Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009368.1 Corchorus capsularis cultivar CVL-1 contig09389, 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: 64646
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2402 original size:3 final size:3
Alignment explanation
Indices: 2394--2445 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
2384 AGTTAATTTG
2394 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2442 ATA A
1 ATA A
2446 AAAACTGCCA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2834 original size:16 final size:15
Alignment explanation
Indices: 2813--2854 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
2803 TTGTAAAATA
2813 ACCGAATCCGACTAAG
1 ACCGAATCCGACT-AG
2829 ACCGAA-CTCGACTAG
1 ACCGAATC-CGACTAG
*
2844 ACTGAATCCGA
1 ACCGAATCCGA
2855 ATGAATCCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 11 0.48
16 12 0.52
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (15 bp):
ACCGAATCCGACTAG
Found at i:4607 original size:30 final size:30
Alignment explanation
Indices: 4573--4633 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
4563 GACAACTATG
4573 TAACAAATTTCATTTAGCTTTCAACAGGCC
1 TAACAAATTTCATTTAGCTTTCAACAGGCC
4603 TAACAAATTTCATTTAGCTTTCAACAGGCC
1 TAACAAATTTCATTTAGCTTTCAACAGGCC
4633 T
1 T
4634 GTAAAATCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.34
Consensus pattern (30 bp):
TAACAAATTTCATTTAGCTTTCAACAGGCC
Found at i:5108 original size:32 final size:32
Alignment explanation
Indices: 5071--5159 Score: 151
Period size: 32 Copynumber: 2.8 Consensus size: 32
5061 CAAAAACAGA
5071 AGCAAGTAATATATTCACAAAAACAGAAACTC
1 AGCAAGTAATATATTCACAAAAACAGAAACTC
*
5103 AGCAAGTAATATATTCACAAAAATAGAAACTC
1 AGCAAGTAATATATTCACAAAAACAGAAACTC
* *
5135 AGCAAGTAATATATTCCCAAGAACA
1 AGCAAGTAATATATTCACAAAAACA
5160 ACAGCAAGAA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.52, C:0.18, G:0.10, T:0.20
Consensus pattern (32 bp):
AGCAAGTAATATATTCACAAAAACAGAAACTC
Found at i:10001 original size:42 final size:42
Alignment explanation
Indices: 9954--10053 Score: 155
Period size: 42 Copynumber: 2.4 Consensus size: 42
9944 ACTTTATTTT
*
9954 CCTTCAAACTTCAAAATTTTCAATTTTCTCAAATTCTCTCGA
1 CCTTCAAACTTCAAAATTTTCAATTTTCTCAAATTCTCTCAA
*
9996 CCTTCAAATTTCAAAATTTTCAATTTTCTCAAATTCTCTCAA
1 CCTTCAAACTTCAAAATTTTCAATTTTCTCAAATTCTCTCAA
* *
10038 TCTTCCAACTTTCAAA
1 CCTTCAAAC-TTCAAA
10054 TCTCAATCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
42 46 0.88
43 6 0.12
ACGTcount: A:0.32, C:0.26, G:0.01, T:0.41
Consensus pattern (42 bp):
CCTTCAAACTTCAAAATTTTCAATTTTCTCAAATTCTCTCAA
Found at i:10418 original size:27 final size:27
Alignment explanation
Indices: 10387--10440 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
10377 TAAACTTGTA
* * *
10387 AGTAGAGGAACTAAATAGATTTTTTTG
1 AGTAGAAGAACCAAATAGAATTTTTTG
*
10414 AGTAGAAGAACCAAATTGAATTTTTTG
1 AGTAGAAGAACCAAATAGAATTTTTTG
10441 TAAGTATAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (27 bp):
AGTAGAAGAACCAAATAGAATTTTTTG
Found at i:12044 original size:23 final size:23
Alignment explanation
Indices: 12015--12060 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
12005 GACCTATCTG
12015 AAAATTGGAATAAAAAAGTACTA
1 AAAATTGGAATAAAAAAGTACTA
12038 AAAATTGGAATAAAAAAGTACTA
