Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011276.1 Kokia drynarioides strain JFW-HI SEQ_126255, whole genome shotgun sequence
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: 14331
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1037 original size:202 final size:201
Alignment explanation
Indices: 693--1352 Score: 1124
Period size: 201 Copynumber: 3.3 Consensus size: 201
683 AGGCTCAAAG
* *
693 GAAGCGAGTTGAAACAAACGACACGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCCAAACA
1 GAAGCGAGTTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCCAAACG
* *
758 AGGCTCAAAGTGAGCGAAATCTTCAAAACACAGCTTCCTGATGAGACACTAAGAAGCAGGTGGAA
66 AGGCTCAAAGTGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAA
823 GCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
131 GCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
*
888 TACAGG
196 TACAGA
* *
894 GAAGCGAGTTGAAACAAATGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCCCAAAT
1 GAAGCGAGTTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGA-CCCAAAC
*
959 GAGGCTCAAAGTGAGCGAAATCTTCAAAACCCAACTTCCTGATGAGACACTGAGAAGCAGGTGGA
65 GAGGCTCAAAGTGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGA
* * *
1024 AGCAATAAAAGGTTATCTTCCTGATGAGATTCTGAGAAGTGAACCAAATTCGTCTTCCTAATGAG
130 AGCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAG
*
1089 ATACAAA
195 ATACAGA
* * *
1096 GAAGCGAGTTGAAACAAACGACGTGGTCACCTTCCTGATGAGACACCGAGAAGAAGACCCAAACG
1 GAAGCGAGTTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCCAAACG
1161 AGGCTCAAAGTGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAA
66 AGGCTCAAAGTGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAA
* *
1226 GCAATAAATGGTTAGCTTCCTGATGAGATACTGAGAAATGAACCAAATTCGTCTTCCTGATGAGA
131 GCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
1291 TACAGA
196 TACAGA
* *
1297 GAAGCG-GATTGAAACAAGCGACGCGGTCATTTTCCTGATGAGATACCGAGAAGAAG
1 GAAGCGAG-TTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAG
1353 GCCAAGTCAA
Statistics
Matches: 428, Mismatches: 29, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
200 1 0.00
201 240 0.56
202 187 0.44
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.19
Consensus pattern (201 bp):
GAAGCGAGTTGAAACAAACGACGCGGTCATCTTCCTGATGAGATACCGAGAAGAAGACCCAAACG
AGGCTCAAAGTGAGCGAAATCTTCAAAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTGGAA
GCAATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGA
TACAGA
Found at i:1707 original size:11 final size:11
Alignment explanation
Indices: 1693--1750 Score: 64
Period size: 11 Copynumber: 5.1 Consensus size: 11
1683 TTTGTTTAAA
1693 ATTTTAAATTT
1 ATTTTAAATTT
1704 ATTTTAAATTT
1 ATTTTAAATTT
*
1715 AAATTT-AATTT
1 -ATTTTAAATTT
*
1726 AAGTTTAAATTT
1 -ATTTTAAATTT
1738 ATTTTCAAATTT
1 ATTTT-AAATTT
1750 A
1 A
1751 AAATTGCTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
11 25 0.61
12 16 0.39
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:1715 original size:6 final size:6
Alignment explanation
Indices: 1695--1752 Score: 59
Period size: 6 Copynumber: 10.0 Consensus size: 6
1685 TGTTTAAAAT
* * *
