Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1916
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: 51937
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.35
Found at i:3233 original size:3 final size:3
Alignment explanation
Indices: 3225--3256 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
3215 CGAGTCAACT
*
3225 TCA TCA TCA TCA TCA TCA TCA TCA TTA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
3257 TTTGATGGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:9865 original size:13 final size:14
Alignment explanation
Indices: 9847--9876 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
9837 GTTAAATTTT
9847 AATTTT-TTTGTAA
1 AATTTTCTTTGTAA
9860 AATTTTCTTTGTAA
1 AATTTTCTTTGTAA
9874 AAT
1 AAT
9877 AAAATTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (14 bp):
AATTTTCTTTGTAA
Found at i:9920 original size:15 final size:15
Alignment explanation
Indices: 9900--9930 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
9890 ATATGCCGAT
9900 TTAAAAATA-ATTTA
1 TTAAAAATATATTTA
9914 TTAAAAATATATTTA
1 TTAAAAATATATTTA
9929 TT
1 TT
9931 CATGCAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAAAATATATTTA
Found at i:11262 original size:14 final size:14
Alignment explanation
Indices: 11243--11271 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
11233 TGAATTTGTT
11243 AAATTGGCTTAAAA
1 AAATTGGCTTAAAA
11257 AAATTGGCTTAAAA
1 AAATTGGCTTAAAA
11271 A
1 A
11272 TGATTCAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.14, T:0.28
Consensus pattern (14 bp):
AAATTGGCTTAAAA
Found at i:15838 original size:23 final size:20
Alignment explanation
Indices: 15793--15839 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
15783 TCAATCACTC
*
15793 AAAAATATTAATCTCTCTTA
1 AAAAATATTAATCCCTCTTA
*
15813 AAAAATAATTAATCCCTCTTT
1 AAAAAT-ATTAATCCCTCTTA
15834 AAAAAT
1 AAAAAT
15840 GGATTCTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATATTAATCCCTCTTA
Found at i:18875 original size:22 final size:22
Alignment explanation
Indices: 18834--18875 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
18824 ATATTGACAT
* *
18834 AAATATTAAATATTAATTATTA
1 AAATATTAAAAACTAATTATTA
*
18856 AAATATTAAAAACTATTTAT
1 AAATATTAAAAACTAATTAT
18876 AATTAAACTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
AAATATTAAAAACTAATTATTA
Found at i:20118 original size:76 final size:76
Alignment explanation
Indices: 20027--20181 Score: 283
Period size: 76 Copynumber: 2.0 Consensus size: 76
20017 TTTACTATAA
20027 ATGCAATATCGAGTCTCATATATTATGCCAAGTACATCTAGAACTCTATTGCATTAAGATATGGT
1 ATGCAATATCGAGTCTCATATATTATGCCAAGTACATCTAGAACTCTATTGCATTAAGATATGGT
20092 ACTTCAAAACT
66 ACTTCAAAACT
**
20103 ATGCAATATCGAGTCTCATATATTATGCCAAGTACATCTAGGCCTCTATTGCATTAAGATATGGT
1 ATGCAATATCGAGTCTCATATATTATGCCAAGTACATCTAGAACTCTATTGCATTAAGATATGGT
*
20168 ATTTCAAAACT
66 ACTTCAAAACT
20179 ATG
1 ATG
20182 TATTTCCTCT
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 76 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (76 bp):
ATGCAATATCGAGTCTCATATATTATGCCAAGTACATCTAGAACTCTATTGCATTAAGATATGGT
ACTTCAAAACT
Found at i:22498 original size:19 final size:19
Alignment explanation
Indices: 22474--22541 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
22464 AATTCAACAA
22474 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
22493 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
*
22508 --TGTATCAATACATAAGT
