Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2705
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: 26527
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:1179 original size:31 final size:29
Alignment explanation
Indices: 1146--1215 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
1136 ATTGACAGTA
1146 ATATTTAATATTAATAAATATTTAATATATAAT
1 ATATTTAATA-T-ATAAATATTTAAT-TAT-AT
* *
1179 ATATTTAATATATATATATTTAATTTTAT
1 ATATTTAATATATAAATATTTAATTATAT
1208 ATATTTAA
1 ATATTTAA
1216 ATTTATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 10 0.29
30 2 0.06
31 12 0.34
32 1 0.03
33 10 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATATTTAATATATAAATATTTAATTATAT
Found at i:1184 original size:16 final size:15
Alignment explanation
Indices: 1146--1239 Score: 87
Period size: 14 Copynumber: 6.5 Consensus size: 15
1136 ATTGACAGTA
1146 ATATTTAATATTAAT
1 ATATTTAATATTAAT
1161 AAATATTTAATATATAAT
1 --ATATTTAATAT-TAAT
1179 ATATTTAATA-TATAT
1 ATATTTAATATTA-AT
*
1194 ATATTTAAT-TTTAT
1 ATATTTAATATTAAT
1208 ATATTTAA-ATT--T
1 ATATTTAATATTAAT
1220 AT-TTTAATA-TAA-
1 ATATTTAATATTAAT
1232 ATATTTAA
1 ATATTTAA
1240 AAAAAAAACA
Statistics
Matches: 68, Mismatches: 1, Indels: 20
0.76 0.01 0.22
Matches are distributed among these distances:
11 6 0.09
12 6 0.09
13 5 0.07
14 14 0.21
15 12 0.18
16 10 0.15
17 11 0.16
18 4 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTTAATATTAAT
Found at i:1195 original size:20 final size:20
Alignment explanation
Indices: 1170--1235 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 20
1160 TAAATATTTA
*
1170 ATATATAATATATTTAATAT
1 ATATATAATTTATTTAATAT
*
1190 ATATAT-ATTTAATTTTATAT
1 ATATATAATTT-ATTTAATAT
*
1210 ATTTA-AATTTATTTTAATAT
1 ATATATAATTTA-TTTAATAT
*
1230 AAATAT
1 ATATAT
1236 TTAAAAAAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 4 0.11
20 32 0.89
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATATATAATTTATTTAATAT
Found at i:1240 original size:24 final size:27
Alignment explanation
Indices: 1145--1240 Score: 72
Period size: 24 Copynumber: 3.4 Consensus size: 27
1135 AATTGACAGT
*
1145 AATATTTAATATTAATAAATATTTAATATATA
1 AATATTTAA-A-T-ATATATATTT-A-ATATA
*
1177 ATATATTTAATATATATATATTTAATTTTA
1 A-ATATTTAA-ATATATATATTTAA-TATA
*
1207 TATATTTAAAT-T-TAT-TTTAATATA
1 AATATTTAAATATATATATTTAATATA
1231 AATATTTAAA
1 AATATTTAAA
1241 AAAAAAACAT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
24 12 0.21
25 5 0.09
26 3 0.05
27 1 0.02
28 2 0.04
29 9 0.16
30 4 0.07
31 9 0.16
32 2 0.04
33 10 0.18
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
AATATTTAAATATATATATTTAATATA
Found at i:1537 original size:21 final size:21
Alignment explanation
Indices: 1511--1553 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1501 TTATATTTAA
1511 TTATATTTATTAAATTAAAAT
1 TTATATTTATTAAATTAAAAT
* *
1532 TTATATTTATTTATTTAAAAT
1 TTATATTTATTAAATTAAAAT
1553 T
1 T
1554 AAATATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
TTATATTTATTAAATTAAAAT
Found at i:1564 original size:20 final size:21
Alignment explanation
Indices: 1525--1565 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1515 ATTTATTAAA
* *
1525 TTAAAATTTATATTTATTTAT
1 TTAAAATTTAAATATATTTAT
1546 TTAAAA-TTAAATATATTTAT
1 TTAAAATTTAAATATATTTAT
1566 ATTATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTAAAATTTAAATATATTTAT
Found at i:1591 original size:28 final size:29
Alignment explanation
Indices: 1519--1595 Score: 111
