Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012528.1 Corchorus capsularis cultivar CVL-1 contig12549, 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: 115645
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:929 original size:329 final size:329
Alignment explanation
Indices: 68--3638 Score: 3820
Period size: 330 Copynumber: 10.8 Consensus size: 329
58 AAAAAAAAAA
* * * *
68 GAAGGGATGTTAACGCTTCTAATATTGTTTTCCCTATTTTTTCCTAATTAATTTCTAATTAAATC
1 GAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATC
* * * *
133 GAAACAAGATTCAAAAGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTAAGACTTGGTTAGA
66 GAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTAGA
* * * * *
198 TGAATATTGATATTTCAAGGACTCTTAGCAACAAAAT-TCATGCAAAACTGAGTCGGGTCTCGAA
131 TGAATATAGATATTTCAAGGACTCTTGGC-ACAAAATATCATGCAAAACTGAGCCGGGCCCCGAA
* * *
262 ACGCGTTTTTAGCCGAAAACGGTGATGGTTAGTACATGATTTCGGCTCAAATTTTGCAAAAATTG
195 ACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
** ** *
327 ATCTGAAAGATATTTCCCCTGTTTTTAGCTAAAATACTCATAAAAAATATATAATTCGACAT-AA
260 A-CCCAAAGATATTTCCCCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCGACATCAA
391 AATGATT
324 AAT-ATT
* * * * *
398 GAAGGGCTTTAAACGCTTCTAATATTGTTTTTCCAATTTTTTTCGAATTAATTACTAATTATATC
1 GAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATC
* * * * *
463 GAAACAAGATTTAGATGCTCATTAAAACAAATCATTAAATCCAATGTGGCTGAGATTTGGTTAGG
66 GAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTAGA
* * * *
528 TAAATATAGATATTTCAAGGACTCTTGGCACAAAAAATTATGCAAAACTGAGACC-GGCCCCGGA
131 TGAATATAGATATTTCAAGGACTCTTGGCACAAAATATCATGCAAAACTGAG-CCGGGCCCCGAA
* * * * *
592 ATGCGTTTTTAGCCGAAAACCATGATTGATAGTACACGATTTCGGCTAAAATTTTGCGAAAATTG
195 ACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
* * *
657 ACCCATAAGATATTTCCACAATTTTTGGATAAAATACTCATAAAAAATATATAATTCGACATCAT
260 ACCCA-AAGATATTTCCCCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCGACATCAA
722 AATATT
324 AATATT
* * * * * *
728 TAAGGACTTTTGACGCTTCCAATATTGTTTTCCCTATTTTTT-CGAATTAATTTCTAATTATATC
1 GAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATC
* * *
792 GAAACAAGATTCAGATGCTCATAAAAGCAAATCCTTAAATCCACTTTAGCTGAGATTTGGTTAGA
66 GAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTAGA
* * *
857 TGAGTATAGATATTTCAAGGACTCTTGCCACAAAATATCATGCAAAACTGAGCCGGGCCCCAAAA
131 TGAATATAGATATTTCAAGGACTCTTGGCACAAAATATCATGCAAAACTGAGCCGGGCCCCGAAA
* * *
922 CGCGTTTTTGGCCGAAAACTGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAATTGA
196 CGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA
* * * * * * * *
987 CCCGTAAGATATTTCCTCAATATTTGTCTAAAATACTCCTAAAAAATATTTAATTCAACATTAAA
261 CCC-AAAGATATTTCCCCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCGACA-TCAA
*
1052 AAGATT
324 AATATT
* * ** * * *
1058 GAAGTGCTTTTCAA-GCTTGTAATATCATTTTTCCTATTTTTTTCCGAATTGATTTTTAATTAGA
1 GAAGGGCTTTT-AACGCTTCTAATATTGTTTTTCCTA-TTTTTTCCGAATTAATTTCTAATTAAA
* * * * *
1122 TCGAGAA-AAGATTCAGATGTTCGTAAAAACAAATCCTTAAATCCAATGTGACTGACATTTGGTT
64 TCGA-AACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTT
* * * * *
1186 AGATGAATATGGATATTTCAA-GACTCTTGGCACCAAAA-ATCTTGCAAGACTGAGTCGGGCCCT
128 AGATGAATATAGATATTTCAAGGACTCTTGGCA-CAAAATATCATGCAAAACTGAGCCGGGCCCC
* * * * * * *