1 TTTGTATCGATACATAAGT
*
22525 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
22542 TTAGCTACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 10 0.24
15 2 0.05
17 2 0.05
19 27 0.66
ACGTcount: A:0.37, C:0.12, G:0.13, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:22519 original size:32 final size:32
Alignment explanation
Indices: 22476--22538 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
22466 TTCAACAATT
* *
22476 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCAATACATAAGTATTGTATCGATACAA
22508 TGTATCAATACATAAGTATTGTATCGATACA
1 TGTATCAATACATAAGTATTGTATCGATACA
22539 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.37
Consensus pattern (32 bp):
TGTATCAATACATAAGTATTGTATCGATACAA
Found at i:22586 original size:20 final size:20
Alignment explanation
Indices: 22561--22615 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
22551 GCCAAGGAAA
*
22561 TGTATCGATACATTTTTCTG
1 TGTATCGATACATTTATCTG
** *
22581 TGTATCGATACATGGATCTT
1 TGTATCGATACATTTATCTG
22601 TGTATCGATACATTT
1 TGTATCGATACATTT
22616 GGAAATTTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.15, G:0.16, T:0.45
Consensus pattern (20 bp):
TGTATCGATACATTTATCTG
Found at i:25009 original size:49 final size:52
Alignment explanation
Indices: 24945--25282 Score: 173
Period size: 52 Copynumber: 6.5 Consensus size: 52
24935 AGTTTCTCAA
* * *
24945 TTCTCCACAATCGGGGATATTCCAACTCCGA-TTTATTTTC-AAACACTAA-
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAAT
* *
24994 TT-TTCTATAATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACTAAT
1 TTCTTC-ACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACACTAAT
* * * ** * * * *
25047 TTCTTCACAATCGGGGATACTCCAACCCCG--TTAATCATCGGGGATACTCCAACCCCG
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTAT-TTC--CAAAACACTAA----T
* ** * * * *
25104 TTATTTTCAA--GGGGATACTCCAACCCCGGTTTTATTGCTAAAACACTAAT
1 TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAAT
* * * *
25154 TT-TTCCACAATCGGGGATACTCCAACCCCGGTTTGT-TTT-CAAAACGCCAATT
1 TTCTT-CACAATCGGGGATACTCCAACTCCGATTT-TATTTCCAAAACACTAA-T
* * * * *
25206 TTCCTT--TAATCGGGGATACTCTAACTTCGATTTTATTTCCAAAAATACCAAT
1 TT-CTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCC-AAAACACTAAT
*
25258 TT-TTCACAATCGAGGATACTCCAAC
1 TTCTTCACAATCGGGGATACTCCAAC
25283 CTCGTTATTT
Statistics
Matches: 218, Mismatches: 44, Indels: 51
0.70 0.14 0.16
Matches are distributed among these distances:
48 2 0.01
49 26 0.12
50 16 0.07
51 37 0.17
52 58 0.27
53 38 0.17
54 11 0.05
55 18 0.08
56 1 0.00
57 11 0.05
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.32
Consensus pattern (52 bp):
TTCTTCACAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAAT
Found at i:25066 original size:53 final size:49
Alignment explanation
Indices: 24943--25072 Score: 163
Period size: 49 Copynumber: 2.6 Consensus size: 49
24933 TGAGTTTCTC
* * *
24943 AATTCTCCACAATCGGGGATATTCCAACTCCGATTTATTTTCAAACACT
1 AATTCTTCACAATCGGGGATACTCCAACTCCGATTTATTTCCAAACACT
* *
24992 AATT-TTCTATAATCGGGGATACTCCAGCTCCGATTTTATTTCCAAAAACACT
1 AATTCTTC-ACAATCGGGGATACTCCAACTCCGA-TTTATTTCC--AAACACT
25044 AATTTCTTCACAATCGGGGATACTCCAAC
1 AA-TTCTTCACAATCGGGGATACTCCAAC
25073 CCCGTTAATC
Statistics
Matches: 68, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
48 2 0.03
49 26 0.38
50 8 0.12
52 9 0.13
53 20 0.29
54 3 0.04
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (49 bp):
