Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008531.1 Hibiscus syriacus cultivar Beakdansim tig00111409_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: 3817888
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 19
Found at i:1442162 original size:22 final size:22
Alignment explanation
Indices: 1442113--1442161 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1442103 AATAAATATT
**
1442113 TAAAATAAATCAATACATATTT
1 TAAAATAAATCAATACATATAA
*
1442135 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATACATA-TAA
1442158 TAAA
1 TAAA
1442162 TTATTTAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATACATATAA
Found at i:1442240 original size:22 final size:22
Alignment explanation
Indices: 1442169--1442240 Score: 60
Period size: 22 Copynumber: 3.2 Consensus size: 22
1442159 AAATTATTTA
1442169 AAAT-AATCAATCCATAC-AACT
1 AAATAAATCAATCCATACTAA-T
**
1442190 ACAATAATAATCAATCCATA-TTTT
1 A-AAT-A-AATCAATCCATACTAAT
1442214 AAAATAAATCAATCCATACTAAT
1 -AAATAAATCAATCCATACTAAT
1442237 AAAT
1 AAAT
1442241 TATTTAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
21 1 0.03
22 19 0.47
23 3 0.08
24 4 0.10
25 13 0.32
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (22 bp):
AAATAAATCAATCCATACTAAT
Found at i:1442275 original size:53 final size:53
Alignment explanation
Indices: 1442195--1442358 Score: 296
Period size: 53 Copynumber: 3.1 Consensus size: 53
1442185 CAACTACAAT
1442195 AATAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
*
1442248 AATAATCAATCTATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1 AATAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1442301 AATAAATCAATCCATATTTT-AAATAAATCAATCCATACTAATAAATTATTT-A
1 AAT-AATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
1442353 AATAAT
1 AATAAT
1442359 TATTTTAAAA
Statistics
Matches: 108, Mismatches: 2, Indels: 4
0.95 0.02 0.04
Matches are distributed among these distances:
51 3 0.03
52 4 0.04
53 86 0.80
54 15 0.14
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (53 bp):
AATAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAA
Found at i:1442324 original size:21 final size:21
Alignment explanation
Indices: 1442294--1442392 Score: 87
Period size: 21 Copynumber: 4.6 Consensus size: 21
1442284 ACTAATAAAT
1442294 TATTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
*
1442315 TATTTTAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
* *
1442336 TACTAATAAATTATTTAAAT-AAT-TA
1 TA-T-TTAAA--A--TAAATCAATCCA
1442361 T-TTTAAAATAAATCAATCCA
1 TATTTAAAATAAATCAATCCA
*
1442381 TATTTATAATAA
1 TATTTAAAATAA
1442393 TTTTTTTAAA
Statistics
Matches: 62, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
18 5 0.08
19 3 0.05
20 3 0.05
21 31 0.50
22 5 0.08
23 4 0.06
25 3 0.05
26 3 0.05
27 5 0.08
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (21 bp):
TATTTAAAATAAATCAATCCA
Found at i:1442414 original size:15 final size:15
Alignment explanation
Indices: 1442340--1442468 Score: 131
Period size: 15 Copynumber: 8.5 Consensus size: 15
1442330 AATCCATACT
1442340 AATAAATTA-TTT-A
1 AATAAATTATTTTAA
1442353 AAT-AATTATTTTAA
1 AATAAATTATTTTAA
*
1442367 AATAAATCAATCCATATTTAT
1 AATAAAT---T--AT-TTTAA
*
1442388 AAT-AATTTTTTTAA
1 AATAAATTATTTTAA
*
1442402 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
1442417 TATAAATTATTTTAA
1 AATAAATTATTTTAA
*
1442432 AATAAATTATTTTAT
1 AATAAATTATTTTAA
1442447 AATAAATTATTTTAA
1 AATAAATTATTTTAA
1442462 AATAAAT
1 AATAAAT
1442469 AACCTTATTA
Statistics
Matches: 96, Mismatches: 10, Indels: 18
0.77 0.08 0.15
Matches are distributed among these distances:
12 5 0.05
13 6 0.06
14 11 0.11
15 60 0.62
17 1 0.01
18 1 0.01
20 5 0.05
21 7 0.07
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:1442432 original size:30 final size:30
Alignment explanation
Indices: 1442340--1442489 Score: 159
Period size: 30 Copynumber: 5.0 Consensus size: 30
1442330 AATCCATACT
1442340 AATAAATTA-TTTA-AAT-AATTATTTTAA
1 AATAAATTATTTTATAATAAATTATTTTAA
*
1442367 AATAAATCAATCCATATTTATAAT-AATTTTTTTAA
1 AATAAAT---T--AT-TTTATAATAAATTATTTTAA
*
1442402 AATAAATTATTTTATTATAAATTATTTTAA
1 AATAAATTATTTTATAATAAATTATTTTAA
1442432 AATAAATTATTTTATAATAAATTATTTTAA
1 AATAAATTATTTTATAATAAATTATTTTAA
* **
1442462 AATAAATAACCTTAT--TAAATTATTTTAA
1 AATAAATTATTTTATAATAAATTATTTTAA
1442490 TAAATAACCA
Statistics
Matches: 107, Mismatches: 7, Indels: 17
0.82 0.05 0.13
Matches are distributed among these distances:
27 7 0.07
28 13 0.12
29 7 0.07
30 54 0.50
32 2 0.02
34 4 0.04
35 20 0.19
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
AATAAATTATTTTATAATAAATTATTTTAA
Found at i:1442484 original size:65 final size:62
Alignment explanation
Indices: 1442356--1442510 Score: 162
Period size: 60 Copynumber: 2.5 Consensus size: 62
1442346 TTATTTAAAT
* *
1442356 AATTATTTTAAAATAAATCAATCCATATTTATAATAATTTTTTTAAAATAAATTATTTTATTATA
1 AATTATTTTAAAATAAAT--AT-CATATTTATAATAATTATTTTAAAATAAATAATTTTATTATA
**
1442421 AATTATTTTAAAATAAAT-T-AT-TTTATAATAAATTATTTTAAAATAAATAACCTTA-T-TA
1 AATTATTTTAAAATAAATATCATATTTATAAT-AATTATTTTAAAATAAATAATTTTATTATA
*
1442479 AATTATTTT--AATAAATAACCATATTTTATAAT
1 AATTATTTTAAAATAAAT-ATCATA-TTTATAAT
1442511 TGTTCTTGAA
Statistics
Matches: 79, Mismatches: 5, Indels: 16
0.79 0.05 0.16
Matches are distributed among these distances:
56 7 0.09
58 11 0.14
59 11 0.14
60 23 0.29
61 8 0.10
62 1 0.01
65 18 0.23
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (62 bp):
AATTATTTTAAAATAAATATCATATTTATAATAATTATTTTAAAATAAATAATTTTATTATA
Found at i:1442498 original size:26 final size:27
Alignment explanation
Indices: 1442449--1442503 Score: 85
Period size: 26 Copynumber: 2.0 Consensus size: 27
1442439 TATTTTATAA
*
1442449 TAAATTATTTTAAAATAAATAACCTTAT
1 TAAATTATTTT-AAATAAATAACCATAT
1442477 TAAATTATTTT-AATAAATAACCATAT
1 TAAATTATTTTAAATAAATAACCATAT
1442503 T
1 T
1442504 TTATAATTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 15 0.58
28 11 0.42
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (27 bp):
TAAATTATTTTAAATAAATAACCATAT
Found at i:1455677 original size:2 final size:2
Alignment explanation
Indices: 1455666--1455847 Score: 210
Period size: 2 Copynumber: 91.5 Consensus size: 2
1455656 AATAGGCCCA
1455666 AT AT -T 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
1455707 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
* * * * *
1455749 AT AT AT AT AT AT AT AT AT AT AT AGT AG AA AT TT AT -T TT CGT -T
1 AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT -AT AT
* * * * * *
1455791 CAT AT TT TT TT TT AT -T TT AT AC 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
1455833 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1455848 GTTTGCAAAT
Statistics
Matches: 162, Mismatches: 11, Indels: 14
0.87 0.06 0.07
Matches are distributed among these distances:
1 4 0.02
2 154 0.95
3 4 0.02
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1455921 original size:38 final size:35
Alignment explanation
Indices: 1455877--1456088 Score: 226
Period size: 38 Copynumber: 6.1 Consensus size: 35
1455867 AATACATATG
1455877 TAATATATAGTTTTTAAAACACTTTTAAAAATTATA
1 TAATATATAGTTTTTAAAACA-TTTTAAAAATTATA
*
1455913 TAATATATAGTTTTTAAAATATTTTAGAAAA-TATA
1 TAATATATAGTTTTTAAAACATTTTA-AAAATTATA
*
1455948 TAATATATAGTTTTTAAAATCATTTTGAAAACTTATA
1 TAATATATAGTTTTTAAAA-CATTTT-AAAAATTATA
* *
1455985 TAATATATAGTTTTTGAAAATATTTTTGAAAACTTATA
1 TAATATATAGTTTTT-AAAACA-TTTT-AAAAATTATA
1456023 TAATATATAGTTTTTGAAAAC---TT----A-TATA
1 TAATATATAGTTTTT-AAAACATTTTAAAAATTATA
* *
1456051 TAATATATAATTTTTAAAACATTTTTGAAAATTATA
1 TAATATATAGTTTTTAAAACA-TTTTAAAAATTATA
1456087 TA
1 TA
1456089 GTTTTTAAAA
Statistics
Matches: 154, Mismatches: 7, Indels: 30
0.81 0.04 0.16
Matches are distributed among these distances:
27 5 0.03
28 18 0.12
31 2 0.01
34 2 0.01
35 29 0.19
36 38 0.25
37 21 0.14
38 39 0.25
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (35 bp):
TAATATATAGTTTTTAAAACATTTTAAAAATTATA
Found at i:1456023 original size:31 final size:29
Alignment explanation
Indices: 1455988--1456130 Score: 76
Period size: 31 Copynumber: 4.6 Consensus size: 29
1455978 ACTTATATAA
1455988 TATATAGTTTTTGAAAATATTTTTGAAAACTTAT
1 TATATAGTTTTTGAAAATATTTTT--AAA---AT
* * *
1456022 ATAATATATAGTTTTTGAAAACT-TATATATAA-
1 -T-AT--ATAGTTTTTGAAAA-TATTTTTAAAAT
* *
1456054 TATATAATTTTT-AAAACATTTTTGAAAAT
1 TATATAGTTTTTGAAAATATTTTT-AAAAT
* *
1456083 TATATAGTTTTTAAAAAATAATTTTAAAAAT
1 TATATAGTTTTT-GAAAAT-ATTTTTAAAAT
*
1456114 TATATAGTTTTTTAAAA
1 TATATAGTTTTTGAAAA
1456131 AACAGTTTTG
Statistics
Matches: 86, Mismatches: 12, Indels: 25
0.70 0.10 0.20
Matches are distributed among these distances:
27 7 0.08
28 11 0.13
29 11 0.13
30 6 0.07
31 22 0.26
32 5 0.06
33 1 0.01
35 1 0.01
36 4 0.05
38 17 0.20
39 1 0.01
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.48
Consensus pattern (29 bp):
TATATAGTTTTTGAAAATATTTTTAAAAT
Found at i:1456036 original size:26 final size:28
Alignment explanation
Indices: 1456006--1456070 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
1455996 TTTTGAAAAT
1456006 ATTTTTGAAAAC-T-TATATAATATATA
1 ATTTTTGAAAACTTATATATAATATATA
*
1456032 GTTTTTGAAAACTTATATATAATATATA
1 ATTTTTGAAAACTTATATATAATATATA
1456060 ATTTTT-AAAAC
1 ATTTTTGAAAAC
1456071 ATTTTTGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
26 11 0.31
27 6 0.17
28 18 0.51
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.46
Consensus pattern (28 bp):
ATTTTTGAAAACTTATATATAATATATA
Found at i:1456056 original size:110 final size:109
Alignment explanation
Indices: 1455819--1456061 Score: 294
Period size: 110 Copynumber: 2.2 Consensus size: 109
1455809 ATACATATAT
* * *
1455819 ATATATATATATATATATATATATATATAGTTTGCAAATGATTTTGAAAATACATATGTAATATA
1 ATAT-TATATATA-ATATATA-ATATATAGTTTGAAAATCATTTTGAAAATACATATATAATATA
1455884 TAGTTTTTAAAACACTTTTAAAAATTATATAATATATAGTTTTTAAA
63 TAGTTTTTAAAACACTTTTAAAAATTATATAATATATAGTTTTTAAA
* * * * *
1455931 ATATTTTAGAAAATATATAATATATAGTTTTTAAAATCATTTTG-AAA-ACTTATATAATATATA
1 ATATTATATATAATATATAATATATAG-TTTGAAAATCATTTTGAAAATACATATATAATATATA
* * *
1455994 GTTTTTGAAAATATTTTTGAAAACTTATATAATATATAGTTTTTGAAA
65 GTTTTT-AAAACACTTTT-AAAAATTATATAATATATAGTTTTT-AAA
*
1456042 A-CTTATATATAATATATAAT
1 ATATTATATATAATATATAAT
1456062 TTTTAAAACA
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
108 20 0.18
109 20 0.18
110 59 0.53
111 9 0.08
112 4 0.04
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (109 bp):
ATATTATATATAATATATAATATATAGTTTGAAAATCATTTTGAAAATACATATATAATATATAG
TTTTTAAAACACTTTTAAAAATTATATAATATATAGTTTTTAAA
Found at i:1456058 original size:35 final size:35
Alignment explanation
Indices: 1455877--1456061 Score: 182
Period size: 35 Copynumber: 5.1 Consensus size: 35
1455867 AATACATATG
1455877 TAATATATAGTTTTTAAAACACTTTTA-AAAATTATA
1 TAATATATAGTTTTT-AAA-ACTTTTATAAAATTATA
* *
1455913 TAATATATAGTTTTTAAAATATTTTAGAAAA-TATA
1 TAATATATAGTTTTTAAAA-CTTTTATAAAATTATA
*
1455948 TAATATATAGTTTTTAAAATCATTTTGA-AAACTTATA
1 TAATATATAGTTTTTAAAA-C-TTTT-ATAAAATTATA
*
1455985 TAATATATAGTTTTTGAAAA-TATTTTTGAAAACTTATA
1 TAATATATAGTTTTT-AAAACT-TTTAT-AAAA-TTATA
* *
1456023 TAATATATAGTTTTTGAAAACTTATATATAA-TATA
1 TAATATATAGTTTTT-AAAACTTTTATAAAATTATA
1456058 TAAT
1 TAAT
1456062 TTTTAAAACA
Statistics
