Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011185.1 Kokia drynarioides strain JFW-HI SEQ_126161, 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: 177861
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 53 characters in sequence are not A, C, G, or T
Found at i:748 original size:96 final size:96
Alignment explanation
Indices: 575--755 Score: 233
Period size: 96 Copynumber: 1.9 Consensus size: 96
565 AGGATATTTG
** * * *
575 ATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCGGAATCGAAGAT
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCGAAACCGAAGAT
*
640 AAGGAAACATTGCCTCGATTAAGGGTATTCA
66 AAAGAAACATTGCCTCGATTAAGGGTATTCA
* *
671 ATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCGTAAAT-TTTCGAAACCCGAA-
1 ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCG-AAATATTTCGAAA-CCGAAG
*
734 ATAAA-AGAATATTGCCTCGATT
64 ATAAAGA-AACATTGCCTCGATT
756 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
95 1 0.01
96 65 0.89
97 7 0.10
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.29
Consensus pattern (96 bp):
ATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCGAAATATTTCGAAACCGAAGAT
AAAGAAACATTGCCTCGATTAAGGGTATTCA
Found at i:1106 original size:41 final size:41
Alignment explanation
Indices: 1061--1142 Score: 139
Period size: 41 Copynumber: 2.0 Consensus size: 41
1051 GGGGTAAAAA
*
1061 GGTAATTTTTGGAAGGTTCAGGG-TCAAAATGGGATTTTTGG
1 GGTAATTTTTGGAAGGTTC-GGGATCAAAATGGGACTTTTGG
1102 GGTAATTTTTGGAAGGTTCGGGATCAAAATGGGACTTTTGG
1 GGTAATTTTTGGAAGGTTCGGGATCAAAATGGGACTTTTGG
1143 AAGTTCGGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 3 0.08
41 36 0.92
ACGTcount: A:0.24, C:0.06, G:0.34, T:0.35
Consensus pattern (41 bp):
GGTAATTTTTGGAAGGTTCGGGATCAAAATGGGACTTTTGG
Found at i:1141 original size:29 final size:29
Alignment explanation
Indices: 1106--1424 Score: 217
Period size: 29 Copynumber: 10.9 Consensus size: 29
1096 TTTTGGGGTA
*
1106 ATTTTTGGAAGGTTC-GGGATCAAAATGGG
1 ATTTTTGGAAGGTTCGGGGGT-AAAATGGG
* *
1135 ACTTTTGGAA-GTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCGGGGGTAAAATGG-G
* *
1164 ATTCTTGGAAGGTTC-GAGGTCAAAATGGG
1 ATTTTTGGAAGGTTCGGGGGT-AAAATGGG
* **
1193 ATTTTTGGAA-GTTCAGGGGTAAAATGATA
1 ATTTTTGGAAGGTTCGGGGGTAAAATG-GG
* *
1222 ATTTTTGGAAGGTTC-GAGGTAAAAAAAATAGG
1 ATTTTTGGAAGGTTCGGGGGT----AAAATGGG
** **
1254 ACCTTTGGAA-GTTCGGGGGTAAAATAGTA
1 ATTTTTGGAAGGTTCGGGGGTAAAAT-GGG
* * * *
1283 ATTTTTAGAAGGTTCGAGGTTAAAAAAGGG
1 ATTTTTGGAAGGTTCGGGGGT-AAAATGGG
* *
1313 ACTTTTGGAA-GTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCGGGGGTAAAATGG-G
* * *
1342 AATTTT-GAAAGTTCGGGGGTAAAATGGTA
1 ATTTTTGGAAGGTTCGGGGGTAAAATGG-G
*
1371 ATTTTTGGAAGGTT-TGGGGTCAAAATGGG
1 ATTTTTGGAAGGTTCGGGGGT-AAAATGGG
**
1400 ATTTTTGGAA-GTTTAGGGGTAAAAT
1 ATTTTTGGAAGGTTCGGGGGTAAAAT
1425 AATAATTTTT
Statistics
Matches: 229, Mismatches: 41, Indels: 41
0.74 0.13 0.13
Matches are distributed among these distances:
28 43 0.19
29 116 0.51
30 45 0.20
31 8 0.03
32 12 0.05
33 5 0.02
ACGTcount: A:0.31, C:0.05, G:0.32, T:0.31
Consensus pattern (29 bp):
ATTTTTGGAAGGTTCGGGGGTAAAATGGG
Found at i:1192 original size:58 final size:59
Alignment explanation
Indices: 1102--1410 Score: 342
Period size: 58 Copynumber: 5.3 Consensus size: 59
1092 GGATTTTTGG
*
1102 GGTAATTTTTGGAAGGTTCG-GGATCAAAATGGGACTTTTGGAAGTTCGGGGGTAAAAT
1 GGTAATTTTTGGAAGGTTCGAGGATAAAAATGGGACTTTTGGAAGTTCGGGGGTAAAAT
* * * *
1160 GGTAATTCTTGGAAGGTTCGAGG-TCAAAATGGGATTTTTGGAAGTTCAGGGGTAAAAT
1 GGTAATTTTTGGAAGGTTCGAGGATAAAAATGGGACTTTTGGAAGTTCGGGGGTAAAAT
* * * *
1218 GATAATTTTTGGAAGGTTCGAGGTAAAAAAAATAGGACCTTTGGAAGTTCGGGGGTAAAAT
1 GGTAATTTTTGGAAGGTTCGAGG--ATAAAAATGGGACTTTTGGAAGTTCGGGGGTAAAAT
* * * *
1279 AGTAATTTTTAGAAGGTTCGAGGTTAAAAAAGGGACTTTTGGAAGTTCGGGGGTAAAAT
1 GGTAATTTTTGGAAGGTTCGAGGATAAAAATGGGACTTTTGGAAGTTCGGGGGTAAAAT
* * * * * * *
