AATTTTTGAAAACACGA-A
*
2738147 ATTTTTATGACACGAAAACACGAA
1 AATTTT-T-----GAAAACACGAA
** **
2738171 AATTTTT-TTAACACGGG
1 AATTTTTGAAAACACGAA
2738188 AATTTTTGAAAACACGAA
1 AATTTTTGAAAACACGAA
2738206 AATTTTTG-AAACAC-AA
1 AATTTTTGAAAACACGAA
* *
2738222 AAATTTT-AAAACACTAA
1 AATTTTTGAAAACACGAA
* *
2738239 CATTTGTG-AAACACGAA
1 AATTTTTGAAAACACGAA
* *
2738256 AACTCTTGAAAA
1 AATTTTTGAAAA
2738268 TGTTAAAAGT
Statistics
Matches: 468, Mismatches: 72, Indels: 129
0.70 0.11 0.19
Matches are distributed among these distances:
16 19 0.04
17 147 0.31
18 89 0.19
19 58 0.12
20 33 0.07
21 9 0.02
22 25 0.05
23 12 0.03
24 17 0.04
25 59 0.13
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (18 bp):
AATTTTTGAAAACACGAA
Found at i:2737671 original size:19 final size:19
Alignment explanation
Indices: 2737647--2737718 Score: 94
Period size: 19 Copynumber: 3.8 Consensus size: 19
2737637 AAAATAATAA
2737647 TTTTTGAAAACACGAAGAT
1 TTTTTGAAAACACGAAGAT
*
2737666 TTTTTG-AAACACGAAAAT
1 TTTTTGAAAACACGAAGAT
*
2737684 TTTTTGAACACACG-AGAAT
1 TTTTTGAAAACACGAAG-AT
*
2737703 TTTTTGAAAACCCGAA
1 TTTTTGAAAACACGAA
2737719 AACATGAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
18 18 0.40
19 26 0.58
20 1 0.02
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (19 bp):
TTTTTGAAAACACGAAGAT
Found at i:2737856 original size:21 final size:19
Alignment explanation
Indices: 2737812--2737871 Score: 86
Period size: 21 Copynumber: 3.1 Consensus size: 19
2737802 GAAAACATGT
2737812 ATTTTTTTTAAAACACAAA
1 ATTTTTTTTAAAACACAAA
2737831 A-TTTTTTTACAAACACAAGA
1 ATTTTTTTTA-AAACACAA-A
2737851 ATTTTTTTTGAAAACACAAA
1 ATTTTTTTT-AAAACACAAA
2737871 A
1 A
2737872 ACATGAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
18 8 0.22
19 9 0.24
20 4 0.11
21 15 0.41
22 1 0.03
ACGTcount: A:0.47, C:0.12, G:0.03, T:0.38
Consensus pattern (19 bp):
ATTTTTTTTAAAACACAAA
Found at i:2737873 original size:152 final size:150
Alignment explanation
Indices: 2737665--2738071 Score: 642
Period size: 152 Copynumber: 2.7 Consensus size: 150
2737655 AACACGAAGA
* * * *
2737665 TTTTTTGAAACACGAAAATTTTTTGAACACACGAGAA--TTTTTTGAAAACCCGAAAACATGAAA
1 TTTTTTAAAACACGAAAATTTTTTTAAAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAA
2737728 ATTTTGAAAACACGAAAATTTTTGAAACACGAGAATTTTTATGACACGAAAAATTTTGAAAACAC
66 ATTTTGAAAACACGAAAATTTTTGAAACACGAGAATTTTTATGACACGAAAAATTTT-AAAACAC
*
2737793 GAAAATTTCGAAAACATGTATT
130 GAAAATTTCGAAAACATG-AAT
* *
2737815 TTTTTTAAAACAC-AAAATTTTTTTACAAACACAAGAATTTTTTTTGAAAACACAAAAACATGAA
1 TTTTTTAAAACACGAAAATTTTTTTA-AAACACGAGAATTTTTTTTGAAAACACGAAAACATGAA
2737879 AATTTTGAAAACACGAAAATTTTTGAAACACGAGAATTTTTATGACACGAAAAATTTTAAAACAC
65 AATTTTGAAAACACGAAAATTTTTGAAACACGAGAATTTTTATGACACGAAAAATTTTAAAACAC
2737944 GAAAATTTCGAAAACATGAAT
130 GAAAATTTCGAAAACATGAAT
* * *
2737965 TTTTTTAAAACACGAAATTTTTTTTAAAAACACGAGAATTTTTTTTTGAAAGCACGAAGACATGA
1 TTTTTTAAAACACGAAAATTTTTTT-AAAACACGAGAA-TTTTTTTTGAAAACACGAAAACATGA
2738030 AAATTTTGAAAACACGAAAATTTTTGAAACACGCA-AATTTTT
64 AAATTTTGAAAACACGAAAATTTTTGAAACACG-AGAATTTTT
2738072 TTTAAAACAG
Statistics
Matches: 238, Mismatches: 12, Indels: 12
0.91 0.05 0.05
Matches are distributed among these distances:
149 11 0.05
150 36 0.15
151 45 0.19
152 145 0.61
153 1 0.00
ACGTcount: A:0.45, C:0.12, G:0.11, T:0.32
Consensus pattern (150 bp):