Matches: 130, Mismatches: 8, Indels: 23
0.81 0.05 0.14
Matches are distributed among these distances:
34 1 0.01
35 41 0.32
36 29 0.22
37 26 0.20
38 32 0.25
39 1 0.01
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.46
Consensus pattern (35 bp):
TAATATATAGTTTTTAAAACTTTTATAAAATTATA
Found at i:1456126 original size:32 final size:30
Alignment explanation
Indices: 1456054--1456152 Score: 110
Period size: 29 Copynumber: 3.2 Consensus size: 30
1456044 TTATATATAA
* * *
1456054 TATATAATTTTTAAAACAT-TTTTGAAAAT
1 TATATAGTTTTTAAAAAATATTTTAAAAAT
1456083 TATATAGTTTTTAAAAAATAATTTTAAAAAT
1 TATATAGTTTTTAAAAAAT-ATTTTAAAAAT
* *
1456114 TATATAGTTTTTTAAAAAACAGTTTTGAAAATT
1 TATATAG-TTTTTAAAAAATA-TTTT-AAAAAT
1456147 TATATA
1 TATATA
1456153 TAATATATAG
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
29 17 0.28
31 17 0.28
32 15 0.25
33 11 0.18
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (30 bp):
TATATAGTTTTTAAAAAATATTTTAAAAAT
Found at i:1456131 original size:31 final size:29
Alignment explanation
Indices: 1456061--1456131 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 29
1456051 TAATATATAA
*
1456061 TTTTTAAAACATTTTTGAAAATTATATAGT
1 TTTTTAAAA-ATTTTTAAAAATTATATAGT
*
1456091 TTTTAAAAAATAATTTTAAAAATTATATAGT
1 TTTTTAAAAAT--TTTTAAAAATTATATAGT
1456122 TTTTTAAAAA
1 TTTTTAAAAA
1456132 ACAGTTTTGA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.06
30 8 0.22
31 26 0.72
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.48
Consensus pattern (29 bp):
TTTTTAAAAATTTTTAAAAATTATATAGT
Found at i:1456184 original size:15 final size:15
Alignment explanation
Indices: 1456164--1456193 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1456154 AATATATAGG
*
1456164 TTTTAAAAGAAATTT
1 TTTTAAAAAAAATTT
1456179 TTTTAAAAAAAATTT
1 TTTTAAAAAAAATTT
1456194 ATATTATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTTTAAAAAAAATTT
Found at i:1456226 original size:26 final size:27
Alignment explanation
Indices: 1456178--1456228 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
1456168 AAAAGAAATT
1456178 TTTTTAAAAAAAATTTATATTATATAG
1 TTTTTAAAAAAAATTTATATTATATAG
1456205 TTTTTAAAAAAATATTT-T-TTATAT
1 TTTTTAAAAAAA-ATTTATATTATAT
1456229 TTATATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
26 6 0.26
27 13 0.57
28 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (27 bp):
TTTTTAAAAAAAATTTATATTATATAG
Found at i:1456254 original size:25 final size:26
Alignment explanation
Indices: 1456226--1456299 Score: 75
Period size: 25 Copynumber: 2.9 Consensus size: 26
1456216 ATATTTTTTA
1456226 TATTTA-TATTTATATTTATTATTAT
1 TATTTATTATTTATATTTATTATTAT
* * *
1456251 TA-TTATTATTTCTTTTTATTATTCT
1 TATTTATTATTTATATTTATTATTAT
1456276 TA-TTATTGATTTAT-TTTAATTATT
1 TATTTATT-ATTTATATTT-ATTATT
1456300 TTGTAGGCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
24 3 0.07
25 28 0.67
26 11 0.26
ACGTcount: A:0.27, C:0.03, G:0.01, T:0.69
Consensus pattern (26 bp):
TATTTATTATTTATATTTATTATTAT
Found at i:1461249 original size:50 final size:50
Alignment explanation
Indices: 1461184--1461309 Score: 200
Period size: 50 Copynumber: 2.5 Consensus size: 50
1461174 TTCAGAGTCA
*
1461184 ATTTCAACTTCACGGCGAAGGATATTGGACTCAAAACAATACAAGCTTGG
1 ATTTCAACTTTACGGCGAAGGATATTGGACTCAAAACAATACAAGCTTGG
*
1461234 ATTTCAACTTTACGGCGAAGGATATTGGACTCGAAACAATACAAGCTTGG
1 ATTTCAACTTTACGGCGAAGGATATTGGACTCAAAACAATACAAGCTTGG
**
1461284 ATTTCAA-TTTCACAACGAAGGATATT
1 ATTTCAACTTT-ACGGCGAAGGATATT
1461310 CAAGTCAAGG
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
49 3 0.04
50 68 0.96
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (50 bp):
ATTTCAACTTTACGGCGAAGGATATTGGACTCAAAACAATACAAGCTTGG
Found at i:1461937 original size:84 final size:83
Alignment explanation
Indices: 1461795--1462163 Score: 387
Period size: 84 Copynumber: 4.4 Consensus size: 83
1461785 AATATCGTGT
** * * * * * * *
1461795 TCATTTGCAATATAACTCAAGGCAAGAAGGGCTATTTACCGACCAAAGACCTTTGAGTTCGATTA
1 TCATTTGCAGCATAACTCAA-GCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
1461860 CGCTAAGCTTAAAGGCATA
65 CGCTCAGCTCAAAGGCATA
* * * *
1461879 TCATTTGTAGCATAACTCAATGCTATAAGGGTTATCAGCCAATCAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAA-GCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
* *
1461944 CGCTCAGCTCGAAGGTATA
65 CGCTCAGCTCAAAGGCATA
*
1461963 TCATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGACAACCAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAGCATAACTCAA-GCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
*
1462028 CGCTCAGCTCAAAGGCACA
65 CGCTCAGCTCAAAGGCATA
* * * * *
1462047 TCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAACCAAAGACCTTCGAGTTCGATTA
1 TCATTTGCAGCATAACTCAAG-CTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTA
** * * *
1462112 CATTCAACTCATAGGCAAA
65 CGCTCAGCTCAAAGGCATA
* * *
1462131 TCAAATTTACAGCATATCTCAAGGTAAGAAGGG
1 TC--ATTTGCAGCATAACTCAAGCT-AGAAGGG
1462164 CTATATATCA
Statistics
Matches: 238, Mismatches: 43, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
83 1 0.00
84 214 0.90
86 23 0.10
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (83 bp):
TCATTTGCAGCATAACTCAAGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCAAAGGCATA
Found at i:1462717 original size:2 final size:2
Alignment explanation
Indices: 1462705--1462755 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
1462695 TTTTTAATTT
*
1462705 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
1462747 TA T- TA TA TA
1 TA TA TA TA TA
1462756 GTTTACAAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1462786 original size:38 final size:36
Alignment explanation
Indices: 1462738--1462936 Score: 126
Period size: 38 Copynumber: 5.2 Consensus size: 36
1462728 ATATATATAT
*
1462738 ATATATATATATTATATAGTTTACAAA-CGATTTTGAAA
1 ATAT-TATATAATATATAGTTTA-AAATC-ATTTTGAAA
1462776 ATATGTATATAATATATAGTTTTTAAAATCATTTTGAAA
1 ATAT-TATATAATATATAG--TTTAAAATCATTTTGAAA
*
1462815 A-CTTATATAATATATAGTTTTTGAAAA-CATTTTTGAAA
1 ATATTATATAATATATAG--TTT-AAAATCA-TTTTGAAA
*
1462853 A-CTTATATAATATATAGTTTTTGAAAA-CATTTTTGAAA
1 ATATTATATAATATATAG--TTT-AAAATCA-TTTTGAAA
*
1462891 ACTCA-TATATAATAT-TAATTTTTAAAA-CATTTTTGAAA
1 A-T-ATTATATAATATAT-A-GTTTAAAATCA-TTTTGAAA
*
1462929 ATTTTATA
1 ATATTATA
1462937 GTTTTTAAAA
Statistics
Matches: 144, Mismatches: 6, Indels: 23
0.83 0.03 0.13
Matches are distributed among these distances:
37 26 0.18
38 85 0.59
39 17 0.12
40 16 0.11
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (36 bp):
ATATTATATAATATATAGTTTAAAATCATTTTGAAA
Found at i:1462833 original size:75 final size:76
Alignment explanation
Indices: 1462741--1462929 Score: 230
Period size: 76 Copynumber: 2.5 Consensus size: 76
1462731 TATATATATA
*
1462741 TATATATATTATATAG-TTT-ACAAACGA-TTTTGAAAATATGTATATAATATATAGTTTTT-AA
1 TATATATAATATATAGTTTTGA-AAAC-ATTTTTGAAAA-AT-TATATAATATATAGTTTTTGAA
1462802 AATCA-TTTTGAAAAC
62 AA-CATTTTTGAAAAC
*
1462817 T-TATATAATATATAGTTTTTGAAAACATTTTTGAAAACTTATATAATATATAGTTTTTGAAAAC
1 TATATATAATATATAG-TTTTGAAAACATTTTTGAAAAATTATATAATATATAGTTTTTGAAAAC
1462881 ATTTTTGAAAAC
65 ATTTTTGAAAAC
* *
1462893 TCATATATAATAT-TAATTTTTAAAACATTTTTGAAAA
1 T-ATATATAATATATAGTTTTGAAAACATTTTTGAAAA
1462930 TTTTATAGTT
Statistics
Matches: 101, Mismatches: 4, Indels: 16
0.83 0.03 0.13
Matches are distributed among these distances:
75 34 0.34
76 38 0.38
77 18 0.18
78 11 0.11
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.44
Consensus pattern (76 bp):
TATATATAATATATAGTTTTGAAAACATTTTTGAAAAATTATATAATATATAGTTTTTGAAAACA
TTTTTGAAAAC
Found at i:1462849 original size:12 final size:12
Alignment explanation
Indices: 1462832--1462892 Score: 54
Period size: 12 Copynumber: 4.9 Consensus size: 12
1462822 TAATATATAG
1462832 TTTTTGAAAACA
1 TTTTTGAAAACA
1462844 TTTTTGAAAAC-
1 TTTTTGAAAACA
* *
1462855 TTATAT-AATATATA
1 TT-TTTGAA-A-ACA
1462869 GTTTTTGAAAACA
1 -TTTTTGAAAACA
1462882 TTTTTGAAAAC
1 TTTTTGAAAAC
1462893 TCATATATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 12
0.71 0.07 0.22
Matches are distributed among these distances:
11 4 0.10
12 25 0.64
13 3 0.08
14 3 0.08
15 4 0.10
ACGTcount: A:0.41, C:0.07, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTTGAAAACA
Found at i:1462918 original size:76 final size:75
Alignment explanation
Indices: 1462781--1462929 Score: 232
Period size: 76 Copynumber: 2.0 Consensus size: 75
1462771 TGAAAATATG
*
1462781 TATATAATATATAGTTTTTAAAATCATTTTGAAAACTTATATAATATATAGTTTTTGAAAACATT
1 TATATAATATATAGTTTTTAAAATCATTTTGAAAACTTATATAATATATAATTTTTGAAAACATT
1462846 TTTGAAAACT
66 TTTGAAAACT
1462856 TATATAATATATAGTTTTTGAAAA-CATTTTTGAAAACTCATATATAATAT-TAATTTTT-AAAA
1 TATATAATATATAGTTTTT-AAAATCA-TTTTGAAAACT--TATATAATATATAATTTTTGAAAA
1462918 CATTTTTGAAAA
62 CATTTTTGAAAA
1462930 TTTTATAGTT
Statistics
Matches: 69, Mismatches: 1, Indels: 7
0.90 0.01 0.09
Matches are distributed among these distances:
75 21 0.30
76 31 0.45
77 7 0.10
78 10 0.14
ACGTcount: A:0.44, C:0.05, G:0.06, T:0.45
Consensus pattern (75 bp):
TATATAATATATAGTTTTTAAAATCATTTTGAAAACTTATATAATATATAATTTTTGAAAACATT
TTTGAAAACT
Found at i:1462956 original size:32 final size:30
Alignment explanation
Indices: 1462914--1463001 Score: 95
Period size: 32 Copynumber: 2.8 Consensus size: 30
1462904 ATTAATTTTT
* *
1462914 AAAACATTTTTGAAAATTTTATAGTTTTTAAA
1 AAAACTTTTTTGAAAATTATATA--TTTTAAA
*
1462946 AAAACTTTTTTAAAAATTATATATTTTAAA
1 AAAACTTTTTTGAAAATTATATATTTTAAA
* *
1462976 AAAAATAGTTTTGAAAATATATATAT
1 AAAACT-TTTTTGAAAAT-TATATAT
1463002 AATATATAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 12 0.25
31 9 0.19
32 27 0.56
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (30 bp):
AAAACTTTTTTGAAAATTATATATTTTAAA
Found at i:1463089 original size:3 final size:3
Alignment explanation
Indices: 1463081--1463129 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
1463071 ATATTTATAT
* * * *
1463081 TTA TTA TTA TTA TTA CTA TTA TTA TT- TTC TTT TTA TTA TTC TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1463128 TT
1 TT
1463130 GATTTATTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 2 0.05
3 37 0.95
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1463139 original size:26 final size:25
Alignment explanation
Indices: 1463078--1463146 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
1463068 TTTATATTTA
*
1463078 TATTTATTATTATTATTACTATTAT
1 TATTTATTTTTATTATTACTATTAT
*
1463103 TATTTTCTTTTTATTATT-CTTATTAT
1 TA-TTTATTTTTATTATTAC-TATTAT
*
1463129 TGATTTATTTTAATTATT
1 T-ATTTATTTTTATTATT
1463147 TTGTAGGCCC
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 3 0.08
26 33 0.89
27 1 0.03
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.68
Consensus pattern (25 bp):
TATTTATTTTTATTATTACTATTAT
Found at i:1464407 original size:4 final size:4
Alignment explanation
Indices: 1464400--1464439 Score: 71
Period size: 4 Copynumber: 10.0 Consensus size: 4
1464390 CATACATACA
*
1464400 TATG TATG TATG TATA TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1464440 CATGCATGCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:1464444 original size:4 final size:4
Alignment explanation
Indices: 1464437--1464467 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1464427 GTATGTATGT
*
1464437 ATGC ATGC ATGC ATGC ATGC ATGG ATGC ATG
