Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013495.1 Corchorus olitorius cultivar O-4 contig13528, 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: 94800
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1444 original size:334 final size:331
Alignment explanation
Indices: 676--2223 Score: 1363
Period size: 333 Copynumber: 4.8 Consensus size: 331
666 GCGTTTTAGG
* * *
676 TAGTCCACGATTTCGG-TAAAATTTTGCAAAAATTGATCCGAAAGATTTATCCTCAATTTTTAAC
1 TAGTACACGATTTCGGCAAAAATTTTGCAAAAATTGA-CCGAAAGATTTTTCCTCAATTTTTAAC
*
740 CGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAA
65 CGCAATACTCGT-AAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAA
805 TATCATTTTTTCAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCG
129 TATCATTTTTTCAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCG
*
870 TAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGA
194 TAAAAACAAATCCTTAAATCCATTATGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGA
* * * * *
935 GTCTTGGCGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACC
259 GTCTTGGCGCCAAAAATCATCCAAAACTGAGCCGGGGCCCCGGAACACATTTTTAACCAAAAACC
1000 GTGATGAT
324 GTGATGAT
* * *
1008 TAGTACACGATTTCGGCAAAAATTTTACAAAAGTTCACCCGAAAGATTTTTCCTCAATTTTTAAC
1 TAGTACACGATTTCGGCAAAAATTTTGCAAAAATTGA-CCGAAAGATTTTTCCTCAATTTTTAAC
* *
1073 CGCAATAATCGTAAAATATATATAATTCAATGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAA
65 CGCAATACTCGTAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAA
1138 TATCATTTTTTCAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCG
129 TATCATTTTTTCAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCG
*
1203 TAAAAACAAATCCTTAAATCCATTATGGCTGAGATTTGGTTATGATTAATATAGATATTTCAATG
194 TAAAAACAAATCCTTAAATCCATTATGGCTGAGATTTGG-GATGATTAATATAGATATTTCAATG
*
1268 AGTCTTGGCGCCAAAAATCATCCAAAACTGAGCCGGGTCCCCGGAACACATTTTTAACCAAAAAC
258 AGTCTTGGCGCCAAAAATCATCCAAAACTGAGCCGGGGCCCCGGAACACATTTTTAACCAAAAAC
*
1333 CGTGATGGT
323 CGTGATGAT
* * *
1342 TTGTACACGATTTCGGCAAAAATTTTGCAAAAATTGACCAGAATGATTTTTCCTTAATTTTTAAC
1 TAGTACACGATTTCGGCAAAAATTTTGCAAAAATTGACC-GAAAGATTTTTCCTCAATTTTTAAC
* *
1407 CGCAATACTCATAAGAAATATATAACTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAA
65 CGCAATACTCGTAA-AAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAA
* *
1472 TATCATTTTTTCAATT-TTT-CC-AA--GA-TTC-AGA--AGAA-CGTAA-AA-A--CA-A--AT
129 TATCATTTTTTCAATTCTTTCCCGAATTAATTTCTA-ATTA-AATCGAAACAAGATTCAGATGAT
* * * * ** * * * *** * ** *
1520 CCTTAAATC-CAT--TGTAGCT-GATATTTGG-TTAGA-TTAATATAGA-TATTCCA-ATGA-GT
192 CGTAAAAACAAATCCT-TAAATCCAT-TATGGCTGAGATTTGGGAT-GATTAATATAGAT-ATTT
* * *** * * * ** * * * *
1576 C-TTG-G---T-GC-CAAAAATCATGCA---AAACTGAG-CCGGGGCCCTGGAACGCGC-TTTTA
253 CAATGAGTCTTGGCGCCAAAA--AT-CATCCAAA-ACTGAGCCGGGGCCCCGGA-ACACATTTTT
** * * * * * * *
1629 GTCAAACACCGTGATGGTTAC
313 AACCAAAAAC-CG-TGATGAT
* * ** * *** * * *
1650 TA-CACGA--TTTCT-GCAAAAATTTTGCAAAAATTGAG-CCGAAAGATTTTTCCTTAATTTTTA
1 TAGTAC-ACGATT-TCGGCAAAAATTTTGCAAAAAT-TGACCGAAAGATTTTTCCTCAATTTTTA
* * * * * *
1710 ACCGCAATACTCCTAAAAAATATATAATTCAATG-GAAGAAAGATTGAAGGGCTTTTCAGGCGTC
63 ACCGCAATACTCGT-AAAAATATATAATTCAACGCCAA-AAAGATTGAAGAGCTTTTCACGCTTC
* ** *
1774 TAATATCATTTTTTTTCAATT-TTTTCC-ATATTAATTTCGGATTAAATCGAAACATGATTCAGA
126 TAATATCA--TTTTTTCAATTCTTTCCCGA-ATTAATTTCTAATTAAATCGAAACAAGATTCAGA
