Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016189.1 Corchorus olitorius cultivar O-4 contig16222, 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: 57576
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3901 original size:13 final size:13
Alignment explanation
Indices: 3883--3910 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
3873 AAAGAATAAC
3883 ATTTTGTATAAAT
1 ATTTTGTATAAAT
3896 ATTTTGTATAAAT
1 ATTTTGTATAAAT
3909 AT
1 AT
3911 AAGGAGTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (13 bp):
ATTTTGTATAAAT
Found at i:3919 original size:28 final size:28
Alignment explanation
Indices: 3888--3958 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
3878 ATAACATTTT
*
3888 GTATAAATATTTTGTATAAATATAAGGA
1 GTATAAATATTTTGTACAAATATAAGGA
** *
3916 GTATTTACATTTTGTACAAATATAAGGA
1 GTATAAATATTTTGTACAAATATAAGGA
3944 GTATTTAAATATTTT
1 GTA--TAAATATTTT
3959 AATACAATAA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
28 27 0.79
30 7 0.21
ACGTcount: A:0.41, C:0.03, G:0.13, T:0.44
Consensus pattern (28 bp):
GTATAAATATTTTGTACAAATATAAGGA
Found at i:10759 original size:24 final size:25
Alignment explanation
Indices: 10710--10775 Score: 125
Period size: 25 Copynumber: 2.7 Consensus size: 25
10700 AAAACAAATT
10710 TATCTTCAACTTAAAATTTTTCTTC
1 TATCTTCAACTTAAAATTTTTCTTC
10735 TATCTTCAACTTAAAATTTTT-TTC
1 TATCTTCAACTTAAAATTTTTCTTC
10759 TATCTTCAACTTAAAAT
1 TATCTTCAACTTAAAAT
10776 GATTGACTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
24 20 0.49
25 21 0.51
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (25 bp):
TATCTTCAACTTAAAATTTTTCTTC
Found at i:24968 original size:21 final size:20
Alignment explanation
Indices: 24922--24971 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
24912 AGATTTCACT
24922 GGGTTTTGTTTGTTGGGGAA
1 GGGTTTTGTTTGTTGGGGAA
24942 GGGTTTTGTTTGTTGGGGAA
1 GGGTTTTGTTTGTTGGGGAA
*
24962 GGGGTTTGTT
1 GGGTTTTGTT
24972 GGCTCATAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.08, C:0.00, G:0.46, T:0.46
Consensus pattern (20 bp):
GGGTTTTGTTTGTTGGGGAA
Found at i:28164 original size:39 final size:39
Alignment explanation
Indices: 28110--28187 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
28100 AATGGAAACA
28110 ATGTGATGGTAGTAAGACATGGTGGGTTGGATCCTATTC
1 ATGTGATGGTAGTAAGACATGGTGGGTTGGATCCTATTC
28149 ATGTGATGGTAGTAAGACATGGTGGGTTGGATCCTATTC
1 ATGTGATGGTAGTAAGACATGGTGGGTTGGATCCTATTC
28188 CAGTTTGTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.10, G:0.33, T:0.33
Consensus pattern (39 bp):
ATGTGATGGTAGTAAGACATGGTGGGTTGGATCCTATTC
Found at i:29450 original size:6 final size:6
Alignment explanation
Indices: 29441--29487 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
29431 AGAATATGGA
*
29441 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG CGGGA
1 AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGAG AGGGA
29488 TCGAGACAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.32, C:0.02, G:0.66, T:0.00
Consensus pattern (6 bp):