1 ATGC ATGC ATGC ATGC ATGC ATGC ATGC ATG
1464468 TGTGTGTGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (4 bp):
ATGC
Found at i:1464473 original size:2 final size:2
Alignment explanation
Indices: 1464466--1464573 Score: 207
Period size: 2 Copynumber: 54.0 Consensus size: 2
1464456 CATGGATGCA
1464466 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1464508 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TC TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1464550 TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG
1464574 ACAACCAATA
Statistics
Matches: 104, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 104 1.00
ACGTcount: A:0.00, C:0.01, G:0.49, T:0.50
Consensus pattern (2 bp):
TG
Found at i:1465309 original size:19 final size:19
Alignment explanation
Indices: 1465285--1465324 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
1465275 ATTGACATGT
1465285 TAATAGTTTATATTATCTA
1 TAATAGTTTATATTATCTA
1465304 TAATAGTTTATATTATCTA
1 TAATAGTTTATATTATCTA
1465323 TA
1 TA
1465325 TTTTAACATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (19 bp):
TAATAGTTTATATTATCTA
Found at i:1465393 original size:2 final size:2
Alignment explanation
Indices: 1465386--1465434 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1465376 TCATAATTTA
1465386 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
1465428 AT AT AT A
1 AT AT AT A
1465435 ATAGAACTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1466367 original size:22 final size:21
Alignment explanation
Indices: 1466342--1466384 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
1466332 CTATCCCCTT
1466342 ACCTAGA-AGACCACTCGCCGAC
1 ACCTAGAGAG-CCAC-CGCCGAC
1466364 ACCTAGAGAGCCACCGCCGAC
1 ACCTAGAGAGCCACCGCCGAC
1466385 CGAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 7 0.35
22 11 0.55
23 2 0.10
ACGTcount: A:0.30, C:0.42, G:0.21, T:0.07
Consensus pattern (21 bp):
ACCTAGAGAGCCACCGCCGAC
Found at i:1466383 original size:21 final size:22
Alignment explanation
Indices: 1466342--1466384 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1466332 CTATCCCCTT
1466342 ACCTAGAAGACCACTCGCCGAC
1 ACCTAGAAGACCACTCGCCGAC
1466364 ACCTAG-AGAGCCAC-CGCCGAC
1 ACCTAGAAGA-CCACTCGCCGAC
1466385 CGAAAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.30, C:0.42, G:0.21, T:0.07
Consensus pattern (22 bp):
ACCTAGAAGACCACTCGCCGAC
Found at i:1467468 original size:29 final size:28
Alignment explanation
Indices: 1467436--1467492 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
1467426 CTAATAATAA
1467436 TATATAATA-ATATGTATATATTAAAAAAC
1 TATATAATATATAT-TATAT-TTAAAAAAC
*
1467465 TATATAATATATATTATATTTCAAAAAC
1 TATATAATATATATTATATTTAAAAAAC
1467493 AATGTAACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 8 0.31
29 14 0.54
30 4 0.15
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (28 bp):
TATATAATATATATTATATTTAAAAAAC
Found at i:1467609 original size:17 final size:19
Alignment explanation
Indices: 1467562--1467617 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 19
1467552 AAGCCATATT
*
1467562 TATTATATGTTTTCAAAAC
1 TATTATATATTTTCAAAAC
1467581 TATATAATATATTTTCAAAA-
1 TAT-T-ATATATTTTCAAAAC
1467601 T-TTATATATTTTCAAAA
1 TATTATATATTTTCAAAA
1467618 ACCATATATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 14 0.41
18 1 0.03
19 4 0.12
20 2 0.06
21 13 0.38
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (19 bp):
TATTATATATTTTCAAAAC
Found at i:1467624 original size:17 final size:17
Alignment explanation
Indices: 1467587--1467627 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1467577 AAACTATATA
***
1467587 ATATATTTTCAAAATTT
1 ATATATTTTCAAAAACC
1467604 ATATATTTTCAAAAACC
1 ATATATTTTCAAAAACC
1467621 ATATATT
1 ATATATT
1467628 ATATACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATTTTCAAAAACC
Found at i:1470434 original size:95 final size:95
Alignment explanation
Indices: 1470324--1470523 Score: 285
Period size: 95 Copynumber: 2.1 Consensus size: 95
1470314 ATTGATGTTC
* * * * *
1470324 GTATCGATACCAAGAGAAAGGTATCGATACCAGGGATTCCAGAATGTCGAAATAG-TATTGATAC
1 GTATCGATACCAAGAGAAAGGTATCAATACCAGGAATTACAGAATGTAGAAAT-GCTATCGATAC
*
1470388 TGAAAGGGAGTATCGATACCATAGTATAGAA
65 TGAAAGGGAGTATCGATACAATAGTATAGAA
* * * *
1470419 GTATCGATACTAAGAGAAAGGTATCAATACCATGAATTACATAATGTATAAATGCTATCGATACT
1 GTATCGATACCAAGAGAAAGGTATCAATACCAGGAATTACAGAATGTAGAAATGCTATCGATACT
*
1470484 GAAAGGGCGTATCGATACAATAGTATAGAA
66 GAAAGGGAGTATCGATACAATAGTATAGAA
1470514 GTATCGATAC
1 GTATCGATAC
1470524 AATAGTATAG
Statistics
Matches: 93, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
94 1 0.01
95 92 0.99
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (95 bp):
GTATCGATACCAAGAGAAAGGTATCAATACCAGGAATTACAGAATGTAGAAATGCTATCGATACT
GAAAGGGAGTATCGATACAATAGTATAGAA
Found at i:1470520 original size:22 final size:22
Alignment explanation
Indices: 1470492--1470540 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
1470482 CTGAAAGGGC
1470492 GTATCGATACAATAGTATAGAA
1 GTATCGATACAATAGTATAGAA
*
1470514 GTATCGATACAATAGTATAGAT
1 GTATCGATACAATAGTATAGAA
1470536 GTATC
1 GTATC
1470541 AATTCCATGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (22 bp):
GTATCGATACAATAGTATAGAA
Found at i:1471021 original size:45 final size:45
Alignment explanation
Indices: 1470970--1471286 Score: 402
Period size: 45 Copynumber: 7.2 Consensus size: 45
1470960 AAATGAATGA
* *
1470970 ATAAATGAAATACATAACGGTGCATTATCGGCGTGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
1471015 ATAAATGAAATGCATAACGGCGCATTATCGGCATGAAATGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
** *
1471060 ATAAATGAAATGCATAACGGTGCATTATCAACATGAAAGGATACC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
1471105 ATAAATGAAATGCATAACGGTGCATTATAGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* *
1471150 ATAAATGAAATACATAACGGTGCATTATTGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
*
1471195 ATAAATGAAATGCATAAC-G-G---TA----CATGAAAGGATACC
1 ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
* * ** *
1471231 ACAAATGAAAATGCATAATGGTGCATTATAAGCATG-AACGATTGCC
1 ATAAATG-AAATGCATAACGGTGCATTATCGGCATGAAAGGA-TGCC
1471277 ATAAATGAAA
1 ATAAATGAAA
1471287 ATAAAGAATA
Statistics
Matches: 239, Mismatches: 22, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
36 19 0.08
37 10 0.04
38 1 0.00
39 1 0.00
40 2 0.01
42 2 0.01
43 1 0.00
44 1 0.00
45 189 0.79
46 13 0.05
ACGTcount: A:0.42, C:0.15, G:0.21, T:0.22
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTATCGGCATGAAAGGATGCC
Found at i:1471277 original size:82 final size:81
Alignment explanation
Indices: 1471136--1471286 Score: 214
Period size: 82 Copynumber: 1.9 Consensus size: 81
1471126 GCATTATAGG
* * ** *
1471136 CATGAAAGGATGCCATAAATGAAATACATAACGGTGCATTATTGGCATGAAAGGATGCCATAAAT
1 CATGAAAGGATACCACAAATGAAATACATAACGGTGCATTATAAGCATGAAACGATGCCATAAAT
1471201 GAAATGCATAACGGTA
66 GAAATGCATAACGGTA
* *
1471217 CATGAAAGGATACCACAAATGAAAATGCATAATGGTGCATTATAAGCATG-AACGATTGCCATAA
1 CATGAAAGGATACCACAAATG-AAATACATAACGGTGCATTATAAGCATGAAACGA-TGCCATAA
1471281 ATGAAA
64 ATGAAA
1471287 ATAAAGAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 23 0.38
82 38 0.62
ACGTcount: A:0.44, C:0.14, G:0.21, T:0.22
Consensus pattern (81 bp):
CATGAAAGGATACCACAAATGAAATACATAACGGTGCATTATAAGCATGAAACGATGCCATAAAT
GAAATGCATAACGGTA
Found at i:1478286 original size:336 final size:336
Alignment explanation
Indices: 1477673--1478344 Score: 1344
Period size: 336 Copynumber: 2.0 Consensus size: 336
1477663 TCCCTAGTGG
1477673 AGTCGTCAAGATGTCGTAATCGTCCTTCGGGTGGTCCCCGGGATCGAGTTCTAACTTGATTTTGA
1 AGTCGTCAAGATGTCGTAATCGTCCTTCGGGTGGTCCCCGGGATCGAGTTCTAACTTGATTTTGA
1477738 TGTGTTGGAGTCGCCATCGATCATTTGAATTTGGTCGATCAGATATCATAACTTATCGTTATCTG
66 TGTGTTGGAGTCGCCATCGATCATTTGAATTTGGTCGATCAGATATCATAACTTATCGTTATCTG
1477803 ATCTACAACTTACAAGAAATTTTTCGGATCAGGGAGTCGATTACAATCAGGGAAGGATTAGCACC
131 ATCTACAACTTACAAGAAATTTTTCGGATCAGGGAGTCGATTACAATCAGGGAAGGATTAGCACC
1477868 CCTGTACTACCCTTTCGGTACCAATTTGATTTCTCGATTGTCTTAATTACAAAAATTAAAAGTTA
196 CCTGTACTACCCTTTCGGTACCAATTTGATTTCTCGATTGTCTTAATTACAAAAATTAAAAGTTA
1477933 AAATTCAAATTTAAATATTTGATCTGAATTATTTAACTTTGACCAAGCTGAAATTGCCCTAGAAA
261 AAATTCAAATTTAAATATTTGATCTGAATTATTTAACTTTGACCAAGCTGAAATTGCCCTAGAAA
1477998 ATTCAAATTTA
326 ATTCAAATTTA
1478009 AGTCGTCAAGATGTCGTAATCGTCCTTCGGGTGGTCCCCGGGATCGAGTTCTAACTTGATTTTGA
1 AGTCGTCAAGATGTCGTAATCGTCCTTCGGGTGGTCCCCGGGATCGAGTTCTAACTTGATTTTGA
1478074 TGTGTTGGAGTCGCCATCGATCATTTGAATTTGGTCGATCAGATATCATAACTTATCGTTATCTG
66 TGTGTTGGAGTCGCCATCGATCATTTGAATTTGGTCGATCAGATATCATAACTTATCGTTATCTG
1478139 ATCTACAACTTACAAGAAATTTTTCGGATCAGGGAGTCGATTACAATCAGGGAAGGATTAGCACC
131 ATCTACAACTTACAAGAAATTTTTCGGATCAGGGAGTCGATTACAATCAGGGAAGGATTAGCACC
1478204 CCTGTACTACCCTTTCGGTACCAATTTGATTTCTCGATTGTCTTAATTACAAAAATTAAAAGTTA
196 CCTGTACTACCCTTTCGGTACCAATTTGATTTCTCGATTGTCTTAATTACAAAAATTAAAAGTTA
1478269 AAATTCAAATTTAAATATTTGATCTGAATTATTTAACTTTGACCAAGCTGAAATTGCCCTAGAAA
261 AAATTCAAATTTAAATATTTGATCTGAATTATTTAACTTTGACCAAGCTGAAATTGCCCTAGAAA
1478334 ATTCAAATTTA
326 ATTCAAATTTA
1478345 TGTTAAATAA
Statistics
Matches: 336, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
336 336 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (336 bp):
AGTCGTCAAGATGTCGTAATCGTCCTTCGGGTGGTCCCCGGGATCGAGTTCTAACTTGATTTTGA
TGTGTTGGAGTCGCCATCGATCATTTGAATTTGGTCGATCAGATATCATAACTTATCGTTATCTG
ATCTACAACTTACAAGAAATTTTTCGGATCAGGGAGTCGATTACAATCAGGGAAGGATTAGCACC
CCTGTACTACCCTTTCGGTACCAATTTGATTTCTCGATTGTCTTAATTACAAAAATTAAAAGTTA
AAATTCAAATTTAAATATTTGATCTGAATTATTTAACTTTGACCAAGCTGAAATTGCCCTAGAAA
ATTCAAATTTA
Found at i:1479823 original size:30 final size:30
Alignment explanation
Indices: 1479787--1479888 Score: 123
Period size: 30 Copynumber: 3.4 Consensus size: 30
1479777 TACCTAGAGG
1479787 AGACCACGCACTGCTGCAGATGACCCTATT
1 AGACCACGCACTGCTGCAGATGACCCTATT
* **
1479817 AGACCACGCACTGCTACAGATGACCCTGCT
1 AGACCACGCACTGCTGCAGATGACCCTATT
* * * *
1479847 AGACCACACACTGTTGTAAATGACCCTATT
1 AGACCACGCACTGCTGCAGATGACCCTATT
* *
1479877 GGGCCACGCACT
1 AGACCACGCACT
1479889 ACTGTAACTG
Statistics
Matches: 59, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (30 bp):
AGACCACGCACTGCTGCAGATGACCCTATT
Found at i:1489857 original size:43 final size:43
Alignment explanation
Indices: 1489793--1489878 Score: 145
Period size: 43 Copynumber: 2.0 Consensus size: 43
1489783 GTGGCCAATT
* * *
1489793 TCGCTCCAACCGCCGCGTGGCAAAACCGAAAGGCCCCAAATAA
1 TCGCTCCAACCACCGCATGGCAAAACCGAAAGGCCACAAATAA
1489836 TCGCTCCAACCACCGCATGGCAAAACCGAAAGGCCACAAATAA
1 TCGCTCCAACCACCGCATGGCAAAACCGAAAGGCCACAAATAA
1489879 CTTCCAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.36, C:0.36, G:0.19, T:0.09
Consensus pattern (43 bp):
TCGCTCCAACCACCGCATGGCAAAACCGAAAGGCCACAAATAA
Found at i:1491337 original size:55 final size:55
Alignment explanation
Indices: 1491273--1492185 Score: 828
Period size: 55 Copynumber: 16.6 Consensus size: 55
1491263 GGCGGGTCCA
* *
1491273 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAA-ACATCTTCAGAAAACAGGTATG
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACA-ATCTTCAGAAAACGGGTCTG
* * * * * * *
1491328 TTTCTTCTTCTTTTC---GAGTATAAGACTTGAACAATCTTC-GAAAAATGAGT-TCG
1 CTCCCTCTTC-TTTCAGGGAGTATAGGACTCGAACAATCTTCAG-AAAACGGGTCT-G