* * * * * *
1837 T-ACTCGTAAAATCAAATCCTTAAATCCAATGTGGCTGAGATTTGGAATGATGAATATTGATATT
188 TGA-TCGTAAAAACAAATCCTTAAATCCATTATGGCTGAGATTTGGGATGATTAATATAGATATT
** * * *
1901 TCAATGAGTCTTGGCGCCAAAAATCAAGCAAAACTTA-CCTGGGGCCCCGGAACACGTTTTTAGC
252 TCAATGAGTCTTGGCGCCAAAAATCATCCAAAACTGAGCC-GGGGCCCCGGAACACATTTTTAAC
1965 CAAAAACCGTGAT-AGT
316 CAAAAACCGTGATGA-T
1981 TAGTACACGATTTCGGCAAAAA---T-------TT-ACCAGAAAGA-TTTT--TCAATTTTTAAC
1 TAGTACACGATTTCGGCAAAAATTTTGCAAAAATTGACC-GAAAGATTTTTCCTCAATTTTTAAC
* * *
2032 CACAATACTCGTAAAAATTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGTTTCTAA
65 CGCAATACTCGTAAAAA-TATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAA
* * *
2097 TATCATTTTCTCAATTCCTTTCCTGAATTAGTTTCTAATTAAATCGAAACAAGATTCAGATGATC
129 TATCATTTTTTCAATT-CTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATC
* * * **
2162 GTAAAAGCAAATCCTTAAATCCATTGTGGCTGATATTT-GTTTAGATTAATATAGATATTTCA
193 GTAAAAACAAATCCTTAAATCCATTATGGCTGAGATTTGGGAT-GATTAATATAGATATTTCA
2224 TTTTAATTTT
Statistics
Matches: 977, Mismatches: 162, Indels: 166
0.75 0.12 0.13
Matches are distributed among these distances:
304 2 0.00
305 81 0.08
306 44 0.05
307 24 0.02
308 11 0.01
309 3 0.00
311 2 0.00
312 6 0.01
313 6 0.01
314 13 0.01
315 5 0.01
316 8 0.01
317 7 0.01
318 14 0.01
319 16 0.02
320 155 0.16
321 13 0.01
322 10 0.01
323 14 0.01
324 9 0.01
325 9 0.01
326 9 0.01
327 5 0.01
328 5 0.01
329 1 0.00
330 3 0.00
331 11 0.01
332 30 0.03
333 238 0.24
334 221 0.23
335 2 0.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (331 bp):
TAGTACACGATTTCGGCAAAAATTTTGCAAAAATTGACCGAAAGATTTTTCCTCAATTTTTAACC
GCAATACTCGTAAAAATATATAATTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATA
TCATTTTTTCAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTA
AAAACAAATCCTTAAATCCATTATGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGT
CTTGGCGCCAAAAATCATCCAAAACTGAGCCGGGGCCCCGGAACACATTTTTAACCAAAAACCGT
GATGAT
Found at i:1754 original size:639 final size:635
Alignment explanation
Indices: 214--2119 Score: 2385
Period size: 639 Copynumber: 3.0 Consensus size: 635
204 TAAATCGAAA
** * *
214 CAAGATTCAGATTATCGTAAAAACAAATTCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAA
1 CAAGATTCAGAAGAACGTAAAAACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAA
* * * *
279 TATAGTTATTTCAATGAGTCTTGGCGTCAAAAATCAAGCAAAATTGAGCCGGGGCCCCGGAACGC
66 TATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGC
* * * * **
344 ATTTTTAGCCAAAAACCGTGAT-G--ACT--TCG----GTAC-ACGATTTTGCAAAAATTGACCC
131 GTTTTTAGCCAAAAACCGTGATGGTTACTACACGATTTCTGCAAAAATTTTGCAAAAATTGACCC
* *
399 GAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCAACGACAAAAAG
196 GAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCAATG-GAAAAAG
* *
464 ATTGAAGAGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCTCGTATTAATTTCTAATTA
260 ATTGAAGAGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTAATTTCTAATTA
*
529 AATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTGGGG
325 AATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATT-TGG
594 AATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCC
389 AATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCC
* * * * *
659 CCAGAACGC-GTTT-----------T-A-GG-TAGTCCACGATTTCGG-TAAAATTTTGCAAAAA
454 CCGGAACACTTTTTACCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAA
*
708 TTGATCC-GAAAGATTTATCCTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCAACG
519 TTGA-CCAGAAAGATTTTTCCT-AATTTTTAACCGCAATACTCGT-AAAAATATATAATTCAACG
772 CCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCC
581 CCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCC
*
827 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCA
1 C-----AA-----GA-T---T-----C-AGA---AGA--A-CGTAAAAACAAATCCTTAAATCCA
* *
892 TTGTGGCTGAGATTTGG-GATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATG
40 TTGTGGCTGATATTTGGTTA-GATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATG
* * *
956 CAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTT
104 CAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTACTACACGATTT
* * * * *
1021 CGGCAAAAATTTTACAAAAGTTCACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATAATCGTA
169 CTGCAAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTA
* *
1086 AAATATATATAATTCAATGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATCATTTTTTCA
234 AAAAATATATAATTCAATG-GAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATCATTTTTTCA
1151 ATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCC
298 ATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCC
* *
1216 TTAAATCCATTATGGCTGAGATTTGGTTATGATTAATATAGATATTTCAATGAGTCTTGGCGCCA
363 TTAAATCCATTGTGGCTGAGATTTGG-AATGATTAATATAGATATTTCAATGAGTCTTGGCGCCA
* * *
1281 AAAATCATCCAAAACTGAGCCGGGTCCCCGGAACACATTTTTAACCAAAAACCGTGATGGTTTGT
427 AAAATCATGCAAAACTGAGCCGGGGCCCCGGAACAC-TTTTT-ACCAAAAACCGTGATGGTTAGT
*
1346 ACACGATTTCGGCAAAAATTTTGCAAAAATTGACCAGAATGATTTTTCCTTAATTTTTAACCGCA
490 ACACGATTTCGGCAAAAATTTTGCAAAAATTGACCAGAAAGATTTTTCC-TAATTTTTAACCGCA
* * *
1411 ATACTCATAAGAAATATATAACTCAACGCCAAAAAGATTGAAGAGCTTTTCACGCTTCTAATATC
554 ATACTCGTAA-AAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATC
1476 ATTTTTTCAATT-TTT-C
618 ATTTTTTCAATTCTTTCC
*
1492 CAAGATTCAGAAGAACGTAAAAACAAATCCTTAAATCCATTGTAGCTGATATTTGGTTAGATTAA
1 CAAGATTCAGAAGAACGTAAAAACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAA
* * *
1557 TATAGATATTCCAATGAGTCTTGGTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCTGGAACGC
66 TATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGC
* * * *
1622 GCTTTTAGTCAAACACCGTGATGGTTACTACACGATTTCTGCAAAAATTTTGCAAAAATTGAGCC
131 GTTTTTAGCCAAAAACCGTGATGGTTACTACACGATTTCTGCAAAAATTTTGCAAAAATTGACCC
* *
1687 GAAAGATTTTTCCTTAATTTTTAACCGCAATACTCCTAAAAAATATATAATTCAATGGAAGAAAG
196 GAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCAATGGAA-AAAG
* * * * **
1752 ATTGAAGGGCTTTTCAGGCGTCTAATATCATTTTTTTTCAATT-TTTTCC-ATATTAATTTCGGA
260 ATTGAAGAGCTTTTCACGCTTCTAATATCA--TTTTTTCAATTCTTTCCCGA-ATTAATTTCTAA
* * *
1815 TTAAATCGAAACATGATTCAGAT-ACTCGTAAAATCAAATCCTTAAATCCAATGTGGCTGAGATT
322 TTAAATCGAAACAAGATTCAGATGA-TCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATT
* * * *
1879 TGGAATGATGAATATTGATATTTCAATGAGTCTTGGCGCCAAAAATCAAGCAAAACTTA-CCTGG
386 TGGAATGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCC-GG
*
1943 GGCCCCGGAACACGTTTTTAGCCAAAAACCGTGATAGTTAGTACACGATTTCGGCAAAAA---T-
450 GGCCCCGGAACAC-TTTTTA-CCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTG
*
2004 ------TT-ACCAGAAAGATTTTT-C-AATTTTTAACCACAATACTCGTAAAAATTATATAATTC
