Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1252
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: 134262
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:711 original size:23 final size:22
Alignment explanation
Indices: 659--711 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
649 TCCACGTCTT
*
659 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
681 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
704 TTTCTTTT
1 TTTCTTTT
712 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:12024 original size:15 final size:16
Alignment explanation
Indices: 11985--12025 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
11975 AACAACACTC
11985 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
12001 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
12015 CTTTCTTTTTC
1 CTTTCTTTTTC
12026 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:12216 original size:17 final size:15
Alignment explanation
Indices: 12179--12217 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
12169 TATCTCCCAC
12179 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
12195 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
12212 TCATTT
1 TCATTT
12218 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:13078 original size:27 final size:28
Alignment explanation
Indices: 13036--13102 Score: 109
Period size: 28 Copynumber: 2.4 Consensus size: 28
13026 TTTCAATCAC
*
13036 TCTTTTTTTTTCAATTTCG-ATTTTTTT
1 TCTTTTTTTTTTAATTTCGAATTTTTTT
13063 TCTTTTTTTTTTAATTTCGAATTTTTTT
1 TCTTTTTTTTTTAATTTCGAATTTTTTT
*
13091 TCTTCTTTTTTT
1 TCTTTTTTTTTT
13103 CTTCAATACT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
27 18 0.49
28 19 0.51
ACGTcount: A:0.10, C:0.10, G:0.03, T:0.76
Consensus pattern (28 bp):
TCTTTTTTTTTTAATTTCGAATTTTTTT
Found at i:13164 original size:12 final size:12
Alignment explanation
Indices: 13147--13175 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13137 GAATACAAAC
13147 TTTTTTTT-GAA
1 TTTTTTTTCGAA
13158 TTTTTTTTCGAA
1 TTTTTTTTCGAA
13170 TTTTTT
1 TTTTTT
13176 CCCTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.47
12 9 0.53
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTTTTCGAA
Found at i:16408 original size:15 final size:16
Alignment explanation
Indices: 16369--16409 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
16359 AACAACACTC
16369 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
16385 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
16399 CTTTCTTTTTC
1 CTTTCTTTTTC
16410 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:16601 original size:17 final size:15
Alignment explanation
Indices: 16564--16602 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
16554 TATCTCCCAC
16564 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
16580 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
16597 TCATTT
1 TCATTT
16603 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:17464 original size:26 final size:27
Alignment explanation
Indices: 17420--17484 Score: 96
Period size: 26 Copynumber: 2.4 Consensus size: 27
17410 TTTCAATCAC
* *
17420 TCTTTTTTTTTCAATTTCGATTTTTTT
1 TCTTTTTTTTTTAATTTCGAATTTTTT
17447 TCTTTTTTTTTTAA-TTCGAATTTTTT
1 TCTTTTTTTTTTAATTTCGAATTTTTT
*
17473 TCTTCTTTTTTT
1 TCTTTTTTTTTT
17485 CTTCAATACT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 22 0.63
27 13 0.37
ACGTcount: A:0.11, C:0.11, G:0.03, T:0.75
Consensus pattern (27 bp):
TCTTTTTTTTTTAATTTCGAATTTTTT
Found at i:17546 original size:12 final size:12
Alignment explanation
Indices: 17529--17571 Score: 59
Period size: 13 Copynumber: 3.4 Consensus size: 12
17519 GAATACAAAC
17529 TTTTTTTTGAATT
1 TTTTTTTTGAA-T
17542 TTTTTTTTCGAAT
1 TTTTTTTT-GAAT
*
17555 TTTTTTTCGAAT