* * * * ** *
1491381 CTCCCTCTTCTTTTTCAGGGAGTATAGGAAT-AAAAAATCTTCGGAAAACATGTATG
1 CTCCCTCTTC--TTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCTG
* * * * * *
1491437 CTCCCTCCTCTTTCAGGGAGTATAGAACTCGAATAATCTTTTAAAAAACGGATCTG
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATC-TTCAGAAAACGGGTCTG
* * *
1491493 CTCCCTCTTCTTTCAGGGAGTATAAGACTCGAACAATCTTCTGAAAACGGGTTTG
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCTG
* * * * *
1491548 CTCCCTCTTCTTTCATGGAGTAT-GAGACTTGAACAATCTTTATAAAATGGGTCT-
1 CTCCCTCTTCTTTCAGGGAGTATAG-GACTCGAACAATCTTCAGAAAACGGGTCTG
* ** * * * *
1491602 CTTCCCTCTTCTTTCAAGGAGTATAGGACTTAAAAAATATT-TGAAAAACGGGTCCG
1 C-TCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAG-AAAACGGGTCTG
* * * * * *
1491658 CTCCCTCTTCTTTCAAGGAATATAGGACT-TAACCAATCTTCAAAAAATGGGTCCG
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAA-CAATCTTCAGAAAACGGGTCTG
* * * * * *
1491713 CTCCCTATTCTTTCAGGGAGTATAGGGCTTGAAACAATCTTCAAAAAACGGGCCCG
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCG-AACAATCTTCAGAAAACGGGTCTG
* * * * * *
1491769 CTCCCTCTTTTTTCAAGGAGTATAGGACTTGAACAATCTTCAAAAAATGGGTATG
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCTG
** * **
1491824 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGATTAATCTTCAGAAAATGGGTCCC
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCTG
* * ** **
1491879 CTCCCTCTTCTTTTAGGGACTATAGGACTCGAACAATCTTCAGAAAATTGGTCCA
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCTG
* * *
1491934 CTCCTTTTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGTTCTG
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCTG
* *
1491989 CTCCCTCTTCTTTCAGGGAGTAT-GTGACTTGAACAATCTTCA-AAAAGTGGGTCTG
1 CTCCCTCTTCTTTCAGGGAGTATAG-GACTCGAACAATCTTCAGAAAA-CGGGTCTG
** * * *
1492044 CTCCCTCTTCTTTCAGGGAGTATAGGACTTTAACAATCTTCAGAAAATGTGTCCG
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCTG
* * * * * * *
1492099 CTCTCTATTCTTTCAAGGAATATAGGACTCGAATAATCTTCA-ACAAACGCGTTTG
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGA-AAACGGGTCTG
* *
1492154 CTCCCTATTCTTTCAGAGAGTATAGGACTCGA
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGA
1492186 TCTTGATTTT
Statistics
Matches: 708, Mismatches: 124, Indels: 52
0.80 0.14 0.06
Matches are distributed among these distances:
52 2 0.00
53 34 0.05
54 32 0.05
55 499 0.70
56 127 0.18
57 14 0.02
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (55 bp):
CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCTG
Found at i:1491508 original size:110 final size:110
Alignment explanation
Indices: 1491273--1492185 Score: 921
Period size: 110 Copynumber: 8.3 Consensus size: 110
1491263 GGCGGGTCCA
* ** * * *
1491273 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAA-ACATCTTCAGAAAACAGGTATGTTTCTTCTT
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACA-ATCTTCAGAAAACGGGTCCGCTCCCTCTT
* * *
1491337 CTTTTC---GAGTATAAGACTTGAACAATCTTCGAAAAATGAGT-TCG
65 C-TTTCAAGGAGTATAGGACTTGAACAATCTTCAAAAAATGGGTCT-G
* * * * ** ** *
1491381 CTCCCTCTTCTTTTTCAGGGAGTATAGGAAT-AAAAAATCTTCGGAAAACATGTATGCTCCCTCC
1 CTCCCTCTTC--TTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCCTCT
* * * * * * *
1491445 TCTTTCAGGGAGTATAGAACTCGAATAATCTTTTAAAAAACGGATCTG
64 TCTTTCAAGGAGTATAGGACTTGAACAATC-TTCAAAAAATGGGTCTG
* * **
1491493 CTCCCTCTTCTTTCAGGGAGTATAAGACTCGAACAATCTTCTGAAAACGGGTTTGCTCCCTCTTC
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCCTCTTC
* * *
1491558 TTTCATGGAGTAT-GAGACTTGAACAATCTTTATAAAATGGGTCT-
66 TTTCAAGGAGTATAG-GACTTGAACAATCTTCAAAAAATGGGTCTG
* ** * * *
1491602 CTTCCCTCTTCTTTCAAGGAGTATAGGACTTAAAAAATATT-TGAAAAACGGGTCCGCTCCCTCT
1 C-TCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAG-AAAACGGGTCCGCTCCCTCT
* *
1491666 TCTTTCAAGGAATATAGGACTT-AACCAATCTTCAAAAAATGGGTCCG
64 TCTTTCAAGGAGTATAGGACTTGAA-CAATCTTCAAAAAATGGGTCTG
* * * * *
1491713 CTCCCTATTCTTTCAGGGAGTATAGGGCTTGAAACAATCTTCAAAAAACGGGCCCGCTCCCTCTT
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCG-AACAATCTTCAGAAAACGGGTCCGCTCCCTCTT
* *
1491778 TTTTCAAGGAGTATAGGACTTGAACAATCTTCAAAAAATGGGTATG
65 CTTTCAAGGAGTATAGGACTTGAACAATCTTCAAAAAATGGGTCTG
** * *
1491824 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGATTAATCTTCAGAAAATGGGTCCCCTCCCTCTTC
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCCTCTTC
* * * * * * **
1491889 TTTTAGGGACTATAGGACTCGAACAATCTTCAGAAAATTGGTCCA
66 TTTCAAGGAGTATAGGACTTGAACAATCTTCAAAAAATGGGTCTG
* * * *
1491934 CTCCTTTTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGTTCTGCTCCCTCTTC
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCCTCTTC
* *
1491999 TTTCAGGGAGTAT-GTGACTTGAACAATCTTCAAAAAGTGGGTCTG
66 TTTCAAGGAGTATAG-GACTTGAACAATCTTCAAAAAATGGGTCTG
** * * * *
1492044 CTCCCTCTTCTTTCAGGGAGTATAGGACTTTAACAATCTTCAGAAAATGTGTCCGCTCTCTATTC
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCCTCTTC
* * * * * * *
1492109 TTTCAAGGAATATAGGACTCGAATAATCTTCAACAAACGCGTTTG
66 TTTCAAGGAGTATAGGACTTGAACAATCTTCAAAAAATGGGTCTG
* *
1492154 CTCCCTATTCTTTCAGAGAGTATAGGACTCGA
1 CTCCCTCTTCTTTCAGGGAGTATAGGACTCGA
1492186 TCTTGATTTT
Statistics
Matches: 668, Mismatches: 117, Indels: 38
0.81 0.14 0.05
Matches are distributed among these distances:
108 14 0.02
109 32 0.05
110 435 0.65
111 164 0.25
112 22 0.03
113 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (110 bp):
CTCCCTCTTCTTTCAGGGAGTATAGGACTCGAACAATCTTCAGAAAACGGGTCCGCTCCCTCTTC
TTTCAAGGAGTATAGGACTTGAACAATCTTCAAAAAATGGGTCTG
Found at i:1492336 original size:37 final size:37
Alignment explanation
Indices: 1492295--1492542 Score: 286
Period size: 37 Copynumber: 6.6 Consensus size: 37
1492285 ATCATGATCG
* * *
1492295 GAAGGCTTACTGATAGA-TTACTTCACTACTCTTCTAT
1 GAAGGCTTA-TGATTGATTTGCTTCACTACTCTTCTGT
*
1492332 GAAGGCTTAAGATTGATTTGCTTCACTACTCTTCTGT
1 GAAGGCTTATGATTGATTTGCTTCACTACTCTTCTGT
* * * *
1492369 GAAGGCTTAAGATCGATTTACTTCACTACTCTTCCGT
1 GAAGGCTTATGATTGATTTGCTTCACTACTCTTCTGT
* * **
1492406 GAAGGCTTATAGATTGATTTGCTTTATTACTCTTCCAT
1 GAAGGCTTAT-GATTGATTTGCTTCACTACTCTTCTGT
1492444 GAAGGCTTATAGA-TGATTTGCTTCACTACTCTTCTGT
1 GAAGGCTTAT-GATTGATTTGCTTCACTACTCTTCTGT
* * *
1492481 GAAGGATTGA-GATTAATTTGCTTCACTACTCTTCCGT
1 GAAGGCTT-ATGATTGATTTGCTTCACTACTCTTCTGT
*
1492518 GAAGGCTTATAGATTGATTTTCTTC
1 GAAGGCTTAT-GATTGATTTGCTTC
1492543 GAAGATCGAA
Statistics
Matches: 182, Mismatches: 23, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
36 8 0.04
37 126 0.69
38 48 0.26
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (37 bp):
GAAGGCTTATGATTGATTTGCTTCACTACTCTTCTGT
Found at i:1492468 original size:112 final size:112
Alignment explanation
Indices: 1492321--1492537 Score: 364
Period size: 112 Copynumber: 1.9 Consensus size: 112
1492311 ATTACTTCAC
* * *
1492321 TACTCTTCTATGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCTGTGAAGGCTTAAGATCGAT
1 TACTCTTCCATGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCTGTGAAGGATTAAGATCAAT
1492386 TTACTTCACTACTCTTCCGTGAAGGCTTATAGATTGATTTGCTTTAT
66 TTACTTCACTACTCTTCCGTGAAGGCTTATAGATTGATTTGCTTTAT
* *
1492433 TACTCTTCCATGAAGGCTTATAGA-TGATTTGCTTCACTACTCTTCTGTGAAGGATTGAGATTAA
1 TACTCTTCCATGAAGGCTTA-AGATTGATTTGCTTCACTACTCTTCTGTGAAGGATTAAGATCAA
*
1492497 TTTGCTTCACTACTCTTCCGTGAAGGCTTATAGATTGATTT
65 TTTACTTCACTACTCTTCCGTGAAGGCTTATAGATTGATTT
1492538 TCTTCGAAGA
Statistics
Matches: 98, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
112 95 0.97
113 3 0.03
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (112 bp):
TACTCTTCCATGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCTGTGAAGGATTAAGATCAAT
TTACTTCACTACTCTTCCGTGAAGGCTTATAGATTGATTTGCTTTAT
Found at i:1499862 original size:2 final size:2
Alignment explanation
Indices: 1499855--1499901 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1499845 AACTACACTA
1499855 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
1499897 AT AT A
1 AT AT A
1499902 CAACACCAAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1500992 original size:16 final size:15
Alignment explanation
Indices: 1500974--1501002 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1500964 TGCTCTCCTT
1500974 TTTTTTCTCT-CCTC
1 TTTTTTCTCTCCCTC
1500988 TTTTTTCTCTCCCTC
1 TTTTTTCTCTCCCTC
1501003 GTTAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTTCTCTCCCTC
Found at i:1501002 original size:15 final size:14
Alignment explanation
Indices: 1500966--1500999 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
1500956 ATGATGAATG
*
1500966 CTCTCCTTTTTTTT
1 CTCTCCTCTTTTTT
1500980 CTCTCCTCTTTTTT
1 CTCTCCTCTTTTTT
1500994 CTCTCC
1 CTCTCC
1501000 CTCGTTAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (14 bp):
CTCTCCTCTTTTTT
Found at i:1502108 original size:20 final size:20
Alignment explanation
Indices: 1502079--1502117 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1502069 AGAGCCCATG
*
1502079 TAGGATTATATAGATGCATT
1 TAGGAGTATATAGATGCATT
*
1502099 TAGGAGTATATAGTTGCAT
1 TAGGAGTATATAGATGCAT
1502118 GTGGTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.05, G:0.23, T:0.38
Consensus pattern (20 bp):
TAGGAGTATATAGATGCATT
Found at i:1502435 original size:30 final size:30
Alignment explanation
Indices: 1502396--1502452 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1502386 TATACACTAC
* * *
1502396 TGCAGATGACATTGCTGGACCACACACCGT
1 TGCAAATGACACTGCTGAACCACACACCGT
*
1502426 TGCAAATGACCCTGCTGAACCACACAC
1 TGCAAATGACACTGCTGAACCACACAC
1502453 TACTACAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.18
Consensus pattern (30 bp):
TGCAAATGACACTGCTGAACCACACACCGT
Found at i:1503678 original size:21 final size:21
Alignment explanation
Indices: 1503653--1503696 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1503643 CATCATACTA
1503653 TCATTCCATTCT-CACCAACAT
1 TCATTCCATTCTGCA-CAACAT
* *
1503674 TCATTTCATTTTGCACAACAT
1 TCATTCCATTCTGCACAACAT
1503695 TC
1 TC
1503697 TCATTTGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCATTCCATTCTGCACAACAT
Found at i:1504354 original size:21 final size:21
Alignment explanation
Indices: 1504330--1504401 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
1504320 AAAAACCATA
* *
1504330 TATATTATATGTTTTCAAAAC
1 TATATAATATATTTTCAAAAC
*
1504351 TATATAATATATTTTTAAAA-
1 TATATAATATATTTTCAAAAC
1504371 -AT-T-ATATATTTTCAAAAAC
1 TATATAATATATTTTC-AAAAC
* *
1504390 CATATATTATAT
1 TATATAATATAT
1504402 ACATTTTTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 9 0.22
18 5 0.12
19 2 0.05
20 2 0.05
21 18 0.44
22 5 0.12
ACGTcount: A:0.44, C:0.07, G:0.01, T:0.47
Consensus pattern (21 bp):
TATATAATATATTTTCAAAAC
Found at i:1504361 original size:23 final size:22
Alignment explanation
Indices: 1504313--1504378 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
1504303 TTTTAAAAGC
* *
1504313 TATTTTCAAAAACCATATATATTA
1 TATTTTTAAAAA-C-TATATAATA
*
1504337 TATGTTTTCAAAACTATATAATA
1 TAT-TTTTAAAAACTATATAATA
*
1504360 TATTTTTAAAAATTATATA
1 TATTTTTAAAAACTATATA
1504379 TTTTCAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 14 0.39
23 11 0.31
24 4 0.11
25 7 0.19
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (22 bp):
TATTTTTAAAAACTATATAATA
Found at i:1504394 original size:17 final size:17
Alignment explanation
Indices: 1504357--1504397 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1504347 AAACTATATA
* **
1504357 ATATATTTTTAAAAATT
