Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3445
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: 125076
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:10941 original size:13 final size:14
Alignment explanation
Indices: 10925--10955 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
10915 TTAAACTAAG
10925 TAAATAAAT-AAAA
1 TAAATAAATAAAAA
10938 TAAATAAATAAAAA
1 TAAATAAATAAAAA
10952 TAAA
1 TAAA
10956 ACTTTACAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (14 bp):
TAAATAAATAAAAA
Found at i:12351 original size:23 final size:22
Alignment explanation
Indices: 12300--12351 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 22
12290 CCTCGTCTTT
*
12300 TTCTTTTGTTTCTTTTTCTAAC
1 TTCTTTTCTTTCTTTTTCTAAC
12322 -TCATTTTCTCTTCTTTCTTC-AAC
1 TTC-TTTTCT-TTCTTT-TTCTAAC
12345 TTCTTTT
1 TTCTTTT
12352 TCAAATTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 2 0.08
22 5 0.20
23 13 0.52
24 5 0.20
ACGTcount: A:0.10, C:0.23, G:0.02, T:0.65
Consensus pattern (22 bp):
TTCTTTTCTTTCTTTTTCTAAC
Found at i:14208 original size:11 final size:10
Alignment explanation
Indices: 14183--14243 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
14173 ACCAATAAAA
14183 TAAA-TGAGC
1 TAAATTGAGC
*
14192 TGAATTGTAGC
1 TAAATTG-AGC
14203 TAAATTGAGC
1 TAAATTGAGC
**
14213 TCGATTGAGC
1 TAAATTGAGC
14223 TGAAA-TGAGC
1 T-AAATTGAGC
*
14233 TCAATTGAGC
1 TAAATTGAGC
14243 T
1 T
14244 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:14244 original size:20 final size:20
Alignment explanation
Indices: 14184--14244 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
14174 CCAATAAAAT
*
14184 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
14204 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
14225 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
14245 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:16330 original size:18 final size:18
Alignment explanation
Indices: 16309--16343 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
16299 TTTTTCTTTT
16309 TCAATTT-TTTTCTCAATC
1 TCAATTTCTTTT-TCAATC
16327 TCAATTTCTTTTTCAAT
1 TCAATTTCTTTTTCAAT
16344 TTTCTTTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (18 bp):
TCAATTTCTTTTTCAATC
Found at i:16340 original size:6 final size:6
Alignment explanation
Indices: 16331--16435 Score: 52
Period size: 6 Copynumber: 17.2 Consensus size: 6
16321 TCAATCTCAA
* * * ** **
16331 TTTCTT TTTCAAT TTTCTTT TCTTCAT TTTCTT TTTCTC TCACTAT TTTGAT
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCT-T TTTCTT
* ** * *
16383 TT-CTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
16429 TTTCTT T
1 TTTCTT T
16436 CAATTTCTTT
Statistics
Matches: 69, Mismatches: 25, Indels: 10
0.66 0.24 0.10
Matches are distributed among these distances:
5 7 0.10
6 49 0.71
7 10 0.14
8 3 0.04
ACGTcount: A:0.08, C:0.17, G:0.04, T:0.71
Consensus pattern (6 bp):
TTTCTT
Found at i:16448 original size:6 final size:6
Alignment explanation
Indices: 16382--16435 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
16372 ACTATTTTGA
* ** * *
16382 TTTCTT TTTCTT TTGCAA TTTCTT TTTCTT TTTCGT TTTCTT TTT-GT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
16429 TTTCTT T
1 TTTCTT T
16436 CAATTTCTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.04, C:0.15, G:0.06, T:0.76
Consensus pattern (6 bp):
TTTCTT
Found at i:17516 original size:11 final size:11
Alignment explanation
Indices: 17502--17536 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
17492 TTTTTTTTTC
*
17502 TTTTTTTCG-A
1 TTTTTTTTGAA
17512 TTTTTTTTGAA
1 TTTTTTTTGAA
17523 TTTTTTTTGAA
1 TTTTTTTTGAA
17534 TTT
1 TTT
17537 CTTCTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:17628 original size:11 final size:10