1249 GAAACGCGTTATTAGCCAAAAATCGTGATGGTCAGTACACGACTTCGGTTAAAATTTTGAAAAAA
192 GAAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAA
* *
1314 TTGACCCGAAAGCTATTTCCCCAATTTTTGGCTAAAATACTCAT-AAAAATATATAATTTGACA-
257 TTGACCC-AAAGATATTTCCCCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCGACAT
*
1377 CAAAAAGAGATT
321 C--AAA-ATATT
* * *
1389 GAAGGGCTTTTAACGCTTCTAATATT-TTTTTCCTATTTTTT-TGAATTAATTTTTAATTATATC
1 GAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATC
* * * * *
1452 GAAACAAGATTCTGATACTAATAAAAACAATTTCTTAAATCCACTGTGGCTGAGATTTGGTTAGA
66 GAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTAGA
* * * ** *
1517 TAAATATAGATATTTCAAGGAGTCTTGGCACAAAATATCATGCAAATCTGAGCTAGACCCCGAAA
131 TGAATATAGATATTTCAAGGACTCTTGGCACAAAATATCATGCAAAACTGAGCCGGGCCCCGAAA
* * *
1582 GGCGTTTTCAGCCGAAAACGGTGATGGTTAGTACACGATTTCGGC--------T---AAAATTGA
196 CGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA
* * * *
1636 CCCGAAATATATTTCCCCAATATTTGGCAAAAATGCTCATAAAAAATATATAATTCGACATCAAA
261 CCC-AAAGATATTTCCCCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCGACATC-AA
1701 AATATT
324 AATATT
* * * * * *
1707 GATGTGCTTTTAACGCTTCAAATATTATTTTTCCTATTTTTTCCGAATTTATTTCCAATTAAATC
1 GAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATC
* * * * * * *
1772 GAAATAAGATTCA-ACTGCTCGTTAAAACAAATTCTTAAATCCA-TAATGACTGAAATTTGGTTA
66 GAAACAAGATTCAGA-TGCTCATAAAAACAAATCCTTAAATCCACT-GTGGCTGAGATTTGGTTA
* * * *
1835 GATGAATATAGATATTTTAAGGACTCTTGGTACAAAATATCATGCAAATCTGAGCCGGG-TCCGA
129 GATGAATATAGATATTTCAAGGACTCTTGGCACAAAATATCATGCAAAACTGAGCCGGGCCCCGA
* * *
1899 AATGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAATTT
194 AACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATT
* * * * * *
1964 GACCCGAAACATCTTTCCACAATTTTTGGC-AGAGATACTCATAAAAAGTATATAATTTGACATA
259 GACCC-AAAGATATTTCCCCAATTTTTGGCTA-AAATACTCATAAAAAATATATAATTCGACAT-
*
2028 AAAAATATT
321 CAAAATATT
* ** ** *
2037 GAAGGGCTGTTAACATTTCTAATATTGTTTTTCCTATTTTTTCAAAATTAATTACTAATTAAATC
1 GAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATC
*
2102 GAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTAGC
66 GAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTAGA
* * * *
2167 TGAATATAGATATTTCAAGGACTCTTGGCACAAAAAATTATGCAAAACTAAGCCGGGCCCCGGAA
131 TGAATATAGATATTTCAAGGACTCTTGGCACAAAATATCATGCAAAACTGAGCCGGGCCCCGAAA
* * * * *
2232 CGCGCTTTTAGCCGAAAACCATGATGGTTATTACACGATTTTGGCTAAAATTTTGCGAAAATTGA
196 CGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA
* ** * * *
2297 CCTGAAAGATATTT--CCAAAATTTGTCTAAAATACCCATAAAAAATATATAATTTGACATCAAA
261 CC-CAAAGATATTTCCCCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCGACATC-AA
2360 AATATT
324 AATATT
* * **** * ** *
2366 GAATGGCTTTCTCTTTTACTGCCAAAAAAAAAAAGAAGGGATCTTAACGCTTCTAATATTGTTTT
1 GAA-GG---GCT-TTTAAC-G-C-----TTCTAA-TATTG-T-TT-----TTC--CTATT-TTTT
** * * *
2431 CCCTATT-TTTTCCTAATTAATTTCTAATTAAATCGAAACAAGATTCAAAAGCTCATAAAAACAA
43 CCGAATTAATTT-C-----------TAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAA
* * * *
2495 ATCCTTAAATCCACTGTGGCTAAGACTTGGTTAGATGAATATTGATATTTCAAGGACTCTTAGCA
96 ATCCTTAAATCCACTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGACTCTTGGC-
* * * *
2560 ACAAAAT-TCATGCAAAACTGAGTCGGGTCTCGAAACGCGTTTTTAGCCGAAAACGGTGATGGTT
