Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold739
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: 22322
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.30
Found at i:136 original size:26 final size:26
Alignment explanation
Indices: 107--198 Score: 78
Period size: 26 Copynumber: 3.4 Consensus size: 26
97 CGTGTGGCTT
107 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** * * *
133 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
* *
160 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
188 TGAAAGGTGTC
1 TGAAAGGTGTC
199 ACCAACTTGT
Statistics
Matches: 49, Mismatches: 12, Indels: 10
0.69 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 19 0.39
27 8 0.16
28 8 0.16
29 8 0.16
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:156 original size:54 final size:54
Alignment explanation
Indices: 62--1631 Score: 1651
Period size: 55 Copynumber: 27.9 Consensus size: 54
52 AATAAATGTA
* * * * *
62 TCCTTCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGT-GGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAA-TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
116 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* * * **
171 TCCTGCTCTTTGGGGACTGAAAGGTGTCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* *
232 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
287 TCCTGCTTTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * * * **
342 TCCTGCTCTTTGGGGACTGAAAGGTGCCACC-ACCTGTGTAGGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* * *
402 TCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTATGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACTG-AAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * * *
457 CCCTGCTCTTTGAGGACTGTAAATACCACCATC-TGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * **
510 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTATGT-GGCTTTGAAAAGAAAAAGCA
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTG
* * * *
570 TCCTGTTCTTTGAGGACTAAAAAATGCCACCAAC-CGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
624 TCCTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
679 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
734 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAATA
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG--GTG
* *
792 TCTTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAA-AGGTG
* *
847 TCCTGCTCTTTGAGGATTGGAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGAAGG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGT----G
* * * * *
905 CATCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAG
1 --TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAA-G-G-TG
* * * *
965 GCGTCGCTCTTTGGGGAC--AAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCT-GCTCTTTGAGGACTGAAAA--TGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1020 TCCTACTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* * *
1075 TCCTGCTCTTTGAGGACTGGAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAGGTG
* * * *
1135 TCCTACTCTTTGGGGAC-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1189 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
** * *
1244 TCCTGCTCTTTGAGGACTGGAGGATGCCACTAACTTGTGTGGGCTTTAAAAGGAGAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTT-----GA-AAGGTG
* * * *
1305 TCCTGCTCTTTGGGGAC-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGATG
1 TCCTGCTCTTTGAGGACTGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1359 TCCTGCTCTTTGAGGACTGAAAATACCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
*
1413 TCCTGCTCTTT-AGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
* *
1467 TCCTGCTCTTTGAGGACTGGAAAATACCACCAAC-T-TGTGGGCTTTGAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
**
1520 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAG
1 TCCTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG---GTG
1579 -CATCTGCTCTTTGAGGACTAGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 TC--CTGCTCTTTGAGGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1632 AAAAAGGCGT
Statistics
Matches: 1297, Mismatches: 134, Indels: 165
0.81 0.08 0.10
Matches are distributed among these distances:
53 98 0.08
54 296 0.23
55 456 0.35
56 23 0.02
57 13 0.01
58 70 0.05