TTTTTTAAAACACGAAAATTTTTTTAAAACACGAGAATTTTTTTTGAAAACACGAAAACATGAAA
ATTTTGAAAACACGAAAATTTTTGAAACACGAGAATTTTTATGACACGAAAAATTTTAAAACACG
AAAATTTCGAAAACATGAAT
Found at i:2737989 original size:20 final size:20
Alignment explanation
Indices: 2737964--2738022 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
2737954 AAAACATGAA
2737964 TTTTTTTAAAACACGAAATT
1 TTTTTTTAAAACACGAAATT
*
2737984 TTTTTTAAAAACACGAGAATT
1 TTTTTTTAAAACACGA-AATT
*
2738005 TTTTTTTGAAAGCACGAA
1 TTTTTTT-AAAACACGAA
2738023 GACATGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 15 0.44
21 11 0.32
22 8 0.24
ACGTcount: A:0.39, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTTTTAAAACACGAAATT
Found at i:2738007 original size:22 final size:19
Alignment explanation
Indices: 2737964--2738104 Score: 81
Period size: 19 Copynumber: 6.9 Consensus size: 19
2737954 AAAACATGAA
2737964 TTTTTTTAAAACACGAAAT
1 TTTTTTTAAAACACGAAAT
2737983 TTTTTTTAAAAACACGAGAATT
1 TTTTTTT-AAAACACGA-AA-T
*
2738005 TTTTTTTGAAAGCACGAAGACAT
1 TTTTTTT-AAAACACG-A-A-AT
** *
2738028 GAAAATTTTGAAAACACGAAA-
1 ---TTTTTTTAAAACACGAAAT
* *
2738049 -ATTTTTGAAACACGCAAAT
1 TTTTTTTAAAACACG-AAAT
*
2738068 TTTTTTTAAAACAGGAGAA-
1 TTTTTTTAAAACACGA-AAT
*
2738087 TTTTTTGAAAACACGAAA
1 TTTTTTTAAAACACGAAA
2738105 ACATGAAAAT
Statistics
Matches: 97, Mismatches: 13, Indels: 25
0.72 0.10 0.19
Matches are distributed among these distances:
17 12 0.12
18 5 0.05
19 22 0.23
20 22 0.23
21 2 0.02
22 16 0.16
23 5 0.05
24 2 0.02
25 7 0.07
26 4 0.04
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (19 bp):
TTTTTTTAAAACACGAAAT
Found at i:2738164 original size:42 final size:36
Alignment explanation
Indices: 2738114--2738254 Score: 128
Period size: 42 Copynumber: 3.9 Consensus size: 36
2738104 AACATGAAAA
2738114 TTTTGAAAACACGAAAATTTTTGAAACACGAGAATT
1 TTTTGAAAACACGAAAATTTTTGAAACACGAGAATT
** *
2738150 TTTATGACACGAAAACACGAAAATTTTTTTAACACGGGAA-T
1 TTT-T-----GAAAACACGAAAATTTTTGAAACACGAGAATT
**
2738191 TTTTGAAAACACGAAAATTTTTGAAACAC-A-AAAA
1 TTTTGAAAACACGAAAATTTTTGAAACACGAGAATT
* * *
2738225 TTTT-AAAACACTAACATTTGTGAAACACGA
1 TTTTGAAAACACGAAAATTTTTGAAACACGA
2738255 AAACTCTTGA
Statistics
Matches: 87, Mismatches: 10, Indels: 18
0.76 0.09 0.16
Matches are distributed among these distances:
33 23 0.26
34 5 0.06
35 23 0.26
36 3 0.03
37 1 0.01
40 1 0.01
41 4 0.05
42 27 0.31
ACGTcount: A:0.45, C:0.13, G:0.12, T:0.29
Consensus pattern (36 bp):
TTTTGAAAACACGAAAATTTTTGAAACACGAGAATT
Found at i:2738184 original size:25 final size:25
Alignment explanation
Indices: 2738137--2738185 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
2738127 AAAATTTTTG
* *
2738137 AAACACGAGAATTTTTATGACACGA
1 AAACACGAAAATTTTTATAACACGA
*
2738162 AAACACGAAAATTTTTTTAACACG
1 AAACACGAAAATTTTTATAACACG
2738186 GGAATTTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.45, C:0.16, G:0.12, T:0.27
Consensus pattern (25 bp):
AAACACGAAAATTTTTATAACACGA
Found at i:2738233 original size:33 final size:34
Alignment explanation
Indices: 2738160--2738267 Score: 110
Period size: 35 Copynumber: 3.1 Consensus size: 34
2738150 TTTATGACAC
** * *
2738160 GAAAACACGAAAATTTTTTTAACACGGGAATTTTT
1 GAAAACACGAAAATTTTTGAAACAC-GAAAATTTT
*
2738195 GAAAACACGAAAATTTTTGAAACACAAAAATTTT
1 GAAAACACGAAAATTTTTGAAACACGAAAATTTT
* * * *
2738229 -AAAACACTAACATTTGTGAAACACGAAAACTCTT