160 ACAAAATATCATGCAAAACTGAGCCGGGCCCCGAAACGCGTTTTTAGCCGAAAACCGTGATGGTT
* * ** ** *
2624 AGTACATGATTTCGGCTCAAATTTTGCAAAAATTGATCTGAAAGATATTTCCCCTGTTTTTAGCT
225 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CCCAAAGATATTTCCCCAATTTTTGGCT
2689 AAAATACTCATAAAAAATATATAATTCGACAT-AAAATGATT
289 AAAATACTCATAAAAAATATATAATTCGACATCAAAAT-ATT
* * * *
2730 GAAGGGCTTTAAACGCTTCTAATATTGTTTTTCCAATTTTTTTCGAATTAATTTCTAATTATATC
1 GAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATC
* * *
2795 GAAACAAGATTCAGATGCTCATAAAAGCAAATCCTTAAATCCACTTTAGCTGAGATTTGGTTAGA
66 GAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTAGA
* * *
2860 TGAGTATAGATATTTCAAGGACTCTTGCCACAAAATATCATGAAAAACTGAGCCGGGCCCCGAAA
131 TGAATATAGATATTTCAAGGACTCTTGGCACAAAATATCATGCAAAACTGAGCCGGGCCCCGAAA
* * *
2925 CGCGTTTTTAGCCGAAAA-TGATGATGGTTTGTACACGATTTCGGCTAAATTTTTGCAAAAATTG
196 CGCGTTTTTAGCCGAAAACCG-TGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTG
* * * ** *
2989 ACCCGAAAGATATTTCCTCATTTTTTGTCTAAAATACTCATAAAAAATACT-TAATTCGGTATTA
260 ACCC-AAAGATATTTCCCCAATTTTTGGCTAAAATACTCATAAAAAATA-TATAATTCGACATCA
*
3053 AAA-AGAT
323 AAATA-TT
* * * *
3060 GAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAAT
1 GAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTA-TTTTTTCCGAATTAATTTCTAATTAAAT
* * ** * * * * * *
3125 CGAAAAAAGATTTAGATGCTTGTAAAAACAAATCC-TAAATCCAATATGCCTAAGATTTGTTTAT
65 CGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTAG
** * * * * * *
3189 ATTTATATAGATATTGT-AAGGAATCATGACACCATAA-ATCTTGCAAAACTGAGTCGGGCCCCG
130 ATGAATATAGATATT-TCAAGGACTCTTGGCA-CAAAATATCATGCAAAACTGAGCCGGGCCCCG
* * ** * * *
3252 AAATGCATTTTTAGCCGAAAGTCGTGATGGTTAATACACGATTTCGACTAAAATTTTGTAAAAAT
193 AAACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAAT
*
3317 TGACCCAAAGATATTT-CCCAAATTTTGGTCTAAAATACTCATAAAAAATATATAATTCGACATA
258 TGACCCAAAGATATTTCCCCAATTTTTGG-CTAAAATACTCATAAAAAATATATAATTCGACAT-
*
3381 AAAAATATT
321 CAAAATATT
*
3390 GAAGGGTTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATC
1 GAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATC
* * * * * *
3455 GAAACAAGATTCAGATGCTCGTAAAAACAAATCATTAAATCCAATGTGACTGAAATTTGTTTAGA
66 GAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTAGA
* * * * * * * * *
3520 TGATTATAGATATTGT-AAGGAATCTTGGCACAAAAAATCTTACAAAACTGAGTCAGACCTCGAA
131 TGAATATAGATATT-TCAAGGACTCTTGGCACAAAATATCATGCAAAACTGAGCCGGGCCCCGAA
* * * * *
3584 ACGCGTTATTAACCAAAAACCGTGTTGGTTAGTATACGATTTCGGCTAAAATTTT
195 ACGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTT
3639 ATGAAAATAT
Statistics
Matches: 2702, Mismatches: 438, Indels: 202
0.81 0.13 0.06
Matches are distributed among these distances:
318 70 0.03
319 87 0.03
320 119 0.04
321 1 0.00
327 3 0.00
328 103 0.04
329 482 0.18
330 1132 0.42
331 301 0.11
332 94 0.03
333 4 0.00
334 4 0.00
341 11 0.00
342 8 0.00
343 1 0.00
344 5 0.00
349 5 0.00
350 1 0.00
351 8 0.00
352 11 0.00
357 1 0.00
358 1 0.00
359 4 0.00
360 2 0.00
363 194 0.07
364 13 0.00
365 37 0.01
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (329 bp):
GAAGGGCTTTTAACGCTTCTAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATC
GAAACAAGATTCAGATGCTCATAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTAGA
TGAATATAGATATTTCAAGGACTCTTGGCACAAAATATCATGCAAAACTGAGCCGGGCCCCGAAA
CGCGTTTTTAGCCGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA
CCCAAAGATATTTCCCCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCGACATCAAAA
TATT
Found at i:3932 original size:2 final size:2
Alignment explanation
Indices: 3921--3952 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
3911 TATCATTATT
3921 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3953 GTTGAAACCC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5960 original size:15 final size:15
Alignment explanation
Indices: 5937--5981 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
5927 ATAAAAATTA
5937 AATAT-TTTTATTTT
1 AATATATTTTATTTT
5951 AATATATTTTATTTT
1 AATATATTTTATTTT
* *
5966 ATTGAAATTTTATTTT
1 AAT-ATATTTTATTTT
5982 TAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 5 0.19
15 11 0.41
16 11 0.41
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (15 bp):
AATATATTTTATTTT
Found at i:7034 original size:293 final size:293
Alignment explanation
Indices: 6507--7166 Score: 1234
Period size: 293 Copynumber: 2.3 Consensus size: 293
6497 AATGCCAATT
*
6507 TTTATCTCAGTTTATTTTCTTGGTATGGAATTTTTATCAACTTTTCATCCAAGTGGATTCTTGGT
1 TTTATCTCAGTTTATTTTCCTGGTATGGAATTTTTATCAACTTTTCATCCAAGTGGATTCTTGGT
* *
6572 GAGTTTGATTTCACGCTATACGCTGCGTCAGTAAATGATGCGGGGATAAGAAGTAATTAATCGGG
66 GAGTTTGATTTCACGCTATACACTGCGTCAGTAAATGACGCGGGGATAAGAAGTAATTAATCGGG
6637 GCTTTTGACTTGGGCTGAATTGGTTGGATTTTATAATTACATTTTGGACTCTATTTTATTATTGG
131 GCTTTTGACTTGGGCTGAATTGGTTGGATTTTATAATTACATTTTGGACTCTATTTTATTATTGG
6702 CTTTAGTATTTTATTTTATTTAGTACTTTAATTAGTTTTGACAGGGTATTTAAGGTTTAGAAAAC
196 CTTTAGTATTTTATTTTATTTAGTACTTTAATTAGTTTTGACAGGGTATTTAAGGTTTAGAAAAC
*
6767 CCTAGTTTATGTAGAATCAATTATTTTCTCAAG
261 CCTAGTTTATGTAGAATCAATTATTTTCTCAAA
*
6800 TTTATCTCAGTTTATTTTCCTGGTATGGAATTTTTATCAACTTTTCATCCAAGTGGATTCTCGGT
1 TTTATCTCAGTTTATTTTCCTGGTATGGAATTTTTATCAACTTTTCATCCAAGTGGATTCTTGGT
*
6865 GAGTTTGATTTCACGCTATACACTGCGTCAGTAAATGACGCGGGGATTAGAAGTAATTAATCGGG
66 GAGTTTGATTTCACGCTATACACTGCGTCAGTAAATGACGCGGGGATAAGAAGTAATTAATCGGG
*
6930 GCTTTTGACTTGGGCTGAATTGGTTGGATTTTATGATTACATTTTGGACTCTATTTTATTATTGG
131 GCTTTTGACTTGGGCTGAATTGGTTGGATTTTATAATTACATTTTGGACTCTATTTTATTATTGG
6995 CTTTAGTATTTTATTTTA-TTATGTACTTTAATTAGTTTTGACAGGGTATTTAAGGTTTAGAAAA
196 CTTTAGTATTTTATTTTATTTA-GTACTTTAATTAGTTTTGACAGGGTATTTAAGGTTTAGAAAA
7059 CCCTAGTTTATGTAGAATCAATTATTTTCTCAAA
260 CCCTAGTTTATGTAGAATCAATTATTTTCTCAAA
7093 TTTATCTCAGTTTATTTTCCTGGTATGGAATTTTTATCAAC-TTTCATCCAAGTGGATTCTTGGT
1 TTTATCTCAGTTTATTTTCCTGGTATGGAATTTTTATCAACTTTTCATCCAAGTGGATTCTTGGT
7157 GAGTTTGATT
66 GAGTTTGATT
7167 CATGGAATAA
Statistics
Matches: 358, Mismatches: 8, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
292 35 0.10
293 323 0.90
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (293 bp):
TTTATCTCAGTTTATTTTCCTGGTATGGAATTTTTATCAACTTTTCATCCAAGTGGATTCTTGGT
GAGTTTGATTTCACGCTATACACTGCGTCAGTAAATGACGCGGGGATAAGAAGTAATTAATCGGG
GCTTTTGACTTGGGCTGAATTGGTTGGATTTTATAATTACATTTTGGACTCTATTTTATTATTGG
CTTTAGTATTTTATTTTATTTAGTACTTTAATTAGTTTTGACAGGGTATTTAAGGTTTAGAAAAC
CCTAGTTTATGTAGAATCAATTATTTTCTCAAA
Found at i:8141 original size:13 final size:14
Alignment explanation
