Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013844.1 Kokia drynarioides strain JFW-HI SEQ_128872, 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: 188939
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Warning! 151 characters in sequence are not A, C, G, or T
Found at i:3509 original size:20 final size:22
Alignment explanation
Indices: 3473--3516 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
3463 AAACTTATGG
3473 AAAATGATAAAATAATA-GAAA
1 AAAATGATAAAATAATATGAAA
3494 AAAAT-ATAGAAA-AATATGAAA
1 AAAATGATA-AAATAATATGAAA
3515 AA
1 AA
3517 TATAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.73, C:0.00, G:0.09, T:0.18
Consensus pattern (22 bp):
AAAATGATAAAATAATATGAAA
Found at i:4428 original size:96 final size:95
Alignment explanation
Indices: 4251--4435 Score: 207
Period size: 96 Copynumber: 1.9 Consensus size: 95
4241 GAAAAGGATG
* * * * * *
4251 TTCGATTATCTTGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGTGCAAATTTTTAGAATCGA
1 TTCGATTATCTTGATTTGAGGAAA-GTTGCACCCAGTAAGTTAAAGCGCAAATTTTCAAAAACGA
*
4316 AGATAAGGAAACATTGCCTCGATTAAGGGTA
65 AGATAAAGAAACATTGCCTCGATTAAGGGTA
4347 TTCGATTAT-TTCGATTTGAAGAGAAA-TTGCACCCAGTAAGTTAAAGCGCAAATTTTCAAAACA
1 TTCGATTATCTT-GATTTG-AG-GAAAGTTGCACCCAGTAAGTTAAAGCGCAAATTTTCAAAA-A
* *
4410 CGAA-ATAAA-AGAATATTGCCTTGATT
62 CGAAGATAAAGA-AACATTGCCTCGATT
4436 TTAAAGTTTT
Statistics
Matches: 75, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
95 3 0.04
96 62 0.83
97 6 0.08
98 4 0.05
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (95 bp):
TTCGATTATCTTGATTTGAGGAAAGTTGCACCCAGTAAGTTAAAGCGCAAATTTTCAAAAACGAA
GATAAAGAAACATTGCCTCGATTAAGGGTA
Found at i:4687 original size:29 final size:28
Alignment explanation
Indices: 4652--4713 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
4642 AAATGAGACT
*
4652 TTTTGGATACCCGGGGGGTAAAATGATAA
1 TTTTGGATACCC-GGGGGCAAAATGATAA
* * *
4681 TTTTGGATTCTCGGGGGCAAAATGGTAA
1 TTTTGGATACCCGGGGGCAAAATGATAA
4709 TTTTG
1 TTTTG
4714 AGAAAGTTCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 19 0.66
29 10 0.34
ACGTcount: A:0.26, C:0.10, G:0.31, T:0.34
Consensus pattern (28 bp):
TTTTGGATACCCGGGGGCAAAATGATAA
Found at i:4727 original size:30 final size:29
Alignment explanation
Indices: 4665--4776 Score: 79
Period size: 28 Copynumber: 3.8 Consensus size: 29
4655 TGGATACCCG
* * *
4665 GGGGGTAAAATGATAATTTTG-G-ATTCTC
1 GGGGGCAAAATGGTAATTTTGAGAAAT-TC
4693 GGGGGCAAAATGGTAATTTTGAGAAAGTTC
1 GGGGGCAAAATGGTAATTTTGAGAAA-TTC
* *
4723 GGGGGCTAAAAAT--TAAATTTTTAGACATTC
1 GGGGGC--AAAATGGT-AATTTTGAGAAATTC
* * *
4753 AGGGGTAAAAAGGTAATTTTGAGA
1 GGGGGCAAAATGGTAATTTTGAGA
4777 GTTTCGAGGT
Statistics
Matches: 67, Mismatches: 9, Indels: 15
0.74 0.10 0.16
Matches are distributed among these distances:
28 23 0.34
29 10 0.15
30 18 0.27
31 11 0.16
32 5 0.07
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.30
Consensus pattern (29 bp):
GGGGGCAAAATGGTAATTTTGAGAAATTC
Found at i:4853 original size:59 final size:60
Alignment explanation
Indices: 4790--5101 Score: 196
Period size: 59 Copynumber: 5.3 Consensus size: 60
4780 TCGAGGTCGG
* * *
4790 AAATGGAGTTTTTGGACATCCGAGGG-CAAAATGGTATTTTTTGAAAGTTTTAGGGTCAA
1 AAATGGAATTTTTGGACATCCGAGGGTAAAAATGGAATTTTTTGAAAGTTTTAGGGTCAA
* ** ** * **
4849 AAATGGAAATTTTGGATGTTTGAGGGTAAAAATGGAATTTTTTGGAAGTTTTAGGGTTGA
1 AAATGGAATTTTTGGACATCCGAGGGTAAAAATGGAATTTTTTGAAAGTTTTAGGGTCAA
** * * ****
4909 AAATGGAATTTTTGGA-AGTTTTG-GGGTTAAAAATGGAA-TTGTTGGAAGTGCGGGGGT-AA
1 AAATGGAATTTTTGGACA--TCCGAGGG-TAAAAATGGAATTTTTTGAAAGTTTTAGGGTCAA
* *** * ** *
4968 AATTGGAATTTTTGGA-AGTTTTAGGGTTAAAAATGGAA-TTTTTGGAAGTTCGAGGGT-AG
1 AAATGGAATTTTTGGACA-TCCGAGGG-TAAAAATGGAATTTTTTGAAAGTTTTAGGGTCAA
* * ***
5027 AAATGGAATTTTTGGA-AGTTTCGAGGGTAAAAATGGAATTTTTAG-AAGTTCGGGGGT-AA
1 AAATGGAATTTTTGGACA--TCCGAGGGTAAAAATGGAATTTTTTGAAAGTTTTAGGGTCAA
5086 AAATGGAATTTTTGGA
1 AAATGGAATTTTTGGA
5102 TAGTTTAGGG
Statistics
Matches: 213, Mismatches: 33, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
58 3 0.01
59 124 0.58
60 71 0.33
61 15 0.07
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.35
Consensus pattern (60 bp):
AAATGGAATTTTTGGACATCCGAGGGTAAAAATGGAATTTTTTGAAAGTTTTAGGGTCAA
Found at i:4862 original size:30 final size:29
Alignment explanation
Indices: 4817--5111 Score: 333
Period size: 30 Copynumber: 9.9 Consensus size: 29
4807 ATCCGAGGGC
* * *
4817 AAAATGGTATTTTTTGAAAGTTTTAGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTGAGGGT-A
* *
4848 AAAATGGAAATTTTGGATGTTTGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
* *
4877 AAAATGGAATTTTTTGGAAGTTTTAGGGTTG
1 AAAATGGAA-TTTTTGGAAGTTTGAGGG-TA
4908 AAAATGGAATTTTTGGAAGTTTTG-GGGTTA
1 AAAATGGAATTTTTGGAAG-TTTGAGGG-TA
* ** *
4938 AAAATGGAATTGTTGGAAGTGCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
* *
4967 AAATTGGAATTTTTGGAAGTTTTAGGGTTA
1 AAAATGGAATTTTTGGAAGTTTGAGGG-TA
*
4997 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
*
5026 GAAATGGAATTTTTGGAAGTTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTT-GAGGGTA
* * *
5056 AAAATGGAATTTTTAGAAGTTCGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTA
5085 AAAATGGAATTTTTGGATAGTTT-AGGG
1 AAAATGGAATTTTTGGA-AGTTTGAGGG
5112 ATCTTCAGGG
Statistics
Matches: 225, Mismatches: 32, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
29 82 0.36
30 123 0.55
31 20 0.09
ACGTcount: A:0.32, C:0.02, G:0.31, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTGAGGGTA
Found at i:6905 original size:17 final size:17
Alignment explanation
Indices: 6852--6935 Score: 71
Period size: 17 Copynumber: 4.9 Consensus size: 17
6842 TTTTTTAATT
* * *
6852 AATTTTAATTTACAGTA
1 AATTTAAATTTAAAATA
*
6869 AATTTAAATTCAAAAATA
1 AATTTAAATT-TAAAATA
*
6887 AATTTAAATTTAGAATA
1 AATTTAAATTTAAAATA
* * *
6904 AATTCAAACTTAAAACA
1 AATTTAAATTTAAAATA
*
6921 AA-TTAAAGTTAAAAT
1 AATTTAAATTTAAAAT
6936 TTAGACTCAG
Statistics
Matches: 53, Mismatches: 13, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
16 10 0.19
17 29 0.55
18 14 0.26
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.36
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:7223 original size:11 final size:10
Alignment explanation
Indices: 7191--7234 Score: 52
Period size: 11 Copynumber: 4.2 Consensus size: 10
7181 GTCATAAATG
7191 TTTTTATAAT
1 TTTTTATAAT
* *
7201 TTTTATCTTAT
1 TTTT-TATAAT
7212 TTTTTATATAT
1 TTTTTATA-AT