1695 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AA TTTAAG TTTAAA TTT-AT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
1740 TTTCAAA TTTAAA
1 TTT-AAA TTTAAA
1753 ATTGCTAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 13 0.31
6 25 0.60
7 4 0.10
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (6 bp):
TTTAAA
Found at i:1717 original size:17 final size:17
Alignment explanation
Indices: 1663--1752 Score: 105
Period size: 17 Copynumber: 5.4 Consensus size: 17
1653 TTGAACTCCC
1663 TTTAAATTTATTTT---
1 TTTAAATTTATTTTAAA
* *
1677 TTTAAATTTGTTTAAAA
1 TTTAAATTTATTTTAAA
1694 TTTTAAATTTATTTTAAA
1 -TTTAAATTTATTTTAAA
* *
1712 TTTAAATTTAATTTAAG
1 TTTAAATTTATTTTAAA
1729 TTTAAATTTATTTTCAAA
1 TTTAAATTTATTTT-AAA
1747 TTTAAA
1 TTTAAA
1753 ATTGCTAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
14 12 0.19
17 28 0.44
18 23 0.37
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:3601 original size:59 final size:58
Alignment explanation
Indices: 3507--4116 Score: 883
Period size: 59 Copynumber: 10.4 Consensus size: 58
3497 TGGAGGTCCT
*
3507 CGAACCTTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCTATTTTTGACCC
1 CGAACCTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCC
*
3566 CGAACCTTCTAAAAATTACCATTTTATCCCTGAACTTCC-AAAATCCCATTTTTGACCC
1 CGAACCTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCC
*
3624 CGAACCTTCTAAAAATTACCA-TTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCC
1 CGAACCTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCC
*
3682 CGAACCTTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCC
1 CGAACCTTCTAAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCC
3741 CGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CC
1 CGAACCTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCC
* * *
3799 CGAAACCTTCTAAAAATTACCA-TTTACCCCCAAATTCCAAAAATCCCATTTTTAACCC
1 CG-AACCTTCTAAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCC
* * *
3857 CGAACCTTCTAAAAAATTACCATTTTACCACCGAACTCCCAAAAATCACATTTTTGATCC
1 CGAACCTTCT-AAAAATTACCATTTTACC-CCGAACTTCCAAAAATCCCATTTTTGACCC
* * * *
3917 CGAACCTTTTAAATATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCT
1 CGAACCTTCTAAAAATTACCATTTTA-CCCCGAACTTCCAAAAATCCCATTTTTGACCC
* *
3976 CGAACCTTC-CAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCC
1 CGAACCTTCTAAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCC
*
4034 CGAACCTT-TCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACTC
1 CGAACCTTCT-AAAAATTACCATTTTACCC-CGAACTTCCAAAAATCCCATTTTTGACCC
* * *
4093 TGAACCTTC-CAAAACTACCATTTT
1 CGAACCTTCTAAAAATTACCATTTT
4117 TGCCCCCGTG
Statistics
Matches: 501, Mismatches: 36, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
57 52 0.10
58 165 0.33
59 246 0.49
60 38 0.08
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (58 bp):
CGAACCTTCTAAAAATTACCATTTTACCCCGAACTTCCAAAAATCCCATTTTTGACCC
Found at i:3739 original size:117 final size:118
Alignment explanation
Indices: 3507--4116 Score: 923
Period size: 117 Copynumber: 5.2 Consensus size: 118
3497 TGGAGGTCCT
* *
3507 CGAACCTTCTAAAAATTACCATTTTATCCCCGAACTTCCAAAAATCCTATTTTTGACCCCGAACC
1 CGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
*
