Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009408.1 Corchorus capsularis cultivar CVL-1 contig09429, 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: 56676
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:476 original size:15 final size:15
Alignment explanation
Indices: 456--486 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
446 AATTTCATCG
456 ACGATGTTGACAAGA
1 ACGATGTTGACAAGA
471 ACGATGTTGACAAGA
1 ACGATGTTGACAAGA
486 A
1 A
487 ACAAGTCACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (15 bp):
ACGATGTTGACAAGA
Found at i:1388 original size:71 final size:71
Alignment explanation
Indices: 1300--1431 Score: 194
Period size: 71 Copynumber: 1.9 Consensus size: 71
1290 ACGTTGCAAT
* * * *
1300 GTGGCTTAATGTATTCTGTTTTATTCTGT-TTTTTCAGCTTATAATTTCATCTTTTTATATGTGC
1 GTGGCTTAATCTATTCTGTTTCATTCT-TATTTTGCAGCTTATAATTTCATATTTTTATATGTGC
1364 CAATGGG
65 CAATGGG
* *
1371 GTGGCTTAATCTGTTCTGTTTCGTTCTTATTTTGCAGCTTATAATTTCATATTTTTATATG
1 GTGGCTTAATCTATTCTGTTTCATTCTTATTTTGCAGCTTATAATTTCATATTTTTATATG
1432 AACTATGAAT
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
70 1 0.02
71 53 0.98
ACGTcount: A:0.18, C:0.13, G:0.16, T:0.53
Consensus pattern (71 bp):
GTGGCTTAATCTATTCTGTTTCATTCTTATTTTGCAGCTTATAATTTCATATTTTTATATGTGCC
AATGGG
Found at i:1513 original size:87 final size:88
Alignment explanation
Indices: 1371--1566 Score: 297
Period size: 87 Copynumber: 2.2 Consensus size: 88
1361 TGCCAATGGG
* * *
1371 GTGGCTTAATCTGTTCTG-TTTCGTTCTTATTTTGCAGCTTATAATTTCATATTTTTATATGAAC
1 GTGGCTTAATGTGTTCTGTTTTCGTTATGATTTTGCAGCTTATAATTTCATATTTTTATATGAAC
* *
1435 TATGAATGAAATAATGTGCCAAT
66 TATCAATGAAAGAATGTGCCAAT
* * *
1458 GTGGCTTAATGTGTTATGTTTTTGTTATGATTTTGCAGCTTATAATTTC-TCTTTTTATATGAAC
1 GTGGCTTAATGTGTTCTGTTTTCGTTATGATTTTGCAGCTTATAATTTCATATTTTTATATGAAC
*
1522 TATCAATGACAGAATGTGCCAAT
66 TATCAATGAAAGAATGTGCCAAT
1545 GTGGCTTAATGTGTTCTGTTTT
1 GTGGCTTAATGTGTTCTGTTTT
1567 GTTCTGGTTT
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
87 71 0.72
88 27 0.28
ACGTcount: A:0.24, C:0.12, G:0.17, T:0.47
Consensus pattern (88 bp):
GTGGCTTAATGTGTTCTGTTTTCGTTATGATTTTGCAGCTTATAATTTCATATTTTTATATGAAC
TATCAATGAAAGAATGTGCCAAT
Found at i:18648 original size:74 final size:74
Alignment explanation
Indices: 18511--18670 Score: 254
Period size: 74 Copynumber: 2.2 Consensus size: 74
18501 TTCCTCTAAA
18511 TGTATGAATTTTGGGTGAAAAAGTATGTGAATTTTGAGTCAAGAGTAATGAGAAAATAGATTTTG
1 TGTATGAATTTTGGGTG-AAAAGTATGTGAATTTTGAGTCAAGAGTAATGAGAAAATAGATTTTG
18576 GGTGAAAGTT
65 GGTGAAAGTT
* * *
18586 TGTATGGATTTTGGGTG-AAAGTATGTGAATTTTGAGTCTATGAGTAATGAGAATATAGATTTTG
1 TGTATGAATTTTGGGTGAAAAGTATGTGAATTTTGAGTC-AAGAGTAATGAGAAAATAGATTTTG
18650 GGTGAAAGTT
65 GGTGAAAGTT
18660 TG--TGAATTTTG
1 TGTATGAATTTTG
18671 AGGGTCTGAA
Statistics
Matches: 80, Mismatches: 4, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