AGGGAG
Found at i:38758 original size:64 final size:64
Alignment explanation
Indices: 38657--38786 Score: 260
Period size: 64 Copynumber: 2.0 Consensus size: 64
38647 TTAAGGCTTG
38657 GTTTGGGATTAAGTTTGGAGATAAAAAAAAAGCTACTTTTCACCTCAAACATAATGCCAAATAA
1 GTTTGGGATTAAGTTTGGAGATAAAAAAAAAGCTACTTTTCACCTCAAACATAATGCCAAATAA
38721 GTTTGGGATTAAGTTTGGAGATAAAAAAAAAGCTACTTTTCACCTCAAACATAATGCCAAATAA
1 GTTTGGGATTAAGTTTGGAGATAAAAAAAAAGCTACTTTTCACCTCAAACATAATGCCAAATAA
38785 GT
1 GT
38787 CATGGTTTGT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 66 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (64 bp):
GTTTGGGATTAAGTTTGGAGATAAAAAAAAAGCTACTTTTCACCTCAAACATAATGCCAAATAA
Found at i:53704 original size:325 final size:316
Alignment explanation
Indices: 52991--53765 Score: 841
Period size: 317 Copynumber: 2.4 Consensus size: 316
52981 AAACACTCAT
*
52991 AAAAATATATAGAATTCAACG-CAAAAAGATTGA-AGGACTTTTCACGCTTTTAATATCGTTTTT
1 AAAAA-ATATATAATTCAACGCCAAAAAGATTGACAGG-CTTTTCACGCTTTTAATATCGTTTTT
* * * *
53054 CATATTTTTTCTGAATTAATTTTTATTTAAATCGAAACAAGATTATGATACATGTAAAAACAAAT
64 CAT-TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTA-GATGCTTGTAAAAACAAAT
* **
53119 CCTTAGATCAAATGTGACTGAGATTTGATTAGACTAATAAGGATATTTCAAGGAGTCTCGGCGCC
127 CCTTAGATCAAATGTGACTGACATTTGATTAGACTAATAAGGATATTTCAACAAGTCTCGGCGCC
*
53184 AAAAACCATACAAAATAGAGCCGTGGCCTCGGAAGGCGTTTTTAGTAAAAAAACCGTGATGGTAC
192 AAAAACCATACAAAATAGAGCCGTGGCCTCGGAACGCGTTTTTAGTAAAAAAACCGTGATGGTAC
* * *
53249 AAGATTTCGGCTAAAAACTGATCCGAAAATTTTTTACAATTTTTTTGCCACAATACTCAG
257 AAGATTTCGGCTAAAAACTGATCCAAAAATTTTTTACAATTTTTTTACCACAATACACAG
* * * * * *
53309 AAAAAATATATAATTCAACGCCAGAAAGACTAACGGGATTTTCACGCTTCTAATATCGTTTTTTC
1 AAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTTTAATATCG-TTTTTC
** *
53374 ATTTTTTTCCCAATTAATTTCTAATTAAATCAAAACAAGATTCAGATGCTTGTAAAAA-AAATCC
65 ATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATT-AGATGCTTGTAAAAACAAATCC
** * ** * * **
53438 TTCTATCCAATGTGGTTGACATTTGGTTCGA-TGAATATA-GATATTTCAACAAGTCTTTGCGCC
129 TTAGATCAAATGTGACTGACATTTGATTAGACT-AATA-AGGATATTTCAACAAGTCTCGGCGCC
* * * * * * ** *
53501 AAAAATCATGCAAAATTGAGCTG-GGGCTCGGGAACGTGTTTTTAG-CCAAAAACTGTGATGGTT
192 AAAAACCATACAAAATAGAGCCGTGGCCTC-GGAACGCGTTTTTAGTAAAAAAACCGTGAT-G--
* * *
53564 AGTACACGATTTCGGCTAAAAACTTA-CCTTAAAAAATTTTTTTTTCTCAA-TTTTTTACCACAA
253 -GTACAAGATTTCGGCTAAAAACTGATCC---AAAAA---TTTTTT-ACAATTTTTTTACCACAA
53627 TACACAG
310 TACACAG
* * *
53634 ACAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCATGCTTTTAATATCGTTTTCCC
1 AAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTTTAATATCGTTTT-TC
* * * *
53699 A-TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGACTGATATGCTCGAAAAAACAAATCC
65 ATTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGA-TTAGATGCTTGTAAAAACAAATCC
53763 TTA
129 TTA
53766 CACAGACTCC
Statistics
Matches: 377, Mismatches: 59, Indels: 35
0.80 0.13 0.07
Matches are distributed among these distances:
316 17 0.05
317 100 0.27
318 81 0.21