1 GAAAACACGAAAATTTTTGAAACACGAAAA-TTTT
2738263 GAAAA
1 GAAAA
2738268 TGTTAAAAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
33 25 0.41
34 9 0.15
35 27 0.44
ACGTcount: A:0.48, C:0.14, G:0.11, T:0.27
Consensus pattern (34 bp):
GAAAACACGAAAATTTTTGAAACACGAAAATTTT
Found at i:2738970 original size:20 final size:20
Alignment explanation
Indices: 2738932--2738994 Score: 76
Period size: 20 Copynumber: 3.2 Consensus size: 20
2738922 TGCTTTGTTC
* *
2738932 TTTTTTGCTATTCTG-TTTT
1 TTTTTTGCTGTTTTGTTTTT
2738951 TTTTTTGCTGTTTTGTTTTT
1 TTTTTTGCTGTTTTGTTTTT
*
2738971 TTTTTGGGC-GTTTTGTTTTT
1 TTTTT-TGCTGTTTTGTTTTT
2738991 TTTT
1 TTTT
2738995 GGGGCTGCTG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 13 0.33
20 24 0.62
21 2 0.05
ACGTcount: A:0.02, C:0.06, G:0.16, T:0.76
Consensus pattern (20 bp):
TTTTTTGCTGTTTTGTTTTT
Found at i:2738989 original size:19 final size:20
Alignment explanation
Indices: 2738914--2738997 Score: 77
Period size: 19 Copynumber: 4.3 Consensus size: 20
2738904 CTGGGCTTGG
* *
2738914 TTTGGGCCTGCTTTGTTCTTT
1 TTTGGG-CTGTTTTGTTTTTT
* *
2738935 TTT--GCTATTCTGTTTTTT
1 TTTGGGCTGTTTTGTTTTTT
*
2738953 TTT-TGCTGTTTTGTTTTTTT
1 TTTGGGCTGTTTTG-TTTTTT
2738973 TTTGGGC-GTTTTGTTTTTT
1 TTTGGGCTGTTTTGTTTTTT
2738992 TTTGGG
1 TTTGGG
2738998 GCTGCTGGGT
Statistics
Matches: 53, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
18 13 0.25
19 20 0.38
20 15 0.28
21 5 0.09
ACGTcount: A:0.01, C:0.10, G:0.21, T:0.68
Consensus pattern (20 bp):
TTTGGGCTGTTTTGTTTTTT
Found at i:2738999 original size:20 final size:20
Alignment explanation
Indices: 2738960--2738999 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2738950 TTTTTTTGCT
*
2738960 GTTTTGTTTTTTTTTTGGGC
1 GTTTTGTTTTTTTTTGGGGC
2738980 GTTTTGTTTTTTTTTGGGGC
1 GTTTTGTTTTTTTTTGGGGC
2739000 TGCTGGGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.05, G:0.28, T:0.68
Consensus pattern (20 bp):
GTTTTGTTTTTTTTTGGGGC
Found at i:2739079 original size:13 final size:13
Alignment explanation
Indices: 2739061--2739117 Score: 53
Period size: 13 Copynumber: 4.5 Consensus size: 13
2739051 AAAAAAATAT
2739061 TTTTTTTTTCTTC
1 TTTTTTTTTCTTC
2739074 TTTTTTTTT-TTC
1 TTTTTTTTTCTTC
** **
2739086 CCTTCCTTTCTTC
1 TTTTTTTTTCTTC
* *
2739099 TCTCTTTTTCTTC
1 TTTTTTTTTCTTC
2739112 TTTTTT
1 TTTTTT
2739118 CTTCCTTTTT
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
12 8 0.24
13 25 0.76
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTCTTC
Found at i:2739133 original size:11 final size:10
Alignment explanation
Indices: 2739087--2739134 Score: 53
Period size: 10 Copynumber: 4.6 Consensus size: 10
2739077 TTTTTTTTCC
2739087 CTTCCTTTCTT
1 CTTCCTTT-TT
2739098 C-TCTCTTTTT
1 CTTC-CTTTTT
*
2739108 CTTCTTTTTT
1 CTTCCTTTTT
2739118 CTTCCTTTTT
1 CTTCCTTTTT
2739128 CCTTCCT
1 -CTTCCT
2739135 CTTCGGGGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 19 0.59
11 13 0.41
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (10 bp):
CTTCCTTTTT
Found at i:2739869 original size:30 final size:31
Alignment explanation
Indices: 2739744--2739876 Score: 123
Period size: 30 Copynumber: 4.5 Consensus size: 31
2739734 CTTGAGAGTT
*
2739744 TAGGGGTCAAAGTG-AAATTTTGAGAAAGTA
1 TAGGGGTCAAAATGTAAATTTTGAGAAAGTA
* * * *
2739774 TAAGGGTCGAAATGT-AATTTT-ATAAAGTT
1 TAGGGGTCAAAATGTAAATTTTGAGAAAGTA