Alignment explanation
Indices: 17611--17641 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
17601 TCCAACTCAA
17611 ATTTTTTTTG
1 ATTTTTTTTG
17621 ATTTTTTTTG
1 ATTTTTTTTG
17631 ACTTTTTTTTG
1 A-TTTTTTTTG
17642 TTACGAACCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.10, C:0.03, G:0.10, T:0.77
Consensus pattern (10 bp):
ATTTTTTTTG
Found at i:18918 original size:11 final size:10
Alignment explanation
Indices: 18893--18953 Score: 54
Period size: 10 Copynumber: 6.1 Consensus size: 10
18883 ACCAATAAAA
18893 TAAA-TGAGC
1 TAAATTGAGC
*
18902 TGAATTGTAGC
1 TAAATTG-AGC
18913 TAAATTGAGC
1 TAAATTGAGC
**
18923 TCGATTGAGC
1 TAAATTGAGC
18933 TGAAA-TGAGC
1 T-AAATTGAGC
*
18943 TCAATTGAGC
1 TAAATTGAGC
18953 T
1 T
18954 GGTCGGAGTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
9 5 0.12
10 26 0.63
11 10 0.24
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.30
Consensus pattern (10 bp):
TAAATTGAGC
Found at i:18954 original size:20 final size:20
Alignment explanation
Indices: 18894--18954 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
18884 CCAATAAAAT
*
18894 AAATGAGCTGAATTGTAGCT-
1 AAATGAGCTCAATTG-AGCTG
*
18914 AAATTGAGCTCGATTGAGCTG
1 AAA-TGAGCTCAATTGAGCTG
18935 AAATGAGCTCAATTGAGCTG
1 AAATGAGCTCAATTGAGCTG
18955 GTCGGAGTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AAATGAGCTCAATTGAGCTG
Found at i:22519 original size:16 final size:15
Alignment explanation
Indices: 22498--22527 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
22488 GCACGTGAAA
22498 AAAATTCAAAAAAATC
1 AAAATT-AAAAAAATC
22514 AAAATTAAAAAAAT
1 AAAATTAAAAAAAT
22528 ATATACAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (15 bp):
AAAATTAAAAAAATC
Found at i:30527 original size:4 final size:4
Alignment explanation
Indices: 30518--30552 Score: 63
Period size: 4 Copynumber: 9.0 Consensus size: 4
30508 TTAAACTAAG
30518 TAAA TAAA TAAA TAAA TAAA TAAA TAAA -AAA TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
30553 AATAAAACTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:31956 original size:23 final size:22
Alignment explanation
Indices: 31904--31956 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
31894 TCCACGTCTT
*
31904 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
31926 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
31949 TTTCTTTT
1 TTTCTTTT
31957 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:41606 original size:12 final size:13
Alignment explanation
Indices: 41591--41619 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
41581 AGATGTGAAG
41591 AGAAATTGAA-AA
1 AGAAATTGAAGAA
41603 AGAAATTGAAGAA
1 AGAAATTGAAGAA
41616 AGAA
1 AGAA
41620 GAGAAAATGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.66, C:0.00, G:0.21, T:0.14
Consensus pattern (13 bp):
AGAAATTGAAGAA
Found at i:41626 original size:23 final size:22
Alignment explanation
Indices: 41600--41652 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
41590 GAGAAATTGA
*
41600 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
41623 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
41645 AAAAGAAA
1 AAAAGAAA
41653 AAGACGTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 14 0.54
24 4 0.15
ACGTcount: A:0.70, C:0.02, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAGAAATTAGAAAAAGAAAC
Found at i:43014 original size:4 final size:4
Alignment explanation
Indices: 43005--43030 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
42995 AAGTTTTATT
43005 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
43031 ACTTAGTTTA
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:51926 original size:46 final size:46
Alignment explanation
