Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2000
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: 20800
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.32
Found at i:1253 original size:23 final size:23
Alignment explanation
Indices: 1210--1254 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
1200 AATTGATGAT
**
1210 TAAAAAAAATAAAATCTAAAGTC
1 TAAAAAAAATAAAATAAAAAGTC
1233 TAAAAAATAA-AAAATAAAAAGT
1 TAAAAAA-AATAAAATAAAAAGT
1255 AGTTTAATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 17 0.89
24 2 0.11
ACGTcount: A:0.71, C:0.04, G:0.04, T:0.20
Consensus pattern (23 bp):
TAAAAAAAATAAAATAAAAAGTC
Found at i:1284 original size:21 final size:22
Alignment explanation
Indices: 1237--1285 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
1227 AAAGTCTAAA
**
1237 AAATAAAAAATAAAAAGTAGTT
1 AAATAAAAAATAAAAAACAGTT
* *
1259 TAATAAAAATTAAAAAACA-TT
1 AAATAAAAAATAAAAAACAGTT
1280 AAATAA
1 AAATAA
1286 TAATAAATGT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.24
Consensus pattern (22 bp):
AAATAAAAAATAAAAAACAGTT
Found at i:3744 original size:46 final size:45
Alignment explanation
Indices: 3691--3866 Score: 212
Period size: 46 Copynumber: 3.8 Consensus size: 45
3681 ATTTTGGGCA
3691 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
3737 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
*
3784 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
3830 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3867 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 12, Indels: 14
0.81 0.09 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 69 0.62
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:3846 original size:93 final size:93
Alignment explanation
Indices: 3687--3858 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
3677 TAGGATTTTG
* *
3687 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3752 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* *
3780 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
3845 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
3859 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:6801 original size:29 final size:29
Alignment explanation
Indices: 6750--6832 Score: 93
Period size: 29 Copynumber: 2.9 Consensus size: 29
6740 CATAGTATCG
* *
6750 TATCTTGGGTTTCTTTATCCTGGATCTT-T-
1 TATCTTGGATTTCTTTATTCTGG-T-TTCTC
6779 TAT-TCTGGATTTCTTTATTCTGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGTTTCTC
6808 TATCTTGGATTTCTTTATTC-GGTTT
1 TATCTTGGATTTCTTTATTCTGGTTT
6833 TCTTGTTATC
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
27 2 0.04
28 8 0.17
29 37 0.77
30 1 0.02
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.58
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCTGGTTTCTC
Found at i:6836 original size:14 final size:15
Alignment explanation
Indices: 6759--6836 Score: 83
Period size: 14 Copynumber: 5.4 Consensus size: 15
6749 GTATCTTGGG
*
6759 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
6774 TCT-TTTATTCTGGA
1 TTTCTTTATTCTGGA
6788 TTTCTTTATTCTGG-
1 TTTCTTTATTCTGGA
*
6802 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
6817 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
6831 TTTCTT
1 TTTCTT
6837 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
13 2 0.04
14 30 0.57
15 19 0.36
16 2 0.04
ACGTcount: A:0.10, C:0.17, G:0.13, T:0.60
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:9328 original size:46 final size:48
Alignment explanation
Indices: 9207--9337 Score: 230
Period size: 48 Copynumber: 2.8 Consensus size: 48
9197 TGTTTGGGCA
*
9207 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTC
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
9255 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-C
