Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1320
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: 22192
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Found at i:56 original size:19 final size:19
Alignment explanation
Indices: 3--59 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
1 CT
*
3 CATGTATCGATACCAATTGTC
1 CATGTATCGATA-CAA-TGAC
*
24 CATTGTAT-GATACAATGAG
1 CA-TGTATCGATACAATGAC
43 CATGTATCGATACAATG
1 CATGTATCGATACAATG
60 TATCGATACA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 5 0.16
19 13 0.41
20 3 0.09
21 6 0.19
22 5 0.16
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAC
Found at i:62 original size:13 final size:13
Alignment explanation
Indices: 44--70 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
34 TACAATGAGC
44 ATGTATCGATACA
1 ATGTATCGATACA
57 ATGTATCGATACA
1 ATGTATCGATACA
70 A
1 A
71 AGCATAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5584 original size:97 final size:97
Alignment explanation
Indices: 5462--5644 Score: 269
Period size: 97 Copynumber: 1.9 Consensus size: 97
5452 TTATTCATGA
* * * * *
5462 GGATACTCCTACCCTATTCTTCCGAGAGGATACTCCAACCCCGTTTTTAAA-TTCATCAAGATTT
1 GGATACTCCAACCCCATTCTTCCGAGAGGATACTCCAAACCCATTTCTAAACTT-ATCAAGATTT
* *
5526 GAATCTTATTTTTGCCCAAATTTTCATCACTAG
65 AAATCTTAGTTTTGCCCAAATTTTCATCACTAG
* *
5559 GGATACTCCAACCCCATTCTTCCGAGAGGATACTCCAAACCTATTTCTAAACTTATCAATATTTA
1 GGATACTCCAACCCCATTCTTCCGAGAGGATACTCCAAACCCATTTCTAAACTTATCAAGATTTA
5624 AATCTTAGTTTTGCCCAAATT
66 AATCTTAGTTTTGCCCAAATT
5645 GTTATCGTCG
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
97 74 0.97
98 2 0.03
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.35
Consensus pattern (97 bp):
GGATACTCCAACCCCATTCTTCCGAGAGGATACTCCAAACCCATTTCTAAACTTATCAAGATTTA
AATCTTAGTTTTGCCCAAATTTTCATCACTAG
Found at i:5671 original size:97 final size:95
Alignment explanation
Indices: 5447--5701 Score: 257
Period size: 97 Copynumber: 2.6 Consensus size: 95
5437 AAAAATATCA
* * * * *
5447 AAATTTT-ATTCATGAGGATACTCCTACCCTATTCTTCCGAGAGGATACTCCAACCCCGTTTTTA
1 AAATTTTCA-TCACGAGGATACT-CTACCCCATTCTTCCGAGAGGATACTCCAAACCCATTTCTA
* *
5511 AATTCATCAAGATTTGAATCTTATTTTTGCCC
64 AATTCATCAAGATTTAAATCTTAGTTTTGCCC
* * *
5543 AAATTTTCATCACTAGGGATACTCCAACCCCATTCTTCCGAGAGGATACTCCAAACCTATTTCTA
1 AAATTTTCATCACGA-GGATACT-CTACCCCATTCTTCCGAGAGGATACTCCAAACCCATTTCTA
*
5608 AACTT-ATCAATATTTAAATCTTAGTTTTGCCC
64 AA-TTCATCAAGATTTAAATCTTAGTTTTGCCC
* * * * *
5640 AAATTGTT-ATCGTCGAGGACACTCTAGCCCCATTCCTCTGAGTA-GATACTCCAACCCCATTT
1 AAATT-TTCATC-ACGAGGATACTCTA-CCCCATTCTTCCGAG-AGGATACTCCAAACCCATTT
5702 TTCAACTAAA
Statistics
Matches: 133, Mismatches: 19, Indels: 13
0.81 0.12 0.08
Matches are distributed among these distances:
96 13 0.10
97 113 0.85
98 7 0.05
ACGTcount: A:0.28, C:0.26, G:0.11, T:0.34
