Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016639.1 Corchorus olitorius cultivar O-4 contig16672, 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: 61111
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2298 original size:48 final size:45
Alignment explanation
Indices: 2217--2332 Score: 126
Period size: 48 Copynumber: 2.5 Consensus size: 45
2207 TTTATAGTGT
* *
2217 GGTTATCAAAATTTCATAAGAAGGTAAACAAAATTTCATAGGGAGAGA
1 GGTTATCAAAATTTCATAGGGAGGTAAACAAAATTT--TAGGGAGA-A
* ** *
2265 GGTTATCAAAATTTCATAGGGAGGTTATGAAAATTTTATGGAGAA
1 GGTTATCAAAATTTCATAGGGAGGTAAACAAAATTTTAGGGAGAA
* *
2310 -GTTATCAAAATTACATAGAGAGG
1 GGTTATCAAAATTTCATAGGGAGG
2333 ATATCACAGT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
44 21 0.35
45 1 0.02
46 7 0.12
48 31 0.52
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.28
Consensus pattern (45 bp):
GGTTATCAAAATTTCATAGGGAGGTAAACAAAATTTTAGGGAGAA
Found at i:2319 original size:70 final size:70
Alignment explanation
Indices: 2194--2327 Score: 162
Period size: 70 Copynumber: 1.9 Consensus size: 70
2184 AATCATTCGA
* * * * *
2194 AGGTTATCGAAATTTTATAGTGTGGTTATCAAAATTTCATAAGAAGGTAAACAAAATTTCATAGG
1 AGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAAGAAGGTAAACAAAATTACATAGG
2259 GAGAG
66 GAGAG
* * * * *
2264 AGGTTATCAAAATTTCATAGGGAGGTTATGAAAATTTTATGGAGAA-GTTATCAAAATTACATAG
1 AGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCAT-AAGAAGGTAAACAAAATTACATAG
2328 AGAGGATATC
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
70 49 0.92
71 4 0.08
ACGTcount: A:0.40, C:0.07, G:0.21, T:0.32
Consensus pattern (70 bp):
AGGTTATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAAGAAGGTAAACAAAATTACATAGG
GAGAG
Found at i:2330 original size:22 final size:23
Alignment explanation
Indices: 2047--2347 Score: 151
Period size: 22 Copynumber: 13.5 Consensus size: 23
2037 AAGTTCAAAC
* *
2047 CAAAATTACATAG-GAAGGTCAT
1 CAAAATTTCATAGAGAAGGTTAT
* * * *
2069 TAAAATTTCATAG-TATGGTTAG
1 CAAAATTTCATAGAGAAGGTTAT
*
2091 CAAAGTTTCATATG-G-AGGTTAT
1 CAAAATTTCATA-GAGAAGGTTAT
* * *
2113 TAAAATTTCATACAG-AGGTTAC
1 CAAAATTTCATAGAGAAGGTTAT
* * *
2135 CAAAATTTCACATA-AAAGTTAT
1 CAAAATTTCATAGAGAAGGTTAT
* * * * *
2157 CGAAATTTCTTA-TGAATGTTAA
1 CAAAATTTCATAGAGAAGGTTAT
** **
2179 CAAAAAATCAT-TCGAAGGTTAT
1 CAAAATTTCATAGAGAAGGTTAT
* * * *
2201 CGAAATTTTATAGTG-TGGTTAT
1 CAAAATTTCATAGAGAAGGTTAT
* *
2223 CAAAATTTCATA-AGAAGGTAAA
1 CAAAATTTCATAGAGAAGGTTAT
2245 CAAAATTTCATAGGGAGAGAGGTTAT
1 CAAAATTTCATA--GAGA-AGGTTAT
*
2271 CAAAATTTCATAG-GGAGGTTAT
1 CAAAATTTCATAGAGAAGGTTAT
* * *
2293 GAAAATTTTATGGAGAA-GTTAT
1 CAAAATTTCATAGAGAAGGTTAT
* *
2315 CAAAATTACATAGAG-AGGATAT
1 CAAAATTTCATAGAGAAGGTTAT
* *
2337 CACAGTTTCAT
1 CAAAATTTCAT
2348 TCTCATAATT
Statistics
Matches: 205, Mismatches: 61, Indels: 26
0.70 0.21 0.09
Matches are distributed among these distances:
21 2 0.01
22 177 0.86
23 5 0.02
24 1 0.00
25 3 0.01
26 17 0.08
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.32
Consensus pattern (23 bp):