Period size: 28 Copynumber: 2.6 Consensus size: 29
1509 AATTATATTT
1519 ATTAAATTAAAATTTATATTTATTTATTTAAA
1 ATTAAA-T-AAATTTATA-TTATTTATTTAAA
*
1551 ATTAAATATATTTATATTATTTATTT-AA
1 ATTAAATAAATTTATATTATTTATTTAAA
1579 ATTAAATAAATTTATAT
1 ATTAAATAAATTTATAT
1596 CTAAATACTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 18 0.42
29 10 0.23
30 8 0.19
31 1 0.02
32 6 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (29 bp):
ATTAAATAAATTTATATTATTTATTTAAA
Found at i:1593 original size:19 final size:22
Alignment explanation
Indices: 1569--1647 Score: 58
Period size: 23 Copynumber: 3.7 Consensus size: 22
1559 TATTTATATT
1569 ATTTAT-T-TAAAT-TAAATAA
1 ATTTATATCTAAATATAAATAA
1588 ATTTATATCTAAATACTAAATAA
1 ATTTATATCTAAATA-TAAATAA
* * * * *
1611 ATATGTTTATAAATATAATTAA
1 ATTTATATCTAAATATAAATAA
*
1633 ATATAT-TCATAAATA
1 ATTTATATC-TAAATA
1648 ATTAAAAATA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
19 6 0.12
20 1 0.02
21 6 0.12
22 17 0.35
23 18 0.38
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.43
Consensus pattern (22 bp):
ATTTATATCTAAATATAAATAA
Found at i:1607 original size:28 final size:28
Alignment explanation
Indices: 1549--1613 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 28
1539 TATTTATTTA
* ** *
1549 AAATTAAATATATTTATATTATTTATTT
1 AAATTAAATAAATTTATATTAAATATCT
1577 AAATTAAATAAATTTATATCTAAATA-CT
1 AAATTAAATAAATTTATAT-TAAATATCT
1605 AAA-TAAATA
1 AAATTAAATA
1614 TGTTTATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
27 6 0.19
28 22 0.69
29 4 0.12
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (28 bp):
AAATTAAATAAATTTATATTAAATATCT
Found at i:1635 original size:22 final size:23
Alignment explanation
Indices: 1581--1674 Score: 95
Period size: 22 Copynumber: 4.2 Consensus size: 23
1571 TTATTTAAAT
*
1581 TAAATAAATTTATATC-TAAATAC
1 TAAATAAATATAT-TCATAAATAC
* *
1604 TAAATAAATATGTTTATAAATA-
1 TAAATAAATATATTCATAAATAC
* *
1626 TAATTAAATATATTCATAAATAA
1 TAAATAAATATATTCATAAATAC
* *
1649 TTAA-AAATATATTCATAAATAA
1 TAAATAAATATATTCATAAATAC
1671 TAAA
1 TAAA
1675 CAGCTACAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
22 41 0.68
23 19 0.32
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (23 bp):
TAAATAAATATATTCATAAATAC
Found at i:1645 original size:12 final size:11
Alignment explanation
Indices: 1607--1669 Score: 58
Period size: 12 Copynumber: 5.6 Consensus size: 11
1597 TAAATACTAA
*
1607 ATAAATATGTTT
1 ATAAATAT-ATT
*
1619 ATAAATATAAT
1 ATAAATATATT
1630 -TAAATATATT
1 ATAAATATATT
1640 CATAAATA-ATT
1 -ATAAATATATT
*
1651 AAAAATATATT
1 ATAAATATATT
1662 CATAAATA
1 -ATAAATA
1670 ATAAACAGCT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
10 15 0.36
11 7 0.17
12 20 0.48
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (11 bp):
ATAAATATATT
Found at i:1807 original size:13 final size:13
Alignment explanation
Indices: 1775--1812 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1765 AATTTTAAAT
* *
1775 AAACTTAATAAAC
1 AAACTTTATATAC
1788 AAACTTTATATAC
1 AAACTTTATATAC
1801 AAACTTTATATA
1 AAACTTTATATA
1813 ATTTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (13 bp):
AAACTTTATATAC
Found at i:3815 original size:29 final size:30
Alignment explanation
Indices: 3772--3896 Score: 94
Period size: 29 Copynumber: 4.5 Consensus size: 30
3762 CAAAATTCTG
* *
3772 TATTTTTATTATTATTTTTTATTT-TATAA
1 TATTTTTATAATTATTTTATATTTATATAA
3801 TTATTTTTA-AATTATTTTATATTTATATAA
1 -TATTTTTATAATTATTTTATATTTATATAA
3831 TA--TTT-TAA-TATTTTATA-TTATATAA
