Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014058.1 Corchorus capsularis cultivar CVL-1 contig14079, 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: 113586
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1058 original size:39 final size:34
Alignment explanation
Indices: 984--1053 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
974 TACAGGGTCC
984 TAATTAATTTATTTTATTTTATTTAATTAAATCA
1 TAATTAATTTATTTTATTTTATTTAATTAAATCA
1018 TAATTAATTTATTTTATTTTATTTAATTAAATCA
1 TAATTAATTTATTTTATTTTATTTAATTAAATCA
1052 TA
1 TA
1054 TCATATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.59
Consensus pattern (34 bp):
TAATTAATTTATTTTATTTTATTTAATTAAATCA
Found at i:7608 original size:2 final size:2
Alignment explanation
Indices: 7596--7631 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
7586 ATCTTTAATC
7596 AT AT AT A- AT AT AT AT AT AT AT A- AT -T AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
7632 ATTTAGTTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.10
2 28 0.90
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:7625 original size:14 final size:14
Alignment explanation
Indices: 7596--7634 Score: 69
Period size: 14 Copynumber: 2.7 Consensus size: 14
7586 ATCTTTAATC
7596 ATATATAATATATAT
1 ATATATAAT-TATAT
7611 ATATATAATTATAT
1 ATATATAATTATAT
7625 ATATATAATT
1 ATATATAATT
7635 TAGTTAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 15 0.62
15 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATATAATTATAT
Found at i:11186 original size:33 final size:33
Alignment explanation
Indices: 11147--11208 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
11137 TACTGTAAAT
*
11147 TTAATTTTTG-AGGTTTGACGAGGGATCCAAAA
1 TTAAATTTTGAAGGTTTGACGAGGGATCCAAAA
*
11179 TTAAATTTTGAAGGTTTGAGGAGGGATCCA
1 TTAAATTTTGAAGGTTTGACGAGGGATCCA
11209 CTTTACACCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 9 0.33
33 18 0.67
ACGTcount: A:0.31, C:0.08, G:0.27, T:0.34
Consensus pattern (33 bp):
TTAAATTTTGAAGGTTTGACGAGGGATCCAAAA
Found at i:13616 original size:46 final size:46
Alignment explanation
Indices: 13549--13641 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
13539 GCAGGAGCTA
13549 ATAATTAAGAATGGTTTGCAGCAACATGAATGGCTACAAGGATTGT
1 ATAATTAAGAATGGTTTGCAGCAACATGAATGGCTACAAGGATTGT
13595 ATAATTAAGAATGGTTTGCAGCAACATGAATGGCTACAAGGATTGT
1 ATAATTAAGAATGGTTTGCAGCAACATGAATGGCTACAAGGATTGT
13641 A
1 A
13642 CCGAATTCGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.38, C:0.11, G:0.24, T:0.28
Consensus pattern (46 bp):
ATAATTAAGAATGGTTTGCAGCAACATGAATGGCTACAAGGATTGT
Found at i:17829 original size:2 final size:2
Alignment explanation
Indices: 17822--17865 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
17812 TTTCTTAACC
*
17822 AT AT AT AT AT CT AT 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 AT AT AT AT AT AT AT
17864 AT
1 AT
17866 GCACAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23569 original size:332 final size:333
Alignment explanation
Indices: 22776--23638 Score: 890
Period size: 332 Copynumber: 2.6 Consensus size: 333
22766 GATAAGAATA
* * * *
22776 ACCCGAAAAATTTTTCCTCAATTTTTGGAA--AAAATACTCAATATATATATATATATAATTCAA
1 ACCCGAAAGATATTTCCTCAATTTCT--AACGAAAATACTC-ATA-A-AAATATATATAATTCAA
* * *
22839 CGCCAAAAAGATTG-GAGTACTTTTTACGCTTTTAATATCGTTTTT-CATATTTTTTCTGAATTA
61 CACCAAAAAGATTGAAAG-ACTTTTTACGCTTCTAATATCGTTTTTCCATATTTTTT-TGAATTA
* *
22902 ATTTCTAATATTAAATCAAAACAAGATTCAGATGCACATAAAAACAAATCCTTAAATCCAATATG
124 ATTTCT-A-ATTAAATCGAAACAAGATTCAAATGCACATAAAAACAAATCCTTAAATCCAATATG
* ** * **
22967 GCTGAGATTTGATTAGATGAAAAAACATAATTCAAGGAGTTTCGGTGCCAAAAATCATGCCAAAT
187 GCTGAGATTTGATTACATGAAAAAACATAATTCAAGGAGTTTCGGCACAAAAAATCATGAAAAAT
* * * * * * *
23032 AGAGCTTTGACCCTCTAACGCGTTTTTGGCCAAAAATTCGTGATGATTAGTACACGATTTCGGCT
252 AGAGCTTGGACCCTCGAACGCGTTTTTAGCCAAAAATCCATGATGATAAGTACACGATTTCAGCT
* *
23097 AATTTTTGCAAAAAATG
317 AAATTTTACAAAAAATG
* ** * *
23114 ACCCGAAAGATATTTCCTCAATTTTTAATTAAAATACTCATAAAAATATATATAATTCGACATCA
1 ACCCGAAAGATATTTCCTCAATTTCTAACGAAAATACTCATAAAAATATATATAATTCAACACCA
* * * * * * * * *
23179 AAAAGATTGAAGGGCTTTTAATGTTTCTAATATTGCTTTTCC-TATTTTCTCGAATTAATTTCTA