7223 TTTTTATAAT
1 TTTTTATAAT
7233 TT
1 TT
7235 CTGTGATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTTATAAT
Found at i:9942 original size:22 final size:21
Alignment explanation
Indices: 9906--9952 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
9896 CACGCATATC
*
9906 TATAAGTATTATACTATATTTTA
1 TATAAGTATAATACT-T-TTTTA
9929 TATAA-TATAATACTTTTTTA
1 TATAAGTATAATACTTTTTTA
9949 TATA
1 TATA
9953 TCAACAGGCG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 1 0.04
22 8 0.35
23 5 0.22
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (21 bp):
TATAAGTATAATACTTTTTTA
Found at i:14534 original size:11 final size:12
Alignment explanation
Indices: 14483--14541 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
14473 AAGTTTAACT
14483 AATATAA-ATATA
1 AATATAATAT-TA
*
14495 AATCTAATCAATTA
1 AATATAAT--ATTA
*
14509 TAATATAAAATTA
1 -AATATAATATTA
14522 AAT-TAATATTA
1 AATATAATATTA
14533 AATATAATA
1 AATATAATA
14542 AATAAAAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
11 10 0.26
12 14 0.37
13 4 0.11
14 2 0.05
15 8 0.21
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.37
Consensus pattern (12 bp):
AATATAATATTA
Found at i:14694 original size:2 final size:2
Alignment explanation
Indices: 14687--14716 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
14677 GTTGGTAATA
14687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14717 TCTGATTTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15301 original size:21 final size:20
Alignment explanation
Indices: 15277--15316 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
15267 GTTCTTTTAT
*
15277 TAATTTGATAAGAAAGTAAAA
1 TAATTTGAT-ACAAAGTAAAA
*
15298 TAATTTTATACAAAGTAAA
1 TAATTTGATACAAAGTAAA
15317 TTATCTCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (20 bp):
TAATTTGATACAAAGTAAAA
Found at i:18396 original size:22 final size:22
Alignment explanation
Indices: 18349--18396 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
18339 AATTATAATA
* *
18349 TGTTTTTTAAAATATTTGTGTG
1 TGTTTTTTAAAATATTCGTATG
*
18371 TGTTTTTTAAATTTATTCGTAT-
1 TGTTTTTTAAA-ATATTCGTATG
18393 TGTT
1 TGTT
18397 GGTATTGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.21, C:0.02, G:0.15, T:0.62
Consensus pattern (22 bp):
TGTTTTTTAAAATATTCGTATG
Found at i:22376 original size:29 final size:30
Alignment explanation
Indices: 22344--22409 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
22334 AAAATGAGAC
22344 TTTTGGGATACTC-GGGGGCAAAATGGTAA
1 TTTTGGGATACTCGGGGGGCAAAATGGTAA
* **
22373 TTTT-GGATTCTCGGGGGGTGAAATGGTAA
1 TTTTGGGATACTCGGGGGGCAAAATGGTAA
22402 TTTTGGGA
1 TTTTGGGA
22410 AAATTTGGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.22
29 22 0.69
30 3 0.09
ACGTcount: A:0.23, C:0.08, G:0.36, T:0.33
Consensus pattern (30 bp):
TTTTGGGATACTCGGGGGGCAAAATGGTAA
Found at i:22552 original size:30 final size:30
Alignment explanation
Indices: 22518--22764 Score: 196
Period size: 29 Copynumber: 8.3 Consensus size: 30
22508 TAAAATGGTA
*
22518 ATTTTTGGAAGTTTCGGGGTTAAAAATAGG
1 ATTTTTGGAAGTTTCGGGGGTAAAAATAGG
* *
22548 ATTTTTGGAAGTTT-TGGAGTAAAAACGTA--
1 ATTTTTGGAAGTTTCGGGGGTAAAAA--TAGG
* *
22577 ATTTTTGGAAGTTTC-GAGGTAAAAAAAGGG
1 ATTTTTGGAAGTTTCGGGGGTAAAAATA-GG
**
22607 ATTTTTAAAAG-TTCGGGGGGTAAAAA-ATGG
1 ATTTTTGGAAGTTTC-GGGGGTAAAAATA-GG
*
22637 AATTTTTGGAAGTTT-TGGGGTCAAAAAT-GG
1 -ATTTTTGGAAGTTTCGGGGGT-AAAAATAGG
*
22667 AATTTTTGGAAGTTT-GGGGGTAAAAAT-GAA
1 -ATTTTTGGAAGTTTCGGGGGTAAAAATAG-G
* *
22697 ATTTTTGGAAGTTTC-GAGGTCAAAAATGGG
1 ATTTTTGGAAGTTTCGGGGGT-AAAAATAGG
*
22727 ATTTTTGGGAG-TTCGGGGGTAAAAAT-GG
1 ATTTTTGGAAGTTTCGGGGGTAAAAATAGG
22755 AATTTTTGGA
1 -ATTTTTGGA
22765 CAATTTAGGG
Statistics
Matches: 179, Mismatches: 20, Indels: 37
0.76 0.08 0.16
Matches are distributed among these distances:
27 1 0.01
28 2 0.01
29 75 0.42
30 73 0.41
31 26 0.15
32 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.34
Consensus pattern (30 bp):
ATTTTTGGAAGTTTCGGGGGTAAAAATAGG
Found at i:22570 original size:59 final size:59
Alignment explanation
Indices: 22468--22764 Score: 316
Period size: 59 Copynumber: 5.0 Consensus size: 59
22458 TAATTTTGAG
* * * *
22468 AGTTTCGAGGTCGAAAAT-GGAGTCTTCGGACA-TATGGGGGT-AAAATGGTAATTTTTGGA
1 AGTTTCGAGGTCAAAAATAGGA-TTTTTGGA-AGTTTGGGGGTAAAAATGG-AATTTTTGGA
* * * * * *
22527 AGTTTCGGGGTTAAAAATAGGATTTTTGGAAGTTTTGGAGTAAAAACGTAATTTTTGGA
1 AGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
* ** *
22586 AGTTTCGAGGT-AAAAAAAGGGATTTTTAAAAGTTCGGGGGGTAAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATA-GGATTTTTGGAAGTT-TGGGGGT-AAAAATGGAATTTTTGGA
* * *
22647 AGTTTTGGGGTCAAAAAT-GGAATTTTTGGAAGTTTGGGGGTAAAAATGAAATTTTTGGA
1 AGTTTCGAGGTCAAAAATAGG-ATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
* * *
22706 AGTTTCGAGGTCAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
22765 CAATTTAGGG
Statistics
Matches: 198, Mismatches: 31, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
58 7 0.04
59 128 0.65
60 22 0.11
61 36 0.18
62 5 0.03
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (59 bp):
AGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
Found at i:23630 original size:21 final size:20
Alignment explanation
Indices: 23606--23645 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23596 GTTCTTTTAT
*
23606 TAATTTGATAAGAAAGTAAAA
1 TAATTTGAT-ACAAAGTAAAA
*
23627 TAATTTTATACAAAGTAAA
1 TAATTTGATACAAAGTAAA
23646 TTATCTCATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.55, C:0.03, G:0.10, T:0.33
Consensus pattern (20 bp):
TAATTTGATACAAAGTAAAA
Found at i:26725 original size:22 final size:22
Alignment explanation
Indices: 26678--26725 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
26668 AATTATAATA
* *
26678 TGTTTTTTAAAATATTTGTGTG
1 TGTTTTTTAAAATATTCGTATG
*
26700 TGTTTTTTAAATTTATTCGTAT-
1 TGTTTTTTAAA-ATATTCGTATG
26722 TGTT
1 TGTT
26726 GGTATTGGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 15 0.68
23 7 0.32
ACGTcount: A:0.21, C:0.02, G:0.15, T:0.62
Consensus pattern (22 bp):
TGTTTTTTAAAATATTCGTATG
Found at i:30705 original size:29 final size:30
Alignment explanation
Indices: 30673--30738 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 30
30663 AAAATGAGAC
30673 TTTTGGGATACTC-GGGGGCAAAATGGTAA
1 TTTTGGGATACTCGGGGGGCAAAATGGTAA
* **
30702 TTTT-GGATTCTCGGGGGGTGAAATGGTAA
1 TTTTGGGATACTCGGGGGGCAAAATGGTAA
30731 TTTTGGGA
