Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020712.1 Corchorus olitorius cultivar O-4 contig20745, 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: 56029
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:740 original size:334 final size:331
Alignment explanation
Indices: 3--945 Score: 1138
Period size: 334 Copynumber: 2.8 Consensus size: 331
1 AT
* * *
3 GAGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTT
1 GAGCCACGGAACGTGTTTTTACCCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTT
* * * * * *
68 GTAAAAATTGACCCGAAAGATATTACCTCAATTTTTAGCCATAATAATCATAAAGAATATATAAT
66 GTAAAAATTGACCCGAAAGAT-TTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAAT
** *
133 TCAACG-CAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATA-TTTTTCTGTAC
130 TCAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTTCTAAAT
* **
196 TAATTTCTAATTAAATCGAAACAAGATTAAGATGCTTGTACAAACAAATTTTTAAATCCAATGTG
195 TAATTTCTAATTAAATCGAAACAAAATTAAGATGCTTGTACAAACAAATCCTTAAATCCAATGTG
* *
261 GCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAAT
260 GCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAAT
326 TGAGCCG
325 TGAGCCG
* * * * *
333 GAGCCACAGAAAGCT-TTTTTATCCAAAAATTGTGATGGTTATTACACGATTTCGGCTAAAATTT
1 GAGCCACGGAACG-TGTTTTTACCCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAATTT
*
397 TGTAAAAATTGACCCGAAAGATGTTTCCTAAATTTTTGGCTAAAATACTCATAAAAAATATATAA
65 TGTAAAAATTGACCCGAAAGAT-TTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAA
* * *
462 CTCAACGCCAGAAAA-ATTGAAGGGCTTTTGACG-TTTCTAATATCGTTTTTCCTATTTTTTCCA
129 TTCAACGCCA-AAAAGATTGAAGGGCTTTTGACGCTTT-TAATATCGTTTTTCATATTTTTTCTA
* * *
525 AATTAATTTCTAATTAAATC-ACAGCAAAATTCAGATG-TTGGTA-AAGACAAATCCTTAAATCT
192 AATTAATTTCTAATTAAATCGA-AACAAAATTAAGATGCTT-GTACAA-ACAAATCCTTAAATCC
* * * * **
587 AATGTGGGGGTGAGATTTGATTAGATGAATATAGATATTTTAAGTAGTCTCGGAGCCTGAAATCA
254 AATGT--GGCTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGAGCCAAAAATCA
652 TGCAAAATTGAGCCAG
317 TGCAAAATTGAGCC-G
* * * * * **
668 G-TCCTCGGAACGTGTTTTTACCCAAAAACCGTGATAGTTTGTTA-GTGATTTCGGCTAAAATTT
1 GAGCCACGGAACGTGTTTTTACCCAAAAACTGTGAT-GATTATTACACGATTTCGGCTAAAATTT
* * * *
731 TGCAAAAATTGACACGAACGATTTCTTCTCAATTTTTGGCTAAAATACTCAT-AAAAATATATAA
65 TGTAAAAATTGACCCGAAAGATTT-TCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAA
* *
795 TTCAACGCCAAAAAGATTGGAA-GGCTTTTTACGCTTTTAATATCGTATTTT-TTATTTTTTCTA
129 TTCAACGCCAAAAAGATT-GAAGGGCTTTTGACGCTTTTAATATCGT-TTTTCATATTTTTTCTA
* * * * * **
858 AATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATTTTTAAATCCAAT
192 AATTAATTTCTAATTAAATCGAAACAAAATTAAGATGCTTGTACAAACAAATCCTTAAATCCAAT
** *
923 GTTACTGAGATTTGGTTAGATGA
257 GTGGCTGAGATTTGATTAGATGA
946 TGTAGAGTAA
Statistics
Matches: 525, Mismatches: 67, Indels: 41
0.83 0.11 0.06
Matches are distributed among these distances:
330 122 0.23
331 58 0.11
332 65 0.12
333 108 0.21
334 164 0.31
335 8 0.02
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.34
Consensus pattern (331 bp):
GAGCCACGGAACGTGTTTTTACCCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAATTTT
GTAAAAATTGACCCGAAAGATTTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATT
CAACGCCAAAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTTTTCTAAATT
AATTTCTAATTAAATCGAAACAAAATTAAGATGCTTGTACAAACAAATCCTTAAATCCAATGTGG
CTGAGATTTGATTAGATGAATATAGATATCTCAAGGAGTCTCGGAGCCAAAAATCATGCAAAATT
GAGCCG
Found at i:994 original size:16 final size:16
Alignment explanation
Indices: 970--1024 Score: 76
Period size: 16 Copynumber: 3.4 Consensus size: 16
960 GGCAATTGGG
970 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
986 CGGGCTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
1002 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
1018 CGGGTTC
1 CGGGTTC
1025 AGTCTCAGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 1 0.03
16 31 0.94
17 1 0.03
ACGTcount: A:0.05, C:0.16, G:0.40, T:0.38
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:1511 original size:31 final size:31
Alignment explanation
Indices: 1476--1547 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
1466 TAAATTATTG
*
1476 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
1507 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
1538 CAAATTAAAA
1 CAAATTAAAA
1548 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:5481 original size:107 final size:107
Alignment explanation
Indices: 5295--5509 Score: 394
Period size: 107 Copynumber: 2.0 Consensus size: 107
5285 GGATTAATTA
* *
5295 GCTTTTGGTGATGGTCTTTGTTAAAAATTGGTTTTTTGTTGTTGATCGTTCTAGGGTATCTTTGT
1 GCTTTTGGTGATGGTCTTTGCTAAAAATTGGTTTTTTGTTGTTCATCGTTCTAGGGTATCTTTGT
5360 TTATTTTCGCCTTGTGGGTAGAGTTGCTTCCTGTTTGCTCCT
66 TTATTTTCGCCTTGTGGGTAGAGTTGCTTCCTGTTTGCTCCT
* *
5402 GCTTTTGGTGATGGTCTTTGCTAAGAATTGGTTTTTTGTTGTTCATCGTTCTAGTGTATCTTTGT
1 GCTTTTGGTGATGGTCTTTGCTAAAAATTGGTTTTTTGTTGTTCATCGTTCTAGGGTATCTTTGT
5467 TTATTTTCGCCTTGTGGGTAGAGTTGCTTCCTGTTTGCTCCT
66 TTATTTTCGCCTTGTGGGTAGAGTTGCTTCCTGTTTGCTCCT
5509 G
1 G
5510 AACATTTGTG
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
107 104 1.00
ACGTcount: A:0.11, C:0.14, G:0.25, T:0.50
Consensus pattern (107 bp):
GCTTTTGGTGATGGTCTTTGCTAAAAATTGGTTTTTTGTTGTTCATCGTTCTAGGGTATCTTTGT
TTATTTTCGCCTTGTGGGTAGAGTTGCTTCCTGTTTGCTCCT
Found at i:5560 original size:44 final size:44
Alignment explanation
Indices: 5493--5584 Score: 175
Period size: 44 Copynumber: 2.1 Consensus size: 44
5483 GGTAGAGTTG
5493 CTTCCTGTTTGCTCCTGAACATTTGTGAATGATTCATAATCGTT
1 CTTCCTGTTTGCTCCTGAACATTTGTGAATGATTCATAATCGTT
*
5537 CTTCCTGTTTGCTCCTGATCATTTGTGAATGATTCATAATCGTT
1 CTTCCTGTTTGCTCCTGAACATTTGTGAATGATTCATAATCGTT
5581 CTTC
1 CTTC
5585 GATTATTAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.18, C:0.22, G:0.15, T:0.45
Consensus pattern (44 bp):
CTTCCTGTTTGCTCCTGAACATTTGTGAATGATTCATAATCGTT
Found at i:6492 original size:85 final size:84
Alignment explanation
Indices: 6393--6651 Score: 353
Period size: 85 Copynumber: 3.0 Consensus size: 84
6383 GTCAAGTTTC
* * * *
6393 TTCCAATCATCATCTGACATATCACTTGGTTTACCCAAATCACCCAATACCGGATCAAACAAGTC
1 TTCCAATCATCATCT-ATATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAAACAAGTC
*
6458 ATTGCAGTATAGATGATCCT
65 CTTGCAGTATAGATGATCCT
6478 TTCCAATCATCATCTAATATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAAACAAGTC
1 TTCCAATCATCATCT-ATATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAAACAAGTC
6543 CTTGCAGTATAGATGATCC-
65 CTTGCAGTATAGATGATCCT
*
6562 -TCC-ATCATCGGTTTCCAAATATTATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAA
1 TTCCAATCATC---AT-C---TA-TATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAA
6625 ACAAGTCCTTGCAGTATAGATGATCCT
58 ACAAGTCCTTGCAGTATAGATGATCCT
6652 CCATCATCGG
Statistics
Matches: 158, Mismatches: 7, Indels: 13
0.89 0.04 0.07
Matches are distributed among these distances:
82 6 0.04
83 3 0.02
85 79 0.50
86 1 0.01
88 1 0.01
89 68 0.43
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (84 bp):
TTCCAATCATCATCTATATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAAACAAGTCC
TTGCAGTATAGATGATCCT
Found at i:6615 original size:89 final size:89
Alignment explanation
Indices: 6411--6674 Score: 398
Period size: 89 Copynumber: 3.0 Consensus size: 89
6401 ATCATCTGAC
* * * *
6411 ATATCACTTGGTTTACCCAAATCACCCAATACCGGATCAAACAAGTCATTGCAGTATAGATGATC
1 ATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAAACAAGTCCTTGCAGTATAGATGATC
* *
6476 CTTTCCAATCATC---AT-C---TAAT
66 C--TCC-ATCATCGGTTTCCAAATATT
6496 ATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAAACAAGTCCTTGCAGTATAGATGATC
1 ATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAAACAAGTCCTTGCAGTATAGATGATC
6561 CTCCATCATCGGTTTCCAAATATT
66 CTCCATCATCGGTTTCCAAATATT
6585 ATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAAACAAGTCCTTGCAGTATAGATGATC
1 ATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAAACAAGTCCTTGCAGTATAGATGATC
6650 CTCCATCATCGGTTTCCAAATATT
66 CTCCATCATCGGTTTCCAAATATT
6674 A
1 A
6675 AAATTTGTAG
Statistics
Matches: 166, Mismatches: 6, Indels: 10
0.91 0.03 0.05
Matches are distributed among these distances:
82 6 0.04
83 3 0.02
85 63 0.38
86 1 0.01
89 93 0.56
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (89 bp):
ATATCACTTGGTTTACCCGAATCACCGAATACCTGATCAAACAAGTCCTTGCAGTATAGATGATC
CTCCATCATCGGTTTCCAAATATT
Found at i:11793 original size:49 final size:49
Alignment explanation
Indices: 11740--11838 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
11730 ATGTAATCAT
11740 GGCCGCATTCTTCTTGTATTCCTTATTATATATATAAGCAATATCAAAA
1 GGCCGCATTCTTCTTGTATTCCTTATTATATATATAAGCAATATCAAAA
11789 GGCCGCATTCTTCTTGTATTCCTTATTATATATATAAGCAATATCAAAA
1 GGCCGCATTCTTCTTGTATTCCTTATTATATATATAAGCAATATCAAAA
11838 G
1 G
11839 AGCAATGTTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.38
Consensus pattern (49 bp):
GGCCGCATTCTTCTTGTATTCCTTATTATATATATAAGCAATATCAAAA
Found at i:26518 original size:12 final size:12
Alignment explanation
Indices: 26496--26532 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
26486 TAAAATACTC
*
26496 ATATATATATAT
1 ATATATGTATAT
*
26508 ATATGTGTATAT
1 ATATATGTATAT
26520 ATATATGTATAT
1 ATATATGTATAT
26532 A
1 A
26533 ATTTAACGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.08, T:0.49
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:26520 original size:14 final size:14
Alignment explanation
Indices: 26499--26532 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
26489 AATACTCATA
26499 TATATATATATATG
1 TATATATATATATG
*
26513 TGTATATATATATG
1 TATATATATATATG
26527 TATATA
1 TATATA
