Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012683.1 Kokia drynarioides strain JFW-HI SEQ_127694, 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: 83295
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1153 original size:6 final size:6
Alignment explanation
Indices: 1142--1205 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
1132 ATTTTTTTTA
** *
1142 AAATTT AAATTT --ATCTT AAATTT AAATTT ATCTTTT AAAATT AAATTT
1 AAATTT AAATTT AAAT-TT AAATTT AAATTT A-AATTT AAATTT AAATTT
*
1190 -AATTA AAATTT AAATT
1 AAATTT AAATTT AAATT
1206 GTTTTAAAAC
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
4 2 0.04
5 6 0.13
6 31 0.69
7 6 0.13
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (6 bp):
AAATTT
Found at i:1164 original size:17 final size:17
Alignment explanation
Indices: 1142--1205 Score: 76
Period size: 17 Copynumber: 3.6 Consensus size: 17
1132 ATTTTTTTTA
1142 AAATTTAAATTTATCTT
1 AAATTTAAATTTATCTT
1159 AAATTTAAATTTATCTTTT
1 AAATTTAAATTTATC--TT
* *
1178 AAAATTAAATTTAAT-TA
1 AAATTTAAATTT-ATCTT
1195 AAATTTAAATT
1 AAATTTAAATT
1206 GTTTTAAAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 26 0.63
19 13 0.32
20 2 0.05
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATTTAAATTTATCTT
Found at i:1199 original size:36 final size:35
Alignment explanation
Indices: 1130--1219 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 35
1120 AAATTGATTC
*
1130 AAATTTTTTTTAAAATTTAAATTTATCTTAAATTT
1 AAATTTTTTTTAAAATTTAAATTTATCTAAAATTT
1165 AAATTTATCTTTTAAAA-TTAAATTTAAT-TAAAATTT
1 AAATTT-T-TTTTAAAATTTAAATTT-ATCTAAAATTT
* *
1201 AAA-TTGTTTTAAAACTTAA
1 AAATTTTTTTTAAAATTTAA
1220 CTAAATAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
33 8 0.16
34 4 0.08
35 8 0.16
36 19 0.39
37 10 0.20
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (35 bp):
AAATTTTTTTTAAAATTTAAATTTATCTAAAATTT
Found at i:1212 original size:17 final size:16
Alignment explanation
Indices: 1135--1219 Score: 66
Period size: 17 Copynumber: 4.9 Consensus size: 16
1125 GATTCAAATT
1135 TTTTTTAAAATTTAAA
1 TTTTTTAAAATTTAAA
1151 TTTATCTT-AAATTTAAA
1 TTT-T-TTAAAATTTAAA
1168 TTTATCTTTTAAAA-TTAAA
1 --T-T-TTTTAAAATTTAAA
*
1187 TTTAATTAAAATTTAAA
1 TTT-TTTAAAATTTAAA
*
1204 TTGTTTTAAAACTTAA
1 TT-TTTTAAAATTTAA
1220 CTAAATAAAA
Statistics
Matches: 56, Mismatches: 3, Indels: 19
0.72 0.04 0.24
Matches are distributed among these distances:
15 1 0.02
16 10 0.18
17 28 0.50
18 3 0.05
19 8 0.14
20 5 0.09
21 1 0.02
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.52
Consensus pattern (16 bp):
TTTTTTAAAATTTAAA
Found at i:2238 original size:29 final size:29
Alignment explanation
Indices: 2197--2662 Score: 402
Period size: 30 Copynumber: 15.8 Consensus size: 29
2187 AGAGGTTCCT
*
2197 AAACTGTCTAAAAATTCCATTTTT-CCCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
* *
2226 GAACTTCCAAAAATTCCATTTTTGCCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * *
2255 GAACTTTCAAAAATTCCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* * *
2285 AAACTTCCAAAAATCCCATTTATGCCCCC
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * * *
2314 GAACTTCCAAAAATTTCATTTTTGACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* *
2344 AAACATCCAAAAATTCCATTTTTACCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* *
2373 AAACTTCTAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* * * *
2403 AAATTTTCAAAAATTCCATTTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* * *
2433 AAACTTTCAAAAATTCCATTTTTAAGCCCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
*