66 AAAAGATTGAAAGACTTTTTACGCTTCTAATATCGTTTTTCCATATTTTTTTGAATTAATTTCTA
*
23243 ATTAAATCGAAACAAGATTCAAATGCACATAAAAACTAATCCTTAAATCCAATATGGCTGAGATT
131 ATTAAATCGAAACAAGATTCAAATGCACATAAAAACAAATCCTTAAATCCAATATGGCTGAGATT
* * * * *
23308 TGGTTACATGAATATAGATATTTCAAGGAGTCTT-GGCACAAAAAATCATGAAAAACT-GAGC-T
196 TGATTACATGAAAAAACATAATTCAAGGAGT-TTCGGCACAAAAAATCATGAAAAA-TAGAGCTT
*
23370 GGA-CCTCGGAACGCGTTTTTAGCCGAAAA-CCATGATG-TAACGTACACGATTTCAGCTAAATT
259 GGACCCTC-GAACGCGTTTTTAGCCAAAAATCCATGATGATAA-GTACACGATTTCAGCTAAATT
*
23432 TTACAAAAATTG
322 TTACAAAAAATG
* * * * * *
23444 AGCCGAAAGAT-TTTTCTCTATTTCTAGCGAAAATACTCTTAAAAA-ATATATAATTCAATACCA
1 ACCCGAAAGATATTTCCTCAATTTCTAACGAAAATACTCATAAAAATATATATAATTCAACACCA
* * * *
23507 AAAAAATTGAAAGCCTTTTTCACGCTTCTAATATCATTTTTCCTATATTATTTTTAAATTAATTT
66 AAAAGATTGAAAGACTTTTT-ACGCTTCTAATATCGTTTTTCC-ATATT-TTTTTGAATTAATTT
* * * * * * * * *
23572 CTGATTAAATCGAAACAAGATTTAGAA-ACTCGTAAAAACAAATCTTTAAATACAATGTGGTTGA
128 CTAATTAAATCGAAACAAGATTCA-AATGCACATAAAAACAAATCCTTAAATCCAATATGGCTGA
23636 GAT
192 GAT
23639 ATTTAAAAAT
Statistics
Matches: 437, Mismatches: 75, Indels: 32
0.80 0.14 0.06
Matches are distributed among these distances:
328 31 0.07
329 46 0.11
330 49 0.11
331 25 0.06
332 173 0.40
333 6 0.01
334 12 0.03
335 54 0.12
336 5 0.01
337 3 0.01
338 33 0.08
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (333 bp):
ACCCGAAAGATATTTCCTCAATTTCTAACGAAAATACTCATAAAAATATATATAATTCAACACCA
AAAAGATTGAAAGACTTTTTACGCTTCTAATATCGTTTTTCCATATTTTTTTGAATTAATTTCTA
ATTAAATCGAAACAAGATTCAAATGCACATAAAAACAAATCCTTAAATCCAATATGGCTGAGATT
TGATTACATGAAAAAACATAATTCAAGGAGTTTCGGCACAAAAAATCATGAAAAATAGAGCTTGG
ACCCTCGAACGCGTTTTTAGCCAAAAATCCATGATGATAAGTACACGATTTCAGCTAAATTTTAC
AAAAAATG
Found at i:24774 original size:332 final size:327
Alignment explanation
Indices: 23702--26188 Score: 1436
Period size: 332 Copynumber: 7.4 Consensus size: 327
23692 AACAAATCAT
* * * * *
23702 GATTTAGGCTAATATTTTTCAAAAATTGAC-CTATAATAT-TTAT-CTCAATTTTTAGCCACAAT
1 GATTTCGGCTAAAATTTTGCAAAAATTGACTCGA-AATATATT-TCCTCAATTTTTAGCCAAAAT
* * ** * * * *
23764 ACTCATAAAAAATATATAATTGAATGCAAAAAAGATTGAAGGGCTTCTCACGCTTCTAATATCGG
64 ACTCAT-AAAATTATATAATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATC-G
* * ** * *
23829 TTTTTTTTC-TAATTTTTTTCAAATTCATTTCTAATTAAATTGAAACATTATTAAAATACTCGTA
127 ---TTTTTCAT-ATTTTTCT-AAATTAATTTCTAATTAAATTGAAACAAGATTCAGATACTCGTA
* * * ** * * *
23893 AAAA-AAATCCTTCAATCTAACGTGGCTAAGATTTGGTCAGTTGAATATAGATATTTCAAGGAGT
187 AAAACAAATCCTTAAATCCAATGTATCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
* * * * * * * * *
23957 GTTGCCACCAAAAATCATTCAAAACTGA-CTCGGGGCCCCAGAACGCGTTTTTAGTAAAAA-AAA
252 CTAG-CGCCAAAAATCATGCAAAACTTAGC-CGGGG-CCCGGAACGCGTTTTTAGCAAAAACCAT
*
24020 AACCGTGA-TAGTACAC
314 GA---TGATTAGTACAC
* * * ** *
24036 GATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAAATTTTAATCATAATAC
1 GATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAATATATTTCCTCAATTTTTAGCCAAAATAC
* * ** * * ** *
24101 TCATAGAATCTATATAATTAAATGCC--AAA-ATTGGAGGA--TTTCACGCTTTTAACATCACTG
66 TCATAAAAT-TATATAATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTT
* * *
24161 TTCATA-TTTTCTGAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAATAA
130 TTCATATTTTTCT-AAATTAATTTCTAATTAAATTGAAACAAGATTCAGATACTCGTAAAAACAA
** * * * * * * *
24225 ATTTTTAAATTCAATGT-GCATGAGATTTGATTAAATGAATATAGATATTTCAAGGAGTGTCGGG
194 ATCCTTAAATCCAATGTATC-TAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT-AGC
* * * * * * * * *
24289 GGCAAAAATCATGCAAAACTAAGTCGGGGTCCCGAAATGCGTTTTTAACCAAAAATCGTG-TTAG
257 GCCAAAAATCATGCAAAACTTAGCCGGGG-CCCGGAACGCGTTTTT-AGCAAAAACCATGATGA-
*
24353 TTAGTAGAC
319 TTAGTACAC
* * * * * * *
24362 GGTTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCGTC-ATTTTTTGGCATAAAT
1 GATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAATATATTTCC-TCAATTTTTAGCCA-AAAT
* * * * *
24426 AATCATTATA-TATATAATTTAACACCAAAAAGATGGAAGGACTTATCACGCTTTTAATATCGTT
64 ACTCATAAAATTATATAATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTT
* * * * *
24490 TTTCATATTTTTCTGAATTAATTTCTAATTAAATTGAAAAAAAAGATTCGGATGCTCGTAAAAAT
129 TTTCATATTTTTCTAAATTAATTTCTAATTAAATTG--AAACAAGATTCAGATACTCGTAAAAAC