26533 ATTTAACGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (14 bp):
TATATATATATATG
Found at i:27941 original size:26 final size:26
Alignment explanation
Indices: 27905--27962 Score: 109
Period size: 26 Copynumber: 2.3 Consensus size: 26
27895 TGTTCAATTA
27905 AGGAGGAGGATTTCCGTCTCCCATCC
1 AGGAGGAGGATTTCCGTCTCCCATCC
27931 AGGAGGAGGATTTCCGTCTCCCATCC
1 AGGAGGAGGATTTCCGTCTCCCATCC
27957 A-GAGGA
1 AGGAGGA
27963 ATGACGTCCT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
25 5 0.16
26 27 0.84
ACGTcount: A:0.22, C:0.28, G:0.29, T:0.21
Consensus pattern (26 bp):
AGGAGGAGGATTTCCGTCTCCCATCC
Found at i:28403 original size:50 final size:51
Alignment explanation
Indices: 28299--28403 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 51
28289 TTCAATATTT
* * * *
28299 TCTTGTTTAGATCTTGTCTCCGGACATCCAAACACTCTTTTAGTGTTTTTC
1 TCTTGTTTAGATCTTGTCTCCAGACATCAAAACACTCTATGAGTGTTTTTC
* *
28350 TCTTGTTTCA-ATCTTGTCTCCAGACAT-AAAACACTGTATGCGTGTTTTTC
1 TCTTGTTT-AGATCTTGTCTCCAGACATCAAAACACTCTATGAGTGTTTTTC
28400 TCTT
1 TCTT
28404 ATTAATAACA
Statistics
Matches: 47, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
50 22 0.47
51 24 0.51
52 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.13, T:0.45
Consensus pattern (51 bp):
TCTTGTTTAGATCTTGTCTCCAGACATCAAAACACTCTATGAGTGTTTTTC
Found at i:29339 original size:15 final size:16
Alignment explanation
Indices: 29321--29350 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
29311 ATAATTACCC
29321 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
29336 ATATTATAATCTAAA
1 ATATTATAATCTAAA
29351 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:29595 original size:39 final size:39
Alignment explanation
Indices: 29568--29647 Score: 124
Period size: 39 Copynumber: 2.1 Consensus size: 39
29558 AAATTTCTCA
* *
29568 ATTAGAATTTTTGACTTTGTGGTTTTATATAGTAGTAAG
1 ATTAGAATTTTTGACTTTGTGGTTTTATAAAGTACTAAG
* *
29607 ATTAGAATTTTTGACTTTGTGGTTTTATATAGTAATAAG
1 ATTAGAATTTTTGACTTTGTGGTTTTATAAAGTACTAAG
29646 AT
1 AT
29648 AGTAAGATAG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.49
Consensus pattern (39 bp):
ATTAGAATTTTTGACTTTGTGGTTTTATAAAGTACTAAG
Found at i:33456 original size:36 final size:36
Alignment explanation
Indices: 33402--33474 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
33392 AGGTTTTGGG
*
33402 TTCTACTCTTACGAAATGTGAGTTTTCTTTGTAATT
1 TTCTACTCTCACGAAATGTGAGTTTTCTTTGTAATT
* *
33438 TTCTATTCTCACGGAATGTGAGTTTTCTTTGTAATT
1 TTCTACTCTCACGAAATGTGAGTTTTCTTTGTAATT
33474 T
1 T
33475 GTGTATTTAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.21, C:0.14, G:0.15, T:0.51
Consensus pattern (36 bp):
TTCTACTCTCACGAAATGTGAGTTTTCTTTGTAATT
Found at i:36502 original size:5 final size:5
Alignment explanation
Indices: 36489--36531 Score: 61
Period size: 5 Copynumber: 8.6 Consensus size: 5
36479 CAAAATTTTA
*
36489 AAAAA AAAAG AAAAG AAAAG AAAAG AAAAG -AAAG AAGAAG AAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA-AAG AAA
36532 GTATGCCACA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
4 4 0.11
5 26 0.74
6 5 0.14
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:37020 original size:19 final size:19
Alignment explanation