2463 AAACTTCCAAAAACTCCATTTTTACCCCCTC
1 AAACTTCCAAAAATTCCATTTTTA-CCCC-C
* * *
2494 GAACTTCCAAAAATTCCATTTTTGACACCG
1 AAACTTCCAAAAATTCCATTTTT-ACCCCC
* * *
2524 AAACTTCTAAAAATTCCATTTTTATCCCT
1 AAACTTCCAAAAATTCCATTTTTACCCCC
* * *
2553 AAACTTCCAAAAATTCCATTTTAAACCTCG
1 AAACTTCCAAAAATTCCATTTT-TACCCCC
*
2583 AAAC-TCTC-AAAATTACC-CTTTTACCCCC
1 AAACTTC-CAAAAATT-CCATTTTTACCCCC
* * * *
2611 GAA-TATCTAAAAATTTCATTTTTAACCCC
1 AAACT-TCCAAAAATTCCATTTTTACCCCC
*
2640 AAACTTCCCAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
2663 GTCCCCGAGA
Statistics
Matches: 353, Mismatches: 68, Indels: 31
0.78 0.15 0.07
Matches are distributed among these distances:
28 24 0.07
29 141 0.40
30 163 0.46
31 24 0.07
32 1 0.00
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTACCCCC
Found at i:2304 original size:59 final size:58
Alignment explanation
Indices: 2206--2662 Score: 422
Period size: 59 Copynumber: 7.7 Consensus size: 58
2196 TAAACTGTCT
* ** *
2206 AAAAATTCCATTTTT-CCCCCGAACTTCCAAAAATTCCATTTTTGCCCCCGAACTTTC
1 AAAAATTCCATTTTTGACCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTTC
* * * *
2263 AAAAATTCCATTTTTGACCTCAAAACTTCCAAAAATCCCATTTATGCCCCCGAACTTCC
1 AAAAATTCCATTTTTGACC-CAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTTC
* * **
2322 AAAAATTTCATTTTTGACCTCAAAACATCCAAAAATTCCATTTTTACCCCTAAAC-TTC
1 AAAAATTCCATTTTTGACC-CAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTTC
* * * **
2380 TAAAAATTCCATTTTTGACCCCAAAATTTTCAAAAATTCCATTTTTAACCTCAAAACTTTC
1 -AAAAATTCCATTTTTGA-CCCAAAACTTCCAAAAATTCCATTTTT-ACCCCCGAACTTTC
* * * *
2441 AAAAATTCCATTTTTAAGCCCGAAACTTCCAAAAACTCCATTTTTACCCCCTCGAACTTCC
1 AAAAATTCCATTTTTGA-CCCAAAACTTCCAAAAATTCCATTTTTA-CCCC-CGAACTTTC
* * * ** *
2502 AAAAATTCCATTTTTGACACCGAAACTTCTAAAAATTCCATTTTTATCCCTAAACTTCC
1 AAAAATTCCATTTTTGAC-CCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTTC
** * * *
2561 AAAAATTCCATTTTAAACCTCGAAAC-TCTC-AAAATTACC-CTTTTACCCCCGAA-TATC
1 AAAAATTCCATTTTTGACC-CAAAACTTC-CAAAAATT-CCATTTTTACCCCCGAACTTTC
* * * *
2618 TAAAAATTTCATTTTTAACCCCAAACTTCCCAAAATTACCATTTT
1 -AAAAATTCCATTTTTGACCCAAAACTTCCAAAAATT-CCATTTT
2663 GTCCCCGAGA
Statistics
Matches: 335, Mismatches: 49, Indels: 30
0.81 0.12 0.07
Matches are distributed among these distances:
57 23 0.07
58 51 0.15
59 155 0.46
60 56 0.17
61 50 0.15
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.33
Consensus pattern (58 bp):
AAAAATTCCATTTTTGACCCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTTC
Found at i:3026 original size:96 final size:94
Alignment explanation
Indices: 2920--3103 Score: 237
Period size: 95 Copynumber: 1.9 Consensus size: 94
2910 ATAAAAACTA
* * * *
2920 TAATCGAGGCAATATTAT-TTTAT-TTCGAGTTTTGAAAATTTGCGTATTAACTTACTAGGTGCA
1 TAATCGAGGCAATATT-TCCTTATCTTCGA-TTCTG-AAATTTACGCATTAACTTACTAGGTGCA
**
2983 ATTTTTCTTCAAATCGAAATAATCGAATACCCT
63 A-CCTTCTTCAAATCGAAATAATCGAATACCCT
* *
3016 TAATCGAGGCAATGTTTCCTTATCTTCGATTCTGAAATTTACGCCTTAACTTACTAGGTGCAACC
1 TAATCGAGGCAATATTTCCTTATCTTCGATTCTGAAATTTACGCATTAACTTACTAGGTGCAACC
*
3081 TTCTTCAAATCGAGATAATCGAA
66 TTCTTCAAATCGAAATAATCGAA
3104 ATCTTTTTCC
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
94 22 0.29
95 27 0.35
96 23 0.30
97 5 0.06
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (94 bp):
TAATCGAGGCAATATTTCCTTATCTTCGATTCTGAAATTTACGCATTAACTTACTAGGTGCAACC
TTCTTCAAATCGAAATAATCGAATACCCT
Found at i:6972 original size:22 final size:21
Alignment explanation
Indices: 6931--6973 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
6921 CCTAAACAAA
*
6931 TAGAGGAAAAATACAGGCGAT
1 TAGAGGAAAAATACACGCGAT
