Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1833
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: 113915
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3253 original size:28 final size:29
Alignment explanation
Indices: 3222--3281 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
3212 GATTTTAAGT
*
3222 AAAAATGCATATT-AGGGATTAAATTGTG
1 AAAAATGCAAATTGAGGGATTAAATTGTG
* * * *
3250 AAAAGTGTAAATTGAGGGGTTGAATTGTG
1 AAAAATGCAAATTGAGGGATTAAATTGTG
3279 AAA
1 AAA
3282 TAAATGAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.42, C:0.02, G:0.27, T:0.30
Consensus pattern (29 bp):
AAAAATGCAAATTGAGGGATTAAATTGTG
Found at i:4101 original size:15 final size:15
Alignment explanation
Indices: 4071--4103 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
4061 ATTTTCTGTG
4071 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
4086 TTTATATATGTG-GAA
1 TTTAT-TATGTGTGAA
4101 TTT
1 TTT
4104 TCGTGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:5311 original size:41 final size:43
Alignment explanation
Indices: 5215--5367 Score: 220
Period size: 43 Copynumber: 3.6 Consensus size: 43
5205 TGTTCTCATA
*
5215 TAAGACCATGTCTGGGACACTGGCATCGATATGTGATTACGTG
1 TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACGTG
*
5258 TAAGACCATGTCTGGGACATTGGCATCG-TATTTGATT-CGTG
1 TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACGTG
* * * *
5299 TAAGACCTTGTCTGGGACAGTGGCATCGATATGTGATTGCATG
1 TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACGTG
* *
5342 TAAGACCACGTCTGGGACGTTGGCAT
1 TAAGACCATGTCTGGGACATTGGCAT
5368 TGTACGATAT
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
41 30 0.31
42 16 0.16
43 52 0.53
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (43 bp):
TAAGACCATGTCTGGGACATTGGCATCGATATGTGATTACGTG
Found at i:11001 original size:39 final size:40
Alignment explanation
Indices: 10923--11106 Score: 198
Period size: 39 Copynumber: 4.7 Consensus size: 40
10913 GCTACTCGTT
* *
10923 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGACCGGATT-TAGTAACTCGCA
*
10963 CAATTGCCTTCGGGACTTA-ACCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGACCGGATTTAGTAACTCGCA
* * *
11002 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGACCGGATTTAGTAACTCGCA
* * * * *
11041 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGACCGGATTTAGTAAC-TCGCA
*
11082 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGACCGGA
11107 CATCATTCAA
Statistics
Matches: 123, Mismatches: 15, Indels: 12
0.82 0.10 0.08
Matches are distributed among these distances:
38 6 0.05
39 57 0.46
40 49 0.40
41 11 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGACCGGATTTAGTAACTCGCA
Found at i:11106 original size:40 final size:40
Alignment explanation
Indices: 10904--11106 Score: 220
Period size: 40 Copynumber: 5.1 Consensus size: 40
10894 CGGAATTTAA
** *
10904 CCGGATATAGCT-ACTCGTTCAAATGCCTTCGGGACATAGC
1 CCGGATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* * *
10944 CCGGTTATAGTAACTCGCACAATTGCCTTCGGGACTTA-A
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
10983 CCGGATTTAGTAACTCGCACAAATGCCTTCGGG-CTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
11022 CCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
11062 CCGGATATGGTCACTTAGCACAAA-GCCTTCGGGACTTAGC
1 CCGGATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