* * * * *
24555 AAATTCTTAAATCCAATGTATCTAAGATTTCATTAGATGAATATGGATATCTCAAAGAGTCTCAG
192 AAATCCTTAAATCCAATGTATCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT-AG
* ** *
24620 TGCCAAAAATCATGCAAAACTTAGTTGGGGCCCGGAACTCGTTTTTAGTCAAAAACCATGATGAT
256 CGCCAAAAATCATGCAAAACTTAGCCGGGGCCCGGAACGCGTTTTTAG-CAAAAACCATGATGAT
*
24685 TATTACAC
320 TAGTACAC
* * ** *
24693 GATTTGGGCTAGAATTTTTTAAAAATTGACTCGAAAGTA-ATTTCCTCAATTTTTAGCCACAATA
1 GATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAA-TATATTTCCTCAATTTTTAGCCAAAATA
* ** * * * * **
24757 CGCATAAAAATTATATAATTTAATGCCTAAAATATTGAAGGACTTTTCATGCTTCTAATATAATT
65 CTCAT-AAAATTATATAATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTT
* * * * * * *** *
24822 TTTCCTATTATTTTCTAAATTAATTTCTAATTAAATAGAAACATGATTCAAATGCTTGT-TTTAT
129 TTTCATA-T-TTTTCTAAATTAATTTCTAATTAAATTGAAACAAGATTCAGATACTCGTAAAAAC
* * * * * *
24886 AAATCCTTAAACATCCAACATGGATGAGATTTGGTTAGATTATAATATATATATATATATATATA
192 AAATCCTT-AA-ATCC-A-AT-G-T---A--T-CTAAGATT-TGAT-TAGAT-GA-ATATAGATA
* * * * ** * *
24951 TTTCAAGGAGTCTTGGCGCCAAAAATAATGCAACA-TTGAACCAGGACCCCGAAACGCGTTCTTA
241 TTTCAAGGAGTC-TAGCGCCAAAAATCATGCAAAACTT-AGCC-GGGGCCCGGAACGCGTTTTTA
* *
25015 GCCAAAAACCGTGATTTCGACTAACGTACAC
303 G-CAAAAACCATGA--T-GA-TTA-GTACAC
* * * * *
25046 GATTT-GGACTAATATTTTGCAAAAATTGTCTAGAAATAGT-TTTCCTCAATTGTT-GTCTAAAA
1 GATTTCGG-CTAAAATTTTGCAAAAATTGACTCGAAATA-TATTTCCTCAATTTTTAG-CCAAAA
* * * * * *
25108 TAATCATAAAATATATATAATTCAACTCCAAAAATATTGGAGAACTTTTCACGCTTTTAATATCG
63 TACTCATAAAAT-TATATAATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCG
* * * *
25173 TTTGTCATATTTTTCTAAATTAATTTCTAATTAAA-T----CAAAACT-AGATCCTCGTAAAAAC
127 TTTTTCATATTTTTCTAAATTAATTTCTAATTAAATTGAAACAAGATTCAGATACTCGTAAAAAC
* * ** ** * *
25232 AGATCCTTAAATGCAA--TATGGAGGAGATTTGATTAGATGAATATCTATATTTCATGGAGTCTT
192 AAATCCTTAAATCCAATGTATCTA--AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTA
* * * ** *
25295 GACGCCAAAAATAATGCAAAACTGAGCCGGTGTCCCAAAACGCGTTTTTAGCAAAAAAAAGCTAT
255 G-CGCCAAAAATCATGCAAAACTTAGCCGG-GGCCCGGAACGCGTTTTTAGC---AAAAA-CCAT
*
25360 GATGGTGTTAGTACAC
314 GAT-G-ATTAGTACAC
* * * *
25376 GATTTCGGCTAAAATTTTGCACAAAAATT-ATTAGAAA-ATTTTTTCCTCAATTTTTAGCTAAAA
1 GATTTCGGCTAAAATTTTG--CAAAAATTGACTCGAAATA-TATTTCCTCAATTTTTAGCCAAAA
* *
25439 TACTCATGAAATATATATAATTTAACACCAAAAAGATTGAAGGACTTTTCAGGCTTTTAATATCG
63 TACTCATAAAAT-TATATAATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCG
* * *
25504 TTTTTCATACTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAA
127 TTTTTCATA-TTTTTCTAAATTAATTTCTAATTAAATTGAAACAAGATTCAGATACTCGTAAAAA
* * * *
25569 CAAATCCTTAAATGCAATGTGGT-TGAGATTTGATTAGATGAATATGGATATATATCTCAAGTGA
191 CAAATCCTTAAATCCAATGT-ATCTAAGATTTGATTAGATGAATAT--AGATAT-T-TCAAG-GA
* * * *
25633 -TCTTAGCGCCAAAAAT-ATGCAAAA-TTAAGCCGAGACCCTGGAACACGTTTTTAGCAAAAA-A
250 GTC-TAGCGCCAAAAATCATGCAAAACTT-AGCCGGGGCCC-GGAACGCGTTTTTAGCAAAAACC
25694 ACTGGGATGATTAGTACAC
312 A-T--GATGATTAGTACAC
* * * *
25713 GATTTCAGCTAAAATTTTGCAAAAATTGAC-C-ATAATGATATTTACTCAATTTTTGGCTAAAAT
1 GATTTCGGCTAAAATTTTGCAAAAATTGACTCGA-AAT-ATATTTCCTCAATTTTTAGCCAAAAT
* * * * * ** * * *
25776 ACTCAAAAAAAAATATATAATTCAA-AGTCAAAAATATTGAAGGGTTTTTTACGCTTCTAAAATC
64 ACTC--ATAAAATTATATAATTTAACA-CCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATC
* ** * * * *
25840 ATTTTTCATATTTTTCCGAATTAATTTCTATTTAAATCGAAACAAAATTCGGATACTCGTAAAAA
126 GTTTTTCATATTTTTCTAAATTAATTTCTAATTAAATTGAAACAAGATTCAGATACTCGTAAAAA
* ** ** * * * * * *
25905 CAAATTCTTAATTAATGAAATGTGGCTGACATTTGATTAGATGAATATAGATAGTACAAGTATTC
191 CAAATCCTT-A--AATCCAATGTATCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
* * * * * * **
25970 TTGGCGCCAAAAA--ATGCAATACTGACCCAGGGGTCCCAGAACGCGTTTTCAGCACACAGAAAA
253 -TAGCGCCAAAAATCATGCAAAACTTAGCC-GGGG-CCCGGAACGCGTTTTTAGCA-A-A-AACC
**
26033 AAAAGTGA-T-GTTACAC
312 ATGA-TGATTAG-TACAC
* * * * * * *
26049 GATTTGGGCTAATATTTTGCAAAAAATT-A-TCCAAAATATTTTTTCTCAATTTCTAGCCACAAT
1 GATTTCGGCTAAAATTTTGC-AAAAATTGACT-CGAAATATATTTCCTCAATTTTTAGCCAAAAT
* * * * * * ** * *
26112 ACTCATAAAAAATATATAATTCAACGCTAAAAAGATTGAAGGGCTTGTCACAATTCTAATACCG-
64 ACTCAT-AAAATTATATAATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGT
*