1 TATTTTTATAATTATTTTATATTTATATAA
* * * *
3856 -AATATTA-AAATATTTATATAATTATAT--
1 TATTTTTATAATTATTT-TATATTTATATAA
3883 TATTTTTAT-ATTAT
1 TATTTTTATAATTAT
3897 ATCATAATTA
Statistics
Matches: 79, Mismatches: 6, Indels: 22
0.74 0.06 0.21
Matches are distributed among these distances:
24 1 0.01
25 8 0.10
26 13 0.16
27 10 0.13
28 13 0.16
29 21 0.27
30 13 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
TATTTTTATAATTATTTTATATTTATATAA
Found at i:3823 original size:18 final size:19
Alignment explanation
Indices: 3802--3844 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
3792 ATTTTATAAT
3802 TATTTTTA-AATTATTTT-A
1 TATTTTTATAA-TATTTTAA
*
3820 TATTTATATAATATTTTAA
1 TATTTTTATAATATTTTAA
3839 TATTTT
1 TATTTT
3845 ATATTATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
18 13 0.62
19 8 0.38
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TATTTTTATAATATTTTAA
Found at i:3847 original size:18 final size:18
Alignment explanation
Indices: 3813--3904 Score: 57
Period size: 18 Copynumber: 5.1 Consensus size: 18
3803 ATTTTTAAAT
3813 TATTTTATATTTATATAA
1 TATTTTATATTTATATAA
*
3831 TATTTTAATATTT-TATAT
1 TATTTT-ATATTTATATAA
* * *
3849 TATATAAAATATTA-A-AA
1 TATTTTATAT-TTATATAA
* *
3866 TATTTATATAATTATATTA
1 TATTT-TATATTTATATAA
3885 T-TTTTATATTATATCATAA
1 TATTTTATATT-TAT-ATAA
3904 T
1 T
3905 TATATTACAG
Statistics
Matches: 54, Mismatches: 12, Indels: 15
0.67 0.15 0.19
Matches are distributed among these distances:
17 16 0.30
18 26 0.48
19 12 0.22
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTATATTTATATAA
Found at i:3867 original size:27 final size:27
Alignment explanation
Indices: 3807--3882 Score: 91
Period size: 27 Copynumber: 2.8 Consensus size: 27
3797 ATAATTATTT
* *
3807 TTAAATTATTTTATATT-TATATAATA
1 TTAAAATATTTTATATTATATAAAATA
**
3833 TTTTAATATTTTATATTATATAAAATA
1 TTAAAATATTTTATATTATATAAAATA
3860 TTAAAATATTTATATAATTATAT
1 TTAAAATATTT-TAT-ATTATAT
3883 TATTTTTATA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
26 14 0.34
27 17 0.41
28 3 0.07
29 7 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TTAAAATATTTTATATTATATAAAATA
Found at i:5648 original size:18 final size:18
Alignment explanation
Indices: 5625--5663 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5615 AAAGTGACAA
*
5625 AAATAAAAATATAAATCT
1 AAATAAAAAAATAAATCT
*
5643 AAATAAAAAAATAAATGT
1 AAATAAAAAAATAAATCT
5661 AAA
1 AAA
5664 AAATTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.23
Consensus pattern (18 bp):
AAATAAAAAAATAAATCT
Found at i:6096 original size:2 final size:2
Alignment explanation
Indices: 6089--6128 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
6079 AAGCAAAACA
6089 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6129 GGTAAGGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8464 original size:20 final size:20
Alignment explanation
Indices: 8427--8469 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
8417 ATGCAGATAC
* *
8427 AATTTCTATCAAATAAATAA
1 AATTTCTATAAAAAAAATAA
* *
8447 AATTTTTATAAAAAAAATTA
1 AATTTCTATAAAAAAAATAA
8467 AAT
1 AAT
8470 ATATTTGTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTTCTATAAAAAAAATAA
Found at i:12715 original size:16 final size:16
Alignment explanation
Indices: 12684--12729 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
12674 TTTTAAATTT
*
12684 TTTTATTTAGAGTTAAA
1 TTTTA-TTAGATTTAAA
12701 TTTTATTAGATTTAAA
1 TTTTATTAGATTTAAA
* *
12717 TTTAATTTGATTT
1 TTTTATTAGATTT