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
*
9302 -CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
9338 GCGGGTTACA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
46 35 0.43
47 1 0.01
48 45 0.56
ACGTcount: A:0.20, C:0.22, G:0.28, T:0.30
Consensus pattern (48 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTC
Found at i:12281 original size:15 final size:15
Alignment explanation
Indices: 12242--12319 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
12232 GTATCTTGGG
*
12242 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
12257 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
12272 TTTCTTTATTC-GG-
1 TTTCTTTATTCTGGA
*
12285 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
12300 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
12314 TTTCTT
1 TTTCTT
12320 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
12 2 0.04
13 7 0.13
14 12 0.23
15 30 0.57
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:12308 original size:28 final size:28
Alignment explanation
Indices: 12233--12315 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
12223 CATAGTATCG
* * * *
12233 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GG-TTTCTC
12263 TAT-TCTGGATTTCTTTATTCGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGTTTCTC
12291 TATCTTGGATTTCTTTATTCGGTTT
1 TATCTTGGATTTCTTTATTCGGTTT
12316 TCTTGTTATC
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
28 27 0.57
29 4 0.09
30 16 0.34
ACGTcount: A:0.11, C:0.17, G:0.16, T:0.57
Consensus pattern (28 bp):
TATCTTGGATTTCTTTATTCGGTTTCTC
Found at i:14734 original size:46 final size:46
Alignment explanation
Indices: 14684--14811 Score: 222
Period size: 46 Copynumber: 2.8 Consensus size: 46
14674 TGTTTGGGCA
*
14684 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
14730 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
* *
14776 CCCGAGCTCGTTGAGTTGAGT-CGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
14812 GCGGGTTACA
Statistics
Matches: 79, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
45 15 0.19
46 64 0.81
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
Found at i:18459 original size:6 final size:6
Alignment explanation
Indices: 18448--18634 Score: 163
Period size: 6 Copynumber: 30.8 Consensus size: 6
18438 AACCAAAATG
*
18448 AGAATC AGAATC AGAATC AGTAA-C AGAATC AGAATC AGAATC A-ATATT
1 AGAATC AGAATC AGAATC AG-AATC AGAATC AGAATC AGAATC AGA-ATC
* *
18496 AGTAA-C AGAATC AGAATC AGAATC AGAATT AG-GTGAC AGAATC AGAATC
1 AG-AATC AGAATC AGAATC AGAATC AGAATC AGAAT--C AGAATC AGAATC
* * * *
18545 AGAATC A-ATAAC AGAATC AGAATC GGAATC AGTATT AGTAA-C AGAATC
1 AGAATC AGA-ATC AGAATC AGAATC AGAATC AGAATC AG-AATC AGAATC
* *
18593 AGAATC AGAATC AGAATT ACGTGA-C AGAATC AGAATC AGAAT
1 AGAATC AGAATC AGAATC A-G-AATC AGAATC AGAATC AGAAT
18635 GTGAATGCAA
Statistics
Matches: 147, Mismatches: 18, Indels: 32
0.75 0.09 0.16
Matches are distributed among these distances:
5 10 0.07
6 125 0.85
7 9 0.06
8 3 0.02
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (6 bp):
AGAATC
Found at i:18463 original size:30 final size:30
Alignment explanation
Indices: 18427--18634 Score: 227
Period size: 30 Copynumber: 7.1 Consensus size: 30
18417 AAGAAACATT
* *
18427 ATCAGAATT-GGAACCAAAATGAGAATCAGA
1 ATCAGAATTAGGAA-CAGAATCAGAATCAGA
* *
18457 ATCAGAATCAGTAACAGAATCAGAATCAGA
1 ATCAGAATTAGGAACAGAATCAGAATCAGA
*
18487 ATCA-ATATTAGTAACAGAATCAGAATCAGA
1 ATCAGA-ATTAGGAACAGAATCAGAATCAGA
*
18517 ATCAGAATTAGGTGACAGAATCAGAATCAGA
1 ATCAGAATTAGG-AACAGAATCAGAATCAGA
*
18548 ATC--AA-T---AACAGAATCAGAATCGGA
1 ATCAGAATTAGGAACAGAATCAGAATCAGA
* *
18572 ATCAGTATTAGTAACAGAATCAGAATCAGA
1 ATCAGAATTAGGAACAGAATCAGAATCAGA
18602 ATCAGAATTACGTG-ACAGAATCAGAATCAGA
1 ATCAGAATTA-G-GAACAGAATCAGAATCAGA
18633 AT
1 AT