1338 GGTAAATTTT-GAAAGTTCGGGGGT-AAAATGGTAATTTTTGGAAGGTT-TGGGGTCAAAAT
1 GGTAATTTTTGGAAGGTTCGAGGATAAAAATGG-GACTTTTGGAA-GTTCGGGGGT-AAAAT
*
1397 GG-GATTTTTGGAAG
1 GGTAATTTTTGGAAG
1411 TTTAGGGGTA
Statistics
Matches: 212, Mismatches: 31, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
57 6 0.03
58 103 0.49
59 54 0.25
61 49 0.23
ACGTcount: A:0.31, C:0.06, G:0.32, T:0.31
Consensus pattern (59 bp):
GGTAATTTTTGGAAGGTTCGAGGATAAAAATGGGACTTTTGGAAGTTCGGGGGTAAAAT
Found at i:1356 original size:119 final size:120
Alignment explanation
Indices: 1127--1365 Score: 338
Period size: 119 Copynumber: 2.0 Consensus size: 120
1117 GTTCGGGATC
* * * * * *
1127 AAAATGGGACTTTTGGAAGTTCGGGGGTAAAATGGTAATTCTTGGAAGGTTCGAGGTCAAAATGG
1 AAAATAGGACCTTTGGAAGTTCGGGGGTAAAATAGTAATTCTTAGAAGGTTCGAGGTAAAAAAGG
* * *
1192 GATTTTTGGAAGTTCAGGGGTAAAATGATAATTTTTGGAAGGTTC-GAGGTAAAA
66 GACTTTTGGAAGTTCAGGGGTAAAATGATAAATTTTGGAAAGTTCGGAGGTAAAA
*
1246 AAAATAGGACCTTTGGAAGTTCGGGGGTAAAATAGTAATTTTTAGAAGGTTCGAGGTTAAAAAAG
1 AAAATAGGACCTTTGGAAGTTCGGGGGTAAAATAGTAATTCTTAGAAGGTTCGAGG-TAAAAAAG
* * *
1311 GGACTTTTGGAAGTTCGGGGGTAAAATGGTAAATTTT-GAAAGTTCGGGGGTAAAA
65 GGACTTTTGGAAGTTCAGGGGTAAAATGATAAATTTTGGAAAGTTCGGAGGTAAAA
1366 TGGTAATTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
119 58 0.55
120 47 0.45
ACGTcount: A:0.33, C:0.06, G:0.31, T:0.29
Consensus pattern (120 bp):
AAAATAGGACCTTTGGAAGTTCGGGGGTAAAATAGTAATTCTTAGAAGGTTCGAGGTAAAAAAGG
GACTTTTGGAAGTTCAGGGGTAAAATGATAAATTTTGGAAAGTTCGGAGGTAAAA
Found at i:3446 original size:18 final size:18
Alignment explanation
Indices: 3420--3536 Score: 157
Period size: 18 Copynumber: 6.6 Consensus size: 18
3410 TTATTTATTT
*
3420 TAAACTTTAAATTTGAAAA
1 TAAA-TTTAAATTTTAAAA
* *
3439 TAATTTTAAA-CTTAAAA
1 TAAATTTAAATTTTAAAA
3456 TAAATTTAAATTTTAAAA
1 TAAATTTAAATTTTAAAA
*
3474 TAAATTTAAAATTTAAAA
1 TAAATTTAAATTTTAAAA
*
3492 TAAATTTAAATTTTTAAA
1 TAAATTTAAATTTTAAAA
*
3510 CAAATTT-AATTTTAAAA
1 TAAATTTAAATTTTAAAA
3527 TAAATTTAAA
1 TAAATTTAAA
3537 GAGAGTATGA
Statistics
Matches: 85, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
17 29 0.34
18 53 0.62
19 3 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (18 bp):
TAAATTTAAATTTTAAAA
Found at i:3472 original size:7 final size:6
Alignment explanation
Indices: 3418--3504 Score: 56
Period size: 6 Copynumber: 14.5 Consensus size: 6
3408 TTTTATTTAT
* * * *
3418 TTTAAA CTTTAAA TTTGAAA -ATAAT TTTAAA CTTAAA -ATAAA TTTAAA
1 TTTAAA -TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
3466 TTTTAAA -ATAAA TTTAAAA TTTAAA -ATAAA TTTAAA TTT
1 -TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTT
3505 TTAAACAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 15
0.70 0.12 0.17
Matches are distributed among these distances:
5 14 0.23
6 27 0.44
7 21 0.34
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (6 bp):
TTTAAA
Found at i:3490 original size:36 final size:35
Alignment explanation
Indices: 3420--3536 Score: 162
Period size: 35 Copynumber: 3.3 Consensus size: 35
3410 TTATTTATTT
* * *
3420 TAAACTTTAAATTTGAAAATAATTTTAAACTTAAAA
1 TAAA-TTTAAATTTTAAAATAAATTTAAATTTAAAA
3456 TAAATTTAAATTTTAAAATAAATTTAAAATTTAAAA
1 TAAATTTAAATTTTAAAATAAATTT-AAATTTAAAA
* * *
3492 TAAATTTAAATTTTTAAACAAATTTAATTTTAAAA
1 TAAATTTAAATTTTAAAATAAATTTAAATTTAAAA
3527 TAAATTTAAA
1 TAAATTTAAA
3537 GAGAGTATGA
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
35 38 0.51
36 36 0.49
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (35 bp):
TAAATTTAAATTTTAAAATAAATTTAAATTTAAAA
Found at i:12097 original size:15 final size:16
Alignment explanation
Indices: 12077--12106 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12067 GTTTTCTTGT
12077 AATTAAT-TTAAATAA
1 AATTAATGTTAAATAA
12092 AATTAATGTTAAATA
1 AATTAATGTTAAATA
12107 GTTATTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (16 bp):
AATTAATGTTAAATAA