59 29 0.02
60 197 0.15
61 110 0.08
62 4 0.00
63 1 0.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.28
Consensus pattern (54 bp):
TCCTGCTCTTTGAGGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
Found at i:584 original size:168 final size:167
Alignment explanation
Indices: 61--1631 Score: 1754
Period size: 168 Copynumber: 9.3 Consensus size: 167
51 AAATAAATGT
* * * * *
61 ATCCTTCTCATTGAGGAGT-AAAAAGTGCCACCAACTCGTGT-GGCTTTGAAAGGTGTCCTGCTC
1 ATCCTGCTCTTTGAGGACTGAAAAA-TGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTC
*
124 TTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGGGGAC
65 TTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGAC
* *
188 TGAAAGGTGTCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
128 TGAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAG--AAAGC
* *
231 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTTT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
* *
296 TTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACTG
66 TTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
* * *
361 AAAGGTGCCACC-ACCTGTGTAGGCTTTGAAAAGAAAAAGC
130 AAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAG--AAAGC
* * *
401 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACCTGTATGGGCTTTAAAAGGTGCCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
* *
466 TTGAGGACTGTAAA-TACCACCATC-TGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
66 TTGAGGACTG-AAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTG
* *
529 AAAGGTGCCACCAACTTATGT-GGCTTTGAAAAGAAAAAGC
130 AAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAG--AAAGC
* * *
569 ATCCTGTTCTTTGAGGACTAAAAAATGCCACCAAC-CGTGTGGGCTTTAAAAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
*
633 TTGAGGATTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACT
66 TTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACT
* * *
697 GAAAGGTGCCACCAACTTGTGTGGGCTTTG---AG-AGGT
129 GAAA-ATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAGC
* * * * *
733 GTCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAATATCTTGC
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT-AAAAG--GTGTCCTGC
798 TCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGG
63 TCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGG
* * * *
862 ATTGGAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTGAAGGC
126 ACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAA--AGAAAGC
* ** * * * *
906 ATCCTACTCTTTGAGGACTGGGAAGTGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCG
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAA-G-G-TGTCCT-G
* * * *
971 CTCTTTGGGGAC-AAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTACTCTTTGAGG
62 CTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGG
*
1035 ACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG---GT
126 ACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAGC
* * * *
1074 GTCCTGCTCTTTGAGGACTG-GAGATGCCACCAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCC
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT---A--A-AAGGTGTCC
* * *
1138 TACTCTTTGGGGAC-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGA
60 TGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGA
*
1202 GGACTGGAAAATGCCACCAACTTGTGTGGGCTTTG-AAAG---GT
124 GGACT-GAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAGC
* * ** * *
1243 GTCCTGCTCTTTGAGGACTGGAGGATGCCACTAACTTGTGTGGGCTTTAAAAGGAGAAGGCGTCC
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTT---A--A-AAGGTGTCC
* * *
1308 TGCTCTTTGGGGAC-GAAAGGTGCCACCAACTTGTGTGGGCTTTGAGAGATGTCCTGCTCTTTGA
60 TGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGA
* *
1372 GGACTGAAAATACCACCAACTTGTGTGGGCTTTG-AAAG---GT
124 GGACTGAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAGC
* * * *
1412 GTCCTGCTCTTT-AGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCT
1 ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
* * *
1476 TTGAGGACTGGAAAATACCACCAAC-T-TGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTG
66 TTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACT-
1539 GAAAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGC
129 GAAAATGCCACCAACTTGTGTGGGCTTTGAAAAG--AAAGC
*
1580 AT-CTGCTCTTTGAGGACT-AGAAAATGCCACCAACTTGTGTGGGCTTTGAAAG