Consensus pattern (95 bp):
AAATTTTCATCACGAGGATACTCTACCCCATTCTTCCGAGAGGATACTCCAAACCCATTTCTAAA
TTCATCAAGATTTAAATCTTAGTTTTGCCC
Found at i:7708 original size:17 final size:17
Alignment explanation
Indices: 7681--7722 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 17
7671 TTTTCGATAG
7681 AATTTTTAAATGTAT-A
1 AATTTTTAAATGTATCA
*
7697 AATTTTTAAAATTTATCA
1 AATTTTT-AAATGTATCA
7715 AATATTTT
1 AAT-TTTT
7723 CATTAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 7 0.32
17 7 0.32
18 4 0.18
19 4 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
AATTTTTAAATGTATCA
Found at i:13989 original size:14 final size:13
Alignment explanation
Indices: 13972--14020 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
13962 AAAAAAAATT
13972 AAAAAAAAAACAA
1 AAAAAAAAAACAA
* *
13985 CAAAACAAAAATAA
1 -AAAAAAAAAACAA
13999 AAAAATAAAAACAA
1 AAAAA-AAAAACAA
14013 AAACAAAA
1 AAA-AAAA
14021 GGAAAAGGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 4 0.14
14 23 0.79
15 2 0.07
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.04
Consensus pattern (13 bp):
AAAAAAAAAACAA
Found at i:13994 original size:25 final size:25
Alignment explanation
Indices: 13961--14020 Score: 79
Period size: 25 Copynumber: 2.4 Consensus size: 25
13951 AAGGCAATGT
*
13961 CAAAA-AAAATTAAAAAAA-AAACAA
1 CAAAACAAAAATAAAAAAATAAA-AA
13985 CAAAACAAAAATAAAAAAATAAAAA
1 CAAAACAAAAATAAAAAAATAAAAA
14010 CAAAAACAAAA
1 C-AAAACAAAA
14021 GGAAAAGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 5 0.16
25 15 0.47
26 12 0.38
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (25 bp):
CAAAACAAAAATAAAAAAATAAAAA
Found at i:13994 original size:26 final size:26
Alignment explanation
Indices: 13965--14020 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
13955 CAATGTCAAA
13965 AAAAATTAAAAAAA-AAACAAC-AAAAC
1 AAAAA-TAAAAAAATAAA-AACAAAAAC
13991 AAAAATAAAAAAATAAAAACAAAAAC
1 AAAAATAAAAAAATAAAAACAAAAAC
14017 AAAA
1 AAAA
14021 GGAAAAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 11 0.39
26 17 0.61
ACGTcount: A:0.84, C:0.09, G:0.00, T:0.07
Consensus pattern (26 bp):
AAAAATAAAAAAATAAAAACAAAAAC
Found at i:14026 original size:26 final size:25
Alignment explanation
Indices: 13972--14026 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 25
13962 AAAAAAAATT
*
13972 AAAAAAAAAACAACAAAACAAAAAT
1 AAAAAAAAAACAACAAAACAAAAAG
*
13997 AAAAAAATAAA-AACAAAAACAAAAGG
1 AAAAAAA-AAACAAC-AAAACAAAAAG
14023 AAAA
1 AAAA
14027 GGAAAAATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.84, C:0.09, G:0.04, T:0.04
Consensus pattern (25 bp):
AAAAAAAAAACAACAAAACAAAAAG
Found at i:15383 original size:65 final size:64
Alignment explanation
Indices: 15237--15788 Score: 362
Period size: 65 Copynumber: 8.5 Consensus size: 64
15227 CTGATGATAT
* * * * *