72 8 0.10
73 21 0.26
74 35 0.44
75 16 0.20
ACGTcount: A:0.32, C:0.01, G:0.29, T:0.38
Consensus pattern (74 bp):
TGTATGAATTTTGGGTGAAAAGTATGTGAATTTTGAGTCAAGAGTAATGAGAAAATAGATTTTGG
GTGAAAGTT
Found at i:19035 original size:74 final size:74
Alignment explanation
Indices: 18914--19060 Score: 276
Period size: 74 Copynumber: 2.0 Consensus size: 74
18904 TTTGTTCTTG
18914 TTGAAAAACCATGAATTTTATCTAAAAATAAGCCCTATTTAAAGAGTTTGAGCAAGTGTTTGTTG
1 TTGAAAAACCATGAATTTTATCTAAAAATAAGCCCTATTTAAAGAGTTTGAGCAAGTGTTTGTTG
18979 ATAATGTCC
66 ATAATGTCC
* *
18988 TTGAAAAACCATGAATTTTCTCTAAAAATAAGCCCTGTTTAAAGAGTTTGAGCAAGTGTTTGTTG
1 TTGAAAAACCATGAATTTTATCTAAAAATAAGCCCTATTTAAAGAGTTTGAGCAAGTGTTTGTTG
19053 ATAATGTC
66 ATAATGTC
19061 TGCTTGCAAG
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 71 1.00
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (74 bp):
TTGAAAAACCATGAATTTTATCTAAAAATAAGCCCTATTTAAAGAGTTTGAGCAAGTGTTTGTTG
ATAATGTCC
Found at i:19419 original size:20 final size:20
Alignment explanation
Indices: 19396--19458 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
19386 GATTTTGTAC
19396 GTGAAATATTGATGATCTAT
1 GTGAAATATTGATGATCTAT
* * * *
19416 GTGAAGTGACT-AT-ATGT-G
1 GTGAAAT-ATTGATGATCTAT
19434 GTGAAATATTGATGATCTAT
1 GTGAAATATTGATGATCTAT
19454 GTGAA
1 GTGAA
19459 GTGACATGCT
Statistics
Matches: 31, Mismatches: 8, Indels: 8
0.66 0.17 0.17
Matches are distributed among these distances:
17 2 0.06
18 8 0.26
19 6 0.19
20 13 0.42
21 2 0.06
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (20 bp):
GTGAAATATTGATGATCTAT
Found at i:19911 original size:30 final size:30
Alignment explanation
Indices: 19877--19937 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
19867 AGTAGATGAA
*
19877 AACTTAATGAGATTGGTATGAGTCTAAAAT
1 AACTTAATGAGATTGGTAAGAGTCTAAAAT
19907 AACTTAATGAGATTGGTAAGAGTCTAAAAT
1 AACTTAATGAGATTGGTAAGAGTCTAAAAT
19937 A
1 A
19938 GATCTTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.31
Consensus pattern (30 bp):
AACTTAATGAGATTGGTAAGAGTCTAAAAT
Found at i:23589 original size:329 final size:324
Alignment explanation
Indices: 22827--23722 Score: 762
Period size: 329 Copynumber: 2.7 Consensus size: 324
22817 ACGATTTTGT
* * *** * *
22827 CTAAAATTTTGCTAAAACTGACAGGAAA-ATTTTTCCT-AACTTTTTGGCCACAATACTCGTAGA
1 CTAAAATTTTGCAAAAACTAACCCAAAATATTTTTCCTCAA-TTTTTGACCACAATACTCGTAAA
* * * *
22890 AAATATATAATTCAATGACAAAAATATTGAAGGTCTTTTCACGCTTCTAATATAGTTTTTCCTAT
65 AAATATATAATTCAA-CACAAAAACA-T-AGGGT-TTTTCATGCTTCTAATATAGTTTTTCCTAT
* * * *
22955 TTTTCCGAATTAATTTGTAATAAAATCGAAACAA-GATTCTGATCCTCGTAAAAACAAAT-TCTT
126 TTTTCCGAATTAATTTCTAATTAAATCGAAA-AAGGTTTCTGATACTCGTAAAAACAAATCT-TT
* * * * * *
23018 AAATCCAATGTGAATGAGATTTGGTTAGGTGGATATAGAA-ATTTTAAGGAGTCCTAGTGCAAAA
189 AAATCCAATGTGAATGAGATTTGATTAGATGAATATA-AATATTTAAAGGAATCCTAGGGCAAAA