11102 CCGGA
1 CCGGA
11107 CATCATTCAA
Statistics
Matches: 137, Mismatches: 18, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
38 6 0.04
39 58 0.42
40 61 0.45
41 12 0.09
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:18480 original size:46 final size:46
Alignment explanation
Indices: 18430--18558 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
18420 TGGTTGAGCA
*
18430 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
18476 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* * *
18522 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
18559 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.19, C:0.22, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:20387 original size:26 final size:26
Alignment explanation
Indices: 20356--20463 Score: 173
Period size: 26 Copynumber: 4.2 Consensus size: 26
20346 ATGAAATGCC
20356 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAAACCATT
*
20382 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAAACCATT
* *
20408 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAAACCATT
20434 ATCATGGAACATTTACCT-AACTCATT
1 ATCATGGAACATTTACCTAAAC-CATT
20460 ATCA
1 ATCA
20464 ATTTGTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
25 2 0.03
26 74 0.97
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAAACCATT
Found at i:30007 original size:18 final size:19
Alignment explanation
Indices: 29984--30026 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
29974 AAGGCCAATT
*
29984 CAGGCAGTGTAGGCC-ATA
1 CAGGCAGTGTAGGCCGACA
*
30002 CAGGCA-TGTGGGCCGACA
1 CAGGCAGTGTAGGCCGACA
30020 CAGGCAG
1 CAGGCAG
30027 ACAACATGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.26, C:0.26, G:0.37, T:0.12
Consensus pattern (19 bp):
CAGGCAGTGTAGGCCGACA
Found at i:31357 original size:24 final size:24
Alignment explanation
Indices: 31328--31376 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
31318 TTATTTTTGA
*
31328 TAGTATATCTTGAAACTGCTATAG
1 TAGTATATCTTGAAACTACTATAG
* *
31352 TAGTATATGTTGAGACTACTATAG
1 TAGTATATCTTGAAACTACTATAG
31376 T
1 T
31377 TAGATTGTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.39
Consensus pattern (24 bp):
TAGTATATCTTGAAACTACTATAG
Found at i:38856 original size:13 final size:13
Alignment explanation
Indices: 38838--38862 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38828 CCGAACATAG
38838 ATAGCCAAACATC
1 ATAGCCAAACATC
38851 ATAGCCAAACAT
1 ATAGCCAAACAT
38863 TTGGTCATTC
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:0.48, C:0.28, G:0.08, T:0.16
Consensus pattern (13 bp):
ATAGCCAAACATC
Found at i:41247 original size:16 final size:17
Alignment explanation
Indices: 41210--41250 Score: 57
Period size: 16 Copynumber: 2.4 Consensus size: 17
41200 AACTTATTAT
41210 ATGTTTCATTATATTAAC
1 ATGTTT-ATTATATTAAC
*
41228 ATGTTTATTAT-TTTAC
1 ATGTTTATTATATTAAC
41244 ATGTTTA
1 ATGTTTA
41251 ACCTTTTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.50
17 5 0.23
18 6 0.27
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.56
Consensus pattern (17 bp):
ATGTTTATTATATTAAC
Found at i:50971 original size:73 final size:73
Alignment explanation
Indices: 50852--50999 Score: 296
Period size: 73 Copynumber: 2.0 Consensus size: 73
50842 GTAATTAGGG
50852 TTTGTTTCCGCAAAACAGAATCTTACTACAGCTTTTAGTCTTCTACAGTCTCAATTTACTCTAAC