CAAAATTTCATAGAGAAGGTTAT
Found at i:2431 original size:20 final size:21
Alignment explanation
Indices: 2393--2445 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
2383 TGGTTATCAA
*
2393 AATTTTCATAGTGCGATTACC
1 AATTTTCATAGTGCAATTACC
* *
2414 AATTTT-ATAGTGTAATTATCA
1 AATTTTCATAGTGCAATTA-CC
*
2435 AAGTTTCATAG
1 AATTTTCATAG
2446 GAAGATCATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 10 0.38
21 12 0.46
22 4 0.15
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (21 bp):
AATTTTCATAGTGCAATTACC
Found at i:2445 original size:22 final size:22
Alignment explanation
Indices: 2364--2535 Score: 143
Period size: 22 Copynumber: 7.9 Consensus size: 22
2354 AATTAGGATG
* * *
2364 TTATCGAAATTTCATGGTGTGG
1 TTATCAAAATTTCATAGTGTGA
*
2386 TTATCAAAATTTTCATAGTGCGA
1 TTATCAAAA-TTTCATAGTGTGA
* * *
2409 TTA-C-CAATTTTATAGTGTAA
1 TTATCAAAATTTCATAGTGTGA
* *
2429 TTATCAAAGTTTCATAG-GAAGA
1 TTATCAAAATTTCATAGTG-TGA
* * * * *
2451 TCATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGTGTGA
2473 TTATCAAAATTTCATAGTGTGA
1 TTATCAAAATTTCATAGTGTGA
* * *
2495 TTATCAAAATTTCACAATGTGG
1 TTATCAAAATTTCATAGTGTGA
*
2517 TTATCAAATTTTCATAGTG
1 TTATCAAAATTTCATAGTG
2536 AAGTTAGCGA
Statistics
Matches: 116, Mismatches: 29, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
20 13 0.11
21 4 0.03
22 85 0.73
23 14 0.12
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGA
Found at i:2477 original size:44 final size:45
Alignment explanation
Indices: 2429--2566 Score: 156
Period size: 44 Copynumber: 3.1 Consensus size: 45
2419 TATAGTGTAA
* *
2429 TTATCAAAGTTTCATAG-GAAGATCATCAAAATTTCACACTGAGG
1 TTATCAAAATTTCATAGTGAAGATCATCAAAATTTCACAATGAGG
* * *
2473 TTATCAAAATTTCATAGTG-TGATTATCAAAATTTCACAATGTGG
1 TTATCAAAATTTCATAGTGAAGATCATCAAAATTTCACAATGAGG
* * * * * *
2517 TTATCAAATTTTCATAGTGAAG-TTAGCGAAATTTTATAATGAGG
1 TTATCAAAATTTCATAGTGAAGATCATCAAAATTTCACAATGAGG
2561 TTATCA
1 TTATCA
2567 GATTTTCACA
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 78 0.98
45 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (45 bp):
TTATCAAAATTTCATAGTGAAGATCATCAAAATTTCACAATGAGG
Found at i:2523 original size:66 final size:66
Alignment explanation
Indices: 2453--2595 Score: 151
Period size: 66 Copynumber: 2.2 Consensus size: 66
2443 TAGGAAGATC
* * * * *
2453 ATCAAAATTTCACACTGAGGTTATCAAAATTTCATAGTGTGATTATCAAAATTTCACAATGTGGT
1 ATCAAAATTTCACACTGAAGTTAGCAAAATTTCATAATGAGATTATCAAAATTTCACAATGTAGT
2518 T
66 T
* * * * * * * * *
2519 ATCAAATTTTCATAGTGAAGTTAGCGAAATTTTATAATGAGGTTATCAGATTTTCACAGTGTAGT
1 ATCAAAATTTCACACTGAAGTTAGCAAAATTTCATAATGAGATTATCAAAATTTCACAATGTAGT
2584 T
66 T
*
2585 ATCAATATTTC
1 ATCAAAATTTC
2596 TACGTTGGAG
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
66 61 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (66 bp):
ATCAAAATTTCACACTGAAGTTAGCAAAATTTCATAATGAGATTATCAAAATTTCACAATGTAGT
T
Found at i:2541 original size:22 final size:22
Alignment explanation
Indices: 2363--2594 Score: 120
Period size: 22 Copynumber: 10.5 Consensus size: 22