** * * * * * *
23082 AGTATTCAAAATTGAACCGGACTTTGGAACGCGTTTTTAGCTCAAAACCGTGATGGAAAGTACAT
253 AGTATTCAAAACAGAACCGGACTTCGGAACACATTTTTAGCTCAAAACCATAATGGAAAG-ACAC
23147 GATGTCGA
317 GATGTCGA
* * * *
23155 CTAAAATTTTGCAAAAATTGACCCAAAATATTTTTCCTCAGTTTTTGACCACAATACTCATAAAA
1 CTAAAATTTTGCAAAAACTAACCCAAAATATTTTTCCTCAATTTTTGACCACAATACTCGTAAAA
* * * * * *
23220 AGTATATGATTCATCGTA-AAAAAGATTGAAGGGCTTTTCATGCTTCTAATATTGTTTTTCCTAT
66 AATATATAATTCAAC--ACAAAAACA-T--AGGGTTTTTCATGCTTCTAATATAGTTTTTCCTAT
**
23284 TTTTCCGAATTAATTTCTAATTAAATCGAAATTGGTTTCTGATACTCGTAAAAACAAATCTTTAA
126 TTTTCCGAATTAATTTCTAATTAAATCGAAAAAGGTTTCTGATACTCGTAAAAACAAATCTTTAA
* * * * *
23349 ATCCAATGTGACTGAGATTAGATTAGATGAAAATAAATATTTAAAGGAATCTTGGCGGCAAAAA-
191 ATCCAATGTGAATGAGATTTGATTAGATGAATATAAATATTTAAAGGAATCCTAG-GGCAAAAAG
* * * *
23413 TCATTCAAAACAGAGCTGG-GTCTCGGAACACATTTTTAGC-CAAAAAAACCATAATGGTTTAA-
255 T-ATTCAAAACAGAACCGGACT-TCGGAACACATTTTTAGCTC---AAAACCATAATGG--AAAG
*
23475 ACACGATTTC-A
313 ACACGATGTCGA
* * *
23486 GTCAAAATTTTGCAAAAACTAAGCCAGAAA-A-TTTTCTGTCAATTTTTGACCACAATACTCGTA
1 CT-AAAATTTTGCAAAAACTAACCCA-AAATATTTTTC-CTCAATTTTTGACCACAATACTCGTA
* * *
23549 AAAAATATATAATTCAACACCAAAAACATCGGGTTTTTCATGCTTCTAACATCA-ATTTTCCTTT
63 AAAAATATATAATTCAACA-CAAAAACATAGGGTTTTTCATGCTTCTAATAT-AGTTTTTCC---
* * * * * * * * *
23613 TTTTTTTTCGAATTAATTTTTAA-TAAATTCTAAACACGATTTC-AATGCTCGTAAAAACAGATC
123 TATTTTTCCGAATTAATTTCTAATTAAA-TCGAAA-AAGGTTTCTGATACTCGTAAAAACAAATC
* ** *
23676 ATTAAATCCAATGTGGTTGAGATTTGATTATATGAATATAAATATTT
186 TTTAAATCCAATGTGAATGAGATTTGATTAGATGAATATAAATATTT
23723 TAAAAAAGTA
Statistics
Matches: 460, Mismatches: 81, Indels: 50
0.78 0.14 0.08
Matches are distributed among these distances:
328 25 0.05
329 204 0.44
330 42 0.09
331 12 0.03
332 167 0.36
333 8 0.02
334 2 0.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.34
Consensus pattern (324 bp):
CTAAAATTTTGCAAAAACTAACCCAAAATATTTTTCCTCAATTTTTGACCACAATACTCGTAAAA
AATATATAATTCAACACAAAAACATAGGGTTTTTCATGCTTCTAATATAGTTTTTCCTATTTTTC
CGAATTAATTTCTAATTAAATCGAAAAAGGTTTCTGATACTCGTAAAAACAAATCTTTAAATCCA
ATGTGAATGAGATTTGATTAGATGAATATAAATATTTAAAGGAATCCTAGGGCAAAAAGTATTCA
AAACAGAACCGGACTTCGGAACACATTTTTAGCTCAAAACCATAATGGAAAGACACGATGTCGA
Found at i:24564 original size:12 final size:13
Alignment explanation
Indices: 24540--24564 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
24530 TCTAATATCG
24540 TTTTCCTATTTTT
1 TTTTCCTATTTTT
24553 TTTTCCTATTTT
1 TTTTCCTATTTT
24565 GCAAATGGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTCCTATTTTT
Found at i:29147 original size:32 final size:32
Alignment explanation
Indices: 29111--29266 Score: 93
Period size: 32 Copynumber: 4.8 Consensus size: 32
29101 CCACAACATG
29111 GTGGCGTTTGTCTTACAAAAGGCCACAATTTT
1 GTGGCGTTTGTCTTACAAAAGGCCACAATTTT
* * * *** * * *
29143 GTGGCGTTTTTATTATAAATA-AAAACCATATC