Indices: 51874--51967 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
51864 ATAGTGTGGC
* *
51874 GTTCATCATATACTAAGGTTCTTATCA-TCATTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
51920 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
51966 GT
1 GT
51968 CTTTTCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 43 0.96
47 2 0.04
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.36
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:54237 original size:22 final size:19
Alignment explanation
Indices: 54198--54239 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
54188 TGCAAAGTTG
54198 ATAATAATTAATATATATT
1 ATAATAATTAATATATATT
54217 ATAATAGATATAATTATATATT
1 ATAATA-AT-TAA-TATATATT
54239 A
1 A
54240 ATGATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 3 0.15
22 9 0.45
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
ATAATAATTAATATATATT
Found at i:55352 original size:20 final size:20
Alignment explanation
Indices: 55329--55382 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
55319 AGTTTTTCCC
*
55329 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
55349 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
55369 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
55383 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:55364 original size:30 final size:30
Alignment explanation
Indices: 55329--55402 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
55319 AGTTTTTCCC
55329 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
55359 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
55389 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
55403 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:55392 original size:20 final size:20
Alignment explanation
Indices: 55329--55393 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
55319 AGTTTTTCCC
* * * *
55329 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
55349 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
55368 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
55389 AGCTC
1 AGCTC
55394 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:57024 original size:11 final size:11
Alignment explanation
Indices: 57002--57037 Score: 56
Period size: 10 Copynumber: 3.3 Consensus size: 11
56992 AAGAGAGAAG
57002 AAATTCAGAAAA
1 AAATTCA-AAAA
57014 AAATTCAAAAA
1 AAATTCAAAAA
57025 AAA-TCAAAAA
1 AAATTCAAAAA
57035 AAA
1 AAA
57038 GAAAAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 10 0.42
11 7 0.29
12 7 0.29
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:57025 original size:10 final size:10
Alignment explanation
Indices: 57010--57060 Score: 50
Period size: 10 Copynumber: 5.0 Consensus size: 10
57000 AGAAATTCAG
*
57010 AAAAAAATTC
1 AAAAAAAATC
57020 AAAAAAAATC
1 AAAAAAAATC
*
57030 AAAAAAAA-G
1 AAAAAAAATC
*
57039 AAAAAAAAGTG
1 AAAAAAAA-TC
57050 ACAAAAAAATC
1 A-AAAAAAATC
57061 GAGTTAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 8 0.23
10 17 0.49
11 3 0.09
12 7 0.20
ACGTcount: A:0.76, C:0.08, G:0.06, T:0.10
Consensus pattern (10 bp):
AAAAAAAATC
Found at i:58136 original size:5 final size:6
Alignment explanation
Indices: 58106--58243 Score: 55
Period size: 6 Copynumber: 22.7 Consensus size: 6
58096 AAAGAAATTG
* * * ** *
58106 AAAG-A AAACAA AAAGGA AATGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
* ** ** * * *
58153 AAGGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
** * * *
58204 AAAGAA ATTGAG AATGAA AAA-AA AATTGAA AAAGAA AAAG
1 AAAGAA AAAGAA AAAGAA AAAGAA AA-AGAA AAAGAA AAAG
58244 CGAAAAAAGA
Statistics
Matches: 92, Mismatches: 35, Indels: 11
0.67 0.25 0.08
Matches are distributed among these distances:
5 7 0.08
6 70 0.76
7 11 0.12
