Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019375.1 Corchorus olitorius cultivar O-4 contig19408, 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: 35982
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1487 original size:58 final size:58
Alignment explanation
Indices: 1391--1505 Score: 169
Period size: 58 Copynumber: 2.0 Consensus size: 58
1381 ATTAATCAAA
*
1391 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTCGGACCAAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
* * * *
1449 TATCGAGTGACATGTTTTTTTATTAGATGCCT-AAAAAAGACGTTTTAGGACCGAGAC
1 TATCAAGTGACATG-TTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGAC
1506 ATGATGCTAT
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 36 0.71
59 15 0.29
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCATAAAAAAAGACGTTTTAGGACCAAGACT
Found at i:2816 original size:36 final size:36
Alignment explanation
Indices: 2769--2838 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
2759 TTCAATAACC
*
2769 TTACATTTTTTGTAATTTTGGTTATCATATTTCTTA
1 TTACATTTTTTGTAATTTTGATTATCATATTTCTTA
2805 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATTTTTTGTAATTTTGATTATCATATTTCT
2839 CCAAAATCTC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.23, C:0.09, G:0.07, T:0.61
Consensus pattern (36 bp):
TTACATTTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:3437 original size:120 final size:120
Alignment explanation
Indices: 3224--3462 Score: 469
Period size: 120 Copynumber: 2.0 Consensus size: 120
3214 AACCTTACAT
3224 TCTAGTAATTTTGGTTATCAAATTTCTCATTTATGCTTACTAATTAGAAAGCTAAACTATAGTAT
1 TCTAGTAATTTTGGTTATCAAATTTCTCATTTATGCTTACTAATTAGAAAGCTAAACTATAGTAT
*
3289 TATATCAAGAAATGTAGCAATCTTACATGCTTAATAACTTTATCAATGGTGAATC
66 TATATCAAGAAATGTAACAATCTTACATGCTTAATAACTTTATCAATGGTGAATC
3344 TCTAGTAATTTTGGTTATCAAATTTCTCATTTATGCTTACTAATTAGAAAGCTAAACTATAGTAT
1 TCTAGTAATTTTGGTTATCAAATTTCTCATTTATGCTTACTAATTAGAAAGCTAAACTATAGTAT
3409 TATATCAAGAAATGTAACAATCTTACATGCTTAATAACTTTATCAATGGTGAAT
66 TATATCAAGAAATGTAACAATCTTACATGCTTAATAACTTTATCAATGGTGAAT
3463 GTTATTAATT
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
120 118 1.00
ACGTcount: A:0.36, C:0.13, G:0.11, T:0.39
Consensus pattern (120 bp):
TCTAGTAATTTTGGTTATCAAATTTCTCATTTATGCTTACTAATTAGAAAGCTAAACTATAGTAT
TATATCAAGAAATGTAACAATCTTACATGCTTAATAACTTTATCAATGGTGAATC
Found at i:3804 original size:21 final size:21
Alignment explanation
Indices: 3738--3804 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3728 TAAGAATTTA
*
3738 ATTAATGTAAGTGTTTTAGTT
1 ATTAATGTAAGTATTTTAGTT
* ** *
3759 ATT-ATAGT-ATTATTACATTT
1 ATTAAT-GTAAGTATTTTAGTT
3779 AATTAATGTAAGTATTTTAGTT
1 -ATTAATGTAAGTATTTTAGTT
3801 ATTA
1 ATTA
3805 TTTATATTAC
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
20 9 0.27
21 14 0.42
22 10 0.30
ACGTcount: A:0.34, C:0.01, G:0.12, T:0.52
Consensus pattern (21 bp):
ATTAATGTAAGTATTTTAGTT
Found at i:4152 original size:1 final size:1
Alignment explanation
Indices: 4146--4176 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
4136 AATCTGATGC
4146 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
