Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011158.1 Corchorus capsularis cultivar CVL-1 contig11179, 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: 54203
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Found at i:58 original size:2 final size:2
Alignment explanation
Indices: 51--75 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41 AATACTCATA
51 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
76 ATTTAACGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:922 original size:327 final size:331
Alignment explanation
Indices: 68--4543 Score: 4956
Period size: 329 Copynumber: 13.5 Consensus size: 331
58 TATATATATA
* * *
68 TATATATAATTTAACGGCAAAAGGATTGGAGGACTTTTCACACTTTTAATATCGTTTTTCATATT
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
* * * * *
133 TTTTCTAAATTAATTTCTAATTAAATTGAAACAAGATTCAGATACTTGTAACAACAAATTCTTAA
66 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA-TCTTAA
* * ** * * * ** *
198 ATGCAATGTGCCTGAGATTTGATTAGATCAATAT-GTATATCTCAAGGAGTCTTGGAACTAAAAA
130 ATGCAATGTGGCTAAGATTTTTTTAGATGAATATAG-ATATTTCAAGGAGTCTCGGCGCCAAAAA
* * * * * * *
262 TCATGCAAAACTGAGTCGGGGTCCCGGAACAC-TGTTTTAGCCAAAATAACCGTGATGGTTAATA
194 TCATACAAAACTGAGTCAGGGCCCCGAAACGCGT-TTTTAACC-AAA-AACCGTGATGGTTAGTA
* * * * *
326 CACAATTATGGCTAAAATTTTGTAAAAAGTGATCCGAAAATTTTTTCCTCAATTTTTGGATAAAA
256 CACGATTTTGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAA
391 TACTCATAATAT
321 TACTCATAA-AT
* * * * * *
403 ATATATATAATTTAACCCCAAAAATATTGTAGGAATTTTCACTCTTTTAATATTGTTTTTCATAT
1 -TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATAT
* * * * * *
468 TTTTTCTGAATTAATTTCTAATTAACTCGAAAAAAAATTCAGA--CTCTTAAAAA-AATTATTAA
65 TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTAA
** * ** * * * * * *
530 AAACAATGTGGCTGAGATTTGATTAGTTGAATATGGATATCTCAAGGAGTCTTGGCACGAAAAAT
130 ATGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAAT
* * * * *
595 CATGCAAAACTGAGTAAGGGCCCCGGAACGC-TTTTTAACCAAAAACTGTGATGGTTATTACACG
195 CATACAAAACTGAGTCAGGGCCCCGAAACGCGTTTTTAACCAAAAACCGTGATGGTTAGTACACG
* * * * * *
659 ATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACA
260 ATTTTGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACT
724 CATAAA-
325 CATAAAT
* * * * *
730 AATATATAATTTAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCATTTTTCATATT
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
* * * * * * *
795 TTTTATGAATTCATTTGTAATTAAATCGAAA-AAAATTTAGATACTCGTAAAAA-AAATATTAAA
66 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTAAA
* * ** * * * * * *
858 AGAAATGTGGCTGAA-ATTTGATTATATGAATATCGATATCTCAAGGAGTCTTGACACCAAAAAT
131 TGCAATGTGGCT-AAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAAT
* ** * ** * ***
922 CATACAAAACTAAGT-AAAGCCCTTGAAACGCGTATTTAGTTAAAAAAAAAATCGTGATAAATAG
195 CATACAAAACTGAGTCAGGGCCC-CGAAACGCG--TTT--TT-AACCAAAAACCGTGATGGTTAG
* *
986 TATACGATTTTGGCTAAAATTTTGTAAAAAATGATCC-AAGAAATTTTTCCTCAATTTTTGGATA
254 TACACGATTTTGGCTAAAATTTTGTAAAAAATGACCCGAA-AAATTTTTCCTCAATTTTTGGATA
*
1050 AAATACTCTTAAATT
318 AAATACTCATAAA-T
* * * *
1065 ATATATATAATTTAACGCAAAAAAAGGTTGGAGGACTTTTAACGCTTTTAATATTGTTTTTCATA
1 -TATATATAATTTAACGC-CAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA
* * * *
1130 -CTTTTCCGAATTAATTTCTAATTAAATTGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTT
64 TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT-CTT