319 13 0.03
320 23 0.06
322 4 0.01
324 51 0.14
325 85 0.23
326 3 0.01
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (316 bp):
AAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTTTCACGCTTTTAATATCGTTTTTCA
TTTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTAGATGCTTGTAAAAACAAATCCTT
AGATCAAATGTGACTGACATTTGATTAGACTAATAAGGATATTTCAACAAGTCTCGGCGCCAAAA
ACCATACAAAATAGAGCCGTGGCCTCGGAACGCGTTTTTAGTAAAAAAACCGTGATGGTACAAGA
TTTCGGCTAAAAACTGATCCAAAAATTTTTTACAATTTTTTTACCACAATACACAG
Found at i:55858 original size:322 final size:321
Alignment explanation
Indices: 54645--56973 Score: 3031
Period size: 322 Copynumber: 7.3 Consensus size: 321
54635 GCCCTGCTTG
* ** * * *
54645 TAGATATTTAAAGGAGTCTTTGCGTTAAAAATCATGTAAAATTGAGTCAGGGCTCCGGAACGCGT
1 TAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGT
* *
54710 TTTTAACCAAAAACC--G-TGA-TAGTACACAATTTCGGCTAAAAA-TGACCCGAAAA-TTTTAT
66 TTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTT-T
* * *
54769 ACTCAATTTTTTGCCACAATACACAG-AAAAATATATAATTCAACGCCAAAAAGATTGACGGGCT
130 -CTCAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCT
**
54833 TTTCACGCTTCTAATATCGTTTTTTCCATTTTTTTTAGAATTAATTTCTAATTAAATCGAAACAA
194 TTTCACGCTTCTAATATCG-TTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
* * *
54898 GATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGCTTTGGTTCGATGAATA
258 GATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATA
* * * * ** * *
54962 TAGATATTTCACGGAGTTTTTACGCCAAAAATCATGTAAAATTGAGACTAGGCCCCGGAACGCAT
1 TAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGT
* * *
55027 TTTTAG-CAAAAACTGTGATGGTTAGTACACGATTTCGGCCAAAAACTGACCCGAAAAGTATTTT
66 TTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGT-TTTT
* * * * * *
55091 GT-TAATTTTTGCCACAATAGTCAGAAATAATATATAATTCAATGCCAAAAAGATAGAC-GAGCT
130 CTCAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAG-GCT
55154 TTTCACGCTTCTAATATCGTTTTTCCATTTTTTT-CGAATTAATTTCTAATT-AATCCGAAACAA
194 TTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAAT-CGAAACAA
55217 GATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATA
258 GATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATA
* * * * * * * * * *
55281 TAGATATTTCAAGGAGTTTTTACACTAATAACCATGCAAAATTGAGCCGCGGCTCTGGAACGCAT
1 TAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGT
* *
55346 TTTTAGCCAAAAACCATGATGGTTAGTTAGTACATGATTTCGGCTAAAAACTGACCCGAAAAGTA
66 TTTTAGCCAAAAACCGTGAT-G--A-TTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGT-
*
55411 TTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAC-G
126 TTTTCTCAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAG
* **
55475 GTCTCTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTGGAATTAATTTCTAATTAAATCGAAA
191 G-CTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAA
* * * *
55540 CAAGATTGAGATGCTCGGAAAAACAAATCCTTATATCCAATATGGCTGAAATTTGGTTCGATAAA
255 CAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAA
55605 TA
320 TA
* * *
55607 TAGATATTTC-AGGCAGTTTTTGCGTCAAAAATCATGCAAAATTGAGACGGGGCTCCGGAATGCG