Found at i:18192 original size:14 final size:14
Alignment explanation
Indices: 18170--18199 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18160 TTTATTTTTT
*
18170 ACCTTGAATCTTGA
1 ACCTCGAATCTTGA
18184 ACCTCGAATCTTGA
1 ACCTCGAATCTTGA
18198 AC
1 AC
18200 TTTGAACCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (14 bp):
ACCTCGAATCTTGA
Found at i:19035 original size:4 final size:4
Alignment explanation
Indices: 19026--19051 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
19016 AGTGGACAAA
19026 TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TA
19052 AGAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:20478 original size:19 final size:18
Alignment explanation
Indices: 20451--20487 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
20441 GCCAGTTAAC
*
20451 TTGCGACGTTGGACAAGTA
1 TTGCCACGTTGGA-AAGTA
20470 TTGCCACGTTGGAAAGTA
1 TTGCCACGTTGGAAAGTA
20488 GTAAAAGTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.27, C:0.16, G:0.30, T:0.27
Consensus pattern (18 bp):
TTGCCACGTTGGAAAGTA
Found at i:21787 original size:24 final size:24
Alignment explanation
Indices: 21760--21842 Score: 121
Period size: 24 Copynumber: 3.5 Consensus size: 24
21750 TTTATCCCAC
*
21760 ACGAGCCCAAAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
* *
21784 ACGAGCCTAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
* *
21808 ACAATCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGGTTAGCTCTT
21832 ACGAGCCCAGA
1 ACGAGCCCAGA
21843 TAGAGTTTAA
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.24
Consensus pattern (24 bp):
ACGAGCCCAGAATGGTTAGCTCTT
Found at i:27598 original size:24 final size:22
Alignment explanation
Indices: 27544--27615 Score: 126
Period size: 22 Copynumber: 3.2 Consensus size: 22
27534 CTTACTGATC
27544 AGCACTGTGTGTGCTTCTATTT
1 AGCACTGTGTGTGCTTCTATTT
27566 AGCACTGTGTGTGCTTCTATTT
1 AGCACTGTGTGTGCTTCTATTT
*
27588 AGCACTGTGTGTGCTCTCTGTTT
1 AGCACTGTGTGTGCT-TCTATTT
27611 AGCAC
1 AGCAC
27616 GTTTCGTGCC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
22 37 0.77
23 11 0.23
ACGTcount: A:0.14, C:0.21, G:0.24, T:0.42
Consensus pattern (22 bp):
AGCACTGTGTGTGCTTCTATTT
Found at i:27615 original size:23 final size:23
Alignment explanation
Indices: 27544--27703 Score: 157
Period size: 23 Copynumber: 7.0 Consensus size: 23
27534 CTTACTGATC
* *
27544 AGCACTGTGTGTG-CTTCTATTT
1 AGCACTGTGTGTGCCCTCTGTTT
* *
27566 AGCACTGTGTGTG-CTTCTATTT
1 AGCACTGTGTGTGCCCTCTGTTT
*
27588 AGCACTGTGTGTGCTCTCTGTTT
1 AGCACTGTGTGTGCCCTCTGTTT
* * *
27611 AGCAC-GTTTCGTGCCCTCTGATC
1 AGCACTGTGT-GTGCCCTCTGTTT
*
27634 AGCACTTTGTGTGCCCTCTGTTATT
1 AGCACTGTGTGTGCCCTCTG-T-TT
*
27659 AGCACT-TCGTGTGCCCTCTGATT
1 AGCACTGT-GTGTGCCCTCTGTTT
*
27682 AGCACTTTGTGTGCCCTCTGTT
1 AGCACTGTGTGTGCCCTCTGTT
27704 ACCCAGCACT
Statistics
Matches: 118, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
22 38 0.32
23 57 0.48
24 4 0.03
25 19 0.16
ACGTcount: A:0.12, C:0.25, G:0.23, T:0.41
Consensus pattern (23 bp):
AGCACTGTGTGTGCCCTCTGTTT
Found at i:27670 original size:25 final size:25
Alignment explanation
Indices: 27621--27729 Score: 113
Period size: 25 Copynumber: 4.5 Consensus size: 25
27611 AGCACGTTTC
*
27621 GTGCCCTCTG--ATCAGCACTTTGT
1 GTGCCCTCTGTTATCAGCACTTCGT
*
27644 GTGCCCTCTGTTATTAGCACTTCGT
1 GTGCCCTCTGTTATCAGCACTTCGT
* *
27669 GTGCCCTCTG--ATTAGCACTTTGT
1 GTGCCCTCTGTTATCAGCACTTCGT
*
27692 GTGCCCTCTGTTACCCAGCACTTAC--
1 GTGCCCTCTGTTA-TCAGCACTT-CGT
27717 GTGCCCTCTGTTA
1 GTGCCCTCTGTTA
27730 AGTATTTCGA
Statistics
Matches: 74, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
23 32 0.43
25 35 0.47
26 7 0.09
ACGTcount: A:0.13, C:0.31, G:0.20, T:0.36
Consensus pattern (25 bp):
GTGCCCTCTGTTATCAGCACTTCGT
Found at i:27673 original size:48 final size:48
Alignment explanation
Indices: 27588--27726 Score: 162