6952 TAGAGGAGAAAAT-CGACGCGAT
1 TAGAGGA-AAAATAC-ACGCGAT
6974 GCAGGGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.44, C:0.12, G:0.30, T:0.14
Consensus pattern (21 bp):
TAGAGGAAAAATACACGCGAT
Found at i:11466 original size:15 final size:15
Alignment explanation
Indices: 11446--11475 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
11436 TGGGAGATTG
11446 GCTCGATGGCAAATC
1 GCTCGATGGCAAATC
11461 GCTCGATGGCAAATC
1 GCTCGATGGCAAATC
11476 TTACTCTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (15 bp):
GCTCGATGGCAAATC
Found at i:14530 original size:116 final size:116
Alignment explanation
Indices: 14324--14532 Score: 305
Period size: 116 Copynumber: 1.8 Consensus size: 116
14314 TAATATGGTT
* *
14324 ATCTTCCTGATGAGATACAAAGAAGAATACCAACTCAGGGCTCGATGTAATCAAATCTTCGAATC
1 ATCTTCCTGATGAGATACAAAGAAGAATACCAACTCAGGGCTCGATGTAATCAAATCTTCAAACC
* **
14389 CCAGCTTCCTGATAAGATACAGAGAAGCGGATTGAAACAAGTAAGGCTGTA
66 CCAACTTCAAGATAAGATACAGAGAAGCGGATTGAAACAAGTAAGGCTGTA
* *
14440 ATCTTCCTGATGAGATACAGAGAAGAATACTAACTCAGGGCTCGATACG-AA-CAAATCTTCAAA
1 ATCTTCCTGATGAGATACAAAGAAGAATACCAACTCAGGGCTCGAT--GTAATCAAATCTTCAAA
* *
14503 CCCCAACTTCAAGATGAGATACTGAGAAGC
64 CCCCAACTTCAAGATAAGATACAGAGAAGC
14533 AGGTCGAAGC
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
116 79 0.96
117 2 0.02
118 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (116 bp):
ATCTTCCTGATGAGATACAAAGAAGAATACCAACTCAGGGCTCGATGTAATCAAATCTTCAAACC
CCAACTTCAAGATAAGATACAGAGAAGCGGATTGAAACAAGTAAGGCTGTA
Found at i:14815 original size:205 final size:205
Alignment explanation
Indices: 14491--15090 Score: 795
Period size: 205 Copynumber: 2.9 Consensus size: 205
14481 TCGATACGAA
* * * *
14491 CAAATCTTCAAACCCCAACTTCAAGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCA
1 CAAATCTTCGAACCCCAGCTTCATGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAA-GGTTA
* * *
14556 GCTTCCTGATGAGATACTGAGAAGTGAACTAAATTCGTCTTCCGGATGAGATACAGAGAAGCGAA
65 GCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGAA
* * * *
14621 TTGAAATAAACGACGCGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
130 TTAAAAAAAATGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACG
* *
14686 CTTGATGTAAG
195 CTCGATATAAG
* * * *
14697 CAAATCTTCGAACCCCAGCTTCTTGATGAGACATTGAGAAGCAGGTCAAAGCAATAAAAGGTTAG
1 CAAATCTTCGAACCCCAGCTTCATGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
* * * * *
14762 CTTCCTGATGAGATATTGAGAAGTGGACCAAATTCGTCTTTCTGATGAGATACAAAGAGGTGAAT
66 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGAAT
* * *
14827 TAAAACAAATGACGTGGTCATCTCCCTGATGAGACACTGAGAAGAAGACCAAATCAAACCCACGC
131 TAAAAAAAATGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
*
14892 TCGATATGAG
196 TCGATATAAG
* * * *
14902 TAAATCTTCGAATCCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAATGGTTAG
1 CAAATCTTCGAACCCCAGCTTCATGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
* * * * * **
14967 CTTCCTGTTGAAATACTGAGAAGTGAACCAAATTCGTCTTCCTGATAAAACACAGAGAAGTGGGT
66 CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGAAT
** * * *
15032 TAAAAAACAAGTGATATGGTCGTCTTCCTGATGAGATACTGAGAAGAAGGCCAAGTCAA
131 TAAAAAA-AA-TGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAA
15091 TGAAACCAGA
Statistics
Matches: 340, Mismatches: 52, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
205 245 0.72
206 54 0.16
207 41 0.12
ACGTcount: A:0.36, C:0.19, G:0.22, T:0.23
Consensus pattern (205 bp):
CAAATCTTCGAACCCCAGCTTCATGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAGGTTAG
CTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGAAT
TAAAAAAAATGACGTGGTCATCTTCCTGATGAGATACTGAGAAGAAGACCAAATCAAACCCACGC
TCGATATAAG
Found at i:15474 original size:12 final size:12
Alignment explanation
Indices: 15466--15538 Score: 71
Period size: 11 Copynumber: 6.2 Consensus size: 12
15456 CAAATTTATT
15466 TTTAAATTTAAA
1 TTTAAATTTAAA
15478 TTT--ATCTTAAA
1 TTTAAAT-TTAAA
**
15489 TTTAAATTTATCT
1 TTTAAATTTA-AA
15502 TTTAAATTTAAA
1 TTTAAATTTAAA
**
15514 TTT-GCTTTAAA
1 TTTAAATTTAAA
15525 TTTAAATTTAAA
1 TTTAAATTTAAA
15537 TT
1 TT
15539 GATTTAAAAC
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
10 2 0.04
11 17 0.35
12 17 0.35
13 12 0.25
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:15475 original size:6 final size:6
Alignment explanation
Indices: 15466--15538 Score: 71
Period size: 6 Copynumber: 12.3 Consensus size: 6
15456 CAAATTTATT
**
15466 TTTAAA TTTAAA TTT--A TCTTAAA TTTAAA TTTATCT TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTA-AA TTTAAA TTTAAA
**
15514 TTT-GC TTTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
15539 GATTTAAAAC
Statistics
Matches: 54, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
4 2 0.04
5 5 0.09
6 41 0.76
7 6 0.11
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:15489 original size:17 final size:18
Alignment explanation
Indices: 15457--15534 Score: 115
Period size: 17 Copynumber: 4.4 Consensus size: 18
15447 AAATTGATTC
*
15457 AAATTTATTTTTAAATTT
1 AAATTTATCTTTAAATTT
15475 AAATTTATC-TTAAATTT
1 AAATTTATCTTTAAATTT
15492 AAATTTATCTTTTAAATTT
1 AAATTTATC-TTTAAATTT
*
15511 AAATTT-GCTTTAAATTT
1 AAATTTATCTTTAAATTT
15528 AAATTTA
1 AAATTTA
15535 AATTGATTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
17 32 0.58
18 9 0.16
19 14 0.25
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (18 bp):
AAATTTATCTTTAAATTT
Found at i:15508 original size:36 final size:35
Alignment explanation
Indices: 15457--15534 Score: 122
Period size: 36 Copynumber: 2.2 Consensus size: 35
15447 AAATTGATTC
*
15457 AAATTTATTTTTAAATTTAAATTT-ATCTTAAATTT
1 AAATTTATTTTTAAATTTAAATTTGCT-TTAAATTT
15492 AAATTTATCTTTTAAATTTAAATTTGCTTTAAATTT
1 AAATTTAT-TTTTAAATTTAAATTTGCTTTAAATTT
15528 AAATTTA
1 AAATTTA
15535 AATTGATTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
35 8 0.20
36 31 0.77
37 1 0.03
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (35 bp):
AAATTTATTTTTAAATTTAAATTTGCTTTAAATTT
Found at i:15532 original size:23 final size:22
Alignment explanation
Indices: 15466--15546 Score: 63
Period size: 17 Copynumber: 4.0 Consensus size: 22
15456 CAAATTTATT
*
15466 TTTAAATTTAAATTTATCTTAAA
1 TTTAAATTTAAATTGAT-TTAAA
15489 TTTAAATTT--ATCT--TTTAAA
1 TTTAAATTTAAAT-TGATTTAAA
*
15508 TTTAAA--T---TTGCTTTAAA
1 TTTAAATTTAAATTGATTTAAA
15525 TTTAAATTTAAATTGATTTAAA
1 TTTAAATTTAAATTGATTTAAA
15547 ACTTAATTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 17
0.73 0.01 0.25
Matches are distributed among these distances:
15 1 0.02
16 1 0.02
17 13 0.27
19 12 0.24
20 1 0.02
21 2 0.04
22 10 0.20
23 9 0.18
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTAAATTTAAATTGATTTAAA
Found at i:15552 original size:23 final size:22
Alignment explanation
Indices: 15503--15559 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 22
15493 AATTTATCTT
* *
15503 TTAAATTTAAATTTGCTTTAAAT
1 TTAAATTTAAA-TTGATTTAAAC
15526 TTAAATTTAAATTGATTTAAAAC
1 TTAAATTTAAATTGATTT-AAAC
15549 TT-AA-TTAAATT
1 TTAAATTTAAATT
15560 AAAGTCCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 7 0.23
22 8 0.26
23 16 0.52
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.49