1 GTGGCGTTTGTCTTACAAA-AGGCCACAATTTT
*
29175 GTGGCGTTTAT-TTGACAAAAGCGCCACAATTTT
1 GTGGCGTTTGTCTT-ACAAAAG-GCCACAATTTT
** * * *
29208 GTGGCACTTGTCTGACAAAAACGCCACCATTTT
1 GTGGCGTTTGTCTTAC-AAAAGGCCACAATTTT
*
29241 GTGGCGTTT-TTTTGACAAAAGCGCCA
1 GTGGCGTTTGTCTT-ACAAAAG-GCCA
29267 TAGATTTAAT
Statistics
Matches: 88, Mismatches: 28, Indels: 15
0.67 0.21 0.11
Matches are distributed among these distances:
31 3 0.03
32 41 0.47
33 39 0.44
34 5 0.06
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (32 bp):
GTGGCGTTTGTCTTACAAAAGGCCACAATTTT
Found at i:29224 original size:33 final size:33
Alignment explanation
Indices: 29187--29266 Score: 106
Period size: 33 Copynumber: 2.4 Consensus size: 33
29177 GGCGTTTATT
29187 TGACAAAAGCGCCACAATTTTGTGGCACTTGTC
1 TGACAAAAGCGCCACAATTTTGTGGCACTTGTC
* * ** * *
29220 TGACAAAAACGCCACCATTTTGTGGCGTTTTTT
1 TGACAAAAGCGCCACAATTTTGTGGCACTTGTC
29253 TGACAAAAGCGCCA
1 TGACAAAAGCGCCA
29267 TAGATTTAAT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.28
Consensus pattern (33 bp):
TGACAAAAGCGCCACAATTTTGTGGCACTTGTC
Found at i:29369 original size:33 final size:33
Alignment explanation
Indices: 29332--29394 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
29322 CTAACGATGA
** *
29332 AAAAGCGCCGTAAATATTGGTGGCGATTTTAAG
1 AAAAGCGCCACAAATATTGGCGGCGATTTTAAG
*
29365 AAAAGCGCCACAAATATTGGCGGCGTTTTT
1 AAAAGCGCCACAAATATTGGCGGCGATTTT
29395 CTGAATAACG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (33 bp):
AAAAGCGCCACAAATATTGGCGGCGATTTTAAG
Found at i:29989 original size:33 final size:33
Alignment explanation
Indices: 29946--30011 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
29936 ATTACCTACA
*
29946 ATTTTCAAACAAAGGAGAAATCAAAACTAGTAG
1 ATTTTAAAACAAAGGAGAAATCAAAACTAGTAG
29979 ATTTTAAAACAAAGGAGAAATCAAAACTAGTAG
1 ATTTTAAAACAAAGGAGAAATCAAAACTAGTAG
30012 TAATAGAGCC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.53, C:0.11, G:0.15, T:0.21
Consensus pattern (33 bp):
ATTTTAAAACAAAGGAGAAATCAAAACTAGTAG
Found at i:30923 original size:21 final size:21
Alignment explanation
Indices: 30897--30938 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
30887 TGTTTAGCGC
*
30897 CAAATTAACAGTAAATAATTA
1 CAAATTAACAATAAATAATTA
*
30918 CAAATTAATAATAAATAATTA
1 CAAATTAACAATAAATAATTA
30939 TATATGAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.31
Consensus pattern (21 bp):
CAAATTAACAATAAATAATTA
Found at i:31892 original size:93 final size:93
Alignment explanation
Indices: 31762--31931 Score: 268
Period size: 93 Copynumber: 1.8 Consensus size: 93
31752 AATATAGAAT
* **
31762 TTTTGACAAGTTAATCAATTGAGGGTGAACATTTAGGACCAAATAAGGGTGGGTACCATGTAAAA
1 TTTTGACAAGTTAATCAATTGAGGGTGAACATCTAGGACCAAATAAGGGTGGACACCATGTAAAA
31827 TTACATACAAAATAATAAGAAATGGACA
66 TTACATACAAAATAATAAGAAATGGACA
* * * *