Period size: 48 Copynumber: 2.9 Consensus size: 48
27578 GCTTCTATTT
* *
27588 AGCACTGTGTGTGCTCTCTG-T-TTAGCACGTTTCGTGCCCTCTGATC
1 AGCACTTTGTGTGCCCTCTGTTATTAGCACGTTTCGTGCCCTCTGATC
*
27634 AGCACTTTGTGTGCCCTCTGTTATTAGCAC--TTCGTGTGCCCTCTGATT
1 AGCACTTTGTGTGCCCTCTGTTATTAGCACGTTTC--GTGCCCTCTGATC
** *
27682 AGCACTTTGTGTGCCCTCTGTTACCCAGCAC-TTACGTGCCCTCTG
1 AGCACTTTGTGTGCCCTCTGTTA-TTAGCACGTTTCGTGCCCTCTG
27727 TTAAGTATTT
Statistics
Matches: 81, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
46 21 0.26
47 1 0.01
48 52 0.64
49 5 0.06
50 2 0.02
ACGTcount: A:0.12, C:0.30, G:0.22, T:0.36
Consensus pattern (48 bp):
AGCACTTTGTGTGCCCTCTGTTATTAGCACGTTTCGTGCCCTCTGATC
Found at i:28580 original size:2 final size:2
Alignment explanation
Indices: 28573--28597 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28563 TGAACCAAAT
28573 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
28598 ATAGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:36891 original size:20 final size:19
Alignment explanation
Indices: 36854--36893 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
36844 CCTTCTATTC
36854 CTTTTATTTTGTTTTCTTT
1 CTTTTATTTTGTTTTCTTT
36873 CTTTTGATTTT-TTTCTCTTT
1 CTTTT-ATTTTGTTT-TCTTT
36893 C
1 C
36894 AATTGTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (19 bp):
CTTTTATTTTGTTTTCTTT
Found at i:37641 original size:33 final size:33
Alignment explanation
Indices: 37604--37670 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
37594 TTAATACATC
37604 TATTTTCAGAGAGAACAACAAAATAACAAATGG
1 TATTTTCAGAGAGAACAACAAAATAACAAATGG
37637 TATTTTCAGAGAGAACAACAAAATAACAAATGG
1 TATTTTCAGAGAGAACAACAAAATAACAAATGG
37670 T
1 T
37671 TTAGCAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.51, C:0.12, G:0.15, T:0.22
Consensus pattern (33 bp):
TATTTTCAGAGAGAACAACAAAATAACAAATGG
Found at i:40958 original size:17 final size:19
Alignment explanation
Indices: 40931--40980 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
40921 TTTTTAAATA
*
40931 AAAATATTTATTAA-TTTT
1 AAAATAATTATTAAGTTTT
40949 AAAA-AATTA-TAATGTTTT
1 AAAATAATTATTAA-GTTTT
*
40967 AAAATAAATATTAA
1 AAAATAATTATTAA
40981 AAAATATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
16 3 0.12
17 4 0.15
18 12 0.46
19 4 0.15
20 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
AAAATAATTATTAAGTTTT
Found at i:44765 original size:21 final size:20
Alignment explanation
Indices: 44710--44759 Score: 66
Period size: 21 Copynumber: 2.5 Consensus size: 20
44700 GAATTTAGGA
*
44710 TTCAAGATTCA-GGTTCGGG
1 TTCAAGATTTATGGTTCGGG
*
44729 TTCAAGGTTTATGGTTCGAGG
1 TTCAAGATTTATGGTTCG-GG
44750 TTCAAGATTT
1 TTCAAGATTT
44760 TGGGTTTGAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 9 0.35
20 6 0.23
21 11 0.42
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (20 bp):
TTCAAGATTTATGGTTCGGG
Found at i:56715 original size:23 final size:22
Alignment explanation
Indices: 56689--56738 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
56679 TTTTGAGGGG
*
56689 TTAAAATATAATTTAATCTTTT
1 TTAAAATATAATTTAATCATTT
** *
56711 ATTAATTTATAATTTCATCATTT
1 -TTAAAATATAATTTAATCATTT
56734 TTAAA
1 TTAAA
56739 GCTTTGATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.40, C:0.06, G:0.00, T:0.54
Consensus pattern (22 bp):
TTAAAATATAATTTAATCATTT
Found at i:63217 original size:18 final size:19
Alignment explanation
Indices: 63196--63243 Score: 73
Period size: 18 Copynumber: 2.6 Consensus size: 19
63186 GATTAAGTAA
*
63196 AAATATATTTATAAATG-T
1 AAATATATTTAAAAATGTT
63214 AAATATATTTAAAAATGTT
1 AAATATATTTAAAAATGTT
63233 AAATAT-TTTAA
1 AAATATATTTAA
63244 TTAATAAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 21 0.75
19 7 0.25
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (19 bp):
AAATATATTTAAAAATGTT
Found at i:79176 original size:14 final size:14
Alignment explanation
