Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014582.1 Kokia drynarioides strain JFW-HI SEQ_129621, 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: 119517
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Warning! 115 characters in sequence are not A, C, G, or T
Found at i:241 original size:29 final size:28
Alignment explanation
Indices: 209--303 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 28
199 TCAAAAACCG
209 AATTTTTGGACATCCGGGGGTAAAATGGT
1 AATTTTTGGACAT-CGGGGGTAAAATGGT
* *
238 AATTTTTAGGAAAATC-GGGATCAAAAATGG-
1 AATTTTT-GG-ACATCGGGGGT--AAAATGGT
* *
268 AATTTTTGGACATTTGGGGGTAAGATGGT
1 AATTTTTGGACA-TCGGGGGTAAAATGGT
297 AATTTTT
1 AATTTTT
304 AAAAGTTTTA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
28 8 0.15
29 21 0.40
30 14 0.26
31 10 0.19
ACGTcount: A:0.32, C:0.06, G:0.27, T:0.35
Consensus pattern (28 bp):
AATTTTTGGACATCGGGGGTAAAATGGT
Found at i:274 original size:30 final size:29
Alignment explanation
Indices: 189--277 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 29
179 AACTTTTAAA
**
189 AAAATCGGGATCAAAAACCGAATTTTTGG
1 AAAATCGGGATCAAAAATGGAATTTTTGG
* *
218 -ACATCCGGGGGT--AAAATGGTAATTTTTAGG
1 AAAAT-C-GGGATCAAAAATGG-AATTTTT-GG
248 AAAATCGGGATCAAAAATGGAATTTTTGG
1 AAAATCGGGATCAAAAATGGAATTTTTGG
277 A
1 A
278 CATTTGGGGG
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
28 8 0.17
29 15 0.32
30 14 0.30
31 10 0.21
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (29 bp):
AAAATCGGGATCAAAAATGGAATTTTTGG
Found at i:391 original size:30 final size:30
Alignment explanation
Indices: 230--434 Score: 156
Period size: 29 Copynumber: 6.9 Consensus size: 30
220 ATCCGGGGGT
** *
230 AAAATGGTAATTTTTAGGAA-AATCGGGATCA
1 AAAATGG-AATTTTT-GGAAGTTTCGGGGTCA
*
261 AAAATGGAATTTTTGGACA-TTTGGGGGT--
1 AAAATGGAATTTTTGGA-AGTTTCGGGGTCA
* ** ***
289 AAGATGGTAATTTTTAAAAGTTTTAAGGTCA
1 AAAATGG-AATTTTTGGAAGTTTCGGGGTCA
*
320 AAAATGGAATTTTTGGAGGTTT-GGGG-CTA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTC-A
**
349 AAAATTTAATTTTTGGAAGTTTCGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTCGGGGTCA
*
379 AAAATGGGATTTTTGGAAG-TTCGAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTCG-GGGTCA
* *
408 AAAATGTAATTTTTAGAAGTTTCGGGG
1 AAAATGGAATTTTTGGAAGTTTCGGGG
435 ACCTCCAGGG
Statistics
Matches: 139, Mismatches: 25, Indels: 22
0.75 0.13 0.12
Matches are distributed among these distances:
28 8 0.06
29 63 0.45
30 54 0.39
31 14 0.10
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTCGGGGTCA
Found at i:431 original size:59 final size:58
Alignment explanation
Indices: 79--434 Score: 212
Period size: 59 Copynumber: 6.1 Consensus size: 58
69 TTTTGGATAC
* * * * *
79 TCGGGG-C-AAAATGGTAA-TTTTGG-ACTTTGGGGCAAAATGATAATTTTGGAAAAG-T
1 TCGGGGTCAAAAATGG-AATTTTTGGAAGTTTGGGGTAAAATGGTAATTTT-TAGAAGTT
* * * * * * * * ***
134 TCGGGGTTAAAAATGGAACTTTTAGACA-CTCGAGGGTAAAACGGTAACTTTTAAAAAAA
1 TCGGGGTCAAAAATGGAATTTTTGGA-AGTTTG-GGGTAAAATGGTAATTTTTAGAAGTT
* ** ** **
193 TCGGGATCAAAAACCGAATTTTTGGACA-TCCGGGGGTAAAATGGTAATTTTTAGGAA-AA
1 TCGGGGTCAAAAATGGAATTTTTGGA-AGT-TTGGGGTAAAATGGTAATTTTTA-GAAGTT
* * *
252 TCGGGATCAAAAATGGAATTTTTGGACA-TTTGGGGGTAAGATGGTAATTTTTAAAAGTT
1 TCGGGGTCAAAAATGGAATTTTTGGA-AGTTT-GGGGTAAAATGGTAATTTTTAGAAGTT
*** * * *
311 TTAAGGTCAAAAATGGAATTTTTGGAGGTTTGGGGCTAAAAAT-TTAATTTTTGGAAGTT
1 TCGGGGTCAAAAATGGAATTTTTGGAAGTTTGGGG-T-AAAATGGTAATTTTTAGAAGTT
* *
370 TCGGGGTCAAAAATGGGATTTTTGGAAGTTCGAGGGTAAAAAT-GTAATTTTTAGAAGTT
1 TCGGGGTCAAAAATGGAATTTTTGGAAGTTTG-GGGT-AAAATGGTAATTTTTAGAAGTT
429 TCGGGG
1 TCGGGG
435 ACCTCCAGGG
Statistics
Matches: 238, Mismatches: 48, Indels: 26
0.76 0.15 0.08
Matches are distributed among these distances:
55 6 0.03
56 2 0.01
57 12 0.05
58 12 0.05
59 196 0.82
60 10 0.04
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.32
Consensus pattern (58 bp):
TCGGGGTCAAAAATGGAATTTTTGGAAGTTTGGGGTAAAATGGTAATTTTTAGAAGTT
Found at i:1503 original size:3 final size:3
Alignment explanation
Indices: 1434--1490 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
1424 TTAATAAATG
* * * * * *
1434 TTA TTA TTA TTA TTA TTA TTA TTA TTG TTG TTG TTG TTG TTG TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1482 TTA TTA TTA
1 TTA TTA TTA
1491 AAAACAATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2215 original size:6 final size:6
Alignment explanation
Indices: 2200--2308 Score: 75
Period size: 6 Copynumber: 18.7 Consensus size: 6
2190 TGTAATTGAT
* * * *
2200 TTTAAA TTTAAG TTTAAA ATT--A TTTCAAA TTTAGA -CTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA
* ** *
2246 TTTAAA -ATAAA TTTAAA TTTAAAA AATGAA TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
2294 -GTAAA TTTAAT TTTA
1 TTTAAA TTTAAA TTTA
2309 GAAATAAATC
Statistics
Matches: 77, Mismatches: 19, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
4 3 0.04
5 11 0.14
6 55 0.71
7 8 0.10
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:2277 original size:19 final size:19
Alignment explanation
Indices: 2236--2287 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
2226 AAATTTAGAC
2236 TAAATTTAAATTT--AAAA
1 TAAATTTAAATTTAAAAAA
2253 TAAATTTAAATTTAAAAAA
1 TAAATTTAAATTTAAAAAA
*
2272 TGAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
2288 TTTAAAGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 13 0.41
19 19 0.59
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAATTTAAATTTAAAAAA
Found at i:2303 original size:17 final size:17
Alignment explanation
Indices: 2202--2287 Score: 93
Period size: 17 Copynumber: 4.9 Consensus size: 17
2192 TAATTGATTT
*
2202 TAAATTTAAGTTTAAAA
1 TAAATTTAAATTTAAAA
* * *
2219 T-TATTTCAAATTTAGAC
1 TAAATTT-AAATTTAAAA
2236 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
2253 TAAATTTAAATTTAAAAAA
1 TAAATTTAAATTT--AAAA
*
2272 TGAATTTAAATTTAAA
1 TAAATTTAAATTTAAA
2288 TTTAAAGTAA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
16 4 0.07
17 33 0.58
18 4 0.07
19 16 0.28
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:4292 original size:16 final size:16
Alignment explanation
Indices: 4252--4294 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
4242 ATAAAATTTT
4252 AAAATTCAAAAAATATA
1 AAAATT-AAAAAATATA
* *
4269 TAATTTAAAAAATATA