3572 TTCTAAAAATTACCATTTTATCCCT-GAACTTCC-AAAATCCCATTTTTGACCC
66 TTCTAAAAATTACCATTTTA-CCCTCAAACTTCCAAAAATCCCATTTTTGACCC
*
3624 CGAACCTTCTAAAAATTACCA-TTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCCCGAACC
1 CGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
3688 TTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCC
66 TTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCC
3741 CGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCGAAAC
1 CGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCG-AAC
* *
3805 CTTCTAAAAATTACCA-TTTACCCCCAAA-TTCCAAAAATCCCATTTTTAACCC
65 CTTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCC
* * * *
3857 CGAACCTTCTAAAAAATTACCATTTTACCACCGAACTCCCAAAAATCACATTTTTGATCCCGAAC
1 CGAACCTTCT-AAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* * * *
3922 CTTTTAAATATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCT
65 CTTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCC
* **
3976 CGAACCTTC-CAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
1 CGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
* *
4040 TT-TCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACTC
66 TTCT-AAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCC
* * *
4093 TGAACCTTC-CAAAACTACCATTTT
1 CGAACCTTCTAAAAATTACCATTTT
4117 TGCCCCCGTG
Statistics
Matches: 456, Mismatches: 28, Indels: 18
0.91 0.06 0.04
Matches are distributed among these distances:
115 4 0.01
116 101 0.22
117 252 0.55
118 68 0.15
119 31 0.07
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (118 bp):
CGAACCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
TTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCC
Found at i:3901 original size:176 final size:174
Alignment explanation
Indices: 3507--4116 Score: 908
Period size: 176 Copynumber: 3.5 Consensus size: 174
3497 TGGAGGTCCT
*
3507 CGAACCTTCTAAAAATTACCATTTTATCCC-CGAACTTCCAAAAATCCTATTTTTGACCCCGAAC
1 CGAACCTTCTAAAAATTACCATTTTA-CCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* *
3571 CTTCTAAAAATTACCATTTTATCCCTGAACTTCC-AAAATCCCATTTTTGACCCCGAACCTTCTA
65 CTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCGAACCTTCTA
*
3635 AAAATTACCATTTACCCCCGAACTTCCAAAAATCCCATTTTTTACCC
129 AAAATTACCATTTACCCCC-AACTTCCAAAAATCCCATTTTTAACCC
*
3682 CGAACCTTCTAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCCCGAACC
1 CGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
3747 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCGAAACCTTCTAA
66 TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCG-AACCTTCTAA
*
3812 AAATTACCATTTACCCCCAAATTCCAAAAATCCCATTTTTAACCC
130 AAATTACCATTTACCCCCAACTTCCAAAAATCCCATTTTTAACCC
* * *
3857 CGAACCTTCTAAAAAATTACCATTTTACCAC-CGAACTCCCAAAAATCACATTTTTGATCCCGAA
1 CGAACCTTCT-AAAAATTACCATTTTACC-CTCGAACTTCCAAAAATCCCATTTTTGACCCCGAA
* * *
3921 CCTTTTAAATATTACCATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAACCTTC-
64 CCTTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACC-CGAACCTTCT
* ** *
3985 CAAAATTACCATTTTACCCTTGAACTTCCAAAAATCCCATTTTTGACCC
128 AAAAATTACCA-TTTACCC-CCAACTTCCAAAAATCCCATTTTTAACCC
* *
4034 CGAACCTT-TCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACTCTGAAC
1 CGAACCTTCT-AAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAAC
* *
4098 CTTC-CAAAACTACCATTTT
65 CTTCTAAAAATTACCATTTT
4117 TGCCCCCGTG
Statistics
Matches: 398, Mismatches: 28, Indels: 18
0.90 0.06 0.04
Matches are distributed among these distances:
174 3 0.01
175 152 0.38
176 207 0.52
177 36 0.09
ACGTcount: A:0.33, C:0.32, G:0.04, T:0.31
Consensus pattern (174 bp):
CGAACCTTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCCATTTTTGACCCCGAACC
TTCTAAAAATTACCATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCGAACCTTCTAAA
AATTACCATTTACCCCCAACTTCCAAAAATCCCATTTTTAACCC
Found at i:5916 original size:16 final size:16
Alignment explanation
Indices: 5888--5929 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 16
5878 TCGACCTCTC
5888 CTTTTTTCATTTTTCT
1 CTTTTTTCATTTTTCT
5904 CTTTTCTTC-TTTTTCTTT
1 CTTTT-TTCATTTTTC--T
5922 CTTTTTTC
1 CTTTTTTC
5930 TCTTCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 11 0.48
17 6 0.26
18 6 0.26
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.76
Consensus pattern (16 bp):
CTTTTTTCATTTTTCT
Found at i:5924 original size:13 final size:13
Alignment explanation
Indices: 5892--5939 Score: 55
Period size: 12 Copynumber: 3.7 Consensus size: 13
5882 CCTCTCCTTT
*
5892 TTTCATTTTTCTC
1 TTTCTTTTTTCTC
5905 TTTTCTTCTTTT-TC
1 -TTTCTT-TTTTCTC
5919 TTTCTTTTTTCTC
1 TTTCTTTTTTCTC
5932 -TTCTTTTT
1 TTTCTTTTT
5940 ATTTATTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 12 0.39
13 8 0.26
14 7 0.23
15 4 0.13
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTTTTTTCTC
Found at i:5935 original size:12 final size:12
Alignment explanation
Indices: 5908--5939 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
5898 TTTTCTCTTT
5908 TCTTC-TTTTTC
1 TCTTCTTTTTTC
5919 T-TTCTTTTTTC
1 TCTTCTTTTTTC
5930 TCTTCTTTTT
1 TCTTCTTTTT
5940 ATTTATTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.16
11 8 0.42
12 8 0.42
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (12 bp):
TCTTCTTTTTTC
Found at i:5952 original size:26 final size:25
Alignment explanation
Indices: 5896--5956 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 25
5886 TCCTTTTTTC
* *
5896 ATTTTTCTCTTTTCTTCTTTTTCTTT
1 ATTTTT-TCTCTTCTTCTTTTTATTT
* *
5922 CTTTTTTCTCTTCTTTTTATTTATTT
1 ATTTTTTCTCTTCTTCTT-TTTATTT
5948 ATTTTTTCT
1 ATTTTTTCT
5957 TCATTGCATC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
25 10 0.34
26 19 0.66
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.77
Consensus pattern (25 bp):
ATTTTTTCTCTTCTTCTTTTTATTT
Found at i:11253 original size:29 final size:29
Alignment explanation
Indices: 11221--11292 Score: 144
Period size: 29 Copynumber: 2.5 Consensus size: 29
11211 GCTCGGGGGT
11221 AAAATGGTAATTTTGGACACTTCAAGAAC
1 AAAATGGTAATTTTGGACACTTCAAGAAC
11250 AAAATGGTAATTTTGGACACTTCAAGAAC
1 AAAATGGTAATTTTGGACACTTCAAGAAC
11279 AAAATGGTAATTTT
1 AAAATGGTAATTTT
11293 CGGATGGTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.31
Consensus pattern (29 bp):
AAAATGGTAATTTTGGACACTTCAAGAAC
Found at i:11348 original size:59 final size:59
Alignment explanation
Indices: 11279--11441 Score: 161