1 TTTGTTTCCGCAAAACAGAATCTTACTACAGCTTTTAGTCTTCTACAGTCTCAATTTACTCTAAC
50917 TAAAGAGT
66 TAAAGAGT
50925 TTTGTTTCCGCAAAACAGAATCTTACTACAGCTTTTAGTCTTCTACAGTCTCAATTTACTCTAAC
1 TTTGTTTCCGCAAAACAGAATCTTACTACAGCTTTTAGTCTTCTACAGTCTCAATTTACTCTAAC
50990 TAAAGAGT
66 TAAAGAGT
50998 TT
1 TT
51000 CAGTGTAGTC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 75 1.00
ACGTcount: A:0.30, C:0.22, G:0.11, T:0.38
Consensus pattern (73 bp):
TTTGTTTCCGCAAAACAGAATCTTACTACAGCTTTTAGTCTTCTACAGTCTCAATTTACTCTAAC
TAAAGAGT
Found at i:54316 original size:33 final size:33
Alignment explanation
Indices: 54274--54338 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 33
54264 CATGCAGTAA
* *
54274 CAGTCTGGGCCAGAGCCCTATTCAGTAACAGTT
1 CAGTCTGGGCCAGAGCCCTATACAGAAACAGTT
**
54307 CAGTCTGGGCCTTAGCCCTATACAGAAACAGT
1 CAGTCTGGGCCAGAGCCCTATACAGAAACAGT
54339 GTAGGCCTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (33 bp):
CAGTCTGGGCCAGAGCCCTATACAGAAACAGTT
Found at i:56311 original size:432 final size:432
Alignment explanation
Indices: 55495--56358 Score: 1658
Period size: 431 Copynumber: 2.0 Consensus size: 432
55485 TCCCACAATT
*
55495 GTTGATTGACCACTAACTTCATAACAACAGATCTCGTTAGAGGGTTGATTAAGGATGTAGTTTAC
1 GTTGATTGACCACTAACTTCAAAACAACAGATCTCGTTAGAGGGTTGATTAAGGATGTAGTTTAC
* * *
55560 ATCCAACAAGAATAACTTGAGCAAGACAGAGGACAACTTACCGTATCCTTCAGAATCGAACACTG
66 ACCCAACAAGAATAACTTGAGCAAGACAGAGGACAACTTACCGTATCCCTCAGAACCGAACACTG
55625 ACTTAAGGGGCAGCATACGTGAGTGGAGTATTGCGTTCGATCTAAGAGAGTAAAATGAAGGAAGA
131 ACTTAAGGGGCAGCATACGTGAGTGGAGTATTGCGTTCGATCTAAGAGAGTAAAATGAAGGAAGA
55690 TCATTAGATAGAAGTAATGATAATCCTAGAAAGGAAATCTACAAAGTAAGAAAAACAACCCAATT
196 TCATTAGATAGAAGTAATGATAATCCTAGAAAGGAAATCTACAAAGTAAGAAAAACAACCCAATT
55755 ACCTACCACTAATATTCGGCTATTACTTAGGAAGAGAGGAAGAGACGGAAGCAAAGATGATCCAG
261 ACCTACCACTAATATTCGGCTATTACTTAGGAAGAGAGGAAGAGACGGAAGCAAAGATGATCCAG
*
55820 AGATAGCATATTCGGTCTAGCACCAAGAGCGGGTTGAAGGTCTGAGGTATTTGATTTAGAAAAGA
326 AGATAGCATATTCGATCTAGCACCAAGAGCGGGTTGAAGGTCTGAGGTATTTGATTTAGAAAAGA
55885 GGAGAAGAAGAATACCAATTTTGCAAAGATAAAATGTGAAGA
391 GGAGAAGAAGAATACCAATTTTGCAAAGATAAAATGTGAAGA
55927 GTTGATTGA-CACTAACTTCAAAACAACAGATCTCGTTAGAGGGTTGATTAAGGATGTAGTTTAC
1 GTTGATTGACCACTAACTTCAAAACAACAGATCTCGTTAGAGGGTTGATTAAGGATGTAGTTTAC
*
55991 ACCCAACAATAATAACTTGAGCAAGACAGAGGACAACTTACCGTATCCCTCAGAACCGAACACTG
66 ACCCAACAAGAATAACTTGAGCAAGACAGAGGACAACTTACCGTATCCCTCAGAACCGAACACTG
56056 ACTTAAGGGGCAGCATACGTGAGTGGAGTATTGCGTTCGATCTAAGAGAGTAAAATGAAGGAAGA
131 ACTTAAGGGGCAGCATACGTGAGTGGAGTATTGCGTTCGATCTAAGAGAGTAAAATGAAGGAAGA
56121 TCATTAGATAGAAGTAATGATAATCCTAGAAAGGAAATCTACAAAGTAAGAAAAAACAACCCAAT
196 TCATTAGATAGAAGTAATGATAATCCTAGAAAGGAAATCTACAAAGTAAG-AAAAACAACCCAAT
56186 TACCTACCACTAATATTCGGCTATTACTTAGGAAGAGAGGAAGAGACGGAAGCAAAGATGATCCA
260 TACCTACCACTAATATTCGGCTATTACTTAGGAAGAGAGGAAGAGACGGAAGCAAAGATGATCCA
56251 GAGATAGCATATTCGATCTAGCACCAAGAGCGGGTTGAAGGTCTGAGGTATTTGATTTAGAAAAG
325 GAGATAGCATATTCGATCTAGCACCAAGAGCGGGTTGAAGGTCTGAGGTATTTGATTTAGAAAAG
56316 AGGAGAAGAAGAATACCAATTTTGCAAAGATAAAATGTGAAGA
390 AGGAGAAGAAGAATACCAATTTTGCAAAGATAAAATGTGAAGA
56359 AGAAATGGAA
Statistics
Matches: 425, Mismatches: 6, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
431 230 0.54
432 195 0.46
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.22
Consensus pattern (432 bp):