4177 CTGGGTTTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4752 original size:32 final size:32
Alignment explanation
Indices: 4711--4775 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
4701 GTCTTGGTGG
4711 ATTCCTAATAGAGTTGGAAAATAGAAGTTCAA
1 ATTCCTAATAGAGTTGGAAAATAGAAGTTCAA
4743 ATTCCTAATAGAGTTGGAAAATAGAAGTTCAA
1 ATTCCTAATAGAGTTGGAAAATAGAAGTTCAA
4775 A
1 A
4776 GTGCAAATTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.45, C:0.09, G:0.18, T:0.28
Consensus pattern (32 bp):
ATTCCTAATAGAGTTGGAAAATAGAAGTTCAA
Found at i:16264 original size:21 final size:21
Alignment explanation
Indices: 16223--16264 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
16213 GACCCGATTA
**
16223 AATAGGACTAGGGTATTGTAT
1 AATAGGACTAGGGTAGGGTAT
*
16244 AATAGGATTAGGGTAGGGTAT
1 AATAGGACTAGGGTAGGGTAT
16265 GGGTGGTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.02, G:0.33, T:0.31
Consensus pattern (21 bp):
AATAGGACTAGGGTAGGGTAT
Found at i:16379 original size:19 final size:19
Alignment explanation
Indices: 16355--16395 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
16345 TACTAATTAA
16355 TTATTTTAATATTATATTT
1 TTATTTTAATATTATATTT
*
16374 TTATTTTTATATTATATTT
1 TTATTTTAATATTATATTT
16393 TTA
1 TTA
16396 CTTAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTTAATATTATATTT
Found at i:17679 original size:18 final size:18
Alignment explanation
Indices: 17638--17672 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17628 AACTAAATAA
*
17638 AATTAATAATATATTAAC
1 AATTGATAATATATTAAC
*
17656 AATTGATAATATTTTAA
1 AATTGATAATATATTAA
17673 TAGTTGAAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (18 bp):
AATTGATAATATATTAAC
Found at i:17767 original size:10 final size:10
Alignment explanation
Indices: 17752--17780 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
17742 TTTTAAGACG
17752 AAACGAAATC
1 AAACGAAATC
17762 AAACGAAATC
1 AAACGAAATC
17772 AAACGAAAT
1 AAACGAAAT
17781 TTTGAGAAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.17, G:0.10, T:0.10
Consensus pattern (10 bp):
AAACGAAATC
Found at i:26017 original size:18 final size:18
Alignment explanation
Indices: 25990--26026 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
25980 AGGATCCCAA
*
25990 AATGTCCGTTTATGGTTG
1 AATGTCCGTTTATAGTTG
*
26008 AATGTTCGTTTATAGTTG
1 AATGTCCGTTTATAGTTG
26026 A
1 A
26027 TCAGGTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.24, T:0.46
Consensus pattern (18 bp):
AATGTCCGTTTATAGTTG
Found at i:28221 original size:28 final size:27
Alignment explanation
Indices: 28190--28248 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 27
28180 ATGATTATGG
28190 AATTAATAATATGTTAACAATTGAATAT
1 AATTAAT-ATATGTTAACAATTGAATAT
28218 AATTTAATATATGTTAACAATTGAATAT
1 AA-TTAATATATGTTAACAATTGAATAT
28246 AAT
1 AAT
28249 ATGTTACAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 1 0.03
28 24 0.80
29 5 0.17
ACGTcount: A:0.49, C:0.03, G:0.07, T:0.41
Consensus pattern (27 bp):
AATTAATATATGTTAACAATTGAATAT
Found at i:28259 original size:20 final size:21
Alignment explanation
Indices: 28226--28268 Score: 79
Period size: 20 Copynumber: 2.1 Consensus size: 21
28216 ATAATTTAAT
28226 ATATGTTAACAATTGAATATA
1 ATATGTTAACAATTGAATATA