Consensus pattern (22 bp):
TTAAATTTAAATTGATTTAAAC
Found at i:16344 original size:16 final size:16
Alignment explanation
Indices: 16320--16351 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
16310 TGTAATAATG
16320 ATAACATTAATAATAA
1 ATAACATTAATAATAA
*
16336 ATAATATTAATAATAA
1 ATAACATTAATAATAA
16352 CATTAATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAACATTAATAATAA
Found at i:16895 original size:36 final size:36
Alignment explanation
Indices: 16855--16932 Score: 147
Period size: 36 Copynumber: 2.2 Consensus size: 36
16845 AAACCGGCGA
*
16855 CGTTTTGGTCTAGGCTCTTAAGCCCCAAAACGGTGC
1 CGTTTTGGTCTAGGCTCTTAAGCCCCAAAACGGTAC
16891 CGTTTTGGTCTAGGCTCTTAAGCCCCAAAACGGTAC
1 CGTTTTGGTCTAGGCTCTTAAGCCCCAAAACGGTAC
16927 CGTTTT
1 CGTTTT
16933 ACTTGTTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.19, C:0.27, G:0.23, T:0.31
Consensus pattern (36 bp):
CGTTTTGGTCTAGGCTCTTAAGCCCCAAAACGGTAC
Found at i:17497 original size:57 final size:57
Alignment explanation
Indices: 17345--17633 Score: 275
Period size: 57 Copynumber: 5.0 Consensus size: 57
17335 CTCGGTAGGT
17345 CCCTAAACTGTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTGA
1 CCCTAAACT-TCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCA-TTTTGA
* * * * * * *
17404 CCCCAAAACATCCAAAAAATCCATTTTTGCGCCCGAACTTCCAAAAACTCCATTTAGA
1 -CCCTAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTGA
*
17462 CCCTAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTTA
1 CCCTAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTGA
* * * * *
17519 CCCTCGAACTT-CAAAAATT-CATTTTAAACCTCGAAAC-TCTC-AAAATTACCCTTTT-A
1 CCCT-AAACTTCCAAAAATTCCATTTTTACCCCCG-AACTTC-CAAAAATT-CCATTTTGA
* * * * *
17575 CCCTCGAA-TGTCTAAAAATTTCATTTTTAACCCCGAACTTTCCCAAAATTACCATTTTG
1 CCCT-AAACT-TCCAAAAATTCCATTTTTACCCCCGAAC-TTCCAAAAATT-CCATTTTG
17634 TCCCCGAGAA
Statistics
Matches: 194, Mismatches: 24, Indels: 22
0.81 0.10 0.09
Matches are distributed among these distances:
55 1 0.01
56 29 0.15
57 81 0.42
58 23 0.12
59 53 0.27
60 7 0.04
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (57 bp):
CCCTAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCAAAAATTCCATTTTGA
Found at i:17516 original size:28 final size:29
Alignment explanation
Indices: 17350--17632 Score: 256
Period size: 29 Copynumber: 9.7 Consensus size: 29
17340 TAGGTCCCTA
17350 AACTGTCCAAAAATTCCATTTTTACCCCCG
1 AACT-TCCAAAAATTCCATTTTTACCCCCG
**
17380 AACTTCCAAAAATTCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTT-ACCCCCG
* * * *
17410 AACATCCAAAAAATCCATTTTTGCGCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* ** **
17439 AACTTCCAAAAACTCCATTTAGA-CCCTA
1 AACTTCCAAAAATTCCATTTTTACCCCCG
17467 AACTTCCAAAAATTCCATTTTTACCCCCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
*
17496 AACTTCCAAAAATTCCATTTTTACCCTCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* * *
17525 AACTT-CAAAAATT-CATTTTAAACCTCG
1 AACTTCCAAAAATTCCATTTTTACCCCCG
* *
17552 AAAC-TCTC-AAAATTACC-CTTTTACCCTCG
1 -AACTTC-CAAAAATT-CCATTTTTACCCCCG
* * *
17581 AA-TGTCTAAAAATTTCATTTTTAACCCCG
1 AACT-TCCAAAAATTCCATTTTTACCCCCG
*
17610 AACTTTCCCAAAATTACCATTTT
1 AAC-TTCCAAAAATT-CCATTTT
17633 GTCCCCGAGA
Statistics
Matches: 204, Mismatches: 35, Indels: 27
0.77 0.13 0.10
Matches are distributed among these distances:
27 13 0.06
28 42 0.21
29 104 0.51
30 38 0.19
31 7 0.03
ACGTcount: A:0.34, C:0.30, G:0.05, T:0.31
Consensus pattern (29 bp):
AACTTCCAAAAATTCCATTTTTACCCCCG
Found at i:17666 original size:28 final size:29
Alignment explanation
Indices: 17617--17681 Score: 78