Indices: 79159--79214 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
79149 GAGCTTTTTA
79159 ATTTATTTAAATTT
1 ATTTATTTAAATTT
79173 ATTT-TTTAAAATTTT
1 ATTTATTT-AAA-TTT
*
79188 ATTTTATTT-TATTT
1 A-TTTATTTAAATTT
*
79202 ATTTATTCAAATT
1 ATTTATTTAAATT
79215 GATATTGCTG
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
13 9 0.26
14 14 0.41
15 5 0.15
16 3 0.09
17 3 0.09
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTTATTTAAATTT
Found at i:79202 original size:29 final size:30
Alignment explanation
Indices: 79154--79214 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
79144 GAGGAGAGCT
*
79154 TTTTAATTTATTTAAATTTATTTTTTAAAA
1 TTTTAATTTATTTAAATTTATTTATTAAAA
* * *
79184 TTTTATTTTATTT-TATTTATTTATTCAAA
1 TTTTAATTTATTTAAATTTATTTATTAAAA
79213 TT
1 TT
79215 GATATTGCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (30 bp):
TTTTAATTTATTTAAATTTATTTATTAAAA
Found at i:84622 original size:18 final size:18
Alignment explanation
Indices: 84601--84642 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
84591 TATTTTATAT
84601 TTTTTTAATATTTATAAA
1 TTTTTTAATATTTATAAA
*
84619 TTTTTT-ATATTTTTAAA
1 TTTTTTAATATTTATAAA
*
84636 TTATTTA
1 TTTTTTA
84643 TTGATATGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTTTAATATTTATAAA
Found at i:86490 original size:16 final size:16
Alignment explanation
Indices: 86469--86503 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
86459 TTGATTTCTA
86469 TTAGTCTTTAATAAAT
1 TTAGTCTTTAATAAAT
86485 TTAGTCTTTAATAAAT
1 TTAGTCTTTAATAAAT
86501 TTA
1 TTA
86504 ACGATAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.37, C:0.06, G:0.06, T:0.51
Consensus pattern (16 bp):
TTAGTCTTTAATAAAT
Found at i:104316 original size:60 final size:59
Alignment explanation
Indices: 104242--104360 Score: 220
Period size: 60 Copynumber: 2.0 Consensus size: 59
104232 TTTTGGTCTC
*
104242 GATTAAGAATTTATGCTTTGGCTTATATGTCCAAAAAACACTTAAGAAAATGTAAAAAA
1 GATTAAGAATTTATGCTTTGGCTTATATGTCCAAAAAACACATAAGAAAATGTAAAAAA
104301 NGATTAAGAATTTATGCTTTGGCTTATATGTCCAAAAAACACATAAGAAAATGTAAAAAA
1 -GATTAAGAATTTATGCTTTGGCTTATATGTCCAAAAAACACATAAGAAAATGTAAAAAA
104361 AATAAAAAAT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.46, C:0.10, G:0.13, T:0.29
Consensus pattern (59 bp):
GATTAAGAATTTATGCTTTGGCTTATATGTCCAAAAAACACATAAGAAAATGTAAAAAA
Found at i:104577 original size:19 final size:20
Alignment explanation
Indices: 104553--104590 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
104543 ATATTTTCCC
104553 CATAAAAATGA-TTAAAAAT
1 CATAAAAATGATTTAAAAAT
*
104572 CATAAAAATTATTTAAAAA
1 CATAAAAATGATTTAAAAA
104591 AGAAGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (20 bp):
CATAAAAATGATTTAAAAAT
Found at i:104637 original size:19 final size:20
Alignment explanation
Indices: 104600--104637 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
104590 AAGAAGAAAA
*
104600 TATTAAAATTGATATAAATT
1 TATTAAAATTGATAAAAATT
*
104620 TATT-AAATTTATAAAAAT
1 TATTAAAATTGATAAAAAT
104638 ATATAATAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (20 bp):
TATTAAAATTGATAAAAATT
Found at i:112737 original size:6 final size:7
Alignment explanation
Indices: 112719--112752 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
112709 TCTTTAATTG
112719 TAAAAAA
1 TAAAAAA
112726 TAAAAAA
1 TAAAAAA
112733 TAAAAAA
1 TAAAAAA
112740 T-AAAAA
1 TAAAAAA
112746 TAAAAAA
1 TAAAAAA
112753 ATCCCCCCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAAAAA
Found at i:112754 original size:14 final size:14
Alignment explanation
Indices: 112719--112752 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
112709 TCTTTAATTG
112719 TAAAAAATAAAAAA
1 TAAAAAATAAAAAA
112733 TAAAAAAT-AAAAA
1 TAAAAAATAAAAAA
112746 TAAAAAA
1 TAAAAAA
112753 ATCCCCCCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (14 bp):
TAAAAAATAAAAAA
Found at i:114356 original size:168 final size:168