1194 AAATGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAA
128 AAATGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAA
* * * * * ** **
1259 ATGATACAAAACTGAGCCAGAGACCTGAAACGCGTTTTTAGCAAAAAAAAAAAAACATTTGATGG
193 ATCATACAAAACTGAGTCAGGGCCCCGAAACGCGTTTTT-------AACCAAAAAC-CGTGATGG
* *
1324 TTAGTACACGATTTTTGCTGAAATTTTGTAAAAAAATGACCCGAAAAA-TTTTCCTCAATTTTTG
250 TTAGTACACGATTTTGGCTAAAATTTTGT-AAAAAATGACCCGAAAAATTTTTCCTCAATTTTTG
1388 GATAAAATACTCATAAAT
314 GATAAAATACTCATAAAT
* * *
1406 TATATATAATTTAACGCCAAAAATATTGGAGGACTTTTCACGTTTTTAATATCGTTTTTCATGTT
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCA--TA
* * * * * *
1471 TTTTTTTTGAGAATTAATTTTTAATTAAATCGAAATAAGATTTAGATACTCGTAAAAACATATCC
64 TTTTTTCT--GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT-C
* * * *
1536 TTAAATGCAATGTGTCTAAGATTTTTTAAGATGAATATAGATATTTTAAGGAGTCTCGGCGCAAA
126 TTAAATGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAA
* * * * * * *
1601 AAATAATTCCAAACTGAGTCAGGGTCCCAAAACGCGTTTTTAGCCAAAAACCTGTGACGGTTAGT
191 AAATCATACAAAACTGAGTCAGGGCCCCGAAACGCGTTTTTAACCAAAAACC-GTGATGGTTAGT
* * ** *
1666 ACACGATTTTGGCTAAAACTTTGTAAAAAATAAAACGAAATA-TTTTCCTCAATTTTTGGATAAA
255 ACACGATTTTGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAA
1730 ATACTCATAAAT
320 ATACTCATAAAT
* * * *
1742 TATATATAATTTAACGCCCAAAATACTGGAGGACTTTTCACTCTTTTAATATCGTTTTTCATATT
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
* * *
1807 TTTTCTGAATTAATTTCTAATTAAATCCAATCAAGATTCAGGA-GTTCGTAAAAACAAATTCTTA
66 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCA-GATGCTCGTAAAAACAAA-TCTTA
* * * *
1871 AATGCAATGTGGCTAA-ACTTTTTCAGATGAATATACATATTGT-AAGGAGTCTCGGCGGCAAAA
129 AATGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATT-TCAAGGAGTCTCGGCGCCAAAA
* * * *
1934 ATCATACAAAACTGAGGCAGGGCCCCGAAACGCGTTTTTCACCAAAAAACCGTGATGGTAACATA
193 ATCATACAAAACTGAGTCAGGGCCCCGAAACGCGTTTTTAACC-AAAAACCGTGATGGTTA-GTA
* * * *
1999 CACGATTTTAGCTAAAATTTTGTAAAAAATGACTCGAAAATTTTTTCC-CAAATTTTTGGAGAAA
256 CACGATTTTGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTC-AATTTTTGGATAAA
2063 ATACTCATAAAT
320 ATACTCATAAAT
* * * * * * *
2075 GATATATAATTTAACGCCGAAAACATTTGATGACTTTTCACACTTTTAATATTGTTTTTCATATT
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
* * * *
2140 TTTTCTGAATTAATTTCTAACTAAATCAAAACAAGATTTAGATGCTCGTAAAACCAAATCCTTAA
66 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT-CTTAA
* * * * * *
2205 ATGCAAGGTGGCTAAGATATTTTTAGATTAATATAGGTATTTCAAGGAGTCTCGGTGCAAAAAAT
130 ATGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAAT
* * * * *
2270 CATTCAAAACTGAGACAGGGCCCCGAAACGCGTTTTTCGACCAAAAAAAACCGTGATGGTTAATT
195 CATACAAAACTGAGTCAGGGCCCCGAAACGCGTTTTT-AACC---AAAAACCGTGATGGTTAGTA
* **
2335 CACGATTTTGGCTAAAATTTTATAAAAAAATGATTCGAAAAATTTTTCCTCAATTTTTGGATAAA
256 CACGATTTTGGCTAAAATTTTGT-AAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAA
2400 ATACTCATAAAT
320 ATACTCATAAAT
* *
2412 TATATATAATTTAACGCCAAAAATATTTGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
* * *
2477 TTTTCTGATTTAATTTCTAATTAAATAGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAA
66 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT-CTTAA
* * * * * * * *
2542 ATGCAATATCGATAAGATTTTTTTAAATGAATATAGTTATTTCAAGGAGTCTCCGTGCAAAAAAT
130 ATGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAAT
* ** * * * **