Indices: 8118--8146 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
8108 TTAACTAATA
8118 AACTAAATTAAACT
1 AACTAAATTAAACT
8132 AACT-AATTAAACT
1 AACTAAATTAAACT
8145 AA
1 AA
8147 ATTAATTGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.59, C:0.14, G:0.00, T:0.28
Consensus pattern (14 bp):
AACTAAATTAAACT
Found at i:8146 original size:23 final size:22
Alignment explanation
Indices: 8109--8151 Score: 77
Period size: 23 Copynumber: 1.9 Consensus size: 22
8099 TTGTTTCAAT
8109 TAACTAATAAACTAAATTAAAC
1 TAACTAATAAACTAAATTAAAC
8131 TAACTAATTAAACTAAATTAA
1 TAACTAA-TAAACTAAATTAA
8152 TTGGACAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.58, C:0.12, G:0.00, T:0.30
Consensus pattern (22 bp):
TAACTAATAAACTAAATTAAAC
Found at i:8367 original size:18 final size:19
Alignment explanation
Indices: 8338--8375 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
8328 ACTTCACTCA
*
8338 CCCAATCAAATTCATTAAG
1 CCCAATCAAATTAATTAAG
8357 CCCAATC-AATTAATTAAG
1 CCCAATCAAATTAATTAAG
8375 C
1 C
8376 TATCACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.42, C:0.26, G:0.05, T:0.26
Consensus pattern (19 bp):
CCCAATCAAATTAATTAAG
Found at i:19979 original size:16 final size:15
Alignment explanation
Indices: 19956--19999 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
19946 ATTTTAAATT
19956 ATTACTTTTATTTTG
1 ATTACTTTTATTTTG
19971 ATATAC-TTTA--TT-
1 AT-TACTTTTATTTTG
19983 ATTACTTTTATTTTG
1 ATTACTTTTATTTTG
19998 AT
1 AT
20000 GTATAATCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 10
0.71 0.00 0.29
Matches are distributed among these distances:
11 3 0.12
12 6 0.25
13 2 0.08
14 2 0.08
15 8 0.33
16 3 0.12
ACGTcount: A:0.25, C:0.07, G:0.05, T:0.64
Consensus pattern (15 bp):
ATTACTTTTATTTTG
Found at i:22475 original size:92 final size:92
Alignment explanation
Indices: 22369--22555 Score: 374
Period size: 92 Copynumber: 2.0 Consensus size: 92
22359 AAGTAGAATT
22369 ACATGTCTAAATTATTATTTTAAAGAAAGAAAATTCCACACAGCCTGAAAAATTGATCCGGATTT
1 ACATGTCTAAATTATTATTTTAAAGAAAGAAAATTCCACACAGCCTGAAAAATTGATCCGGATTT
22434 TGTTTCTCATAACGTGTCAAAACTTTG
66 TGTTTCTCATAACGTGTCAAAACTTTG
22461 ACATGTCTAAATTATTATTTTAAAGAAAGAAAATTCCACACAGCCTGAAAAATTGATCCGGATTT
1 ACATGTCTAAATTATTATTTTAAAGAAAGAAAATTCCACACAGCCTGAAAAATTGATCCGGATTT
22526 TGTTTCTCATAACGTGTCAAAACTTTG
66 TGTTTCTCATAACGTGTCAAAACTTTG
22553 ACA
1 ACA
22556 AATAGTGTTG
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 95 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (92 bp):
ACATGTCTAAATTATTATTTTAAAGAAAGAAAATTCCACACAGCCTGAAAAATTGATCCGGATTT
TGTTTCTCATAACGTGTCAAAACTTTG
Found at i:32920 original size:58 final size:55
Alignment explanation
Indices: 32814--32994 Score: 204
Period size: 58 Copynumber: 3.2 Consensus size: 55
32804 TTCGTTACAT
* * *
32814 CATCAGGACCAATTTT-TTGGTCCAGATAATCTGAATGATAAATTGAAGGCAACAC
1 CATCAGGATCAATTTTATTAGTCCAGATGATCTGAATGAT-AATTGAAGGCAACAC
* * **
32869 CATCAGGATCAA-TTTATTAGTCCCGATGATTTGAGTAATTTTTAATTGAAGGCAACAC
1 CATCAGGATCAATTTTATTAGTCCAGATGATCT--G-AA-TGATAATTGAAGGCAACAC
* * *
32927 CATCAGGACCAATTTTTTTGGTCCAGATGATCTGAATGATAAGTTGAAGGCAACAC
1 CATCAGGATCAATTTTATTAGTCCAGATGATCTGAATGATAA-TTGAAGGCAACAC
32983 CATCAGGATCAA
1 CATCAGGATCAA
32995 GCTATTTATC
Statistics