8 4 0.04
ACGTcount: A:0.69, C:0.02, G:0.20, T:0.09
Consensus pattern (6 bp):
AAAGAA
Found at i:58221 original size:18 final size:18
Alignment explanation
Indices: 58092--58243 Score: 73
Period size: 18 Copynumber: 8.4 Consensus size: 18
58082 AGAAAGAGAT
58092 TGAAAAAGAAATTGAAAGAAA
1 TGAAAAAGAAATTG--A-AAA
**
58113 ACAAAAAGGAAA-TGAAAA
1 TGAAAAA-GAAATTGAAAA
*
58131 AGAAAAAGAAATTGCAAAA
1 TGAAAAAGAAATTG-AAAA
* *
58150 -GAAAAGGAAATCGAAAA
1 TGAAAAAGAAATTGAAAA
* ** * **
58167 AGTGAGAGAAAAAGAAAA
1 TGAAAAAGAAATTGAAAA
*
58185 TG---AAGAAA-AGAAAA
1 TGAAAAAGAAATTGAAAA
*
58199 TTGAAAAAGAAATTGAGAA
1 -TGAAAAAGAAATTGAAAA
*
58218 TGAAAAAAAAATTGAAAA
1 TGAAAAAGAAATTGAAAA
*
58236 AGAAAAAG
1 TGAAAAAG
58244 CGAAAAAAGA
Statistics
Matches: 103, Mismatches: 19, Indels: 21
0.72 0.13 0.15
Matches are distributed among these distances:
14 6 0.06
15 7 0.07
17 8 0.08
18 62 0.60
19 9 0.09
21 7 0.07
22 4 0.04
ACGTcount: A:0.68, C:0.02, G:0.20, T:0.11
Consensus pattern (18 bp):
TGAAAAAGAAATTGAAAA
Found at i:58229 original size:30 final size:27
Alignment explanation
Indices: 58174--58261 Score: 97
Period size: 30 Copynumber: 3.1 Consensus size: 27
58164 AAAAGTGAGA
*
58174 GAAAAAGAAAATGAAGAAAAGAAAATT
1 GAAAAAGAAAATGAAGAAAAAAAAATT
*
58201 GAAAAAGAAATTGAGAATGAAAAAAAAATT
1 GAAAAAGAAAAT--GAA-GAAAAAAAAATT
* *
58231 GAAAAAGAAAAAG-CGAAAAAAGAAATT
1 GAAAAAGAAAATGAAGAAAAAA-AAATT
58258 GAAA
1 GAAA
58262 GAGAGCTTGA
Statistics
Matches: 52, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
26 7 0.13
27 20 0.38
28 1 0.02
29 3 0.06
30 21 0.40
ACGTcount: A:0.69, C:0.01, G:0.18, T:0.11
Consensus pattern (27 bp):
GAAAAAGAAAATGAAGAAAAAAAAATT
Found at i:58257 original size:57 final size:52
Alignment explanation
Indices: 58084--58261 Score: 162
Period size: 57 Copynumber: 3.2 Consensus size: 52
58074 AGAAAAGGAG
* * *
58084 AAAGAGATTGAAAAAGAAATTGAAA-GAAAACAAAAAGGAAATGAAAAAG-AA
1 AAAGAAATTGAAAAAGAAATTGAAATGAAAA-AAAAAGAAAAAGAAAAAGAAA
* ** * * *
58135 AAAGAAATTGCAAAAGAAAAGGAAATCGAAAAAGTGAGAGAAAAAGAAAATGAAGA
1 AAAGAAATTGAAAAAGAAATTGAAAT-GAAAAA--AAAAGAAAAAGAAAAAGAA-A
58191 AAAGAAAATTGAAAAAGAAATTGAGAATGAAAAAAAAATTGAAAAAGAAAAAGCGAAA
1 AAAG-AAATTGAAAAAGAAATTGA-AATGAAAAAAAAA--GAAAAAGAAAAA--GAAA
58249 AAAGAAATTGAAA
1 AAAGAAATTGAAA
58262 GAGAGCTTGA
Statistics
Matches: 100, Mismatches: 15, Indels: 18
0.75 0.11 0.14
Matches are distributed among these distances:
51 21 0.21
52 1 0.01
53 5 0.05
54 12 0.12
55 3 0.03
56 5 0.05
57 42 0.42
58 8 0.08
59 3 0.03
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.11
Consensus pattern (52 bp):
AAAGAAATTGAAAAAGAAATTGAAATGAAAAAAAAAGAAAAAGAAAAAGAAA
Found at i:58295 original size:33 final size:33
Alignment explanation
Indices: 58258--58320 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
58248 AAAAGAAATT
58258 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
58291 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
58321 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:60114 original size:20 final size:20
Alignment explanation
Indices: 60091--60144 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 20
60081 AGTTTTTCCC
*
60091 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTCACATG
* ***
60111 AGCTTAATTTAGCTCGTTTG
1 AGCTCAATTTAGCTCACATG
60131 AGCTCAATTTAGCT
1 AGCTCAATTTAGCT
60145 TACTTTAGCT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.20, G:0.19, T:0.37
Consensus pattern (20 bp):
AGCTCAATTTAGCTCACATG
Found at i:60126 original size:30 final size:30
Alignment explanation
Indices: 60091--60164 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
60081 AGTTTTTCCC
60091 AGCTCGATTT-AGCTCACA-TGAGCTTAATTT
1 AGCTCG-TTTGAGCTCA-ATTGAGCTTAATTT
* *