AATTCTTCACAATCGGGGATACTCCAACTCCGATTTATTTCCAAACACT
Found at i:25090 original size:27 final size:28
Alignment explanation
Indices: 25056--25131 Score: 111
Period size: 27 Copynumber: 2.8 Consensus size: 28
25046 TTTCTTCACA
25056 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
*
25083 ATCGGGGATACTCCAACCCCGTTATTTTC
1 ATCGGGGATACTCCAACCCCGTTA-TATC
*
25112 A-AGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
25132 GTTTTATTGC
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 24 0.53
28 18 0.40
29 3 0.07
ACGTcount: A:0.25, C:0.33, G:0.20, T:0.22
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:25269 original size:103 final size:102
Alignment explanation
Indices: 24950--25283 Score: 300
Period size: 107 Copynumber: 3.2 Consensus size: 102
24940 CTCAATTCTC
* * * * *
24950 CACAATCGGGGATATTCCAACTCCGATTTATTTTCAAACACTAATTTT-CTATAATCGGGGATAC
1 CACAATCGGGGATACTCCAACCCCGGTTTATTTTCAAACACCAATTTTCCTTTAATCGGGGATAC
*
25014 TCCAGCTCCGATTTTATTTCCAAAAACACTAATTTCTT
66 TCCAACTCCGATTTTATTTCCAAAAACACTAATTT-TT
* ** * * ** **
25052 CACAATCGGGGATACTCCAACCCC-GTTAATCATCGGGGATACTCCAA--CCCCGTTATTTTCAA
1 CACAATCGGGGATACTCCAACCCCGGTTTATTTTC----AAACACCAATTTTCC-TT-TAATC--
* * * *
25114 GGGGATACTCCAACCCCGGTTTTA-TTGCTAAAACACTAATTTTT
58 GGGGATACTCCAACTCCGATTTTATTTCCAAAAACACTAATTTTT
* *
25158 CCACAATCGGGGATACTCCAACCCCGGTTTGTTTTCAAAACGCCAATTTTCCTTTAATCGGGGAT
1 -CACAATCGGGGATACTCCAACCCCGGTTTATTTTC-AAACACCAATTTTCCTTTAATCGGGGAT
* * * *
25223 ACTCTAACTTCGATTTTATTTCCAAAAATACCAATTTTT
64 ACTCCAACTCCGATTTTATTTCCAAAAACACTAATTTTT
*
25262 CACAATCGAGGATACTCCAACC
1 CACAATCGGGGATACTCCAACC
25284 TCGTTATTTC
Statistics
Matches: 179, Mismatches: 39, Indels: 27
0.73 0.16 0.11
Matches are distributed among these distances:
101 6 0.03
102 22 0.12
103 41 0.23
104 17 0.09
105 17 0.09
106 7 0.04
107 42 0.23
108 27 0.15
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.31
Consensus pattern (102 bp):
CACAATCGGGGATACTCCAACCCCGGTTTATTTTCAAACACCAATTTTCCTTTAATCGGGGATAC
TCCAACTCCGATTTTATTTCCAAAAACACTAATTTTT
Found at i:25301 original size:27 final size:29
Alignment explanation
Indices: 25266--25340 Score: 86
Period size: 27 Copynumber: 2.7 Consensus size: 29
25256 ATTTTTCACA
* *
25266 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCG-GGATACTCCAACCCCGTTACTTCCG
25294 ATCGGGATACT-CAACCCCGTTACTTCCG
1 ATCGGGATACTCCAACCCCGTTACTTCCG
*
25322 A-GGGGATACTCCAACCCCG
1 ATCGGGATACTCCAACCCCG
25341 GCTTTATTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 10 0.24
27 18 0.44
28 13 0.32
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (29 bp):
ATCGGGATACTCCAACCCCGTTACTTCCG
Found at i:25328 original size:209 final size:209
Alignment explanation
Indices: 24945--25399 Score: 598
Period size: 209 Copynumber: 2.2 Consensus size: 209
24935 AGTTTCTCAA
* * *
24945 TTCTCCACAATCGGGGATATTCCAACTCCGATTTATTTTCAAACACTAATTTTCTATAATCGGGG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTATTTTCAAACACCAATTTTCTATAATCGGGG
* * *
25010 ATACTCCAGCTCCGATTTTATTTCCAAAAACACTAATTTCTTCACAATCGGGGATACTCCAACCC
66 ATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
* * *
25075 CGTTAATCATCGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCCAACCCCGGTTTTATT
131 CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGGCTTTATT
* *
25140 GCTAAAACACTAAT
196 CCCAAAACACTAAT
* * * * *
25154 TTTTCCACAATCGGGGATACTCCAACCCCGGTTTGTTTTCAAAACGCCAATTTTCCTTTAATCGG