31855 TTTTGACGAGTTAATTAATTGAGGGTGGACATCTAGGACCATATAAGGGTGGACACCATGTAAAA
1 TTTTGACAAGTTAATCAATTGAGGGTGAACATCTAGGACCAAATAAGGGTGGACACCATGTAAAA
*
31920 TTACATAGAAAA
66 TTACATACAAAA
31932 CGTTAAGAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (93 bp):
TTTTGACAAGTTAATCAATTGAGGGTGAACATCTAGGACCAAATAAGGGTGGACACCATGTAAAA
TTACATACAAAATAATAAGAAATGGACA
Found at i:35591 original size:29 final size:29
Alignment explanation
Indices: 35515--35623 Score: 110
Period size: 29 Copynumber: 3.7 Consensus size: 29
35505 ACTAATCAAC
* ** *
35515 CATTTTGCCCCCTGAACTTGTAGCGTTTAGA
1 CATTTTGCCCCCTGAACTT-CA-ATTTTGGA
* *
35546 CGTTTTGCCCCCCGAACTTCAATTTTGGA
1 CATTTTGCCCCCTGAACTTCAATTTTGGA
*
35575 CATTTTGCCCCCTGAACTACAATTTTGGGA
1 CATTTTGCCCCCTGAACTTCAATTTT-GGA
* *
35605 CGTTTTGCCCCCTCAACTT
1 CATTTTGCCCCCTGAACTT
35624 AACAGCCCCG
Statistics
Matches: 65, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
29 28 0.43
30 20 0.31
31 17 0.26
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (29 bp):
CATTTTGCCCCCTGAACTTCAATTTTGGA
Found at i:35613 original size:30 final size:29
Alignment explanation
Indices: 35544--35622 Score: 113
Period size: 29 Copynumber: 2.7 Consensus size: 29
35534 GTAGCGTTTA
* *
35544 GACGTTTTGCCCCCCGAACTTCAATTTTG
1 GACGTTTTGCCCCCTGAACTACAATTTTG
*
35573 GACATTTTGCCCCCTGAACTACAATTTTGG
1 GACGTTTTGCCCCCTGAACTACAATTTT-G
*
35603 GACGTTTTGCCCCCTCAACT
1 GACGTTTTGCCCCCTGAACT
35623 TAACAGCCCC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
29 25 0.57
30 19 0.43
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.33
Consensus pattern (29 bp):
GACGTTTTGCCCCCTGAACTACAATTTTG
Found at i:35868 original size:29 final size:30
Alignment explanation
Indices: 35817--35915 Score: 119
Period size: 29 Copynumber: 3.3 Consensus size: 30
35807 TTAAGTTGAT
*
35817 GGGGCAAAACGTCTCAAAATTGAAGTTCAG
1 GGGGCAAAACGTCTCAAGATTGAAGTTCAG
* *
35847 GGGGCAAAATGTC-CAAGATTGAAGTTCGG
1 GGGGCAAAACGTCTCAAGATTGAAGTTCAG
* * **
35876 GGGGCAAAACGTCTAAACGCTACAAGTTCAG
1 GGGGCAAAACGTCTCAA-GATTGAAGTTCAG
35907 GGGGCAAAA
1 GGGGCAAAA
35916 TGGTAGATTA
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 26 0.45
30 14 0.24
31 18 0.31
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.17
Consensus pattern (30 bp):
GGGGCAAAACGTCTCAAGATTGAAGTTCAG
Found at i:37885 original size:333 final size:330
Alignment explanation
Indices: 37203--38100 Score: 1004
Period size: 333 Copynumber: 2.7 Consensus size: 330
37193 CTTTGTTACC
* * * * ** * * * * *
37203 AAAAACCGTGATGGTTAATACACGATTTCGGTTAAAATTTTGCAAAAATTTACCCGAAAGAATTT
1 AAAAACCATGATAGTTAGTACACGATTTCGGCTAAAAAATGGAAAAAATTGACACGAAAAAATTT
* *** * *
37268 TCCTAAATTTTTTG-CCACGATACTCATAAAAAATATATTATTTAACGCCAAAAAGATTGAAAGG
66 TCCTCAA-TTCCCGACCACGATACTCATAAAAAATATATAATTAAACGCCAAAAAGATTGAAAGG
* * * *
37332 TTTTTCACGCTTCCAATATCG-GTTTTCTTATTTTTCCGAATTAATTTCTAATTAAATCGAAACA