* * * *
2739803 TTGGGGTAAAAATGTAAATTTT-AGAAAATT
1 TAGGGGTCAAAATGTAAATTTTGAGAAAGTA
*
2739833 TTGGGGTCAAAATGTAAATTTTGA-AAAGTA
1 TAGGGGTCAAAATGTAAATTTTGAGAAAGTA
* *
2739863 CAGGGGTTAAAATG
1 TAGGGGTCAAAATG
2739877 CAAAAAATAA
Statistics
Matches: 83, Mismatches: 17, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
29 17 0.20
30 65 0.78
31 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (31 bp):
TAGGGGTCAAAATGTAAATTTTGAGAAAGTA
Found at i:2740175 original size:16 final size:16
Alignment explanation
Indices: 2740154--2740184 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2740144 TATGGAACCA
2740154 TATTAAATAATACTAG
1 TATTAAATAATACTAG
2740170 TATTAAATAATACTA
1 TATTAAATAATACTA
2740185 TTTGCATTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (16 bp):
TATTAAATAATACTAG
Found at i:2740679 original size:26 final size:26
Alignment explanation
Indices: 2740650--2740707 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
2740640 TTAGATTTAT
* *
2740650 ATTATTTTATAAGTTATAGAGTAAGA
1 ATTATTTGATAAGCTATAGAGTAAGA
*
2740676 ATTATTTGATAAGCTATAGAGTGAGA
1 ATTATTTGATAAGCTATAGAGTAAGA
2740702 ATTATT
1 ATTATT
2740708 ATGCAATGAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.40, C:0.02, G:0.17, T:0.41
Consensus pattern (26 bp):
ATTATTTGATAAGCTATAGAGTAAGA
Found at i:2742616 original size:19 final size:20
Alignment explanation
Indices: 2742589--2742629 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
2742579 AAAATTTTAA
2742589 TTAAATAAT-TATTAAAA-TT
1 TTAAATAATAT-TTAAAAGTT
*
2742608 TTAAGTAATATTTAAAAGTT
1 TTAAATAATATTTAAAAGTT
2742628 TT
1 TT
2742630 TGATAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTAAATAATATTTAAAAGTT
Found at i:2743378 original size:15 final size:14
Alignment explanation
Indices: 2743360--2743467 Score: 67
Period size: 15 Copynumber: 7.2 Consensus size: 14
2743350 CTTGGCACCT
2743360 TAACCCCTAAATCCC
1 TAACCCCTAAA-CCC
2743375 TAACCCCT-AACCC
1 TAACCCCTAAACCC
2743388 TTAAATCCCCCTAAACCC
1 -T-AA--CCCCTAAACCC
*
2743406 TAACCCCCTAAATCAC
1 TAA-CCCCTAAA-CCC
*
2743422 TAA-CCCTTAACCTC
1 TAACCCCTAAACC-C
* *
2743436 TAAGCCCTAAATTCC
1 TAACCCCTAAA-CCC
* *
2743451 TAACCCTTAACCCC
1 TAACCCCTAAACCC
2743465 TAA
1 TAA
2743468 ACCTTAATCC
Statistics
Matches: 75, Mismatches: 9, Indels: 19
0.73 0.09 0.18
Matches are distributed among these distances:
13 4 0.05
14 18 0.24
15 34 0.45
16 8 0.11
17 6 0.08
18 5 0.07
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.22
Consensus pattern (14 bp):
TAACCCCTAAACCC
Found at i:2743384 original size:7 final size:7
Alignment explanation
Indices: 2743360--2743467 Score: 54
Period size: 7 Copynumber: 14.4 Consensus size: 7
2743350 CTTGGCACCT
2743360 TAACCCC
1 TAACCCC
*
2743367 TAAATCCC
1 T-AACCCC
2743375 TAACCCC
1 TAACCCC
*
2743382 TAACCCT
1 TAACCCC
2743389 TAAATCCCCC
1 T-AA--CCCC
*
2743399 TAAACCC
1 TAACCCC
2743406 TAACCCCC
1 TAA-CCCC
* *
2743414 TAAATCAC
1 T-AACCCC
*
2743422 TAACCCT
1 TAACCCC
*
2743429 TAACCTC
1 TAACCCC
*
2743436 TAAGCCC
1 TAACCCC
**
2743443 TAAATTCC
1 T-AACCCC
*
2743451 TAACCCT
1 TAACCCC
2743458 TAACCCC
1 TAACCCC
2743465 TAA
1 TAA
2743468 ACCTTAATCC
Statistics
Matches: 73, Mismatches: 21, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
7 45 0.62
8 20 0.27
9 4 0.05
10 4 0.05
ACGTcount: A:0.33, C:0.44, G:0.01, T:0.22
