Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold743
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: 34475
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Found at i:960 original size:45 final size:46
Alignment explanation
Indices: 918--1117 Score: 296
Period size: 45 Copynumber: 4.3 Consensus size: 46
908 TGACAAGTGG
* *
918 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGA-
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
963 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
*
1009 AAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC
1 -----AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
* *
1060 AAAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
1105 AAAGTGATAAGTG
1 AAAGTGATAAGTG
1118 GCTACACTTA
Statistics
Matches: 145, Mismatches: 4, Indels: 12
0.90 0.02 0.07
Matches are distributed among these distances:
45 80 0.55
46 20 0.14
51 45 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC
Found at i:981 original size:97 final size:97
Alignment explanation
Indices: 852--1117 Score: 419
Period size: 97 Copynumber: 2.7 Consensus size: 97
842 TTTGAGTACT
* *
852 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGT-
*
917 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTAATAGCTTCGGCTACACTTA
**
950 TCTGATCAAGTGA-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
1014 AAAGTGATAAGTGATAGCTTCGGCTACACTTA
66 AAAGTGATAAGTAATAGCTTCGGCTACACTTA
* *
1046 TCTGATCAAGAGACAAAGTGATAAGTGATAGC-TTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
1110 GATAAGTG
65 GA-AAGTG
1118 GCTACACTTA
Statistics
Matches: 156, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
96 67 0.43
97 71 0.46
98 18 0.12
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (97 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTAATAGCTTCGGCTACACTTA
Found at i:1033 original size:51 final size:51
Alignment explanation
Indices: 956--1117 Score: 237
Period size: 51 Copynumber: 3.2 Consensus size: 51
946 CTTATCTGAT
*
956 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGA
1 CAAGTG-AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
1008 CAAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
1 CAAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
*
1059 C-----AAAGTGATAAGTGATAGCTT-AGCTACACTTATCTGATCAAGAGA
1 CAAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
1104 CAAAGTGATAAGTG
1 C-AAGTGA-AAGTG
1118 GCTACACTTA
Statistics
Matches: 101, Mismatches: 2, Indels: 14
0.86 0.02 0.12
Matches are distributed among these distances:
45 24 0.24
46 20 0.20
51 46 0.46
52 11 0.11
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (51 bp):
CAAGTGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGA
Found at i:1125 original size:37 final size:37
Alignment explanation
Indices: 1081--1225 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
1071 TGATAGCTTA
1081 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1118 GCTACACTTATCTGATCAAGA-ACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
* *
1154 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
1191 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1226 ATCATACGTA
Statistics
Matches: 103, Mismatches: 4, Indels: 4
0.93 0.04 0.04
Matches are distributed among these distances:
35 11 0.11
36 40 0.39
37 52 0.50
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:1192 original size:73 final size:72
Alignment explanation
Indices: 1081--1225 Score: 245
Period size: 73 Copynumber: 2.0 Consensus size: 72
1071 TGATAGCTTA
*
1081 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAACAAAGT
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAAC-AAGT
1146 GATAAGTG
65 GATAAGTG
* * *
1154 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTGGCTACACTTATCTGATCAGGGACAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAACAAGTG
1219 ATAAGTG
66 ATAAGTG
1226 ATCATACGTA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
72 12 0.18
73 56 0.82
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (72 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTGGCTACACTTATCTGATCAAGAACAAGTG
ATAAGTG
Found at i:2556 original size:58 final size:58
Alignment explanation
Indices: 2479--2645 Score: 237
Period size: 58 Copynumber: 3.0 Consensus size: 58