Period size: 28 Copynumber: 2.2 Consensus size: 29
17607 CCGAACTTTC
**
17617 CCAAAATTACCATTTT-GTCCCCGAGAAT
1 CCAAAATTACCATTTTACCCCCCGAGAAT
* *
17645 CCAAATTTACCATTTTACCCCCCGAGTAT
1 CCAAAATTACCATTTTACCCCCCGAGAAT
17674 CCGAAAAT
1 CC-AAAAT
17682 CTCATTTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 15 0.50
29 11 0.37
30 4 0.13
ACGTcount: A:0.32, C:0.31, G:0.09, T:0.28
Consensus pattern (29 bp):
CCAAAATTACCATTTTACCCCCCGAGAAT
Found at i:23302 original size:15 final size:15
Alignment explanation
Indices: 23282--23312 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23272 GCTAGTTTTC
23282 TACTGTTTCCAGTTG
1 TACTGTTTCCAGTTG
*
23297 TACTGTTTCTAGTTG
1 TACTGTTTCCAGTTG
23312 T
1 T
23313 GCGTTTGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.19, T:0.52
Consensus pattern (15 bp):
TACTGTTTCCAGTTG
Found at i:27059 original size:18 final size:17
Alignment explanation
Indices: 27016--27061 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 17
27006 CTTAATGATG
27016 CTTTTATAAGAATTTTA
1 CTTTTATAAGAATTTTA
*
27033 CTCTTATAAGAATGTTCT-
1 CTTTTATAAGAAT-TT-TA
27051 CTTTTATAAGA
1 CTTTTATAAGA
27062 GAAGTTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.48
18 12 0.48
19 1 0.04
ACGTcount: A:0.33, C:0.11, G:0.09, T:0.48
Consensus pattern (17 bp):
CTTTTATAAGAATTTTA
Found at i:27912 original size:40 final size:38
Alignment explanation
Indices: 27868--27963 Score: 106
Period size: 40 Copynumber: 2.5 Consensus size: 38
27858 TAATTAATAG
27868 ATTTTTTAAATTTTAAAATT-TTAAAGAAAGTATAAAAAAT
1 ATTTTTTAAATTTTAAAATTATTAAA-AAAGT-T-AAAAAT
* * * *
27908 ATTTTTAAAAATTTAAGAATTATTAAAAATGTTAAACAT
1 ATTTTTTAAATTTTAA-AATTATTAAAAAAGTTAAAAAT
27947 ATTTTTT-AATTTTAAAA
1 ATTTTTTAAATTTTAAAA
27964 AAGTAATTAA
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
37 2 0.04
38 7 0.15
39 11 0.23
40 15 0.31
41 8 0.17
42 5 0.10
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (38 bp):
ATTTTTTAAATTTTAAAATTATTAAAAAAGTTAAAAAT
Found at i:27915 original size:39 final size:37
Alignment explanation
Indices: 27870--27963 Score: 100
Period size: 39 Copynumber: 2.4 Consensus size: 37
27860 ATTAATAGAT
27870 TTTTTAAATTTTAAAATT-TTAAAGAAAGTATAAAAAATA
1 TTTTTAAATTTTAAAATTATTAAA-AAAGT-T-AAAAATA
* * *
27909 TTTTTAAAAATTTAAGAATTATTAAAAATGTTAAACATA
1 TTTTT-AAATTTTAA-AATTATTAAAAAAGTTAAAAATA
*
27948 TTTTTTAATTTTAAAA
1 TTTTTAAATTTTAAAA
27964 AAGTAATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
37 2 0.04
38 7 0.15
39 16 0.34
40 9 0.19
41 8 0.17
42 5 0.11
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTTTAAATTTTAAAATTATTAAAAAAGTTAAAAATA
Found at i:32579 original size:4 final size:4
Alignment explanation
Indices: 32570--32596 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
32560 CTTTAAAATA
32570 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
32597 ATGAGCATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:32761 original size:4 final size:4
Alignment explanation
Indices: 32752--32778 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
32742 CTTTAAAATA
32752 TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
32779 ACGGTAATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.22, T:0.52
Consensus pattern (4 bp):
TATG
Found at i:34947 original size:11 final size:11
Alignment explanation
Indices: 34933--34978 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 11
34923 ATATCCAACC
34933 AATAATAATAA
1 AATAATAATAA
**
34944 AATAATAGCAA
1 AATAATAATAA
*
34955 TATAATAATAA
1 AATAATAATAA
*
34966 AATAACAATAA
1 AATAATAATAA
34977 AA
1 AA