513 CAAAAATTGACCAGAAAGATTTTTCCTAATTTTTAACCGCAATACTCGTAAAAA-TATATAATTC
* *
2060 AACGCCAAAAAGATTGAAGGGCTTTTCACGTTTCTAATATCATTTTCTCAATTCCTTTCC
577 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATT-CTTTCC
2120 TGAATTAGTT
Statistics
Matches: 1126, Mismatches: 96, Indels: 127
0.83 0.07 0.09
Matches are distributed among these distances:
613 1 0.00
618 2 0.00
623 1 0.00
624 4 0.00
625 81 0.07
627 5 0.00
628 15 0.01
629 2 0.00
632 1 0.00
633 3 0.00
636 2 0.00
638 6 0.01
639 479 0.43
640 78 0.07
641 11 0.01
642 5 0.00
644 2 0.00
645 3 0.00
646 1 0.00
648 3 0.00
649 270 0.24
651 4 0.00
654 1 0.00
655 1 0.00
660 2 0.00
663 1 0.00
664 1 0.00
665 4 0.00
666 21 0.02
667 115 0.10
668 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (635 bp):
CAAGATTCAGAAGAACGTAAAAACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTAGATTAA
TATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGC
GTTTTTAGCCAAAAACCGTGATGGTTACTACACGATTTCTGCAAAAATTTTGCAAAAATTGACCC
GAAAGATTTTTCCTCAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCAATGGAAAAAGA
TTGAAGAGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCCCGAATTAATTTCTAATTAA
ATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGAA
TGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCCC
GGAACACTTTTTACCAAAAACCGTGATGGTTAGTACACGATTTCGGCAAAAATTTTGCAAAAATT
GACCAGAAAGATTTTTCCTAATTTTTAACCGCAATACTCGTAAAAATATATAATTCAACGCCAAA
AAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTCAATTCTTTCC
Found at i:7963 original size:12 final size:11
Alignment explanation
Indices: 7946--7982 Score: 56
Period size: 12 Copynumber: 3.2 Consensus size: 11
7936 ACAAATCTTC
7946 TTCTTTTTTTCT
1 TTCTTTTTTT-T
7958 TTCTTTTTTTT
1 TTCTTTTTTTT
7969 TTCGTTTTTTTT
1 TTC-TTTTTTTT
7981 TT
1 TT
7983 GGGGGGGGGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.00, C:0.11, G:0.03, T:0.86
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:7967 original size:15 final size:15
Alignment explanation
Indices: 7943--7982 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
7933 TCCACAAATC
* *
7943 TTCTTCTTTTTTTCT
1 TTCTTTTTTTTTTCG
7958 TTCTTTTTTTTTTCG
1 TTCTTTTTTTTTTCG
7973 TT-TTTTTTTT
1 TTCTTTTTTTT
7983 GGGGGGGGGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (15 bp):
TTCTTTTTTTTTTCG
Found at i:19819 original size:6 final size:6
Alignment explanation
Indices: 19808--19832 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
19798 TTTTTGAGGA
19808 GAGTTT GAGTTT GAGTTT GAGTTT G
1 GAGTTT GAGTTT GAGTTT GAGTTT G
19833 TTTCCAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.36, T:0.48
Consensus pattern (6 bp):
GAGTTT
Found at i:26051 original size:65 final size:66
Alignment explanation
Indices: 25946--26077 Score: 239
Period size: 65 Copynumber: 2.0 Consensus size: 66
25936 TCGATTCTGG
* *
25946 ATATCCGCCTTTAGATCACAATATTATCATGGAGGCACTTGAAGATCTCCTATATTACATGTTCA
1 ATATCCGCCTTTAGATCACAATATTATCATGGAGCCACTTGAAGATCTCCTATATTAAATGTTCA
26011 A
66 A
26012 ATATCCGCCTTTAGATCAC-ATATTATCATGGAGCCACTTGAAGATCTCCTATATTAAATGTTCA
1 ATATCCGCCTTTAGATCACAATATTATCATGGAGCCACTTGAAGATCTCCTATATTAAATGTTCA
26076 A
66 A
26077 A
1 A
26078 CCACATTAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 45 0.70
66 19 0.30
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (66 bp):