2469 CATGTGAACA
2479 TGTGATTATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
1 TGTGA-TATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
2538 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATA--
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
* *
2594 TGTG--A--T--TT-CGTGTAAGACCATAG-TGGGCTATGGCATCGGTATGTGATTTG
1 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
2644 TG
1 TG
2646 ATTACGTGTA
Statistics
Matches: 104, Mismatches: 2, Indels: 13
0.87 0.02 0.11
Matches are distributed among these distances:
48 23 0.22
49 15 0.14
50 4 0.04
52 1 0.01
54 1 0.01
56 4 0.04
58 51 0.49
59 5 0.05
ACGTcount: A:0.23, C:0.13, G:0.31, T:0.33
Consensus pattern (58 bp):
TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTAAGTGATATG
Found at i:2588 original size:28 final size:28
Alignment explanation
Indices: 2498--2588 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
2488 GTGATTCCGT
2498 GTAAGACCATAGCTGGGCTATGGCATCG
1 GTAAGACCATAGCTGGGCTATGGCATCG
** * *
2526 GTAAG-TGATATG-TGTGATATGTG-ATTCCG
1 GTAAGACCATA-GCTGGGCTATG-GCA-T-CG
2555 TGTAAGACCATAGCTGGGCTATGGCATCG
1 -GTAAGACCATAGCTGGGCTATGGCATCG
2584 GTAAG
1 GTAAG
2589 TGATATGTGA
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 11 0.23
28 13 0.28
29 4 0.09
30 8 0.17
31 11 0.23
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.27
Consensus pattern (28 bp):
GTAAGACCATAGCTGGGCTATGGCATCG
Found at i:2640 original size:48 final size:49
Alignment explanation
Indices: 2538--2680 Score: 225
Period size: 48 Copynumber: 2.9 Consensus size: 49
2528 AAGTGATATG
*
2538 TGTGATATGTGATTCCGTGTAAGACCATAGCTGGGCTATGGCATCGGTA
1 TGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTA
* *
2587 AGTGATATGTGATTTCGTGTAAGACCATAG-TGGGCTATGGCATCGGTA
1 TGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTA
* * *
2635 TGTGATTTGTGATTACGTGTAAGACCATAGTTGGACTATGGCATCG
1 TGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCG
2681 AGAAAACGAA
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
48 45 0.52
49 42 0.48
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (49 bp):
TGTGATATGTGATTACGTGTAAGACCATAGCTGGGCTATGGCATCGGTA
Found at i:5908 original size:52 final size:48
Alignment explanation
Indices: 5889--6090 Score: 272
Period size: 46 Copynumber: 4.3 Consensus size: 48
5879 TGACAAGTGG
* *
5889 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
5935 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
* *
5983 GTGAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 ---AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
6032 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
6078 AAAGTGATAAGTG
1 AAAGTGATAAGTG
6091 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 10
0.89 0.04 0.06
Matches are distributed among these distances:
46 100 0.69
51 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:6006 original size:51 final size:51
Alignment explanation
Indices: 5935--6090 Score: 223
Period size: 51 Copynumber: 3.1 Consensus size: 51
5925 ATCAAGTGAC
*
5935 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTG
*
5986 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC-----
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTG
**
6032 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGTG
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGAC-AAGTG
6084 ATAAGTG
1 A-AAGTG
6091 GCTACACTTA
Statistics
Matches: 93, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
46 43 0.46
51 44 0.47
52 1 0.01
53 5 0.05
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (51 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGAGACAAGTG
Found at i:6045 original size:97 final size:97
Alignment explanation
Indices: 5823--6090 Score: 455
Period size: 97 Copynumber: 2.7 Consensus size: 97
5813 TTTGAGTACT
*
5823 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGT-
5888 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
65 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
5921 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
5986 AAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
6018 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
6083 GATAAGTG
65 GA-AAGTG
6091 GCTACACTTA
Statistics