1 TAGATATTTCAAGG-AGTCTTTGCGCCAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCG
* * * * * *
55671 TTTTTAGCCAAAAACCGTAAAGATTAGTACATGATTTCGCCTAAAAACTGACCTGAAAAATTTGT
65 TTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTT-T
* * * *
55736 TCACAAATTTTTGCCCCAATATTAAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCT
129 TCTCAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCT
* *
55801 TTTCACACTTCTAATATCGTTTTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAG
194 TTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
* * * * * * * *
55866 ATTCAGATGCTC-ATAAAAAGAAATCCTTATGTCCAATGTGGCTGACATTTGCTTCAATAAATG
259 ATTGAGATGCTCGA-AAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATA
* * * * *
55929 TAGGTAATTCAAGGAGTCTTTGCGCAAAAAAT-AT-CTAAAATTGAGCCGGGGCTCCGGAATGCG
1 TAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGC-AAAATTGAGACGGGGCTCCGGAACGCG
* *
55992 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACTCGAAAAGTATTT
65 TTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGT-TTT
* * *
56057 TCTCAAA-TTTTACCACAATACTCAGAAAAAATTTATAATTCAGCGCCAAAAAGATTGACAGGCT
129 TCTCAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCT
56121 TTTCACGCTTCTAATATCGTTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
194 TTTCACGCTTCTAATATCG-TTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
* * *
56186 GATTGAGATGTTCGAAAAAACAAATCCTTA-ATTCTAATATTGCTGAGATTTGGTTCAATGAATA
258 GATTGAGATGCTCGAAAAAACAAATCCTTATA-TCCAATATGGCTGAGATTTGGTTCAATGAATA
* * * * *
56250 TAAATATTTCAAGGAGTCTTTGCACCAAAAATCATACAAAATTGAGACAGGGCTCCGGACCGCGT
1 TAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGT
* *
56315 TTTTAGCCAAAAAACCCGTGATGCTTAGTACACGATTTCGGCTAAAAACTGA-TCGAAAAGTATT
66 TTTTAGCC-AAAAA-CCGTGATGATTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGT-TT
* * * * *
56379 TTCTTAATTTTTTACCACAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAGATTGACAAGC
128 TTCTCAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGC
*
56444 TTTTCACACTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
193 TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
* * * * * * * * **
56509 GATTCAAACGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTAACATTTGATTTGATGAATA
258 GATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATA
* * * * *
56573 TAGATATTTCAAGGAGTCTTTGCG-CTAAAATCATGTAAAATTGAGTCGGGGCTCCGGAATGAGT
1 TAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGT
* *
56637 TTTTAGCCAAAAACCGTGAT-A--CGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTATA
66 TTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTT-TT
** * *
56699 CTC-AATCTTTTGCCACAATACAAAGAAAAAAAATATAATTCAACGCCAAAAAGATTGACGGGCT
130 CTCAAAT-TTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCT
* * **
56763 TTTCACGGTTCTAAAATAATTTTTCC-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
194 TTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
*
56827 ATTGAGATGCTCG-AAAAACAAATCCTTATATCCAATATGGTTGAGATTTGGTTCAATGAATA