ATATCCGCCTTTAGATCACAATATTATCATGGAGCCACTTGAAGATCTCCTATATTAAATGTTCA
A
Found at i:28689 original size:7 final size:7
Alignment explanation
Indices: 28677--28703 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28667 TGCATAAATG
28677 AGTGGGC
1 AGTGGGC
28684 AGTGGGC
1 AGTGGGC
28691 AGTGGGC
1 AGTGGGC
28698 AGTGGG
1 AGTGGG
28704 TGGGGTGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.59, T:0.15
Consensus pattern (7 bp):
AGTGGGC
Found at i:30206 original size:8 final size:8
Alignment explanation
Indices: 30193--30225 Score: 66
Period size: 8 Copynumber: 4.1 Consensus size: 8
30183 CTTGACATGC
30193 AATTTGCA
1 AATTTGCA
30201 AATTTGCA
1 AATTTGCA
30209 AATTTGCA
1 AATTTGCA
30217 AATTTGCA
1 AATTTGCA
30225 A
1 A
30226 TGCATCCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (8 bp):
AATTTGCA
Found at i:30739 original size:2 final size:2
Alignment explanation
Indices: 30725--30756 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
30715 CATCTATGAC
30725 TA TA TA -A TA -A TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
30757 GAAAAGAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:32158 original size:7 final size:7
Alignment explanation
Indices: 32148--32180 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
32138 AAAGAAAAAA
32148 TGCCAAT
1 TGCCAAT
32155 TGCCAAT
1 TGCCAAT
32162 TGCCAAT
1 TGCCAAT
32169 TGCCAAT
1 TGCCAAT
32176 TGCCA
1 TGCCA
32181 GCCAACCAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.30, G:0.15, T:0.27
Consensus pattern (7 bp):
TGCCAAT
Found at i:34333 original size:13 final size:13
Alignment explanation
Indices: 34315--34358 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
34305 ATATATTAAA
34315 AAATTAATGTATT
1 AAATTAATGTATT
34328 AAATTAATGTATT
1 AAATTAATGTATT
*
34341 AAATTTAT-T-TT
1 AAATTAATGTATT
34352 AAATTAA
1 AAATTAA
34359 ACCAACAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
11 8 0.28
12 1 0.03
13 20 0.69
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (13 bp):
AAATTAATGTATT
Found at i:40070 original size:13 final size:12
Alignment explanation
Indices: 40048--40083 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 12
40038 TTTTACTAAC
40048 AAAAAAAAAGAA
1 AAAAAAAAAGAA
40060 AAAAGAAAAAGAA
1 AAAA-AAAAAGAA
40073 AAAAAAGAAAG
1 AAAAAA-AAAG
40084 CATATGCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 6 0.27
13 16 0.73
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:41945 original size:20 final size:21
Alignment explanation
Indices: 41908--41949 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
41898 ATTTTTCTTT
*
41908 TTCCTTTTTCTTGTAATTTTG
1 TTCCTTTTTCTTGGAATTTTG
41929 TTCCTTTTT-TTGGAATTTTG
1 TTCCTTTTTCTTGGAATTTTG
41949 T
1 T
41950 GAATGTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.67
Consensus pattern (21 bp):
TTCCTTTTTCTTGGAATTTTG
Found at i:76335 original size:42 final size:43
Alignment explanation
Indices: 76271--76357 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 43
76261 ATATTACAAA
* *
76271 CACAGAATTCATGTAATCGAAGC-TGATGTGATAATGTCAGTG
1 CACAAAATTCATGTAATCGAAGCGTGATGTGAGAATGTCAGTG
* *
76313 CACAAAATTCATGTAATTGAAGCTGTGATGTGAGAATGTGAGTG
1 CACAAAATTCATGTAATCGAAGC-GTGATGTGAGAATGTCAGTG
76357 C
1 C
76358 CTACCAGCTG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
42 21 0.54
44 18 0.46