130 CTTATCACGCTTCTAATATCGTTTTTTC-TATTTTTCCGAATTAATTTCTAATTAAATCGAAACA
** **
37396 TGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAGTTGAGATTTGGTAAATGGATAT
194 TGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAACTGAGATTTGGTAAATAAATAT
*
37461 AGATATTTCAATGAGACTTGGCGCAAAAAATCATGCAAAACAGAGCCGGGAACCCGAATCGCGTT
259 AGATATTTCAATGAGACTTGACGCAAAAAATCATGCAAAACAGAGCCGGGAACCCGAATCGCGTT
*
37526 TTTAATA
324 TTTAACA
** * * * *
37533 AAAAACTGTGATGGTTAGTACATGA-TTCGGCTAAAAAATGGCAAAAAATTGACATG-AAACATT
1 AAAAACCATGATAGTTAGTACACGATTTCGGCTAAAAAATGG-AAAAAATTGACACGAAAAAATT
* *
37596 TCTCCTCAATTCCCGACCACCATATTCATAAAAAATATATAATTAAACGCCAAAAAGATTG-AAG
65 T-TCCTCAATTCCCGACCACGATACTCATAAAAAATATATAATTAAACGCCAAAAAGATTGAAAG
* *
37660 TGCTTATCACGCTTCTAATATTGTACTTTTTCTATTTTTCCGAATTAATTTCTAATTAAATTGAA
129 -GCTTATCACGCTTCTAATATCGT--TTTTTCTATTTTTCCGAATTAATTTCTAATTAAATCGAA
* * * *
37725 AC-TGGATTGAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAACTGGGATTTCGTTAGATA
191 ACAT-GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAACTGAGATTT-GGTAAATA
* * * ** *
37789 AATATAGATATTTCAATGAGTCTTGACGCCAAAAATCATGCAAAACTGAGCCGGGGTCACGGAA-
254 AATATAGATATTTCAATGAGACTTGACGCAAAAAATCATGCAAAACAGAGCCGGGAAC-CCGAAT
*
37853 CGCGTTTTTAGCA
318 CGCGTTTTTAACA
* ** * * *
37866 AAAAACCATGATAGTTAGTATACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAAAATTT
1 AAAAACCATGATAGTTAGTACACGATTTCGGCTAAAAAATGGAAAAAATTGACACGAAAAAATTT
*** * * * *
37931 TCCTCAATTTTTGGCCAAGATACTCATAAAAAATATATAATTCAACACCAAAAAAAGATTGAAAG
66 TCCTCAATTCCCGACCACGATACTCATAAAAAATATATAATTAAACGCC--AAAAAGATTGAAAG
* * * *
37996 GC-TATTCACGCTTCTAATATCGTTTTTCCTA-TTTTCCGGATTAATTCCTAATTGAATCGAAAC
129 GCTTA-TCACGCTTCTAATATCGTTTTTTCTATTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * *
38059 ATGATTCATATACTTGTAAAAACAAATCCTTAAATCCAATGT
193 ATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
38101 GTGTAAGATT
Statistics
Matches: 476, Mismatches: 75, Indels: 32
0.82 0.13 0.05
Matches are distributed among these distances:
329 24 0.05
330 97 0.20
331 1 0.00
332 145 0.30
333 151 0.32
334 26 0.05
335 29 0.06
336 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (330 bp):
AAAAACCATGATAGTTAGTACACGATTTCGGCTAAAAAATGGAAAAAATTGACACGAAAAAATTT
TCCTCAATTCCCGACCACGATACTCATAAAAAATATATAATTAAACGCCAAAAAGATTGAAAGGC
TTATCACGCTTCTAATATCGTTTTTTCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACATG
ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTAACTGAGATTTGGTAAATAAATATAG
ATATTTCAATGAGACTTGACGCAAAAAATCATGCAAAACAGAGCCGGGAACCCGAATCGCGTTTT
TAACA
Found at i:42850 original size:14 final size:14
Alignment explanation
Indices: 42831--42879 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
42821 TCCTTATCAC
*
42831 AATGTATCTTA-ATT
1 AATGTATCATACA-T
42845 AATGTATCATACAT
1 AATGTATCATACAT
42859 AATGTAT--TCACAT