1 TTTTTTTTGAAT
17567 TTTTT
1 TTTTT
17572 CCCTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 9 0.32
13 16 0.57
14 3 0.11
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (12 bp):
TTTTTTTTGAAT
Found at i:17548 original size:14 final size:14
Alignment explanation
Indices: 17529--17571 Score: 65
Period size: 12 Copynumber: 3.3 Consensus size: 14
17519 GAATACAAAC
17529 TTTTTTTT-GAATT
1 TTTTTTTTCGAATT
17542 TTTTTTTTCGAA--
1 TTTTTTTTCGAATT
17554 TTTTTTTTCGAATT
1 TTTTTTTTCGAATT
17568 TTTT
1 TTTT
17572 CCCTTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 12 0.44
13 8 0.30
14 7 0.26
ACGTcount: A:0.14, C:0.05, G:0.07, T:0.74
Consensus pattern (14 bp):
TTTTTTTTCGAATT
Found at i:26875 original size:21 final size:23
Alignment explanation
Indices: 26830--26876 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
26820 TCACCTGCAA
* *
26830 TAAACACATTAAAATGAGTTTAT
1 TAAACACATTAAAATCAGCTTAT
26853 TAAACACATTAAAA-CA-CTTAT
1 TAAACACATTAAAATCAGCTTAT
26874 TAA
1 TAA
26877 TCATAACACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 7 0.32
22 1 0.05
23 14 0.64
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.32
Consensus pattern (23 bp):
TAAACACATTAAAATCAGCTTAT
Found at i:32150 original size:15 final size:16
Alignment explanation
Indices: 32130--32169 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
32120 TAGCTTCTTC
32130 TTTTTTTCACG-AATT
1 TTTTTTTCACGAAATT
32145 TTTTTTTCACGAAATT
1 TTTTTTTCACGAAATT
32161 TTTTTTTCA
1 TTTTTTTCA
32170 ACTTGATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.20, C:0.12, G:0.05, T:0.62
Consensus pattern (16 bp):
TTTTTTTCACGAAATT
Found at i:32223 original size:12 final size:12
Alignment explanation
Indices: 32205--32238 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
32195 GAAAGGAAAC
32205 CAATTTTTTTTT
1 CAATTTTTTTTT
*
32217 GAA-TTTTTTTT
1 CAATTTTTTTTT
32228 CAATTTTTTTT
1 CAATTTTTTTT
32239 GAAGAAACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:32225 original size:11 final size:11
Alignment explanation
Indices: 32209--32241 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
32199 GGAAACCAAT
32209 TTTTTTTTGAA
1 TTTTTTTTGAA
*
32220 TTTTTTTTCAA
1 TTTTTTTTGAA
32231 TTTTTTTTGAA
1 TTTTTTTTGAA
32242 GAAACTACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.73
Consensus pattern (11 bp):
TTTTTTTTGAA
Found at i:38473 original size:45 final size:45
Alignment explanation
Indices: 38424--38656 Score: 394
Period size: 45 Copynumber: 5.2 Consensus size: 45
38414 TCGGCCATGG
* * * *
38424 TGCTTCCTCAATTTGTTCCATAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
38469 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
38514 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTAGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
38559 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
38604 TGCTTCCTCAAATTCTCCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
38649 TGCTTCCT
1 TGCTTCCT
38657 TAATTTCATG
Statistics
Matches: 179, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 179 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:41187 original size:30 final size:30
Alignment explanation
Indices: 41153--41227 Score: 150
Period size: 30 Copynumber: 2.5 Consensus size: 30
41143 AGATTCGATT
41153 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
41183 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
1 TCTTGATTTTCTTGAAAACAAGAAAGTGAA
41213 TCTTGATTTTCTTGA
1 TCTTGATTTTCTTGA
41228 TTTGAGCCCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 45 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.39
Consensus pattern (30 bp):
TCTTGATTTTCTTGAAAACAAGAAAGTGAA
Found at i:42548 original size:23 final size:22