34979 CAGTGACAAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (11 bp):
AATAATAATAA
Found at i:35529 original size:19 final size:18
Alignment explanation
Indices: 35492--35525 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
35482 TTTAAAATAT
*
35492 AATAATTTTAAAATTTTC
1 AATAAATTTAAAATTTTC
35510 AATAAATTT-AAATTTT
1 AATAAATTTAAAATTTT
35526 TTCATCCAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
AATAAATTTAAAATTTTC
Found at i:35991 original size:15 final size:15
Alignment explanation
Indices: 35971--36001 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35961 CCCCTAAATA
*
35971 AAATCTTTTCAATTT
1 AAATCTTTTAAATTT
35986 AAATCTTTTAAATTT
1 AAATCTTTTAAATTT
36001 A
1 A
36002 TTAAAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (15 bp):
AAATCTTTTAAATTT
Found at i:36020 original size:16 final size:17
Alignment explanation
Indices: 35992--36026 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
35982 ATTTAAATCT
35992 TTTAAATTTATTAAAAA
1 TTTAAATTTATTAAAAA
36009 TTTAAA-TTATTAAAAA
1 TTTAAATTTATTAAAAA
36025 TT
1 TT
36027 AATTTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTAAATTTATTAAAAA
Found at i:36032 original size:20 final size:20
Alignment explanation
Indices: 36007--36047 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
35997 ATTTATTAAA
36007 AATTTAAATTATTAAAAATT
1 AATTTAAATTATTAAAAATT
*
36027 AATTTAAATTTTTAAAAATT
1 AATTTAAATTATTAAAAATT
36047 A
1 A
36048 TAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
AATTTAAATTATTAAAAATT
Found at i:36511 original size:23 final size:23
Alignment explanation
Indices: 36460--36514 Score: 92
Period size: 23 Copynumber: 2.4 Consensus size: 23
36450 TAATATTTTA
*
36460 AAAATAATAAAATAACCAATAAT
1 AAAATTATAAAATAACCAATAAT
*
36483 AAAATTATAAAATAACTAATAAT
1 AAAATTATAAAATAACCAATAAT
36506 AAAATTATA
1 AAAATTATA
36515 CTTTTAACTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.27
Consensus pattern (23 bp):
AAAATTATAAAATAACCAATAAT
Found at i:36572 original size:16 final size:17
Alignment explanation
Indices: 36551--36586 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
36541 TAATTTATTC
36551 AAAATTAATA-ACATTA
1 AAAATTAATATACATTA
*
36567 AAAATTAATATATATTA
1 AAAATTAATATACATTA
36584 AAA
1 AAA
36587 CTATATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATTAATATACATTA
Found at i:36585 original size:17 final size:16
Alignment explanation
Indices: 36546--36586 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
36536 TTATCTAATT
*
36546 TATTCAAAATTAATAA
1 TATTAAAAATTAATAA
*
36562 CATTAAAAATTAATATA
1 TATTAAAAATTAATA-A
36579 TATTAAAA
1 TATTAAAA
36587 CTATATTTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (16 bp):
TATTAAAAATTAATAA
Found at i:37022 original size:28 final size:29
Alignment explanation
Indices: 36920--37028 Score: 98
Period size: 28 Copynumber: 3.7 Consensus size: 29
36910 TTTATATATT
* *
36920 AATTTTTTTATCAACTTTTAAG-GATCTC
1 AATTTTTTTATCAACTTTTAAGAGATTTA
* * * *
36948 AATTTTTTTTTTAATTTTTAAAAG-TTTAA
1 AATTTTTTTATCAACTTTTAAGAGATTT-A
36977 ATTTATCTTTTTTATCAACTTTTAAGAGATTTA
1 A---AT-TTTTTTATCAACTTTTAAGAGATTTA
37010 AATTTTTTT-TCAACTTTTA
1 AATTTTTTTATCAACTTTTA
37029 TTATTTTAGT
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
28 30 0.47
29 8 0.12
30 2 0.03
32 2 0.03
33 19 0.30
34 3 0.05
ACGTcount: A:0.30, C:0.08, G:0.05, T:0.57
Consensus pattern (29 bp):
AATTTTTTTATCAACTTTTAAGAGATTTA
Found at i:37583 original size:15 final size:16
Alignment explanation
Indices: 37566--37628 Score: 69
Period size: 16 Copynumber: 4.0 Consensus size: 16
37556 CAATACTTTT
37566 TTAATTTTAAAATTT-