ACGTcount: A:0.33, C:0.13, G:0.25, T:0.29
Consensus pattern (43 bp):
CACAAAATTCATGTAATCGAAGCGTGATGTGAGAATGTCAGTG
Found at i:78166 original size:3 final size:3
Alignment explanation
Indices: 78158--78201 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
78148 ATTTTTTCAT
78158 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATTA ATA AT- ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA AT
78202 TGTAAAGAGA
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:84935 original size:30 final size:30
Alignment explanation
Indices: 84901--85166 Score: 331
Period size: 30 Copynumber: 8.9 Consensus size: 30
84891 AATGCAACCA
84901 CAGCTACCACAGATGCAACAGCAGCAGCCG
1 CAGCTACCACAGATGCAACAGCAGCAGCCG
84931 CAGCTACCACAGATGCAACAGCAGCAGCCG
1 CAGCTACCACAGATGCAACAGCAGCAGCCG
84961 CAGCTACCACAGATGCAACAGCAGCAGCCG
1 CAGCTACCACAGATGCAACAGCAGCAGCCG
*
84991 CAGCTACCACAGATGCAACAGCAGCAACCG
1 CAGCTACCACAGATGCAACAGCAGCAGCCG
*
85021 CAGCTACCACAGATGCAACAGCAGCAGCAG
1 CAGCTACCACAGATGCAACAGCAGCAGCCG
** * *
85051 CAGCTTTCTCAGATG---CAGCAGCAGCAG
1 CAGCTACCACAGATGCAACAGCAGCAGCCG
* *
85078 CAGCTGCCACAGATGCAGCAGCAGCAGCAGCCT
1 CAGCTACCACAGATGCA--A-CAGCAGCAGCCG
* * * * **
85111 CAACTTCCGCAAATGCAACAGCAGCAATCG
1 CAGCTACCACAGATGCAACAGCAGCAGCCG
* * *
85141 CAGCTGCCACAGATGCAGCAACAGCA
1 CAGCTACCACAGATGCAACAGCAGCA
85167 TCAGCTTCAA
Statistics
Matches: 206, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
27 24 0.12
30 158 0.77
31 1 0.00
33 23 0.11
ACGTcount: A:0.33, C:0.35, G:0.23, T:0.09
Consensus pattern (30 bp):
CAGCTACCACAGATGCAACAGCAGCAGCCG
Found at i:85199 original size:63 final size:63
Alignment explanation
Indices: 85077--85200 Score: 149
Period size: 63 Copynumber: 2.0 Consensus size: 63
85067 AGCAGCAGCA
* ** ** *
85077 GCAGCTGCCACAGATGCAGCAGCAGCAGCAGCCTCAACTTCCGCAAATGCAACAGCAGCAATC
1 GCAGCTGCCACAGATGCAGCAACAGCAGCAGCCTCAACAGCCGCAAACACAACAACAGCAATC
* * * * *
85140 GCAGCTGCCACAGATGCAGCAACAGCATCAGCTTCAACAGCTGCAACCACAGCAACAGCAA
1 GCAGCTGCCACAGATGCAGCAACAGCAGCAGCCTCAACAGCCGCAAACACAACAACAGCAA
85201 CAATTACAAC
Statistics
Matches: 50, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
63 50 1.00
ACGTcount: A:0.34, C:0.35, G:0.21, T:0.10
Consensus pattern (63 bp):
GCAGCTGCCACAGATGCAGCAACAGCAGCAGCCTCAACAGCCGCAAACACAACAACAGCAATC
Found at i:85249 original size:30 final size:30
Alignment explanation
Indices: 85213--85280 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
85203 ATTACAACAA
85213 CAGCAGCTTCCACACTTACAGCAGCAGCAG
1 CAGCAGCTTCCACACTTACAGCAGCAGCAG
* *
85243 CAGCAGCTTTCACAGTTACAGCAGCAGCAG
1 CAGCAGCTTCCACACTTACAGCAGCAGCAG
85273 CAGCAGCT
1 CAGCAGCT
85281 CTCCCAGCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.34, G:0.22, T:0.15
Consensus pattern (30 bp):
CAGCAGCTTCCACACTTACAGCAGCAGCAG
Found at i:85301 original size:30 final size:30
Alignment explanation
Indices: 85237--85308 Score: 81
Period size: 30 Copynumber: 2.4 Consensus size: 30
85227 CTTACAGCAG
* * * *
85237 CAGCAGCAGCAGCTTTCACAGTTACAGCAG
1 CAGCAGCAGCAGCTCTCACAGCTACAACAA
* *
85267 CAGCAGCAGCAGCTCTCCCAGCTGCAACAA
1 CAGCAGCAGCAGCTCTCACAGCTACAACAA
*
85297 CAGCAACAGCAG
1 CAGCAGCAGCAG
85309 TTGCAGCAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.32, C:0.35, G:0.22, T:0.11
Consensus pattern (30 bp):
CAGCAGCAGCAGCTCTCACAGCTACAACAA
Done.