2353 TAATTAGGAT
* **
2363 GTTATCGAAA-TTTCATGGTGTG
1 GTTATC-AAATTTTCATAGTGAA
*
2385 GTTATCAAAATTTTCATAGTG-C
1 GTTATC-AAATTTTCATAGTGAA
*
2407 GATTA-CCAATTTT-ATAGTGTAA
1 G-TTATCAAATTTTCATAGTG-AA
*
2429 -TTATCAAAGTTTCATAG-GAA
1 GTTATCAAATTTTCATAGTGAA
* * * * *
2449 GATCATCAAAATTTCACACTGAG
1 G-TTATCAAATTTTCATAGTGAA
* *
2472 GTTATCAAAATTTCATAGTG-T
1 GTTATCAAATTTTCATAGTGAA
* * * **
2493 GATTATCAAAATTTCACAATGTG
1 G-TTATCAAATTTTCATAGTGAA
2516 GTTATCAAATTTTCATAGTGAA
1 GTTATCAAATTTTCATAGTGAA
* * *
2538 GTTAGCGAAATTTT-ATAATGAG
1 GTTATC-AAATTTTCATAGTGAA
* * *
2560 GTTATCAGATTTTCACAGTGTA
1 GTTATCAAATTTTCATAGTGAA
2582 GTTATCAATATTT
1 GTTATCAA-ATTT
2595 CTACGTTGGA
Statistics
Matches: 162, Mismatches: 34, Indels: 27
0.73 0.15 0.12
Matches are distributed among these distances:
20 11 0.07
21 20 0.12
22 104 0.64
23 27 0.17
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (22 bp):
GTTATCAAATTTTCATAGTGAA
Found at i:2572 original size:44 final size:43
Alignment explanation
Indices: 2429--2595 Score: 147
Period size: 44 Copynumber: 3.8 Consensus size: 43
2419 TATAGTGTAA
* * * *
2429 TTATCAAAGTTTCATAG-GAAGATCATCAAAATTTCACACTGAGG
1 TTATCAAATTTTCATAGTG-AG-TTAGCAAAATTTCACAATGAGG
* * * *
2473 TTATCAAAATTTCATAGTGTGATTATCAAAATTTCACAATGTGG
1 TTATCAAATTTTCATAGTGAG-TTAGCAAAATTTCACAATGAGG
* * *
2517 TTATCAAATTTTCATAGTGAAGTTAGCGAAATTTTATAATGAGG
1 TTATCAAATTTTCATAGTG-AGTTAGCAAAATTTCACAATGAGG
* * * *
2561 TTATCAGATTTTCACAGTGTAGTTATCAATATTTC
1 TTATCAAATTTTCATAGTG-AGTTAGCAAAATTTC
2596 TACGTTGGAG
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
44 100 0.98
45 2 0.02
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (43 bp):
TTATCAAATTTTCATAGTGAGTTAGCAAAATTTCACAATGAGG
Found at i:4864 original size:23 final size:23
Alignment explanation
Indices: 4838--4886 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
4828 AAGTGTTCAT
*
4838 AAAAATTACAAAGGATAGTTATC
1 AAAAATTACAAAAGATAGTTATC
* *
4861 AAAATTTACAAAAGATTGTTATC
1 AAAAATTACAAAAGATAGTTATC
4884 AAA
1 AAA
4887 GCCTCGTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.53, C:0.08, G:0.10, T:0.29
Consensus pattern (23 bp):
AAAAATTACAAAAGATAGTTATC
Found at i:5547 original size:21 final size:22
Alignment explanation
Indices: 5497--5552 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
5487 TTTCTTATGA
* *
5497 GGTTATCAAAATTATATTGGGT
1 GGTTATCAAAATTACATTGGAT
**
5519 CATTATCAAAATTACATT-GAT
1 GGTTATCAAAATTACATTGGAT
5540 GGTTATCAAAATT
1 GGTTATCAAAATT
5553 TATATAGGGC
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 13 0.46
22 15 0.54
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (22 bp):
GGTTATCAAAATTACATTGGAT
Found at i:5591 original size:21 final size:22
Alignment explanation
Indices: 5540--5791 Score: 96
Period size: 22 Copynumber: 11.7 Consensus size: 22
5530 TTACATTGAT
*
5540 GGTTATCAAAATTT-ATATAG-
1 GGTTATCAAAATTTCAAATAGA
***
5560 GGCCCTCAAAATTTC-AATCA-A
1 GGTTATCAAAATTTCAAAT-AGA
* *
5581 GGTTATCAAAATTACAAATAGT
1 GGTTATCAAAATTTCAAATAGA
* * *
5603 GGTTATCAAAATTTCGAATGGT