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTATTTTC-AAACACCAATTTT-CTATAATCGG
* * *
25219 GGATACTCTAACTTCGATTTTATTTCCAAAAATACCAATTT-TTCACAATCGAGGATACTCCAAC
64 GGATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCTTCACAATCGAGGATACTCCAAC
* * *
25283 CTCGTTATTTCATC-GGGATACT-CAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTT
129 CCCGTTA-ATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGGCTTT
* * *
25346 ATTCCCAAAATATTGAT
193 ATTCCCAAAACACTAAT
* *
25363 TTCT-CATAATTGGGGATACTCCAACCCCG--TTATTTTC
1 TTCTCCACAATCGGGGATACTCCAACCCCGATTTATTTTC
25400 GAGGGGATAC
Statistics
Matches: 214, Mismatches: 29, Indels: 9
0.85 0.12 0.04
Matches are distributed among these distances:
206 7 0.03
208 23 0.11
209 87 0.41
210 47 0.22
211 50 0.23
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (209 bp):
TTCTCCACAATCGGGGATACTCCAACCCCGATTTATTTTCAAACACCAATTTTCTATAATCGGGG
ATACTCCAACTCCGATTTTATTTCCAAAAACACCAATTTCTTCACAATCGAGGATACTCCAACCC
CGTTAATCATCGGGGATACTCCAACCCCGTTACTTCCAAGGGGATACTCCAACCCCGGCTTTATT
CCCAAAACACTAAT
Found at i:25443 original size:79 final size:79
Alignment explanation
Indices: 25297--25498 Score: 210
Period size: 79 Copynumber: 2.6 Consensus size: 79
25287 TTATTTCATC
* * * *
25297 GGGATACT-CAACCCCGTTACTTCCGAGGGGATACTCCAACCCCGGCTTTATTCCCAAAATATTG
1 GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATCG
* **
25361 ATTTCTCATAATTG
66 ATTTCTCACAACCG
* * * * ** *
25375 GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAATCTCGATTTTTTTTTC-TAATCATC
1 GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAAT-ATC
25439 GATTTCTCACAACCG
65 GATTTCTCACAACCG
* * * * *
25454 GGGATACTCGAGCCCCGTTATTTTCAAGGGAACACTCCAACCCCG
1 GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCG
25499 TTATTATCTC
Statistics
Matches: 101, Mismatches: 21, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
78 11 0.11
79 90 0.89
ACGTcount: A:0.24, C:0.29, G:0.17, T:0.30
Consensus pattern (79 bp):
GGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAACCCCGACTTTATTCCCAAAATATCG
ATTTCTCACAACCG
Found at i:30912 original size:27 final size:26
Alignment explanation
Indices: 30882--30932 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
30872 GATGATTAGA
30882 AAAAAAATCGAGATTGGAGTATCCCTC
1 AAAAAAA-CGAGATTGGAGTATCCCTC
* * *
30909 AAAATAACGGGGTTGGAGTATCCC
1 AAAAAAACGAGATTGGAGTATCCC
30933 CAATTATGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.37, C:0.18, G:0.24, T:0.22
Consensus pattern (26 bp):
AAAAAAACGAGATTGGAGTATCCCTC
Found at i:31160 original size:52 final size:50
Alignment explanation
Indices: 31085--31196 Score: 118
Period size: 52 Copynumber: 2.2 Consensus size: 50
31075 ATCGAAGTTA
* * *
31085 GAGTATCCCCGATTAAAGGAAAATTGGCGTTTTGAAAACAAAACCGGGGTTG
1 GAGTATCCCCGATTAAAGGAAAATTAGCGTTTAG-AAACAAAACAGGGG-TG
** * * *
31137 GAGTATCCCCGATT-GTGGAAAAATTAGTGTTTAGCAATAAAACAGGGGTG
1 GAGTATCCCCGATTAAAGG-AAAATTAGCGTTTAGAAACAAAACAGGGGTG
31187 GAGTATCCCC
1 GAGTATCCCC
31197 TGAAATAACG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
50 12 0.24
51 13 0.25
52 26 0.51
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (50 bp):
GAGTATCCCCGATTAAAGGAAAATTAGCGTTTAGAAACAAAACAGGGGTG
Found at i:31210 original size:25 final size:24
Alignment explanation
Indices: 31181--31247 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 24
31171 CAATAAAACA
31181 GGGGTGGAGTATCCCCTGAAATAAC