Matches: 104, Mismatches: 15, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
54 3 0.03
55 27 0.26
56 26 0.25
57 2 0.02
58 28 0.27
59 18 0.17
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (55 bp):
CATCAGGATCAATTTTATTAGTCCAGATGATCTGAATGATAATTGAAGGCAACAC
Found at i:39556 original size:49 final size:49
Alignment explanation
Indices: 39503--39645 Score: 121
Period size: 49 Copynumber: 3.1 Consensus size: 49
39493 AGTAGAATCC
39503 CCTGTTATGGAATGACAACACTTTTGCTGAGTAATGTGATAGATACTTG
1 CCTGTTATGGAATGACAACACTTTTGCTGAGTAATGTGATAGATACTTG
*** * * **
39552 CCTGTTCAATTTCA-GA-AA-A-TTTGGC--A--AAT-AG-TAGA-A-TCC
1 CCTGTT--ATGGAATGACAACACTTTTGCTGAGTAATGTGATAGATACTTG
39591 CCTGTTATGGAATGACAACACTTTTGCTGAGTAATGTGATAGATACTTG
1 CCTGTTATGGAATGACAACACTTTTGCTGAGTAATGTGATAGATACTTG
39640 CCTGTT
1 CCTGTT
39646 CAATTTCAGA
Statistics
Matches: 66, Mismatches: 14, Indels: 28
0.61 0.13 0.26
Matches are distributed among these distances:
37 3 0.05
38 2 0.03
39 9 0.14
40 2 0.03
41 9 0.14
42 1 0.02
43 4 0.06
45 4 0.06
46 1 0.02
47 9 0.14
48 2 0.03
49 15 0.23
50 2 0.03
51 3 0.05
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (49 bp):
CCTGTTATGGAATGACAACACTTTTGCTGAGTAATGTGATAGATACTTG
Found at i:39640 original size:88 final size:88
Alignment explanation
Indices: 39491--39669 Score: 358
Period size: 88 Copynumber: 2.0 Consensus size: 88
39481 AGCACATTCC
39491 ATAGTAGAATCCCCTGTTATGGAATGACAACACTTTTGCTGAGTAATGTGATAGATACTTGCCTG
1 ATAGTAGAATCCCCTGTTATGGAATGACAACACTTTTGCTGAGTAATGTGATAGATACTTGCCTG
39556 TTCAATTTCAGAAAATTTGGCAA
66 TTCAATTTCAGAAAATTTGGCAA
39579 ATAGTAGAATCCCCTGTTATGGAATGACAACACTTTTGCTGAGTAATGTGATAGATACTTGCCTG
1 ATAGTAGAATCCCCTGTTATGGAATGACAACACTTTTGCTGAGTAATGTGATAGATACTTGCCTG
39644 TTCAATTTCAGAAAATTTGGCAA
66 TTCAATTTCAGAAAATTTGGCAA
39667 ATA
1 ATA
39670 AGTCATCAGG
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (88 bp):
ATAGTAGAATCCCCTGTTATGGAATGACAACACTTTTGCTGAGTAATGTGATAGATACTTGCCTG
TTCAATTTCAGAAAATTTGGCAA
Found at i:47962 original size:38 final size:38
Alignment explanation
Indices: 47911--47986 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
47901 ATAACATTTT
47911 TGCCTGCAAAACATCAAAATAACAAGTCAAAAATCTGA
1 TGCCTGCAAAACATCAAAATAACAAGTCAAAAATCTGA
47949 TGCCTGCAAAACATCAAAATAACAAGTCAAAAATCTGA
1 TGCCTGCAAAACATCAAAATAACAAGTCAAAAATCTGA
47987 ACTATATAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.50, C:0.21, G:0.11, T:0.18
Consensus pattern (38 bp):
TGCCTGCAAAACATCAAAATAACAAGTCAAAAATCTGA
Found at i:48231 original size:21 final size:21
Alignment explanation
Indices: 48205--48247 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
48195 ATATAGGGGA
48205 TTACTAAATACCGCCCCCTTT
1 TTACTAAATACCGCCCCCTTT
** *
48226 TTACTAGGTACCGCCCTCTTT
1 TTACTAAATACCGCCCCCTTT
48247 T
1 T
48248 GGACTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.35, G:0.09, T:0.37
Consensus pattern (21 bp):
TTACTAAATACCGCCCCCTTT
Found at i:57095 original size:2 final size:2
Alignment explanation
Indices: 57082--57131 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
57072 TCAAGGTTTC
* *
57082 AT AT AT AA AT AT AT AT AT AT AA AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
57124 AT AT AT AT
1 AT AT AT AT
57132 TTAGGTTCAG