1 GGTTATCAAAATTTCAAATAGA
* *
5625 GGATT-TCAAATTTTCAAA-AAA
1 GG-TTATCAAAATTTCAAATAGA
* *
5646 TAGTTATCAAAATTTCATA-AGA
1 -GGTTATCAAAATTTCAAATAGA
* * *
5668 CGGCTGTCAAAATTTC-AATCGA
1 -GGTTATCAAAATTTCAAATAGA
* * * *
5690 AGTTATTAAAATTACAAAGA-A
1 GGTTATCAAAATTTCAAATAGA
* * * *
5711 TGGTTCTCATAA-TT-ATATAGGGC
1 -GGTTATCAAAATTTCAAATA--GA
* *
5734 GGTTGTCAAAA-TTCCAATAGA
1 GGTTATCAAAATTTCAAATAGA
* * *
5755 GGTTATCAAGATTACAAATAGT
1 GGTTATCAAAATTTCAAATAGA
5777 GGTTATCAAAATTTC
1 GGTTATCAAAATTTC
5792 GAATGGTGAT
Statistics
Matches: 162, Mismatches: 54, Indels: 30
0.66 0.22 0.12
Matches are distributed among these distances:
20 16 0.10
21 38 0.23
22 103 0.64
23 5 0.03
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (22 bp):
GGTTATCAAAATTTCAAATAGA
Found at i:19862 original size:24 final size:24
Alignment explanation
Indices: 19830--19879 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
19820 AATTCCTTCT
19830 CTACCTTGGCATGTCCTATAGAAA
1 CTACCTTGGCATGTCCTATAGAAA
19854 CTACCTTGGCATGTCCTATAGAAA
1 CTACCTTGGCATGTCCTATAGAAA
19878 CT
1 CT
19880 TAAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (24 bp):
CTACCTTGGCATGTCCTATAGAAA
Found at i:32192 original size:2 final size:2
Alignment explanation
Indices: 32185--32228 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
32175 CCTGATGACA
32185 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
1 GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT GT
32227 GT
1 GT
32229 TTCTTTTCCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
GT
Found at i:51057 original size:26 final size:26
Alignment explanation
Indices: 51004--51060 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
50994 TGAATAAATG
* *
51004 TAAAATTACAGTCAAATCATCAATTA
1 TAAAATTACAGTCAAACCATCAACTA
* *
51030 TAAAATTACAGTCAAACCCTTAACTA
1 TAAAATTACAGTCAAACCATCAACTA
51056 TAAAA
1 TAAAA
51061 CAAACTCAGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.51, C:0.18, G:0.04, T:0.28
Consensus pattern (26 bp):
TAAAATTACAGTCAAACCATCAACTA
Found at i:55856 original size:150 final size:150
Alignment explanation
Indices: 55585--55881 Score: 585
Period size: 150 Copynumber: 2.0 Consensus size: 150
55575 GCGTCCCGGG
55585 AGTTAAAACCTGATGCCTATGTTGGCATTTTAAAAGATACAAAAGGTATTCATTTGTTAATGGTT
1 AGTTAAAACCTGATGCCTATGTTGGCATTTTAAAAGATACAAAAGGTATTCATTTGTTAATGGTT
55650 TTTGCTTGTAAGTTATTATCAGTGTAGTTGCCTTTCTAACTGTTTTACATCATACTCCATGCATA
66 TTTGCTTGTAAGTTATTATCAGTGTAGTTGCCTTTCTAACTGTTTTACATCATACTCCATGCATA
55715 AGCTTGTAAGATTCATTGTA
131 AGCTTGTAAGATTCATTGTA
55735 AGTTAAAACCTGATGCCTATGTTGGCATTTTAAAAGATACAAAAGGTATTCATTTGTTAATGGTT
1 AGTTAAAACCTGATGCCTATGTTGGCATTTTAAAAGATACAAAAGGTATTCATTTGTTAATGGTT
*
55800 TTTGCTTGTAAGTTATTATCAGTGTAGTTGCCTTTCTAACTGTTTTACATCGTACTCCATGCATA
66 TTTGCTTGTAAGTTATTATCAGTGTAGTTGCCTTTCTAACTGTTTTACATCATACTCCATGCATA
55865 AGCTTGTAAGATTCATT
131 AGCTTGTAAGATTCATT
55882 TTAATGTTTA
Statistics
Matches: 146, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 146 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (150 bp):