Alignment explanation
Indices: 42496--42548 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
42486 TCCACGTCTT
*
42496 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
42518 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
42541 TTTCTTTT
1 TTTCTTTT
42549 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:47212 original size:22 final size:22
Alignment explanation
Indices: 47182--47225 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
47172 TTTGGTATTT
47182 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
47204 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
47226 TGGTTCAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.36, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:53112 original size:10 final size:10
Alignment explanation
Indices: 53088--53136 Score: 55
Period size: 10 Copynumber: 4.9 Consensus size: 10
53078 AGCTCGTTTC
*
53088 CAGCTCACTT
1 CAGCTCAATT
* *
53098 GAGCTCAAGT
1 CAGCTCAATT
53108 CAGCTC-ATT
1 CAGCTCAATT
53117 CGAGCTCAATT
1 C-AGCTCAATT
53128 CAGCTCAAT
1 CAGCTCAAT
53137 CTTAACCCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 3 0.09
10 25 0.78
11 4 0.12
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.27
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:53113 original size:20 final size:20
Alignment explanation
Indices: 53088--53134 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
53078 AGCTCGTTTC
53088 CAGCTCACTT-GAGCTCAAGT
1 CAGCTCA-TTCGAGCTCAAGT
*
53108 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAAGT
53128 CAGCTCA
1 CAGCTCA
53135 ATCTTAACCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.26
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAAGT
Found at i:63390 original size:11 final size:11
Alignment explanation
Indices: 63374--63413 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
63364 TAGTTTCTTC
63374 AAAAAAATTTG
1 AAAAAAATTTG
63385 AAAAAAAATTTG
1 -AAAAAAATTTG
* *
63397 AAAAAAAATTC
1 AAAAAAATTTG
63408 AAAAAA
1 AAAAAA
63414 TAATTGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.20
Consensus pattern (11 bp):
AAAAAAATTTG
Found at i:63413 original size:12 final size:12
Alignment explanation
Indices: 63374--63406 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
63364 TAGTTTCTTC
63374 AAAAAAATTTGA
1 AAAAAAATTTGA
63386 AAAAAAATTTGA
1 AAAAAAATTTGA
63398 AAAAAAATT
1 AAAAAAATT
63407 CAAAAAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:63418 original size:12 final size:11
Alignment explanation
Indices: 63371--63418 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
63361 TAGTAGTTTC
*
63371 TTCAAAAAAAT
1 TTCAAAAAAAA
*
63382 TTGAAAAAAAA
1 TTCAAAAAAAA
*
63393 TTTGAAAAAAAA
1 -TTCAAAAAAAA
63405 TTCAAAAAATAA
1 TTCAAAAAA-AA
63417 TT
1 TT
63419 GGTTTCCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
11 17 0.53
12 15 0.47
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (11 bp):
TTCAAAAAAAA
Found at i:63478 original size:15 final size:15
Alignment explanation
Indices: 63455--63496 Score: 75
Period size: 15 Copynumber: 2.7 Consensus size: 15
63445 GATATCAAGT
63455 TGAAAAAAAAATTTCG
1 TGAAAAAAAAA-TTCG
63471 TGAAAAAAAAATTCG
1 TGAAAAAAAAATTCG
63486 TGAAAAAAAAA
1 TGAAAAAAAAA
63497 GAAGAAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.64, C:0.05, G:0.12, T:0.19
Consensus pattern (15 bp):
TGAAAAAAAAATTCG
Found at i:72634 original size:20 final size:20
Alignment explanation
Indices: 72611--72657 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
72601 GGGTTAAGAT
*
72611 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* * *
72631 TGAGTTGACTTGAGCTCGTG
1 TGAGCTGAATTGAGCTCGAG
72651 TGAGCTG
1 TGAGCTG
72658 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:0.19, C:0.13, G:0.36, T:0.32