12730 GTAATCTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
16 21 0.81
17 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
TTTTATTAGATTTAAA
Found at i:13784 original size:14 final size:15
Alignment explanation
Indices: 13765--13793 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
13755 TAAGAAATGG
13765 GTTTTTGTT-TTTGT
1 GTTTTTGTTCTTTGT
13779 GTTTTTGTTCTTTGT
1 GTTTTTGTTCTTTGT
13794 TGTAATTACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.00, C:0.03, G:0.21, T:0.76
Consensus pattern (15 bp):
GTTTTTGTTCTTTGT
Found at i:15396 original size:48 final size:47
Alignment explanation
Indices: 15325--15422 Score: 153
Period size: 48 Copynumber: 2.1 Consensus size: 47
15315 CAGAACCTGT
15325 ATAAAGCATCCCCCTTTAGTTTAAAAACATCTTGTCTC-CTATCTTTTC
1 ATAAAGCATCCCCCTTTAGTTTAAAAACATCTTGTCTCGC-ATC-TTTC
* *
15373 ATAAAGCATCCCTCTTTAGTTTAAGAACATCTTGTCTCGCATCTTTC
1 ATAAAGCATCCCCCTTTAGTTTAAAAACATCTTGTCTCGCATCTTTC
15420 ATA
1 ATA
15423 TAATTCAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
47 7 0.15
48 39 0.83
49 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.39
Consensus pattern (47 bp):
ATAAAGCATCCCCCTTTAGTTTAAAAACATCTTGTCTCGCATCTTTC
Found at i:16327 original size:21 final size:23
Alignment explanation
Indices: 16286--16327 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
16276 GTCAAACGTA
*
16286 ATAATTAAAAGATTTTAATTTTT
1 ATAATTAAAAGATTATAATTTTT
16309 ATAATT-AAA-ATTATAATTT
1 ATAATTAAAAGATTATAATTT
16328 GATAATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 3 0.17
23 6 0.33
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (23 bp):
ATAATTAAAAGATTATAATTTTT
Found at i:16337 original size:21 final size:23
Alignment explanation
Indices: 16286--16338 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 23
16276 GTCAAACGTA
* * *
16286 ATAATTAAAAGATTTTAATTTTT
1 ATAATTTAAAGATTATAATTTTG
16309 ATAA-TTAAA-ATTATAA-TTTG
1 ATAATTTAAAGATTATAATTTTG
16329 ATAATTTAAA
1 ATAATTTAAA
16339 TAAAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 7 0.27
21 11 0.42
22 4 0.15
23 4 0.15
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (23 bp):
ATAATTTAAAGATTATAATTTTG
Found at i:16341 original size:29 final size:29
Alignment explanation
Indices: 16309--16377 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
16299 TTTAATTTTT
16309 ATAATTAAAATT-ATAATTTGATAATTTAA
1 ATAATTAAAATTAATAATTT-ATAATTTAA
16338 ATAA--AAAATTTAAATAATTTATAATTTAA
1 ATAATTAAAA-TT-AATAATTTATAATTTAA
*
16367 A-AATTATAATT
1 ATAATTAAAATT
16378 TAAATAAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
27 4 0.12
28 4 0.12
29 16 0.47
30 10 0.29
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
ATAATTAAAATTAATAATTTATAATTTAA
Found at i:16357 original size:30 final size:29
Alignment explanation
Indices: 16321--16384 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 29
16311 AATTAAAATT
16321 ATAATTTGATAATTTAAATAA-AAAATTTAA
1 ATAATTT-ATAATTTAAA-AATAAAATTTAA
*
16351 ATAATTTATAATTTAAAAATTATAATTTAA
1 ATAATTTATAATTTAAAAA-TAAAATTTAA
16381 ATAA
1 ATAA
16385 AATAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 2 0.06
29 10 0.32
30 19 0.61
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (29 bp):
ATAATTTATAATTTAAAAATAAAATTTAA
Found at i:16375 original size:14 final size:16
Alignment explanation
Indices: 16321--16384 Score: 75
Period size: 13 Copynumber: 4.2 Consensus size: 16
16311 AATTAAAATT
16321 ATAATTTGATAATTTAA
1 ATAATTT-ATAATTTAA
*
16338 ATAA---AAAATTTAA
1 ATAATTTATAATTTAA