1 GGGGTGGAGTATCCCCTG-AATAAC
* *
31206 GGGGTTGGAGTATCCCGATGATTAAC
1 GGGG-TGGAGTATCCC-CTGAATAAC
*
31232 GGGTTGGAGTATCCCC
1 GGGGTGGAGTATCCCC
31248 GATTGTGAAG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 15 0.42
26 19 0.53
27 2 0.06
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.24
Consensus pattern (24 bp):
GGGGTGGAGTATCCCCTGAATAAC
Found at i:31248 original size:26 final size:28
Alignment explanation
Indices: 31181--31250 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 28
31171 CAATAAAACA
31181 GGGG-TGGAGTATCCCC--TGAAATAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
*
31206 GGGGTTGGAGTAT-CCCGATG-ATTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
31232 -GGGTTGGAGTATCCCCGAT
1 GGGGTTGGAGTATCCCCGAT
31251 TGTGAAGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
25 19 0.47
26 19 0.47
27 2 0.05
ACGTcount: A:0.23, C:0.19, G:0.34, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:33714 original size:20 final size:20
Alignment explanation
Indices: 33687--33741 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
33677 TAAAATTTCC
*
33687 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
33707 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
33727 AAATGTATCGATACA
1 AAATGTATCGATACA
33742 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:33785 original size:19 final size:18
Alignment explanation
Indices: 33761--33828 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
33751 CAGTAGCTAA
33761 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
*
33780 TTATGTATTGATAC--A-
1 TTATGTATCGATACAAAC
33795 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
33812 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
33829 TTGTTGAATT
Statistics
Matches: 41, Mismatches: 2, Indels: 13
0.73 0.04 0.23
Matches are distributed among these distances:
13 10 0.24
14 1 0.02
16 2 0.05
18 4 0.10
19 24 0.59
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:33805 original size:32 final size:32
Alignment explanation
Indices: 33764--33826 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
33754 TAGCTAATTA
* *
33764 TGTATCGATACAATACTTATGTATTGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
33796 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
33827 AATTGTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.37
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:36238 original size:76 final size:76
Alignment explanation
Indices: 36112--36266 Score: 292
Period size: 76 Copynumber: 2.0 Consensus size: 76
36102 AGAGGAAATA
36112 CATAGTTTTGAAGTACCATATCTTAATGCAATAGAGGCCTAGATGTACTTGGCATAATATATGAG
1 CATAGTTTTGAAGTACCATATCTTAATGCAATAGAGGCCTAGATGTACTTGGCATAATATATGAG
36177 ACTCGATATTG
66 ACTCGATATTG
**
36188 CATAGTTTTGAAGTACCATATCTTAATGCAATAGAGTTCTAGATGTACTTGGCATAATATATGAG
1 CATAGTTTTGAAGTACCATATCTTAATGCAATAGAGGCCTAGATGTACTTGGCATAATATATGAG
36253 ACTCGATATTG
66 ACTCGATATTG
36264 CAT
1 CAT
36267 TTATAGTAAA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.34
Consensus pattern (76 bp):
CATAGTTTTGAAGTACCATATCTTAATGCAATAGAGGCCTAGATGTACTTGGCATAATATATGAG
ACTCGATATTG
Found at i:37422 original size:28 final size:28
Alignment explanation
Indices: 37366--37422 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
37356 AAACATTACC
** *
37366 ATTAAAATATTATTTTTTTAATATTAAT
1 ATTAAAATATTATTAGTTTAATATAAAT
37394 ATTAAAA-ATTATTAGTTTAATTATAAAT