1 AAAATTAAAAAATATA
4285 AAAATTAAAA
1 AAAATTAAAA
4295 TTAAACAAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
16 18 0.82
17 4 0.18
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAATTAAAAAATATA
Found at i:4308 original size:21 final size:22
Alignment explanation
Indices: 4273--4314 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
4263 AATATATAAT
4273 TTAAAAAATATAAAAATTAAAA
1 TTAAAAAATATAAAAATTAAAA
* *
4295 TTAAACAA-ATAAAAGTTAAA
1 TTAAAAAATATAAAAATTAAA
4315 TTCACAAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (22 bp):
TTAAAAAATATAAAAATTAAAA
Found at i:6468 original size:6 final size:6
Alignment explanation
Indices: 6457--6491 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
6447 CATGCCCTTG
*
6457 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC CCTTT
1 TCTTTC TCTTTC TCTTTC TCTTTC TCTTTC TCTTT
6492 TCAGCAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (6 bp):
TCTTTC
Found at i:19763 original size:18 final size:18
Alignment explanation
Indices: 19737--19773 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
19727 TTTTATTAGA
19737 CTCAAAATGTAATTTTAT
1 CTCAAAATGTAATTTTAT
*
19755 CTCAGAATGTAATTTTAT
1 CTCAAAATGTAATTTTAT
19773 C
1 C
19774 ATTATAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (18 bp):
CTCAAAATGTAATTTTAT
Found at i:22682 original size:97 final size:97
Alignment explanation
Indices: 22533--22714 Score: 287
Period size: 97 Copynumber: 1.9 Consensus size: 97
22523 ATCTAAAAGC
* * *
22533 ATTTGTAAGTTGCATAAGACCTCAAGAATGTATAGGAAAACAGCATTATACTATA-GTA-GTGGA
1 ATTTGCAAGTTGCATAAAACCTCAAGAATGTATAGGAAAACAGCATTATACTAAATGTATG-GGA
22596 CCTATGAAACCTTCATTTACATACATACATACAT
65 CCTATGAAACCTTCA-TTACATACATACATACAT
* *
22630 ATTTGCAAGTTGCATAAAACCTCAAGAATGTTTGGGAAAACAGCATTATACTAAATGTATGGGAC
1 ATTTGCAAGTTGCATAAAACCTCAAGAATGTATAGGAAAACAGCATTATACTAAATGTATGGGAC
22695 CTATGAAACCTTCATTACAT
66 CTATGAAACCTTCATTACAT
22715 GCATGCATGC
Statistics
Matches: 78, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
97 56 0.72
98 21 0.27
99 1 0.01
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (97 bp):
ATTTGCAAGTTGCATAAAACCTCAAGAATGTATAGGAAAACAGCATTATACTAAATGTATGGGAC
CTATGAAACCTTCATTACATACATACATACAT
Found at i:22768 original size:28 final size:28
Alignment explanation
Indices: 22736--22806 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
22726 TGCATAAATA
* * *
22736 CATACACACATACGTACATATGTTCATG
1 CATACATACATACATACATATGTACATG
*
22764 CATACATGCATACATACATATGTACATG
1 CATACATACATACATACATATGTACATG
22792 CATACATACATACAT
1 CATACATACATACAT
22807 GCATGCATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.28
Consensus pattern (28 bp):
CATACATACATACATACATATGTACATG
Found at i:22811 original size:20 final size:20
Alignment explanation
Indices: 22764--22815 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
22754 TATGTTCATG
22764 CATACATGCATACATACATA
1 CATACATGCATACATACATA
**
22784 TGTACATGCATACATACATA
1 CATACATGCATACATACATA
*
22804 CATGCATGCATA
1 CATACATGCATA
22816 TCTAAAAGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.40, C:0.23, G:0.10, T:0.27
Consensus pattern (20 bp):
CATACATGCATACATACATA
Found at i:22814 original size:4 final size:4
Alignment explanation
Indices: 22728--22806 Score: 59
Period size: 4 Copynumber: 19.8 Consensus size: 4
22718 TGCATGCATG
* * * ** * * *
22728 CATA AATA CATA CACA CATA CGTA CATA TGTT CATG CATA CATG CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
** *
22776 CATA CATA TGTA CATG CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CAT
22807 GCATGCATAT
Statistics
Matches: 54, Mismatches: 21, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.28
Consensus pattern (4 bp):
CATA
Found at i:22888 original size:4 final size:4
Alignment explanation
Indices: 22879--22930 Score: 63
Period size: 4 Copynumber: 13.5 Consensus size: 4
22869 AACCTTCATT
* * *
22879 TACA TACA TACA TACA TACA TAC- TAC- TACA TACA TGCA TGCA TTCA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
22925 TACA TA
1 TACA TA
22931 TCTAGAAGCA
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
3 6 0.14
4 38 0.86
ACGTcount: A:0.42, C:0.25, G:0.04, T:0.29
Consensus pattern (4 bp):
TACA
Found at i:25048 original size:20 final size:20
Alignment explanation
Indices: 25011--25049 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
25001 AGAGAAGCAG
*
25011 AAAAGAATAGAAAATAAAAA
1 AAAAGAATAAAAAATAAAAA
25031 AAAAGAA-AAAAAATTAAAA
1 AAAAGAATAAAAAA-TAAAA
25050 TAACATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.82, C:0.00, G:0.08, T:0.10
Consensus pattern (20 bp):
AAAAGAATAAAAAATAAAAA
Found at i:29424 original size:6 final size:6
Alignment explanation
Indices: 29413--29453 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
29403 CTTCAAGAAC
29413 TACATA TACATA TACATA TACATA TACATA T--ATA TACATA T
1 TACATA TACATA TACATA TACATA TACATA TACATA TACATA T
29454 GAATATGTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
4 4 0.12
6 29 0.88
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (6 bp):
TACATA
Found at i:29449 original size:10 final size:11
Alignment explanation
Indices: 29413--29459 Score: 60
Period size: 12 Copynumber: 4.1 Consensus size: 11
29403 CTTCAAGAAC
29413 TACATATACATA
1 TACATATA-ATA
29425 TACATATACATA
1 TACATATA-ATA
29437 TACATAT-ATA
1 TACATATAATA
29447 TACATATGAATA
1 TACATAT-AATA
29459 T
1 T
29460 GTATATACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.30
12 23 0.70
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (11 bp):
TACATATAATA
Found at i:29459 original size:16 final size:17
Alignment explanation
Indices: 29413--29470 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
29403 CTTCAAGAAC
29413 TACATATACATA-TACATA
1 TACATATACATAGT--ATA
29431 TACATATACATA-TATA
1 TACATATACATAGTATA
29447 TACATATGA-ATATGTATA
1 TACATAT-ACATA-GTATA
29465 TACATA
1 TACATA
29471 CCCTTCCCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
16 13 0.35
17 1 0.03
18 23 0.62
ACGTcount: A:0.48, C:0.12, G:0.03, T:0.36
Consensus pattern (17 bp):
TACATATACATAGTATA
Found at i:33532 original size:3 final size:3
Alignment explanation
Indices: 33524--33548 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