Consensus pattern (7 bp):
TAACCCC
Found at i:2743406 original size:24 final size:22
Alignment explanation
Indices: 2743360--2743487 Score: 86
Period size: 22 Copynumber: 5.8 Consensus size: 22
2743350 CTTGGCACCT
*
2743360 TAACCCCTAAATCCCTAACCCC
1 TAACCCCTAAATCCCTAAACCC
*
2743382 TAACCCTTAAATCCCCCTAAACCC
1 TAACCCCTAAAT--CCCTAAACCC
*
2743406 TAACCCCCTAAATCACT-AACCC
1 TAA-CCCCTAAATCCCTAAACCC
* * *
2743428 TTAACCTCT-AAGCCCTAAATTCC
1 -TAACCCCTAAATCCCTAAA-CCC
* * *
2743451 TAA-CCCTTAACCCCTAAACCT
1 TAACCCCTAAATCCCTAAACCC
*
2743472 TAATCCC-AAA-CCCTAA
1 TAACCCCTAAATCCCTAA
2743488 TCCATACCCC
Statistics
Matches: 85, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
20 6 0.07
21 14 0.16
22 37 0.44
23 8 0.09
24 12 0.14
25 8 0.09
ACGTcount: A:0.34, C:0.43, G:0.01, T:0.22
Consensus pattern (22 bp):
TAACCCCTAAATCCCTAAACCC
Found at i:2743443 original size:29 final size:29
Alignment explanation
Indices: 2743411--2743467 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
2743401 AACCCTAACC
*
2743411 CCCTAAA-TCACTAACCCTTAACCTCTAAG
1 CCCTAAATTC-CTAACCCTTAACCCCTAAG
2743440 CCCTAAATTCCTAACCCTTAACCCCTAA
1 CCCTAAATTCCTAACCCTTAACCCCTAA
2743468 ACCTTAATCC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 24 0.92
30 2 0.08
ACGTcount: A:0.33, C:0.40, G:0.02, T:0.25
Consensus pattern (29 bp):
CCCTAAATTCCTAACCCTTAACCCCTAAG
Found at i:2744114 original size:41 final size:42
Alignment explanation
Indices: 2744069--2744224 Score: 126
Period size: 41 Copynumber: 3.8 Consensus size: 42
2744059 CGTTTCCATC
*
2744069 AAAACGCCGCT-AAAACTC-CAACATTAGCGGCGCTTTACAAA
1 AAAACGCCACTAAAAAC-CACAACATTAGCGGCGCTTTACAAA
** * * *
2744110 AAAACGCCACTAAAAACCTTAACTTTAGCGGCGCATTATC--G
1 AAAACGCCACTAAAAACCACAACATTAGCGGCGCTTTA-CAAA
** * * * *
2744151 AAAACGCTGCTAAAAGCC-CTAAAATTAGCGGCG-TTCAGAAA
1 AAAACGCCACTAAAAACCAC-AACATTAGCGGCGCTTTACAAA
*
2744192 AAAACGCCACTAAAAACCATAACATTAGCGGCG
1 AAAACGCCACTAAAAACCACAACATTAGCGGCG
2744225 TTTGTTTAAA
Statistics
Matches: 88, Mismatches: 20, Indels: 14
0.72 0.16 0.11
Matches are distributed among these distances:
40 2 0.02
41 64 0.73
42 21 0.24
43 1 0.01
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.17
Consensus pattern (42 bp):
AAAACGCCACTAAAAACCACAACATTAGCGGCGCTTTACAAA
Found at i:2744139 original size:42 final size:42
Alignment explanation
Indices: 2744088--2744224 Score: 145
Period size: 41 Copynumber: 3.3 Consensus size: 42
2744078 CTAAAACTCC
*
2744088 AACATTAGCGGCGCTTTACAAAAAAACGCCACTAAAAACCTT
1 AACATTAGCGGCGCTTTACAAAAAAACGCCACTAAAAACCAT
* * * ** * *
2744130 AACTTTAGCGGCGCATTATC--GAAAACGCTGCTAAAAGCCCT
1 AACATTAGCGGCGCTTTA-CAAAAAAACGCCACTAAAAACCAT
* * *
2744171 AAAATTAGCGGCG-TTCAGAAAAAAACGCCACTAAAAACCAT
1 AACATTAGCGGCGCTTTACAAAAAAACGCCACTAAAAACCAT
2744212 AACATTAGCGGCG
1 AACATTAGCGGCG
2744225 TTTGTTTAAA
Statistics
Matches: 74, Mismatches: 18, Indels: 7
0.75 0.18 0.07
Matches are distributed among these distances:
40 2 0.03
41 55 0.74
42 16 0.22
43 1 0.01
ACGTcount: A:0.40, C:0.25, G:0.17, T:0.18
Consensus pattern (42 bp):
AACATTAGCGGCGCTTTACAAAAAAACGCCACTAAAAACCAT
Found at i:2744206 original size:82 final size:82
Alignment explanation
Indices: 2744069--2744224 Score: 226
Period size: 82 Copynumber: 1.9 Consensus size: 82
2744059 CGTTTCCATC
* * * *
2744069 AAAACGCCGCTAAAACTCCAACATTAGCGGCGCTTTACAAAAAAACGCCACTAAAAACCTTAACT