26176 TTTTCCTATTTTT
128 TTTTCATATTTTT
26189 TTCCGAATTG
Statistics
Matches: 1697, Mismatches: 331, Indels: 250
0.74 0.15 0.11
Matches are distributed among these distances:
324 2 0.00
325 61 0.04
326 145 0.09
327 22 0.01
328 7 0.00
329 5 0.00
330 147 0.09
331 187 0.11
332 224 0.13
333 17 0.01
334 93 0.05
335 132 0.08
336 140 0.08
337 104 0.06
338 65 0.04
339 35 0.02
340 12 0.01
341 28 0.02
342 18 0.01
343 11 0.01
344 6 0.00
345 13 0.01
346 15 0.01
347 35 0.02
348 29 0.02
350 1 0.00
351 27 0.02
352 13 0.01
353 103 0.06
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (327 bp):
GATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAATATATTTCCTCAATTTTTAGCCAAAATAC
TCATAAAATTATATAATTTAACACCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTT
TCATATTTTTCTAAATTAATTTCTAATTAAATTGAAACAAGATTCAGATACTCGTAAAAACAAAT
CCTTAAATCCAATGTATCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTAGCGCCA
AAAATCATGCAAAACTTAGCCGGGGCCCGGAACGCGTTTTTAGCAAAAACCATGATGATTAGTAC
AC
Found at i:29133 original size:15 final size:17
Alignment explanation
Indices: 29110--29143 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
29100 AACTATAAAT
29110 AATATTATTATAAT-TA
1 AATATTATTATAATCTA
29126 AATA-TATTATAATCTA
1 AATATTATTATAATCTA
29142 AA
1 AA
29144 AATAGTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATTATTATAATCTA
Found at i:29146 original size:18 final size:18
Alignment explanation
Indices: 29105--29154 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 18
29095 TTCATAACTA
29105 TAAATAATATTATTATAAT
1 TAAA-AATATTATTATAAT
29124 T--AAATA-TATTATAAT
1 TAAAAATATTATTATAAT
29139 CTAAAAATAGTTATTA
1 -TAAAAATA-TTATTA
29155 GAAGTAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
15 9 0.35
16 5 0.19
17 1 0.04
18 5 0.19
19 1 0.04
20 5 0.19
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TAAAAATATTATTATAAT
Found at i:29230 original size:30 final size:31
Alignment explanation
Indices: 29188--29249 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
29178 ATAGTGGATT
* *
29188 ATTAATATTTTTCCATAGTTTAAAAATTTTA
1 ATTAATATTTTTCAATAATTTAAAAATTTTA
29219 ATTAATA-TTTTCAATAATTTAAAAATTTTA
1 ATTAATATTTTTCAATAATTTAAAAATTTTA
29249 A
1 A
29250 ATATTGGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.50
Consensus pattern (31 bp):
ATTAATATTTTTCAATAATTTAAAAATTTTA
Found at i:36630 original size:20 final size:20
Alignment explanation
Indices: 36605--36645 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
36595 GTTTCTTCTG
36605 TTTATTGTTGCCTAGTGAAC
1 TTTATTGTTGCCTAGTGAAC
36625 TTTATTGTTGCCTAGTGAAC
1 TTTATTGTTGCCTAGTGAAC
36645 T
1 T
36646 GAGTTAGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.15, G:0.20, T:0.46
Consensus pattern (20 bp):
TTTATTGTTGCCTAGTGAAC
Found at i:39344 original size:13 final size:13
Alignment explanation
Indices: 39326--39351 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
39316 GTTCTCGGGG
39326 AATGGTTTTGATT
1 AATGGTTTTGATT
39339 AATGGTTTTGATT
1 AATGGTTTTGATT
39352 GGTGATGTCA
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:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (13 bp):
AATGGTTTTGATT
Found at i:42730 original size:181 final size:176
Alignment explanation
Indices: 42375--42733 Score: 592
Period size: 181 Copynumber: 2.0 Consensus size: 176
42365 TCCATAAACA
*
42375 AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATGCTATTTAAT
1 AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
* * *
42440 CCTTACAATTATATGTTGGACGATTGAATGTTTCGGCTTTAATTGTTTTTTTTTCTATTTGACCG
66 CCTTACAATTATAGGTTGGACAATTGAATGTTTCGGCTTTAATTGTTTTTTTTTCTATTCGACCG
* *
42505 ATCAAGGTGATTCAGGTGTCTATTTAAAGGTAATTTCATGGTCTAC
131 ATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
42551 AATCATTTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAA
1 AATCA-TTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAA
* * *
42616 TCACTTACAATTATGGGTTGGACAATTGAATGTTTCGGTTTTAATTCTTTTATTTTTTTCTATTC
65 TC-CTTACAATTATAGGTTGGACAATTGAATGTTTCGGCTTTAA-T-TGTT-TTTTTTTCTATTC
42681 GACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
126 GACCGATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
42732 AA
1 AA
42734 CTTTCATGAA
Statistics