1 AATGTATCAT-ACAT
42872 AATGTATC
1 AATGTATC
42880 TACTTGGTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 1 0.03
13 11 0.35
14 18 0.58
15 1 0.03
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (14 bp):
AATGTATCATACAT
Found at i:44478 original size:21 final size:21
Alignment explanation
Indices: 44449--44489 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
44439 CCCAAGGATA
*
44449 AAACCAACACACAGATAGAGC
1 AAACCAACACACAAATAGAGC
*
44470 AAACTAACACACAAATAGAG
1 AAACCAACACACAAATAGAG
44490 GGTAGAAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.56, C:0.24, G:0.12, T:0.07
Consensus pattern (21 bp):
AAACCAACACACAAATAGAGC
Found at i:44529 original size:47 final size:47
Alignment explanation
Indices: 44478--44572 Score: 145
Period size: 47 Copynumber: 2.0 Consensus size: 47
44468 GCAAACTAAC
* * * *
44478 ACACAAATAGAGGGTAGAAACCCAAGCATTCCAAGACACTTAGAGCA
1 ACACAAATAGAGGATAGAAACCCAAGCATTACAAGACACCTAAAGCA
*
44525 ACACAGATAGAGGATAGAAACCCAAGCATTACAAGACACCTAAAGCA
1 ACACAAATAGAGGATAGAAACCCAAGCATTACAAGACACCTAAAGCA
44572 A
1 A
44573 AGTCAAGCTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.47, C:0.23, G:0.18, T:0.12
Consensus pattern (47 bp):
ACACAAATAGAGGATAGAAACCCAAGCATTACAAGACACCTAAAGCA
Found at i:52002 original size:46 final size:46
Alignment explanation
Indices: 51937--52024 Score: 167
Period size: 46 Copynumber: 1.9 Consensus size: 46
51927 CTAACTTATT
51937 AAAATTATCATTCATCTTTCATGAGTTATATAAGCACTCCAAAGTA
1 AAAATTATCATTCATCTTTCATGAGTTATATAAGCACTCCAAAGTA
*
51983 AAAATTATCGTTCATCTTTCATGAGTTATATAAGCACTCCAA
1 AAAATTATCATTCATCTTTCATGAGTTATATAAGCACTCCAA
52025 TAATAGTAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (46 bp):
AAAATTATCATTCATCTTTCATGAGTTATATAAGCACTCCAAAGTA
Found at i:55458 original size:28 final size:30
Alignment explanation
Indices: 55386--55458 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 30
55376 ATTCAATTGT
*
55386 ACGATATACG-AAATTTTTTGGTTGGTTGA
1 ACGATATAGGAAAATTTTTTGGTTGGTTGA
55415 ACGATCATATGTGAAAATTTTTT-GTTGGTTG-
1 ACGAT-ATA-G-GAAAATTTTTTGGTTGGTTGA
*
55446 ATGATATAGGAAA
1 ACGATATAGGAAA
55459 TTTAATTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
28 4 0.11
29 6 0.16
30 6 0.16
31 4 0.11
32 9 0.24
33 9 0.24
ACGTcount: A:0.32, C:0.05, G:0.23, T:0.40
Consensus pattern (30 bp):
ACGATATAGGAAAATTTTTTGGTTGGTTGA
Found at i:56550 original size:17 final size:17
Alignment explanation
Indices: 56528--56582 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
56518 ATCACCCCCC
*
56528 AGATCACTAGTGATCTA
1 AGATCACCAGTGATCTA
*
56545 AGATCACCAGTGATGTA
1 AGATCACCAGTGATCTA
* *
56562 AGATCACCGGTGATCAA
1 AGATCACCAGTGATCTA
56579 AGAT
1 AGAT
56583 TACATGGGTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 33 1.00
ACGTcount: A:0.36, C:0.18, G:0.22, T:0.24
Consensus pattern (17 bp):
AGATCACCAGTGATCTA
Done.