Period size: 60 Copynumber: 2.7 Consensus size: 59
11269 CTTCAAGAAC
* * * *
11279 AAAATGGTAATTTTCGGATGGTTCGAGGTTTAAAATGGAATTTTTAGACATT-TAGGGGT
1 AAAATAGTAATTTTTGGA-GGTTCGAGGTTAAAAATGGAATTTTTAGACATTCGAGGGGT
* * * ** *
11338 AAAATAGTAATTTTTGGAAGATTCGGGGGTCAAAAATGGTGTTTTTAGACATTCGAGGTGT
1 AAAATAGTAATTTTTGG-AGGTTC-GAGGTTAAAAATGGAATTTTTAGACATTCGAGGGGT
* *
11399 AAAATTGTAATTTTTGAGAGGTTCGA-G-TCAAAATGGAATTTTT
1 AAAATAGTAATTTTTG-GAGGTTCGAGGTTAAAAATGGAATTTTT
11442 GTAAAATTCA
Statistics
Matches: 83, Mismatches: 17, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
58 12 0.14
59 20 0.24
60 25 0.30
61 25 0.30
62 1 0.01
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.37
Consensus pattern (59 bp):
AAAATAGTAATTTTTGGAGGTTCGAGGTTAAAAATGGAATTTTTAGACATTCGAGGGGT
Found at i:11413 original size:30 final size:30
Alignment explanation
Indices: 11300--11413 Score: 83
Period size: 30 Copynumber: 3.8 Consensus size: 30
11290 TTTCGGATGG
** *
11300 TTCGAGGTTTAAAA-TGGAATTTTTAGACA
1 TTCGAGGGGTAAAATTGTAATTTTTAGACA
* * * *
11329 TT-TAGGGGTAAAATAGTAATTTTTGGAAGA
1 TTCGAGGGGTAAAATTGTAATTTTTAG-ACA
* *
11359 TTCG-GGGGTCAAAAATGGT-GTTTTTAGACA
1 TTCGAGGGGT--AAAATTGTAATTTTTAGACA
*
11389 TTCGAGGTGTAAAATTGTAATTTTT
1 TTCGAGGGGTAAAATTGTAATTTTT
11414 GAGAGGTTCG
Statistics
Matches: 63, Mismatches: 15, Indels: 13
0.69 0.16 0.14
Matches are distributed among these distances:
28 8 0.13
29 18 0.29
30 20 0.32
31 10 0.16
32 7 0.11
ACGTcount: A:0.32, C:0.05, G:0.25, T:0.39
Consensus pattern (30 bp):
TTCGAGGGGTAAAATTGTAATTTTTAGACA
Found at i:11458 original size:29 final size:29
Alignment explanation
Indices: 11428--11690 Score: 167
Period size: 29 Copynumber: 9.0 Consensus size: 29
11418 GGTTCGAGTC
* *
11428 AAAATGGAATTTTTGTAAAATTCAAGTTCA
1 AAAATGGAATTTTTGGAAAATTCAAGGT-A
* *
11458 AAAATGGAA-TTTTGGAAAGTTCAAAAGTA
1 AAAATGGAATTTTTGGAAAATTC-AAGGTA
** *
11487 AAAATATAATTTTTGGAAAATTCGAGGTCA
1 AAAATGGAATTTTTGGAAAATTCAAGGT-A
* ** *
11517 AAAATGGAA-TTTTAGAAAATTTGAGATTA
1 AAAATGGAATTTTTGGAAAATTCAAG-GTA
* * *
11546 AAAATGGAA-TTTTGGAAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAAATTCA-AGGTA
* * **
11575 AAAATGTAATTTTTGAAAAATTTGAGGTTA
1 AAAATGGAATTTTTGGAAAATTCAAGG-TA
* *
11605 AAAATGGAATTTTT-GAAAATTCGAGGTC
1 AAAATGGAATTTTTGGAAAATTCAAGGTA
* * ***
11633 AAAA-GGTAATTTTTTGAAAGTTTGGGGGTA
1 AAAATGG-AATTTTTGGAAA-ATTCAAGGTA
* * *
11663 AAAATGTAATTTTTGGAAAGTTCGAGGT
1 AAAATGGAATTTTTGGAAAATTCAAGGT
11691 CGAAATATGA
Statistics
Matches: 185, Mismatches: 37, Indels: 23
0.76 0.15 0.09
Matches are distributed among these distances:
27 2 0.01
28 12 0.06
29 89 0.48
30 81 0.44
31 1 0.01
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.34
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAAATTCAAGGTA
Found at i:11491 original size:88 final size:87
Alignment explanation
Indices: 11397--11708 Score: 289
Period size: 88 Copynumber: 3.6 Consensus size: 87
11387 CATTCGAGGT
* ** *
11397 GTAAAATTGTAATTTTTGAGAGGTTCGA-GTCAAAATGGAATTTTTGTAAAATTCAAGTTCAAAA
1 GTAAAAATGTAATTTTTGAGAAATTCGAGGTCAAAATGGAATTTTTG-AAAATTCGAGTTCAAAA
11461 ATGGAATTTTGGAAAGTTCAAAA
65 ATGGAATTTTGGAAAGTTCAAAA
* * *