2607 TATTTAAAACTTAGTCAGGACCCCGAAACGCATTTTTCGCCAAAAACCGTGAT-G---GTACACG
195 CATACAAAACTGAGTCAGGGCCCCGAAACGCGTTTTTAACCAAAAACCGTGATGGTTAGTACACG
** * * * *
2668 ATTTTTTCTGAAATTTTGTAAAAAAATAACCCGAAAAATGTTTCCTCGATTTTTGGATAAAATAC
260 ATTTTGGCTAAAATTTTGT-AAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATAC
*
2733 ACATAAAT
324 TCATAAAT
* *
2741 TATATCTAATTTAACGCCAAAAAGATTGGAGGACTTTTCACTCTTTTAATATCGTTTTTCATA-T
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
* * *
2805 TTTTCTGAATTAATTTCTAATTAAATCGAATCAAGATTCAGATGTTCGTAAAAACAAATTTTGAA
66 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTT-AA
* * * * *
2870 ATGCAATGTGGCTAAGCTTTTTTTAGATGAATACAGATATTTTAAGGAGTCTTGGCGCAAAAAAT
130 ATGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAAT
* * *
2935 CATACAAAACTGAGCCAGGGCCCCGAAACGCGTTTTTCACCAAAAAACC------G-T--TACAT
195 CATACAAAACTGAGTCAGGGCCCCGAAACGCGTTTTTAACC-AAAAACCGTGATGGTTAGTACAC
* * *
2991 GATTTTGGCTAAAATTTTGTGAAAAATGACCCG-AAAATTTGTCTTCAATTTTTGGATAAAATAC
259 GATTTTGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATAC
3055 TCATAAAT
324 TCATAAAT
* * *
3063 TATATTTAATTTAACGCCAAAAAGATTGGAGGATTTTTCACGCTTTTAATATCGTTTTTCATAGT
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
* * *
3128 TTTTCTGAATTAATTTCTAATTAAATCGAATCAAGATTCAGATGTTCGTAAAAACAAATTTTTAA
66 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA-TCTTAA
* *
3193 ATGCAATGTGGCTAA-ACTTTTTTTAGATGAATATAGATATTTTAAGGAGTCTTGGCGCCAAAAA
130 ATGCAATGTGGCTAAGA-TTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAA
* * * ** * * *
3257 TCATACATAACTGAGACAAGGTTCCGAAACGCGTTTTTAACCAAAAAAC-TGCT-G--A-TACAT
194 TCATACAAAACTGAGTCAGGGCCCCGAAACGCGTTTTTAACCAAAAACCGTGATGGTTAGTACAC
* ** *
3317 GATTTTGGCTAAAATTTTGCAAAAAATGACATGAAAAATTTTTCCTCAATTTTTCGATAAAATAC
259 GATTTTGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATAC
*
3382 TCATAATT
324 TCATAAAT
3390 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCCAT-T
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTT-CATAT
*
3454 TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATCCTTA
65 TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT-CTTA
* * *
3519 AATGCAATGTGGGTAAGATTTTTTTAGATGAATATAGATATTTTAAGGAGTCTCGGCGCAAAAAA
129 AATGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAA
* **
3584 T-ATACAAAACTGAGTCAGGGCCCCAAAACGCGTTTTTCGCCAAAAAACCGTGATGGTTAGTACA
194 TCATACAAAACTGAGTCAGGGCCCCGAAACGCGTTTTTAACC-AAAAACCGTGATGGTTAGTACA
* ** *
3648 CGATTTTGGCTAAAATTTTGTAAAAAATAACCCGAAATTTTTTTTCTCAATTTTTGGAT-AAATA
258 CGATTTTGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATA
3712 CTCATAAAT
323 CTCATAAAT
* * *
3721 TATATATAATTTAACGCCCAAAATATTGGAGGACTTTTCACTCTTTTAATATCGTTTTTCAT-TT
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
* *
3785 TTTTCTGAATTAATTTCTAATTAAATC-AAATCAAGATTCAGATGTTCATAAAAACAAATTCTTA
66 TTTTCTGAATTAATTTCTAATTAAATCGAAA-CAAGATTCAGATGCTCGTAAAAACAAA-TCTTA
* * * *
3849 AATGCAATGTGGCTAAGCTTTTTTCAAATGAATATAGATATTTCAAGGAGTCTCGGTGCCAAAAA
129 AATGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAA
* * * * *
3914 T--TACAAAACTGAGCCAGGACCCCGAAACGCG-TTTTCACCAAAAAACCGTGATGGTTAATTCA
194 TCATACAAAACTGAGTCAGGGCCCCGAAACGCGTTTTTAACC-AAAAACCGTGATGGTTAGTACA
* * * *
3976 CGATTTTGGCTAAAATTTTGCAAAAAATTACCCGAAAAATTTATCCTCAATTTTTGAATAAAATA
258 CGATTTTGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATA
4041 CTCATAACA-