1 ATCCTGCTCTTTGAGGACTGA-AAAATGCCACCAACTTGTGTGGGCTTTAAAAG
1632 AAAAAGGCGT
Statistics
Matches: 1265, Mismatches: 92, Indels: 90
0.87 0.06 0.06
Matches are distributed among these distances:
161 35 0.03
162 49 0.04
163 14 0.01
164 37 0.03
165 11 0.01
166 8 0.01
167 95 0.08
168 276 0.22
169 238 0.19
170 249 0.20
171 95 0.08
172 14 0.01
173 103 0.08
174 41 0.03
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.28
Consensus pattern (167 bp):
ATCCTGCTCTTTGAGGACTGAAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCT
TTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGA
AAATGCCACCAACTTGTGTGGGCTTTGAAAAGAAAGC
Found at i:704 original size:26 final size:26
Alignment explanation
Indices: 617--704 Score: 70
Period size: 26 Copynumber: 3.3 Consensus size: 26
607 GTGGGCTTTA
*
617 AAAGGTGTCCTGCTCTTTGAGGATTG
1 AAAGGTGTCCTGCTCTTTGAGGACTG
** * * * *
643 AAAGGTG-CCACCAACTTGTGTGGGCTTT
1 AAAGGTGTCCTGC-TCTT-TGAGGAC-TG
671 AAGAGGTGTCCTGCTCTTTGAGGACTG
1 AA-AGGTGTCCTGCTCTTTGAGGACTG
698 AAAGGTG
1 AAAGGTG
705 CCACCAACTT
Statistics
Matches: 44, Mismatches: 13, Indels: 10
0.66 0.19 0.15
Matches are distributed among these distances:
25 3 0.07
26 15 0.34
27 7 0.16
28 8 0.18
29 8 0.18
30 3 0.07
ACGTcount: A:0.22, C:0.17, G:0.32, T:0.30
Consensus pattern (26 bp):
AAAGGTGTCCTGCTCTTTGAGGACTG
Found at i:7890 original size:28 final size:28
Alignment explanation
Indices: 7850--7916 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
7840 AAAATCGGGA
** *
7850 TTGGAGTATCCCCTCGGAAGTAAC-AGGG
1 TTGGAGTATCCCCGAGGAAATAACGA-GG
*
7878 TTGGAGTATCCCCGATGAAATAACGAGG
1 TTGGAGTATCCCCGAGGAAATAACGAGG
7906 TTGGAGTATCC
1 TTGGAGTATCC
7917 TCGACTGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 33 0.97
29 1 0.03
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (28 bp):
TTGGAGTATCCCCGAGGAAATAACGAGG
Found at i:8050 original size:81 final size:80
Alignment explanation
Indices: 7877--8053 Score: 275
Period size: 80 Copynumber: 2.2 Consensus size: 80
7867 AAGTAACAGG
* *
7877 GTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGTATCCTCGACTGTGAAAAATTGGTATTTTT
1 GTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGACTGTGAAAAATTGGTATTTTT
7942 GGAAATAAAATCGGA
66 GGAAATAAAATCGGA
** * *
7957 GTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAGAAATTGTGT-TTT
1 GTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGACTGTGAA-AAATTG-GTATTT
8021 TTGGAAATAAAATCGGA
64 TTGGAAATAAAATCGGA
8038 GTTGGAGTATCCCCGA
1 GTTGGAGTATCCCCGA
8054 TTATAGAAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
80 45 0.52
81 40 0.46
82 2 0.02
ACGTcount: A:0.29, C:0.14, G:0.28, T:0.29
Consensus pattern (80 bp):
GTTGGAGTATCCCCGAGGAAATAACGAGGTTGGAGTATCCCCGACTGTGAAAAATTGGTATTTTT
GGAAATAAAATCGGA
Found at i:8094 original size:51 final size:52
Alignment explanation
Indices: 7985--8151 Score: 157
Period size: 51 Copynumber: 3.2 Consensus size: 52
7975 AAATAACGGG
* * * *
7985 GTTGGAGTATCCCCGATTGTGAAGAAATTGTGTTTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATGAAGAAATTGTG-TTCTTGAAAATAAAACCGGA
8038 GTTGGAGTATCCCCGATTAT--AGAAAATTAGTG-TCTTGAAAATAAAACCAGGA
1 GTTGGAGTATCCCCGATTATGAAG-AAATT-GTGTTCTTGAAAATAAAACC-GGA
* * * **
8090 -TTGGAGTATCCCCGATTGTGGAAAAAATTAGTGTT-TAG-CGATAAAACCGGA
1 GTTGGAGTATCCCCGATTAT-GAAGAAATT-GTGTTCTTGAAAATAAAACCGGA
8141 GTTGGAGTATC
1 GTTGGAGTATC
8152 TCCTCGGAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 17
0.79 0.07 0.14
Matches are distributed among these distances:
51 36 0.37
52 26 0.27
53 33 0.34
54 2 0.02
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (52 bp):
GTTGGAGTATCCCCGATTATGAAGAAATTGTGTTCTTGAAAATAAAACCGGA
Found at i:8282 original size:52 final size:50
Alignment explanation
Indices: 8200--8327 Score: 141
Period size: 51 Copynumber: 2.5 Consensus size: 50
8190 AACGGGGTTG
* *
8200 GAGTATCCCCGATTGTGAAGAATTGGGTTTTTTGGAAATAAAATCGGAGTTA
1 GAGTAT-CCCGATTATGAAGAATTGGG-TTTTTGAAAATAAAATCGGAGTTA
* *
8252 GAGTATCCCGATTATAGAA-AATTAGTGTTTTTGAAAATAAAATCGGAGTTG
1 GAGTATCCCGATTAT-GAAGAATT-GGGTTTTTGAAAATAAAATCGGAGTTA
* * *
8303 GAATATCCACGATTGTGGAGAATTG
1 GAGTATCC-CGATTATGAAGAATTG
8328 ATAAACTCAA
Statistics
Matches: 65, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
51 44 0.68
52 21 0.32