11484 GTAAAAATATAATTTTTG-GAAAATTCGAGGTCAAAAATGGAATTTTAGAAAATTTGAGATT-AA
1 GTAAAAATGTAATTTTTGAG-AAATTCGAGGTC-AAAATGGAATTTTTGAAAATTCGAG-TTCAA
* ***
11547 AAATGGAATTTTGGAAAGTTTAGGG
63 AAATGGAATTTTGGAAAGTTCAAAA
* * * *
11572 GTAAAAATGTAATTTTTGAAAAATTTGAGGTTAAAAATGGAATTTTTGAAAATTCGAGGTC-AAA
1 GTAAAAATGTAATTTTTGAGAAATTCGAGG-TCAAAATGGAATTTTTGAAAATTCGAGTTCAAAA
* *****
11636 A-GGTAATTTTTTGAAAGTTTGGGG
65 ATGG-AA-TTTTGGAAAGTTCAAAA
11660 GTAAAAATGTAATTTTTG-GAAAGTTCGAGGTCGAAATAT-G-ATTTTTGAA
1 GTAAAAATGTAATTTTTGAGAAA-TTCGAGGTC-AAA-ATGGAATTTTTGAA
11709 CAACTTAGGG
Statistics
Matches: 190, Mismatches: 23, Indels: 24
0.80 0.10 0.10
Matches are distributed among these distances:
86 3 0.02
87 42 0.22
88 126 0.66
89 19 0.10
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (87 bp):
GTAAAAATGTAATTTTTGAGAAATTCGAGGTCAAAATGGAATTTTTGAAAATTCGAGTTCAAAAA
TGGAATTTTGGAAAGTTCAAAA
Found at i:11548 original size:59 final size:59
Alignment explanation
Indices: 11423--11708 Score: 255
Period size: 59 Copynumber: 4.9 Consensus size: 59
11413 TGAGAGGTTC
* * * * * * **
11423 GAGTCAAAATGGAATTTTTGTAAAATTCAAGTTCAAAAATGGAATTTTGGAAAGTTCAA
1 GAGTAAAAATGGAATTTTTGGAAAATTCGAGGTCAAAAATGGAATTTTTGAAAATTTGA
* ** *
11482 AAGTAAAAATATAATTTTTGGAAAATTCGAGGTCAAAAATGGAATTTTAGAAAATTTGA
1 GAGTAAAAATGGAATTTTTGGAAAATTCGAGGTCAAAAATGGAATTTTTGAAAATTTGA
* * * * *
11541 GATTAAAAATGGAA-TTTTGGAAAGTTTAGGGGT-AAAAATGTAATTTTTGAAAAATTTGA
1 GAGTAAAAATGGAATTTTTGGAAA-ATTCGAGGTCAAAAATGGAATTTTTG-AAAATTTGA
* *
11600 G-GTTAAAAATGGAATTTTT-GAAAATTCGAGGTC-AAAA-GGTAATTTTTTGAAAGTTTGG
1 GAG-TAAAAATGGAATTTTTGGAAAATTCGAGGTCAAAAATGG-AA-TTTTTGAAAATTTGA
* * * *
11658 GGGTAAAAATGTAATTTTTGGAAAGTTCGAGGTCGAAATAT-G-ATTTTTGAA
1 GAGTAAAAATGGAATTTTTGGAAAATTCGAGGTC-AAAAATGGAATTTTTGAA
11709 CAACTTAGGG
Statistics
Matches: 185, Mismatches: 30, Indels: 25
0.77 0.12 0.10
Matches are distributed among these distances:
57 1 0.01
58 66 0.36
59 110 0.59
60 4 0.02
61 4 0.02
ACGTcount: A:0.41, C:0.03, G:0.21, T:0.34
Consensus pattern (59 bp):
GAGTAAAAATGGAATTTTTGGAAAATTCGAGGTCAAAAATGGAATTTTTGAAAATTTGA
Found at i:11696 original size:29 final size:29
Alignment explanation
Indices: 11338--11690 Score: 200
Period size: 30 Copynumber: 12.0 Consensus size: 29
11328 ATTTAGGGGT
* *
11338 AAAATAGTAATTTTTGGAAGATTCGGGGGTCA
1 AAAAT-GTAATTTTTGGAAAATTC-GAGGT-A
* * *
11370 AAAATGGT-GTTTTTAG-ACATTCGAGGTGTA
1 AAAAT-GTAATTTTTGGAAAATTCGA-G-GTA
* ** *
11400 AAATTGTAATTTTT-GAGAGGTTCGA-GTC
1 AAAATGTAATTTTTGGA-AAATTCGAGGTA
* * * *
11428 AAAATGGAATTTTTGTAAAATTCAAGTTCA
1 AAAATGTAATTTTTGGAAAATTCGAGGT-A
* * * *
11458 AAAATGGAA-TTTTGGAAAGTTCAAAAGTA
1 AAAATGTAATTTTTGGAAAATTC-GAGGTA
*
11487 AAAATATAATTTTTGGAAAATTCGAGGTCA
1 AAAATGTAATTTTTGGAAAATTCGAGGT-A
* * * *
11517 AAAATGGAA-TTTTAGAAAATTTGAGATTA
1 AAAATGTAATTTTTGGAAAATTCGAG-GTA
* * * *
11546 AAAATGGAA-TTTTGGAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAAA-ATTCGAGGTA
* *
11575 AAAATGTAATTTTTGAAAAATTTGAGGTTA
1 AAAATGTAATTTTTGGAAAATTCGAGG-TA
* *
11605 AAAATGGAATTTTT-GAAAATTCGAGGTC
1 AAAATGTAATTTTTGGAAAATTCGAGGTA
* * * * *
11633 AAAAGGTAATTTTTTGAAAGTTTGGGGGTA
1 AAAATGTAATTTTTGGAAA-ATTCGAGGTA
*
11663 AAAATGTAATTTTTGGAAAGTTCGAGGT