GTTGATTGACCACTAACTTCAAAACAACAGATCTCGTTAGAGGGTTGATTAAGGATGTAGTTTAC
ACCCAACAAGAATAACTTGAGCAAGACAGAGGACAACTTACCGTATCCCTCAGAACCGAACACTG
ACTTAAGGGGCAGCATACGTGAGTGGAGTATTGCGTTCGATCTAAGAGAGTAAAATGAAGGAAGA
TCATTAGATAGAAGTAATGATAATCCTAGAAAGGAAATCTACAAAGTAAGAAAAACAACCCAATT
ACCTACCACTAATATTCGGCTATTACTTAGGAAGAGAGGAAGAGACGGAAGCAAAGATGATCCAG
AGATAGCATATTCGATCTAGCACCAAGAGCGGGTTGAAGGTCTGAGGTATTTGATTTAGAAAAGA
GGAGAAGAAGAATACCAATTTTGCAAAGATAAAATGTGAAGA
Found at i:56422 original size:28 final size:28
Alignment explanation
Indices: 56382--56435 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
56372 TTTCAAAAGA
56382 GAGTTCGGCACTTGCTATCTTGTATTTG
1 GAGTTCGGCACTTGCTATCTTGTATTTG
56410 GAGTTCGGCACTTGCTATCTTGTATT
1 GAGTTCGGCACTTGCTATCTTGTATT
56436 CGGCCAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.43
Consensus pattern (28 bp):
GAGTTCGGCACTTGCTATCTTGTATTTG
Found at i:58039 original size:44 final size:44
Alignment explanation
Indices: 57989--58077 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
57979 AGCCTAAGGG
57989 TAAAATCATAATTTTGTGAAAGTCTAGGGGCAAAATGGTCATTT
1 TAAAATCATAATTTTGTGAAAGTCTAGGGGCAAAATGGTCATTT
58033 TAAAATCATAATTTTGTGAAAGTCTAGGGGCAAAATGGTCATTT
1 TAAAATCATAATTTTGTGAAAGTCTAGGGGCAAAATGGTCATTT
58077 T
1 T
58078 TCCAAAATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.35
Consensus pattern (44 bp):
TAAAATCATAATTTTGTGAAAGTCTAGGGGCAAAATGGTCATTT
Found at i:58461 original size:48 final size:48
Alignment explanation
Indices: 58404--58675 Score: 208
Period size: 48 Copynumber: 5.7 Consensus size: 48
58394 TATGTGTGCC
* * * *
58404 AGTGCAAGACCACGTTTGGGACATGGCATCGGCCACGATATGAGGGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCT
* * * * * * *
58452 AGTGTAAGACCATGTTTGGAACATGGCATTGGCGA-TATTGTGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGA-TATGAGAGCT
** * * * * *
58500 AGTGTAAGATAATGTCTAGGACATGGCATCAG-CATTGATATGTGCGCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-CGATATGAGAGCT
* * * * * *
58548 AGTGTAAGACCAAGTCTAGGACATGGCATAGG-CATTGAGATGAGATCT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCA-CGATATGAGAGCT
* * * * *
58596 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCAACATGTGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCT
* * *
58644 AGTGTAAGACCATGTTTGGAACATGACATCGG
1 AGTGTAAGACCATGTCTGGGACATGGCATCGG
58676 TAACTCACCC
Statistics
Matches: 176, Mismatches: 44, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
47 2 0.01
48 172 0.98
49 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (48 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCACGATATGAGAGCT
Found at i:58572 original size:96 final size:96
Alignment explanation
Indices: 58422--58668 Score: 232
Period size: 96 Copynumber: 2.6 Consensus size: 96
58412 ACCACGTTTG
* * * * *
58422 GGACATGGCATCGGCCACGATATGAGGGCTAGTGTAAGACCATGTTTGGAACATGGCATTGGCGA
1 GGACATGGCATCAGCCACGATATGAGCGCTAGTGTAAGACCAAGTTAGGAACATGGCATAGGC-A
* *
58487 TAT-TG-TGAGAGCCAGTGTAAGATAATGTCTA
65 T-TGAGATGAGAGCCAGTGTAAGACAATGTCTA
* *
58518 GGACATGGCATCAG-CATTGATATGTGCGCTAGTGTAAGACCAAGTCTAGG-ACATGGCATAGGC
1 GGACATGGCATCAGCCA-CGATATGAGCGCTAGTGTAAGACCAAGT-TAGGAACATGGCATAGGC
* * * *
58581 ATTGAGATGAGATCTAGTGTAAGACCATGTCTG
64 ATTGAGATGAGAGCCAGTGTAAGACAATGTCTA
* * * * * * * * *
58614 GGACATGGCATCGGCCTCAACATGTGAGCCAGTGTAAGACCATGTTTGGAACATG