ACGTcount: A:0.34, C:0.09, G:0.25, T:0.32
Consensus pattern (50 bp):
GAGTATCCCGATTATGAAGAATTGGGTTTTTGAAAATAAAATCGGAGTTA
Found at i:10403 original size:52 final size:52
Alignment explanation
Indices: 10339--10459 Score: 208
Period size: 52 Copynumber: 2.3 Consensus size: 52
10329 CACTGATTTT
*
10339 TGTATCGATACATGCAGGCAAATTTTGCCCAGATGTATCGATACATTA-TAAA
1 TGTATCGATACATGCAGGCAAA-TTTGCCCAGATGTATCGATACACTATTAAA
10391 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
*
10443 TGTATAGATACATGCAG
1 TGTATCGATACATGCAG
10460 TAACTTTTCA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 24 0.36
52 42 0.64
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:14243 original size:19 final size:18
Alignment explanation
Indices: 14219--14286 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
14209 CAGTAGCTAA
14219 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
14238 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
14253 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
14270 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
14287 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:14259 original size:13 final size:13
Alignment explanation
Indices: 14241--14265 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14231 ACAATACTTA
14241 TGTATCGATACAT
1 TGTATCGATACAT
14254 TGTATCGATACA
1 TGTATCGATACA
14266 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:14263 original size:32 final size:32
Alignment explanation
Indices: 14222--14284 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
14212 TAGCTAATTA
*
14222 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
14254 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
14285 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:14597 original size:19 final size:18
Alignment explanation
Indices: 14573--14637 Score: 77
Period size: 19 Copynumber: 3.8 Consensus size: 18
14563 CAAACAGAAA
14573 TTGTATCGATACATAAGTG
1 TTGTATCGATACA-AAGTG
14592 TTGTATCGATAC-AA---
1 TTGTATCGATACAAAGTG
14606 -TGTATCGATACACAAGTG
1 TTGTATCGATACA-AAGTG
14624 TTGTATCGATACAA
1 TTGTATCGATACAA
14638 TGTATCGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 11 0.28
15 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (18 bp):
TTGTATCGATACAAAGTG
Found at i:14615 original size:32 final size:32
Alignment explanation
Indices: 14574--14644 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
14564 AAACAGAAAT
*
14574 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACACAAGTGTTGTATCGATACAA
14606 TGTATCGATACACAAGTGTTGTATCGATACAA
1 TGTATCGATACACAAGTGTTGTATCGATACAA
14638 TGTATCG
1 TGTATCG
14645 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (32 bp):
TGTATCGATACACAAGTGTTGTATCGATACAA
Found at i:14644 original size:13 final size:13
Alignment explanation
Indices: 14593--14617 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14583 ACATAAGTGT
14593 TGTATCGATACAA
1 TGTATCGATACAA
14606 TGTATCGATACA
1 TGTATCGATACA
14618 CAAGTGTTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:14707 original size:13 final size:13
Alignment explanation
Indices: 14689--14713 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
14679 ATTACTCAAA
14689 TGTATCGATACAT
1 TGTATCGATACAT
14702 TGTATCGATACA
1 TGTATCGATACA
14714 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:17853 original size:28 final size:28
Alignment explanation
Indices: 17772--17853 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
17762 TTTTGGAGAT
*
17772 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* *
17800 AGTAACGGGGTTGGAGTAT-CTCCGATGA
1 AATAACGAGGTTGGAGTATCCT-CGATGA
17828 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
17854 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
25 2 0.04
26 2 0.04
27 1 0.02
28 38 0.84
29 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.32, T:0.26
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:18001 original size:50 final size:49
Alignment explanation
Indices: 17836--18004 Score: 176
Period size: 52 Copynumber: 3.3 Consensus size: 49
17826 GAAATAACGA
* *
17836 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTT-GAAATAAAATCG
* * * * * *
17887 GAATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAATAAAACCGG
1 G-GTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAATAAAATC-G
* * *
17940 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTG-AAATAAAATCG
17990 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
18005 TCAGAAATAA
Statistics
Matches: 96, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
50 29 0.30
51 9 0.09
52 43 0.45
53 5 0.05
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (49 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAATAAAATCG
Found at i:18042 original size:27 final size:28
Alignment explanation
Indices: 17989--18062 Score: 98
Period size: 27 Copynumber: 2.7 Consensus size: 28
17979 AAATAAAGTC
*
17989 GGGTTGGAGTATCCCCTCA-GAAATAACG
1 GGGTTGGAGTATCCCC-GATGAAATAACG
*
18017 GGGTTGGAGTATCCCCGATG-ATTAACG
1 GGGTTGGAGTATCCCCGATGAAATAACG
*
18044 GGGTTGGAGTGTCCCCGAT
1 GGGTTGGAGTATCCCCGAT
18063 TGTGAAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.60
28 17 0.40
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCGATGAAATAACG
Found at i:20558 original size:13 final size:13
Alignment explanation
Indices: 20540--20565 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20530 ACAAAGATCC
20540 ATGTATCGATACA
1 ATGTATCGATACA
20553 ATGTATCGATACA
1 ATGTATCGATACA
20566 CAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:20561 original size:33 final size:33
Alignment explanation
Indices: 20519--20585 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
20509 AAAATTTCCA
***
20519 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
20552 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
20585 A
1 A
20586 TTTCCTTGGC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:20629 original size:19 final size:18
Alignment explanation
Indices: 20605--20672 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
20595 CAGTAGCTAA
20605 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
20624 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
20639 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
20656 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
20673 TGTTGAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:20645 original size:13 final size:13
Alignment explanation
Indices: 20627--20651 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20617 ACAATACTTA
20627 TGTATCGATACAT
1 TGTATCGATACAT
20640 TGTATCGATACA
1 TGTATCGATACA
20652 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:20649 original size:32 final size:32
Alignment explanation
Indices: 20608--20670 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
20598 TAGCTAATTA
*
20608 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
20640 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
20671 AATGTTGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:20732 original size:21 final size:21
Alignment explanation
Indices: 20706--20783 Score: 115
Period size: 21 Copynumber: 3.8 Consensus size: 21
20696 GTTGGGACCC
20706 TGTATCGATACATTTGTAGAA
1 TGTATCGATACATTTGTAGAA
20727 TGTATCGATACATTTGT-GAA
1 TGTATCGATACATTTGTAGAA
* *
20747 TGTATCGATACA-TTCTACAAA
1 TGTATCGATACATTTGTA-GAA
20768 TGTATCGATACATTTG
1 TGTATCGATACATTTG
20784 GAATTTTTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
19 3 0.06
20 15 0.29
21 31 0.61
22 2 0.04
ACGTcount: A:0.32, C:0.13, G:0.17, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTGTAGAA
Found at i:20770 original size:41 final size:40
Alignment explanation
Indices: 20706--20787 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 40
20696 GTTGGGACCC
* *
20706 TGTATCGATACATTTGTAGAATGTATCGATACATTTGTGAA
1 TGTATCGATACATTTCTAAAATGTATCGATACATTTG-GAA
20747 TGTATCGATACA-TTCTACAAATGTATCGATACATTTGGAA
1 TGTATCGATACATTTCTA-AAATGTATCGATACATTTGGAA
20787 T
1 T
20788 TTTTTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
40 8 0.21
41 30 0.79
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (40 bp):
TGTATCGATACATTTCTAAAATGTATCGATACATTTGGAA
Found at i:22172 original size:19 final size:19
Alignment explanation
Indices: 22148--22184 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
22138 ATATAATTAT
*
22148 TGTACATAATATTAGAAAC
1 TGTACAAAATATTAGAAAC
22167 TGTACAAAATATTAGAAA
1 TGTACAAAATATTAGAAA
22185 TTATAATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (19 bp):
TGTACAAAATATTAGAAAC
Done.