15237 CCCTAGTTAACTCTTTTTGACTTAGGTTTCATCCTAGTTACTCTTAGTTGACTATAT-TGATTTT
1 CCCTAGTCAAC-CTTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATCAG-TTTT
15301 G
64 G
* *** *
15302 CCATAGTTGTCTCTTTTTGACTTATGTTTCATCCTGGTCACCCTTAGTTGA-TGATATCAGTTTT
1 CCCTAGTCAAC-CTTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACT-ATATCAGTTTT
*
15366 T
64 G
** ** * * * * *
15367 CCCTAGTCAATCCTTTTTTGACTTAGGTTTTGTTTTGGTCACCTTTCGTTAATTATATCA-ATTT
1 CCCTAGTCAA-CC-TTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATCAGTTTT
15431 G
64 G
* * * * * * ** * *
15432 CCTTGGTCAACCTTTTTTTGACTTAGATTTCATCCTCGTTACCCTCAGTTGACTGCATTAGTTTC
1 CCCTAGTCAACC--TTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATCAGTTTT
*
15497 A
64 G
* * * * * *
15498 CCCTGGTCAACCTATTTTGACTTAGATTTCATCTTGGTCACCTTTAGTTGACTATAT-TGATTT-
1 CCCTAGTCAACCT-TTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATCAGTTTTG
* ** * * * * *
15561 CACCATGGTCAAGCCTTTTCAACTTAGATTTTATCCTAGT-ATCCTTAGTTGTCTATATCAGTTT
1 C-CC-TAGTCAA-CCTTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATCAGTTT
15625 TG
63 TG
* * ** * * * *
15627 CCCTAGTCAACTCCTTTTCGATTTAGGTTTTGTCCTTGTCACCTTTAGTTGACTATGTTAGTTTT
1 CCCTAGTCAA--CCTTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATCAGTTTT
*
15692 A
64 G
* *
15693 CCTTAGTCAACCTTTTTCGACTTAGGTTTCATCCTGGTCGCCCTTAGTTGACTATATC-GATTTT
1 CCCTAGTCAACCTTTTT-GACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATCAG-TTTT
15757 G
64 G
* * * *
15758 CCCTGGTCAACCCCTTTTGAATTTGGTTTCA
1 CCCTAGTCAA-CCTTTTTGACTTAGGTTTCA
15789 ACTAGTTACC
Statistics
Matches: 376, Mismatches: 93, Indels: 36
0.74 0.18 0.07
Matches are distributed among these distances:
63 1 0.00
64 37 0.10
65 247 0.66
66 90 0.24
67 1 0.00
ACGTcount: A:0.19, C:0.22, G:0.15, T:0.45
Consensus pattern (64 bp):
CCCTAGTCAACCTTTTTGACTTAGGTTTCATCCTGGTCACCCTTAGTTGACTATATCAGTTTTG
Found at i:15786 original size:130 final size:131
Alignment explanation
Indices: 15314--15786 Score: 423
Period size: 130 Copynumber: 3.6 Consensus size: 131
15304 ATAGTTGTCT
*
15314 CTTTTT-GACTTATG-TTTCATCCTGGTCACCCTTAGTTGA-TGATATCAGTTTTTCCCTAGTCA
1 CTTTTTCGACTTA-GATTTCATCCTGGTCACCCTTAGTTGACTGATATCAGTTTTGCCCTAGTCA
** * * * * * * * *
15376 ATCCTTTTTTGACTTAGGTTTTGTTTTGGTCACCTTTCGTTAATTATATCA-ATTTGCCTTGGTC
65 A-CCCCTTTTGAATTAGGTTTTGTCTTGGTCACCTTTAGTTGACTATATTAGTTTTACCTTGGTC
15440 AAC
129 AAC
* * * * ** *
15443 CTTTTTTTGACTTAGATTTCATCCTCGTTACCCTCAGTTGACTGCAT-T-AGTTTCACCCTGGTC
1 C-TTTTTCGACTTAGATTTCATCCTGGTCACCCTTAGTTGACTG-ATATCAGTTTTGCCCTAGTC
** * * ** * *
15506 AACCTATTTTGACTTAGATTTCATCTTGGTCACCTTTAGTTGACTATATT-GATTTCACCATGGT
64 AACCCCTTTTGAATTAGGTTTTGTCTTGGTCACCTTTAGTTGACTATATTAG-TTTTACCTTGGT
15570 CAAGC
128 CAA-C
* * * * *
15575 C-TTTTCAACTTAGATTTTATCCTAGT-ATCCTTAGTTGTCT-ATATCAGTTTTGCCCTAGTCAA