28247 ATATGTT-ACAATTGAATATA
1 ATATGTTAACAATTGAATATA
28267 AT
1 AT
28269 TTAATCGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.47, C:0.05, G:0.09, T:0.40
Consensus pattern (21 bp):
ATATGTTAACAATTGAATATA
Found at i:31900 original size:90 final size:90
Alignment explanation
Indices: 31799--32180 Score: 320
Period size: 90 Copynumber: 4.0 Consensus size: 90
31789 CAACAACCAC
* *
31799 CGCCGCCTTTTGCAGCAGGGAAGACCCCGAAATCGCCACCGTCTCCCAAGCCATCTCCTCCAACA
1 CGCCGCCTTTTGCAGCAGGGAAGACCCCCAAATCGCCACCGTCTCCCAAGCCAGCTCCTCCAACA
*
31864 CATCAAGATATGATCGAGTTGCCAT
66 CATCAAGATATGATCGAGCTGCCAT
* * * *
31889 CGCCGCCTTTTGCAGCCGGGAAGACCCCCAAATCGCCACAGTCT-CCAACTCCAGCTCCTCCAAA
1 CGCCGCCTTTTGCAGCAGGGAAGACCCCCAAATCGCCACCGTCTCCCAA-GCCAGCTCCTCCAAC
* * * *
31953 AAATCAACATATGATTGAGCTACCTAT
65 ACATCAAGATATGATCGAGCTGCC-AT
* *
31980 AAAACAAAGATCACCACCTTTTGCAGCAGCTGGGAAGACCCCCAAATCGCCACCGTCTCCGAAGC
1 ----C---G----CCGCCTTTTGCAGCA---GGGAAGACCCCCAAATCGCCACCGTCTCCCAAGC
* *
32045 CAGCTCCTTCAACACATCAAGATGTGATCGAGCTCATGCAACAACCAT
52 CAGCTCCTCCAACACATCAAGATATGATCGAG--C-TG------CCAT
* * * * *
32093 CGCCGCCTTTTGCAGCAGGGAAGA-CCCC-ATTGCCGCCACCGCCTCCTAATCCAGCTCCTTCAA
1 CGCCGCCTTTTGCAGCAGGGAAGACCCCCAAAT--CGCCACCGTCTCCCAAGCCAGCTCCTCCAA
32156 CACATCAAGATATGATCGAGCTGCC
64 CACATCAAGATATGATCGAGCTGCC
32181 TTTACAACAA
Statistics
Matches: 235, Mismatches: 29, Indels: 56
0.73 0.09 0.17
Matches are distributed among these distances:
89 4 0.02
90 74 0.31
91 2 0.01
95 1 0.00
96 2 0.01
97 3 0.01
98 5 0.02
99 53 0.23
102 27 0.11
105 53 0.23
106 4 0.02
107 1 0.00
108 1 0.00
109 1 0.00
113 2 0.01
114 2 0.01
ACGTcount: A:0.28, C:0.36, G:0.18, T:0.19
Consensus pattern (90 bp):
CGCCGCCTTTTGCAGCAGGGAAGACCCCCAAATCGCCACCGTCTCCCAAGCCAGCTCCTCCAACA
CATCAAGATATGATCGAGCTGCCAT
Found at i:32188 original size:99 final size:98
Alignment explanation
Indices: 31885--32177 Score: 311
Period size: 105 Copynumber: 2.9 Consensus size: 98
31875 GATCGAGTTG
* * *
31885 CCATCGCCGCCTTTTGCAGCCGGGAAGACCCCCAAATCGCCACAGTCTCCAACTCCAGCTCCTCC
1 CCATCGCCGCCTTTTGCAGCAGGGAAGACCCCCAAATCGCCACCGTCTCCAA-TCCAGCTCCTTC
* * * *
31950 AAAAAATCAACATATGATTGAGCTACCTATAAAACAA
65 AACACATCAAGATATGATCGAGCT-CCTAT--AACAA
** * * *
31987 AGATCACCACCTTTTGCAGCAGCTGGGAAGACCCCCAAATCGCCACCGTCTCCGAAGCCAGCTCC
1 CCATCGCCGCCTTTTGCAGCA---GGGAAGACCCCCAAATCGCCACCGTCTCC-AATCCAGCTCC
* * **
32052 TTCAACACATCAAGATGTGATCGAGCTCATGCAACAA
62 TTCAACACATCAAGATATGATCGAGCTCCTATAACAA
* *
32089 CCATCGCCGCCTTTTGCAGCAGGGAAGA-CCCC-ATTGCCGCCACCGCCTCCTAATCCAGCTCCT
1 CCATCGCCGCCTTTTGCAGCAGGGAAGACCCCCAAAT--CGCCACCGTCTCC-AATCCAGCTCCT
32152 TCAACACATCAAGATATGATCGAGCT
63 TCAACACATCAAGATATGATCGAGCT
32178 GCCTTTACAA
Statistics
Matches: 160, Mismatches: 25, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
97 2 0.01
98 4 0.03
99 55 0.34
102 38 0.24
104 2 0.01
105 57 0.36
106 2 0.01
ACGTcount: A:0.29, C:0.36, G:0.17, T:0.19
Consensus pattern (98 bp):
CCATCGCCGCCTTTTGCAGCAGGGAAGACCCCCAAATCGCCACCGTCTCCAATCCAGCTCCTTCA
ACACATCAAGATATGATCGAGCTCCTATAACAA
Found at i:32192 original size:204 final size:192
Alignment explanation
Indices: 31751--32198 Score: 515
Period size: 204 Copynumber: 2.3 Consensus size: 192