Matches: 160, Mismatches: 8, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
97 88 0.55
98 67 0.42
99 5 0.03
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (97 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:6098 original size:37 final size:37
Alignment explanation
Indices: 6054--6199 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
6044 GATAGCTTTA
*
6054 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
6091 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
6128 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
6165 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
6200 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:10953 original size:44 final size:43
Alignment explanation
Indices: 10673--11123 Score: 243
Period size: 44 Copynumber: 10.5 Consensus size: 43
10663 ATTATACAGG
* *** * *
10673 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCA---GAGA
* * * *
10719 TCTTATCTCCCTGAGATTACAGCGGAGCAGA-TCAAGGATAGTAA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCAGAG--A
* * * *
10763 TCCTATCTCCTTGAGATTACAATGGAGCGGATT-AA--AG-GA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCAGAGA
* * * * *
10802 TCTTATCTCTCTGA-AGTTACAGTAGAGAAGA-TCACATCAG-G-
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGA-AGCAGAGA
* *** * *
10843 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCA---GAGA
*
10889 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAGAGA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-CAGAGA
* * **
10933 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-CAGAGA
* * * **
10976 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATTAAAATAAGAGA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATT-GAAGCAGAGA
* * * **
11020 TCTTATCTCCCTGAGATTACAGCGAAGCAGATCGAAGACA-CTA
1 TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAG-CAGAGA
* *
11063 TCCTATCTCCCTGA-AGTTACAGTGGAGCGGATT-AA--AG-GA
1 TCTTATCTCCCTGAGA-TTACAGTGGAGCAGATTGAAGCAGAGA
* *
11102 TCTTATCTCTCTGAGGTTACAG
1 TCTTATCTCCCTGAGATTACAG
11124 CAGAATAGAT
Statistics
Matches: 312, Mismatches: 69, Indels: 55
0.72 0.16 0.13
Matches are distributed among these distances:
38 2 0.01
39 44 0.14
40 1 0.00
41 28 0.09
42 12 0.04
43 58 0.19
44 98 0.31
45 7 0.02
46 61 0.20
47 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (43 bp):
TCTTATCTCCCTGAGATTACAGTGGAGCAGATTGAAGCAGAGA
Found at i:10983 original size:87 final size:83
Alignment explanation
Indices: 10843--11124 Score: 343
Period size: 87 Copynumber: 3.3 Consensus size: 83
10833 TCACATCAGG
* * * * * * *
10843 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGA-ATTTCAGATCTTATCTCCCTGAGGTT
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACA---C-TATCCTATCTCCCTGAAGTT
*
10907 ACAGTGGAGCAGATTGAAGCCAGAGA
62 ACAGTGGAGCGGATT-AA---AGAGA
10933 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
10998 TGGAGCGGATTAAAATAAGAGA
66 TGGAGCGGATT---A-AAGAGA
*
11020 TCTTATCTCCCTGAGATTACAGCGAAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
11085 TGGAGCGGATTAAAG-GA
66 TGGAGCGGATTAAAGAGA
* *
11102 TCTTATCTCTCTGAGGTTACAGC
1 TCTTATCTCCCTGAGATTACAGC
11125 AGAATAGATC
Statistics
Matches: 176, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
82 23 0.13
83 3 0.02
84 1 0.01
87 111 0.63
88 1 0.01
89 1 0.01
90 35 0.20
91 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (83 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCGAAGACACTATCCTATCTCCCTGAAGTTACAG
TGGAGCGGATTAAAGAGA
Found at i:11666 original size:15 final size:16
Alignment explanation
Indices: 11646--11675 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11636 CTAACAAAAG
11646 AACCCAAT-ACCCACA
1 AACCCAATAACCCACA
11661 AACCCAATAACCCAC
1 AACCCAATAACCCAC
11676 CTAAACACTA
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:0.47, C:0.47, G:0.00, T:0.07
Consensus pattern (16 bp):
AACCCAATAACCCACA
Found at i:12756 original size:3 final size:3
Alignment explanation
Indices: 12748--12777 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
12738 GATTTAGTCC
12748 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
12778 CTACTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:25038 original size:49 final size:49
Alignment explanation
Indices: 24981--25078 Score: 144