1 ATTAAAATATTATTAGTTTAA-TATAAAT
37422 A
1 A
37423 GTTTTATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 11 0.44
28 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
ATTAAAATATTATTAGTTTAATATAAAT
Found at i:37435 original size:23 final size:22
Alignment explanation
Indices: 37409--37455 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
37399 AAATTATTAG
* *
37409 TTTAATTATAAATAGTTTTATAT
1 TTTAATAATAAATA-TTTAATAT
*
37432 TTTAATAATTAATATTTAATAT
1 TTTAATAATAAATATTTAATAT
37454 TT
1 TT
37456 ATGTCAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTAATAATAAATATTTAATAT
Found at i:39327 original size:17 final size:16
Alignment explanation
Indices: 39293--39333 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
39283 GCACACTTAT
39293 ATTTAAAT-ATTCAAA
1 ATTTAAATAATTCAAA
*
39308 ATTTAAATAAATTTAAA
1 ATTTAAAT-AATTCAAA
39325 ATTTAAATA
1 ATTTAAATA
39334 TCAAATGGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 8 0.35
16 1 0.04
17 14 0.61
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTTAAATAATTCAAA
Found at i:40453 original size:21 final size:20
Alignment explanation
Indices: 40429--40475 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
40419 TAAAGAATCC
*
40429 ATTTTTAAAGAGGGATTAATT
1 ATTTTTAAAGAGAGATTAA-T
*
40450 ATTTTTTAAGAGAGATTAAT
1 ATTTTTAAAGAGAGATTAAT
40470 ATTTTT
1 ATTTTT
40476 GAGTGATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
ATTTTTAAAGAGAGATTAAT
Found at i:40463 original size:23 final size:19
Alignment explanation
Indices: 40430--40475 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 19
40420 AAAGAATCCA
40430 TTTTTAAAGAGGGATTAATTAT
1 TTTTTAAAGA--GATTAA-TAT
40452 TTTTTAAGAGAGATTAATAT
1 TTTTTAA-AGAGATTAATAT
40472 TTTT
1 TTTT
40476 GAGTGATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.30
21 6 0.26
22 7 0.30
23 3 0.13
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (19 bp):
TTTTTAAAGAGATTAATAT
Found at i:45016 original size:14 final size:14
Alignment explanation
Indices: 44997--45025 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
44987 GGTTGAATCA
44997 TTTTTAAGCCAATT
1 TTTTTAAGCCAATT
45011 TTTTTAAGCCAATT
1 TTTTTAAGCCAATT
45025 T
1 T
45026 AACAAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTTTAAGCCAATT
Found at i:45620 original size:17 final size:18
Alignment explanation
Indices: 45584--45621 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
45574 CGGATTTATA
*
45584 TTTTATGATAAATAATTT
1 TTTTATGATAAATAAGTT
*
45602 TTTTAT-ATAAATGAGTT
1 TTTTATGATAAATAAGTT
45619 TTT
1 TTT
45622 GATAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (18 bp):
TTTTATGATAAATAAGTT
Found at i:46361 original size:14 final size:15
Alignment explanation
Indices: 46334--46364 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
46324 TTTTTGCATG
46334 AATAAATATATTTTT
1 AATAAATATATTTTT
46349 AATAAAT-TATTTTT
1 AATAAATATATTTTT
46363 AA
1 AA
46365 ATCGGCATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
AATAAATATATTTTT
Found at i:46417 original size:13 final size:14
Alignment explanation
Indices: 46388--46417 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
46378 TGAAAATTTT
46388 ATTTTACAAAGAAA
1 ATTTTACAAAGAAA
46402 ATTTTACAAA-AAA
1 ATTTTACAAAGAAA
46415 ATT
1 ATT
46418 AAAATTTAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.57, C:0.07, G:0.03, T:0.33
Consensus pattern (14 bp):
ATTTTACAAAGAAA
Done.