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:60143 original size:1 final size:1
Alignment explanation
Indices: 60139--60163 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
60129 AGGCTTTGTT
60139 GGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGG
60164 TGGTGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:72667 original size:5 final size:5
Alignment explanation
Indices: 72657--72685 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
72647 TTCTGGCCAA
72657 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
72686 AGGTGGCGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:76858 original size:1 final size:1
Alignment explanation
Indices: 76852--76884 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
76842 TCTCTCTTGG
76852 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
76885 CTACACACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:80213 original size:2 final size:2
Alignment explanation
Indices: 80208--80238 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
80198 GGGTGTTTAT
80208 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
80239 GTGTGTGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:87666 original size:25 final size:25
Alignment explanation
Indices: 87638--87689 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
87628 TTCTGGAAGA
*
87638 AACTATGCCCTGTTTTTACTATGGC
1 AACTATGCCCTGTTTTTACTAAGGC
87663 AACTATGCCCTGTTTTTACTAAGGC
1 AACTATGCCCTGTTTTTACTAAGGC
87688 AA
1 AA
87690 TTCAAGCACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (25 bp):
AACTATGCCCTGTTTTTACTAAGGC
Found at i:89552 original size:22 final size:22
Alignment explanation
Indices: 89526--89594 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 22
89516 TATACATGAA
89526 ATATTTGAAAGGTAAGATTTAT
1 ATATTTGAAAGGTAAGATTTAT
* *** *
89548 ATATTTGGACTTTATGA---A-
1 ATATTTGAAAGGTAAGATTTAT
89566 ATATTTGAAAGGTAAGATTTAT
1 ATATTTGAAAGGTAAGATTTAT
89588 ATATTTG
1 ATATTTG
89595 GACTTAGTCA
Statistics
Matches: 33, Mismatches: 10, Indels: 8
0.65 0.20 0.16
Matches are distributed among these distances:
18 12 0.36
19 1 0.03
21 1 0.03
22 19 0.58
ACGTcount: A:0.38, C:0.01, G:0.17, T:0.43
Consensus pattern (22 bp):
ATATTTGAAAGGTAAGATTTAT
Found at i:89576 original size:40 final size:40
Alignment explanation
Indices: 89521--89599 Score: 158
Period size: 40 Copynumber: 2.0 Consensus size: 40
89511 CCAAATATAC
89521 ATGAAATATTTGAAAGGTAAGATTTATATATTTGGACTTT
1 ATGAAATATTTGAAAGGTAAGATTTATATATTTGGACTTT
89561 ATGAAATATTTGAAAGGTAAGATTTATATATTTGGACTT
1 ATGAAATATTTGAAAGGTAAGATTTATATATTTGGACTT
89600 AGTCAACTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.42
Consensus pattern (40 bp):
ATGAAATATTTGAAAGGTAAGATTTATATATTTGGACTTT
Found at i:90151 original size:4 final size:4
Alignment explanation
Indices: 90142--90166 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
90132 CATAGAAGTT
90142 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
90167 CAGATCTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:93187 original size:2 final size:2
Alignment explanation
Indices: 93182--93209 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
93172 TTCCCCAACA
93182 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