259 ATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATA
* * * * * *
56889 TAGATATTTCAAGGAGTTTTTGTGCCAATAATCATGCCAAATTGAGCCGCGGCTCCGGAA-GCGT
1 TAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGT
*
56953 GTTTAGCCAAAAACCGTGATG
66 TTTTAGCCAAAAACCGTGATG
56974 CCCTAAAAGT
Statistics
Matches: 1767, Mismatches: 205, Indels: 80
0.86 0.10 0.04
Matches are distributed among these distances:
316 93 0.05
317 165 0.09
318 86 0.05
319 147 0.08
320 143 0.08
321 281 0.16
322 308 0.17
323 149 0.08
324 151 0.09
325 90 0.05
326 151 0.09
327 3 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (321 bp):
TAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGACGGGGCTCCGGAACGCGT
TTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTC
TCAAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACAGGCTTT
TCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
TGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATA
Found at i:56641 original size:644 final size:637
Alignment explanation
Indices: 54645--57576 Score: 3622
Period size: 644 Copynumber: 4.6 Consensus size: 637
54635 GCCCTGCTTG
* * * * *
54645 TAGATATTTAAAGGAGTCTTTGCGTTAAAAATCATGTAAAATTGAGTCAGGGCTCCGGAACGCGT
1 TAGATATTTCAAGGAGTCTTTGCGCT-AAAATCATGTAAAATTGAGCCGGGGCTCCGGAACGAGT
* *
54710 TTTTAACCAAAAACCGTGATAGTACACAATTTCGGCTAAAAA-TGACCCGAAAA-TTTTATACTC
65 TTTTAGCCAAAAACCGTGATAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTT-T-CTC
54773 AATTTTTTGCCACAATACACAG-AAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTC
128 AATTTTTTGCCACAATACACAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTC
**
54837 ACGCTTCTAATATCGTTTTTTCCATTTTTTTTAGAATTAATTTCTAATTAAATCGAAACAAGATT
193 ACGCTTCTAATATCGTTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * *
54902 GAGATGCTCGAAAAAACAAATCCTTATATCCAATATTGCTGAGCTTTGGTTCGATGAATATAGAT
258 GAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATATAGAT
* * * * *
54967 ATTTCACGGAGTTTTTACGCCAAAAATCATGTAAAATTGAGACTA-GGCCCCGGAACGCATTTTT
323 ATTTCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTGAGAC-AGGGCTCCGGAACGCGTTTTT
* * * *
55031 AG-CAAAAACTGTGATGGTTAGTACACGATTTCGGCCAAAAACTGACCCGAAAAGTATTTTGTTA
387 AGCCAAAAACCGTGATGCTTAGTACACGATTTCGGCTAAAAACTGA-CCGAAAAGTATTTTCTTA
* * * * *
55095 ATTTTTGCCACAATAGTCAGAAATAATATATAATTCAATGCCAAAAAGATAGACGAGCTTTTCAC
451 ATTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAGATTGACAAGCTTTTCAC
* *
55160 GCTTCTAATATCGTTTTTCCATTTTTTT-CGAATTAATTTCTAATT-AATCCGAAACAAGATTGA
516 ACTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAAT-CGAAACAAGATTCA
* * * *
55223 GATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATA
580 GATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGATTCAATGAATA
* * * * * * *
55281 TAGATATTTCAAGGAGTTTTTACACTAATAACCATGCAAAATTGAGCCGCGGCTCTGGAACGCA-
1 TAGATATTTCAAGGAGTCTTTGCGCTAA-AATCATGTAAAATTGAGCCGGGGCTCCGGAACG-AG
*
55345 TTTTTAGCCAAAAACCATGATGGTTAGTTAGTACATGATTTCGGCTAAAAACTGACCCGAAAAGT