Indices: 36996--37039 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
36986 TATATGTTAA
*
36996 TAAAATTCAATTTTA-ATAC
1 TAAAATT-AACTTTAGATAC
*
37015 TAAAATTTACTTTAGATAC
1 TAAAATTAACTTTAGATAC
37034 TAAAAT
1 TAAAAT
37040 ATTAATACAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.41
Consensus pattern (19 bp):
TAAAATTAACTTTAGATAC
Found at i:45136 original size:48 final size:48
Alignment explanation
Indices: 45060--45156 Score: 142
Period size: 48 Copynumber: 2.0 Consensus size: 48
45050 TTAAGCAGGT
* *
45060 CTCAGGTTCGAGACCTTGCATACATAGCTGCCCCTGTT-GTGAGACTCA
1 CTCAAGTTCGAGACCTTACATACATAGCTGCCCCTGTTAG-GAGACTCA
* *
45108 CTCAAGTTCGAGACCTTACGTACATAGCTGCTCCTGTTAGGAGACTCA
1 CTCAAGTTCGAGACCTTACATACATAGCTGCCCCTGTTAGGAGACTCA
45156 C
1 C
45157 CCACCATGAC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 43 0.98
49 1 0.02
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.27
Consensus pattern (48 bp):
CTCAAGTTCGAGACCTTACATACATAGCTGCCCCTGTTAGGAGACTCA
Found at i:54234 original size:323 final size:322
Alignment explanation
Indices: 53634--55666 Score: 2086
Period size: 323 Copynumber: 6.3 Consensus size: 322
53624 ACCATGATGG
* * * * * * *
53634 TAAAAA-TGACCCG-AAATATTTTCCTCAATTTTTGGCAAAAATACTCATAAAATATATATACTT
1 TAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCA-AAAAAATATATAATT
* * * * * * *
53697 CAATGCCAAAAAGTTTGGA-GGACTTTTCAAGCTTTTAATATCGTTTTTCATATTTTTTTCT-AA
65 CAACGCCAAAAAGATT-GACGGGCTTTTCACGCTTCTAATATCGTTTTTC-CATTTTTTTCTCGA
* * * * *
53760 ATTAATTTCT-ATTAAATTGAAACAACATTCAGATGCACGTAAAAACAATTCAC-TAAATACAAT
128 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC-CTTAAATCCAAT
* * * * * * **** *
53823 GTGACTGAGATTCGATTAGATCAATAAAGATATTTCAAGGAGTCAGGGTGCC-AAAATCCATGCA
192 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTACCAAAAAT-CATGCA
* * * * * * * *
53887 AAACAGAGCCGTA-ACCCCGAAACGCATTTTTTTGTCAAAAACCGTGATGATTAATACAGGATTT
256 AAACTGAGCC-TAGGCCCCGAAACGC-GTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTT
*
53951 CGAC
319 CGGC
* *
53955 TAAAAAGTGACCCGAAAATTTTTTTCTCAATTCTTTGCCACAATACTCAAAAAAATATATAATTC
1 TAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAAAAAAATATATAATTC
* * *
54020 CACGCCAAAAAGATTGACGGGTTTTTCACGCTTCTAACATCGTTTTTCCATTTTTTTCTCGAATT
66 AACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTCGAATT
* *
54085 AATTTCTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGG
131 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* *
54150 CTGATATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTACCAAAAATCATACAAAACT
196 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTACCAAAAATCATGCAAAACT
***
54215 GAGCCTAGGCTTTGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGGC
261 GAGCCTAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGGC
* *
54277 TAAAAAACTGACCCGAAAAGTGTTTTCTCAATTTTTTGCCACAATACTC-AAAAAATATATAATT
1 T-AAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAAAAAAATATATAATT
* * *
54341 CAACGCCAAAAAGATTGACGGGCTTTTCACGCTACTAA-A-----ATTCCA-TTTTTT-TCAAAT
65 CAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTCGAAT
* * * * * *
54398 TTA-TT-TAATTAAATTGAAAAAAGATTTAGATGCTTGTAAAAA-AAATCCTTATATCCAATGTG