AGTTAAAACCTGATGCCTATGTTGGCATTTTAAAAGATACAAAAGGTATTCATTTGTTAATGGTT
TTTGCTTGTAAGTTATTATCAGTGTAGTTGCCTTTCTAACTGTTTTACATCATACTCCATGCATA
AGCTTGTAAGATTCATTGTA
Found at i:59728 original size:16 final size:16
Alignment explanation
Indices: 59707--59737 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
59697 TCAAGTTGTA
*
59707 TAGTAATCTTATTAAT
1 TAGTAACCTTATTAAT
59723 TAGTAACCTTATTAA
1 TAGTAACCTTATTAA
59738 CTGAGGTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (16 bp):
TAGTAACCTTATTAAT
Found at i:60474 original size:202 final size:202
Alignment explanation
Indices: 59746--61111 Score: 1885
Period size: 199 Copynumber: 6.8 Consensus size: 202
59736 AACTGAGGTT
* * *
59746 TTTCATAATTAATT-AA-ATATTAAATATTAACACATATTCCCTAAGGCGACACATGTCAACCCT
1 TTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCT
* ** ** * *
59809 TACACATCGTCTTGTGCAGTCTGCTAAACTCTACTGAC-GTTGTATTCTATAATTTTTCTTATA-
66 TAAACCCCG-CACGTGCAGTCTGCTAAACTCCACTGACTG-TGTATTGTATAATTTTTCTTATAG
* * * * *
59872 TGATTATTATACAATACATTGTAAGTGTAAATTTTGAACTCCATAAACGGGTTAA-AAGGTTGAC
129 GGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAA-GTTGAC
59936 ACATA-CCCA
193 ACATACCCCA
* * *
59945 TTTCATAATTAATT-AA-ATATTTAATATTAATACATATTCCCTAAGGAGACATATGCCAACCCT
1 TTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCT
* * *
60008 TAAACCCCACACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATAATTTTTCTTATAGGG
66 TAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTTCTTATAGGG
* * * *
60073 ATTATTATGCAATACAATGTCAGTGTAAATTTTGGACTCCATAAGTGGGTTAAGAGGTTGACACA
131 ATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACA
60138 TA-CCCA
196 TACCCCA
60144 TTTCATAATTAATTAAATATTTAATATTTAATATTAATTAAGACATATTCCCTAAGGGGACACAT
1 TTTCATAATTAATT-AA-A--T-ATATTTAATATTAA-T---ACATATTCCCTAAGGGGACACAT
* * * ** *
60209 GTCAACCCATAAACCCCACACGTGCAGTCTGCTAAGA-TCCACTAAGGGTATATTGTATAATTTT
57 GTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAA-ACTCCACTGACTGTGTATTGTATAATTTT
* *
60273 TCTTATAGGGATTATTATACAATACACTGTCGGTGTAAATTTTGGACTCTATAAGCGGGTT-AGA
121 TCTTATAGGGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAG-
* *
60337 AAGTCGCCACATACCCCA
185 AAGTTGACACATACCCCA
* * *
60355 TTTAATAATTAATTAAATATATTTAATATCAATACATATTCCCTAAGGGGACACATGTTAACCCT
1 TTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCT
* *
60420 TAAACCCCGCACATGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTTCTTATA-GT
66 TAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTTCTTATAGGG
*
60484 AATATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACA
131 ATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACA
60549 TACCCCA
196 TACCCCA
* * *
60556 TTTCATAATCAATT-CA-ATATTTAATATTAATACATATTCCCTAATGGGACACATGTCAACCCT
1 TTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCT
* * *
60619 TAAACCCCACACGTGCATTCTGCTAAACTCCACT-AATGGTGTATTGTATAA-TTTTCTTATAGG
66 TAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACT-GTGTATTGTATAATTTTTCTTATAGG
* ** *