1 CTTTTTCGACTTAGATTTCATCCTGGTCACCCTTAGTTGACTGATATCAGTTTTGCCCTAGTCAA
* * * *
15637 CTCCTTTTCGATTTAGGTTTTGTCCTT-GTCACCTTTAGTTGACTATGTTAGTTTTACCTTAGTC
66 CCCCTTTT-GAATTAGGTTTTGT-CTTGGTCACCTTTAGTTGACTATATTAGTTTTACCTTGGTC
15701 AAC
129 AAC
* * *
15704 CTTTTTCGACTTAGGTTTCATCCTGGTCGCCCTTAGTTGACT-ATATC-GATTTTGCCCTGGTCA
1 CTTTTTCGACTTAGATTTCATCCTGGTCACCCTTAGTTGACTGATATCAG-TTTTGCCCTAGTCA
*
15767 ACCCCTTTTGAATTTGGTTT
65 ACCCCTTTTGAATTAGGTTT
15787 CAACTAGTTA
Statistics
Matches: 277, Mismatches: 51, Indels: 31
0.77 0.14 0.09
Matches are distributed among these distances:
127 2 0.01
128 1 0.00
129 33 0.12
130 140 0.51
131 94 0.34
132 5 0.02
133 2 0.01
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (131 bp):
CTTTTTCGACTTAGATTTCATCCTGGTCACCCTTAGTTGACTGATATCAGTTTTGCCCTAGTCAA
CCCCTTTTGAATTAGGTTTTGTCTTGGTCACCTTTAGTTGACTATATTAGTTTTACCTTGGTCAA
C
Found at i:19250 original size:52 final size:53
Alignment explanation
Indices: 19130--19252 Score: 203
Period size: 53 Copynumber: 2.3 Consensus size: 53
19120 TGAAATTTTA
* * *
19130 CCTGCTTGTATCGATACATTTCATATTGTATCGATACATTTGGGGCAAATTTG
1 CCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGGCAAATTTG
*
19183 CCTGTATGTATCGATACATTTCATAGTGTATCGATACATCT-GGGCAAATTTG
1 CCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGGCAAATTTG
19235 CCTGCATGTATCGATACA
1 CCTGCATGTATCGATACA
19253 AAAATCAATG
Statistics
Matches: 65, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
52 28 0.43
53 37 0.57
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (53 bp):
CCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGGCAAATTTG
Found at i:19265 original size:52 final size:53
Alignment explanation
Indices: 19130--19273 Score: 177
Period size: 52 Copynumber: 2.7 Consensus size: 53
19120 TGAAATTTTA
* ** * *
19130 CCTGCTTGTATCGATACATTTCATATTGTATCGATACATTTGGGGCAAATTTG
1 CCTGCATGTATCGATACAAATCATAGTGTATCGATACATCTGGGGCAAATTTG
* **
19183 CCTGTATGTATCGATACATTTCATAGTGTATCGATACATCT-GGGCAAATTTG
1 CCTGCATGTATCGATACAAATCATAGTGTATCGATACATCTGGGGCAAATTTG
19235 CCTGCATGTATCGATACAAAAATCA-A-TGTATCGATACAT
1 CCTGCATGTATCGATAC--AAATCATAGTGTATCGATACAT
19274 TTTCTTGGCA
Statistics
Matches: 82, Mismatches: 7, Indels: 5
0.87 0.07 0.05
Matches are distributed among these distances:
52 40 0.49
53 38 0.46
54 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (53 bp):
CCTGCATGTATCGATACAAATCATAGTGTATCGATACATCTGGGGCAAATTTG
Found at i:19328 original size:19 final size:18
Alignment explanation
Indices: 19304--19400 Score: 70
Period size: 19 Copynumber: 5.8 Consensus size: 18
19294 AGCGATACAT
19304 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
19323 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
*
19336 TGTATTGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