60121 AGCTCGTTTGAGCTCAATTTAGCTTACTTT
1 AGCTCGTTTGAGCTCAATTGAGCTTAATTT
60151 AGCTCGTTTGAGCT
1 AGCTCGTTTGAGCT
60165 TGGCTTAAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (30 bp):
AGCTCGTTTGAGCTCAATTGAGCTTAATTT
Found at i:60154 original size:20 final size:20
Alignment explanation
Indices: 60091--60155 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
60081 AGTTTTTCCC
* * * *
60091 AGCTCGATTTAGCTCACATG
1 AGCTCAATTTAGCTTACTTT
*
60111 AGCTTAATTTAGC-T-CGTTT
1 AGCTCAATTTAGCTTAC-TTT
60130 GAGCTCAATTTAGCTTACTTT
1 -AGCTCAATTTAGCTTACTTT
60151 AGCTC
1 AGCTC
60156 GTTTGAGCTT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 28 0.80
21 4 0.11
22 1 0.03
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.38
Consensus pattern (20 bp):
AGCTCAATTTAGCTTACTTT
Found at i:70528 original size:20 final size:20
Alignment explanation
Indices: 70505--70551 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
70495 GGGTTAAGAT
*
70505 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
70525 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
70545 TGAGCTG
1 TGAGCTG
70552 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:72276 original size:48 final size:48
Alignment explanation
Indices: 72221--72344 Score: 146
Period size: 48 Copynumber: 2.6 Consensus size: 48
72211 TTGTCTTTTC
*
72221 TTTCTTTTTCAATTT-TCTCT-TTTTCCTCACA-CTTTTCTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTT--TCACATCCTTT-TTCAATCTCAA
* *
72269 TTTCTTTTTCGATTTCTTTCTCTTTTTCACATCCTTTTTCAATCTCAA
1 TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
* * *
72317 TTTCTTTTTCAATCTCTTTCTCCTTTTC
1 TTTCTTTTTCAATTTCTCTCTCTTTTTC
72345 TCGCTCAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
48 55 0.82
49 8 0.12
50 4 0.06
ACGTcount: A:0.14, C:0.27, G:0.01, T:0.59
Consensus pattern (48 bp):
TTTCTTTTTCAATTTCTCTCTCTTTTTCACATCCTTTTTCAATCTCAA
Found at i:72344 original size:18 final size:17
Alignment explanation
Indices: 72302--72337 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
72292 TTTTCACATC
72302 CTTTTTCAATCTCAATTT
1 CTTTTTCAATCTC-ATTT
72320 CTTTTTCAATCTC-TTT
1 CTTTTTCAATCTCATTT
72336 CT
1 CT
72338 CCTTTTCTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
18 13 0.72
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.58
Consensus pattern (17 bp):
CTTTTTCAATCTCATTT
Found at i:74946 original size:20 final size:20
Alignment explanation
Indices: 74923--74969 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
74913 GGGTTAAGAT
*
74923 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
74943 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
74963 TGAGCTG
1 TGAGCTG
74970 GAAACGAGCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.21, C:0.13, G:0.36, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:86726 original size:29 final size:29
Alignment explanation
Indices: 86693--86784 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
86683 AATGCAAATT
86693 TAACTAACATGAAAGTTACATAATTAATC
1 TAACTAACATGAAAGTTACATAATTAATC
* * * * * *
86722 TAACTTGAC-T-TAATTTA-ATGATGCAAAC
1 TAAC-TAACATGAAAGTTACATAAT-TAATC
86750 TTAACTAACATGAAAGTTACATAATTAATC
1 -TAACTAACATGAAAGTTACATAATTAATC
86780 TAACT
1 TAACT
86785 TGACTTATTT
Statistics
Matches: 45, Mismatches: 12, Indels: 12
0.65 0.17 0.17
Matches are distributed among these distances:
27 4 0.09
28 11 0.24
29 15 0.33
30 11 0.24
31 4 0.09
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.34
Consensus pattern (29 bp):
TAACTAACATGAAAGTTACATAATTAATC
Found at i:86774 original size:58 final size:58
Alignment explanation
Indices: 86684--86832 Score: 280
Period size: 58 Copynumber: 2.6 Consensus size: 58
86674 TGGTTTTGAA
*
86684 ATGCAAATTTAACTAACATGAAAGTTACATAATTAATCTAACTTGACTTAATTTAATG