1 TTTTGGGA
30739 AAATTTGGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
28 7 0.22
29 22 0.69
30 3 0.09
ACGTcount: A:0.23, C:0.08, G:0.36, T:0.33
Consensus pattern (30 bp):
TTTTGGGATACTCGGGGGGCAAAATGGTAA
Found at i:30881 original size:30 final size:30
Alignment explanation
Indices: 30847--31093 Score: 196
Period size: 29 Copynumber: 8.3 Consensus size: 30
30837 TAAAATGGTA
*
30847 ATTTTTGGAAGTTTCGGGGTTAAAAATAGG
1 ATTTTTGGAAGTTTCGGGGGTAAAAATAGG
* *
30877 ATTTTTGGAAGTTT-TGGAGTAAAAACGTA--
1 ATTTTTGGAAGTTTCGGGGGTAAAAA--TAGG
* *
30906 ATTTTTGGAAGTTTC-GAGGTAAAAAAAGGG
1 ATTTTTGGAAGTTTCGGGGGTAAAAATA-GG
**
30936 ATTTTTAAAAG-TTCGGGGGGTAAAAA-ATGG
1 ATTTTTGGAAGTTTC-GGGGGTAAAAATA-GG
*
30966 AATTTTTGGAAGTTT-TGGGGTCAAAAAT-GG
1 -ATTTTTGGAAGTTTCGGGGGT-AAAAATAGG
*
30996 AATTTTTGGAAGTTT-GGGGGTAAAAAT-GAA
1 -ATTTTTGGAAGTTTCGGGGGTAAAAATAG-G
* *
31026 ATTTTTGGAAGTTTC-GAGGTCAAAAATGGG
1 ATTTTTGGAAGTTTCGGGGGT-AAAAATAGG
*
31056 ATTTTTGGGAG-TTCGGGGGTAAAAAT-GG
1 ATTTTTGGAAGTTTCGGGGGTAAAAATAGG
31084 AATTTTTGGA
1 -ATTTTTGGA
31094 CAATTTAGGG
Statistics
Matches: 179, Mismatches: 20, Indels: 37
0.76 0.08 0.16
Matches are distributed among these distances:
27 1 0.01
28 2 0.01
29 75 0.42
30 73 0.41
31 26 0.15
32 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.34
Consensus pattern (30 bp):
ATTTTTGGAAGTTTCGGGGGTAAAAATAGG
Found at i:30899 original size:59 final size:59
Alignment explanation
Indices: 30797--31093 Score: 316
Period size: 59 Copynumber: 5.0 Consensus size: 59
30787 TAATTTTGAG
* * * *
30797 AGTTTCGAGGTCGAAAAT-GGAGTCTTCGGACA-TATGGGGGT-AAAATGGTAATTTTTGGA
1 AGTTTCGAGGTCAAAAATAGGA-TTTTTGGA-AGTTTGGGGGTAAAAATGG-AATTTTTGGA
* * * * * *
30856 AGTTTCGGGGTTAAAAATAGGATTTTTGGAAGTTTTGGAGTAAAAACGTAATTTTTGGA
1 AGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
* ** *
30915 AGTTTCGAGGT-AAAAAAAGGGATTTTTAAAAGTTCGGGGGGTAAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATA-GGATTTTTGGAAGTT-TGGGGGT-AAAAATGGAATTTTTGGA
* * *
30976 AGTTTTGGGGTCAAAAAT-GGAATTTTTGGAAGTTTGGGGGTAAAAATGAAATTTTTGGA
1 AGTTTCGAGGTCAAAAATAGG-ATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
* * *
31035 AGTTTCGAGGTCAAAAATGGGATTTTTGGGAGTTCGGGGGTAAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
31094 CAATTTAGGG
Statistics
Matches: 198, Mismatches: 31, Indels: 18
0.80 0.13 0.07
Matches are distributed among these distances:
58 7 0.04
59 128 0.65
60 22 0.11
61 36 0.18
62 5 0.03
ACGTcount: A:0.32, C:0.04, G:0.31, T:0.33
Consensus pattern (59 bp):
AGTTTCGAGGTCAAAAATAGGATTTTTGGAAGTTTGGGGGTAAAAATGGAATTTTTGGA
Found at i:32960 original size:25 final size:24
Alignment explanation
Indices: 32927--32973 Score: 85
Period size: 25 Copynumber: 1.9 Consensus size: 24
32917 TTTTAAATCC
32927 ATTTAAATTTAAAAGATAAATTTAA
1 ATTTAAATTTAAAA-ATAAATTTAA
32952 ATTTAAATTTAAAAATAAATTT
1 ATTTAAATTTAAAAATAAATTT
32974 GAATCAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
ATTTAAATTTAAAAATAAATTTAA
Found at i:32970 original size:12 final size:12
Alignment explanation
Indices: 32930--32973 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
32920 TAAATCCATT
32930 TAAATTTAAAAGA
1 TAAATTTAAAA-A
**
32943 TAAATTTAAATT
1 TAAATTTAAAAA
32955 TAAATTTAAAAA
1 TAAATTTAAAAA
32967 TAAATTT
1 TAAATTT
32974 GAATCAATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 17 0.63
13 10 0.37
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (12 bp):
TAAATTTAAAAA
Found at i:33200 original size:23 final size:23
Alignment explanation
Indices: 33170--33333 Score: 148
Period size: 23 Copynumber: 7.4 Consensus size: 23
33160 AGTGCTAGGC
33170 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
33193 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
**
33212 ---ATTGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
33232 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
33255 ATA-AGAGAGCACGA-GACGTGCTA
1 A-ACAGAGAGCAC-ACAAAGTGCTA
* *
33278 AACAGAGAGCATACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
33301 AACAGATAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
33324 AACAGAGAGC
1 AACAGAGAGC
33334 GCGTTAGTGT
Statistics
Matches: 114, Mismatches: 16, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
16 11 0.10
18 1 0.01
19 1 0.01
20 1 0.01
21 1 0.01
22 2 0.02
23 96 0.84
24 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:33230 original size:39 final size:39
Alignment explanation
Indices: 33176--33250 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
33166 AGGCAACAGA
*
33176 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTATT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTATT
* *
33215 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
33251 GCTAATAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTATT
Found at i:38638 original size:39 final size:39
Alignment explanation
Indices: 38576--38698 Score: 138
Period size: 39 Copynumber: 3.2 Consensus size: 39
38566 TAGCATTACG
* *** *
38576 GTGTTTACAATGTCACCATCAATTCAGTATTGTATTATA
1 GTGTTTACAGTGTCACTGCCAATTCAGTATTGTATTGTA
* *
38615 GTGTTTACAGTTTCACTGCCAATTTAGTATTGTATTGTA
1 GTGTTTACAGTGTCACTGCCAATTCAGTATTGTATTGTA
* * * * *
38654 GTGTTTTCAGTGTCACTGTCAGTTCAATATCGTATTGTA
1 GTGTTTACAGTGTCACTGCCAATTCAGTATTGTATTGTA
38693 GTGTTT
1 GTGTTT
38699 CTAGTGTTAC
Statistics
Matches: 70, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 70 1.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.45
Consensus pattern (39 bp):
GTGTTTACAGTGTCACTGCCAATTCAGTATTGTATTGTA
Found at i:38935 original size:73 final size:73
Alignment explanation
Indices: 38812--39005 Score: 325
Period size: 73 Copynumber: 2.7 Consensus size: 73
38802 CATCTGTGTC
* * *
38812 ACACAATCTGGCACACGCCCGTGTGTCCAACCCGTGTAACTCACTATTTCTGATTTTAGAAAACA
1 ACACAGTCTGGCACACGCCCGTGTGTCCAACCCGTGTAACTCACTGTTTCTGATTTCAGAAAACA
38877 AAATATCT
66 AAATATCT
* *
38885 ACACAGTCTGGCACACGCCCGTGTGTCCAACCCGTGTAGCTCACTGTTTCTGATTTCAGAAAATA
1 ACACAGTCTGGCACACGCCCGTGTGTCCAACCCGTGTAACTCACTGTTTCTGATTTCAGAAAACA
38950 AAATATCT
66 AAATATCT
* *
38958 ACACAGTCTGGCACACGCCTGTGTGTCCAACCCGTGTAACTAACTGTT
1 ACACAGTCTGGCACACGCCCGTGTGTCCAACCCGTGTAACTCACTGTT
39006 GCTAGTTTCC
Statistics
Matches: 113, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 113 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (73 bp):
ACACAGTCTGGCACACGCCCGTGTGTCCAACCCGTGTAACTCACTGTTTCTGATTTCAGAAAACA