Alignment explanation
Indices: 114066--114377 Score: 461
Period size: 168 Copynumber: 1.9 Consensus size: 168
114056 ACCATTGAAT
* *
114066 TTGTTCAACATTTCATATATCATTAGCATTGGATGTTATGTCACGTATGTTGTATATGAATATGT
1 TTGTTCAACATTTCATAGATCATTAGCATTGGATGTTATGTCACGTATATTGTATATGAATATGT
* * * * *
114131 GCTATCGGTGTTGGTTTGAGAATTATATTTGATGTATCAACTTGTTTATTGATCTCTGCATTCAT
66 GCTATCGGTATTGGCTTGAGAAATATATTTGATGTATCAACTTGGTTATTAATCTCTGCATTCAT
*
114196 ATAACCATTGTTGTTGTTTATACGGTTTTCTCATCGAA
131 ATAACAATTGTTGTTGTTTATACGGTTTTCTCATCGAA
114234 TTGTTCAACATTTCATAGATCATTA-CTATTGGATGTTATGTCACGTATATTGTATAT-AAGTAC
1 TTGTTCAACATTTCATAGATCATTAGC-ATTGGATGTTATGTCACGTATATTGTATATGAA-TA-
*
114297 T-TG-TCATCGGTATTGGCTTGAGAAATATTTTTGATGTATCAACTTGGTTATTAATCTCTGCAT
63 TGTGCT-ATCGGTATTGGCTTGAGAAATATATTTGATGTATCAACTTGGTTATTAATCTCTGCAT
* *
114360 TCTTATAATAATTGTTGT
127 TCATATAACAATTGTTGT
114378 AGTTATTTAC
Statistics
Matches: 129, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
167 4 0.03
168 124 0.96
169 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.17, T:0.45
Consensus pattern (168 bp):
TTGTTCAACATTTCATAGATCATTAGCATTGGATGTTATGTCACGTATATTGTATATGAATATGT
GCTATCGGTATTGGCTTGAGAAATATATTTGATGTATCAACTTGGTTATTAATCTCTGCATTCAT
ATAACAATTGTTGTTGTTTATACGGTTTTCTCATCGAA
Found at i:115524 original size:3 final size:3
Alignment explanation
Indices: 115518--115567 Score: 73
Period size: 3 Copynumber: 16.7 Consensus size: 3
115508 TCATCATCAT
* * *
115518 CAC CAC CAC CAC CAC CAC CAC CAT CAC CAC CAC CAT CAC CAT CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC
115566 CA
1 CA
115568 TAGTGCTGAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.60, G:0.00, T:0.06
Consensus pattern (3 bp):
CAC
Found at i:117821 original size:28 final size:28
Alignment explanation
Indices: 117781--117863 Score: 157
Period size: 28 Copynumber: 3.0 Consensus size: 28
117771 AGGATTGTTG
117781 GCGCTGCATGGAAGGTACCTAAAAGAGA
1 GCGCTGCATGGAAGGTACCTAAAAGAGA
117809 GCGCTGCATGGAAGGTACCTAAAAGAGA
1 GCGCTGCATGGAAGGTACCTAAAAGAGA
*
117837 GCGCTGCATGGAAGGTAACTAAAAGAG
1 GCGCTGCATGGAAGGTACCTAAAAGAG
117864 GGTGGATCAA
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.36, C:0.17, G:0.33, T:0.14
Consensus pattern (28 bp):
GCGCTGCATGGAAGGTACCTAAAAGAGA
Found at i:118513 original size:3 final size:3
Alignment explanation
Indices: 118507--118536 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
118497 TAATAAAGTG
118507 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
118537 AAAGGATGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:123108 original size:22 final size:22
Alignment explanation
Indices: 123080--123123 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
123070 TGTGGTATTA
123080 AACGATGGATCAAGTTTAAGTT
1 AACGATGGATCAAGTTTAAGTT
123102 AACGATGGATCAAGTTTAAGTT
1 AACGATGGATCAAGTTTAAGTT
123124 GTTATTGTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.23, T:0.32
Consensus pattern (22 bp):
AACGATGGATCAAGTTTAAGTT
Found at i:129856 original size:23 final size:22
Alignment explanation
Indices: 129830--129872 Score: 52
Period size: 22 Copynumber: 1.9 Consensus size: 22
129820 ACAAAAAGTA
129830 AAAAGAATAA-TCACTTAAAAAAG
1 AAAAGAA-AATTCA-TTAAAAAAG
*
129853 AAAATAAAATTCATTAAAAA
1 AAAAGAAAATTCATTAAAAA
129873 TCCCAAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (22 bp):
AAAAGAAAATTCATTAAAAAAG
Found at i:135930 original size:22 final size:22
Alignment explanation
Indices: 135886--135930 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
135876 ATAAAAAAAT
*
135886 TCTCCTCTCTTCTCTTCTCTTC
1 TCTCCTCTCTTCTCTTCTATTC
*
135908 TCTCCTCTGTT-TCTTCTTATTC
1 TCTCCTCTCTTCTCTTC-TATTC
135930 T
1 T
135931 TCTTTTTAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.02, C:0.38, G:0.02, T:0.58
Consensus pattern (22 bp):
TCTCCTCTCTTCTCTTCTATTC
Found at i:137444 original size:19 final size:19