64 TTTTTAGCCAAAAACC--G-T-G--A--TAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGT
*
55410 ATTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACG
121 -TTTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAACGCCAAAAAGATTGACG
* * **
55475 GTCTCTTCACGCTTCTAATATCG-TTTTTCCATTTTTTTTGGAATTAATTTCTAATTAAATCGAA
185 GGCTTTTCACGCTTCTAATATCGTTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAA
* * * *
55539 ACAAGATTGAGATGCTCGGAAAAACAAATCCTTATATCCAATATGGCTGAAATTTGGTTCGATAA
250 ACAAGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGA
* * *
55604 ATATAGATATTTC-AGGCAGTTTTTGCGTCAAAAATCATGCAAAATTGAGACGGGGCTCCGGAAT
315 ATATAGATATTTCAAGG-AGTTTTTGCGCCAAAAATCATGCAAAATTGAGACAGGGCTCCGGAAC
* * * * * *
55668 GCGTTTTTAGCCAAAAACCGTAAAGATTAGTACATGATTTCGCCTAAAAACTGACCTGAAAAAT-
379 GCGTTTTTAGCCAAAAACCGTGATGCTTAGTACACGATTTCGGCTAAAAACTGACC-GAAAAGTA
** * * * *
55732 TTGTTCACAAATTTTTGCCCCAATATTAAGAAAAAATATATAATTCAACGCCAAAAAGATTGACA
443 TT-TTC-TTAATTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAGATTGACA
* *
55797 GGCTTTTCACACTTCTAATATCGTTTTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAA
506 AGCTTTTCACACTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAA
* * * * *
55862 CAAGATTCAGATGCTCATAAAAAGAAATCCTTATGTCCAATGTGGCTGACATTTGCTTCAATAAA
571 CAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGATTCAATGAA
*
55927 TG
636 TA
* * * * * *
55929 TAGGTAATTCAAGGAGTCTTTGCGCAAAAAAT-ATCTAAAATTGAGCCGGGGCTCCGGAATGCGT
1 TAGATATTTCAAGGAGTCTTTGCGC-TAAAATCATGTAAAATTGAGCCGGGGCTCCGGAACGAGT
*
55993 TTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACTCGAAAAGTATTTT
65 TTTTAGCCAAAAACCGTGA----TAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGT-TTTT
* * * * * *
56058 CTCAA-ATTTTACCACAATACTCAGAAAAAATTTATAATTCAGCGCCAAAAAGATTGACAGGCTT
125 CTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTT
56122 TTCACGCTTCTAATATCGTTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
190 TTCACGCTTCTAATATCGTTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
* * *
56187 ATTGAGATGTTCGAAAAAACAAATCCTTA-ATTCTAATATTGCTGAGATTTGGTTCAATGAATAT
255 ATTGAGATGCTCGAAAAAACAAATCCTTATA-TCCAATATGGCTGAGATTTGGTTCAATGAATAT
* * * * *
56251 AAATATTTCAAGGAGTCTTTGCACCAAAAATCATACAAAATTGAGACAGGGCTCCGGACCGCGTT
319 AGATATTTCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTGAGACAGGGCTCCGGAACGCGTT
*
56316 TTTAGCCAAAAAACCCGTGATGCTTAGTACACGATTTCGGCTAAAAACTGATCGAAAAGTATTTT
384 TTTAGCC-AAAAA-CCGTGATGCTTAGTACACGATTTCGGCTAAAAACTGACCGAAAAGTATTTT
*
56381 CTTAATTTTTTACCACAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAGATTGACAAGCTT
447 CTTAA-TTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAGATTGACAAGCTT
56446 TTCACACTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
511 TTCACACTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
* * * **
56511 TTCAAACGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTAACATTTGATTTGATGAATA
576 TTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGATTCAATGAATA
* *