18635 GTGAATGCAA
Statistics
Matches: 153, Mismatches: 13, Indels: 23
0.81 0.07 0.12
Matches are distributed among these distances:
24 19 0.12
26 1 0.01
27 1 0.01
28 1 0.01
29 3 0.02
30 84 0.55
31 44 0.29
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (30 bp):
ATCAGAATTAGGAACAGAATCAGAATCAGA
Found at i:18548 original size:85 final size:85
Alignment explanation
Indices: 18448--18634 Score: 338
Period size: 85 Copynumber: 2.2 Consensus size: 85
18438 AACCAAAATG
*
18448 AGAATCAGAATCAGAATCAGTAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAATAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
*
18513 CAGAATCAGAATTAGGTGAC
66 CAGAATCAGAATTACGTGAC
* *
18533 AGAATCAGAATCAGAATCAATAACAGAATCAGAATCGGAATCAGTATTAGTAACAGAATCAGAAT
1 AGAATCAGAATCAGAATCAATAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
18598 CAGAATCAGAATTACGTGAC
66 CAGAATCAGAATTACGTGAC
18618 AGAATCAGAATCAGAAT
1 AGAATCAGAATCAGAAT
18635 GTGAATGCAA
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 98 1.00
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.20
Consensus pattern (85 bp):
AGAATCAGAATCAGAATCAATAACAGAATCAGAATCAGAATCAATATTAGTAACAGAATCAGAAT
CAGAATCAGAATTACGTGAC
Found at i:18789 original size:27 final size:26
Alignment explanation
Indices: 18752--18817 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 26
18742 AGCATGGCTG
*
18752 CCAGAACAGATATCGTGACAGAGTCA
1 CCAGAACAGATATCGTGACAGAGCCA
* *
18778 CCAGATACAGATATTGTGGCAGAGCCA
1 CCAGA-ACAGATATCGTGACAGAGCCA
18805 CCAGAATCAGATA
1 CCAGAA-CAGATA
18818 ATGTGGTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.17
27 29 0.83
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (26 bp):
CCAGAACAGATATCGTGACAGAGCCA
Found at i:18832 original size:27 final size:27
Alignment explanation
Indices: 18776--18833 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
18766 GTGACAGAGT
* * *
18776 CACCAGATACAGATATTGTGGCAGAGC
1 CACCAGATACAGATAATGTGGCAAACC
*
18803 CACCAGA-ATCAGATAATGTGGTAAACC
1 CACCAGATA-CAGATAATGTGGCAAACC
18830 CACC
1 CACC
18834 TAACAGAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.36, C:0.26, G:0.21, T:0.17
Consensus pattern (27 bp):
CACCAGATACAGATAATGTGGCAAACC
Found at i:19004 original size:22 final size:22
Alignment explanation
Indices: 18956--19014 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
18946 GTAAATACGT
*
18956 TTGGCACGAAGCCATAGTCAAG
1 TTGGCACAAAGCCATAGTCAAG
* * * *
18978 ATGGCACAAAGCCATATTTAGG
1 TTGGCACAAAGCCATAGTCAAG
*
19000 TTGGCACAGAGCCAT
1 TTGGCACAAAGCCAT
19015 TAATAACGGG
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.25, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAGTCAAG
Found at i:19146 original size:27 final size:26
Alignment explanation
Indices: 19099--19154 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
19089 ATCGATCGTC
19099 AACAGATATTGTGGCAGAGCCACCAG
1 AACAGATATTGTGGCAGAGCCACCAG
*
19125 AACAGATATTTGTGGCATAGCCACCAG
1 AACAGATA-TTGTGGCAGAGCCACCAG
19152 AAC
1 AAC
19155 GCTTCCTCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.36, C:0.23, G:0.23, T:0.18
Consensus pattern (26 bp):
AACAGATATTGTGGCAGAGCCACCAG
Found at i:19407 original size:27 final size:26
Alignment explanation
Indices: 19352--19543 Score: 217
Period size: 27 Copynumber: 7.3 Consensus size: 26
19342 GGGGCAAAAT
* *
19352 GGTAATTTTACCC-ACAAGGGTATCTC
1 GGTAATTCTACCCTAC-AGGGTATTTC
19378 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACA-GGGTATTTC
*
19405 GGTATTTCTACCCTACTAGGGTATTTC
1 GGTAATTCTACCCTAC-AGGGTATTTC
* *
19432 GATAATTCTACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACA-GGGTATTTC
* *
19459 GGTAATTCTATCCTATAAGGGTATTTC
1 GGTAATTCTACCCTA-CAGGGTATTTC
* *
19486 AGTAATTCTACCCTATAGGGTATTTC
1 GGTAATTCTACCCTACAGGGTATTTC
**
19512 -AAAATTCTACCCTACAGGGTATTTC
1 GGTAATTCTACCCTACAGGGTATTTC