1 AAAATGTAATTTTTGGAAAATTCGAGGT
11691 CGAAATATGA
Statistics
Matches: 247, Mismatches: 57, Indels: 37
0.72 0.17 0.11
Matches are distributed among these distances:
28 32 0.13
29 95 0.38
30 99 0.40
31 14 0.06
32 7 0.03
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.35
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAAATTCGAGGTA
Found at i:12741 original size:12 final size:12
Alignment explanation
Indices: 12726--12787 Score: 63
Period size: 12 Copynumber: 5.1 Consensus size: 12
12716 AAATAATTAG
*
12726 TTAATAAATATA
1 TTAATATATATA
*
12738 TTAATGTATA-A
1 TTAATATATATA
* *
12749 TAAATAAATATA
1 TTAATATATATA
12761 TTAATATATATA
1 TTAATATATATA
12773 TATATATATATATA
1 T-TA-ATATATATA
12787 T
1 T
12788 AAATGCTTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 8 0.20
12 20 0.50
13 2 0.05
14 10 0.25
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (12 bp):
TTAATATATATA
Found at i:12769 original size:2 final size:2
Alignment explanation
Indices: 12756--12788 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
12746 TAATAAATAA
12756 AT AT AT -T A- AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12789 AATGCTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 27 0.93
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13386 original size:17 final size:16
Alignment explanation
Indices: 13363--13455 Score: 98
Period size: 17 Copynumber: 5.4 Consensus size: 16
13353 ACTTCTATTT
13363 ATTTAAATTTAGAATAA
1 ATTTAAATTTA-AATAA
*
13380 TTTTAAATTTAAATATAA
1 ATTTAAATTT-AA-ATAA
*
13398 ATTTAAACTTAAATTAA
1 ATTTAAATTTAAA-TAA
13415 ATTTAAATTTTAAATAA
1 ATTTAAA-TTTAAATAA
13432 ATTT-AATCTTAAAATAA
1 ATTTAAAT-TT-AAATAA
13449 ATTTAAA
1 ATTTAAA
13456 ATGAGTTGAG
Statistics
Matches: 65, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
15 1 0.02
16 5 0.08
17 39 0.60
18 20 0.31
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (16 bp):
ATTTAAATTTAAATAA
Found at i:13390 original size:6 final size:6
Alignment explanation
Indices: 13363--13455 Score: 74
Period size: 6 Copynumber: 16.2 Consensus size: 6
13353 ACTTCTATTT
* * *
13363 ATTTAA ATTTAGA A--TAA TTTTAA ATTTAA ATATAA ATTTAA ACTTAA
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
13410 A-TTAA ATTTAA ATTTTAA A--TAA ATTT-A ATCTTAA A-ATAA ATTTAA
1 ATTTAA ATTTAA A-TTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA
13455 A
1 A
13456 ATGAGTTGAG
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
4 5 0.07
5 14 0.20
6 41 0.59
7 10 0.14
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (6 bp):
ATTTAA
Found at i:13437 original size:34 final size:34
Alignment explanation
Indices: 13363--13455 Score: 116
Period size: 35 Copynumber: 2.7 Consensus size: 34
13353 ACTTCTATTT
* *
13363 ATTTAAATTTAGAATAATTTTAAATTTAAATATAA
1 ATTTAAACTTA-AATAAATTTAAATTTAAATATAA
*
13398 ATTTAAACTTAAATTAAATTTAAATTTTAA-ATAA
1 ATTTAAACTTAAA-TAAATTTAAATTTAAATATAA
*
13432 ATTTAATCTTAAAATAAATTTAAA
1 ATTTAAACTT-AAATAAATTTAAA
13456 ATGAGTTGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
34 25 0.48
35 27 0.52
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (34 bp):
ATTTAAACTTAAATAAATTTAAATTTAAATATAA
Done.