1 ATGCAAACTTAACTAACATGAAAGTTACATAATTAATCTAACTTGACTTAATTTAATG
*
86742 ATGCAAACTTAACTAACATGAAAGTTACATAATTAATCTAACTTGACTTATTTTAATG
1 ATGCAAACTTAACTAACATGAAAGTTACATAATTAATCTAACTTGACTTAATTTAATG
86800 ATGCAAACTTAACTAACATGAAAGTTACATAAT
1 ATGCAAACTTAACTAACATGAAAGTTACATAAT
86833 GCATGACTTT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 89 1.00
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.34
Consensus pattern (58 bp):
ATGCAAACTTAACTAACATGAAAGTTACATAATTAATCTAACTTGACTTAATTTAATG
Found at i:89392 original size:17 final size:16
Alignment explanation
Indices: 89368--89402 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
89358 GCAATATATA
89368 TTTTTTTTCAATTTTT
1 TTTTTTTTCAATTTTT
*
89384 TTTTCTTTTCGATTTTT
1 TTTT-TTTTCAATTTTT
89401 TT
1 TT
89403 GATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.09, C:0.09, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTTTTTTCAATTTTT
Found at i:90970 original size:20 final size:20
Alignment explanation
Indices: 90945--90999 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
90935 ACGAGTTAAA
* *
90945 TTGAGCTTGAATGAGCTGAC
1 TTGAGCTCGAATGAGCTAAC
90965 TTGAGCTCGAATGAGCTAAC
1 TTGAGCTCGAATGAGCTAAC
90985 TTGAGCTCGAATGAG
1 TTGAGCTCGAATGAG
91000 TTGAACCACA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.27
Consensus pattern (20 bp):
TTGAGCTCGAATGAGCTAAC
Found at i:94755 original size:22 final size:22
Alignment explanation
Indices: 94725--94768 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
94715 TTTGGTATTT
94725 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
* *
94747 GGGATTTGGTACGTAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
94769 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.05, G:0.36, T:0.27
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:97043 original size:20 final size:20
Alignment explanation
Indices: 97020--97066 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
97010 GGGTTAAGAT
*
97020 TGAGCTGAATTGAGCTTGAA
1 TGAGCTGAATTGAGCTCGAA
* * *
97040 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAA
97060 TGAGCTG
1 TGAGCTG
97067 GAAACGAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAA
Found at i:99658 original size:46 final size:46
Alignment explanation
Indices: 99606--99699 Score: 154
Period size: 46 Copynumber: 2.0 Consensus size: 46
99596 ATAGTGTGGC
* *
99606 GTTCATCATATACCGAGGTTCTTATCA-TCATTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTC-TTGATAGTGGGTCGAG
99652 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
1 GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
99698 GT
1 GT
99700 CTTTTCTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
46 43 0.96
47 2 0.04
ACGTcount: A:0.23, C:0.18, G:0.23, T:0.35
Consensus pattern (46 bp):
GTTCATCATATACCAAGGTTCCTATCATTCTTGATAGTGGGTCGAG
Found at i:100191 original size:14 final size:15
Alignment explanation
Indices: 100156--100195 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
100146 AATATTTACA
100156 TAAAAATTAAACTAAG
1 TAAAAA-TAAACTAAG
*
100172 TAAAAATAAA-TAAT
1 TAAAAATAAACTAAG
100186 TAAAAATAAA
1 TAAAAATAAA
100196 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.25
Consensus pattern (15 bp):
TAAAAATAAACTAAG
Found at i:102573 original size:14 final size:15
Alignment explanation
Indices: 102537--102577 Score: 57
Period size: 14 Copynumber: 2.7 Consensus size: 15
102527 GAATATTTAC
102537 ATAAAAATTAAACTAA
1 ATAAAAA-TAAACTAA
*
102553 GTAAAAATAAA-TAA
1 ATAAAAATAAACTAA
102567 ATAAAAATAAA
1 ATAAAAATAAA
102578 ACTTTACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 4 0.17
16 6 0.26
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (15 bp):
ATAAAAATAAACTAA
Done.