1 ATATATTTTCAAAAACC
1504374 ATATATTTTCAAAAACC
1 ATATATTTTCAAAAACC
1504391 ATATATT
1 ATATATT
1504398 ATATACATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATATTTTCAAAAACC
Found at i:1506136 original size:29 final size:30
Alignment explanation
Indices: 1506098--1506155 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1506088 TAATATGAGC
** *
1506098 AATTCGAAAGTTTAGTGAGTAAAATAGAAA
1 AATTCGAAAGTGCAATGAGTAAAATAGAAA
1506128 AATT-GAAAGTGCAATGAGTAAAATAGAA
1 AATTCGAAAGTGCAATGAGTAAAATAGAA
1506156 GAGAGAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 21 0.84
30 4 0.16
ACGTcount: A:0.52, C:0.03, G:0.21, T:0.24
Consensus pattern (30 bp):
AATTCGAAAGTGCAATGAGTAAAATAGAAA
Found at i:1509767 original size:23 final size:23
Alignment explanation
Indices: 1509738--1509799 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
1509728 TTGACCTATA
* *
1509738 AAATAAATCAAATTAATGTTAAAT
1 AAATAAAT-AAATAAATATTAAAT
1509762 -AATAAAATAAATAAATATTAAAT
1 AAAT-AAATAAATAAATATTAAAT
*
1509785 AAATAAAAAAATAAA
1 AAATAAATAAATAAA
1509800 GGAAAATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 26 0.79
24 7 0.21
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (23 bp):
AAATAAATAAATAAATATTAAAT
Found at i:1509787 original size:27 final size:27
Alignment explanation
Indices: 1509735--1509799 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
1509725 AAATTGACCT
* *
1509735 ATAAAATAAATCAAATTAATGTTAAATA
1 ATAAAATAAATAAAATTAA-GATAAATA
1509763 ATAAAATAAATAAATATTAA-ATAAATA
1 ATAAAATAAATAAA-ATTAAGATAAATA
*
1509790 AAAAAATAAA
1 ATAAAATAAA
1509800 GGAAAATTCA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 15 0.45
28 13 0.39
29 5 0.15
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (27 bp):
ATAAAATAAATAAAATTAAGATAAATA
Found at i:1511133 original size:16 final size:15
Alignment explanation
Indices: 1511096--1511137 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
1511086 CTTATTGGAC
*
1511096 ATAAAACAAAGATGAA
1 ATAAAATAAA-ATGAA
1511112 AT-AAATAAAATGAA
1 ATAAAATAAAATGAA
1511126 AGTAAAATAAAA
1 A-TAAAATAAAA
1511138 ATAGTTAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 6 0.26
15 7 0.30
16 10 0.43
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (15 bp):
ATAAAATAAAATGAA
Found at i:1511304 original size:42 final size:44
Alignment explanation
Indices: 1511206--1511315 Score: 120
Period size: 42 Copynumber: 2.5 Consensus size: 44
1511196 ATATATTATA
* *
1511206 TTTCAAAAATAATATATGTTTTCAAAGATTATATATATTATATACAT
1 TTTC-AAAATAATAT-T-TTTTCAAAAACTATATATATTATATACAT
**
1511253 TTTC--AATAATATTTTTT-AAAAACTATATATA-TATATATGT
1 TTTCAAAATAATATTTTTTCAAAAACTATATATATTATATACAT
*
1511293 TTTCAAAATAATATATTTTCAAA
1 TTTCAAAATAATATTTTTTCAAA
1511316 TATATGTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
40 11 0.20
41 12 0.22
42 16 0.29
43 4 0.07
44 8 0.15
47 4 0.07
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (44 bp):
TTTCAAAATAATATTTTTTCAAAAACTATATATATTATATACAT
Found at i:1511393 original size:14 final size:14
Alignment explanation
Indices: 1511374--1511402 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1511364 ACTATATATT
1511374 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
1511388 ATATGTTTTCAAAA
1 ATATGTTTTCAAAA
1511402 A
1 A
1511403 CTATACTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
ATATGTTTTCAAAA
Found at i:1521116 original size:15 final size:15
Alignment explanation
Indices: 1521096--1521135 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1521086 GTAAGGGGGA
1521096 GTAATTTCAAAACTT
1 GTAATTTCAAAACTT
1521111 GTAATTTCAAAACTT
1 GTAATTTCAAAACTT
1521126 G--ATTTCAAAA
1 GTAATTTCAAAA
1521136 TCTTAAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
13 9 0.36
15 16 0.64
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (15 bp):
GTAATTTCAAAACTT
Found at i:1527257 original size:24 final size:24
Alignment explanation
Indices: 1527212--1527257 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1527202 TCAAATATCA
*
1527212 AGAACCTATTAGCATTACACTAAT
1 AGAACCTATTAGCAATACACTAAT
*
1527236 AGAACCTATTAGCAATATACTA
1 AGAACCTATTAGCAATACACTA
1527258 GCCAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.20, G:0.09, T:0.28
Consensus pattern (24 bp):
AGAACCTATTAGCAATACACTAAT
Found at i:1532469 original size:16 final size:16
Alignment explanation
Indices: 1532448--1532489 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1532438 ACATATAATA
*
1532448 ATTTTGCCTTCAAAAT
1 ATTTTGCCCTCAAAAT
1532464 ATTTTGCCCTCAAAAT
1 ATTTTGCCCTCAAAAT
1532480 ATTTTGCCCT
1 ATTTTGCCCT
1532490 AGCATTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (16 bp):
ATTTTGCCCTCAAAAT
Found at i:1535011 original size:22 final size:20
Alignment explanation
Indices: 1534972--1535013 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
1534962 TGCTGTGGCA
*
1534972 AAATAGAATGATTGATGTGG
1 AAATAGAATGATTAATGTGG
1534992 AAATAGAATGATGGTAATGTGG
1 AAATAGAATGAT--TAATGTGG
1535014 TAGCAAACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 12 0.63
22 7 0.37
ACGTcount: A:0.40, C:0.00, G:0.31, T:0.29
Consensus pattern (20 bp):
AAATAGAATGATTAATGTGG
Found at i:1537141 original size:55 final size:55
Alignment explanation
Indices: 1537036--1537142 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 55
1537026 CTATGTGTGT
* *
1537036 AAAACTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTTTGTGTAC
1 AAAAATAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCAATTTGTGTAC
* * *
1537091 AAAAATAATAAATTCATAATAAGTTTATGAA-TTTCGGTATTGGTAATTTGTG
1 AAAAATAAGAAATTCATAATAAGTTTATGAATTTTC-GTATGGGCAATTTGTG
1537143 CCACCTACGT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 4 0.09
55 42 0.91
ACGTcount: A:0.38, C:0.07, G:0.16, T:0.38
Consensus pattern (55 bp):
AAAAATAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCAATTTGTGTAC
Found at i:1537388 original size:81 final size:81
Alignment explanation
Indices: 1537275--1537849 Score: 750
Period size: 81 Copynumber: 7.1 Consensus size: 81
1537265 ACTATTCCAA
* * * * *
1537275 AGTAAAATATTAATAGCCTAGCTATGCATTTGGTAGAAAGAAGTCAATTATGTCAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAA
1537340 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * * * * * *
1537356 AGTAAAACATTAATAGTCTAGTTGTGCATTTGGCAGTAAGGTGTCAATTATGTCGGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAA
*
1537421 AGGTTAAAAACCTTTG
66 AGGTTAAATACCTTTG
* *
1537437 AGTAAAAGATTAATAGCATAGTTGTGCATTTGGCAGAAATG-TGTCAATTATGCCAGTTAGATGA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGGCAGAAA-GATGTCAATTATGCCAGTTAGATGA
1537501 AAGGTTAAATACCTTTG
65 AAGGTTAAATACCTTTG
* *
1537518 AGTAAAAGATTAATAGCCTAACTGTGCATTTGGCATAAATG-TGTCAATTATGCCAGTTAGATGA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGGCAGAAA-GATGTCAATTATGCCAGTTAGATGA
*
1537582 AAGGTTAAAAACCTTTG
65 AAGGTTAAATACCTTTG
* * * *
1537599 AGTAAAAGATTAATATCCTAGCTATGCATTTGGCAGAAAGGTGTTAATTATGCCAGTTAGATGAA
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAA
1537664 AGGTTAAATACCTTTG
66 AGGTTAAATACCTTTG
* * *
1537680 ACTAAAAGATTAATAGCCTAGTTGTGCATTTGGCA-AAA-ATGTTTCAATTATGCTAGTTAGATG
1 AGTAAAAGATTAATAGCCTAGCTGTGCATTTGGCAGAAAGATG--TCAATTATGCCAGTTAGATG
1537743 AAAGGTTAAATA--TTTG
64 AAAGGTTAAATACCTTTG
* * *
1537759 TTAGTAAAAGATTAATAGCCTAGCTGTGCATTTGGCAGAAA-AGTGTCAATCATGCAAGTTATAT
1 --AGTAAAAGATTAATAGCCTAGCTGTGCATTTGGCAGAAAGA-TGTCAATTATGCCAGTTAGAT
* * *
1537823 GAAAGGCTAAATGCATTTG
63 GAAAGGTTAAATACCTTTG
*
1537842 GGTAAAAG
1 AGTAAAAG
1537850 GCTAAAGGAA
Statistics
Matches: 441, Mismatches: 43, Indels: 20
0.88 0.09 0.04
Matches are distributed among these distances:
79 6 0.01
80 4 0.01
81 420 0.95
82 5 0.01
83 6 0.01
ACGTcount: A:0.36, C:0.10, G:0.21, T:0.32
Consensus pattern (81 bp):
AGTAAAAGATTAATAGCCTAGCTGTGCATTTGGCAGAAAGATGTCAATTATGCCAGTTAGATGAA
AGGTTAAATACCTTTG
Found at i:1537918 original size:2 final size:2
Alignment explanation
Indices: 1537911--1537975 Score: 130
Period size: 2 Copynumber: 32.5 Consensus size: 2
1537901 AATTATGATG
1537911 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
1537953 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
1537976 GTACAACAAT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 63 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1539306 original size:59 final size:58
Alignment explanation
Indices: 1539233--1539644 Score: 565
Period size: 59 Copynumber: 7.0 Consensus size: 58
1539223 TGCATTTCCC
* * * *
1539233 ATATGGAAATTCATACGCTTATTATGAATTTCATATCATTTTAGCACACAAGATGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAG-TGCCCA
* * * * *
1539292 ATATGGAAACTCATACACTTAGTATGAAATCCTTCTCATGTTAGCACACGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACAC-AAGTGCCCA
1539351 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAA-GTGCCCA
* * * * * *
1539410 ATATGAAAATTCATACACTTAGTATGAATTCTTTCTCATGTTAGCACATGAAGTGCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACA-CAAGTGCCCA
1539469 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCA
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAA-GTGCCCA
* * * *
1539528 ATATGGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTTCCCT
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACAC-AAGTGCCCA
*
1539587 ATATGGAAATTCATAAACTTAGTATGAATTCCTTGA-CATTTTAGCACACGAAGTGCCC
1 ATATGGAAATTCATACACTTAGTATGAATTCCTT-ATCATTTTAGCACAC-AAGTGCCC
1539645 TTTTGGTAAT
Statistics
Matches: 313, Mismatches: 34, Indels: 12
0.87 0.09 0.03
Matches are distributed among these distances:
58 4 0.01
59 302 0.96
60 7 0.02
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (58 bp):
ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGTGCCCA
Found at i:1539446 original size:118 final size:118
Alignment explanation
Indices: 1539233--1539644 Score: 684
Period size: 118 Copynumber: 3.5 Consensus size: 118
1539223 TGCATTTCCC
* * * * *
1539233 ATATGGAAATTCATACGCTTATTATGAATTTCATATCATTTTAGCACACAAGATGCCCAATATGG
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATATGG
* *
1539298 AAACTCATACACTTAGTATGAAATCCTTCTCATGTTAGCACACGAAGTGCCCT
66 AAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
*
1539351 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATATGA
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATATGG
* *
1539416 AAATTCATACACTTAGTATGAATTCTTTCTCATGTTAGCACATGAAGTGCCCT
66 AAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
1539469 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATATGG
1 ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATATGG
*
1539534 AAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTTCCCT
66 AAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
*
1539587 ATATGGAAATTCATAAACTTAGTATGAATTCCTTGA-CATTTTAGCACACGAA-GTGCCC
1 ATATGGAAATTCATACACTTAGTATGAATTCCTT-ATCATTTTAGCACAC-AAGGTGCCC
1539645 TTTTGGTAAT
Statistics
Matches: 277, Mismatches: 15, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
118 274 0.99
119 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (118 bp):
ATATGGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATATGG
AAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCT
Found at i:1540118 original size:22 final size:22
Alignment explanation
Indices: 1540061--1540119 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 22