56573 TAGATATTTCAAGGAGTCTTTGCGCTAAAATCATGTAAAATTGAGTCGGGGCTCCGGAATGAGTT
1 TAGATATTTCAAGGAGTCTTTGCGCTAAAATCATGTAAAATTGAGCCGGGGCTCCGGAACGAGTT
*
56638 TTTAGCCAAAAACCGTGATACGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTATACTCA
66 TTTAGCCAAAAACCGTGATA-GTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTT-TTCTCA
* * *
56703 ATCTTTTGCCACAATACAAAGAAAAAAAATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCA
129 ATTTTTTGCCACAATACACAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCA
* * **
56768 CGGTTCTAAAAT-AATTTTTCC-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTG
194 CGCTTCTAATATCGTTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTG
*
56831 AGATGCTCG-AAAAACAAATCCTTATATCCAATATGGTTGAGATTTGGTTCAATGAATATAGATA
259 AGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATATAGATA
* * * * *
56895 TTTCAAGGAGTTTTTGTGCCAATAATCATGCCAAATTGAG-CCGCGGCTCCGGAA-GCGTGTTTA
324 TTTCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTGAGACAG-GGCTCCGGAACGCGTTTTTA
*
56958 GCCAAAAACC--G-TG---A-T----G----C--C------CT-----AAAAGTA-TTTCTCAAT
388 GCCAAAAACCGTGATGCTTAGTACACGATTTCGGCTAAAAACTGACCGAAAAGTATTTTCTTAA-
* * *
56994 TTTTTGCCACAATACTCAGGAAAAATATATAATTCAACGCCAAAAAGATTGAC-GGTCTTTTCAC
452 TTTTTGCCACAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAGATTGACAAG-CTTTTCAC
* * *
57058 GCTTCTAATATCGTTTTT-CATTTTTTTTCCGAATTAATTTCTAAGTATAA-CGAAACAAGATTG
516 ACTTCTAATATCGTTTTTCCA-TTTTTTTCCGAATTAATTTCTAATTA-AATCGAAACAAGATTC
* * * * * *
57121 AGATGCTCGAAAAAACAAATCCTTGTATCCAATATGGCTGAAATTTGGTTCTATGAATA
579 AGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGATTCAATGAATA
* * * * * * * *
57180 TTGATATTTC-AGGCAGTTTTTGCGTCAAAAATCATGCAAAATTAAGACGGGGCTCCGAAACGCG
1 TAGATATTTCAAGG-AGTCTTTGCG-CTAAAATCATGTAAAATTGAGCCGGGGCTCCGGAACGAG
* * * *
57244 TTTTTAGCCAAAAACCGTGAAGGTTAGTTCACGATTTCGGCTAAAACCTAACCTGAAAA-TTTCT
64 TTTTTAGCCAAAAACCGTG-A---TAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTT-T
* ** *
57308 TCTAAAATTTTTT-CCACAATATTCAGAAAAAAAATATAATTCAACGCCAAAAAGATTGACGGGC
124 TCT-CAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGC
** *
57372 TTTTCACGCTTCTAATATCG--TTTTCCATTTTTTTTTGAAATAATTTCTAATTAAATCGAAACA
188 TTTTCACGCTTCTAATATCGTTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * *
57435 AGATTGAGATGCTCAAAAAAACAATTCCTTATATCCAATATTGCTGAGATTTGGTTCAATGAATA
253 AGATTGAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATA
* * * ** *
57500 TAAAATATTTCAACGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGATGGGGCTCTGGAACGCG
318 T-AGATATTTCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTGAGACAGGGCTCCGGAACGCG
57565 -TTTTAG-CAAAAA
382 TTTTTAGCCAAAAA
Statistics
Matches: 2020, Mismatches: 221, Indels: 135
0.85 0.09 0.06
Matches are distributed among these distances:
606 6 0.00
607 187 0.09
608 60 0.03
609 7 0.00
610 117 0.06
611 89 0.04
612 55 0.03
613 6 0.00
619 1 0.00
621 1 0.00
625 1 0.00
629 1 0.00
630 1 0.00
633 2 0.00
634 1 0.00
635 2 0.00
636 65 0.03
637 5 0.00
638 14 0.01
639 93 0.05