323 CTCATAA-AT
* * ** * *
4050 TATATATAATTTAACGCTAAAAAGATTGTAGGGTTTTTGACG-TTTCTAATGTCGTTTTTCATAT
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTT-TAATATCGTTTTTCATAT
* * * *
4114 TTTTTCCGAATTAATTTCTAAATAAATCGAAACAA-ATTTCAGATGCCCG-AAATACAAATCCTT
65 TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGA-TTCAGATGCTCGTAAAAACAAAT-CTT
* * * * ** * * * * **
4177 AAATACAATGTGACTGAGAATTGATTATATGAATATCGATATTTCAAGTAGTCTCGGAGTAAAAA
128 AAATGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAA
** * * * * *
4242 ATCATGTAAAATTGAGGC-GAGTCCCCGAAACGCGTTTTTAGCCAAAAACCGTAATGGTTTGTTA
193 ATCATACAAAACTGAGTCAG-GGCCCCGAAACGCGTTTTTAACCAAAAACCGTGAT-G---GTTA
* * * * * * * * *
4306 CTACACGATTTCGGCTAAAATTTTGCAAAAATTGACACGAAAGATTTCTCCTCAATTTTTTGCTA
253 GTACACGATTTTGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATA
4371 AAATACTCATAAA-
318 AAATACTCATAAAT
* * * * * * *
4384 AATATATAATTCAACACCAAAAAGATTAGAGGGCTTTTCACGCTTTTAATATCGTATTTCTTATT
1 TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
* * *
4449 TTTTCTAAATTAATTTCTAATTAAATTGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAA
66 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA-TCTTAA
* * * **
4514 ATCCAATGTTGCTGAGATTTGGTTAGATGA
130 ATGCAATGTGGCTAAGATTTTTTTAGATGA
4544 TGTAAAGTAT
Statistics
Matches: 3569, Mismatches: 477, Indels: 189
0.84 0.11 0.04
Matches are distributed among these distances:
322 100 0.03
323 168 0.05
324 26 0.01
325 9 0.00
326 155 0.04
327 311 0.09
328 237 0.07
329 370 0.10
330 166 0.05
331 198 0.06
332 263 0.07
333 254 0.07
334 179 0.05
335 116 0.03
336 266 0.07
337 370 0.10
338 7 0.00
339 115 0.03
340 22 0.01
341 12 0.00
342 65 0.02
343 14 0.00
344 146 0.04
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (331 bp):
TATATATAATTTAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATT
TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTAAA
TGCAATGTGGCTAAGATTTTTTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATC
ATACAAAACTGAGTCAGGGCCCCGAAACGCGTTTTTAACCAAAAACCGTGATGGTTAGTACACGA
TTTTGGCTAAAATTTTGTAAAAAATGACCCGAAAAATTTTTCCTCAATTTTTGGATAAAATACTC
ATAAAT
Found at i:5085 original size:22 final size:23
Alignment explanation
Indices: 5041--5085 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
5031 CACAATTAAT
* *
5041 AAAAAAGTTGAATCATCTCAAAA
1 AAAAAAGTTAAATCATCTAAAAA
*
5064 AAAAAAGTTAAATGA-CTAAAAA
1 AAAAAAGTTAAATCATCTAAAAA
5086 GAATATTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.62, C:0.09, G:0.09, T:0.20
Consensus pattern (23 bp):
AAAAAAGTTAAATCATCTAAAAA
Found at i:7937 original size:13 final size:13
Alignment explanation
Indices: 7921--7946 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7911 TTATAACTTT
7921 AATAAGTAACACA
1 AATAAGTAACACA
7934 AATAAGTAACACA
1 AATAAGTAACACA
7947 CTTGTTTCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (13 bp):
AATAAGTAACACA
Found at i:20605 original size:13 final size:13
Alignment explanation
Indices: 20587--20617 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
20577 CACCATGATT
20587 TTTTAGAATTTTC
1 TTTTAGAATTTTC
*
20600 TTTTAGAATTTTT
1 TTTTAGAATTTTC
20613 TTTTA
1 TTTTA
20618 AAAGAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.03, G:0.06, T:0.68
Consensus pattern (13 bp):
TTTTAGAATTTTC
Found at i:20924 original size:15 final size:15
Alignment explanation