60682 GATTATTATACAATACACTGTCAGTGTAAAATTTGGACTCCATAAGTTGGTTAAGAAATTGACAC
130 GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACAC
60747 ATACCCCA
195 ATACCCCA
* * * *
60755 TTTCATAATAAATTAGATATATTTAATATTGATACATATTCCCTAATGGGACACATGTCAACCCT
1 TTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCT
* * *
60820 TAAACCTCGCACGTGCAGTCTGCTAAACTCCACTAACTGTGTATTGTGTAATTTTTCTTATAGGG
66 TAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTTCTTATAGGG
*
60885 ATTATTATACAATACACTGTCACTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACA
131 ATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACA
60950 TACCCCA
196 TACCCCA
* *
60957 TTTCATAATTAATTAAATACATTTAATATTAATA-AGTATTCCCTAAGGGAACACATGTCAACCC
1 TTTCATAATTAATTAAATATATTTAATATTAATACA-TATTCCCTAAGGGGACACATGTCAACCC
61021 TTAAACCCCGCACGTGCAGTCTGCTAAACT-C-C--ACTGTGTATTGTATAATTTTTCTTATA-G
65 TTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTTCTTATAGG
61081 GATTATTATACAATACACTGTCAGTGTAAAT
130 GATTATTATACAATACACTGTCAGTGTAAAT
Statistics
Matches: 1050, Mismatches: 91, Indels: 54
0.88 0.08 0.05
Matches are distributed among these distances:
197 31 0.03
198 85 0.08
199 310 0.30
200 4 0.00
201 170 0.16
202 254 0.24
205 1 0.00
206 27 0.03
207 2 0.00
209 3 0.00
210 145 0.14
211 18 0.02
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (202 bp):
TTTCATAATTAATTAAATATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCT
TAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTTCTTATAGGG
ATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAAGTTGACACA
TACCCCA
Found at i:61001 original size:602 final size:605
Alignment explanation
Indices: 59746--61111 Score: 2003
Period size: 602 Copynumber: 2.3 Consensus size: 605
59736 AACTGAGGTT
* * *
59746 TTTCATAATTAATTAAAT-ATTAAATATTAACACATATTCCCTAAGGCGACACATGTCAACCCTT
1 TTTCATAATTAATTAAATAATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTT
* ** ** * *
59810 ACACATCGTCTTGTGCAGTCTGCTAAACTCTACTGAC-GTTGTATTCTATAATTTTTCTTATA-T
66 AAACCCCG-CACGTGCAGTCTGCTAAACTCCACTGACTG-TGTATTGTATAATTTTTCTTATAGT
* *
59873 GATTATTATACAATACATTGTAAGTGTAAATTTTGAACTCCATAAACGGGTTAAAAGGTTGACAC
129 -ATTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAACGGGTTAAAAGGTTGACAC
* *
59938 ATACCCATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGAGACATATGCCA
193 ATACCCATTTCATAATCAATTAAATATTTAATATTAATACATATTCCCTAAGGAGACACATGCCA
*
60003 ACCCTTAAACCCCACACGTGCAGTCTGCTAAACTCCACTGACGGTGTATTATATAATTTTTCTTA
258 ACCCTTAAACCCCACACGTGCAGTCTGCTAAACTCCACTAACGGTGTATTATATAATTTTTCTTA
* * **
60068 TAGGGATTATTATGCAATACAATGTCAGTGTAAATTTTGGACTCCATAAGTGGGTTAAGAGGTTG
323 TAGGGATTATTATACAATACAATGTCAGTGTAAAATTTGGACTCCATAAGTGGGTTAAGAAATTG
* *
60133 ACACATACCCATTTCATAATTAATTAAATATTTAATATTTAATATTAATTAAGACATATTCCCTA
388 ACACATACCCATTTCATAATAAATT-AAGA-TTAATATTTAATATTAATT-A-ACATATTCCCTA
*
60198 AGGGGACACATGTCAACCCATAAACCCCACACGTGCAGTCTGCTAAGATCCACTAAGGGTATATT
449 AGGGGACACATGTCAACCCATAAACCCCACACGTGCAGTCTGCTAAGATCCACTAACGGTATATT