1540051 ATGTGGTCCA
1540061 GTATCGATA-CCCT-TACCTTG
1 GTATCGATACCCCTATACCTTG
* **
1540081 GTATCAATACTACTATA-CTATG
1 GTATCGATACCCCTATACCT-TG
1540103 GTATCGATACCCCTATA
1 GTATCGATACCCCTATA
1540120 TGTATCGATA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
20 8 0.27
21 4 0.13
22 18 0.60
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.34
Consensus pattern (22 bp):
GTATCGATACCCCTATACCTTG
Found at i:1546299 original size:59 final size:58
Alignment explanation
Indices: 1546232--1546757 Score: 723
Period size: 59 Copynumber: 8.9 Consensus size: 58
1546222 TTTCCCATAC
** * * * *
1546232 GGAAATTCATATGCTTAGTATGATTTTCTTATCATTTTAGCACACAAGTTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACAAG-TGCCCTATAT
* *
1546291 GAAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACAC-AAGTGCCCTATAT
* *
1546350 GGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACAA-GTGCCCTATAT
* *
1546409 GGAAATTCATACACTTAGTATGAATTCCTTCTCAAGTTAGCACACGAAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACAC-AAGTGCCCTATAT
* * *
1546468 GGAAATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACAAGGTGCCCAATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACAA-GTGCCCTATAT
* * * *
1546527 GGAAATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACATGAAGTGCCTTGTAT
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACA-CAAGTGCCCTATAT
1546586 GGAAATTCATACACTTAGTATGAATT-CTTATCATGTTAGCACACAGAGTGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACA-AGTGCCCTATAT
* * * *
1546644 AGAAATTCATACACTTAGTATGAATTCCTTCTCAGGTTAGCACACGAAGCGCCCTATAT
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACAC-AAGTGCCCTATAT
* *
1546703 GGAAATTTATACACTTAGTATGAATTCCTTGA-CATTTTAGCACACAAAGTGCCCT
1 GGAAATTCATACACTTAGTATGAATTCCTT-ATCATGTTAGCACAC-AAGTGCCCT
1546758 TCTGGTAATC
Statistics
Matches: 417, Mismatches: 41, Indels: 18
0.88 0.09 0.04
Matches are distributed among these distances:
57 1 0.00
58 55 0.13
59 353 0.85
60 8 0.02
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (58 bp):
GGAAATTCATACACTTAGTATGAATTCCTTATCATGTTAGCACACAAGTGCCCTATAT
Found at i:1546381 original size:118 final size:118
Alignment explanation
Indices: 1546232--1546756 Score: 833
Period size: 118 Copynumber: 4.5 Consensus size: 118
1546222 TTTCCCATAC
** * * *
1546232 GGAAATTCATATGCTTAGTATGATTTTCTTATCATTTTAGCACACAAGTTGCCCAATATGAAAAT
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATATGAAAAT
1546297 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
66 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
*
1546350 GGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATATGGAAAT
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATATGAAAAT
*
1546415 TCATACACTTAGTATGAATTCCTTCTCAAGTTAGCACACGAAGTGCCCTATAT
66 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
* *
1546468 GGAAATTCATACACTTAGTATGAATTCCTTGTCATTTTAGCACACAAGGTGCCCAATATGGAAAT
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATATGAAAAT
* * *
1546533 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACATGAAGTGCCTTGTAT
66 TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
* *
1546586 GGAAATTCATACACTTAGTATGAATT-CTTATCATGTTAGCACAC-AGAGTGCCCTATAT-AGAA
1 GGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAG-GTGCCCAATATGA-AA
* *
1546648 ATTCATACACTTAGTATGAATTCCTTCTCAGGTTAGCACACGAAGCGCCCTATAT
64 ATTCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
* *
1546703 GGAAATTTATACACTTAGTATGAATTCCTTGA-CATTTTAGCACACAAAGTGCCC
1 GGAAATTCATACACTTAGTATGAATTCCTT-ATCATTTTAGCACACAAGGTGCCC
1546757 TTCTGGTAAT
Statistics
Matches: 378, Mismatches: 24, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
116 2 0.01
117 103 0.27
118 271 0.72
119 2 0.01
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (118 bp):
GGAAATTCATACACTTAGTATGAATTCCTTATCATTTTAGCACACAAGGTGCCCAATATGAAAAT
TCATACACTTAGTATGAATTCCTTCTCATGTTAGCACACGAAGTGCCCTATAT
Found at i:1547250 original size:95 final size:95
Alignment explanation
Indices: 1547078--1547302 Score: 224
Period size: 95 Copynumber: 2.4 Consensus size: 95
1547068 CTTGTTCCTT
* * * * * *
1547078 AGTATCGATACTCC-CACAATAGTATCGATACTACCCTGCTATGGTATCGATACCCCCTTCCAGT
1 AGTATCGATAC-CCTTACAATGGTATCGATACTACCATACTATGGTACCGATACCCCCTTACAGT
*
1547142 ATCAATACCAAAATTAGATTCAATGTGGT-C-C
65 ATCAATACAAAAATTAGATTCAATGT--TACTC
** **
1547173 AGTATCGATACCCTTACAATGGTATCGATACTATTATACTATGGTACCGATA-CCCCTATATGGT
1 AGTATCGATACCCTTACAATGGTATCGATACTACCATACTATGGTACCGATACCCCCT-TACAGT
* * ** *
1547237 ATCGATACAAAAATTAGGTTTGATGTTACTT
65 ATCAATACAAAAATTAGATTCAATGTTACTC
* *
1547268 GGTATCGATACCCTTACCATGGTATCGATACTACC
1 AGTATCGATACCCTTACAATGGTATCGATACTACC
1547303 TCATTCGGTA
Statistics
Matches: 106, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
93 1 0.01
94 8 0.08
95 97 0.92
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (95 bp):
AGTATCGATACCCTTACAATGGTATCGATACTACCATACTATGGTACCGATACCCCCTTACAGTA
TCAATACAAAAATTAGATTCAATGTTACTC
Found at i:1550652 original size:27 final size:29
Alignment explanation
Indices: 1550599--1550662 Score: 89
Period size: 28 Copynumber: 2.3 Consensus size: 29
1550589 AAAATTGACC
* *
1550599 TAAA-AAAATAAATCAAATTAATGTTAAA
1 TAAATAAAATAAATCAAATAAATATTAAA
1550627 T-AATAAAATAAAT-AAATAAATATTAAA
1 TAAATAAAATAAATCAAATAAATATTAAA
1550654 TAAATAAAA
1 TAAATAAAA
1550663 GAATAAAAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 15 0.47
28 17 0.53
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (29 bp):
TAAATAAAATAAATCAAATAAATATTAAA
Found at i:1551129 original size:20 final size:20
Alignment explanation
Indices: 1551104--1551151 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
1551094 CAGGCCACCG
*
1551104 GAAAACTGCTGAGATACCTC
1 GAAAACTGCTGAGATACCCC
1551124 GAAAACTGCTGAGATACCCC
1 GAAAACTGCTGAGATACCCC
*
1551144 GAACACTG
1 GAAAACTG
1551152 AATCACCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.27, G:0.21, T:0.17
Consensus pattern (20 bp):
GAAAACTGCTGAGATACCCC
Found at i:1551948 original size:5 final size:5
Alignment explanation
Indices: 1551939--1551978 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
1551929 GCATAAAACA
* *
1551939 AAAAT GAAAT AAAAT AAAAT AAAAT GAAAGT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAAAT AAAA
1551979 ATAGTTAAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
5 26 0.87
6 4 0.13
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1551957 original size:21 final size:21
Alignment explanation
Indices: 1551931--1551979 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
1551921 CTTATTGGGC
1551931 ATAAAACAAAAATGAAA-TAAA
1 ATAAAA-AAAAATGAAAGTAAA
*
1551952 ATAAAATAAAATGAAAGTAAA
1 ATAAAAAAAAATGAAAGTAAA
1551973 ATAAAAA
1 ATAAAAA
1551980 TAGTTAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 9 0.36
21 16 0.64
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (21 bp):
ATAAAAAAAAATGAAAGTAAA
Found at i:1551972 original size:16 final size:15
Alignment explanation
Indices: 1551939--1551978 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
1551929 GCATAAAACA
*
1551939 AAAATGAAATAAAAT
1 AAAATAAAATAAAAT
*
1551954 AAAATAAAATGAAAGT
1 AAAATAAAAT-AAAAT
1551970 AAAATAAAA
1 AAAATAAAA
1551979 ATAGTTAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.75, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAATAAAATAAAAT
Found at i:1552164 original size:61 final size:55
Alignment explanation
Indices: 1552099--1552232 Score: 157
Period size: 61 Copynumber: 2.3 Consensus size: 55
1552089 TTATATATAT
*
1552099 TATATATGTTTTCAAAAACC-ATTTTTAAAAACTATATATACATATATATGTTTTCAAAAA
1 TATATATGTTTTCAAAAACCGATTTTTAAAAA-T-TATAT--AT-TATACGTTTTC-AAAA
*
1552159 CTATATATGTTTTCAAAAAACCGTTTTTTAAAAATTATATATTATACGTTTTCAAAA
1 -TATATATGTTTTC-AAAAACCGATTTTTAAAAATTATATATTATACGTTTTCAAAA
1552216 -A-ATATGTTTTCAAAAAC
1 TATATATGTTTTCAAAAAC
1552233 TATACTATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 12
0.83 0.02 0.14
Matches are distributed among these distances:
53 6 0.09
54 10 0.14
55 1 0.01
57 4 0.06
58 10 0.14
59 2 0.03
61 18 0.26
62 8 0.12
63 10 0.14
ACGTcount: A:0.43, C:0.10, G:0.04, T:0.42
Consensus pattern (55 bp):
TATATATGTTTTCAAAAACCGATTTTTAAAAATTATATATTATACGTTTTCAAAA
Found at i:1552166 original size:21 final size:19
Alignment explanation
Indices: 1552141--1552177 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
1552131 TATATATACA
1552141 TATATATGTTTTCAAAAAC
1 TATATATGTTTTCAAAAAC
1552160 TATATATGTTTTCAAAAA
1 TATATATGTTTTCAAAAA
1552178 ACCGTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.43
Consensus pattern (19 bp):
TATATATGTTTTCAAAAAC
Found at i:1552231 original size:39 final size:35
Alignment explanation
Indices: 1552144--1552253 Score: 89
Period size: 39 Copynumber: 3.0 Consensus size: 35
1552134 ATATACATAT
*
1552144 ATATGTTTTCAAAAA-CTATATATGTTTTCAAAAA
1 ATATGTTTTCAAAAATATATATATGTTTTCAAAAA
** *
1552178 A-CCGTTTTTTAAAAATTATATATTATACGTTTTCAAAAA
1 ATATG-TTTTCAAAAA-TATATA-TAT--GTTTTCAAAAA
* *
1552217 ATATGTTTTCAAAAACTATACTATATATCTTCAAAAA
1 ATATGTTTTCAAAAA-TATA-TATATGTTTTCAAAAA
1552254 CTATATATAT
Statistics
Matches: 58, Mismatches: 10, Indels: 13
0.72 0.12 0.16
Matches are distributed among these distances:
33 1 0.02
34 10 0.17
36 4 0.07
37 12 0.21
39 28 0.48
40 3 0.05
ACGTcount: A:0.44, C:0.11, G:0.05, T:0.41
Consensus pattern (35 bp):
ATATGTTTTCAAAAATATATATATGTTTTCAAAAA
Found at i:1552262 original size:19 final size:21
Alignment explanation
Indices: 1552224--1552263 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1552214 AAAATATGTT
1552224 TTCAAAAACTATACTATATATC
1 TTCAAAAAC-ATACTATATATC
1552246 TTCAAAAAC-TA-TATATAT
1 TTCAAAAACATACTATATAT
1552264 TATATATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 2 0.11
22 9 0.50
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.38
Consensus pattern (21 bp):
TTCAAAAACATACTATATATC
Found at i:1552269 original size:9 final size:9
Alignment explanation
Indices: 1552255--1552321 Score: 50
Period size: 9 Copynumber: 7.4 Consensus size: 9
1552245 CTTCAAAAAC
1552255 TATATATAT
1 TATATATAT
1552264 TATATAT-T
1 TATATATAT
* *
1552272 TTTGAAATTAT
1 TAT-ATA-TAT
1552283 TAT-TATTAT
1 TATATA-TAT
1552292 TATATATA-
1 TATATATAT
1552300 TATATATAT
1 TATATATAT
* *
1552309 AATATATAA
1 TATATATAT
1552318 TATA
1 TATA
1552322 ATAAAGACCA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
8 11 0.24
9 29 0.63
10 3 0.07
11 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (9 bp):
TATATATAT
Found at i:1552322 original size:12 final size:13
Alignment explanation
Indices: 1552292--1552324 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
1552282 TTATTATTAT
1552292 TATAT-ATATATA
1 TATATAATATATA
1552304 TATATAATATATA
1 TATATAATATATA
1552317 -ATATAATA
1 TATATAATA
1552325 AAGACCATTG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATATAATATATA
Found at i:1561394 original size:15 final size:15
Alignment explanation
Indices: 1561374--1561419 Score: 50
Period size: 15 Copynumber: 3.5 Consensus size: 15
1561364 GCTTTTAGTC
1561374 TTTTAGAACTCTGTA
1 TTTTAGAACTCTGTA
1561389 TTTTAG-A-TC----
1 TTTTAGAACTCTGTA
1561398 TTTTAGAACTCTGTA
1 TTTTAGAACTCTGTA
1561413 TTTTAGA
1 TTTTAGA
1561420 TCTTTTACCC
Statistics
Matches: 25, Mismatches: 0, Indels: 12
0.68 0.00 0.32