Indices: 20906--20953 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
20896 CTTCTTTTAA
*
20906 TTTCTCTTTTCTTTT
1 TTTCTTTTTTCTTTT
20921 TTTCTTTTTTC-TTT
1 TTTCTTTTTTCTTTT
20935 TTTCTTTTTTTCTTTT
1 TTTC-TTTTTTCTTTT
20951 TTT
1 TTT
20954 GAAAAATGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 7 0.23
15 17 0.57
16 6 0.20
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTCTTTTTTCTTTT
Found at i:20925 original size:8 final size:8
Alignment explanation
Indices: 20912--20953 Score: 70
Period size: 8 Copynumber: 5.5 Consensus size: 8
20902 TTAATTTCTC
20912 TTTTCTTT
1 TTTTCTTT
20920 TTTTC-TT
1 TTTTCTTT
20927 TTTTC-TT
1 TTTTCTTT
20934 TTTTCTTT
1 TTTTCTTT
20942 TTTTCTTT
1 TTTTCTTT
20950 TTTT
1 TTTT
20954 GAAAAATGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 14 0.42
8 19 0.58
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTTCTTT
Found at i:20928 original size:6 final size:7
Alignment explanation
Indices: 20906--20952 Score: 67
Period size: 7 Copynumber: 6.4 Consensus size: 7
20896 CTTCTTTTAA
*
20906 TTTCTCT
1 TTTCTTT
20913 TTTCTTTT
1 TTTC-TTT
20921 TTTCTTT
1 TTTCTTT
20928 TTTCTTT
1 TTTCTTT
20935 TTTCTTTT
1 TTTC-TTT
20943 TTTCTTT
1 TTTCTTT
20950 TTT
1 TTT
20953 TGAAAAATGA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
7 24 0.65
8 13 0.35
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTCTTT
Found at i:20931 original size:22 final size:22
Alignment explanation
Indices: 20906--20952 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
20896 CTTCTTTTAA
20906 TTTCTCTTTTCTTTTTTTCTTT
1 TTTCTCTTTTCTTTTTTTCTTT
*
20928 TTTCTTTTTTCTTTTTTTCTTT
1 TTTCTCTTTTCTTTTTTTCTTT
20950 TTT
1 TTT
20953 TGAAAAATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (22 bp):
TTTCTCTTTTCTTTTTTTCTTT
Found at i:22813 original size:2 final size:2
Alignment explanation
Indices: 22806--22838 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22796 TCAAAAGTAT
22806 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
22839 AACATCCACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:32591 original size:45 final size:46
Alignment explanation
Indices: 32524--32613 Score: 137
Period size: 45 Copynumber: 1.9 Consensus size: 46
32514 TTGACATTGC
* *
32524 TTTGATGTTCAGCATCAGACTGAG-CAGCAAGTTCAACTCCTTCGT
1 TTTGATGTTCAGCATCAAACTGAGACAACAAGTTCAACTCCTTCGT
32569 TTTGATGTTCAGCATCAAACTGAGCAACAACAAGTTCAACTCCTT
1 TTTGATGTTCAGCATCAAACTGAG--ACAACAAGTTCAACTCCTT
32614 TGTTCTCCTC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
45 23 0.57
48 17 0.43
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (46 bp):
TTTGATGTTCAGCATCAAACTGAGACAACAAGTTCAACTCCTTCGT
Found at i:32714 original size:69 final size:64
Alignment explanation
Indices: 32603--32785 Score: 266
Period size: 60 Copynumber: 2.8 Consensus size: 64
32593 CAACAACAAG
32603 TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCATAGCCTCGCCCTCAATAG
1 TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCATAGCCTCG--CTCAATA-
32668 CAGC
63 C--C
* * *
32672 TTCAACTCCTTTTTTCTCCTCTGCTTCTAAATGATCCAGCTCAATCACAG----GCTCAATACC
1 TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCATAGCCTCGCTCAATACC
32732 TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCATAGCCTC
1 TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCATAGCCTC
32786 ACCCCCTTGC
Statistics
Matches: 104, Mismatches: 6, Indels: 13
0.85 0.05 0.11