AAATATCT
Found at i:45010 original size:133 final size:133
Alignment explanation
Indices: 44867--45128 Score: 384
Period size: 133 Copynumber: 2.0 Consensus size: 133
44857 CTAATATTCA
*
44867 TTTTTTTCATTAAATTGCTGCGAACATCATGAATTTACGAACCAAAAGCAAAACAACTTTCTTCT
1 TTTTTTTCATTAAATTGCTGCGAACATCATCAATTTACGAACCAAAAGCAAAACAACTTTCTTCT
* * * *
44932 -TCGATC-TCTGACATTGTCCATCAAATTGATTTGGATCTAAGATATGTTCTTCTACTCATTAAT
66 CT-AATCTTC-GACATTGACCATCAAATTGATTTGGATCTAAGATATGTTATTCTACTCATCAAT
44995 GAGTT
129 GAGTT
** * * *
45000 TTTTTTTCATTAAATTGCTTTGAACGTCATCAATTTACGAACCAAAATCTAAACAACTTTCTTCT
1 TTTTTTTCATTAAATTGCTGCGAACATCATCAATTTACGAACCAAAAGCAAAACAACTTTCTTCT
* *
45065 CTAATCTTCGACATTGACCATCAAATTGATTTGGATCTAAGGTATGTTATTTTACTCATCAATG
66 CTAATCTTCGACATTGACCATCAAATTGATTTGGATCTAAGATATGTTATTCTACTCATCAATG
45129 GGCACTGAGT
Statistics
Matches: 115, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
133 112 0.97
134 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.11, T:0.39
Consensus pattern (133 bp):
TTTTTTTCATTAAATTGCTGCGAACATCATCAATTTACGAACCAAAAGCAAAACAACTTTCTTCT
CTAATCTTCGACATTGACCATCAAATTGATTTGGATCTAAGATATGTTATTCTACTCATCAATGA
GTT
Found at i:48009 original size:11 final size:11
Alignment explanation
Indices: 47993--48071 Score: 62
Period size: 11 Copynumber: 7.6 Consensus size: 11
47983 AATTAATCAT
47993 ATTAATATTAA
1 ATTAATATTAA
48004 ATTAATA--AA
1 ATTAATATTAA
*
48013 A-TATTATTAA
1 ATTAATATTAA
*
48023 GATAAATATTAA
1 -ATTAATATTAA
*
48035 ATTAA-ATTTA
1 ATTAATATTAA
* *
48045 A-T-ATCTTAT
1 ATTAATATTAA
48054 ATTAATATTAA
1 ATTAATATTAA
48065 ATTAATA
1 ATTAATA
48072 AAATACTATC
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
8 5 0.10
9 7 0.14
10 8 0.16
11 24 0.47
12 7 0.14
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (11 bp):
ATTAATATTAA
Found at i:48017 original size:16 final size:16
Alignment explanation
Indices: 47996--48109 Score: 57
Period size: 16 Copynumber: 7.2 Consensus size: 16
47986 TAATCATATT
47996 AATATTAAATTAATAA
1 AATATTAAATTAATAA
*
48012 AATATT--ATTAAGATA
1 AATATTAAATTAATA-A
48027 AATATTAAA-T--T-A
1 AATATTAAATTAATAA
* *
48039 AAT-TTAATATCTTATATT
1 AATATTAA-AT-TAATA-A
48057 AATATTAAATTAATAA
1 AATATTAAATTAATAA
*
48073 AATACT--ATCTAGATAA
1 AATATTAAAT-TA-ATAA
*
48089 AATATTAAATTTATTAA
1 AATATTAAA-TTAATAA
48106 AATA
1 AATA
48110 ATATTATCTT
Statistics
Matches: 74, Mismatches: 8, Indels: 31
0.65 0.07 0.27
Matches are distributed among these distances:
11 4 0.05
12 5 0.07
14 9 0.12
15 9 0.12
16 22 0.30
17 12 0.16
18 8 0.11
19 5 0.07
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (16 bp):
AATATTAAATTAATAA
Found at i:58737 original size:14 final size:13
Alignment explanation
Indices: 58712--58736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
58702 TTACTTATAA
58712 CTTTAATTTTTTG
1 CTTTAATTTTTTG
58725 CTTTAATTTTTT
1 CTTTAATTTTTT
58737 TTTGTAACTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.72
Consensus pattern (13 bp):
CTTTAATTTTTTG
Found at i:60196 original size:17 final size:18
Alignment explanation
Indices: 60174--60208 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
60164 TAAAATATGT
60174 ATAATAAAAA-TAAAATA
1 ATAATAAAAATTAAAATA
60191 ATAATAAAAATTAAAATA
1 ATAATAAAAATTAAAATA
60209 CTTTAATTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
ATAATAAAAATTAAAATA
Found at i:66472 original size:41 final size:41
Alignment explanation
Indices: 66427--66530 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 41
66417 TTTTCAACGT
*
66427 GTTTTTGTCTCAGTCAAGGAAAAATGCTCCT-ACGTGGAGGC
1 GTTTTTGTCTCATTCAAGGAAAAATG-TCCTCACGTGGAGGC
* **
66468 GTTTTTGTCTCATTCAAGG-AAAGTGTTTTCACGTGGAGGC
1 GTTTTTGTCTCATTCAAGGAAAAATGTCCTCACGTGGAGGC
66508 GTTTTTGTCTCATTCAAGGAAAA
1 GTTTTTGTCTCATTCAAGGAAAA
66531 GTACTTCCAC
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
39 2 0.04
40 34 0.60
41 21 0.37
ACGTcount: A:0.24, C:0.16, G:0.25, T:0.35
Consensus pattern (41 bp):
GTTTTTGTCTCATTCAAGGAAAAATGTCCTCACGTGGAGGC
Found at i:66544 original size:41 final size:41
Alignment explanation
Indices: 66427--66554 Score: 170
Period size: 41 Copynumber: 3.1 Consensus size: 41
66417 TTTTCAACGT
* *
66427 GTTTTTGTCTCAGTCAAGGAAAAATGC-TCCTACGTGGAGGC
1 GTTTTTGTCTCATTCAAGGAAAAGTGCTTCC-ACGTGGAGGC
* *
66468 GTTTTTGTCTCATTCAAGG-AAAGTGTTTTCACGTGGAGGC
1 GTTTTTGTCTCATTCAAGGAAAAGTGCTTCCACGTGGAGGC
* *
66508 GTTTTTGTCTCATTCAAGGAAAAGTACTTCCACGTGGAAGC
1 GTTTTTGTCTCATTCAAGGAAAAGTGCTTCCACGTGGAGGC
*
66549 GCTTTT
1 GTTTTT
66555 CTGGAATTTC
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
40 34 0.45
41 42 0.55
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (41 bp):
GTTTTTGTCTCATTCAAGGAAAAGTGCTTCCACGTGGAGGC
Found at i:66871 original size:21 final size:21
Alignment explanation
Indices: 66847--66886 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
66837 TACAACATAA
* *
66847 AGGTAGCATACCTTTCTGTCT
1 AGGTACCACACCTTTCTGTCT
66868 AGGTACCACACCTTTCTGT
1 AGGTACCACACCTTTCTGT
66887 TCCAAATGCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (21 bp):
AGGTACCACACCTTTCTGTCT
Found at i:67431 original size:3 final size:3
Alignment explanation
Indices: 67423--67457 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
67413 ATACAAACAA
* *
67423 ATG ATG ATG ATG ATG ATG ATG GTG ATA ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
67458 TCTAGAATGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:68358 original size:44 final size:44
Alignment explanation
Indices: 68273--68358 Score: 127
Period size: 44 Copynumber: 2.0 Consensus size: 44
68263 GGGCTGACAC
* * *
68273 ACGGGGGTGTGTCCAGGGTGTGTGTCTATATTGTTTAGAGGCAT
1 ACGGGGGTGTGTCCAGGGTATGTGTCTATACTATTTAGAGGCAT
* *
68317 ACGGGGGTGTGTCTAGGGTATGTGTCTATACTATTTGGAGGC
1 ACGGGGGTGTGTCCAGGGTATGTGTCTATACTATTTAGAGGC
68359 TCACGAGTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.16, C:0.12, G:0.38, T:0.34
Consensus pattern (44 bp):
ACGGGGGTGTGTCCAGGGTATGTGTCTATACTATTTAGAGGCAT
Found at i:68559 original size:55 final size:54
Alignment explanation
Indices: 68323--68599 Score: 217
Period size: 55 Copynumber: 5.1 Consensus size: 54
68313 GCATACGGGG
* * * * * * * * *
68323 GTGTGTCTAGGGTATGTGTCTATACTATTTGGAGGCTCACGAGTTGACACATAGGT
1 GTGTGTC-AGGGTGTGTGTGTATACTGTTTGGTGGCACAAGGGCTGACACAT-GGC
* * * *
68379 GTGTGTCAGGGTGTGTGCCTGT-T-CTATTTGGTGGCATACA-GGTTGACACACGGGC
1 GTGTGTCAGGGTGTGTG--TGTATACTGTTTGGTGGCACA-AGGGCTGACACA-TGGC