1 AAAACGCCGCTAAAACTCCAAAATTAGCGGCGCTTCACAAAAAAACGCCACTAAAAACCATAACA
2744134 TTAGCGGCGCATTATCG
66 TTAGCGGCGCATTATCG
* *
2744151 AAAACGCTGCTAAAAGC-CCTAAAATTAGCGGCG-TTCAGAAAAAAACGCCACTAAAAACCATAA
1 AAAACGCCGCTAAAA-CTCC-AAAATTAGCGGCGCTTCACAAAAAAACGCCACTAAAAACCATAA
2744214 CATTAGCGGCG
64 CATTAGCGGCG
2744225 TTTGTTTAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
82 53 0.80
83 13 0.20
ACGTcount: A:0.40, C:0.26, G:0.16, T:0.17
Consensus pattern (82 bp):
AAAACGCCGCTAAAACTCCAAAATTAGCGGCGCTTCACAAAAAAACGCCACTAAAAACCATAACA
TTAGCGGCGCATTATCG
Found at i:2744236 original size:41 final size:40
Alignment explanation
Indices: 2744088--2744246 Score: 120
Period size: 41 Copynumber: 3.9 Consensus size: 40
2744078 CTAAAACTCC
** *
2744088 AACATTAGCGGCGCTTTACAAAAAAACGCCACTAAAAACCTT
1 AACATTAGCGGCG-TTT-GTAAAAAACGCCACTAAAAACCAT
* * * ** ** * *
2744130 AACTTTAGCGGCGCATTATCGAAAACGCTGCTAAAAGCCCT
1 AACATTAGCGGCG-TTTGTAAAAAACGCCACTAAAAACCAT
* * *
2744171 AAAATTAGCGGCGTTCAGAAAAAAACGCCACTAAAAACCAT
1 AACATTAGCGGCGTT-TGTAAAAAACGCCACTAAAAACCAT
* *
2744212 AACATTAGCGGCGTTTGTTTAAAAACGCCAATAAA
1 AACATTAGCGGCGTTTG-TAAAAAACGCCACTAAA
2744247 GCCCTCTGAA
Statistics
Matches: 88, Mismatches: 27, Indels: 5
0.73 0.22 0.04
Matches are distributed among these distances:
40 2 0.02
41 71 0.81
42 15 0.17
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.20
Consensus pattern (40 bp):
AACATTAGCGGCGTTTGTAAAAAACGCCACTAAAAACCAT
Found at i:2744369 original size:40 final size:39
Alignment explanation
Indices: 2744287--2744400 Score: 104
Period size: 40 Copynumber: 2.8 Consensus size: 39
2744277 GAGTTTGGAG
* * * *
2744287 TTTTTGTGGCGTTTTAGCA-AAAGCGCCGCTAAAGGCCTAT
1 TTTTTGTGGCGTTTT-TCACAAA-CGCCACTAAAGCCCGAT
*
2744327 TTTTTGTGGCGTTTTCTCACAAACGCCACTAATGCCCGAT
1 TTTTTGTGGCGTTTT-TCACAAACGCCACTAAAGCCCGAT
***
2744367 TTTTACCGGCGTTTTTCCACAAAACGCCACTAAA
1 TTTTTGTGGCGTTTTT-CAC-AAACGCCACTAAA
2744401 AGTGCCGCTA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
39 1 0.02
40 45 0.74
41 15 0.25
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (39 bp):
TTTTTGTGGCGTTTTTCACAAACGCCACTAAAGCCCGAT
Found at i:2745697 original size:17 final size:17
Alignment explanation
Indices: 2745675--2745708 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2745665 GATAAGGACA
2745675 AAGGGTGGGGTTTAGAT
1 AAGGGTGGGGTTTAGAT
2745692 AAGGGTGGGGTTTAGAT
1 AAGGGTGGGGTTTAGAT
2745709 GAGCGATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.47, T:0.29
Consensus pattern (17 bp):
AAGGGTGGGGTTTAGAT
Found at i:2749620 original size:4 final size:4
Alignment explanation
Indices: 2749611--2749656 Score: 92
Period size: 4 Copynumber: 11.5 Consensus size: 4
2749601 AAAATACGTG
2749611 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CA
2749657 CAACATTGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 42 1.00
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:2755306 original size:19 final size:19
Alignment explanation
Indices: 2755265--2755323 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 19
2755255 CCCTCTCAAC
*
2755265 AAAAATTACAAAATATTT-C
1 AAAAATT-CAAAATATTTAT
2755284 AAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
2755303 AAAAGAATTCAAAAT-TTTAT
1 -AAA-AATTCAAAATATTTAT
2755323 A
1 A