*
19537 AGTAATT
1 GGTAATT
19544 TCACAATCAA
Statistics
Matches: 142, Mismatches: 18, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
25 22 0.15
26 28 0.20
27 90 0.63
28 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (26 bp):
GGTAATTCTACCCTACAGGGTATTTC
Found at i:19481 original size:81 final size:78
Alignment explanation
Indices: 19354--19543 Score: 247
Period size: 81 Copynumber: 2.4 Consensus size: 78
19344 GGCAAAATGG
* * * * *
19354 TAATTTTACCC-ACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCGGTATTTCTACCC
1 TAATTCTACCCTAC-AGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCC
19418 TACTAGGGTATTTCGA
65 TA-TAGGGTATTTC-A
* * *
19434 TAATTCTACCCTACAGGGGTATTTTGGTAATTCTATCCTATAAGGGTATTTCAGTAATTCTACCC
1 TAATTCTACCCTACA-GGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCC
19499 TATAGGGTATTTCA
65 TATAGGGTATTTCA
* *
19513 AAATTCTACCCTACAGGGTATTTCAGTAATT
1 TAATTCTACCCTACAGGGTATTTCGGTAATT
19544 TCACAATCAA
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
78 14 0.14
79 15 0.15
80 22 0.23
81 46 0.47
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (78 bp):
TAATTCTACCCTACAGGGTATTTCGGTAATTCTACCCTACAAGGGTATTTCAGTAATTCTACCCT
ATAGGGTATTTCA
Found at i:19602 original size:27 final size:27
Alignment explanation
Indices: 19553--19874 Score: 405
Period size: 27 Copynumber: 12.0 Consensus size: 27
19543 TTCACAATCA
*
19553 AGGGTAAAAC-GTAATTCTATAAATTG
1 AGGGTAAAACGGTAATTCTGTAAATTG
* * * *
19579 AGGGTAAAATGATAATTTTGTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATTG
* * **
19606 AGGGTAAACCAGTAATTCTGTAAATCA
1 AGGGTAAAACGGTAATTCTGTAAATTG
* * ** *
19633 AGGGTAAAACAGTAATTTTACAAATCG
1 AGGGTAAAACGGTAATTCTGTAAATTG
*
19660 AGGGTAAAACGGTAATTCTGTAAATCG
1 AGGGTAAAACGGTAATTCTGTAAATTG
* *
19687 AGGGTAAAACAGTAATTCTGTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATTG
*
19714 AGGGTAAAATGGTAATTCTGTAAATTG
1 AGGGTAAAACGGTAATTCTGTAAATTG
**
19741 AGGGTAAAATAGTAATTCTGTAAATTG
1 AGGGTAAAACGGTAATTCTGTAAATTG
*
19768 AGGGTAAAA-GGTAATTCTGTAAATCG
1 AGGGTAAAACGGTAATTCTGTAAATTG
*
19794 AGGGTAAAACGGTAATTCTGTAAACTG
1 AGGGTAAAACGGTAATTCTGTAAATTG
* * *
19821 AGGGTAAAACGTTAATTCTATAAATCG
1 AGGGTAAAACGGTAATTCTGTAAATTG
19848 AGGGTAAAACGGTAATTCTGTAAATTG
1 AGGGTAAAACGGTAATTCTGTAAATTG
19875 GGAGTACTTT
Statistics
Matches: 254, Mismatches: 40, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
26 33 0.13
27 221 0.87
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (27 bp):
AGGGTAAAACGGTAATTCTGTAAATTG
Found at i:19926 original size:107 final size:107
Alignment explanation
Indices: 19553--19874 Score: 412
Period size: 107 Copynumber: 3.0 Consensus size: 107
19543 TTCACAATCA
* * * * * * * *
19553 AGGGTAAAACGTAATTCTATAAATTGAGGGTAAAA-TGATAATTTTGTAAACTGAGGGTAAACCA
1 AGGGTAAAAGGTAATTCTGTAAATCGAGGGCAAAACAG-TAATTCTGTAAACTGAGGGTAAAACG
* * * ** *
19617 GTAATTCTGTAAATCAAGGGTAAAACAGTAATTTTACAAATCG
65 GTAATTCTATAAATCGAGGGTAAAACAGTAATTCTGTAAATTG
* *
19660 AGGGTAAAACGGTAATTCTGTAAATCGAGGGTAAAACAGTAATTCTGTAAACTGAGGGTAAAATG
1 AGGGTAAAA-GGTAATTCTGTAAATCGAGGGCAAAACAGTAATTCTGTAAACTGAGGGTAAAACG
* * *
19725 GTAATTCTGTAAATTGAGGGTAAAATAGTAATTCTGTAAATTG
65 GTAATTCTATAAATCGAGGGTAAAACAGTAATTCTGTAAATTG
* * *
19768 AGGGTAAAAGGTAATTCTGTAAATCGAGGGTAAAACGGTAATTCTGTAAACTGAGGGTAAAACGT
1 AGGGTAAAAGGTAATTCTGTAAATCGAGGGCAAAACAGTAATTCTGTAAACTGAGGGTAAAACGG
*
19833 TAATTCTATAAATCGAGGGTAAAACGGTAATTCTGTAAATTG
66 TAATTCTATAAATCGAGGGTAAAACAGTAATTCTGTAAATTG
19875 GGAGTACTTT
Statistics
Matches: 191, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
107 100 0.52
108 90 0.47
109 1 0.01
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.29
Consensus pattern (107 bp):
AGGGTAAAAGGTAATTCTGTAAATCGAGGGCAAAACAGTAATTCTGTAAACTGAGGGTAAAACGG
TAATTCTATAAATCGAGGGTAAAACAGTAATTCTGTAAATTG
Done.