19355 TTTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
19368 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
19387 TGTATCAATACAAA
1 TGTATCGATACAAA
19401 TCGTTGAATT
Statistics
Matches: 61, Mismatches: 5, Indels: 25
0.67 0.05 0.27
Matches are distributed among these distances:
13 20 0.33
14 2 0.03
16 4 0.07
18 3 0.05
19 32 0.52
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:19337 original size:32 final size:32
Alignment explanation
Indices: 19296--19398 Score: 170
Period size: 32 Copynumber: 3.2 Consensus size: 32
19286 AGCTTCATAG
*
19296 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
* *
19328 CGATACATTGTATTGATACAACACTTATTTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
19360 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
*
19392 CAATACA
1 CGATACA
19399 AATCGTTGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 65 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:21060 original size:10 final size:10
Alignment explanation
Indices: 21041--21135 Score: 55
Period size: 10 Copynumber: 9.1 Consensus size: 10
21031 GTATCGATAC
*
21041 ATGAACAGTG
1 ATGAATAGTG
21051 ATGAATAGTG
1 ATGAATAGTG
* * *
21061 ATGTATCGATAC
1 ATGAATAG-T-G
21073 ATGAATAGTG
1 ATGAATAGTG
*
21083 ATGAACAGTG
1 ATGAATAGTG
* * *
21093 ATGTATTGATAC
1 ATGAATAG-T-G
* *
21105 ATGAACAGTT
1 ATGAATAGTG
21115 ATGAATAGTG
1 ATGAATAGTG
*
21125 ATGAACAGTG
1 ATGAATAGTG
21135 A
1 A
21136 AAGTGAGATT
Statistics
Matches: 62, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
10 47 0.76
11 4 0.06
12 11 0.18
ACGTcount: A:0.39, C:0.07, G:0.25, T:0.28
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:21070 original size:32 final size:32
Alignment explanation
Indices: 21029--21127 Score: 162
Period size: 32 Copynumber: 3.1 Consensus size: 32
21019 ACTATTCATA
21029 ATGTATCGATACATGAACAGTGATGAATAGTG
1 ATGTATCGATACATGAACAGTGATGAATAGTG
* *
21061 ATGTATCGATACATGAATAGTGATGAACAGTG
1 ATGTATCGATACATGAACAGTGATGAATAGTG
* *
21093 ATGTATTGATACATGAACAGTTATGAATAGTG
1 ATGTATCGATACATGAACAGTGATGAATAGTG
21125 ATG
1 ATG
21128 AACAGTGAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 61 1.00
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.30
Consensus pattern (32 bp):
ATGTATCGATACATGAACAGTGATGAATAGTG
Found at i:21347 original size:21 final size:21
Alignment explanation
Indices: 21297--21359 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
21287 GTATTTTTGC
*
21297 TTTGAAAAACATTATTATT-TA
1 TTTGAAAAACATT-TAATTATA
*
21318 CTTGAAAAACATTTAATTATA
1 TTTGAAAAACATTTAATTATA
* *
21339 TTTGTAAAACATCTTGATTAT
1 TTTGAAAAACAT-TTAATTAT
21360 TAGAAAACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 4 0.11
21 24 0.69
22 7 0.20
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.44
Consensus pattern (21 bp):
TTTGAAAAACATTTAATTATA
Done.