1 GGACATGGCATCAGCCACGATATGAGCGCTAGTGTAAGACCAAGTTAGGAACATG
58669 ACATCGGTAA
Statistics
Matches: 123, Mismatches: 22, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
94 1 0.01
95 8 0.07
96 110 0.89
97 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (96 bp):
GGACATGGCATCAGCCACGATATGAGCGCTAGTGTAAGACCAAGTTAGGAACATGGCATAGGCAT
TGAGATGAGAGCCAGTGTAAGACAATGTCTA
Found at i:63329 original size:37 final size:37
Alignment explanation
Indices: 63279--63356 Score: 156
Period size: 37 Copynumber: 2.1 Consensus size: 37
63269 GAGACATATC
63279 AAAGTTTGTGTCAAAATGTTTAATTTGTCAGCAAGTG
1 AAAGTTTGTGTCAAAATGTTTAATTTGTCAGCAAGTG
63316 AAAGTTTGTGTCAAAATGTTTAATTTGTCAGCAAGTG
1 AAAGTTTGTGTCAAAATGTTTAATTTGTCAGCAAGTG
63353 AAAG
1 AAAG
63357 CCAAGCACCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 41 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.36
Consensus pattern (37 bp):
AAAGTTTGTGTCAAAATGTTTAATTTGTCAGCAAGTG
Found at i:66822 original size:42 final size:41
Alignment explanation
Indices: 66775--66866 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 41
66765 TGGTTCGAAG
*
66775 GCCCTTCGGAACTAAGTCCAGTTATGA-CACTGGCTCTAAAAA
1 GCCCTTCGAAACTAAGTCCAGTTATGAGCACTGGCTC--AAAA
* * *
66817 GCCCTTCGAAACTAAGTTCGGTTATTAGCACTGGCTCAAAA
1 GCCCTTCGAAACTAAGTCCAGTTATGAGCACTGGCTCAAAA
66858 GCCCTTCGA
1 GCCCTTCGA
66867 GACCAAGCTC
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
41 13 0.29
42 23 0.51
43 9 0.20
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.25
Consensus pattern (41 bp):
GCCCTTCGAAACTAAGTCCAGTTATGAGCACTGGCTCAAAA
Found at i:66866 original size:41 final size:41
Alignment explanation
Indices: 66717--66866 Score: 135
Period size: 41 Copynumber: 3.6 Consensus size: 41
66707 AGTCCGACTC
* * * * *
66717 TTAGCACCGGCTCAAAAGCCATTCGAGACCAAGCTCGG--A
1 TTAGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTA
* * * * * *
66756 TTAGACTACTGGTTCGAAGGCCCTTCGGAACTAAGTCCAGTTA
1 TTAG-C-ACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTA
*
66799 TGA-CACTGGCTCTAAAAAGCCCTTCGAAACTAAGTTCGGTTA
1 TTAGCACTGGCTC--AAAAGCCCTTCGAAACTAAGTTCGGTTA
66841 TTAGCACTGGCTCAAAAGCCCTTCGA
1 TTAGCACTGGCTCAAAAGCCCTTCGA
66867 GACCAAGCTC
Statistics
Matches: 85, Mismatches: 19, Indels: 12
0.73 0.16 0.10
Matches are distributed among these distances:
39 4 0.05
40 8 0.09
41 36 0.42
42 25 0.29
43 12 0.14
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (41 bp):
TTAGCACTGGCTCAAAAGCCCTTCGAAACTAAGTTCGGTTA
Found at i:68877 original size:102 final size:106
Alignment explanation
Indices: 68674--68881 Score: 370
Period size: 102 Copynumber: 2.0 Consensus size: 106
68664 GTTAAACAAA
**
68674 CAACTTTTGTAAAGTAGTTTTCATGAAAACCCTAACTAAGGACTATTTTGCATAAGTTATAAATT
1 CAACTTTTGTAAAAAAGTTTTCATGAAAACCCTAACTAAGGACTATTTTGCATAAGTTATAAATT
68739 ATGTGGTAAATGTGTGAAATGATGGGAATTGTAGGCTGGTT
66 ATGTGGTAAATGTGTGAAATGATGGGAATTGTAGGCTGGTT
68780 CAACTTTTGTAAAAAAGTTTTCATGAAAA-CCTAACTAAGGACTA-TTTGCATAAGTTATAAATT
1 CAACTTTTGTAAAAAAGTTTTCATGAAAACCCTAACTAAGGACTATTTTGCATAAGTTATAAATT
68843 ATGT-GT-AATGTGTGAAATGATGGGAATTGTAGGCTGGTT
66 ATGTGGTAAATGTGTGAAATGATGGGAATTGTAGGCTGGTT
68882 TGATAAAAAA
Statistics
Matches: 100, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
102 33 0.33
103 2 0.02
104 23 0.23
105 15 0.15
106 27 0.27