Alignment explanation
Indices: 137372--137444 Score: 56
Period size: 19 Copynumber: 3.6 Consensus size: 19
137362 CTGTCCAAAT
*
137372 AAAATATTAATTAAATTTTA
1 AAAATATT-TTTAAATTTTA
*
137392 AAATGATATTTTATATATTTTTA
1 AAA--ATATTTT-TA-AATTTTA
* * *
137415 TAAATAATTTTACATTTTA
1 AAAATATTTTTAAATTTTA
137434 AAAATATTTTT
1 AAAATATTTTT
137445 TATTATTCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
19 14 0.34
20 5 0.12
21 7 0.17
22 7 0.17
23 8 0.20
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (19 bp):
AAAATATTTTTAAATTTTA
Found at i:137445 original size:20 final size:20
Alignment explanation
Indices: 137372--137446 Score: 53
Period size: 20 Copynumber: 3.6 Consensus size: 20
137362 CTGTCCAAAT
**
137372 AAAATATTAATTAAATTTTA
1 AAAATATTTTTTAAATTTTA
* *
137392 AAATGATATTTTATATATTTTTA
1 AAA--ATATTTTTTA-AATTTTA
* * *
137415 TAAATA-ATTTTACATTTTA
1 AAAATATTTTTTAAATTTTA
137434 AAAATATTTTTTA
1 AAAATATTTTTTA
137447 TTATTCAATT
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
19 10 0.25
20 12 0.30
21 3 0.08
22 7 0.17
23 8 0.20
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (20 bp):
AAAATATTTTTTAAATTTTA
Found at i:143424 original size:18 final size:17
Alignment explanation
Indices: 143396--143429 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
143386 AAATGTATAT
143396 ATTCCTTTTTTTAAATA
1 ATTCCTTTTTTTAAATA
143413 ATTCCTTTTTTTAAATA
1 ATTCCTTTTTTTAAATA
143430 CGTATGATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTCCTTTTTTTAAATA
Found at i:143956 original size:18 final size:20
Alignment explanation
Indices: 143918--143957 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
143908 ACTATAAACA
143918 AAGCAAATGAAACACAAATC
1 AAGCAAATGAAACACAAATC
*
143938 AAGC-AATGAAATA-AAATC
1 AAGCAAATGAAACACAAATC
143956 AA
1 AA
143958 CTAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 8 0.42
20 4 0.21
ACGTcount: A:0.62, C:0.15, G:0.10, T:0.12
Consensus pattern (20 bp):
AAGCAAATGAAACACAAATC
Found at i:151923 original size:85 final size:85
Alignment explanation
Indices: 151736--152021 Score: 319
Period size: 85 Copynumber: 3.3 Consensus size: 85
151726 AATCAAGTCG
* * * * * *
151736 AATTTAATTAACAACGGATAAATTATACTGATAATTATTCGATTGTTGATGATTTGTCATAGTAA
1 AATTTAATTAATAACGGATAAATTATACTCATAATTATTCGATTATTGATGACTCGTC--A-CAA
* * * *
151801 AATATAAAAATTGAATCGAGCCG
63 AAGATAAAAATTGAGTTGAGCCA
*
151824 AATTTAATTAATAACGGATAAATTATACTTATAATTATTCGATTATTTG-TGACTCGTCACAAAA
1 AATTTAATTAATAACGGATAAATTATACTCATAATTATTCGATTA-TTGATGACTCGTCACAAAA
151888 GATAAAAATTGAGTTGAGCCA
65 GATAAAAATTGAGTTGAGCCA
* * *
151909 AATTTAATTAATAACGGGTAAGTTATAC-CATTAATTATTCGGTTATTGATGAC-CTGTCACAAA
1 AATTTAATTAATAACGGATAAATTATACTCA-TAATTATTCGATTATTGATGACTC-GTCACAAA
* *
151972 AGATACAAAAATCGAGTTGAGACA
64 AGAT--AAAAATTGAGTTGAGCCA
*
151996 AATTTAATTAATAA-GGGTAAATTATA
1 AATTTAATTAATAACGGATAAATTATA
152022 TTGATAGTTA
Statistics
Matches: 175, Mismatches: 17, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
84 5 0.03
85 76 0.43
86 12 0.07
87 30 0.17
88 49 0.28
89 3 0.02
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (85 bp):
AATTTAATTAATAACGGATAAATTATACTCATAATTATTCGATTATTGATGACTCGTCACAAAAG
ATAAAAATTGAGTTGAGCCA
Found at i:157061 original size:16 final size:17
Alignment explanation
Indices: 157042--157073 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
157032 AAAAGCGAAT
157042 AAATTATAAT-TTTTTA
1 AAATTATAATATTTTTA
157058 AAATTATAATATTTTT
1 AAATTATAATATTTTT
157074 TGGTATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AAATTATAATATTTTTA
Found at i:157766 original size:28 final size:28
Alignment explanation
Indices: 157713--157766 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
157703 TTTAAATTAG
*
157713 AAATGATAAAATTATACATTTGTCCTCA
1 AAATGATAAAATTATACATTTATCCTCA
*
157741 AAATGATAAAATTTTA-ATTTAATCCT