1 AAAATTGGAATAAAAAAGTACTA
12061 GTTTACTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.61, C:0.04, G:0.13, T:0.22
Consensus pattern (23 bp):
AAAATTGGAATAAAAAAGTACTA
Found at i:13079 original size:2 final size:2
Alignment explanation
Indices: 13067--13112 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
13057 TAAATTACTC
13067 TA TA T- TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13105 TA TA TA TA
1 TA TA TA TA
13113 CTACATATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
1 4 0.10
2 36 0.90
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:13093 original size:23 final size:26
Alignment explanation
Indices: 13068--13123 Score: 82
Period size: 25 Copynumber: 2.3 Consensus size: 26
13058 AAATTACTCT
13068 ATATTATA-TA-TATATATATA-TAT
1 ATATTATATTATTATATATATACTAT
*
13091 ATATTATATTATTATATATATACTAC
1 ATATTATATTATTATATATATACTAT
13117 ATATTAT
1 ATATTAT
13124 TTTTTTTAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 8 0.28
24 2 0.07
25 10 0.34
26 9 0.31
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (26 bp):
ATATTATATTATTATATATATACTAT
Found at i:15053 original size:30 final size:30
Alignment explanation
Indices: 15013--15071 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
15003 CATCTTCAAG
15013 TCCATAATAAGTCCTT-GGCGCATCATTCCT
1 TCCATAATAAG-CCTTGGGCGCATCATTCCT
*
15043 TCCATGATAAGCCTTGGGCGCATCATTCC
1 TCCATAATAAGCCTTGGGCGCATCATTCC
15072 CTCCCCCTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 4 0.15
30 23 0.85
ACGTcount: A:0.22, C:0.31, G:0.17, T:0.31
Consensus pattern (30 bp):
TCCATAATAAGCCTTGGGCGCATCATTCCT
Found at i:15572 original size:33 final size:33
Alignment explanation
Indices: 15535--15617 Score: 87
Period size: 33 Copynumber: 2.5 Consensus size: 33
15525 GTTTCATCAT
* * *
15535 AAACAACACCTAAAACAGACTTAGTGTCATTGC
1 AAACAACAACTAAAACAGACTTAGTATCATCGC
** *
15568 AAACAA-AACTCAAATTAGATTTAGTATCATCGC
1 AAACAACAACT-AAAACAGACTTAGTATCATCGC
*
15601 AAACAACATCTAAAACA
1 AAACAACAACTAAAACA
15618 CTCTTCGCAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
32 3 0.08
33 33 0.85
34 3 0.08
ACGTcount: A:0.48, C:0.22, G:0.08, T:0.22
Consensus pattern (33 bp):
AAACAACAACTAAAACAGACTTAGTATCATCGC
Found at i:19884 original size:24 final size:24
Alignment explanation
Indices: 19849--19900 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
19839 GTGTTGATGA
*
19849 TAATGGGGATGATGAAGATAGAGG
1 TAATGGGAATGATGAAGATAGAGG
* *
19873 TAATGGGAATGATGGAGATGGAGG
1 TAATGGGAATGATGAAGATAGAGG
19897 TAAT
1 TAAT
19901 TTTGATGATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.40, T:0.23
Consensus pattern (24 bp):
TAATGGGAATGATGAAGATAGAGG
Found at i:21333 original size:31 final size:31
Alignment explanation
Indices: 21297--21375 Score: 83
Period size: 29 Copynumber: 2.6 Consensus size: 31
21287 GTACGGAAAC
**
21297 GGTCCCTATACTTACAAGTTTTG-TCCATTTT
1 GGTCCCTATACTTACAAG-ACTGCTCCATTTT
* *
21328 TGTCCCTGTACTTA-AA-ACTGCTCCATTTT
1 GGTCCCTATACTTACAAGACTGCTCCATTTT
*
21357 GGTCCCTCTACTTACAAGA
1 GGTCCCTATACTTACAAGA
21376 ATGTGCAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.05
29 20 0.51
30 4 0.10
31 13 0.33
ACGTcount: A:0.22, C:0.27, G:0.13, T:0.39
Consensus pattern (31 bp):