* * * *
68434 GTGTGTCAGGGTGTGTGTGTATACTGTTTGGAGGCACATGGGTTGGCACATGAGC
1 GTGTGTCAGGGTGTGTGTGTATACTGTTTGGTGGCACAAGGGCTGACACATG-GC
* *
68489 GTGTGTTAGGGTGTGTGTG--TACTGTTTGGTGGCACAAGGGCTGACATATTGGC
1 GTGTGTCAGGGTGTGTGTGTATACTGTTTGGTGGCACAAGGGCTGACACA-TGGC
* * * *
68542 ATGTGTCAGGGTGTGTGTGTATACTATTTTGG-GGAACATGGGCTGACACATGG-
1 GTGTGTCAGGGTGTGTGTGTATACT-GTTTGGTGGCACAAGGGCTGACACATGGC
68595 GTGTG
1 GTGTG
68600 GTTACATGGT
Statistics
Matches: 181, Mismatches: 28, Indels: 27
0.77 0.12 0.11
Matches are distributed among these distances:
53 50 0.28
54 7 0.04
55 109 0.60
56 13 0.07
57 2 0.01
ACGTcount: A:0.17, C:0.13, G:0.37, T:0.32
Consensus pattern (54 bp):
GTGTGTCAGGGTGTGTGTGTATACTGTTTGGTGGCACAAGGGCTGACACATGGC
Found at i:68566 original size:108 final size:110
Alignment explanation
Indices: 68324--68599 Score: 305
Period size: 108 Copynumber: 2.5 Consensus size: 110
68314 CATACGGGGG
* * * * *
68324 TGTGTCTAGGGTATGTGTCTATACTATTTGGAGGCTCACGAGTTGACACAT-AGGTGTGTGTCAG
1 TGTGTC-AGGGTGTGTGTGTATACTATTTGGAGGCACATGGGTTGACACATGAGGTGTGTGTCAG
* * * *
68388 GGTGTGTGCCTGTTCTATTTGGTGGCATACAGGTTGACACACGGGCG
65 GGTGTGTG-CTGTACTATTTGGTGGCACACAGGCTGACACACGGGCA
* *
68435 TGTGTCAGGGTGTGTGTGTATACTGTTTGGAGGCACATGGGTTGGCACATGAGCGTGTGT-T-AG
1 TGTGTCAGGGTGTGTGTGTATACTATTTGGAGGCACATGGGTTGACACATGAG-GTGTGTGTCAG
* * **
68498 GGTGTGTG-TGTACTGTTTGGTGGCACA-AGGGCTGACATATTGGCA
65 GGTGTGTGCTGTACTATTTGGTGGCACACA-GGCTGACACACGGGCA
* *
68543 TGTGTCAGGGTGTGTGTGTATACTATTTTGG-GGAACATGGGCTGACACATG-GGTGTG
1 TGTGTCAGGGTGTGTGTGTATACTA-TTTGGAGGCACATGGGTTGACACATGAGGTGTG
68600 GTTACATGGT
Statistics
Matches: 142, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
106 5 0.04
107 2 0.01
108 68 0.48
109 5 0.04
110 47 0.33
111 9 0.06
112 6 0.04
ACGTcount: A:0.17, C:0.13, G:0.37, T:0.33
Consensus pattern (110 bp):
TGTGTCAGGGTGTGTGTGTATACTATTTGGAGGCACATGGGTTGACACATGAGGTGTGTGTCAGG
GTGTGTGCTGTACTATTTGGTGGCACACAGGCTGACACACGGGCA
Found at i:69221 original size:29 final size:29
Alignment explanation
Indices: 69184--69289 Score: 99
Period size: 29 Copynumber: 3.7 Consensus size: 29
69174 ATCATGTCTA
* *
69184 CATCCGTAACTATATCTGTGACATGACTG
1 CATCTGTAACTATATCTGTGACATGATTG
* * *
69213 CATCTGTAACTGTATCT-TTA-ATTCAATTG
1 CATCTGTAACTATATCTGTGACA-T-GATTG
* * *
69242 TATCTGTAACTGTATCTCTGACATGATTG
1 CATCTGTAACTATATCTGTGACATGATTG
*
69271 TATCTGTAACTATATCTGT
1 CATCTGTAACTATATCTGT
69290 ATTATTTCTA
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.02
28 3 0.05
29 55 0.87
30 3 0.05
31 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (29 bp):
CATCTGTAACTATATCTGTGACATGATTG
Found at i:70972 original size:10 final size:11
Alignment explanation
Indices: 70950--70978 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
70940 AAAATAGTAA
70950 ATAATTATTTT
1 ATAATTATTTT
70961 ATAATT-TTTT
1 ATAATTATTTT
70971 ATAATTAT
1 ATAATTAT
70979 ATAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
ATAATTATTTT
Found at i:71349 original size:24 final size:24
Alignment explanation
Indices: 71320--71365 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
71310 TTATAATTAG
71320 ATTAAATAAATAATGT-ATTTTATT
1 ATTAAAT-AATAATGTGATTTTATT
*
71344 ATTAAATAATAATTTGATTTTA
1 ATTAAATAATAATGTGATTTTA
71366 ACCAATTCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (24 bp):
ATTAAATAATAATGTGATTTTATT
Found at i:73468 original size:94 final size:92
Alignment explanation
Indices: 73270--73558 Score: 269
Period size: 94 Copynumber: 3.1 Consensus size: 92
73260 ACGGTCAAAT
* * * * ***
73270 GACTTTTTTGATGTA-TTTGACAGTTCAAGTACCCAA-TCGAGTGTAAAAACAATCGAGGGCTTA
1 GACTTTTTTGATGCATTTTGAAAGTTCAAATACCCAAGT-GAGTGCAAAAA-AAAAAAGGGCTTA
******
73333 ATTGCTTTTTTAAAAAAAAAAAACGTTTGAG
64 ATTGCTTTTTT-TTTTTGAAAAA-GTTTGAG
* * *
73364 GGCTTTTTTGATGCATTTTGAAAGTTCAAATACTCAATTGAGTGCAAAATAAAAAAAAAGGGCTT
1 GACTTTTTTGATGCATTTTGAAAGTTCAAATACCCAAGTGAGTGC--AA-AAAAAAAAAGGGCTT
*
73429 AATTG-TTTTTTTTTTTGAAATAGTTTGAG
63 AATTGCTTTTTTTTTTTGAAAAAGTTTGAG
* * ** *
73458 GATTTTTTTGATGCATTTTGAAAGTTCAAGTACCCAAGTGAGTGCAAAAAAAGTACGGGCTTAAT
1 GACTTTTTTGATGCATTTTGAAAGTTCAAATACCCAAGTGAGTGCAAAAAAAAAAAGGGCTTAAT
*
73523 TGCTTTTTTTTTTTTGAAAAAATTTGAG
66 TGC-TTTTTTTTTTTGAAAAAGTTTGAG
*
73551 GGCTTTTT
1 GACTTTTT
73559 ACACCCTTAA
Statistics
Matches: 160, Mismatches: 28, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
91 17 0.11
92 2 0.01
93 28 0.17
94 60 0.38
95 27 0.17
96 7 0.04
97 16 0.10
98 3 0.02
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (92 bp):
GACTTTTTTGATGCATTTTGAAAGTTCAAATACCCAAGTGAGTGCAAAAAAAAAAAGGGCTTAAT
TGCTTTTTTTTTTTGAAAAAGTTTGAG
Found at i:82099 original size:2 final size:2
Alignment explanation
Indices: 82086--82135 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
82076 CTACTCTTTG
*
82086 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
82128 AT AT AT AT
1 AT AT AT AT
82136 CTTAAAACAA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:82512 original size:6 final size:6
Alignment explanation
Indices: 82468--82504 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
82458 ATTGAAGATG
82468 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA G
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA G
82505 GGAAAGGGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:85868 original size:75 final size:75
Alignment explanation
Indices: 85784--85935 Score: 270
Period size: 75 Copynumber: 2.0 Consensus size: 75
85774 TAAGATGGCT
*
85784 AGCGCGCTCATAAAAAAGGGTGGAGG-TCATGATTATGATTTGTTATCCTCGTCATTTGATTCTT
1 AGCGCGCTCATAAAAAAGAGT-GAGGATCATGATTATGATTTGTTATCCTCGTCATTTGATTCTT
85848 TATTTTTAAAG
65 TATTTTTAAAG
*
85859 AGCGCGCTCATCAAAAAGAGTGAGGATCATGATTATGATTTGTTATCCTCGTCATTTGATTCTTT
1 AGCGCGCTCATAAAAAAGAGTGAGGATCATGATTATGATTTGTTATCCTCGTCATTTGATTCTTT
85924 ATTTTTAAAG
66 ATTTTTAAAG
85934 AG
1 AG
85936 GATTCAAATG
Statistics
Matches: 74, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
74 4 0.05
75 70 0.95
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (75 bp):
AGCGCGCTCATAAAAAAGAGTGAGGATCATGATTATGATTTGTTATCCTCGTCATTTGATTCTTT
ATTTTTAAAG
Found at i:87606 original size:15 final size:16
Alignment explanation
Indices: 87580--87609 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
87570 AGATATAATA
87580 AAATATTTTTAAAAAT
1 AAATATTTTTAAAAAT
87596 AAATA-TTTTAAAAA
1 AAATATTTTTAAAAA