31741 TCACAACCAT
* * * ** * * *
31751 CTCCTTCAGCACATCAAGATATGATCGAGCTGCCCATGCAACAACCACCGCCGCCTTTTGCAGCA
1 CTCCTTCAACACATCAAGATATGATCGAGCTGCCTATACAACAAAGATCACCACCTTTTGCAGCA
* *
31816 GGGAAGACCCCGAAATCGCCACCGTCTCCCAAGCCATCTCCTCCAACACATCAAGATATGATCGA
66 GGGAAGACCCCCAAATCGCCACCGTCTCCCAAGCCAGCTCCTCCAACACATCAAGATATGATCGA
* *
31881 GTTGCCATCGCCGCCTTTTGCAGCCGGGAAGACCCCCAAATCGCCACAGTCTCCAACTCCAG
131 GTTGCCATCGCCGCCTTTTGCAGCAGGGAAGACCCCCAAATCGCCACAGCCTCCAACTCCAG
* * * * * * *
31943 CTCCTCCAAAAAATCAACATATGATTGAGCTACCTATAAAACAAAGATCACCACCTTTTGCAGCA
1 CTCCTTCAACACATCAAGATATGATCGAGCTGCCTATACAACAAAGATCACCACCTTTTGCAGCA
* * *
32008 GCTGGGAAGACCCCCAAATCGCCACCGTCTCCGAAGCCAGCTCCTTCAACACATCAAGATGTGAT
66 ---GGGAAGACCCCCAAATCGCCACCGTCTCCCAAGCCAGCTCCTCCAACACATCAAGATATGAT
* *
32073 CGAGCTCATGCAACAACCATCGCCGCCTTTTGCAGCAGGGAAGA-CCCC-ATTGCCGCCACCGCC
128 CGAG-T--TG------CCATCGCCGCCTTTTGCAGCAGGGAAGACCCCCAAAT--CGCCACAGCC
32136 TCCTAA-TCCAG
182 TCC-AACTCCAG
*
32147 CTCCTTCAACACATCAAGATATGATCGAGCTGCCTTTACAACAAAGATCACC
1 CTCCTTCAACACATCAAGATATGATCGAGCTGCCTATACAACAAAGATCACC
32199 TCCAGCATAT
Statistics
Matches: 209, Mismatches: 32, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
192 50 0.24
195 61 0.29
196 1 0.00
198 2 0.01
202 2 0.01
203 4 0.02
204 87 0.42
205 2 0.01
ACGTcount: A:0.29, C:0.36, G:0.17, T:0.19
Consensus pattern (192 bp):
CTCCTTCAACACATCAAGATATGATCGAGCTGCCTATACAACAAAGATCACCACCTTTTGCAGCA
GGGAAGACCCCCAAATCGCCACCGTCTCCCAAGCCAGCTCCTCCAACACATCAAGATATGATCGA
GTTGCCATCGCCGCCTTTTGCAGCAGGGAAGACCCCCAAATCGCCACAGCCTCCAACTCCAG
Found at i:32566 original size:6 final size:6
Alignment explanation
Indices: 32555--32580 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
32545 TCACGTATTA
32555 TACTAG TACTAG TACTAG TACTAG TA
1 TACTAG TACTAG TACTAG TACTAG TA
32581 TATAGTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (6 bp):
TACTAG
Found at i:33856 original size:40 final size:41
Alignment explanation
Indices: 33800--33878 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 41
33790 CGGACTGTTC
33800 CAACTTTAAGTTGAAGTCAAAACATTTATATCAATTTTGAA
1 CAACTTTAAGTTGAAGTCAAAACATTTATATCAATTTTGAA
33841 CAAC-TTAAGTTGAAGTCAAAACATTTATATCAATTTTG
1 CAACTTTAAGTTGAAGTCAAAACATTTATATCAATTTTG
33879 TTGGCCAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
40 34 0.89
41 4 0.11
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.37
Consensus pattern (41 bp):
CAACTTTAAGTTGAAGTCAAAACATTTATATCAATTTTGAA
Found at i:34605 original size:22 final size:21
Alignment explanation
Indices: 34537--34610 Score: 85
Period size: 22 Copynumber: 3.4 Consensus size: 21
34527 TGAATATTTT
34537 TATGAAATTTTGATAATTACC
1 TATGAAATTTTGATAATTACC
* **
34558 TTATTAAATTTTGATAACCACGC
1 -TATGAAATTTTGATAATTAC-C
34581 TATGAAATTTTGATAATTTACC
1 TATGAAATTTTGATAA-TTACC
*
34603 TATAAAAT
1 TATGAAAT
34611 ATGAAACTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
22 40 0.93
23 3 0.07
ACGTcount: A:0.39, C:0.11, G:0.08, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTGATAATTACC
Found at i:34614 original size:29 final size:29
Alignment explanation
Indices: 34581--34639 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