2755324 TTTTTTTACA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 10 0.28
19 8 0.22
20 8 0.22
21 10 0.28
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:2757525 original size:29 final size:30
Alignment explanation
Indices: 2757487--2757552 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 30
2757477 AAATATAATA
* *
2757487 TATAAAATTACGCA-AAATCAAAATTTATG
1 TATAATATTACACACAAATCAAAATTTATG
* *
2757516 TATAATATTACACACGAATTCAAAGTTTATG
1 TATAATATTACACAC-AAATCAAAATTTATG
2757547 TATAAT
1 TATAAT
2757553 TTTCAGATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 12 0.39
31 19 0.61
ACGTcount: A:0.47, C:0.11, G:0.08, T:0.35
Consensus pattern (30 bp):
TATAATATTACACACAAATCAAAATTTATG
Found at i:2758006 original size:17 final size:18
Alignment explanation
Indices: 2757971--2758007 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
2757961 TAAAAAGTAA
*
2757971 AATATTTATGAAAATTTT
1 AATATTTATGAAAACTTT
2757989 AATATTTAT-AAAACTTT
1 AATATTTATGAAAACTTT
2758006 AA
1 AA
2758008 GCCCCAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (18 bp):
AATATTTATGAAAACTTT
Found at i:2770354 original size:29 final size:28
Alignment explanation
Indices: 2770311--2770409 Score: 85
Period size: 29 Copynumber: 3.5 Consensus size: 28
2770301 ACAAAAGTTA
2770311 TAAAAATTACTAAATTTTAATAAAAATAT
1 TAAAAATTA-TAAATTTTAATAAAAATAT
* *
2770340 TAAAAATTATAAA-ATTAGTAAGAAA-AT
1 TAAAAATTATAAATTTTAATAA-AAATAT
* * * *
2770367 ATAAAAATTGTAATTTTTTATAAAAAAAT
1 -TAAAAATTATAAATTTTAATAAAAATAT
*
2770396 AAAAAAATTATAAA
1 -TAAAAATTATAAA
2770410 ATACATCAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 8
0.76 0.14 0.11
Matches are distributed among these distances:
27 8 0.14
28 21 0.38
29 27 0.48
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (28 bp):
TAAAAATTATAAATTTTAATAAAAATAT
Found at i:2770379 original size:19 final size:18
Alignment explanation
Indices: 2770330--2770379 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
2770320 CTAAATTTTA
*
2770330 ATAAAAATAT-TAAAAATT
1 ATAAAAAT-TGTAAAAAAT
2770348 AT-AAAATTAGTAAGAAAAT
1 ATAAAAATT-GTAA-AAAAT
2770367 ATAAAAATTGTAA
1 ATAAAAATTGTAA
2770380 TTTTTTATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 1 0.04
17 5 0.19
18 5 0.19
19 10 0.37
20 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (18 bp):
ATAAAAATTGTAAAAAAT
Found at i:2770653 original size:21 final size:20
Alignment explanation
Indices: 2770609--2770667 Score: 61
Period size: 19 Copynumber: 3.0 Consensus size: 20
2770599 AAATAATAAT
2770609 TTTACTATTTTTAT-A-TTTC
1 TTTAC-ATTTTTATAATTTTC
2770628 TTTACATTTTTTTATAATTTTC
1 TTTACA--TTTTTATAATTTTC
*
2770650 -TTACAATTTTATAATTTT
1 TTTACATTTTTATAATTTT
2770668 TTCTGTATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
18 1 0.03
19 17 0.49
20 7 0.20
21 6 0.17
22 4 0.11
ACGTcount: A:0.25, C:0.08, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTACATTTTTATAATTTTC
Found at i:2770698 original size:9 final size:9
Alignment explanation
Indices: 2770686--2770744 Score: 55
Period size: 9 Copynumber: 6.1 Consensus size: 9
2770676 TTCTATATAA
2770686 TTTATAATT
1 TTTATAATT
*
2770695 TTTATAAAAT
1 TTTAT-AATT
*
2770705 TTTGTAATT
1 TTTATAATT
*
2770714 TTTTTACGATT
1 TTTATA--ATT
2770725 TTTATAATT
1 TTTATAATT
2770734 TTTATTAATT
1 TTTA-TAATT
2770744 T
1 T
2770745 ATCTTTCTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