33514 TTGACATGTT
33524 AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG A
33549 TATAACACAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:47061 original size:18 final size:18
Alignment explanation
Indices: 47038--47075 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
47028 CAACATGTGC
47038 CAATGTTTTCTTGATTAG
1 CAATGTTTTCTTGATTAG
47056 CAATGTTTTCTTGATTAG
1 CAATGTTTTCTTGATTAG
47074 CA
1 CA
47076 CCCTACATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.47
Consensus pattern (18 bp):
CAATGTTTTCTTGATTAG
Found at i:53467 original size:20 final size:20
Alignment explanation
Indices: 53426--53469 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
53416 AACCCGATTC
*
53426 AAAATTCGATTCTATATAAT
1 AAAATTCGATTCTACATAAT
*
53446 AAAATTCG-TTCCTACATTAT
1 AAAATTCGATT-CTACATAAT
53466 AAAA
1 AAAA
53470 GAGTACATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (20 bp):
AAAATTCGATTCTACATAAT
Found at i:57323 original size:71 final size:71
Alignment explanation
Indices: 57207--57348 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
57197 TTGAACACCA
*
57207 GCAATAGAAATCCAAAGAAGTTCGAAGGTATTATTTTTTCTTTTATTTCATATTTCTATATATAT
1 GCAATAGAAATCCAAAGAAGTTCGAAGGTATTATTTTTTATTTTATTTCATATTTCTATATATAT
57272 ATATAT
66 ATATAT
57278 GCAATAGAAATCCAAAGAAGTTCGAAGGTATTATTTTTTATTTTATTTCATATTTCTATATATAT
1 GCAATAGAAATCCAAAGAAGTTCGAAGGTATTATTTTTTATTTTATTTCATATTTCTATATATAT
*
57343 GTATAT
66 ATATAT
57349 ATATACATAT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (71 bp):
GCAATAGAAATCCAAAGAAGTTCGAAGGTATTATTTTTTATTTTATTTCATATTTCTATATATAT
ATATAT
Found at i:57342 original size:12 final size:12
Alignment explanation
Indices: 57334--57375 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
57324 TTCATATTTC
57334 TATATATATGTA
1 TATATATATGTA
*
57346 TATATATA--CA
1 TATATATATGTA
*
57356 TATGTATATGTA
1 TATATATATGTA
57368 TATATATA
1 TATATATA
57376 AAAGGAAAAG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
10 8 0.33
12 16 0.67
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (12 bp):
TATATATATGTA
Found at i:58357 original size:29 final size:29
Alignment explanation
Indices: 58287--58380 Score: 127
Period size: 29 Copynumber: 3.3 Consensus size: 29
58277 GAAAATTATA
* *
58287 TTTTAACCTCAAACTTTTTAAAATCTCA-
1 TTTTAACCTCAAACTTTATAAAATTTCAT
*
58315 TTTTACCCTCAAACTTTATAAAATTTCAT
1 TTTTAACCTCAAACTTTATAAAATTTCAT
* *
58344 TTTTAACCTCAAACTTTCTAAAATTCCAT
1 TTTTAACCTCAAACTTTATAAAATTTCAT
*
58373 ATTTAACC
1 TTTTAACC
58381 CCTAAAATTT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 25 0.43
29 33 0.57
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (29 bp):
TTTTAACCTCAAACTTTATAAAATTTCAT
Found at i:58394 original size:30 final size:29
Alignment explanation
Indices: 58288--58396 Score: 89
Period size: 29 Copynumber: 3.8 Consensus size: 29
58278 AAAATTATAT
* * *
58288 TTTAACCTCAAACTTTTTAAAA-TCTCAT-
1 TTTAACCCCAAAATTTCTAAAATTC-CATA
* * * *
58316 TTT-ACCCTCAAACTTTATAAAATTTCATT
1 TTTAACCC-CAAAATTTCTAAAATTCCATA
* *
58345 TTTAACCTCAAACTTTCTAAAATTCCATA
1 TTTAACCCCAAAATTTCTAAAATTCCATA
58374 TTTAACCCCTAAAATTTCTAAAA
1 TTTAACCCC-AAAATTTCTAAAA
58397 ATTATATTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
27 3 0.04
28 19 0.28
29 30 0.45
30 15 0.22
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.40
Consensus pattern (29 bp):
TTTAACCCCAAAATTTCTAAAATTCCATA
Found at i:58403 original size:29 final size:30
Alignment explanation
Indices: 58278--58483 Score: 153
Period size: 30 Copynumber: 7.0 Consensus size: 30
58268 ATTTTATTCG
* * *
58278 AAAATTATATTTTAACCTC-AAACTTT-TT
1 AAAATTATATTTTGACCCCTAAACTTTCTA
* *
58306 AAAATCT-CATTTT-A-CCCTCAAACTTTATA
1 AAAAT-TATATTTTGACCCCT-AAACTTTCTA
* * *
58335 AAATTTCAT-TTTTAACCTC-AAACTTTCT-
1 AAAATT-ATATTTTGACCCCTAAACTTTCTA
* *
58363 AAAATTCCATA-TTTAACCCCTAAAATTTCTA
1 AAAATT--ATATTTTGACCCCTAAACTTTCTA
* *
58394 AAAATTATATTTTGACCCTTAATCTTT-TCA
1 AAAATTATATTTTGACCCCTAAACTTTCT-A
* * *
58424 AAAATTTTATTTTGACCCTTAAACTTTCCA
1 AAAATTATATTTTGACCCCTAAACTTTCTA
58454 AAAATTATATTTTGACCCCTAAACTTTCTA
1 AAAATTATATTTTGACCCCTAAACTTTCTA
58484 GAATTGCATT
Statistics
Matches: 143, Mismatches: 20, Indels: 28
0.75 0.10 0.15
Matches are distributed among these distances:
26 2 0.01
27 1 0.01
28 23 0.16
29 33 0.23
30 76 0.53
31 8 0.06
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.42
Consensus pattern (30 bp):
AAAATTATATTTTGACCCCTAAACTTTCTA
Found at i:60308 original size:29 final size:29
Alignment explanation
Indices: 60276--60652 Score: 147
Period size: 30 Copynumber: 13.0 Consensus size: 29
60266 AATGGAATTG
*
60276 TAGACATTCGAGGGTAAAACTGTAATTTT
1 TAGACATTCGAGGGTAAAAATGTAATTTT
* * * *
60305 TAGAAAAATCG-GGATCAAAAATGAAATTTT
1 TAG-ACATTCGAGGGT-AAAAATGTAATTTT
* *
60335 TGGACGTTCGAGGGT-AAAATGGTAATTTT
1 TAGACATTCGAGGGTAAAAAT-GTAATTTT
* * * *
60364 TAGGAAAATCGA-GATCAAAAATGGAATTTT
1 TA-GACATTCGAGGGT-AAAAATGTAATTTT
* **
60394 TGGACATTC----G--AAAGGGTAATTTT
1 TAGACATTCGAGGGTAAAAATGTAATTTT
* * * *
60417 T-GAAAGTTTCGATGTTAAAAATGGAATTTT
1 TAGACA--TTCGAGGGTAAAAATGTAATTTT
*
60447 TAGACATTCGGGGGTAAAAATGTAATTTT
1 TAGACATTCGAGGGTAAAAATGTAATTTT
* * *
60476 TGGA-AGTTTTG-GGGTTAAAAATGGAATTTT
1 TAGACA--TTCGAGGG-TAAAAATGTAATTTT
** * *
60506 TAGAGGTTTGGGGGTAAAAATGTAATTTT
1 TAGACATTCGAGGGTAAAAATGTAATTTT
** *
60535 TAGA-AGTTTTAGGGTCAAAAATGCAATTTT
1 TAGACA-TTCGAGGGT-AAAAATGTAATTTT
* **
60565 TGGACA-TCCTGGGTAAAAATGTAATTTT
1 TAGACATTCGAGGGTAAAAATGTAATTTT
* *
60593 T-GATAGTTTCGA-GGTCAAAAATGGAATTTT
1 TAGACA--TTCGAGGGT-AAAAATGTAATTTT
* ** * * *
60623 TGGAGGTTTGGGGGTAAAAATGTAAATTT
1 TAGACATTCGAGGGTAAAAATGTAATTTT
60652 T
1 T
60653 GGAAGTTTAG
Statistics
Matches: 259, Mismatches: 59, Indels: 60
0.69 0.16 0.16
Matches are distributed among these distances:
22 3 0.01
23 11 0.04
24 3 0.01
27 3 0.01
28 20 0.08
29 103 0.40
30 105 0.41
31 11 0.04
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (29 bp):
TAGACATTCGAGGGTAAAAATGTAATTTT
Found at i:60501 original size:59 final size:59
Alignment explanation
Indices: 60257--60778 Score: 388
Period size: 59 Copynumber: 9.0 Consensus size: 59
60247 GGGAAAATTT
* * * * * * ***
60257 GGGGTTTAAAATGGAA-TTGTAGACATTCGAGGGTAAAACTGTAATTTTTAGAAAAATC