130 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * ** * *
54460 CCTGAGATTTGGTTCGATGAATATAGCCATTTCAAGG-A-CTTTTTGCGCAAAAAATCATGCAAA
195 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTAC-C-AAAAATCATGCAAA
* * ** ** * * * * * * ** *
54523 ATTGAGGCGGGGATCTGGAATGCGTTTTTGGCCAAAAATCGTGACGGTTAGTACACAATTTCGAC
258 ACTGAGCCTAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGGC
* *
54588 TAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACT-AAAAAAA
1 --------T--AAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAAAAAAA
* * * ** * ** *
54652 TATATAATTCAATGCAAAAAAAATTGAAAGGTTTTTCACGAATCTAATATCG-TTTTCCCTTTTT
56 TATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTT
* * * * * *
54716 TTTTCCGAATTTATTTTTAATTAAATCAAAACAAGATTCAGACGCTCGTAAAAAAAAATCCTTAA
121 TTCT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA
* * * * *
54781 ATCCAATGAGGTTGAGATTTTGTTAAATGAATATAGATATTTTAAGGAA-CTTTTCTACCAAAAA
185 ATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATC-TTTCTACCAAAAA
*
54845 TCATGCAAAACTGAGCC-GGTGCCCCGAAACGCGTTTTTAGCCAAAAAAAACCGTGAT-G-TAGT
249 TCATGCAAAACTGAGCCTAG-GCCCCGAAACGCGTTTTTAGCC---AAAAACCGTGATGGTTAGT
*
54907 ACATGATTACGGC
310 ACATGATTTCGGC
* * * * * *
54920 TAAAAATTGACCCAAAAAATCTTTTTCCCGAATTTTTTGCCATAATACTTAGAAAAAATATATAA
1 TAAAAACTGACCC-GAAAATTTTTTTCTC-AATTTTTTGCCACAATACTCA-AAAAAATATATAA
* * *
54985 TTCAACGGCAAAAAGATTAATGGGCTTTTCACGCTTCTAATATCGTTTTTCC-TTTTTTTC-CGA
63 TTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTCGA
* * * * *
55048 ATTAATTTCTAATTAAATCGGAACAAGATTCAGATGCTTGTAAAAAACAAATCCATATATCCAAA
128 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAAACAAATCCTTAAATCCAAT
* * * * * * *
55113 GTGGCTGAAATTTGGTTCGATGAATATGGATATTTTAAGGAGTTTTTGC-GCCAAAAATCATGCA
192 GTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTT-CTACCAAAAATCATGCA
* * * *
55177 AAACTGAGGC-AGGGCCCCGAAACGCGTTTTTAGTCAAAAACCGTGATGATTAGTACATGAATTC
256 AAACTGAGCCTA-GGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTC
55241 GGC
320 GGC
* * * *
55244 TAAAAATTGACCCAAAAAATATTTTTCTGAATTTTTTTGCCACAATACTCAAAAAAATATATAAT
1 TAAAAACTGACCC-GAAAATTTTTTTCTCAA-TTTTTTGCCACAATACTCAAAAAAATATATAAT
* * ** * * *
55309 CCAACG-CAAAACAAATTGAAAGGTTTTTCACGCGTCTAATATTGTTTTTCCATTTTTTTC-CGA
64 TCAACGCCAAAA-AGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTCGA
* * * * * *
55372 ATTTATTTTTAATTAAATCGAAATAAGATTCGGATACTCGTAAAAACAAATTCTTAAATCCAATG
128 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* *
55437 TGGCTGAGATTTTGTTAGATGAATATAGATATTTCAAGGAATCTTTCTACCAAAAATCATACAAA
193 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTACCAAAAATCATGCAAA
***
55502 ACTGAGCCTAGGCTTTGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGGC
258 ACTGAGCCTAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGGC
* *
55567 TAAAAACTGACCCGAAAAGTGTTTTCTCAA-TTTTTGCCACAATACTC-AAAAAATATATAATTC
1 TAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAAAAAAATATATAATTC
*
55630 AACGCCAAAAAGATTGACGGGCTTTTCACGCTACTAA
66 AACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAA
55667 AATTCCATTT
Statistics
Matches: 1425, Mismatches: 232, Indels: 112
0.81 0.13 0.06