9 20 0.49
10 13 0.32
11 8 0.20
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTATAATT
Found at i:2770738 original size:48 final size:50
Alignment explanation
Indices: 2770636--2770749 Score: 116
Period size: 48 Copynumber: 2.3 Consensus size: 50
2770626 TCTTTACATT
*
2770636 TTTTTATAATTTTCTTACAATTTTATAATTTTTTCTGTATTTCTATATAA
1 TTTTTATAATTTTCTTAAAATTTTATAATTTTTTCTGTATTTCTATATAA
*
2770686 --TTTATAATTTT-TATAAAATTTTGTAATTTTTT-TACG-ATTT-T-TATAA
1 TTTTTATAATTTTCT-TAAAATTTTATAATTTTTTCT--GTATTTCTATATAA
2770732 TTTTTATTAATTTATCTT
1 TTTTTA-TAATTT-TCTT
2770750 TCTTTTTTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
46 5 0.09
47 3 0.06
48 36 0.67
49 7 0.13
50 2 0.04
51 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (50 bp):
TTTTTATAATTTTCTTAAAATTTTATAATTTTTTCTGTATTTCTATATAA
Found at i:2770744 original size:19 final size:19
Alignment explanation
Indices: 2770686--2770744 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
2770676 TTCTATATAA
* *
2770686 TTTATAATTTTTATAAAAT
1 TTTATAATTTTTATTAATT
*
2770705 TTTGTAATTTTT-TTACGATT
1 TTTATAATTTTTATTA--ATT
2770725 TTTATAATTTTTATTAATT
1 TTTATAATTTTTATTAATT
2770744 T
1 T
2770745 ATCTTTCTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
18 2 0.06
19 15 0.45
20 13 0.39
21 3 0.09
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTATAATTTTTATTAATT
Found at i:2772839 original size:21 final size:21
Alignment explanation
Indices: 2772762--2772860 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
2772752 GCTTCAGTTT
* *
2772762 AACTCATATGAGTTTCCGTTC
1 AACTCTTATGAGTTTTCGTTC
* * * *
2772783 AGCTCTTTTGAG-CTTCTGTTT
1 AACTCTTATGAGTTTTC-GTTC
*
2772804 AAC-CGTTATGGGTTTTCGTTC
1 AACTC-TTATGAGTTTTCGTTC
*
2772825 AGCTCTTATGAGTTTTCGTTC
1 AACTCTTATGAGTTTTCGTTC
* *
2772846 AACCCTTATGGGTTT
1 AACTCTTATGAGTTT
2772861 CTGTTTAGCA
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
20 3 0.05
21 51 0.88
22 4 0.07
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.44
Consensus pattern (21 bp):
AACTCTTATGAGTTTTCGTTC
Found at i:2772855 original size:42 final size:42
Alignment explanation
Indices: 2772732--2772886 Score: 132
Period size: 42 Copynumber: 3.7 Consensus size: 42
2772722 TAGTGTTTAC
* * * * * * * * *
2772732 TTTCTGTTTAGCTCTCACGAGCTTCAGTTTAACTCATATGAG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
* * *
2772774 TTTCCGTTCAGCTCTTTTGAGCTTCTGTTTAACCGTTATGGG
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
* *
2772816 TTTTCGTTCAGCTCTTATGAG-TTTTCGTTCAACCCTTATGGG
1 TTTCCGTTCAGCTCTTATGAGCTTCT-GTTCAACCCTTATGGG
* * * *
2772858 TTTCTGTTTAGCACTTATGTGCTTCTGTT
1 TTTCCGTTCAGCTCTTATGAGCTTCTGTT
2772887 TAGCCTTCGG
Statistics
Matches: 90, Mismatches: 21, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
41 3 0.03
42 84 0.93
43 3 0.03
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.46
Consensus pattern (42 bp):
TTTCCGTTCAGCTCTTATGAGCTTCTGTTCAACCCTTATGGG
Found at i:2772874 original size:21 final size:21
Alignment explanation
Indices: 2772850--2772890 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2772840 TCGTTCAACC
*
2772850 CTTATGGGTTTCTGTTTAGCA
1 CTTATGGGCTTCTGTTTAGCA
*
2772871 CTTATGTGCTTCTGTTTAGC
1 CTTATGGGCTTCTGTTTAGC
2772891 CTTCGGGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (21 bp):
CTTATGGGCTTCTGTTTAGCA
Done.