1 TTAATTTTAAAATTTA
*
37581 TTATATCGTT-AAATTTA
1 TTA-AT-TTTAAAATTTA
*
37598 TTAA-TTTAAATTTTA
1 TTAATTTTAAAATTTA
37613 TTAATTTTAAAATTTA
1 TTAATTTTAAAATTTA
37629 ATATTACACA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
14 2 0.05
15 13 0.33
16 19 0.49
17 5 0.13
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (16 bp):
TTAATTTTAAAATTTA
Found at i:37606 original size:14 final size:15
Alignment explanation
Indices: 37589--37619 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
37579 TTTTATATCG
37589 TTAAA-TTTATTAAT
1 TTAAATTTTATTAAT
37603 TTAAATTTTATTAAT
1 TTAAATTTTATTAAT
37618 TT
1 TT
37620 TAAAATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTAAATTTTATTAAT
Found at i:37802 original size:15 final size:15
Alignment explanation
Indices: 37782--37832 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
37772 AAATAATATA
37782 AAAATTAAAATAAAC
1 AAAATTAAAATAAAC
*
37797 AAAATTAAAATATA-
1 AAAATTAAAATAAAC
*
37811 AAAATTAAATCTAAAC
1 AAAATTAAA-ATAAAC
37827 AAAATT
1 AAAATT
37833 TAATGTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
14 9 0.29
15 16 0.52
16 6 0.19
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (15 bp):
AAAATTAAAATAAAC
Found at i:37805 original size:31 final size:31
Alignment explanation
Indices: 37773--37845 Score: 98
Period size: 29 Copynumber: 2.4 Consensus size: 31
37763 TTACAATTTA
37773 AATAATATAAAAATTAAA-ATAAACAAAATT
1 AATAATATAAAAATTAAATATAAACAAAATT
*
37803 AA-AATATAAAAATTAAATCTAAACAAAATTT
1 AATAATATAAAAATTAAATATAAACAAAA-TT
*
37834 AAT-GTATAAAAA
1 AATAATATAAAAA
37846 AAAGGAATCA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
29 15 0.39
30 11 0.29
31 12 0.32
ACGTcount: A:0.67, C:0.04, G:0.01, T:0.27
Consensus pattern (31 bp):
AATAATATAAAAATTAAATATAAACAAAATT
Found at i:37816 original size:14 final size:14
Alignment explanation
Indices: 37776--37819 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
37766 CAATTTAAAT
37776 AATATAAAAATTAA
1 AATATAAAAATTAA
*
37790 AATAAACAAAATTAA
1 AATATA-AAAATTAA
37805 AATATAAAAATTAA
1 AATATAAAAATTAA
37819 A
1 A
37820 TCTAAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 14 0.52
15 13 0.48
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (14 bp):
AATATAAAAATTAA
Found at i:44144 original size:21 final size:21
Alignment explanation
Indices: 44120--44163 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
44110 CATTTATTTT
44120 TTTAAAATCTTAT-ATTTTAAA
1 TTTAAAATCTTATCA-TTTAAA
**
44141 TTTATGATCTTATCATTTAAA
1 TTTAAAATCTTATCATTTAAA
44162 TT
1 TT
44164 AAGGCTTAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.55
Consensus pattern (21 bp):
TTTAAAATCTTATCATTTAAA
Found at i:44672 original size:15 final size:14
Alignment explanation
Indices: 44648--44684 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
44638 TAATCAAAAG
*
44648 TTTTTTTTTTTATC
1 TTTTTTTTTTTATA
44662 TTTTTTCTTTTTATA
1 TTTTTT-TTTTTATA
44677 TTTTTTTT
1 TTTTTTTT
44685 ATGAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.08, C:0.05, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTTTATA
Found at i:66026 original size:15 final size:16
Alignment explanation
Indices: 66001--66047 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
65991 TGGTGGAAAG
*
66001 AAAATTGGAAGGATGA
1 AAAATTAGAAGGATGA
* *
66017 AAAATT-GAAGGGGTAA
1 AAAATTAGAA-GGATGA
66033 AAAATTAGAAGGATG
1 AAAATTAGAAGGATG
66048 GACGACATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 19 0.76
17 3 0.12
ACGTcount: A:0.51, C:0.00, G:0.30, T:0.19
Consensus pattern (16 bp):
AAAATTAGAAGGATGA
Done.