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:80579 original size:9 final size:9
Alignment explanation
Indices: 80564--80598 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
80554 TAAATTTCGT
80564 CTTTTTTGA
1 CTTTTTTGA
*
80573 TTTTTTTGA
1 CTTTTTTGA
80582 CTTTTTTGA
1 CTTTTTTGA
80591 CTATTTTT
1 CT-TTTTT
80599 TATCGGGATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 18 0.78
10 5 0.22
ACGTcount: A:0.11, C:0.09, G:0.09, T:0.71
Consensus pattern (9 bp):
CTTTTTTGA
Found at i:88466 original size:23 final size:22
Alignment explanation
Indices: 88440--88492 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
88430 AAGAGAATGA
*
88440 AAAAGAAATT-GAAGAAAGAAGAG
1 AAAAGAAATTAGAA-AAAGAA-AC
88463 AAAATG-AATTAGAAAAAGAAAC
1 AAAA-GAAATTAGAAAAAGAAAC
88485 AAAAGAAA
1 AAAAGAAA
88493 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:101387 original size:21 final size:21
Alignment explanation
Indices: 101363--101403 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
101353 TTTGAACCAT
*
101363 TACCAATTCGTACCAATTCCA
1 TACCAATTCGAACCAATTCCA
*
101384 TACCATTTCGAACCAATTCC
1 TACCAATTCGAACCAATTCC
101404 CAAATACCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (21 bp):
TACCAATTCGAACCAATTCCA
Found at i:103496 original size:12 final size:12
Alignment explanation
Indices: 103479--103503 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
103469 AATTTTAGAC
103479 CATTTAAATAAG
1 CATTTAAATAAG
103491 CATTTAAATAAG
1 CATTTAAATAAG
103503 C
1 C
103504 TTCATTACAG
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:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (12 bp):
CATTTAAATAAG
Found at i:120410 original size:21 final size:21
Alignment explanation
Indices: 120372--120427 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
120362 CATTACCAAT
*
120372 TCGTACCAAATACCATACCATC
1 TCGTACC-AATTCCATACCATC
* *
120394 TCGTACCAATTCCATACTATT
1 TCGTACCAATTCCATACCATC
*
120415 TCGAACCAATTCC
1 TCGTACCAATTCC
120428 TAAATACCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
21 23 0.77
22 7 0.23
ACGTcount: A:0.32, C:0.34, G:0.05, T:0.29
Consensus pattern (21 bp):
TCGTACCAATTCCATACCATC
Found at i:121253 original size:23 final size:22
Alignment explanation
Indices: 121201--121253 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
121191 TCCACGTCTT
*
121201 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
121223 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
121246 TTTCTTTT
1 TTTCTTTT
121254 TCAATCTTAA
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:124895 original size:30 final size:30
Alignment explanation
Indices: 124861--124957 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
124851 AGCTCACTCC
124861 TAGCTCATA-TTTAGCTCACGAGCTAAACCT
1 TAGCTCA-ACTTTAGCTCACGAGCTAAACCT
* * * * * *
124891 TAGCTCAACTTCAGCTTAGGAGTTTAGCCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
* *
124921 CAGCTCAACTTTAGCTCACGAGCTAAAGCT
1 TAGCTCAACTTTAGCTCACGAGCTAAACCT
124951 TAGCTCA
1 TAGCTCA
124958 TTTTAGTTTA
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (30 bp):
TAGCTCAACTTTAGCTCACGAGCTAAACCT
Found at i:126757 original size:13 final size:12
Alignment explanation
Indices: 126741--126771 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
126731 AAAAAAATTT
126741 AAAAAAAATCAAA
1 AAAAAAAAT-AAA
126754 AAAAAAAATAAA
1 AAAAAAAATAAA
126766 AAAAAA
1 AAAAAA
126772 TTGAAGTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.90, C:0.03, G:0.00, T:0.06
Consensus pattern (12 bp):
AAAAAAAATAAA
Found at i:127652 original size:5 final size:5
Alignment explanation
Indices: 127642--127703 Score: 56
Period size: 5 Copynumber: 12.0 Consensus size: 5
127632 AAGAGAAAAT
* *