34571 ATAACCACGC
* * *
34581 TATGAAATTTTGATAATTTACCTATAAAA
1 TATGAAACTTTGATAACTTAACTATAAAA
*
34610 TATGAAACTTTGATAACTTAACTATGAAA
1 TATGAAACTTTGATAACTTAACTATAAAA
34639 T
1 T
34640 TTTAATAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (29 bp):
TATGAAACTTTGATAACTTAACTATAAAA
Found at i:34638 original size:22 final size:21
Alignment explanation
Indices: 34610--34673 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
34600 ACCTATAAAA
*
34610 TATGAAACTTTGATAACTTAAC
1 TATGAAATTTTGATAACTT-AC
* *
34632 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTTGAT-AA-CTTAC
34655 TATGAAATTTTTGATAACT
1 TATGAAA-TTTTGATAACT
34674 ATGATTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
22 14 0.40
23 12 0.34
24 9 0.26
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (21 bp):
TATGAAATTTTGATAACTTAC
Found at i:35400 original size:298 final size:298
Alignment explanation
Indices: 34864--35460 Score: 1140
Period size: 298 Copynumber: 2.0 Consensus size: 298
34854 CGTTCAGTCG
34864 TACGTACAAACATATATAATTCATATTGAACTCCTCCCATTGATAGTATACACATATACATATTC
1 TACGTACAAACATATATAATTCATATTGAACTCCTCCCATTGATAGTATACACATATACATATTC
34929 GAATTGAGCTCCTCCACTCGATAGTATATAAAGCACGTTACCAAACAGAGTTCCTCCATTCAGCA
66 GAATTGAGCTCCTCCACTCGATAGTATATAAAGCACGTTACCAAACAGAGTTCCTCCATTCAGCA
* *
34994 TTCCTCCACATAGACTCGTTTCGGCCCAGTAGGCCCATTAGACTCGTTTGAGTCCATGAAACCAA
131 TTCCTCCACATAGACTCGTTTCGGCCCAGTAGGCCCATTAAACTCGTTTAAGTCCATGAAACCAA
35059 ATTACCAAGCCAGATGTCTTGAAGCCTAAATCTGATATTCTTAGACCCAATTCGTTAATATGGAA
196 ATTACCAAGCCAGATGTCTTGAAGCCTAAATCTGATATTCTTAGACCCAATTCGTTAATATGGAA
35124 GCCCAAAGAAGGAGTTCAAGTCCAATCAGTAATTATGA
261 GCCCAAAGAAGGAGTTCAAGTCCAATCAGTAATTATGA
* *
35162 TACGTACAAACATATATAATTCATATTGAACTCCTCCCGTTGATAGTATATACATATACATATTC
1 TACGTACAAACATATATAATTCATATTGAACTCCTCCCATTGATAGTATACACATATACATATTC
* *
35227 GAATTGAGCTCCTCCACTCGGTAGTATATAAAGCACGTTATCAAACAGAGTTCCTCCATTCAGCA
66 GAATTGAGCTCCTCCACTCGATAGTATATAAAGCACGTTACCAAACAGAGTTCCTCCATTCAGCA
35292 TTCCTCCACATAGACTCGTTTCGGCCCAGTAGGCCCATTAAACTCGTTTAAGTCCATGAAACCAA
131 TTCCTCCACATAGACTCGTTTCGGCCCAGTAGGCCCATTAAACTCGTTTAAGTCCATGAAACCAA
35357 ATTACCAAGCCAGATGTCTTGAAGCCTAAATCTGATATTCTTAGACCCAATTCGTTAATATGGAA
196 ATTACCAAGCCAGATGTCTTGAAGCCTAAATCTGATATTCTTAGACCCAATTCGTTAATATGGAA
35422 GCCCAAAGAAGGAGTTCAAGTCCAATCAGTAATTATGA
261 GCCCAAAGAAGGAGTTCAAGTCCAATCAGTAATTATGA
35460 T
1 T
35461 GCAGTAATGA
Statistics
Matches: 293, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
298 293 1.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (298 bp):
TACGTACAAACATATATAATTCATATTGAACTCCTCCCATTGATAGTATACACATATACATATTC
GAATTGAGCTCCTCCACTCGATAGTATATAAAGCACGTTACCAAACAGAGTTCCTCCATTCAGCA
TTCCTCCACATAGACTCGTTTCGGCCCAGTAGGCCCATTAAACTCGTTTAAGTCCATGAAACCAA
ATTACCAAGCCAGATGTCTTGAAGCCTAAATCTGATATTCTTAGACCCAATTCGTTAATATGGAA
GCCCAAAGAAGGAGTTCAAGTCCAATCAGTAATTATGA
Found at i:35927 original size:2 final size:2
Alignment explanation
Indices: 35920--35947 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35910 ATTCGTACTT
35920 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35948 ACTAACTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.