93210 CGAAAAGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:113096 original size:38 final size:38
Alignment explanation
Indices: 113041--113275 Score: 218
Period size: 38 Copynumber: 5.9 Consensus size: 38
113031 GGTTGTCCTT
*
113041 GCATGGATTATACTGAATTCTGACTAATTTGGAGTTGA
1 GCATGGATTATATTGAATTCTGACTAATTTGGAGTTGA
*
113079 GCATGGATTATATTGAATTCTGACTAATTTGGAGTCAAGTCA
1 GCATGGATTATATTGAATTCTGACTAATTTGGAGT----TGA
* * *
113121 TTGCAAGGATTATATTGAATTATGACTAATTCGGAGTTGA
1 --GCATGGATTATATTGAATTCTGACTAATTTGGAGTTGA
* * * * * *
113161 GCATAGATTATATTGGATTCTGATTAATTTAGAATCAAGTCA
1 GCATGGATTATATTGAATTCTGACTAATTTGGAGT----TGA
* * *
113203 TTGCATGAATCATATTGAATTCTGACTAATTCGGAGTTGA
1 --GCATGGATTATATTGAATTCTGACTAATTTGGAGTTGA
* *
113243 GTATGGATTATATTGGATTCTGACTAATTTGGA
1 GCATGGATTATATTGAATTCTGACTAATTTGGA
113276 ATCAAGTCAT
Statistics
Matches: 156, Mismatches: 29, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
38 89 0.57
40 4 0.03
42 4 0.03
44 59 0.38
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (38 bp):
GCATGGATTATATTGAATTCTGACTAATTTGGAGTTGA
Found at i:113181 original size:82 final size:82
Alignment explanation
Indices: 113039--113285 Score: 386
Period size: 82 Copynumber: 3.0 Consensus size: 82
113029 ATGGTTGTCC
* * *
113039 TTGCATGGATTATACTGAATTCTGACTAATTTGGAGTTGAGCATGGATTATATTGAATTCTGACT
1 TTGCATGGATTATATTGAATTCTGACTAATTCGGAGTTGAGCATGGATTATATTGGATTCTGACT
*
113104 AATTTGGAGTCAAGTCA
66 AATTTGGAATCAAGTCA
* * * *
113121 TTGCAAGGATTATATTGAATTATGACTAATTCGGAGTTGAGCATAGATTATATTGGATTCTGATT
1 TTGCATGGATTATATTGAATTCTGACTAATTCGGAGTTGAGCATGGATTATATTGGATTCTGACT
*
113186 AATTTAGAATCAAGTCA
66 AATTTGGAATCAAGTCA
* * *
113203 TTGCATGAATCATATTGAATTCTGACTAATTCGGAGTTGAGTATGGATTATATTGGATTCTGACT
1 TTGCATGGATTATATTGAATTCTGACTAATTCGGAGTTGAGCATGGATTATATTGGATTCTGACT
113268 AATTTGGAATCAAGTCA
66 AATTTGGAATCAAGTCA
113285 T
1 T
113286 GTCGCTTATG
Statistics
Matches: 148, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 148 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (82 bp):
TTGCATGGATTATATTGAATTCTGACTAATTCGGAGTTGAGCATGGATTATATTGGATTCTGACT
AATTTGGAATCAAGTCA
Found at i:114855 original size:28 final size:29
Alignment explanation
Indices: 114808--114873 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
114798 CGTTTAGACG
*
114808 TTTTGCCCCCTGAACTTCAATCTT-GGACA
1 TTTTG-CCCATGAACTTCAATCTTGGGACA
* *
114837 TTTTGCCCATGAACTTCAATTTTGGGACG
1 TTTTGCCCATGAACTTCAATCTTGGGACA
114866 TTTTGCCC
1 TTTTGCCC
114874 CCTCAACCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
28 16 0.48
29 17 0.52
ACGTcount: A:0.18, C:0.27, G:0.17, T:0.38
Consensus pattern (29 bp):
TTTTGCCCATGAACTTCAATCTTGGGACA
Found at i:115071 original size:30 final size:30
Alignment explanation
Indices: 115037--115115 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 30
115027 CGAAGCCGTT
* *
115037 AAGTTGAGGGGGCAAAACGTTCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTTCCAAAATTA
* * *
115067 AAGTTCAGGAGGCAAAATG-TCCAAGATTA
1 AAGTTCAGGGGGCAAAACGTTCCAAAATTA
* *
115096 AAGTTTAGGGGACAAAACGT
1 AAGTTCAGGGGGCAAAACGT
115116 CTAAACGATA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
29 23 0.59
30 16 0.41
ACGTcount: A:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTTCCAAAATTA
Done.