Matches are distributed among these distances:
309 6 0.00
310 2 0.00
311 115 0.08
312 32 0.02
313 2 0.00
314 7 0.00
315 6 0.00
316 5 0.00
319 41 0.03
320 110 0.08
321 20 0.01
322 199 0.14
323 382 0.27
324 166 0.12
325 105 0.07
326 63 0.04
327 7 0.00
328 7 0.00
329 2 0.00
330 33 0.02
331 83 0.06
332 16 0.01
333 6 0.00
334 10 0.01
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (322 bp):
TAAAAACTGACCCGAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAAAAAAATATATAATTC
AACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCTCGAATT
AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAATCTTTCTACCAAAAATCATGCAAAACT
GAGCCTAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGGC
Found at i:54781 original size:642 final size:633
Alignment explanation
Indices: 53902--55698 Score: 2363
Period size: 642 Copynumber: 2.8 Consensus size: 633
53892 GAGCCGTAAC
* * * * * * * * *
53902 CCCGAAACGCATTTTTTTGTCAAAAACCGTGATGATTAATACAGGATTTCGACTAAAAAGTGACC
1 CCCGAAACGC-GTTTTTAGCCAAAAACCGTGACGATTAGTACATGAATTCGGCTAAAAACTGACC
* * * * *
53967 CGAAAATTTTTTTCTCAATTCTTTGCCACAATACTCAAAAAAATATATAATTCCACGCCAAAAAG
65 CGAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAAAAAAATATATAATTCAACGCAAAAAAA
** * * * *
54032 ATTGACGGGTTTTTCACGCTTCTAACATCGTTTTTCCATTTTTTTCTCGAATTAATTTCTAATTA
130 ATTGAAAGGTTTTTCACGCATCTAATATCGTTTTTCCATTTTTTTC-CGAATTTATTTTTAATTA
* *
54097 AATCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGATATTTGGT
194 AATCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTGT
54162 TAGATGAATATAGATATTTCAAGGAATCTTTCTACCAAAAATCATACAAAACTGAGCCTAGGCTT
259 TAGATGAATATAGATATTTCAAGGAATCTTTCTACCAAAAATCATACAAAACTGAGCCTAGGCTT
54227 TGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAAAACTGACCCG
324 TGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGGCT-AAAAACTGACCCG
54292 AAAAGTGTTTTCTCAATTTTTTGCCACAATACTCAAAAAATATATAATTCAACGCCAAAAAGATT
388 AAAAGTGTTTTCTCAATTTTTTGCCACAATACTCAAAAAATATATAATTCAACGCCAAAAAGATT
*
54357 GACGGGCTTTTCACGCTACTAAAATTCCATTTTTTTCAAATTTATTTAATTAAATTGAAAAAAGA
453 GACGGGCTTTTCACGCTACTAAAATTCCATTTTTTTCAAATTTATTTAATTAAATCGAAAAAAGA
* * * *
54422 TTTAGATGCTTGT-AAAAA-AAATCCTTATATCCAATGTGCCTGAGATTTGGTTCGATGAATATA
518 TTCAGATGCTTGTAAAAAACAAATCCATATATCCAAAGTGCCTGAAATTTGGTTCGATGAATATA
* * *
54485 GCCATTTCAAGGACTTTTTGCGCAAAAAATCATGCAAAATTGAGGCGGGGA
583 GACATTTCAAGGACTTTTTGCGCAAAAAATCATGCAAAACTGAGGCAGGGA
* * * * * * * * *
54536 TCTGGAATGCGTTTTTGGCCAAAAATCGTGACGGTTAGTACA-CAATTTCGACTAAAATTTTGCA
1 CCCGAAACGCGTTTTTAGCCAAAAACCGTGACGATTAGTACATGAA-TTCGGC--------T--A
* *
54600 AAAACTGACCCGAAAAGTTTTTCCTCAATTTTTTGCCACAATACT-AAAAAAATATATAATTCAA
55 AAAACTGACCCGAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAAAAAAATATATAATTCAA
* * * *
54664 TGCAAAAAAAATTGAAAGGTTTTTCACGAATCTAATATCGTTTTCCCTTTTTTTTTCCGAATTTA
120 CGCAAAAAAAATTGAAAGGTTTTTCACGCATCTAATATCGTTTTTCC-ATTTTTTTCCGAATTTA
* * ** * * *
54729 TTTTTAATTAAATCAAAACAAGATTCAGACGCTCGTAAAAAAAAATCCTTAAATCCAATGAGGTT
184 TTTTTAATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
* * *
54794 GAGATTTTGTTAAATGAATATAGATATTTTAAGGAA-CTTTTCTACCAAAAATCATGCAAAACTG
249 GAGATTTTGTTAGATGAATATAGATATTTCAAGGAATC-TTTCTACCAAAAATCATACAAAACTG