GGTCCCTATACTTACAAGACTGCTCCATTTT
Found at i:30048 original size:197 final size:197
Alignment explanation
Indices: 29713--30106 Score: 761
Period size: 197 Copynumber: 2.0 Consensus size: 197
29703 GACTGAACGG
29713 ACGAGCTCGATCTGCGAATGGAAGAGCTTAATATGAATGATTTATATAGTACTAAATAGAGAAGC
1 ACGAGCTCGATCTGCGAATGGAAGAGCTTAATATGAATGATTTATATAGTACTAAATAGAGAAGC
*
29778 TTAACTTGATAATGATTTATAATTTTATAGAGAGATTGTCGAAATTTCATACTATAGTATCAAAA
66 TTAACTTGATAATGATATATAATTTTATAGAGAGATTGTCGAAATTTCATACTATAGTATCAAAA
* *
29843 AATTATAGGGAGATTAACAAAATCTCACAGAACGAGTATATCAAAAATCATAAGAATGTTACAAA
131 AATTATAGGGAGATTAACAAAACCTCACAGAACGAGTATATCAAAAATCATAAGAAGGTTACAAA
29908 AT
196 AT
29910 ACGAGCTCGATCTGCGAATGGAAGAGCTTAATATGAATGATTTATATAGTACTAAATAGAGAAGC
1 ACGAGCTCGATCTGCGAATGGAAGAGCTTAATATGAATGATTTATATAGTACTAAATAGAGAAGC
29975 TTAACTTGATAATGATATATAATTTTATAGAGAGATTGTCGAAATTTCATACTATAGTATCAAAA
66 TTAACTTGATAATGATATATAATTTTATAGAGAGATTGTCGAAATTTCATACTATAGTATCAAAA
30040 AATTATAGGGAGATTAACAAAACCTCACAGAACGAGTATATCAAAAATCATAAGAAGGTTACAAA
131 AATTATAGGGAGATTAACAAAACCTCACAGAACGAGTATATCAAAAATCATAAGAAGGTTACAAA
30105 AT
196 AT
30107 TCATAGGAAA
Statistics
Matches: 194, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
197 194 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.29
Consensus pattern (197 bp):
ACGAGCTCGATCTGCGAATGGAAGAGCTTAATATGAATGATTTATATAGTACTAAATAGAGAAGC
TTAACTTGATAATGATATATAATTTTATAGAGAGATTGTCGAAATTTCATACTATAGTATCAAAA
AATTATAGGGAGATTAACAAAACCTCACAGAACGAGTATATCAAAAATCATAAGAAGGTTACAAA
AT
Found at i:30190 original size:43 final size:44
Alignment explanation
Indices: 30141--30243 Score: 120
Period size: 43 Copynumber: 2.4 Consensus size: 44
30131 CATAGTTAGG
* * * * *
30141 TTATCAAAGTTTCTTATGG-AGTTTATCACAATTTTATAGG-TAA
1 TTATCAAAATTTCATACGGTAG-TTATCAAAATTTAATAGGATAA
* *
30184 TTATCAAAATCTCATACGGTAGTTATCAAAATTTAATAGGATAG
1 TTATCAAAATTTCATACGGTAGTTATCAAAATTTAATAGGATAA
30228 TTATCAAAATTTCATA
1 TTATCAAAATTTCATA
30244 AAAATATTCA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
43 31 0.62
44 19 0.38
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.40
Consensus pattern (44 bp):
TTATCAAAATTTCATACGGTAGTTATCAAAATTTAATAGGATAA
Found at i:30209 original size:22 final size:21
Alignment explanation
Indices: 30097--30243 Score: 111
Period size: 22 Copynumber: 6.8 Consensus size: 21
30087 TCATAAGAAG
*
30097 GTTA-CAAAA-TTCATAGGAAA
1 GTTATCAAAATTTCATAGG-TA
* * *
30117 GTTTATTAAAAGTTCATAGTTA
1 G-TTATCAAAATTTCATAGGTA
* *
30139 GGTTATCAAAGTTTCTTATGG-A
1 -GTTATCAAAATTTCATA-GGTA
* *
30161 GTTTATCACAATTTTATAGGTA
1 G-TTATCAAAATTTCATAGGTA
* *
30183 ATTATCAAAATCTCATACGGTA
1 GTTATCAAAATTTCATA-GGTA
*
30205 GTTATCAAAATTTAATAGGATA
1 GTTATCAAAATTTCATAGG-TA
30227 GTTATCAAAATTTCATA
1 GTTATCAAAATTTCATA
30244 AAAATATTCA
Statistics
Matches: 98, Mismatches: 20, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
20 1 0.01
21 21 0.21
22 67 0.68
23 9 0.09
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (21 bp):
GTTATCAAAATTTCATAGGTA
Found at i:35330 original size:21 final size:21
Alignment explanation
Indices: 35291--35339 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
35281 TCAATGCTTT
**
35291 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