127642 AAAGA AAAGA AAAGAA AAAGA AAA-A GCAAGA GAAGAA AAAGA AAAGA
1 AAAGA AAAGA AAAG-A AAAGA AAAGA -AAAGA AAAG-A AAAGA AAAGA
127689 AATA-A AAAGA AAAGA
1 AA-AGA AAAGA AAAGA
127704 GAGGCAAGAG
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
4 2 0.04
5 35 0.73
6 11 0.23
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:127672 original size:26 final size:26
Alignment explanation
Indices: 127642--127703 Score: 74
Period size: 26 Copynumber: 2.4 Consensus size: 26
127632 AAGAGAAAAT
127642 AAAGAAAAG-AAAAGAAAAAGAAA-AA
1 AAAGAAAAGAAAAAG-AAAAGAAATAA
* *
127667 GCAAGAGAAGAAAAAGAAAAGAAATAA
1 -AAAGAAAAGAAAAAGAAAAGAAATAA
127694 AAAGAAAAGA
1 AAAGAAAAGA
127704 GAGGCAAGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
26 23 0.77
27 7 0.23
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (26 bp):
AAAGAAAAGAAAAAGAAAAGAAATAA
Found at i:127683 original size:37 final size:36
Alignment explanation
Indices: 127632--127701 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
127622 CATTCTTGTA
127632 AAGAGAAAATAAAGAAAAGAAAAGAAAAAGAAAAAGC
1 AAGAGAAAATAAAGAAAAG-AAAGAAAAAGAAAAAGC
*
127669 AAGAGAAGAA-AAAGAAAAGAAATAAAAAGAAAA
1 AAGAGAA-AATAAAGAAAAGAAAGAAAAAGAAAA
127702 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
36 13 0.42
37 16 0.52
38 2 0.06
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (36 bp):
AAGAGAAAATAAAGAAAAGAAAGAAAAAGAAAAAGC
Found at i:127695 original size:15 final size:14
Alignment explanation
Indices: 127635--127703 Score: 59
Period size: 15 Copynumber: 4.6 Consensus size: 14
127625 TCTTGTAAAG
* *
127635 AGAAAATAAAGAAA
1 AGAAAAGAAAAAAA
127649 AGAAAAGAAAAAGAA
1 AGAAAAGAAAAA-AA
127664 A-AAGCAAGAGAAGAAAA
1 AGAA--AAGA-AA-AAAA
127681 AGAAAAGAAATAAAA
1 AGAAAAGAAA-AAAA
127696 AGAAAAGA
1 AGAAAAGA
127704 GAGGCAAGAG
Statistics
Matches: 46, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
14 12 0.26
15 17 0.37
16 8 0.17
17 5 0.11
18 4 0.09
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (14 bp):
AGAAAAGAAAAAAA
Found at i:127698 original size:21 final size:21
Alignment explanation
Indices: 127642--127701 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
127632 AAGAGAAAAT
127642 AAAGAAAAGAAAAGAAAAAGAA
1 AAAGAAAA-AAAAGAAAAAGAA
* * *
127664 AAAGCAAGAGAAGAAAAAG-A
1 AAAGAAAAAAAAGAAAAAGAA
127684 AAAGAAATAAAAAGAAAA
1 AAAGAAA-AAAAAGAAAA
127702 GAGAGGCAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 7 0.23
21 18 0.58
22 6 0.19
ACGTcount: A:0.78, C:0.02, G:0.18, T:0.02
Consensus pattern (21 bp):
AAAGAAAAAAAAGAAAAAGAA
Found at i:127701 original size:6 final size:6
Alignment explanation
Indices: 127642--127690 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
127632 AAGAGAAAAT
127642 AAAG-A AAAG-A AAAGAA AAAGAA AAAGCAA GAGAAGAA AAAG-A AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAG-AA -A-AAGAA AAAGAA AAAGAA
127690 A
1 A
127691 TAAAAAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
5 14 0.36
6 16 0.41
7 3 0.08
8 3 0.08
9 3 0.08
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:127783 original size:11 final size:12
Alignment explanation
Indices: 127751--127781 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
127741 TTGAGAGAAC
127751 TTGAAAAAGCCT
1 TTGAAAAAGCCT
127763 TTGAAAAAGCCT
1 TTGAAAAAGCCT
127775 TTGAAAA
1 TTGAAAA
127782 GCAAAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (12 bp):
TTGAAAAAGCCT
Found at i:127799 original size:11 final size:12
Alignment explanation
Indices: 127784--127815 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
127774 TTTGAAAAGC
127784 AAAAAGAAAATG
1 AAAAAGAAAATG
127796 AAAAAGAAAATG
1 AAAAAGAAAATG
127808 -AAAAGAAA
1 AAAAAGAAA
127816 TTTGAGAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (12 bp):
AAAAAGAAAATG
Done.