16351 ATAATTTATAATTTAA
1 ATAATTTATAATTTAA
16367 A-AA-TTATAATTTAA
1 ATAATTTATAATTTAA
16381 ATAA
1 ATAA
16385 AATAATTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 12 0.29
14 12 0.29
15 4 0.10
16 9 0.22
17 4 0.10
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
ATAATTTATAATTTAA
Found at i:16389 original size:14 final size:15
Alignment explanation
Indices: 16329--16392 Score: 73
Period size: 14 Copynumber: 4.5 Consensus size: 15
16319 TTATAATTTG
16329 ATAATTTAAATAA-A
1 ATAATTTAAATAATA
*
16343 A-AATTTAAATAATTT
1 ATAATTTAAATAA-TA
*
16358 ATAATTTAAA-AATT
1 ATAATTTAAATAATA
16372 ATAATTTAAATAA-A
1 ATAATTTAAATAATA
16386 ATAATTT
1 ATAATTT
16393 TATTATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
13 11 0.25
14 20 0.45
15 5 0.11
16 8 0.18
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATTTAAATAATA
Found at i:20799 original size:18 final size:17
Alignment explanation
Indices: 20771--20804 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
20761 TAATTTAAAA
*
20771 ATTAATTTTATTATTAT
1 ATTAATTTTATAATTAT
20788 ATTAATTTTTATAATTA
1 ATTAA-TTTTATAATTA
20805 AATTTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
ATTAATTTTATAATTAT
Found at i:21249 original size:7 final size:7
Alignment explanation
Indices: 21237--21264 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
21227 TTTCAGATTT
21237 AAATATA
1 AAATATA
21244 AAATATA
1 AAATATA
21251 AAATATA
1 AAATATA
21258 AAATATA
1 AAATATA
21265 TATTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (7 bp):
AAATATA
Found at i:21795 original size:13 final size:13
Alignment explanation
Indices: 21777--21820 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
21767 CTATTTTTTA
21777 AAATATTTATATT
1 AAATATTTATATT
21790 AAATATTTATATT
1 AAATATTTATATT
* *
21803 TAATTTTTAT-TT
1 AAATATTTATATT
21815 AAATAT
1 AAATAT
21821 AAATATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 6 0.22
13 21 0.78
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AAATATTTATATT
Found at i:23203 original size:6 final size:6
Alignment explanation
Indices: 23192--23222 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
23182 TCCCCGGAGC
23192 CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT C
1 CCCTTT CCCTTT CCCTTT CCCTTT CCCTTT C
23223 TTCCTCTTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (6 bp):
CCCTTT
Found at i:24367 original size:2 final size:2
Alignment explanation
Indices: 24360--24391 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
24350 AAGATTAAAC
24360 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
24392 TACGAGCTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24899 original size:14 final size:14
Alignment explanation
Indices: 24882--24928 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
24872 AATATGTATA
24882 TAAAATTATAAATT
1 TAAAATTATAAATT
24896 TAAAATT-TAAAATT
1 TAAAATTAT-AAATT
24910 T-AAATTATTAAATAT
1 TAAAATTA-TAAAT-T
24925 TAAA
1 TAAA
24929 TGACCCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 6 0.21
14 17 0.61
15 3 0.11
16 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATTATAAATT
Found at i:25834 original size:14 final size:15
Alignment explanation
Indices: 25815--25843 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
25805 AAATTGTAAC
25815 TTAAACATAT-TTAA
1 TTAAACATATCTTAA
25829 TTAAACATATCTTAA
1 TTAAACATATCTTAA
25844 AAAATAAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.41
Consensus pattern (15 bp):
TTAAACATATCTTAA
Done.