35313 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
35334 A-GAAGC
1 AGGAAGC
35340 TATAATTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:38126 original size:15 final size:15
Alignment explanation
Indices: 38106--38144 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
38096 GGTTCAAATG
38106 GGGGAGGGGTGGGGT
1 GGGGAGGGGTGGGGT
*
38121 GGGGAGGGATGGGGT
1 GGGGAGGGGTGGGGT
*
38136 AGGGAGGGG
1 GGGGAGGGG
38145 GAGGAGTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.77, T:0.10
Consensus pattern (15 bp):
GGGGAGGGGTGGGGT
Found at i:44207 original size:18 final size:18
Alignment explanation
Indices: 44184--44248 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 18
44174 CATCGCACAA
44184 GCCATCCGGCCACAACCG
1 GCCATCCGGCCACAACCG
*
44202 GCCATCGATTGGGCCA-ACACACG
1 GCCATC----CGGCCACA-AC-CG
44225 CGCCATCCGGCCACAACCG
1 -GCCATCCGGCCACAACCG
44244 GCCAT
1 GCCAT
44249 TTGATCCTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 16
0.67 0.04 0.29
Matches are distributed among these distances:
18 11 0.30
19 2 0.05
20 7 0.19
21 2 0.05
22 7 0.19
23 2 0.05
24 6 0.16
ACGTcount: A:0.23, C:0.45, G:0.23, T:0.09
Consensus pattern (18 bp):
GCCATCCGGCCACAACCG
Found at i:45184 original size:8 final size:8
Alignment explanation
Indices: 45171--45204 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
45161 ACCTTCTTAA
45171 AAAAATTC
1 AAAAATTC
45179 AAAAATTC
1 AAAAATTC
*
45187 AGAAATTTC
1 A-AAAATTC
45196 AAAAATTC
1 AAAAATTC
45204 A
1 A
45205 TAGCCGATTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.59, C:0.12, G:0.03, T:0.26
Consensus pattern (8 bp):
AAAAATTC
Found at i:54050 original size:136 final size:139
Alignment explanation
Indices: 53896--54169 Score: 439
Period size: 136 Copynumber: 2.0 Consensus size: 139
53886 GAGAAATAAA
* * *
53896 ATTCTAAACTAATCAAATTAATTTGGCATTAGTAAAGAAAAAAAATATGTTTCACATCCAAAATC
1 ATTCTAAACTAATCAAATTAATTTGGCACTAGCAAAGAAAAAAAATATGTTTCACATCCAAAACC
* *
53961 AATCTTAGTGTGAAAAAA-AAAGTCACATTATAA-G-ACAAAAACAAAATTTTATTAATAAAATT
66 AATCTTAATGTGAAAAAAGAAAGTCACATTATAAGGAAAAAAAACAAAA-TTTATTAATAAAATT
54023 TA-TTAAAAT
130 TATTTAAAAT
*
54032 ATTCTAAACTAATCAAATTAATTTGTCACTAGCAAAGAAAAAAAATATGTTTCACATCCAAAACC
1 ATTCTAAACTAATCAAATTAATTTGGCACTAGCAAAGAAAAAAAATATGTTTCACATCCAAAACC
* *
54097 AATCTTAATGTGAAAAAAGAAAGTCCCATTATAAGGAAAAAAAACAAAATTTATTAATACAATTT
66 AATCTTAATGTGAAAAAAGAAAGTCACATTATAAGGAAAAAAAACAAAATTTATTAATAAAATTT
54162 ATTTAAAA
131 ATTTAAAA
54170 AAAAGTCACG
Statistics
Matches: 126, Mismatches: 8, Indels: 5
0.91 0.06 0.04
Matches are distributed among these distances:
136 78 0.62
137 14 0.11
138 17 0.13
139 17 0.13
ACGTcount: A:0.51, C:0.12, G:0.07, T:0.30
Consensus pattern (139 bp):
ATTCTAAACTAATCAAATTAATTTGGCACTAGCAAAGAAAAAAAATATGTTTCACATCCAAAACC
AATCTTAATGTGAAAAAAGAAAGTCACATTATAAGGAAAAAAAACAAAATTTATTAATAAAATTT
ATTTAAAAT
Found at i:54586 original size:2 final size:2
Alignment explanation
Indices: 54575--54606 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
54565 TTCTTGTTTC
54575 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
54607 TAAATGACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:55642 original size:23 final size:23
Alignment explanation
Indices: 55598--55642 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