1 GGGGTTAAAAATGGAATTTTTGGACATTCGGGGGTAAAAATGTAATTTTTGGAAGTTTC
* * * * * **
60315 GGGATCAAAAATGAAATTTTTGGACGTTCGAGGGT-AAAATGGTAATTTTTAGGAA-AATC
1 GGGGTTAAAAATGGAATTTTTGGACATTCGGGGGTAAAAAT-GTAATTTTT-GGAAGTTTC
* * * ** *
60374 GAGATCAAAAATGGAATTTTTGGACATTC----G--AAAGGGTAATTTTTGAAAGTTTC
1 GGGGTTAAAAATGGAATTTTTGGACATTCGGGGGTAAAAATGTAATTTTTGGAAGTTTC
** * *
60427 GATGTTAAAAATGGAATTTTTAGACATTCGGGGGTAAAAATGTAATTTTTGGAAGTTTT
1 GGGGTTAAAAATGGAATTTTTGGACATTCGGGGGTAAAAATGTAATTTTTGGAAGTTTC
* ** * * *
60486 GGGGTTAAAAATGGAATTTTTAGAGGTTTGGGGGTAAAAATGTAATTTTTAGAAGTTTT
1 GGGGTTAAAAATGGAATTTTTGGACATTCGGGGGTAAAAATGTAATTTTTGGAAGTTTC
* * * **
60545 AGGGTCAAAAATGCAATTTTTGGACA-TCCTGGGTAAAAATGTAATTTTT-GATAGTTTC
1 GGGGTTAAAAATGGAATTTTTGGACATTCGGGGGTAAAAATGTAATTTTTGGA-AGTTTC
* * ** * * *
60603 GAGGTCAAAAATGGAATTTTTGGAGGTTTGGGGGTAAAAATGTAAATTTTGGAAGTTTA
1 GGGGTTAAAAATGGAATTTTTGGACATTCGGGGGTAAAAATGTAATTTTTGGAAGTTTC
* * *** *
60662 GGGGTTAAAAATGGAATTTTTGGA-AGTTCAGGGGTAAAAATATAATTTTCAAAAGTTTT
1 GGGGTTAAAAATGGAATTTTTGGACA-TTCGGGGGTAAAAATGTAATTTTTGGAAGTTTC
* * ** * *
60721 AGGGTTAAAAATGGATTTTTTTTA-AGTTCGGGGGT-AAAATATAAATTTTGGACAGTTT
1 GGGGTTAAAAATGGAATTTTTGGACA-TTCGGGGGTAAAAATGTAATTTTTGGA-AGTTT
60779 AGAGACATTC
Statistics
Matches: 378, Mismatches: 71, Indels: 29
0.79 0.15 0.06
Matches are distributed among these distances:
52 3 0.01
53 36 0.10
54 3 0.01
55 1 0.00
57 3 0.01
58 75 0.20
59 252 0.67
60 5 0.01
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (59 bp):
GGGGTTAAAAATGGAATTTTTGGACATTCGGGGGTAAAAATGTAATTTTTGGAAGTTTC
Found at i:60653 original size:29 final size:29
Alignment explanation
Indices: 60409--60778 Score: 257
Period size: 30 Copynumber: 12.6 Consensus size: 29
60399 ATTCGAAAGG
* ** *
60409 GTAATTTTTGAAAGTTTCGATGTTAAAAAT
1 GTAATTTTTGGAAGTTT-GGGGGTAAAAAT
* * *
60439 GGAATTTTTAGACA-TTCGGGGGTAAAAAT
1 GTAATTTTTGGA-AGTTTGGGGGTAAAAAT
*
60468 GTAATTTTTGGAAGTTTTGGGGTTAAAAAT
1 GTAATTTTTGGAAG-TTTGGGGGTAAAAAT
* * *
60498 GGAATTTTTAGAGGTTTGGGGGTAAAAAT
1 GTAATTTTTGGAAGTTTGGGGGTAAAAAT
* **
60527 GTAATTTTTAGAAGTTTTAGGGTCAAAAAT
1 GTAATTTTTGGAAGTTTGGGGGT-AAAAAT
* *
60557 GCAATTTTTGGACA-TCCT--GGGTAAAAAT
1 GTAATTTTTGGA-AGT-TTGGGGGTAAAAAT
* *
60585 GTAATTTTT-GATAGTTTCGAGGTCAAAAAT
1 GTAATTTTTGGA-AGTTTGGGGGT-AAAAAT
* *
60615 GGAATTTTTGGAGGTTTGGGGGTAAAAAT
1 GTAATTTTTGGAAGTTTGGGGGTAAAAAT
* *
60644 GTAAATTTTGGAAGTTTAGGGGTTAAAAAT
1 GTAATTTTTGGAAGTTT-GGGGGTAAAAAT
* **
60674 GGAATTTTTGGAAGTTCAGGGGTAAAAAT
1 GTAATTTTTGGAAGTTTGGGGGTAAAAAT
* *** * *
60703 ATAATTTTCAAAAGTTTTAGGGTTAAAAAT
1 GTAATTTTTGGAAG-TTTGGGGGTAAAAAT
* * ** *
60733 GGATTTTTTTTAAGTTCGGGGGT-AAAAT
1 GTAATTTTTGGAAGTTTGGGGGTAAAAAT
* *
60761 ATAAATTTTGGACAGTTT
1 GTAATTTTTGGA-AGTTT
60779 AGAGACATTC
Statistics
Matches: 264, Mismatches: 62, Indels: 29
0.74 0.17 0.08
Matches are distributed among these distances:
27 4 0.02
28 27 0.10
29 108 0.41
30 120 0.45
31 5 0.02
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.38
Consensus pattern (29 bp):
GTAATTTTTGGAAGTTTGGGGGTAAAAAT
Found at i:61677 original size:3 final size:3
Alignment explanation
Indices: 61669--61711 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
61659 TTGTCTTCCT
* * *
61669 TTA TTA TTA TTA TTA TTT TTA ATA TTA TTA TTA ATA GTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
61712 CTAATTACCA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
3 31 0.94
4 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:61694 original size:12 final size:12
Alignment explanation
Indices: 61669--61716 Score: 60
Period size: 12 Copynumber: 3.9 Consensus size: 12
61659 TTGTCTTCCT
*
61669 TTATTATTATTA
1 TTATTATTAATA
*
61681 TTATTTTTAATA
1 TTATTATTAATA
61693 TTATTATTAATA
1 TTATTATTAATA
*
61705 GTTATTACTAAT
1 -TTATTATTAAT
61717 TACCATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 21 0.68
13 10 0.32
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.60
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:62412 original size:17 final size:17
Alignment explanation
Indices: 62386--62525 Score: 85
Period size: 17 Copynumber: 8.5 Consensus size: 17
62376 ACTAGACATT
* *
62386 ATTTTCAATTTATAATA
1 ATTTTAAATTTAAAATA
62403 ATTTTAAATTTAAAATA
1 ATTTTAAATTTAAAATA
* * *
62420 AATTTAAACTTAAATTA
1 ATTTTAAATTTAAAATA
* * *
62437 AATTCAAAATT--AA-A
1 ATTTTAAATTTAAAATA
*
62451 A--TTAAAATTAAAATTA
1 ATTTTAAATTTAAAA-TA
*
62467 AATTTAAATTTAAAATA
1 ATTTTAAATTTAAAATA
* * *
62484 AATCTAAATTTAAAACA
1 ATTTTAAATTTAAAATA
*
62501 AATTT-AATCTTAAAATA
1 ATTTTAAAT-TTAAAATA
*
62518 AATTTAAA
1 ATTTTAAA
62526 AAAGGCTCGG
Statistics
Matches: 101, Mismatches: 14, Indels: 15
0.78 0.11 0.12
Matches are distributed among these distances:
12 7 0.07
14 4 0.04
15 1 0.01
16 5 0.05
17 71 0.70
18 13 0.13
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (17 bp):
ATTTTAAATTTAAAATA
Found at i:62416 original size:6 final size:6
Alignment explanation
Indices: 62405--62497 Score: 84
Period size: 6 Copynumber: 16.0 Consensus size: 6
62395 TTATAATAAT
* * * *
62405 TTTAAA TTTAAA -ATAAA TTTAAA CTTAAA -TTAAA TTCAAA ATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* * * * *
62451 ATTAAA ATTAAA ATTAAA TTTAAA TTTAAA -ATAAA TCTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
62498 ACAAATTTAA
Statistics
Matches: 74, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
5 13 0.18
6 61 0.82
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (6 bp):
TTTAAA
Found at i:62454 original size:18 final size:18
Alignment explanation
Indices: 62405--62498 Score: 106
Period size: 17 Copynumber: 5.4 Consensus size: 18
62395 TTATAATAAT
*
62405 TTTAAATTTAAAA-TAAA
1 TTTAAAATTAAAATTAAA
*
62422 TTTAAACTT-AAATTAAA
1 TTTAAAATTAAAATTAAA
*
62439 TTCAAAATTAAAATTAAA
1 TTTAAAATTAAAATTAAA
* *
62457 ATTAAAATTAAATTTAAA
1 TTTAAAATTAAAATTAAA
62475 TTTAAAA-T-AAATCTAAA
1 TTTAAAATTAAAAT-TAAA
62492 TTTAAAA
1 TTTAAAA
62499 CAAATTTAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
16 6 0.09
17 31 0.47
18 29 0.44
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
TTTAAAATTAAAATTAAA
Found at i:69955 original size:40 final size:40
Alignment explanation
Indices: 69900--69980 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