Matches are distributed among these distances:
9 6 0.24
10 1 0.04
11 2 0.08
13 2 0.08
14 1 0.04
15 13 0.52
ACGTcount: A:0.26, C:0.11, G:0.13, T:0.50
Consensus pattern (15 bp):
TTTTAGAACTCTGTA
Found at i:1561399 original size:24 final size:24
Alignment explanation
Indices: 1561366--1561426 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
1561356 GCCCTTGAGC
1561366 TTTTAG-TCTTTTAGAACTCTGTA
1 TTTTAGATCTTTTAGAACTCTGTA
1561389 TTTTAGATCTTTTAGAACTCTGTA
1 TTTTAGATCTTTTAGAACTCTGTA
1561413 TTTTAGATCTTTTA
1 TTTTAGATCTTTTA
1561427 CCCTTTATTC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 6 0.16
24 31 0.84
ACGTcount: A:0.23, C:0.11, G:0.11, T:0.54
Consensus pattern (24 bp):
TTTTAGATCTTTTAGAACTCTGTA
Found at i:1567805 original size:2 final size:2
Alignment explanation
Indices: 1567800--1568056 Score: 93
Period size: 2 Copynumber: 132.5 Consensus size: 2
1567790 TAGGTATTAT
* *
1567800 TA TA TA GTA TA TA TA GTA TA TA GTA TT TA T- TA TA TA -A TA TT
1 TA TA TA -TA TA TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA
* * * * * *
1567841 TA TA T- TA TA TA GTA TT TC TA TA TA TT TA TA T- TT TA TA TT TT
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
1567882 TA TC T- TA TT TA TA T- TA TA TA T- TA TA CA GTA TA TA 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
* *
1567922 TA T- TA TA GTA TG T- TG T- TA T- TA TA TA GTA T- TA TA TA TA GTA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* * * * **
1567962 TT TC TA TA TT TA TA T- TA T- TT TA TA GTA GG T- TA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
*
1568000 TA TA GTA TT TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA -A TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1568041 TA TA GTA TA AA TA TA T
1 TA TA -TA TA TA TA TA T
1568057 TATCATTATC
Statistics
Matches: 194, Mismatches: 31, Indels: 60
0.68 0.11 0.21
Matches are distributed among these distances:
1 19 0.10
2 154 0.79
3 21 0.11
ACGTcount: A:0.38, C:0.02, G:0.06, T:0.54
Consensus pattern (2 bp):
TA
Found at i:1567821 original size:16 final size:15
Alignment explanation
Indices: 1567797--1568048 Score: 115
Period size: 14 Copynumber: 17.9 Consensus size: 15
1567787 TAATAGGTAT
1567797 TATTATATAGTATATA
1 TATTATATAGTAT-TA
*
1567813 TAGTATATAGTATT-
1 TATTATATAGTATTA
*
1567827 TATTATATAATATTTA
1 TATTATATAGTA-TTA
1567843 TATTATATAGTATT-
1 TATTATATAGTATTA
*
1567857 T-CTATATA-T-TTA
1 TATTATATAGTATTA
* * *
1567869 TATTTTATATTTTTA
1 TATTATATAGTATTA
* *
1567884 TCTTATTTA-TATTATA
1 TATTATATAGTA-T-TA
*
1567900 TATTATACAGTA-TA
1 TATTATATAGTATTA
1567914 TA-TATATA-TATTA
1 TATTATATAGTATTA
*
1567927 TA--GTAT-GT-TGT-
1 TATTATATAGTAT-TA
1567938 TATTATATAGTA-T-
1 TATTATATAGTATTA
1567951 TA-TATATAGTATT-
1 TATTATATAGTATTA
* *
1567964 TCTATATTTA-TATTA
1 TAT-TATATAGTATTA
1567979 T-TT-TATAGTAGGTTA
1 TATTATATAGTA--TTA
1567994 TTATTATATAGTATT-
1 -TATTATATAGTATTA
1568009 TA-TATATA-TA-TA
1 TATTATATAGTATTA
1568021 TATATATATA-TATTA
1 TAT-TATATAGTATTA
*
1568036 TAATATATAGTAT
1 TATTATATAGTAT
1568049 AAATATATTA
Statistics
Matches: 184, Mismatches: 21, Indels: 63
0.69 0.08 0.24
Matches are distributed among these distances:
11 6 0.03
12 25 0.14
13 37 0.20
14 40 0.22
15 31 0.17
16 34 0.18
17 4 0.02
18 7 0.04
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (15 bp):
TATTATATAGTATTA
Found at i:1567877 original size:13 final size:13
Alignment explanation
Indices: 1567818--1568037 Score: 91
Period size: 13 Copynumber: 16.3 Consensus size: 13
1567808 ATATATAGTA
1567818 TATAGTATTTAT-T
1 TATA-TATTTATAT
1567831 ATATAATATTTATAT
1 -TAT-ATATTTATAT
* *
1567846 TATATA-GTATTT
1 TATATATTTATAT
1567858 CTATATATTTATAT
1 -TATATATTTATAT
* *
1567872 TTTATATTTTTA-
1 TATATATTTATAT
*
1567884 TCT-TATTTATAT
1 TATATATTTATAT
*
1567896 TATATATTATACAGT
1 TATATATT-TATA-T
*
1567911 ATATATATATATAT
1 -TATATATTTATAT
*
1567925 TATAGTATGTTGTTAT
1 TATA-TAT-TT-ATAT
1567941 TATATAGTATTATA-
1 TATATA-T-TTATAT
1567955 TATAGTATTTCTATAT
1 TATA-TA-TT-TATAT
*
1567971 T-TATA-TTATTT
1 TATATATTTATAT
*
1567982 TATAGTAGGTTATTAT
1 TATA-TA-TTTA-TAT
*
1567998 TATATA-GTAT-T
1 TATATATTTATAT
*
1568009 TATATATATATA-
1 TATATATTTATAT
*
1568021 TATATATATATAT
1 TATATATTTATAT
1568034 TATA
1 TATA
1568038 ATATATAGTA
Statistics
Matches: 161, Mismatches: 21, Indels: 49
0.70 0.09 0.21
Matches are distributed among these distances:
11 19 0.12
12 27 0.17
13 35 0.22
14 31 0.19
15 25 0.16
16 24 0.15
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.56
Consensus pattern (13 bp):
TATATATTTATAT
Found at i:1567957 original size:57 final size:53
Alignment explanation
Indices: 1567895--1568037 Score: 164
Period size: 57 Copynumber: 2.6 Consensus size: 53
1567885 CTTATTTATA
* *
1567895 TTATATATTATACAGTATATATATATATATTATAGTATGTTGTTATTATATAGTAT
1 TTATATA-TAT-CA-TATATATATATATATTATAGTAGGTTATTATTATATAGTAT
* *
1567951 TATATATAGTATTTC-TATATTTATATTATTTTATAGTAGGTTATTATTATATAGTAT
1 T-TATATA-TA--TCATATATATATA-TATATTATAGTAGGTTATTATTATATAGTAT
1568008 TTATATATAT-ATATATATATATATATTATA
1 TTATATATATCATATATATATATATATTATA
1568038 ATATATAGTA
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
52 8 0.11
53 10 0.13
55 2 0.03
56 16 0.21
57 37 0.49
58 1 0.01
59 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (53 bp):
TTATATATATCATATATATATATATATTATAGTAGGTTATTATTATATAGTAT
Found at i:1570094 original size:18 final size:18
Alignment explanation
Indices: 1570071--1570127 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 18
1570061 TTAAGGGAAA
1570071 AAAATAATAGAAAAAAAT
1 AAAATAATAGAAAAAAAT
*
1570089 AAAATAA-AG-TAAAAAT
1 AAAATAATAGAAAAAAAT
* * *
1570105 ATAATATATATAAATAAAT
1 AAAATA-ATAGAAAAAAAT
1570124 AAAA
1 AAAA
1570128 ACAAAAAGAG
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 11 0.37
17 3 0.10
18 8 0.27
19 8 0.27
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAATAATAGAAAAAAAT
Found at i:1570200 original size:2 final size:2
Alignment explanation
Indices: 1570193--1570245 Score: 74
Period size: 2 Copynumber: 27.0 Consensus size: 2
1570183 TTAATACATC
1570193 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TGA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
*
1570235 -A GA TA TA TA TA
1 TA TA TA TA TA TA
1570246 ATAAAAATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
1 2 0.04
2 43 0.91
3 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:1571812 original size:110 final size:108
Alignment explanation
Indices: 1571623--1571874 Score: 341
Period size: 110 Copynumber: 2.3 Consensus size: 108
1571613 TTCCGAGTCT
* * * *
1571623 AATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTG--GAACTAGGAAATTGTTTGTTGACAGTCA
1 AATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAGAACTAGAAAATTATTTGTTGACAATCA
* *
1571685 GCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAGTTC
65 GCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAATCC
*
1571729 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTA-AAAAGTTATTTGTTGACAAT
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-G-AACTAGAAAA-TTATTTGTTGACAAT
* *
1571793 CAGTCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTTGAATCC
63 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAATCC
* *
1571839 AATATCCCTCGCTGTGAAGTTAAAATTGGCTCTGAA
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA
1571875 ACTGGGAAGC
Statistics
Matches: 128, Mismatches: 12, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
106 30 0.23
107 1 0.01
109 4 0.03
110 93 0.73
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (108 bp):
AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAGAACTAGAAAATTATTTGTTGACAATCAG
CCGCCCCTTCGCTGTGAAGTTGAGCTTGTGTTGTCTTGAATCC
Found at i:1572721 original size:66 final size:65
Alignment explanation
Indices: 1572589--1572773 Score: 214
Period size: 65 Copynumber: 2.8 Consensus size: 65
1572579 CAAATATATC
* * **
1572589 TTTTGTTTCATGA-AAACGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAG
1 TTTTGTTTCAAGAGAAACGGTCTCAAGGGAGACAAAA-TTTGTTTTAAGGGAAATAAATTCAAAG
1572653 A
65 A
*
1572654 TTTTGTGTTTCAAGAGAAAC-GTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAA
1 -TTT-TGTTTCAAGAGAAACGGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAA
1572718 GA
64 GA
* * * * * *
1572720 TTTTGTTTCAAGGGAATCTGTCTCAAGAGAGA-AGAAATTTGTTTCAAGAGAAAT
1 TTTTGTTTCAAGAGAAACGGTCTCAAGGGAGACA-AAATTTGTTTTAAGGGAAAT
1572774 TGTCTCAAGA
Statistics
Matches: 104, Mismatches: 11, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
64 14 0.13
65 32 0.31
66 28 0.27
67 26 0.25
68 4 0.04
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.32
Consensus pattern (65 bp):
TTTTGTTTCAAGAGAAACGGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGA
Found at i:1572778 original size:36 final size:36
Alignment explanation
Indices: 1572721--1572948 Score: 143
Period size: 37 Copynumber: 6.5 Consensus size: 36
1572711 ATTCAAAGAT
*
1572721 TTTGTTTCAAG-GGAATCTGTCTCAAGAGAGAAGAAA
1 TTTGTTTCAAGAGAAAT-TGTCTCAAGAGAGAAGAAA
*
1572757 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGAAAAAA
1 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGAAGAAA
* * * * * *
1572793 CTTAGTTCCAAAAGAAAATGTCTCAAGGGAGATGAAA
1 -TTTGTTTCAAGAGAAATTGTCTCAAGAGAGAAGAAA
* * * *
1572830 TTTGTTTCAA-ATAAAACATAT-TC-----A-AA-TAA
1 TTTGTTTCAAGA-GAAA-TTGTCTCAAGAGAGAAGAAA
* * * *
1572859 TTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAA
1 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGA-AGAAA
* * * *
1572896 TTTGTTTCAAGGGAAACTGTCTCAAGTGAGACGAAA
1 TTTGTTTCAAGAGAAATTGTCTCAAGAGAGAAGAAA
* *
1572932 TTTATTTCAAGGGAAAT
1 TTTGTTTCAAGAGAAAT
1572949 GTTTTCAATG
Statistics
Matches: 151, Mismatches: 27, Indels: 28
0.73 0.13 0.14
Matches are distributed among these distances:
28 2 0.01
29 16 0.11
30 1 0.01
31 1 0.01
34 1 0.01
35 2 0.01
36 61 0.40
37 67 0.44
ACGTcount: A:0.40, C:0.11, G:0.19, T:0.29
Consensus pattern (36 bp):
TTTGTTTCAAGAGAAATTGTCTCAAGAGAGAAGAAA
Found at i:1572781 original size:15 final size:16
Alignment explanation
Indices: 1572752--1572785 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1572742 TCAAGAGAGA
*
1572752 AGAAATTTGTTTCAAG
1 AGAAATTTGTCTCAAG
1572768 AGAAA-TTGTCTCAAG
1 AGAAATTTGTCTCAAG
1572783 AGA
1 AGA
1572786 GAAAAAACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (16 bp):
AGAAATTTGTCTCAAG
Found at i:1572835 original size:138 final size:140
Alignment explanation
Indices: 1572665--1572926 Score: 350
Period size: 138 Copynumber: 1.9 Consensus size: 140
1572655 TTTGTGTTTC
* ** * * *
1572665 AAGAGAAACGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAA-GATTTTGTTTC
1 AAGAGAAACGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAATAATTTT-TTTC
* * *
1572729 AAGGGAATCTGTCTCAAGAGAGA-AGAAATTTGTTTCAAGAGAAATTGTCTCAAGAGAGAAAAAA
65 AAGGGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAA
1572793 CTTAGTTCCAA
130 CTTAGTTCCAA
* ** * *
1572804 AAGA-AAATGTCTCAAGGGAGATGAAATTTGTTTCAAATAAAACATATTCAAATAATTTTTTTCA
1 AAGAGAAACGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAATAATTTTTTTCA
* *
1572868 AGGGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGGGAAACTGTCTCAAGTGAGA
66 AGGGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
1572927 CGAAATTTAT
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
138 64 0.61