** *
60263 GTATAATTTTTCTTATAGGGATTATTATACAATACACTGTCGGTGTAAATTTTGGACTCTATAAG
514 GTATAATTTTTCTTATAGGGATTATTATACAATACACTGTCACTGTAAATTTTGGACTCCATAAG
*
60328 CGGGTTAGAAAGTCGCCACATACCCCA
579 CGGGTTAGAAAGTCGACACATACCCCA
* * *
60355 TTTAATAATTAATTAAATATATTTAATATCAATACATATTCCCTAAGGGGACACATGTTAACCCT
1 TTTCATAATTAATTAAATA-ATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCT
*
60420 TAAACCCCGCACATGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTTCTTATAGTA
65 TAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTTCTTATAGTA
* * *
60485 ATATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAGCGGGTTAAGAA-GTTGACACA
130 TTATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAACGGGTTAA-AAGGTTGACACA
* *
60549 TACCCCATTTCATAATCAATTCAATATTTAATATTAATACATATTCCCTAATGG-GACACATGTC
194 TA-CCCATTTCATAATCAATTAAATATTTAATATTAATACATATTCCCTAA-GGAGACACATGCC
* * *
60613 AACCCTTAAACCCCACACGTGCATTCTGCTAAACTCCACTAATGGTGTATTGTATAA-TTTTCTT
257 AACCCTTAAACCCCACACGTGCAGTCTGCTAAACTCCACTAACGGTGTATTATATAATTTTTCTT
* *
60677 ATAGGGATTATTATACAATACACTGTCAGTGTAAAATTTGGACTCCATAAGTTGGTTAAGAAATT
322 ATAGGGATTATTATACAATACAATGTCAGTGTAAAATTTGGACTCCATAAGTGGGTTAAGAAATT
* *
60742 GACACATACCCCATTTCATAATAAATT-AGA-T-ATATTTAATATTGA-T-ACATATTCCCTAAT
387 GACACATA-CCCATTTCATAATAAATTAAGATTAATATTTAATATTAATTAACATATTCCCTAAG
* * * * *
60802 GGGACACATGTCAACCCTTAAACCTCGCACGTGCAGTCTGCTAA-ACTCCACTAACTGTGTATTG
451 GGGACACATGTCAACCCATAAACCCCACACGTGCAGTCTGCTAAGA-TCCACTAACGGTATATTG
*
60866 TGTAATTTTTCTTATAGGGATTATTATACAATACACTGTCACTGTAAATTTTGGACTCCATAAGC
515 TATAATTTTTCTTATAGGGATTATTATACAATACACTGTCACTGTAAATTTTGGACTCCATAAGC
*
60931 GGGTTA-AGAAGTTGACACATACCCCA
580 GGGTTAGA-AAGTCGACACATACCCCA
*
60957 TTTCATAATTAATTAAATACATTTAATATTAATA-AGTATTCCCTAAGGGAACACATGTCAACCC
1 TTTCATAATTAATTAAATA-ATTTAATATTAATACA-TATTCCCTAAGGGGACACATGTCAACCC
*
61021 TTAAACCCCGCACGTGCAGTCTGCTAAACT-C-C--ACTGTGTATTGTATAATTTTTCTTATAGG
64 TTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTTCTTATAGT
61082 ATTATTATACAATACACTGTCAGTGTAAAT
129 ATTATTATACAATACACTGTCAGTGTAAAT
Statistics
Matches: 689, Mismatches: 57, Indels: 33
0.88 0.07 0.04
Matches are distributed among these distances:
598 57 0.08
600 1 0.00
601 4 0.01
602 238 0.35
605 1 0.00
606 13 0.02
607 1 0.00
609 19 0.03
610 179 0.26
611 174 0.25
612 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (605 bp):
TTTCATAATTAATTAAATAATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAACCCTT
AAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACTGTGTATTGTATAATTTTTCTTATAGTAT
TATTATACAATACACTGTCAGTGTAAATTTTGAACTCCATAAACGGGTTAAAAGGTTGACACATA
CCCATTTCATAATCAATTAAATATTTAATATTAATACATATTCCCTAAGGAGACACATGCCAACC
CTTAAACCCCACACGTGCAGTCTGCTAAACTCCACTAACGGTGTATTATATAATTTTTCTTATAG
GGATTATTATACAATACAATGTCAGTGTAAAATTTGGACTCCATAAGTGGGTTAAGAAATTGACA
CATACCCATTTCATAATAAATTAAGATTAATATTTAATATTAATTAACATATTCCCTAAGGGGAC
ACATGTCAACCCATAAACCCCACACGTGCAGTCTGCTAAGATCCACTAACGGTATATTGTATAAT
TTTTCTTATAGGGATTATTATACAATACACTGTCACTGTAAATTTTGGACTCCATAAGCGGGTTA
GAAAGTCGACACATACCCCA
Done.