87610 GCAGACACGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATATTTTTAAAAAT
Found at i:88229 original size:61 final size:59
Alignment explanation
Indices: 88164--88276 Score: 154
Period size: 61 Copynumber: 1.9 Consensus size: 59
88154 TACTAGATTT
* * * * *
88164 TTTTTTTTTACATTTTCTCATCAATTAAGTACCCCCTAAAAATCGATTGCTTCAATTTTTC
1 TTTTTTTTTACATATGCTCATCAATCAA--ACACCCAAAAAATCGATTGCTTCAATTTTTC
*
88225 TTTTTTTTTACATATGCTCATCAATCAAACACCCAAAAAATTGATTGCTTCA
1 TTTTTTTTTACATATGCTCATCAATCAAACACCCAAAAAATCGATTGCTTCA
88277 TTGTACAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
59 21 0.46
61 25 0.54
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.43
Consensus pattern (59 bp):
TTTTTTTTTACATATGCTCATCAATCAAACACCCAAAAAATCGATTGCTTCAATTTTTC
Found at i:91402 original size:28 final size:28
Alignment explanation
Indices: 91371--91427 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
91361 GTTGAAATTG
91371 GAAGTAAGTAAAAAAAAGGGGTCAGATT
1 GAAGTAAGTAAAAAAAAGGGGTCAGATT
91399 GAAGTAAGTAAAAAAAAGGGGTCAGATT
1 GAAGTAAGTAAAAAAAAGGGGTCAGATT
91427 G
1 G
91428 GAATTTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.49, C:0.04, G:0.30, T:0.18
Consensus pattern (28 bp):
GAAGTAAGTAAAAAAAAGGGGTCAGATT
Found at i:98928 original size:54 final size:54
Alignment explanation
Indices: 98869--98976 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
98859 ATAATATTTT
*
98869 GAACATGAATATAACTTAAAAAATGACGCATCTTATCTCAATTTAATCAAACAA
1 GAACATGAATATAACTTAAAAAATGACACATCTTATCTCAATTTAATCAAACAA
*
98923 GAACATGAATATAACTTAAAAAATGACACGTCTTATCTCAATTTAATCAAACAA
1 GAACATGAATATAACTTAAAAAATGACACATCTTATCTCAATTTAATCAAACAA
98977 TGAGAGAAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.48, C:0.17, G:0.07, T:0.28
Consensus pattern (54 bp):
GAACATGAATATAACTTAAAAAATGACACATCTTATCTCAATTTAATCAAACAA
Found at i:106077 original size:18 final size:18
Alignment explanation
Indices: 106056--106090 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
106046 AGAAATAACT
*
106056 GCAAAATAATACATAAAA
1 GCAAAACAATACATAAAA
106074 GCAAAACAATACATAAA
1 GCAAAACAATACATAAA
106091 TGCTCAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.66, C:0.14, G:0.06, T:0.14
Consensus pattern (18 bp):
GCAAAACAATACATAAAA
Found at i:111211 original size:6 final size:6
Alignment explanation
Indices: 111202--111262 Score: 63
Period size: 6 Copynumber: 10.3 Consensus size: 6
111192 ATTGATTTTG
** *
111202 AATTTA AATTT- GTTTTA AATTTTA AATTT- AATTTA AATTTA GATTTA
1 AATTTA AATTTA AATTTA AA-TTTA AATTTA AATTTA AATTTA AATTTA
*
111249 TATTTA AATTTA AA
1 AATTTA AATTTA AA
111263 ACTTATTTAA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
5 8 0.18
6 31 0.69
7 6 0.13
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (6 bp):
AATTTA
Found at i:111237 original size:29 final size:29
Alignment explanation
Indices: 111202--111261 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
111192 ATTGATTTTG
*
111202 AATTTAAATTT-GTTTTAAATTTTAAATTT
1 AATTTAAATTTAGATTTAAA-TTTAAATTT
*
111231 AATTTAAATTTAGATTTATATTTAAATTT
1 AATTTAAATTTAGATTTAAATTTAAATTT
111260 AA
1 AA
111262 AACTTATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 22 0.79
30 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (29 bp):
AATTTAAATTTAGATTTAAATTTAAATTT
Found at i:111259 original size:18 final size:17
Alignment explanation
Indices: 111169--111262 Score: 100
Period size: 17 Copynumber: 5.4 Consensus size: 17
111159 TTAAACCCAT
111169 TTTAAGATTTATTTTAAGA
1 TTTAA-ATTTATTTTAA-A
* *
111188 -TTAAATTGATTTTGAA
1 TTTAAATTTATTTTAAA
*
111204 TTTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
*
111221 TTTTAAATTTAATTTAAA
1 -TTTAAATTTATTTTAAA
*
111239 TTTAGATTTATATTTAAA
1 TTTAAATTTAT-TTTAAA
111257 TTTAAA
1 TTTAAA
111263 ACTTATTTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
16 1 0.02
17 31 0.50
18 30 0.48
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.54
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:113237 original size:60 final size:58
Alignment explanation
Indices: 113151--113405 Score: 264
Period size: 60 Copynumber: 4.2 Consensus size: 58
113141 AAACTATTCG
* *
113151 AAAATTCCATTTTT-ACCCTTAAACTTCCAAAAATCTCATTTTTGACCCCAAAACTTTCA
1 AAAATTCCATTTTTGA-CCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAAC-TTCA
* *
113210 AAAA-TCTCATTTTTGACCTCGAAACTTCCAAAAATCCCATTTTTGACCTCTAAACTTCTA
1 AAAATTC-CATTTTTGACCTC-AAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTC-A
* *
113270 AAAATTCCATTTTTGCCCCCTCAAACTTCCAAAAATCCCAATTTTTGACCCCGAAACTTCCA
1 AAAATTCCATTTTTG--ACCTCAAACTTCCAAAAATCCC-ATTTTTGACCCCAAAACTT-CA
* * * * * *
113332 AAATTTCCATTTTTTACC-CAAAAACCTCCAAAATTTCCATTTTTGACCCCAAAACATTTA
1 AAAATTCCATTTTTGACCTC--AAACTTCCAAAAATCCCATTTTTGACCCCAAAAC-TTCA
113392 AAAATTACCATTTT
1 AAAATT-CCATTTT
113406 GCCCCCGAAC
Statistics
Matches: 167, Mismatches: 16, Indels: 24
0.81 0.08 0.12
Matches are distributed among these distances:
58 2 0.01
59 18 0.11
60 69 0.41
61 42 0.25
62 35 0.21
63 1 0.01
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCTCAAACTTCCAAAAATCCCATTTTTGACCCCAAAACTTCA
Found at i:113304 original size:31 final size:31
Alignment explanation
Indices: 113151--113405 Score: 235
Period size: 30 Copynumber: 8.4 Consensus size: 31
113141 AAACTATTCG
*
113151 AAAATTCCATTTTT-A-CCCTTAAACTTCCA
1 AAAATTCCATTTTTGACCCCTAAAACTTCCA
*
113180 AAAA-TCTCATTTTTGACCCC-AAAACTTTCA
1 AAAATTC-CATTTTTGACCCCTAAAACTTCCA
* *
113210 AAAA-TCTCATTTTTGACCTC-GAAACTTCCA
1 AAAATTC-CATTTTTGACCCCTAAAACTTCCA
* * *
113240 AAAATCCCATTTTTGACCTCT-AAACTTCTA
1 AAAATTCCATTTTTGACCCCTAAAACTTCCA
* *
113270 AAAATTCCATTTTTGCCCCCTCAAACTTCCA
1 AAAATTCCATTTTTGACCCCTAAAACTTCCA
* *
113301 AAAATCCCAATTTTTGACCCC-GAAACTTCCA
1 AAAATTCC-ATTTTTGACCCCTAAAACTTCCA
* * * *
113332 AAATTTCCATTTTTTA-CCCAAAAACCTCCA
1 AAAATTCCATTTTTGACCCCTAAAACTTCCA
* *
113362 AAATTTCCATTTTTGACCCC-AAAACATT-TA
1 AAAATTCCATTTTTGACCCCTAAAAC-TTCCA
113392 AAAATTACCATTTT
1 AAAATT-CCATTTT
113406 GCCCCCGAAC
Statistics
Matches: 192, Mismatches: 23, Indels: 20
0.82 0.10 0.09
Matches are distributed among these distances:
28 2 0.01
29 14 0.07
30 120 0.62
31 45 0.23
32 11 0.06
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (31 bp):
AAAATTCCATTTTTGACCCCTAAAACTTCCA
Found at i:113524 original size:30 final size:30
Alignment explanation
Indices: 113450--113524 Score: 75