55588 TTAATCTCTT
* *
55598 GATTTTAGAGTATTATTGAATAG
1 GATTTTAGAGAATTATGGAATAG
55621 GATTTTAGA-AATTATGGTAATA
1 GATTTTAGAGAATTATGG-AATA
55643 TTCTCCGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (23 bp):
GATTTTAGAGAATTATGGAATAG
Found at i:59929 original size:18 final size:20
Alignment explanation
Indices: 59903--59939 Score: 51
Period size: 18 Copynumber: 1.9 Consensus size: 20
59893 TAAAATTAAT
59903 AATTATTTT-ATA-AATATA
1 AATTATTTTGATATAATATA
*
59921 AATTTTTTTGATATAATAT
1 AATTATTTTGATATAATAT
59940 TTAGTAGGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
18 8 0.50
19 3 0.19
20 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
AATTATTTTGATATAATATA
Found at i:61381 original size:50 final size:51
Alignment explanation
Indices: 61293--61389 Score: 133
Period size: 52 Copynumber: 1.9 Consensus size: 51
61283 AGTCAAATTA
*
61293 TCATCAATTCGAGATCAAGTCATCAAAAACCCTCGAATCAAATCAAACTCCC
1 TCATCAATTCAAGATCAAGTCAT-AAAAACCCTCGAATCAAATCAAACTCCC
*** *
61345 TCATCAATTCAAGATCAAGTCAT-TTGACCCTTGAATCAAATCAAA
1 TCATCAATTCAAGATCAAGTCATAAAAACCCTCGAATCAAATCAAA
61390 TCAAACTCTC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
50 18 0.45
52 22 0.55
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (51 bp):
TCATCAATTCAAGATCAAGTCATAAAAACCCTCGAATCAAATCAAACTCCC
Found at i:63523 original size:12 final size:12
Alignment explanation
Indices: 63503--63543 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
63493 CCTCTTCAAG
*
63503 ATTACTTCCAAA
1 ATTATTTCCAAA
63515 ATTATTTCCAAA
1 ATTATTTCCAAA
63527 ATTATTAT-CAAA
1 ATTATT-TCCAAA
63539 ATTAT
1 ATTAT
63544 AAATATATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
12 26 0.96
13 1 0.04
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (12 bp):
ATTATTTCCAAA
Found at i:63616 original size:34 final size:33
Alignment explanation
Indices: 63576--63684 Score: 137
Period size: 34 Copynumber: 3.1 Consensus size: 33
63566 ATATCCACTT
*
63576 AACCCGTAATATATAATTGAAATTGGACTAAGAA
1 AACCCGTAATATATAATTG-AATTGGACTAAAAA
63610 AACCCGTAATATATAATTTGAATTGGACTAATAAAA
1 AACCCGTAATATATAA-TTGAATTGGACT-A-AAAA
63646 TTCAACCCGTAATATATAATTGGAATTGGACTAAAAA
1 ---AACCCGTAATATATAATT-GAATTGGACTAAAAA
63683 AA
1 AA
63685 ATTCAATTTG
Statistics
Matches: 67, Mismatches: 1, Indels: 14
0.82 0.01 0.17
Matches are distributed among these distances:
34 27 0.40
35 4 0.06
36 3 0.04
37 4 0.06
38 3 0.04
39 26 0.39
ACGTcount: A:0.47, C:0.12, G:0.13, T:0.28
Consensus pattern (33 bp):
AACCCGTAATATATAATTGAATTGGACTAAAAA
Found at i:63653 original size:39 final size:38
Alignment explanation
Indices: 63576--63683 Score: 145
Period size: 39 Copynumber: 2.9 Consensus size: 38
63566 ATATCCACTT
*
63576 AACCCGTAATATATAA-TTGAAATTGGACT-AAGAA---
1 AACCCGTAATATATAATTTG-AATTGGACTAAAAAATTC
63610 AACCCGTAATATATAATTTGAATTGGACTAATAAAATTC
1 AACCCGTAATATATAATTTGAATTGGACTAA-AAAATTC
*
63649 AACCCGTAATATATAATTGGAATTGGACTAAAAAA
1 AACCCGTAATATATAATTTGAATTGGACTAAAAAA
63684 AATTCAATTT
Statistics
Matches: 66, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
34 25 0.38
35 4 0.06
36 3 0.05
38 4 0.06
39 30 0.45
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (38 bp):
AACCCGTAATATATAATTTGAATTGGACTAAAAAATTC
Done.