* *** *
54858 AGCC-GGTGCCCCGAAACGCGTTTTTAGCCAAAAAAAACCGTGAT-G-TAGTACATGATTACGGC
313 AGCCTAG-GCTTTGAAACGCGTTTTTAGCC---AAAAACCGTGATGGTTAGTACATGATTTCGGC
* * * * * * *
54920 TAAAAATTGACCCAAAAAATCTTTTTCCCGAATTTTTTGCCATAATACTTAGAAAAAATATATAA
374 TAAAAACTGACCCGAAAAGT-GTTTTCTC-AATTTTTTGCCACAATAC-T-CAAAAAATATATAA
* * * * * *
54985 TTCAACGGCAAAAAGATTAATGGGCTTTTCACGCTTCTAATATCGTTTTTCC-TTTTTTTCCGAA
435 TTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTACTAA-A-----ATTCCATTTTTTT-CAAA
* * *
55049 TTAATTTCTAATTAAATCGGAACAAGATTCAGATGCTTGTAAAAAACAAATCCATATATCCAAAG
493 TTTA-TT-TAATTAAATCGAAAAAAGATTCAGATGCTTGTAAAAAACAAATCCATATATCCAAAG
* * * * * *
55114 TGGCTGAAATTTGGTTCGATGAATATGGATATTTTAAGGAGTTTTTGCGCCAAAAATCATGCAAA
556 TGCCTGAAATTTGGTTCGATGAATATAGACATTTCAAGGACTTTTTGCGCAAAAAATCATGCAAA
*
55179 ACTGAGGCAGGGC
621 ACTGAGGCAGGGA
* * *
55192 CCCGAAACGCGTTTTTAGTCAAAAACCGTGATGATTAGTACATGAATTCGGCTAAAAATTGACCC
1 CCCGAAACGCGTTTTTAGCCAAAAACCGTGACGATTAGTACATGAATTCGGCTAAAAACTGACCC
* * * *
55257 AAAAAATATTTTTCTGAATTTTTTTGCCACAATACTCAAAAAAATATATAATCCAACGCAAAACA
66 GAAAAAT-TTTTTCTCAA-TTTTTTGCCACAATACTCAAAAAAATATATAATTCAACGCAAAAAA
* *
55322 AATTGAAAGGTTTTTCACGCGTCTAATATTGTTTTTCCATTTTTTTCCGAATTTATTTTTAATTA
129 AATTGAAAGGTTTTTCACGCATCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTTTAATTA
* *
55387 AATCGAAATAAGATTCGGATACTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTTGT
194 AATCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTGT
55452 TAGATGAATATAGATATTTCAAGGAATCTTTCTACCAAAAATCATACAAAACTGAGCCTAGGCTT
259 TAGATGAATATAGATATTTCAAGGAATCTTTCTACCAAAAATCATACAAAACTGAGCCTAGGCTT
55517 TGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGA
324 TGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGA
55582 AAAGTGTTTTCTCAA-TTTTTGCCACAATACTCAAAAAATATATAATTCAACGCCAAAAAGATTG
389 AAAGTGTTTTCTCAATTTTTTGCCACAATACTCAAAAAATATATAATTCAACGCCAAAAAGATTG
55646 ACGGGCTTTTCACGCTACTAAAATTCCATTTTTTTCAAATTTATTTAATTAAA
454 ACGGGCTTTTCACGCTACTAAAATTCCATTTTTTTCAAATTTATTTAATTAAA
55699 CTGACGCGCA
Statistics
Matches: 989, Mismatches: 133, Indels: 82
0.82 0.11 0.07
Matches are distributed among these distances:
632 1 0.00
633 31 0.03
634 14 0.01
635 2 0.00
636 10 0.01
637 7 0.01
641 4 0.00
642 265 0.27
643 74 0.07
644 32 0.03
645 27 0.03
646 72 0.07
647 42 0.04
648 172 0.17
649 61 0.06
651 7 0.01
652 10 0.01
653 2 0.00
654 28 0.03
655 5 0.01
656 121 0.12
657 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (633 bp):
CCCGAAACGCGTTTTTAGCCAAAAACCGTGACGATTAGTACATGAATTCGGCTAAAAACTGACCC
GAAAAATTTTTTCTCAATTTTTTGCCACAATACTCAAAAAAATATATAATTCAACGCAAAAAAAA
TTGAAAGGTTTTTCACGCATCTAATATCGTTTTTCCATTTTTTTCCGAATTTATTTTTAATTAAA
TCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTTGTTA
GATGAATATAGATATTTCAAGGAATCTTTCTACCAAAAATCATACAAAACTGAGCCTAGGCTTTG
AAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACATGATTTCGGCTAAAAACTGACCCGAAA
AGTGTTTTCTCAATTTTTTGCCACAATACTCAAAAAATATATAATTCAACGCCAAAAAGATTGAC
GGGCTTTTCACGCTACTAAAATTCCATTTTTTTCAAATTTATTTAATTAAATCGAAAAAAGATTC
AGATGCTTGTAAAAAACAAATCCATATATCCAAAGTGCCTGAAATTTGGTTCGATGAATATAGAC
ATTTCAAGGACTTTTTGCGCAAAAAATCATGCAAAACTGAGGCAGGGA
Done.