Period size: 30 Copynumber: 2.5 Consensus size: 30
113440 TCGAAACTCT
* *
113450 CAAAATTACCCTTTT-ACCCTCGAATGTCT
1 CAAAATTACCATTTTAACCCTCGAATGTCC
* *
113479 AAAAATT-CCATTTTTAACCCT-GAATTTTCC
1 CAAAATTACCA-TTTTAACCCTCGAA-TGTCC
113509 CAAAATTACCATTTTA
1 CAAAATTACCATTTTA
113525 CCCCCGGGTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
28 2 0.05
29 13 0.35
30 19 0.51
31 3 0.08
ACGTcount: A:0.33, C:0.25, G:0.04, T:0.37
Consensus pattern (30 bp):
CAAAATTACCATTTTAACCCTCGAATGTCC
Found at i:125875 original size:16 final size:17
Alignment explanation
Indices: 125854--125888 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
125844 CATGTACTTT
125854 ATAAAAATT-TAAAAAA
1 ATAAAAATTATAAAAAA
125870 ATAAAAATTCATAAAAAA
1 ATAAAAATT-ATAAAAAA
125888 A
1 A
125889 ATTCACTAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
18 8 0.47
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.23
Consensus pattern (17 bp):
ATAAAAATTATAAAAAA
Found at i:128033 original size:2 final size:2
Alignment explanation
Indices: 128026--128051 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
128016 TTTAAAATAA
128026 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
128052 GGGACAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130108 original size:31 final size:33
Alignment explanation
Indices: 130073--130145 Score: 89
Period size: 33 Copynumber: 2.3 Consensus size: 33
130063 AAAAAATTTA
* *
130073 AACTTTTAAAG-GCC-AAAATAT-TTTATTTTCC
1 AACTTTTAAAGAACCTAAAAAATGTTT-TTTTCC
130104 AACTTTTAAAGAACCTAAAAAATGTTTTTTTCC
1 AACTTTTAAAGAACCTAAAAAATGTTTTTTTCC
*
130137 AACTATTAA
1 AACTTTTAA
130146 GAAACTTGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 11 0.31
32 2 0.06
33 20 0.56
34 3 0.08
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (33 bp):
AACTTTTAAAGAACCTAAAAAATGTTTTTTTCC
Found at i:149484 original size:32 final size:32
Alignment explanation
Indices: 149446--149510 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
149436 CTTCGTAATT
149446 TTACATTCTCATAATCCTATTATGAAATATAA
1 TTACATTCTCATAATCCTATTATGAAATATAA
149478 TTACATTCTCATAATCCTATTATGAAATATAA
1 TTACATTCTCATAATCCTATTATGAAATATAA
149510 T
1 T
149511 CTTACTTTCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.40, C:0.15, G:0.03, T:0.42
Consensus pattern (32 bp):
TTACATTCTCATAATCCTATTATGAAATATAA
Found at i:156334 original size:10 final size:10
Alignment explanation
Indices: 156329--156367 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
156319 TATAAATAAT
156329 TTTAAAAAAA
1 TTTAAAAAAA
156339 TTTAAAAAAA
1 TTTAAAAAAA
156349 -TTAAAATAAA
1 TTTAAAA-AAA
156359 TATTAAAAA
1 T-TTAAAAA
156368 GTCAAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 6 0.23
10 13 0.50
11 1 0.04
12 6 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
TTTAAAAAAA
Found at i:156350 original size:21 final size:21
Alignment explanation
Indices: 156330--156367 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
156320 ATAAATAATT
156330 TTAAAA-AAAT-TTAAAAAAA
1 TTAAAATAAATATTAAAAAAA
156349 TTAAAATAAATATTAAAAA
1 TTAAAATAAATATTAAAAA
156368 GTCAAATTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 4 0.24
21 7 0.41
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (21 bp):
TTAAAATAAATATTAAAAAAA
Found at i:156600 original size:2 final size:2
Alignment explanation
Indices: 156593--156617 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
156583 TATCAAAATA
156593 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
156618 AAAACAAAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:159147 original size:24 final size:24
Alignment explanation
Indices: 159120--159171 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
159110 GGAAGTTAGC
159120 TAAAACTGAAAAAATTCTCATTAA
1 TAAAACTGAAAAAATTCTCATTAA
**
159144 TAAATTTGAAAAAATTCTCATTAA
1 TAAAACTGAAAAAATTCTCATTAA
159168 TAAA
1 TAAA
159172 CTTAAATTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
TAAAACTGAAAAAATTCTCATTAA
Found at i:167072 original size:30 final size:29
Alignment explanation
Indices: 167036--167136 Score: 112
Period size: 30 Copynumber: 3.4 Consensus size: 29
167026 TAGATTTTAA
* *
167036 GAGCCACACAGGTTGAGCACATGGCTATGT
1 GAGCCACACAGGATGGGCACATGGC-ATGT
* *
167066 GAGCCACACGGGATGGGCACACGGCCATGT
1 GAGCCACACAGGATGGGCACATGG-CATGT
* * *
167096 GAGCCACACAAGATGGGCACACTGTCGTGT
1 GAGCCACACAGGATGGGCACA-TGGCATGT
167126 GAGCCACACAG
1 GAGCCACACAG
167137 TCATGTGCCA
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
30 57 0.97
31 2 0.03
ACGTcount: A:0.27, C:0.28, G:0.32, T:0.14
Consensus pattern (29 bp):
GAGCCACACAGGATGGGCACATGGCATGT
Found at i:167253 original size:12 final size:12
Alignment explanation
Indices: 167236--167260 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
167226 TATATATACC
167236 AAATATGAGAAG
1 AAATATGAGAAG
167248 AAATATGAGAAG
1 AAATATGAGAAG
167260 A
1 A
167261 GAAGAGTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.16
Consensus pattern (12 bp):
AAATATGAGAAG
Found at i:168449 original size:56 final size:56
Alignment explanation
Indices: 168342--168465 Score: 144
Period size: 56 Copynumber: 2.2 Consensus size: 56
168332 CATTAAATGA
* *
168342 CCAACACCCAATAAAAATAATATTTATTTAAAAAGTTGGTGCTGGCCATTTAAGGG
1 CCAACACCCAATAAAAATAATATTTATTTAAAAAGTTGGTGCTGACCATTTAAGAG
* * * * *
168398 CCAACATCCAA-AAAATTAATTTTTTATTTAAAAAGTTGGTG-TCGACTATTTAATAG
1 CCAACACCCAATAAAAATAA-TATTTATTTAAAAAGTTGGTGCT-GACCATTTAAGAG
*
168454 CCAACACTCAAT
1 CCAACACCCAAT
168466 TTTTTTCAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
55 8 0.14
56 48 0.86
ACGTcount: A:0.40, C:0.17, G:0.12, T:0.31
Consensus pattern (56 bp):
CCAACACCCAATAAAAATAATATTTATTTAAAAAGTTGGTGCTGACCATTTAAGAG
Found at i:169415 original size:139 final size:139
Alignment explanation
Indices: 169165--169479 Score: 612
Period size: 139 Copynumber: 2.3 Consensus size: 139
169155 GTTTACATTT
*
169165 CAGTCCCTCAACTTTGAAAATGTGACAAAACAGTCCTTTTCATGTTTTCCATCACAGACGTCACA
1 CAGTCACTCAACTTTGAAAATGTGACAAAACAGTCCTTTTCATGTTTTCCATCACAGACGTCACA
169230 GAACAGTGACATGGCAGTTGACGACATTGAATGAGTGTGGAAAACGTCCAGCTGATCGATTACAT
66 GAACAGTGACATGGCAGTTGACGACATTGAATGAGTGTGGAAAACGTCCAGCTGATCGATTACAT
169295 TTAACAAAA
131 TTAACAAAA
169304 CAGTCACTCAACTTTGAAAATGTGACAAAACAGTCCTTTTCATGTTTTCCATCACAGACGTCACA
1 CAGTCACTCAACTTTGAAAATGTGACAAAACAGTCCTTTTCATGTTTTCCATCACAGACGTCACA
*
169369 GAACAGTGACATGGCAGTTGACGACATTGAATGAGTGTGGAAAACGTCCAGTTGATCGATTACAT