139 41 0.39
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.27
Consensus pattern (140 bp):
AAGAGAAACGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAACAAATTCAAATAATTTTTTTCA
AGGGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAAC
TTAGTTCCAA
Found at i:1572907 original size:37 final size:36
Alignment explanation
Indices: 1572857--1573049 Score: 170
Period size: 37 Copynumber: 5.5 Consensus size: 36
1572847 ATATTCAAAT
*
1572857 AATTTTTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AA
* *
1572894 AATTTGTTTCAAGGGAAACTGTCTCAAGTGAGACGA
1 AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* * *
1572930 AATTTATTTCAAGGGAAA-TGTTTTC-A-A-TG----
1 AATTTGTTTCAAGGGAAACTG-TCTCAAGAGAGACAA
* * * *
1572959 -TTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAA
1 AATT-TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
* *
1572995 AATTTTGTTTCAAGGGAAACTATCTCAAGAGAGGCAA
1 AA-TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
1573032 AATTCGTTTCAAGGGAAA
1 AATTTGTTTCAAGGGAAA
1573050 TGTTTTCAAT
Statistics
Matches: 125, Mismatches: 19, Indels: 25
0.74 0.11 0.15
Matches are distributed among these distances:
28 2 0.02
29 15 0.12
30 2 0.02
32 1 0.01
33 1 0.01
35 3 0.02
36 36 0.29
37 63 0.50
38 2 0.02
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.30
Consensus pattern (36 bp):
AATTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
Found at i:1572917 original size:102 final size:102
Alignment explanation
Indices: 1572759--1573136 Score: 402
Period size: 102 Copynumber: 3.7 Consensus size: 102
1572749 AGAAGAAATT
* * * ** * * *
1572759 TGTTTCAAGAGAAATTGTCTCAAGAGAGA-AAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAA-TTTGTTTCAAGGGAAACTATCTCAAGAGA
** *** ** *
1572823 GATGAAATTTGTTTCAAATAAAACATATTCAAATAATTT-
65 GACAAAATTTGTTTCAAGGGAAATGTTTTC-AAT-ATTTA
* * *
1572862 T-TTTCAAGGGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGGGAAACTGTCTCAAGTGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAG
* * *
1572926 ACGAAATTTATTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTTGTTTCAAGGGAAATGTTTTCAATATTTA
* * *
1572963 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAG
* * *
1573028 GCAAAATTCGTTTCAAGGGAAATGTTTTCAATGTTTA
66 ACAAAATTTGTTTCAAGGGAAATGTTTTCAATATTTA
* * * * *
1573065 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAATATTTTGTTTCAAGGGAAATTATCTCAAGCGAG
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
1573130 ATAAAAT
66 ACAAAAT
1573137 CTTCTTTTTA
Statistics
Matches: 239, Mismatches: 33, Indels: 7
0.86 0.12 0.03
Matches are distributed among these distances:
100 3 0.01
101 4 0.02
102 226 0.95
103 6 0.03
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAATTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAATTTGTTTCAAGGGAAATGTTTTCAATATTTA
Found at i:1573123 original size:37 final size:38
Alignment explanation
Indices: 1573056--1573130 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 38
1573046 GAAATGTTTT
* * *
1573056 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
1 CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
* *
1573094 CAATATTT-TGTTTCAAGGGAAATTATCTCAAGCGAGA
1 CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
1573131 TAAAATCTTC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
37 25 0.78
38 7 0.22
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (38 bp):
CAATATTTATGTTTCAAGAGAAACTATCTCAAGCGAGA
Found at i:1574821 original size:26 final size:24
Alignment explanation
Indices: 1574782--1574839 Score: 64
Period size: 26 Copynumber: 2.4 Consensus size: 24
1574772 TTTCTTCAAA
* *
1574782 TTTC-CTTTGTTTTTTCTCTTTTTAT
1 TTTCTCTTTGCTTTTTCTC-TCTT-T
*
1574807 TTTCTCTTTGCTTTTTTTCTCTTT
1 TTTCTCTTTGCTTTTTCTCTCTTT
1574831 TTTCTCTTT
1 TTTCTCTTT
1574840 TTGTTCTGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.34
25 7 0.24
26 12 0.41
ACGTcount: A:0.02, C:0.19, G:0.03, T:0.76
Consensus pattern (24 bp):
TTTCTCTTTGCTTTTTCTCTCTTT
Found at i:1574824 original size:15 final size:13
Alignment explanation
Indices: 1574782--1574833 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
1574772 TTTCTTCAAA
*
1574782 TTTC-CTTTGTTT
1 TTTCTCTTTTTTT
*
1574794 TTTCTCTTTTTAT
1 TTTCTCTTTTTTT
1574807 TTTCTCTTTGCTTTT
1 TTTCTCTTT--TTTT
1574822 TTTCTCTTTTTT
1 TTTCTCTTTTTT
1574834 CTCTTTTTGT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
12 4 0.12
13 18 0.53
15 12 0.35
ACGTcount: A:0.02, C:0.17, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTCTCTTTTTTT
Found at i:1575865 original size:34 final size:32
Alignment explanation
Indices: 1575812--1575881 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1575802 CCTTACAAAC
*
1575812 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1575844 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1575878 TCCC
1 TCCC
1575882 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1576150 original size:21 final size:21
Alignment explanation
Indices: 1576125--1576185 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
1576115 CCGTTAGACA
* *
1576125 GGGGGAATCGGTACTCCCTGG
1 GGGGGAATCTGTACCCCCTGG
* *
1576146 GGGGGAATCTGTTCCCCCT-T
1 GGGGGAATCTGTACCCCCTGG
1576166 GGGGGAATCTGTACCCCCTG
1 GGGGGAATCTGTACCCCCTG
1576186 AACAATCTGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 18 0.53
21 16 0.47
ACGTcount: A:0.13, C:0.28, G:0.36, T:0.23
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:1578539 original size:34 final size:32
Alignment explanation
Indices: 1578486--1578555 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1578476 CTTTACAAAC
*
1578486 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
*
1578518 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
1578552 TCCC
1 TCCC
1578556 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:1578964 original size:21 final size:21
Alignment explanation
Indices: 1578903--1578965 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
1578893 CCGTTAGACA
*
1578903 GGGGGGAATCGGTACCCCCT-
1 GGGGGGAATCTGTACCCCCTG
* *
1578923 AGGGGGAATCTGTTCCCCCTG
1 GGGGGGAATCTGTACCCCCTG
*
1578944 GGGGGGAATCTATACCCCCTG
1 GGGGGGAATCTGTACCCCCTG
1578965 G
1 G
1578966 ACAATCTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
20 17 0.47
21 19 0.53
ACGTcount: A:0.16, C:0.29, G:0.37, T:0.19
Consensus pattern (21 bp):
GGGGGGAATCTGTACCCCCTG
Found at i:1581550 original size:18 final size:17
Alignment explanation
Indices: 1581516--1581563 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
1581506 TATTAATGGA
1581516 GTAAAAAAATAATAAAG
1 GTAAAAAAATAATAAAG
1581533 GTAAAAGAAATTAA-AAAG
1 GTAAAA-AAA-TAATAAAG
1581551 G-AATAAAAATAAT
1 GTAA-AAAAATAAT
1581564 GTGTACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.11
17 11 0.41
18 10 0.37
19 3 0.11
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (17 bp):
GTAAAAAAATAATAAAG
Found at i:1581629 original size:36 final size:37
Alignment explanation
Indices: 1581588--1581683 Score: 97
Period size: 36 Copynumber: 2.6 Consensus size: 37
1581578 TAGTATTTAC
1581588 TAAAACATATAAAAATAATAAATATACA-ATACTAAG
1 TAAAACATATAAAAATAATAAATATACAGATACTAAG
* * *
1581624 TAAAACAAATAAAAAATAA-AGATATACATGATATTAAG
1 TAAAACATAT-AAAAATAATAAATATACA-GATACTAAG
* * * *
1581662 AAAAAAATAGAAAAAAAATAAA
1 TAAAACATATAAAAATAATAAA
1581684 ATAAAGTGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
36 17 0.36
37 15 0.32
38 15 0.32
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.21
Consensus pattern (37 bp):
TAAAACATATAAAAATAATAAATATACAGATACTAAG
Found at i:1581676 original size:37 final size:36
Alignment explanation
Indices: 1581589--1581683 Score: 95
Period size: 37 Copynumber: 2.6 Consensus size: 36
1581579 AGTATTTACT
*
1581589 AAAACATATAAAAATAATAAATATACAATACTAAGTA
1 AAAAAATA-AAAAATAATAAATATACAATACTAAGTA
* *
1581626 AAACAAATAAAAAATAA-AGATATACATGATATTAAG-A
1 AAA-AAATAAAAAATAATAAATATACA--ATACTAAGTA
*
1581663 AAAAAATAGAAAAAAAATAAA
1 AAAAAATA-AAAAATAATAAA
1581684 ATAAAGTGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
36 13 0.27
37 22 0.46
38 13 0.27
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.20
Consensus pattern (36 bp):
AAAAAATAAAAAATAATAAATATACAATACTAAGTA
Found at i:1581888 original size:23 final size:22
Alignment explanation
Indices: 1581845--1581918 Score: 64
Period size: 21 Copynumber: 3.4 Consensus size: 22
1581835 ATGATATAAG
* *
1581845 ATATATATAATAAAAATAATATA
1 ATATAAATAA-AAAAAAAATATA
1581868 ATATAAATAAAAAAAGAAATAT-
1 ATATAAATAAAAAAA-AAATATA
* * *
1581890 A-GTAAACAAATAAAAAATATA
1 ATATAAATAAAAAAAAAATATA
1581911 AT-TAAATA
1 ATATAAATA
1581919 TATATATAGG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
20 6 0.14
21 16 0.38
22 6 0.14
23 14 0.33
ACGTcount: A:0.69, C:0.01, G:0.03, T:0.27
Consensus pattern (22 bp):
ATATAAATAAAAAAAAAATATA
Found at i:1583956 original size:45 final size:46
Alignment explanation
Indices: 1583907--1583994 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
1583897 AAACATTGAA
* * *
1583907 TGCATTTTATGCATCGATGCAC-ATACTATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAAACCATGCATCGATGCACTCAG
1583952 TGCATTTGATGCATCGATGCACAAAACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAAACCATGCATCGATGCACT
1583995 TAGGTTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAAACCATGCATCGATGCACTCAG
Found at i:1590285 original size:19 final size:18
Alignment explanation
Indices: 1590261--1590303 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
1590251 AAAACACAAG
1590261 AATTTTCAAAGATTTTGGA
1 AATTTTCAAA-ATTTTGGA
* *
1590280 AATTTTTGAAAATTTTTGA
1 AA-TTTTCAAAATTTTGGA
1590299 AATTT
1 AATTT
1590304 AAAAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 3 0.14
19 11 0.52
20 7 0.33
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (18 bp):
AATTTTCAAAATTTTGGA
Found at i:1591459 original size:21 final size:21
Alignment explanation
Indices: 1591417--1591460 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1591407 ACCCCGGGAG
**
1591417 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCCCCTC
* *
1591438 CTAGCTCTTCTCGTGCCCCTC
1 CTAGCTCTTCACGAGCCCCTC
1591459 CT
1 CT
1591461 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCCCCTC
Found at i:1592660 original size:45 final size:46
Alignment explanation
Indices: 1592606--1592693 Score: 142
Period size: 46 Copynumber: 1.9 Consensus size: 46
1592596 CATCGAATGT
* * *
1592606 ATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTCAGTGC
1 ATTTGATGCATCGATGCACAAAACCATACATCGATGCACTCAGTGC
1592651 ATTTGATGCATCGATGCACAAAACCATACATCGATGCACTCAG
1 ATTTGATGCATCGATGCACAAAACCATACATCGATGCACTCAG
1592694 GTTTTTTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 18 0.46
46 21 0.54
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.26
Consensus pattern (46 bp):
ATTTGATGCATCGATGCACAAAACCATACATCGATGCACTCAGTGC
Found at i:1597112 original size:15 final size:15
Alignment explanation
Indices: 1597089--1597125 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
1597079 TTCAAAGGAG
*
1597089 ATGAACCAATTGTTA
1 ATGAGCCAATTGTTA
1597104 ATGAGCCAATTGTTA
1 ATGAGCCAATTGTTA
1597119 ATGAGCC
1 ATGAGCC
1597126 TATAAAAGAA
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:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (15 bp):
ATGAGCCAATTGTTA
Done.