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (106 bp):
CAACTTTTGTAAAAAAGTTTTCATGAAAACCCTAACTAAGGACTATTTTGCATAAGTTATAAATT
ATGTGGTAAATGTGTGAAATGATGGGAATTGTAGGCTGGTT
Found at i:69402 original size:48 final size:49
Alignment explanation
Indices: 69334--69553 Score: 224
Period size: 48 Copynumber: 4.6 Consensus size: 49
69324 AAGATGCCAC
* *
69334 GATATG-AGAGCCAATGTAAGACCATGTTTGGAACATGGCATCAGC---
1 GATATGTAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCATT
* *
69379 GATATTGTAAGAGCCAGTATAAGACCATGTTTGGGACATGGCATTAGCATT
1 GATA-TGT-AGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCATT
* * *
69430 GATATGT-GCGCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCATT
1 GATATGTAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCATT
* * * * *
69478 GAGACG-AGAGCTC-GTGTAAGACCATGTCTGGGACATGGCATC-GACCTC
1 GATATGTAGAGC-CAGTGTAAGACCATGTTTGGGACATGGCATCAG-CATT
*
69526 GATATGT-GAGCCAGTGTAAGTCCATGTT
1 GATATGTAGAGCCAGTGTAAGACCATGTT
69554 CAAAACATGG
Statistics
Matches: 145, Mismatches: 19, Indels: 19
0.79 0.10 0.10
Matches are distributed among these distances:
45 4 0.03
46 2 0.01
47 2 0.01
48 130 0.90
50 3 0.02
51 4 0.03
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.25
Consensus pattern (49 bp):
GATATGTAGAGCCAGTGTAAGACCATGTTTGGGACATGGCATCAGCATT
Found at i:80722 original size:29 final size:28
Alignment explanation
Indices: 80676--80735 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 28
80666 TTTTCATTTA
*
80676 TTTCACAATTCAAACCCTCAATTTACACT
1 TTTCACAATTCAAACCCT-AATATACACT
* * *
80705 TTTCACAATTTAATCCCTAATATACATT
1 TTTCACAATTCAAACCCTAATATACACT
80733 TTT
1 TTT
80736 ACTCAAAATC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (28 bp):
TTTCACAATTCAAACCCTAATATACACT
Found at i:86919 original size:12 final size:13
Alignment explanation
Indices: 86895--86923 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
86885 GGGCTATAAC
86895 TATTGCATTTATT
1 TATTGCATTTATT
86908 TATTGC-TTTATT
1 TATTGCATTTATT
86920 TATT
1 TATT
86924 CATGTATGAG
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:0.21, C:0.07, G:0.07, T:0.66
Consensus pattern (13 bp):
TATTGCATTTATT
Found at i:91638 original size:51 final size:50
Alignment explanation
Indices: 91562--91699 Score: 181
Period size: 51 Copynumber: 2.8 Consensus size: 50
91552 TATTGTGAGG
91562 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCA-ATAACTTCGA
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAGATAA-TT-GA
* * *
91613 TCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CCAGATAATTGG
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAGATAATTGA
* * * *
91662 TCGCATGTGTAGTACTAAGTGAAAGCTACTATGCGTAC
1 TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTAC
91700 TAGATAGCCT
Statistics
Matches: 76, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
49 32 0.42
50 5 0.07
51 39 0.51
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (50 bp):
TCACGTGTGTAGTACTAAGTGCAGGCTACTATGCGTACCCAGATAATTGA
Found at i:96114 original size:21 final size:21
Alignment explanation
Indices: 96076--96115 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
96066 ATTACTCCAA
*
96076 AGAAGCCGATTGATCCATCTC
1 AGAAGCCGATTCATCCATCTC
96097 AGAAGCCGGATTCA-CCATC
1 AGAAGCC-GATTCATCCATC
96116 AAGACTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAAGCCGATTCATCCATCTC
Done.