66 GAACAGTGACATGGCAGTTGACGACATTGAATGAGTGTGGAAAACGTCCAGCTGATCGATTACAT
169434 TTAACAAAA
131 TTAACAAAA
169443 CAGTCACTCAACTTTGAAAATGTGACAAAACAGTCCT
1 CAGTCACTCAACTTTGAAAATGTGACAAAACAGTCCT
169480 CTACTTACTA
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 174 1.00
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (139 bp):
CAGTCACTCAACTTTGAAAATGTGACAAAACAGTCCTTTTCATGTTTTCCATCACAGACGTCACA
GAACAGTGACATGGCAGTTGACGACATTGAATGAGTGTGGAAAACGTCCAGCTGATCGATTACAT
TTAACAAAA
Found at i:171111 original size:39 final size:39
Alignment explanation
Indices: 171057--171133 Score: 154
Period size: 39 Copynumber: 2.0 Consensus size: 39
171047 GATTTTATTA
171057 TGATTAATGATTATCTTGGGTTTAGACACATGGTTATAG
1 TGATTAATGATTATCTTGGGTTTAGACACATGGTTATAG
171096 TGATTAATGATTATCTTGGGTTTAGACACATGGTTATA
1 TGATTAATGATTATCTTGGGTTTAGACACATGGTTATA
171134 CATTTAACTG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.42
Consensus pattern (39 bp):
TGATTAATGATTATCTTGGGTTTAGACACATGGTTATAG
Found at i:175547 original size:13 final size:13
Alignment explanation
Indices: 175529--175558 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
175519 ATTTAAAAAT
*
175529 AAAAAAATATTTA
1 AAAAAAAAATTTA
175542 AAAAAAAAATTTA
1 AAAAAAAAATTTA
175555 AAAA
1 AAAA
175559 TATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAAAAAATTTA
Found at i:175549 original size:23 final size:21
Alignment explanation
Indices: 175523--175568 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
175513 TTTTAAATTT
175523 AAAAATAAAAAAATATTTAAAAA
1 AAAAATAAAAAAATA--TAAAAA
**
175546 AAAAATTTAAAAATATAAAAA
1 AAAAATAAAAAAATATAAAAA
175567 AA
1 AA
175569 TATAAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
23 13 0.62
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (21 bp):
AAAAATAAAAAAATATAAAAA
Found at i:175552 original size:31 final size:31
Alignment explanation
Indices: 175517--175575 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
175507 AAATTCTTTT
*
175517 AAATTTAAAAATA-AAAAAATATTTAAAAAAA
1 AAATTTAAAAATATAAAAAA-ATATAAAAAAA
175548 AAATTTAAAAATATAAAAAAATATAAAA
1 AAATTTAAAAATATAAAAAAATATAAAA
175576 TTTAATGTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 20 0.77
32 6 0.23
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (31 bp):
AAATTTAAAAATATAAAAAAATATAAAAAAA
Found at i:175575 original size:25 final size:23
Alignment explanation
Indices: 175531--175580 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
175521 TTAAAAATAA
**
175531 AAAAATATTTAAAAAAAAAATTT
1 AAAAATATAAAAAAAAAAAATTT
175554 AAAAATATAAAAAAATATAAAATTT
1 AAAAATATAAAAAAA-A-AAAATTT
175579 AA
1 AA
175581 TGTCATCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 13 0.57
24 1 0.04
25 9 0.39
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (23 bp):
AAAAATATAAAAAAAAAAAATTT
Found at i:175813 original size:31 final size:31
Alignment explanation
Indices: 175737--175813 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
175727 TTTGTCCAAT
*
175737 TTGGTACTCAAACTTGACACTTTTTCATAAA
1 TTGGTACTTAAACTTGACACTTTTTCATAAA
* * *
175768 TTGGTACCTAAACTTGACACCTTTTT-TTAAG
1 TTGGTACTTAAACTTGACA-CTTTTTCATAAA
*
175799 TTGGTACTTGAACTT
1 TTGGTACTTAAACTT
175814 TTTGGGGTCC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
31 33 0.85
32 6 0.15
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACACTTTTTCATAAA
Found at i:175850 original size:90 final size:89
Alignment explanation
Indices: 175679--175868 Score: 204
Period size: 90 Copynumber: 2.1 Consensus size: 89
175669 AATATAACAT
* * * ***
175679 TTGGTACTTAAACTTGAAATTTTTTTTAATTTGGTACCTAAACTTTTTTTTGTCCAATTTGGTAC
1 TTGGTACCTAAACTTGAAACTTTTTTTAAGTTGGTACCTAAACTTTTTGGGGTCCAATTTGGTAC
175744 TCAAACTTGACAC-TTTTTCATAAA
66 TCAAACTTGACACTTTTTTC-TAAA
* * * *
175768 TTGGTACCTAAACTTGACACCTTTTTTTAAGTTGGTACTTGAACTTTTTGGGGTCCAATTTGGTG
1 TTGGTACCTAAACTTGA-AACTTTTTTTAAGTTGGTACCTAAACTTTTTGGGGTCCAATTTGGTA
* ** *
175833 C-CTTAACTTGATTCTTTTTTCTAAT
65 CTC-AAACTTGACACTTTTTTCTAAA
*
175858 TTGATACCTAA
1 TTGGTACCTAA
175869 GTTTTTTTAA
Statistics
Matches: 83, Mismatches: 15, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
89 17 0.20
90 60 0.72
91 6 0.07
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (89 bp):
TTGGTACCTAAACTTGAAACTTTTTTTAAGTTGGTACCTAAACTTTTTGGGGTCCAATTTGGTAC
TCAAACTTGACACTTTTTTCTAAA
Found at i:176124 original size:60 final size:58
Alignment explanation
Indices: 176050--176206 Score: 199
Period size: 58 Copynumber: 2.7 Consensus size: 58
176040 AAATCTTATA
* * *
176050 TACCAAATTAAGAAAAAATGTCAAGTTCAGGTACTAAATTTG-GTCCAAAAAACGTTTGGG
1 TACCAAATTAAGAAAAAATGTCAAGTTCAAGTACCAAA-TTGAGT-C-AAAAACGTTTAGG
* * *
176110 TACCAAATTGAGAAAAAATGTCAAGATCAAGTACCAAATTGAGTCAAAAAGGTTTAGG
1 TACCAAATTAAGAAAAAATGTCAAGTTCAAGTACCAAATTGAGTCAAAAACGTTTAGG
* * *
176168 TACCAAATCAGGAAAAAATGTCAAGTTCAAATACCAAAT
1 TACCAAATTAAGAAAAAATGTCAAGTTCAAGTACCAAAT
176207 ATTATATTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
58 45 0.53
59 4 0.05
60 36 0.42
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.24
Consensus pattern (58 bp):
TACCAAATTAAGAAAAAATGTCAAGTTCAAGTACCAAATTGAGTCAAAAACGTTTAGG
Found at i:176290 original size:12 final size:12
Alignment explanation
Indices: 176273--176298 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
176263 GTGTACTTTT
176273 ATTTTAAAAATA
1 ATTTTAAAAATA
176285 ATTTTAAAAATA
1 ATTTTAAAAATA
176297 AT
1 AT
176299 GTAATGGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTTTAAAAATA
Found at i:176718 original size:21 final size:20
Alignment explanation
Indices: 176665--176720 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
176655 TTAGGCTTAT
*
176665 ATATATATATATATATTTAAAA
1 ATATATA-ATA-ATTTTTAAAA
176687 ATATATAATAATTTTTAAAA
1 ATATATAATAATTTTTAAAA
*
176707 TTATATTAATAATT
1 ATATA-TAATAATT
176721 AATTATACAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 13 0.42
21 11 0.35
22 7 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATATAATAATTTTTAAAA
Found at i:184768 original size:15 final size:14
Alignment explanation
Indices: 184741--184775 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
184731 GGTTTTTAAA
184741 AAAATATATAAAAT
1 AAAATATATAAAAT
*
184755 ATAATATAATAAAAT
1 AAAATAT-ATAAAAT
184770 AAAATA
1 AAAATA
184776 AAATTATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
AAAATATATAAAAT
Done.