Matches: 169, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
176 5 0.03
177 60 0.36
178 37 0.22
179 1 0.01
180 3 0.02
181 63 0.37
ACGTcount: A:0.27, C:0.12, G:0.14, T:0.47
Consensus pattern (176 bp):
AATCATTTTTTTGTTGGATTATTTATTAAATGATCCTCATACTTTTATAATTTATACTATTTAAT
CCTTACAATTATAGGTTGGACAATTGAATGTTTCGGCTTTAATTGTTTTTTTTTCTATTCGACCG
ATCAAGGTGATTCAAGTGTCTATTTAAAGGTAATTCCATGGTCTAC
Found at i:47722 original size:13 final size:13
Alignment explanation
Indices: 47704--47731 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47694 TATAGATCTC
47704 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
47717 AAGAGGTGTGTTA
1 AAGAGGTGTGTTA
47730 AA
1 AA
47732 CACCCTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.29
Consensus pattern (13 bp):
AAGAGGTGTGTTA
Found at i:52286 original size:42 final size:42
Alignment explanation
Indices: 52227--52308 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
52217 TGTTGACACA
52227 TACCCCAACTGATAATTAATTATGTATTTAATATTCAAAACT
1 TACCCCAACTGATAATTAATTATGTATTTAATATTCAAAACT
*
52269 TACCCCACCTGATAATTAATTATGTATTTAATATTCAAAA
1 TACCCCAACTGATAATTAATTATGTATTTAATATTCAAAA
52309 TTAATATCAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.38
Consensus pattern (42 bp):
TACCCCAACTGATAATTAATTATGTATTTAATATTCAAAACT
Found at i:52567 original size:25 final size:25
Alignment explanation
Indices: 52539--52587 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
52529 CCCAACCCGA
52539 GACCCGGGAGACCC-AA-GACCCGAAT
1 GACCC-GGA-ACCCGAATGACCCGAAT
52564 GACCCGGAACCCGAATGACCCGAA
1 GACCCGGAACCCGAATGACCCGAA
52588 ACCCGTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
23 4 0.18
24 5 0.23
25 13 0.59
ACGTcount: A:0.33, C:0.37, G:0.27, T:0.04
Consensus pattern (25 bp):
GACCCGGAACCCGAATGACCCGAAT
Found at i:52633 original size:16 final size:16
Alignment explanation
Indices: 52533--52667 Score: 116
Period size: 16 Copynumber: 8.5 Consensus size: 16
52523 AACCCGCCCA
*
52533 ACCCGAGACCCGGGA-G
1 ACCCGAGACCC-GAATG
*
52549 ACCCAAGACCCGAATG
1 ACCCGAGACCCGAATG
52565 ACCCG-GAACCCGAATG
1 ACCCGAG-ACCCGAATG
* *
52581 ACCCGAAACCCGTATG
1 ACCCGAGACCCGAATG
* * *
52597 ACCTGAGATCCGACTG
1 ACCCGAGACCCGAATG
*
52613 ACCCGAGACCCGAATA
1 ACCCGAGACCCGAATG
*
52629 ACCCGA-ACCC-ATATT
1 ACCCGAGACCCGA-ATG
* *
52644 ACCCGAAACTCGAATG
1 ACCCGAGACCCGAATG
52660 ACCCGAGA
1 ACCCGAGA
52668 AAACTACCTG
Statistics
Matches: 95, Mismatches: 18, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
14 1 0.01
15 15 0.16
16 78 0.82
17 1 0.01
ACGTcount: A:0.33, C:0.36, G:0.21, T:0.10
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:53103 original size:13 final size:13
Alignment explanation
Indices: 53085--53157 Score: 53
Period size: 13 Copynumber: 5.8 Consensus size: 13
53075 ATTGTTTATT
53085 TTCATTATTAATA
1 TTCATTATTAATA
53098 TTCATTATT-AT-
1 TTCATTATTAATA
* * * *
53109 TTAATTTTTTATT
1 TTCATTATTAATA
*
53122 TTCATTATCAATA
1 TTCATTATTAATA
* *
53135 CTT-GTAATTAATA
1 -TTCATTATTAATA
53148 TTCATTATTA
1 TTCATTATTA
53158 TTTAATTGTT
Statistics
Matches: 44, Mismatches: 12, Indels: 8
0.69 0.19 0.12
Matches are distributed among these distances:
11 7 0.16
12 6 0.14
13 29 0.66
14 2 0.05
ACGTcount: A:0.33, C:0.08, G:0.01, T:0.58
Consensus pattern (13 bp):
TTCATTATTAATA
Found at i:53104 original size:37 final size:37
Alignment explanation
Indices: 53063--53134 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
53053 TATGTTTGAC
*
53063 CATTATTATTTAATTGTTTATTTTCATTATTAATATT
1 CATTATTATTTAATTGTTTATTTTCATTATCAATATT
*
53100 CATTATTATTTAATTTTTTATTTTCATTATCAATA
1 CATTATTATTTAATTGTTTATTTTCATTATCAATA
53135 CTTGTAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.31, C:0.07, G:0.01, T:0.61
Consensus pattern (37 bp):
CATTATTATTTAATTGTTTATTTTCATTATCAATATT
Found at i:54968 original size:413 final size:413
Alignment explanation
Indices: 54198--54969 Score: 975
Period size: 413 Copynumber: 1.9 Consensus size: 413
54188 CGCGTTGACT
** * *
54198 TTTATTTTTGTATTTTTTTTTATATTTGTCCGATTAAGATGATTCAAGTGTCTACTAAAAGGTAA
1 TTTATTTTTGTATTTTTGCTTATATTTGTCCAATTAAGATGATTCAAGTGTCTACTAAAAGATAA
* * * * * *
54263 TTTCATGATCTACAATTTTCATGAAGAACTCAAAAGCCAATTTTAATGTTTTGATTCTAAAAAAT