1 AAATGATAAAATTATACATTT-ATCCT
157767 TTAAAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 4 0.17
28 19 0.83
ACGTcount: A:0.44, C:0.11, G:0.06, T:0.39
Consensus pattern (28 bp):
AAATGATAAAATTATACATTTATCCTCA
Found at i:163666 original size:25 final size:25
Alignment explanation
Indices: 163628--163685 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
163618 ACCACAATAG
*
163628 TTTTTAACCGTACAAAAGAATGAAA
1 TTTTTAACCGTACAAAAGAATAAAA
*
163653 TTTTTAACCTTACAAAAGAATAAAA
1 TTTTTAACCGTACAAAAGAATAAAA
163678 TTTTTAAC
1 TTTTTAAC
163686 AAAAATTACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (25 bp):
TTTTTAACCGTACAAAAGAATAAAA
Found at i:164892 original size:19 final size:19
Alignment explanation
Indices: 164857--164894 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
164847 TTTTTCCTTA
164857 TTTTTTTAATAGTTTAATAT
1 TTTTTTTAATAG-TTAATAT
164877 TTTTTTTGAATA-TTAATA
1 TTTTTTT-AATAGTTAATA
164895 GTTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 7 0.41
21 4 0.24
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTTTTTAATAGTTAATAT
Found at i:167379 original size:19 final size:19
Alignment explanation
Indices: 167352--167388 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
167342 GATAAAAATA
167352 TTAACCTTAAAAAATGGAT
1 TTAACCTTAAAAAATGGAT
* *
167371 TTAAGCTTAAAAATTGGA
1 TTAACCTTAAAAAATGGA
167389 CAAGCTAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.14, T:0.32
Consensus pattern (19 bp):
TTAACCTTAAAAAATGGAT
Found at i:169557 original size:3 final size:3
Alignment explanation
Indices: 169549--169580 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
169539 TCCTTTATCG
*
169549 TCA TCA TCA TCA TCA TCA TCA ACA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
169581 TTTTTGTTGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.31
Consensus pattern (3 bp):
TCA
Found at i:169790 original size:177 final size:180
Alignment explanation
Indices: 169566--169904 Score: 499
Period size: 177 Copynumber: 1.9 Consensus size: 180
169556 CATCATCATC
* *
169566 ATCAACATCATCATCTTTTTGTTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTCTGTTGAAA
1 ATCAACATCATCATCTTTTTGCTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTCTATTGAAA
* * *
169631 TCTGC-A-T-TGC-TT-TCTGTTAATATTTTGAATACCTTGTATATTAGATCGCAACTCTGTGGA
66 TCTGCGATTCTGCATTCTCTGTTAA-A-TTTGAATACCTTGGATATTAGATCGCAAATCTCTGGA
* * *
169691 TATGTTTAGTATTTCGATCTGAAGTATTGCATATTCACTCGATGTTTTCTTT
129 TATATTTAGTATTTAGATCTGAAGCATTGCATATTCACTCGATGTTTTCTTT
* *
169743 ATCATCATCATCATCTTTTTGCTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTTTATTGAAA
1 ATCAACATCATCATCTTTTTGCTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTCTATTGAAA
* *
169808 TCTGCGATTCTGCATTGCCTCTGTTAAATTTGAATGCCTTGGATATTAGATCGCAAATCTCTGTA
66 TCTGCGATTCTGCATT--CTCTGTTAAATTTGAATACCTTGGATATTAGATCGCAAATCTCTGGA
169873 TATATTTAGTATTTAGATCTGAAGCATTGCAT
129 TATATTTAGTATTTAGATCTGAAGCATTGCAT
169905 TTCCACTTTA
Statistics
Matches: 143, Mismatches: 12, Indels: 9
0.87 0.07 0.05
Matches are distributed among these distances:
177 66 0.46
178 1 0.01
179 1 0.01
180 3 0.02
181 2 0.01
182 61 0.43
183 1 0.01
184 8 0.06
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (180 bp):
ATCAACATCATCATCTTTTTGCTGGATTTCTTTTGGTAGCTTTCGGAAATTAAGTTCTATTGAAA
TCTGCGATTCTGCATTCTCTGTTAAATTTGAATACCTTGGATATTAGATCGCAAATCTCTGGATA
TATTTAGTATTTAGATCTGAAGCATTGCATATTCACTCGATGTTTTCTTT
Found at i:176845 original size:6 final size:6
Alignment explanation
Indices: 176820--176864 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
176810 ACAATTCATA
* * *
176820 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCA
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCA
176865 ATTTTTATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.22, C:0.31, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Done.