69890 TTGAAAAGTC
69900 TCGAACCGAGGAAGAACATGTAAAGGTCTTGAGGAAGTTG
1 TCGAACCGAGGAAGAACATGTAAAGGTCTTGAGGAAGTTG
69940 TCGAACCGAGGAAGAACATGTAAAGGTCTTGAGGAAGTTG
1 TCGAACCGAGGAAGAACATGTAAAGGTCTTGAGGAAGTTG
69980 T
1 T
69981 TCTTGAGACT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (40 bp):
TCGAACCGAGGAAGAACATGTAAAGGTCTTGAGGAAGTTG
Found at i:73343 original size:49 final size:48
Alignment explanation
Indices: 73258--73826 Score: 372
Period size: 49 Copynumber: 11.6 Consensus size: 48
73248 ACAGGTTTGA
*
73258 AGGGAAAGATTTAAGTTGCAACGGCGAATCC-AGTACCACGAAGATATAG
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCACGAAGATAT-G
* * * * * * *
73307 AGAGAACGGTTTAAGTCGCAACGGTGAACCTTGTACCTCAGAA-ACATG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCAC-GAAGATATG
* * *
73355 AAGGGAAAGATTTAACTCGTAATGGCGAATCC-AGTACCACGAAGATATGG
1 -AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCACGAAGATAT-G
* * * * * * *
73405 AGGGAAAGATTTAAGTCACAATGACGAACCTTGTACCTC-ATAAACATG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCACGA-AGATATG
73453 AAGGGAAAGATTTAAG-CTGCAACGGCGAATCC-AGTACCACGAAGATATGG
1 -AGGGAAAGATTTAAGTC-GCAACGGCGAA-CCTAGTACCACGAAGATAT-G
* * * * *
73503 AGAGAAAGGTTTAAGTCGCAACGACGAACCTTA-TACCTCAGAA-ACATG
1 AGGGAAAGATTTAAGTCGCAACGGCGAACC-TAGTACCAC-GAAGATATG
* * *
73551 AAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCACGAAGATATGG
1 -AGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCACGAAGATAT-G
* * * * * * * * *
73601 AGGGAAAGGTTTAAGTCACAATGTCGAACTTTGTACCTCAGAA-ACATAA
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCAC-GAAGATAT-G
* * *
73650 AGTGAAAGATTTAAGCCGCAACGGCGAATCC-AATACCACGAAGATATG
1 AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCACGAAGATATG
* * ** * * *
73698 AAGGGAAAGGTTTAAGTTGCAACGGTAAACTTTGTACCTA-GAAG-CATG
1 -AGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACC-ACGAAGATATG
* * * * *
73746 AATGGAAAGATTTAAGCCGCAACGGCGAATCC-AATACCATGAAGAGATGG
1 -AGGGAAAGATTTAAGTCGCAACGGCGAA-CCTAGTACCACGAAGATAT-G
* *
73796 AGGGAAAGGTTTAAGTCGCAACGACGAACCT
1 AGGGAAAGATTTAAGTCGCAACGGCGAACCT
73827 TATACCTCAG
Statistics
Matches: 393, Mismatches: 95, Indels: 64
0.71 0.17 0.12
Matches are distributed among these distances:
47 1 0.00
48 59 0.15
49 311 0.79
50 22 0.06
ACGTcount: A:0.38, C:0.18, G:0.25, T:0.20
Consensus pattern (48 bp):
AGGGAAAGATTTAAGTCGCAACGGCGAACCTAGTACCACGAAGATATG
Found at i:73434 original size:98 final size:98
Alignment explanation
Indices: 73255--73854 Score: 835
Period size: 98 Copynumber: 6.1 Consensus size: 98
73245 TCTACAGGTT
** * * *
73255 TGAAGGGAAAGATTTAAGTTGCAACGGCGAATCCAGTACCACGAAGATATAGAGAGAACGGTTTA
1 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTTA
**
73320 AGTCGCAACGGTGAACCTTGTACCTCAGAAACA
66 AGTCGCAACGACGAACCTTGTACCTCAGAAACA
* * *
73353 TGAAGGGAAAGATTTAA-CTCGTAATGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGATTT
1 TGAAGGGAAAGATTTAAGC-CGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTT
* * *
73417 AAGTCACAATGACGAACCTTGTACCTCATAAACA
65 AAGTCGCAACGACGAACCTTGTACCTCAGAAACA
* *
73451 TGAAGGGAAAGATTTAAGCTGCAACGGCGAATCCAGTACCACGAAGATATGGAGAGAAAGGTTTA
1 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTTA
*
73516 AGTCGCAACGACGAACCTTATACCTCAGAAACA
66 AGTCGCAACGACGAACCTTGTACCTCAGAAACA
* *
73549 TGAAGGGAAAGATTTAAGCCGCAACGGTGAATCTAGTACCACGAAGATATGGAGGGAAAGGTTTA
1 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTTA
* * * *
73614 AGTCACAATGTCGAACTTTGTACCTCAGAAACA
66 AGTCGCAACGACGAACCTTGTACCTCAGAAACA
* * * *
73647 TAAAGTGAAAGATTTAAGCCGCAACGGCGAATCCAATACCACGAAGATATGAAGGGAAAGGTTTA
1 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTTA
* *** * *
73712 AGTTGCAACGGTAAACTTTGTACCT-AGAAGCA
66 AGTCGCAACGACGAACCTTGTACCTCAGAAACA
* * * *
73744 TGAATGGAAAGATTTAAGCCGCAACGGCGAATCCAATACCATGAAGAGATGGAGGGAAAGGTTTA
1 TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTTA
*
73809 AGTCGCAACGACGAACCTTATACCTCAGAAACA
66 AGTCGCAACGACGAACCTTGTACCTCAGAAACA
*
73842 TGAAAGGAAAGAT
1 TGAAGGGAAAGAT
73855 GGAAACCACA
Statistics
Matches: 441, Mismatches: 58, Indels: 6
0.87 0.11 0.01
Matches are distributed among these distances:
97 84 0.19
98 356 0.81
99 1 0.00
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (98 bp):
TGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGAAGATATGGAGGGAAAGGTTTA
AGTCGCAACGACGAACCTTGTACCTCAGAAACA
Found at i:75641 original size:30 final size:28
Alignment explanation
Indices: 75589--75727 Score: 111
Period size: 30 Copynumber: 4.8 Consensus size: 28
75579 TTTAACCTCG
* *
75589 AACTTTCTAAAATTCCAT-TTTTGACAGCTA
1 AACTTTCCAAAATT--ATATTTTGAC-CCTA
75619 AACTTTCCAAGAATTATATTTTGACCCCTA
1 AACTTTCCAA-AATTATATTTTGA-CCCTA
** *
75649 AACATTTTTAAAATTATATTTTAACCCTA
1 AAC-TTTCCAAAATTATATTTTGACCCTA
** *
75678 AACTTTTTAAAAATTATATTTTG-TCCTCA
1 AAC-TTTCCAAAATTATATTTTGACCCT-A
*
75707 AACTTTCCAAAATTACATTTT
1 AACTTTCCAAAATTATATTTT
75728 ATCCTCGTCT
Statistics
Matches: 92, Mismatches: 12, Indels: 12
0.79 0.10 0.10
Matches are distributed among these distances:
28 18 0.20
29 31 0.34
30 33 0.36
31 10 0.11
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (28 bp):
AACTTTCCAAAATTATATTTTGACCCTA
Found at i:75709 original size:29 final size:28
Alignment explanation
Indices: 75515--75727 Score: 112
Period size: 29 Copynumber: 7.4 Consensus size: 28
75505 TTTATTCTAG
* *
75515 AATTATATTTTAACCCCAAACTTTTTAA
1 AATTATATTTTGACCCTAAACTTTTTAA
*** * *
75543 AATCCCA-TTT-ACCCACAAACTTTATAA
1 AATTATATTTTGACCC-TAAACTTTTTAA
* * * * *
75570 AATT-TCTTTTTTAACCTCGAACTTTCTAA
1 AATTAT-ATTTTGACCCT-AAACTTTTTAA
* **
75599 AATTCCAT-TTTTGACAGCTAAACTTTCCAA
1 AATT--ATATTTTGAC-CCTAAACTTTTTAA
75629 GAATTATATTTTGACCCCTAAACATTTTTAA
1 -AATTATATTTTGA-CCCTAAAC-TTTTTAA
*
75660 AATTATATTTTAACCCTAAACTTTTTAAA
1 AATTATATTTTGACCCTAAACTTTTT-AA
* **
75689 AATTATATTTTG-TCCTCAAACTTTCCAA
1 AATTATATTTTGACCCT-AAACTTTTTAA
*
75717 AATTACATTTT
1 AATTATATTTT
75728 ATCCTCGTCT
Statistics
Matches: 145, Mismatches: 25, Indels: 30
0.73 0.12 0.15
Matches are distributed among these distances:
26 4 0.03
27 17 0.12
28 27 0.19
29 46 0.32
30 38 0.26
31 12 0.08
32 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.42