640 56 0.03
641 48 0.02
642 137 0.07
643 214 0.11
644 280 0.14
645 237 0.12
646 101 0.05
647 128 0.06
648 100 0.05
649 5 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (637 bp):
TAGATATTTCAAGGAGTCTTTGCGCTAAAATCATGTAAAATTGAGCCGGGGCTCCGGAACGAGTT
TTTAGCCAAAAACCGTGATAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTCTCAAT
TTTTTGCCACAATACACAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACG
CTTCTAATATCGTTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAG
ATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTCAATGAATATAGATATT
TCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTGAGACAGGGCTCCGGAACGCGTTTTTAGCC
AAAAACCGTGATGCTTAGTACACGATTTCGGCTAAAAACTGACCGAAAAGTATTTTCTTAATTTT
TGCCACAATACTCAGAAAAAATATATAATTCAAAGCCAAAAAGATTGACAAGCTTTTCACACTTC
TAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
CGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGATTCAATGAATA
Found at i:57236 original size:291 final size:290
Alignment explanation
Indices: 56699--57263 Score: 839
Period size: 291 Copynumber: 1.9 Consensus size: 290
56689 AAAGTTTATA
56699 CTCAATCTTTTGCCACAATACAAAGAAAAAAAATATAATTCAACGCCAAAAAGATTGACGGGCTT
1 CTCAATCTTTTGCCACAATACAAAGAAAAAAAATATAATTCAACGCCAAAAAGATTGACGGGCTT
* *
56764 TTCACGGTTCTAAAATAATTTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
66 TTCACGCTTCTAAAATAATTTTTCCTTTTTTTCCGAATTAATTTCTAAGTAAATCGAAACAAGAT
* *
56829 TGAGATGCTCGAAAAACAAATCCTTATATCCAATATGGTTGAGATTTGGTTCAATGAATATAGAT
131 TGAGATGCTCGAAAAACAAATCCTTATATCCAATATGGCTGAAATTTGGTTCAATGAATATAGAT
* * * * * *
56894 ATTTCAAGGAGTTTTTGTGCCAATAATCATGCCAAATTGAGCCGCGGCTCCGGAA-GCGTGTTTA
196 ATTTCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTAAGACGCGGCTCCGAAACGCGTGTTTA
56958 GCCAAAAACCGTGATGCCCTAAAAGTATTT
261 GCCAAAAACCGTGATGCCCTAAAAGTATTT
* ** * * *
56988 CTCAATTTTTTGCCACAATACTCAGGAAAAATATATAATTCAACGCCAAAAAGATTGACGGTCTT
1 CTCAATCTTTTGCCACAATACAAAGAAAAAAAATATAATTCAACGCCAAAAAGATTGACGGGCTT
* ** *
57053 TTCACGCTTCTAATATCGTTTTTCATTTTTTTTCCGAATTAATTTCTAAGTATAA-CGAAACAAG
66 TTCACGCTTCTAAAATAATTTTTC-CTTTTTTTCCGAATTAATTTCTAAGTA-AATCGAAACAAG
* * *
57117 ATTGAGATGCTCGAAAAAACAAATCCTTGTATCCAATATGGCTGAAATTTGGTTCTATGAATATT
129 ATTGAGATGCTCG-AAAAACAAATCCTTATATCCAATATGGCTGAAATTTGGTTCAATGAATATA
* * *
57182 GATATTTC-AGGCAGTTTTTGCGTCAAAAATCATGCAAAATTAAGACGGGGCTCCGAAACGCGTT
193 GATATTTCAAGG-AGTTTTTGCGCCAAAAATCATGCAAAATTAAGACGCGGCTCCGAAACGCGTG
57246 TTTAGCCAAAAACCGTGA
257 TTTAGCCAAAAACCGTGA
57264 AGGTTAGTTC
Statistics
Matches: 245, Mismatches: 26, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
289 79 0.32
290 50 0.20
291 94 0.38
292 22 0.09
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (290 bp):
CTCAATCTTTTGCCACAATACAAAGAAAAAAAATATAATTCAACGCCAAAAAGATTGACGGGCTT
TTCACGCTTCTAAAATAATTTTTCCTTTTTTTCCGAATTAATTTCTAAGTAAATCGAAACAAGAT
TGAGATGCTCGAAAAACAAATCCTTATATCCAATATGGCTGAAATTTGGTTCAATGAATATAGAT
ATTTCAAGGAGTTTTTGCGCCAAAAATCATGCAAAATTAAGACGCGGCTCCGAAACGCGTGTTTA
GCCAAAAACCGTGATGCCCTAAAAGTATTT
Done.