Period size: 49 Copynumber: 2.0 Consensus size: 49
24971 TCATGTGTTA
* * * *
24981 TAATTTTATACAGTGTTGAGCTTTTGGTTCATGATATTGAAATTA-ATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATT-AAATTATATTT
25030 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAATTATATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAATTATATTT
25079 AATAATAATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 6 0.14
49 38 0.86
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAATTATATTT
Found at i:25370 original size:39 final size:41
Alignment explanation
Indices: 25325--25430 Score: 108
Period size: 44 Copynumber: 2.5 Consensus size: 41
25315 TCTTCTTATG
* *
25325 CTATTACACCTCTATTCCATTCATCCAAACACAAGAA-TAC
1 CTATTACACCTCTATTCCATTCAACCAAACAAAAGAATTAC
* *
25365 C-ATTACGCCTCTATTCTATTCCATTCAACCAAATAAAAGAATTAC
1 CTATTAC-AC-C---TCTATTCCATTCAACCAAACAAAAGAATTAC
*
25410 CTATTACGCCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
25431 ACGCATCTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
39 5 0.09
40 2 0.04
41 12 0.22
44 25 0.46
45 5 0.09
46 5 0.09
ACGTcount: A:0.34, C:0.30, G:0.04, T:0.32
Consensus pattern (41 bp):
CTATTACACCTCTATTCCATTCAACCAAACAAAAGAATTAC
Found at i:25405 original size:44 final size:46
Alignment explanation
Indices: 25335--25426 Score: 143
Period size: 44 Copynumber: 2.0 Consensus size: 46
25325 CTATTACACC
* *
25335 TCTATTCCATTCATCCAAACACAAGAA-TACC-ATTACGCCTCTAT
1 TCTATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
*
25379 TCTATTCCATTCAACCAAATAAAAGAATTACCTATTACGCCTCTAT
1 TCTATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
25425 TC
1 TC
25427 CATTACGCAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 24 0.56
45 4 0.09
46 15 0.35
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (46 bp):
TCTATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
Found at i:25433 original size:16 final size:16
Alignment explanation
Indices: 25412--25463 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
25402 AGAATTACCT
25412 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
25428 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
** *
25444 ATTACATCTTTATTCC
1 ATTACGCCTCTATTCC
25460 ATTA
1 ATTA
25464 TAGCGAACTA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.25, C:0.29, G:0.04, T:0.42
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:30215 original size:80 final size:79
Alignment explanation
Indices: 30078--30335 Score: 270
Period size: 80 Copynumber: 3.3 Consensus size: 79
30068 TTGAATGCTG
* * * * * * *
30078 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCCTT
1 TCCGGGTTAAGTCCCGAAGGCATTGTGC-GAGTTAATAAATCCGGGCTAAG-TCCCGAAGGCATT
*
30142 TGTGCGAGATACTAAA
64 TGTGCGAGATGCTAAA
* * *
30158 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTT
* *
30223 GTGCGAGTTGTTAAA
65 GTGCGAGATGCTAAA
* * * * *
30238 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTTG
* *
30303 AGCGAGGA-GCTATA
66 TGCGA-GATGCTAAA
*
30317 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
30336 TACGTGATTT
Statistics
Matches: 149, Mismatches: 26, Indels: 8
0.81 0.14 0.04
Matches are distributed among these distances:
78 14 0.09
79 47 0.32
80 84 0.56
81 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (79 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGTTAATAAATCCGGGCTAAGTCCCGAAGGCATTTG
TGCGAGATGCTAAA
Found at i:30282 original size:39 final size:40
Alignment explanation
Indices: 30078--30335 Score: 238
Period size: 40 Copynumber: 6.5 Consensus size: 40
30068 TTGAATGCTG
* * * * * *
30078 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTACTAAA
** * * *
30118 TCCGGACTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTACTAAA
*
30158 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
**
30198 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* *
30238 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
* * * * * * *
30277 ACCGGGCTATGTCCCGAAGGCATTTGAGCGAG-GAGCTATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTA-CTAAA
*
30317 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
30336 TACGTGATTT
Statistics
Matches: 186, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
39 49 0.26
40 129 0.69
41 8 0.04
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTACTAAA
Done.