Consensus pattern (28 bp):
AATTATATTTTGACCCTAAACTTTTTAA
Found at i:79374 original size:59 final size:59
Alignment explanation
Indices: 78991--79385 Score: 291
Period size: 59 Copynumber: 6.7 Consensus size: 59
78981 TGGACGCTTC
* * * * ** * * * *
78991 GAGGGCAAAATAGAAATTTTTAGAAGGTTCGGGGTTGAAAATAGAATTTTTATACATTC
1 GAGGGTAAAATGGTAATTTTTAGAAGATTTAGGGTTAAAAATGGAATTTTTAGACATTT
* * ** ** * * * *
79050 GAGGGTAAAATAGTAACTTTTTGGAA-ATTTCATAGACAAATATGGAATTTTTGGATATTC
1 GAGGGTAAAATGGTAA-TTTTTAGAAGATTT-AGGGTTAAAAATGGAATTTTTAGACATTT
* * * * *
79110 GAGAGTAAAATGGTAATTTTTAGAA-AATTCGGGGTAAAAATTGGAA-TTTTAGAAAGTTT
1 GAGGGTAAAATGGTAATTTTTAGAAGATTTAGGGTTAAAAA-TGGAATTTTTAGACA-TTT
* *
79169 GGGGGTAAAAAT-GTAATTTTT-GTAAAATTTAGGGTTAAAAATGGAATTTTTAGA-AGTTT
1 GAGGGT-AAAATGGTAATTTTTAG-AAGATTTAGGGTTAAAAATGGAATTTTTAGACA-TTT
** * * *
79228 GAGGGTAAAATGGTAATTTTTAGAA-AGCTCGAGGTCAAAAATGGAATTTTTAGACATTC
1 GAGGGTAAAATGGTAATTTTTAGAAGATTTAG-GGTTAAAAATGGAATTTTTAGACATTT
* * * * * *
79287 GAGGGTAAAATGATAATTTTTTGGAGTTTTAGGGTTAAAAAAGGAATTTTTGGACATTT
1 GAGGGTAAAATGGTAATTTTTAGAAGATTTAGGGTTAAAAATGGAATTTTTAGACATTT
* * * *
79346 GGGGGTAAAATGGTAATTTTTAGAAGTTTTGGGGTCAAAA
1 GAGGGTAAAATGGTAATTTTTAGAAGATTTAGGGTTAAAA
79386 TATGATTTTA
Statistics
Matches: 266, Mismatches: 57, Indels: 26
0.76 0.16 0.07
Matches are distributed among these distances:
58 21 0.08
59 177 0.67
60 68 0.26
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (59 bp):
GAGGGTAAAATGGTAATTTTTAGAAGATTTAGGGTTAAAAATGGAATTTTTAGACATTT
Found at i:79382 original size:118 final size:115
Alignment explanation
Indices: 78991--79385 Score: 375
Period size: 118 Copynumber: 3.3 Consensus size: 115
78981 TGGACGCTTC
* * * ** * *
78991 GAGGGCAAAATAGAAATTTTTAGAAGGTTCGGGGTTGAAAATAGAATTTTTATACATTCGAGGGT
1 GAGGGTAAAATGGTAATTTTTAGAA-GTTCGGGGTCAAAAATGGAATTTTTAGACATTCGAGGGT
* ** ** * *
79056 AAAAT-AGTAACTTTTTGGAAATTTCATAGACAAATATGGAATTTTTGGATATTC
65 AAAATGA-TAA-TTTTTGG-AATTTTAGGGTTAAAAATGGAATTTTTGGA-ATTT
* * * * *
79110 GAGAGTAAAATGGTAATTTTTAGAAAATTCGGGGT-AAAAATTGGAA-TTTTAGAAAGTTTGGGG
1 GAGGGTAAAATGGTAATTTTTAG-AAGTTCGGGGTCAAAAA-TGGAATTTTTAGACA-TTCGAGG
* * *
79173 GTAAAAATG-TAATTTTTGTAAAATTTAGGGTTAAAAATGGAATTTTTAGAAGTTT
63 GT-AAAATGATAATTTTTG-GAATTTTAGGGTTAAAAATGGAATTTTTGGAA-TTT
* *
79228 GAGGGTAAAATGGTAATTTTTAGAAAGCTCGAGGTCAAAAATGGAATTTTTAGACATTCGAGGGT
1 GAGGGTAAAATGGTAATTTTTAG-AAGTTCGGGGTCAAAAATGGAATTTTTAGACATTCGAGGGT
* *
79293 AAAATGATAATTTTTTGGAGTTTTAGGGTTAAAAAAGGAATTTTTGGACATTT
65 AAAATGATAA-TTTTTGGAATTTTAGGGTTAAAAATGGAATTTTTGGA-ATTT
* *
79346 GGGGGTAAAATGGTAATTTTTAGAAGTTTTGGGGTCAAAA
1 GAGGGTAAAATGGTAATTTTTAGAAG-TTCGGGGTCAAAA
79386 TATGATTTTA
Statistics
Matches: 226, Mismatches: 37, Indels: 27
0.78 0.13 0.09
Matches are distributed among these distances:
117 10 0.04
118 148 0.65
119 61 0.27
120 7 0.03
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (115 bp):
GAGGGTAAAATGGTAATTTTTAGAAGTTCGGGGTCAAAAATGGAATTTTTAGACATTCGAGGGTA
AAATGATAATTTTTGGAATTTTAGGGTTAAAAATGGAATTTTTGGAATTT
Found at i:79386 original size:30 final size:30
Alignment explanation
Indices: 79116--79386 Score: 176
Period size: 30 Copynumber: 9.2 Consensus size: 30
79106 ATTCGAGAGT
**
79116 AAAATGGTAATTTTTAGAAAATTCGGGGTA
1 AAAATGGTAATTTTTAGAAGTTTCGGGGTA
*
79146 AAAATTGG-AA-TTTTAGAAAGTTTGGGGGTA
1 AAAA-TGGTAATTTTTAG-AAGTTTCGGGGTA
* * *
79176 AAAAT-GTAATTTTT-GTAAAATTTAGGGTTA
1 AAAATGGTAATTTTTAG--AAGTTTCGGGGTA
79206 AAAATGG-AATTTTTAGAAGTTT-GAGGGT-
1 AAAATGGTAATTTTTAGAAGTTTCG-GGGTA
* *
79234 AAAATGGTAATTTTTAGAAAG-CTCGAGGTCA
1 AAAATGGTAATTTTTAG-AAGTTTCGGGGT-A
79265 AAAATGG-AATTTTTAGACA--TTCGAGGGT-
1 AAAATGGTAATTTTTAGA-AGTTTCG-GGGTA
* * * * *
79293 AAAATGATAATTTTTTGGAGTTTTAGGGTTA
1 AAAATGGTAATTTTTAGAAG-TTTCGGGGTA
* * *
79324 AAAAAGG-AATTTTTGGACA-TTTGGGGGT-
1 AAAATGGTAATTTTTAGA-AGTTTCGGGGTA
* *
79352 AAAATGGTAATTTTTAGAAGTTTTGGGGTC
1 AAAATGGTAATTTTTAGAAGTTTCGGGGTA
79382 AAAAT
1 AAAAT
79387 ATGATTTTAG
Statistics
Matches: 191, Mismatches: 26, Indels: 48
0.72 0.10 0.18
Matches are distributed among these distances:
28 23 0.12
29 67 0.35
30 80 0.42
31 21 0.11
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
AAAATGGTAATTTTTAGAAGTTTCGGGGTA
Found at i:80345 original size:9 final size:9
Alignment explanation
Indices: 80331--80384 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
80321 TTTATATCCT
80331 TATTATTAA
1 TATTATTAA
*
80340 TATTATTAT
1 TATTATTAA
80349 TATTATTAA
1 TATTATTAA
*
80358 AATTATTTAA
1 TATTA-TTAA
80368 TA-TATTTAA
1 TATTA-TTAA
80377 TATGTATT
1 TAT-TATT
80385 TAATGCGTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
9 29 0.76
10 7 0.18
11 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
TATTATTAA
Found at i:81185 original size:17 final size:17
Alignment explanation
Indices: 81163--81206 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
81153 TAAATCGAAC
*
81163 TAAATTTAAATTTAAAA
1 TAAATTTAAACTTAAAA
* *
81180 TCAATTTAAACTTAATA
1 TAAATTTAAACTTAAAA
81197 TAAATTTAAA
1 TAAATTTAAA
81207 AGTTTGATCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
TAAATTTAAACTTAAAA
Found at i:82210 original size:49 final size:48
Alignment explanation
Indices: 82157--82525 Score: 242
Period size: 49 Copynumber: 7.4 Consensus size: 48
82147 ATGCTTTTGA
*
82157 GGTATATGGTTCGCCATTGCGACTTAAACCTTTCCCTTTATGTCTATGT
1 GGTATATGGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCT-TGT
* * ** *
82206 GGTATAAGGTTCGCCATTGCAACTTAAACCTTTCCCTTTGTATCTTCGT
1 GGTATATGGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTT-GT
* * * * * *
82255 GGTACTA-GATTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGA
1 GGTA-TATGGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCT-TGT
* * **
82304 GGTATAAGGTTCGCCATTGCAACTTAAACCTTTCCCTTTGTGTCTTTGT
1 GGTATATGGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTC-TTGT
* * * * **
82353 GTCTTCGTGTTACTGGATTCGCCGTTAC-AGCTTAAATCTTTCCCTTCATGTCTCTAA
1 G-----GT-ATA-TGG-TTCGCCATTGCGA-CTTAAACCTTTCCCTTCATGTCT-TGT
* * * *
82410 GGAAT-TAGGTTCGCCATTGTGACTTAAACCTTTCCCTTCGTATCTTCGT
1 GGTATAT-GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTT-GT
* * * * * *
82459 GGTAT-TAGATTAGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGA
1 GGTATAT-GGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTC-TTGT
*
82508 GGTATAAGGTTCGCCATT
1 GGTATATGGTTCGCCATT
82526 TTCCCTTCGT
Statistics
Matches: 244, Mismatches: 56, Indels: 40
0.72 0.16 0.12
Matches are distributed among these distances:
48 4 0.02
49 191 0.78
50 9 0.04
51 1 0.00
52 1 0.00
54 2 0.01
55 2 0.01
56 4 0.02
57 30 0.12
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.40
Consensus pattern (48 bp):
GGTATATGGTTCGCCATTGCGACTTAAACCTTTCCCTTCATGTCTTGT
Found at i:82299 original size:98 final size:98
Alignment explanation
Indices: 82166--82525 Score: 459
Period size: 98 Copynumber: 3.6 Consensus size: 98
82156 AGGTATATGG
* * * * * *
82166 TTCGCCATTGCGACTTAAACCTTTCCCTTTATGTCTATGTGGTATAAGGTTCGCCATTGCAACTT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCAACTT
82231 AAACCTTTCCCTTTGTATCTTCGTGGTACTAGA
66 AAACCTTTCCCTTTGTATCTTCGTGGTACTAGA
*
82264 TTCGTCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCAACTT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCAACTT
* * *
82329 AAACCTTTCCCTTTGTGTCTTTGTGTCTTCGTGTTACTGGA
66 AAACCTTT-CC-------CTTTGTATCTTCGTGGTACTAGA
* * * * * **
82370 TTCGCCGTTACAGCTTAAATCTTTCCCTTCATGTCTCTAAGGAATTAGGTTCGCCATTGTGACTT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCAACTT
* *
82435 AAACCTTTCCCTTCGTATCTTCGTGGTATTAGA
66 AAACCTTTCCCTTTGTATCTTCGTGGTACTAGA
* *
82468 TTAGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTTTGAGGTATAAGGTTCGCCATT
1 TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATT
82526 TTCCCTTCGT
Statistics
Matches: 224, Mismatches: 30, Indels: 16
0.83 0.11 0.06
Matches are distributed among these distances:
98 135 0.60
99 2 0.01
105 2 0.01
106 85 0.38
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (98 bp):
TTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGTCTCTGAGGTATAAGGTTCGCCATTGCAACTT
AAACCTTTCCCTTTGTATCTTCGTGGTACTAGA
Found at i:83029 original size:18 final size:18
Alignment explanation
Indices: 83003--83038 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
82993 AAAAATGCCG
*
83003 AATATTTATAAGGAACAA
1 AATAATTATAAGGAACAA
83021 AATAATTATAAGGAACAA
1 AATAATTATAAGGAACAA
83039 TATTAGATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.58, C:0.06, G:0.11, T:0.25
Consensus pattern (18 bp):
AATAATTATAAGGAACAA
Found at i:94350 original size:29 final size:28
Alignment explanation
Indices: 94293--94365 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 28
94283 CTTCGGAGGC
*
94293 AAAATAGTAATTTTTAGAAGGTTCGGGGTT
1 AAAATAGTAATTTTTAGAA-GTCCGGGG-T
94323 AAAATAG-AATTTTTAGACA-TCCGAGGGT
1 AAAATAGTAATTTTTAGA-AGTCCG-GGGT
*
94351 AAAATGGTAATTTTT
1 AAAATAGTAATTTTT
94366 TGGAAATTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 10 0.26
29 20 0.53
30 8 0.21
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.36
Consensus pattern (28 bp):
AAAATAGTAATTTTTAGAAGTCCGGGGT
Found at i:94415 original size:29 final size:29
Alignment explanation
Indices: 94350--94454 Score: 90
Period size: 29 Copynumber: 3.5 Consensus size: 29
94340 CATCCGAGGG
*
94350 TAAAATGGTAATTTTTTGGAAATTTC-GAGGT
1 TAAAATGG-AA-TTTTTGGAAAATTCGGA-GT
* * *
94381 CAAAATTAGAATTTTTGG-ATATTCAGGAG-
1 TAAAA-TGGAATTTTTGGAAAATTC-GGAGT
94410 TAAAATGGTAATTTTTGGAAAATTCGGAGT
1 TAAAATGG-AATTTTTGGAAAATTCGGAGT
94440 TAAAAATGGAATTTT
1 T-AAAATGGAATTTT
94455 AAAAAGTTCG
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
28 2 0.03
29 21 0.35
30 20 0.33
31 15 0.25
32 2 0.03
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.38
Consensus pattern (29 bp):
TAAAATGGAATTTTTGGAAAATTCGGAGT
Found at i:94422 original size:118 final size:118
Alignment explanation
Indices: 94293--94601 Score: 324
Period size: 118 Copynumber: 2.6 Consensus size: 118
94283 CTTCGGAGGC
* * * *
94293 AAAATAGTAATTTTTAGAAGGTTCGGGGTTAAAATAGAATTTTTAGACATCCGAGGGTAAAATGG
1 AAAATGGTAATTTTTAGAAAGTTCGGGGTTAAAATGGAATTTTTAGACATTCGAGGGTAAAATGG
* * *
94358 TAATTTTTTGG-AAATTTCGAGGTCAAAATTAGAATTTTTGGATA-TTCAGGAGT
66 TAATTTTTTGGAAAATTT-AAGGTCAAAAATAGAATTTTGGGA-AGTTCAGGAGT
* * * * * *
94411 AAAATGGTAATTTTTGGAAAATTCGGAGTTAAAAATGGAA-TTTTAAAAAGTTCGGGGGTAAAAA
1 AAAATGGTAATTTTTAGAAAGTTCGGGGTT-AAAATGGAATTTTTAGACA-TTCGAGGGT-AAAA
* ** *
94475 T-TTAA-TTTTTGGAAAATTTAAGGTCAAAAATAGAATTTTGGGAAGTTTGGGGGT
63 TGGTAATTTTTTGGAAAATTTAAGGTCAAAAATAGAATTTTGGGAAGTTCAGGAGT
* * * *
94529 AAAATGGTAATTTTTAGAAAGCTCGAGGTCAAAAATGGAATTTTTGGACATTC-AGGGATAAAAT
1 AAAATGGTAATTTTTAGAAAGTTCGGGGT-TAAAATGGAATTTTTAGACATTCGAGGG-TAAAAT
94593 GGTAATTTT
64 GGTAATTTT
94602 CAAGAGTTTC
Statistics
Matches: 153, Mismatches: 28, Indels: 19
0.76 0.14 0.09
Matches are distributed among these distances:
117 9 0.06
118 106 0.69
119 33 0.22
120 5 0.03
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (118 bp):
AAAATGGTAATTTTTAGAAAGTTCGGGGTTAAAATGGAATTTTTAGACATTCGAGGGTAAAATGG
TAATTTTTTGGAAAATTTAAGGTCAAAAATAGAATTTTGGGAAGTTCAGGAGT
Found at i:94472 original size:59 final size:59
Alignment explanation
Indices: 94347--94601 Score: 248
Period size: 59 Copynumber: 4.3 Consensus size: 59
94337 AGACATCCGA
* * * *
94347 GGGTAAAATGGTAATTTTTTGGAAATTTCGAGGTCAAAATTAGAATTTTTGGATA-TTCAG
1 GGGTAAAATGGTAA-TTTTTGGAAAATTCGAGGTCAAAAATAGAA-TTTTGGAAAGTTCGG
* * * **
94407 GAGTAAAATGGTAATTTTTGGAAAATTCG-GAGTTAAAAATGGAATTTTAAAAAGTTCGG
1 GGGTAAAATGGTAATTTTTGGAAAATTCGAG-GTCAAAAATAGAATTTTGGAAAGTTCGG
* ** * *
94466 GGGTAAAAAT-TTAATTTTTGGAAAATTTAAGGTCAAAAATAGAATTTTGGGAAGTTTGG
1 GGGT-AAAATGGTAATTTTTGGAAAATTCGAGGTCAAAAATAGAATTTTGGAAAGTTCGG
* ** * * *
94525 GGGTAAAATGGTAATTTTTAGAAAGCTCGAGGTCAAAAATGGAATTTTTGGACA-TTCAG
1 GGGTAAAATGGTAATTTTTGGAAAATTCGAGGTCAAAAATAGAA-TTTTGGAAAGTTCGG
*
94584 GGATAAAATGGTAATTTT
1 GGGTAAAATGGTAATTTT
94602 CAAGAGTTTC
Statistics
Matches: 158, Mismatches: 31, Indels: 13
0.78 0.15 0.06
Matches are distributed among these distances:
58 12 0.08
59 120 0.76
60 26 0.16
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.35
Consensus pattern (59 bp):
GGGTAAAATGGTAATTTTTGGAAAATTCGAGGTCAAAAATAGAATTTTGGAAAGTTCGG
Found at i:95643 original size:9 final size:9
Alignment explanation
Indices: 95629--95682 Score: 56
Period size: 9 Copynumber: 5.8 Consensus size: 9
95619 TTTATATCCT
95629 TATTATTAA
1 TATTATTAA
*
95638 TATTATTAT
1 TATTATTAA
95647 TATTATTAA