Matches are distributed among these distances:
60 48 0.46
62 1 0.01
63 7 0.07
65 1 0.01
69 47 0.45
ACGTcount: A:0.22, C:0.35, G:0.10, T:0.33
Consensus pattern (64 bp):
TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCATAGCCTCGCTCAATACC
Found at i:32742 original size:60 final size:64
Alignment explanation
Indices: 32603--32778 Score: 252
Period size: 69 Copynumber: 2.7 Consensus size: 64
32593 CAACAACAAG
*
32603 TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCATAGCCTCGCCCTCAATAG
1 TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCACAG---CG-CCTCAATAG
32668 CAGC
62 CA-C
* *
32672 TTCAACTCCTTTTTTCTCCTCTGCTTCTAAATGATCCAGCTCAATCACAG-G-CTCAATA-C-C
1 TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCACAGCGCCTCAATAGCAC
32732 TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCA
1 TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCA
32779 TAGCCTCACC
Statistics
Matches: 102, Mismatches: 5, Indels: 9
0.88 0.04 0.08
Matches are distributed among these distances:
60 46 0.45
62 1 0.01
63 7 0.07
65 1 0.01
69 47 0.46
ACGTcount: A:0.22, C:0.35, G:0.10, T:0.34
Consensus pattern (64 bp):
TTCAACTCCTTTGTTCTCCTCTGCCTCTAAATGATCCAGCTCAATCACAGCGCCTCAATAGCAC
Found at i:50131 original size:2 final size:2
Alignment explanation
Indices: 50119--50157 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
50109 CAACCCCCTT
*
50119 TA TA AA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
50158 AAAGTTCCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:50615 original size:35 final size:36
Alignment explanation
Indices: 50576--50644 Score: 131
Period size: 35 Copynumber: 1.9 Consensus size: 36
50566 ACGATGTGAG
50576 TGTAGAAATAAAAAAGTAGTTTATAGTAG-TTTTCT
1 TGTAGAAATAAAAAAGTAGTTTATAGTAGATTTTCT
50611 TGTAGAAATAAAAAAGTAGTTTATAGTAGATTTT
1 TGTAGAAATAAAAAAGTAGTTTATAGTAGATTTT
50645 TTTTTTAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 29 0.88
36 4 0.12
ACGTcount: A:0.42, C:0.01, G:0.17, T:0.39
Consensus pattern (36 bp):
TGTAGAAATAAAAAAGTAGTTTATAGTAGATTTTCT
Found at i:51544 original size:31 final size:31
Alignment explanation
Indices: 51502--51600 Score: 141
Period size: 31 Copynumber: 3.3 Consensus size: 31
51492 CAGGCTAAAT
51502 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
* * *
51533 GCTCAAATTGGTCATAAACCTTTGA--AAGC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
51562 GCTCAATTTGGTCCTAAACCTTTGAGCG-GTC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGAG-C
51593 GCTCAATT
1 GCTCAATT
51601 CAGTCCTATT
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
29 26 0.44
30 1 0.02
31 32 0.54
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.30
Consensus pattern (31 bp):
GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
Found at i:51572 original size:29 final size:30
Alignment explanation
Indices: 51502--51586 Score: 127
Period size: 29 Copynumber: 2.8 Consensus size: 30
51492 CAGGCTAAAT
*
51502 GCTCAATTTGGTCCTAAACCTTTGAGCGAGC
1 GCTCAATTTGGTCCTAAACCTTTGA-CAAGC
* *
51533 GCTCAAATTGGTCATAAACCTTTGA-AAGC
1 GCTCAATTTGGTCCTAAACCTTTGACAAGC
51562 GCTCAATTTGGTCCTAAACCTTTGA
1 GCTCAATTTGGTCCTAAACCTTTGA
51587 GCGGTCGCTC
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
29 26 0.53
31 23 0.47
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.31
Consensus pattern (30 bp):
GCTCAATTTGGTCCTAAACCTTTGACAAGC
Done.