66 TTTCATGATCTACAACTTTCATAAAGAACTCAAAAACAAATTTTAATGTTTTAATTCAAAAAAAT
* * * * * * *
54328 GCTTCCGAAATTTTGTGGTTTTGATTGCCGGTCAATTTAATATCGTGTAATTTTTTATTCACATG
131 GCTTCAGAAATTTTGTCGTTTTGATTGCCGGTCAATTTAATACCATATAATTTTTGATCCACATG
* * * * *
54393 TCCAATTGAAGTTATTGAAGTGTCAGGTAAAAGGTTATTGCATGATTACGACTTTCATGAAGGAC
196 TCCAATTAAAGTTATTCAAGTGTCAGGTAAAAGGTTACTGCATAATTACGACTTTCATGAAGAAC
* ** *
54458 CCGAAAGCTAAATTTGATCTACGAATTTCACTAAGGGTTCAAAAGGGAATTTTTGTGCTTCAAGA
261 CCGAAAGCTAAATTTGATCCACGAATTTCACTAAGGGTTCAAAAGCAAATTTTTATGCTTCAAGA
*
54523 TCTCCATTAACAAACATTTTCTTTAATTGAATTATTTTTCTTATACTATTTAGTTCTTTACAAAT
326 TATCCATTAACAAACATTTTCTTTAATTGAATTATTTTTCTTATACTATTTAGTTCTTTACAAAT
54588 TCTATCTTAATCTAATGTTTAGA
391 TCTATCTTAATCTAATGTTTAGA
* * *
54611 TTTATTTTTTTATTCTTTGCTT-TATTTGTCCAATTAAGTTGATTCATGTGTCTA-TAAAAAGAT
1 TTTATTTTTGTATT-TTTGCTTATATTTGTCCAATTAAGATGATTCAAGTGTCTACT-AAAAGAT
* * *
54674 AATTTCATGATTTACAACTTTCATAAATG-ACTCAAAAATAAATTTTTATGTTTTAATTCAAAAA
64 AATTTCATGATCTACAACTTTCATAAA-GAACTCAAAAACAAATTTTAATGTTTTAATTCAAAAA
* * * * ** *
54738 AATGCTTTATAATTTTTTTCGTTTTGATTGTTGGTCTATTTAATACCATATAATTTTTGATCCAC
128 AATGCTTCAGAAATTTTGTCGTTTTGATTGCCGGTCAATTTAATACCATATAATTTTTGATCCAC
* *
54803 ATGTCCGATTAAAGTTATTCAAGTGTC-GGTTAAAAGGTTACTGTATAATCTACGACTTTCATGA
193 ATGTCCAATTAAAGTTATTCAAGTGTCAGG-TAAAAGGTTACTGCATAAT-TACGACTTTCATGA
* * * *
54867 AGAACCCGAAAG-TTAATTTGATCCACGAGTTTCA-TGAAGGGTTCAGAAGCAAATTTTTTATGT
256 AGAACCCGAAAGCTAAATTTGATCCACGAATTTCACT-AAGGGTTCAAAAGCAAA-TTTTTATGC
* * *
54930 TTCAAGATATCTATT-ACGAAATATTTTC-TTATTTGAATTA
319 TTCAAGATATCCATTAAC-AAACATTTTCTTTAATTGAATTA
54970 GCTATCAAAT
Statistics
Matches: 302, Mismatches: 49, Indels: 16
0.82 0.13 0.04
Matches are distributed among these distances:
412 4 0.01
413 238 0.79
414 60 0.20
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (413 bp):
TTTATTTTTGTATTTTTGCTTATATTTGTCCAATTAAGATGATTCAAGTGTCTACTAAAAGATAA
TTTCATGATCTACAACTTTCATAAAGAACTCAAAAACAAATTTTAATGTTTTAATTCAAAAAAAT
GCTTCAGAAATTTTGTCGTTTTGATTGCCGGTCAATTTAATACCATATAATTTTTGATCCACATG
TCCAATTAAAGTTATTCAAGTGTCAGGTAAAAGGTTACTGCATAATTACGACTTTCATGAAGAAC
CCGAAAGCTAAATTTGATCCACGAATTTCACTAAGGGTTCAAAAGCAAATTTTTATGCTTCAAGA
TATCCATTAACAAACATTTTCTTTAATTGAATTATTTTTCTTATACTATTTAGTTCTTTACAAAT
TCTATCTTAATCTAATGTTTAGA
Found at i:56609 original size:16 final size:18
Alignment explanation
Indices: 56582--56615 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
56572 TCGAATGTGA
56582 GTTTAGTTTGTA-ATTTG
1 GTTTAGTTTGTATATTTG
56599 GTTTA-TTTGTATATTTG
1 GTTTAGTTTGTATATTTG
56616 ATAGGTAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.18, C:0.00, G:0.21, T:0.62
Consensus pattern (18 bp):
GTTTAGTTTGTATATTTG
Found at i:60444 original size:37 final size:37
Alignment explanation
Indices: 60390--60469 Score: 133
Period size: 37 Copynumber: 2.2 Consensus size: 37
60380 CCGGAAATTG
* *
60390 TATATATTGAAAATTGCTTGATAGTGTTTGCTAGAAT
1 TATATATTGAAAATTGCTTGATAGTCTTTGCTAGAAC
*
60427 TATATATTGAAAGTTGCTTGATAGTCTTTGCTAGAAC
1 TATATATTGAAAATTGCTTGATAGTCTTTGCTAGAAC
60464 TATATA
1 TATATA
60470 CTGGGTTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (37 bp):
TATATATTGAAAATTGCTTGATAGTCTTTGCTAGAAC
Found at i:66717 original size:18 final size:18
Alignment explanation
Indices: 66694--66729 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
66684 ATAACTGTAT
66694 TTTGTATAGATATAATTA
1 TTTGTATAGATATAATTA
*
66712 TTTGTATGGATATAATTA
1 TTTGTATAGATATAATTA
66730 CATTCATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.14, T:0.50
Consensus pattern (18 bp):
TTTGTATAGATATAATTA
Found at i:76716 original size:47 final size:47
Alignment explanation
Indices: 76650--76745 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 47
76640 ACCCTTCTAT
76650 TTCTTCATCAGTATTCTATTCACCCAATTCTTCTACCGTAGAGATTC
1 TTCTTCATCAGTATTCTATTCACCCAATTCTTCTACCGTAGAGATTC
* * * * *
76697 TTCTTCATGAGTATTCTATTCACCCAGTTCTTGTACTGTTGAGATTC
1 TTCTTCATCAGTATTCTATTCACCCAATTCTTCTACCGTAGAGATTC
76744 TT
1 TT
76746 TTCTTATCTG
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.44
Consensus pattern (47 bp):
TTCTTCATCAGTATTCTATTCACCCAATTCTTCTACCGTAGAGATTC
Found at i:81376 original size:3 final size:3