1 TATTATTAA
*
95656 AATTATTTAA
1 TATTA-TTAA
95666 TA-TATTTAA
1 TATTA-TTAA
95675 TATGTATT
1 TAT-TATT
95683 TAATGCGTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
9 29 0.76
10 7 0.18
11 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
TATTATTAA
Found at i:96923 original size:44 final size:44
Alignment explanation
Indices: 96868--96952 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
96858 TTTAATTTTG
* *
96868 GCCTAATTTATTAATTATATTTGGTGTAAGGTGTTAAATTTGAT
1 GCCTAATTTATTAATTATATTCGGTGTAAGGTGTCAAATTTGAT
*
96912 GCCTAATTTATTAATTTTATTCGGTGTAAGGTGTCAAATTT
1 GCCTAATTTATTAATTATATTCGGTGTAAGGTGTCAAATTT
96953 ATTTTTGGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.47
Consensus pattern (44 bp):
GCCTAATTTATTAATTATATTCGGTGTAAGGTGTCAAATTTGAT
Found at i:104191 original size:100 final size:100
Alignment explanation
Indices: 104018--104217 Score: 382
Period size: 100 Copynumber: 2.0 Consensus size: 100
104008 TATTATTATT
104018 ATTATTAATTATTTATTTATGGTTAATAAAGTGTTTAGTAATAAATATGAAACAGATAACAATTA
1 ATTATTAATTATTTATTTATGGTTAATAAAGTGTTTAGTAATAAATATGAAACAGATAACAATTA
104083 ATACATATATTAATACGTAATAAATGATAACCAAA
66 ATACATATATTAATACGTAATAAATGATAACCAAA
* *
104118 ATTATTAATTATTTATTTATGGTTAATAAAGTGTTTAGTAATAAATATGAAACAGATGACAGTTA
1 ATTATTAATTATTTATTTATGGTTAATAAAGTGTTTAGTAATAAATATGAAACAGATAACAATTA
104183 ATACATATATTAATACGTAATAAATGATAACCAAA
66 ATACATATATTAATACGTAATAAATGATAACCAAA
104218 CCTACTAATA
Statistics
Matches: 98, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 98 1.00
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (100 bp):
ATTATTAATTATTTATTTATGGTTAATAAAGTGTTTAGTAATAAATATGAAACAGATAACAATTA
ATACATATATTAATACGTAATAAATGATAACCAAA
Found at i:104889 original size:17 final size:17
Alignment explanation
Indices: 104864--104922 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 17
104854 GGACTTTTAA
* **
104864 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
104881 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
104898 TTAAA-TTTAAAGCAAAT
1 TTAAATTTTAAA-TAAAT
104915 TTAAATTT
1 TTAAATTT
104923 AAAAGATAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
16 5 0.15
17 27 0.79
18 2 0.06
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:104893 original size:6 final size:6
Alignment explanation
Indices: 104879--104925 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
104869 TTTTAAATCC
* **
104879 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAA A-GCAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
104925 A
1 A
104926 AGATAAATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 7 0.21
6 26 0.79
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:104923 original size:17 final size:17
Alignment explanation
Indices: 104879--104925 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
104869 TTTTAAATCC
* **
104879 ATTTAAATTTTAATTAA
1 ATTTAAATTTAAAGCAA
104896 ATTTAAATTTAAAGCAA
1 ATTTAAATTTAAAGCAA
104913 ATTTAAATTTAAA
1 ATTTAAATTTAAA
104926 AGATAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
ATTTAAATTTAAAGCAA
Found at i:111753 original size:23 final size:22
Alignment explanation
Indices: 111727--111770 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
111717 ATTTTTAAAT
111727 TATTAAACAT-TTTAATGTTTATA
1 TATTAAA-ATATTTAA-GTTTATA
*
111750 TATTGAAATATTTAAGTTTAT
1 TATTAAAATATTTAAGTTTAT
111771 TTTTTTACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (22 bp):
TATTAAAATATTTAAGTTTATA
Found at i:112224 original size:17 final size:17
Alignment explanation
Indices: 112191--112336 Score: 202
Period size: 17 Copynumber: 8.4 Consensus size: 17
112181 CCAAATTCCC
112191 TTTAAATTTATTTTAAAA
1 TTTAAATTTATTTT-AAA
* * *
112209 ATTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
112226 TTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
112244 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
112261 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
112278 TTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAA
*
112295 TTTAAATTTAATTTCAAA
1 TTTAAATTT-ATTTTAAA
* *
112313 TTTAAAATTATTATAAA
1 TTTAAATTTATTTTAAA
112330 TTTAAAT
1 TTTAAAT
112337 AAAGCTAAAA
Statistics
Matches: 113, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
17 74 0.65
18 39 0.35
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:112239 original size:11 final size:11
Alignment explanation
Indices: 112225--112281 Score: 62
Period size: 11 Copynumber: 5.1 Consensus size: 11
112215 TTTGTTTAAA
112225 ATTTTAAATTT
1 ATTTTAAATTT
112236 ATTTTAAATTT
1 ATTTTAAATTT
* *
112247 AAATTT-ATTTT
1 -ATTTTAAATTT
*
112258 AAATTTAAATTT
1 -ATTTTAAATTT
112270 ATTTTAAATTT
1 ATTTTAAATTT
112281 A
1 A
112282 AATTTATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
11 32 0.80
12 8 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:112247 original size:6 final size:6
Alignment explanation
Indices: 112227--112336 Score: 99
Period size: 6 Copynumber: 19.2 Consensus size: 6
112217 TGTTTAAAAT
* * *
112227 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
112272 TTTAAA TTTAAA TTT-AT TTTGAA TTTAAA TTT-AA TTTCAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA
*
112319 ATT--A TTATAAA TTTAAA T
1 TTTAAA TT-TAAA TTTAAA T
112337 AAAGCTAAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
4 2 0.02
5 22 0.26
6 52 0.62
7 8 0.10
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:112265 original size:34 final size:34
Alignment explanation
Indices: 112191--112336 Score: 202
Period size: 35 Copynumber: 4.2 Consensus size: 34
112181 CCAAATTCCC
* * *
112191 TTTAAATTTATTTTAAAAATTAAATTTGTTTAAAA
1 TTTAAATTTATTTT-AAATTTAAATTTATTTTAAA
112226 TTTTAAATTTATTTTAAATTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
*
112261 TTTAAATTTATTTTAAATTTAAATTTATTTTGAA
1 TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
* * *
112295 TTTAAATTTAATTTCAAATTTAAAATTATTATAAA
1 TTTAAATTT-ATTTTAAATTTAAATTTATTTTAAA
112330 TTTAAAT
1 TTTAAAT
112337 AAAGCTAAAA
Statistics
Matches: 101, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
34 42 0.42
35 45 0.45
36 14 0.14
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (34 bp):
TTTAAATTTATTTTAAATTTAAATTTATTTTAAA
Done.