Alignment explanation
Indices: 81368--81396 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
81358 AAGGAAAATA
81368 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
81397 TAAATGAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:92624 original size:2 final size:2
Alignment explanation
Indices: 92617--92645 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
92607 CATCACTCTG
92617 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
92646 TGATTTCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:94795 original size:23 final size:23
Alignment explanation
Indices: 94767--94813 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
94757 TCAAAAGTGT
*
94767 AAAAAATGGGGCGGTGTTTAGCA
1 AAAAAATGGGGCAGTGTTTAGCA
94790 AAAAAATGGGGCAGTGTTTAGCA
1 AAAAAATGGGGCAGTGTTTAGCA
94813 A
1 A
94814 CACCATTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.09, G:0.32, T:0.21
Consensus pattern (23 bp):
AAAAAATGGGGCAGTGTTTAGCA
Found at i:100801 original size:12 final size:13
Alignment explanation
Indices: 100784--100813 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
100774 GCCCAAATCC
100784 AAAATT-AAAAAA
1 AAAATTGAAAAAA
100796 AAAATTGAAAAAA
1 AAAATTGAAAAAA
100809 AAAAT
1 AAAAT
100814 ACTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (13 bp):
AAAATTGAAAAAA
Found at i:106289 original size:18 final size:18
Alignment explanation
Indices: 106266--106338 Score: 78
Period size: 18 Copynumber: 3.9 Consensus size: 18
106256 ACTTTAAATA
106266 CTAAATTCCATTAAGAGT
1 CTAAATTCCATTAAGAGT
106284 CTAAATT-C-TTAAGTTAGCAT
1 CTAAATTCCATTAAG--AG--T
*
106304 GATAAATTCCATTAAGAGT
1 -CTAAATTCCATTAAGAGT
106323 CTAAATTCCATTAAGA
1 CTAAATTCCATTAAGA
106339 CACTTTAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
16 5 0.11
17 1 0.02
18 24 0.52
19 1 0.02
20 1 0.02
21 8 0.17
22 1 0.02
23 5 0.11
ACGTcount: A:0.40, C:0.15, G:0.11, T:0.34
Consensus pattern (18 bp):
CTAAATTCCATTAAGAGT
Found at i:110198 original size:22 final size:22
Alignment explanation
Indices: 110173--110301 Score: 104
Period size: 22 Copynumber: 5.9 Consensus size: 22
110163 TGTCTCTATG
110173 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
110195 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
110218 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
110239 TGGTTACCAAAATTTCATACGGA
1 TGGTTATCAAAATTTCATA-AGA
* *
110262 -AGTTATCAAAATTTCA-AAGTG
1 TGGTTATCAAAATTTCATAAG-A
*
110283 TGGTTACCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
110302 GGATCAGGTT
Statistics
Matches: 81, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
20 2 0.02
21 1 0.01
22 73 0.90
23 4 0.05
24 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:110243 original size:44 final size:44
Alignment explanation
Indices: 110174--110301 Score: 161
Period size: 44 Copynumber: 2.9 Consensus size: 44
110164 GTCTCTATGT
* ** *
110174 GGTTATCAAAATTTCATAAG-ATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCAT-AGTGTGGTTACCAAAATTTCAT-ACGGA
*
110218 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATACGGA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATACGGA
* *
110262 AGTTATCAAAATTTCAAAGTGTGGTTACCAAAATTTCATA
1 GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATA
110302 GGATCAGGTT
Statistics
Matches: 74, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
43 3 0.04
44 71 0.96
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAGTGTGGTTACCAAAATTTCATACGGA
Found at i:110412 original size:22 final size:21
Alignment explanation
Indices: 110387--110778 Score: 123
Period size: 22 Copynumber: 17.7 Consensus size: 21
110377 ATCAAAGAGA
*
110387 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAG-GAGG
*
110409 TTAT-AAGAATTTCATAGTGTGG
1 TTATCAA-AATTTCATAG-GAGG
*
110431 TTAACAAAATTTCATTAGGAGG
1 TTATCAAAATTTCA-TAGGAGG
* *
110453 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCAT-AGGAGG
* * *
110475 TTATCAAAATTTTATAATGTGG
1 TTATCAAAATTTCAT-AGGAGG
* *
110497 TTATCAAAGTTTCATATGAAGG
1 TTATCAAAATTTCATA-GGAGG
*
110519 TTATAAAAGTCTCAATTTCATA--AGG
1 TTAT-CAA-----AATTTCATAGGAGG
* * * *
110544 AGTACCAAAATTTAATAGTAGG
1 -TTATCAAAATTTCATAGGAGG
* *
110566 TTATC-AAATCTCATA-GAGTTA
1 TTATCAAAATTTCATAGGAG--G
* *
110587 TTATCGAAATTTCATAGAGATCAGA
1 TTATCAAAATTTCATAG-G---AGG
*
110612 TTATCAAAATTT-ATAGGAAGA
1 TTATCAAAATTTCATAGG-AGG
* **
110633 TTATAAAAATTTCATAGTGTTG
1 TTATCAAAATTTCATAG-GAGG
* * *
110655 TTATCAAAATTTTAAAGCGAGA
1 TTATCAAAATTTCATAG-GAGG
* * * * *
110677 TTATCGAAATTACATAATGTGA
1 TTATCAAAATTTCAT-AGGAGG
* *
110699 TTATCAGAATTTCATAGAGGGG
1 TTATCAAAATTTCATAG-GAGG
* * * *
110721 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
* *
110743 TAATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCAT-AGGAGG
*
110765 TTATCAAATTTTCA
1 TTATCAAAATTTCA
110779 AAATGTGATT
Statistics
Matches: 274, Mismatches: 67, Indels: 58
0.69 0.17 0.15
Matches are distributed among these distances:
19 2 0.01
20 16 0.06
21 28 0.10
22 182 0.66
23 12 0.04
24 5 0.02
25 17 0.06
26 2 0.01
27 2 0.01
28 8 0.03
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
TTATCAAAATTTCATAGGAGG
Found at i:110951 original size:22 final size:22
Alignment explanation
Indices: 110926--111195 Score: 143
Period size: 22 Copynumber: 12.4 Consensus size: 22
110916 AGTTTAGTTT
*
110926 TCAAAACTTCATAAGAGGGTTA
1 TCAAAATTTCATAAGAGGGTTA
** *
110948 TCAAAATTTCATATTA-TGTTGA
1 TCAAAATTTCATAAGAGGGTT-A
110970 TCAAAATTTCAT-AG-GGAGATTA
1 TCAAAATTTCATAAGAGG-G-TTA
*
110992 ACAAAATTTCATAATGA-GGTTA
1 TCAAAATTTCATAA-GAGGGTTA
* *
111014 TCAAAATATCAT-AGGGAGGTTA
1 TCAAAATTTCATAAGAG-GGTTA
*
111036 TCAAAATTT-GT---A--GTTA
1 TCAAAATTTCATAAGAGGGTTA
* **
111052 TCAAGATTTCATAAGAAAGTTA
1 TCAAAATTTCATAAGAGGGTTA
* * *
111074 TCAAAATTTTATAGGAAGGTTTA
1 TCAAAATTTCATAAG-AGGGTTA
* * *
111097 TCAAAATTTTATAGGAAGGTTTA
1 TCAAAATTTCATAAG-AGGGTTA
* * **
111120 TCAAAATTTTATAGAAAGATTTA
1 TCAAAATTTCATA-AGAGGGTTA
111143 TCAAAATTTCATAACGA-GGTTA
1 TCAAAATTTCATAA-GAGGGTTA
* * *
111165 TCACAATTTCAT-AGCATGATTA
1 TCAAAATTTCATAAG-AGGGTTA
111187 TCAAAATTT
1 TCAAAATTT
111196 TAGAGTGTGA
Statistics
Matches: 196, Mismatches: 32, Indels: 40
0.73 0.12 0.15
Matches are distributed among these distances:
16 12 0.06
17 1 0.01
20 3 0.02
21 7 0.04
22 108 0.55
23 63 0.32
24 2 0.01
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAAGAGGGTTA
Found at i:110974 original size:44 final size:40
Alignment explanation
Indices: 110902--111044 Score: 126
Period size: 44 Copynumber: 3.3 Consensus size: 40
110892 TCAGGGAGGA
*
110902 TATCAAAATTTCATAGTT-TAGTTTTCAAAACTTCATAAGAGGGT
1 TATCAAAATTTCATA-TTAT-GTTATCAAAA-TTCAT-AG-GGGT
110946 TATCAAAATTTCATATTATGTTGATCAAAATTTCATAGGGAGAT
1 TATCAAAATTTCATATTATGTT-ATCAAAA-TTCATAGGG-G-T
* * *
110990 TAACAAAATTTCATAATGAGGTTATCAAAATATCATAGGGAGGT
1 TATCAAAATTTCAT-ATTATGTTATCAAAAT-TCATA-GG-GGT
111034 TATCAAAATTT
1 TATCAAAATTT
111045 GTAGTTATCA
Statistics
Matches: 85, Mismatches: 6, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
42 2 0.02
43 9 0.11
44 64 0.75
45 9 0.11
46 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (40 bp):
TATCAAAATTTCATATTATGTTATCAAAATTCATAGGGGT
Found at i:111039 original size:66 final size:65
Alignment explanation
Indices: 110883--111376 Score: 257
Period size: 66 Copynumber: 7.6 Consensus size: 65
110873 TTATGGAGTA
* * * *
110883 ATCAAAATTTC--AGGGAGGATATCAAAATTTCATAGTTTAGTTTTCAAAACTTCATAA-GAGGG
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAG-GTAGTTATCAAAATTTCATAATGA-GG
110945 TT
64 TT
** * * *
110947 ATCAAAATTTCATA-TTATGTTGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG
1 ATCAAAATTTCATAGGGAGGTT-ATCAAAATTTCATAGGTAG-TTATCAAAATTTCATAATGAGG
111011 TT
64 TT
* * *
111013 ATCAAAATATCATAGGGAGGTTATCAAAA-TT--T--GTAGTTATCAAGATTTCATAA-GAAAGT
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGTAGTTATCAAAATTTCATAATG-AGGT
111072 T
65 T
* * * * * *
111073 ATCAAAATTTTATAGGAAGGTTTATCAAAATTTTATAGGAAGGTTTATCAAAATTTTATAGA-AA
1 ATCAAAATTTCATAGGGAGG-TTATCAAAATTTCATAGGTA-G-TTATCAAAATTTCATA-ATGA
*
111137 GATTT
62 G-GTT
** * * * * * * *
111142 ATCAAAATTTCATAACGAGGTTATCACAATTTCATA-GCATGATTATCAAAATTTTAGAGTGTGA
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGTA-G-TTATCAAAATTTCATAATGAGG
111206 TT
64 TT
* ** * * * *
111208 A-CTAACAA-TTCATATGGAGGTT-TTTAAATCTTCATAATGTTGTTATCAATATATCAT-ATGG
1 ATC-AA-AATTTCATAGGGAGGTTATCAAAAT-TTCAT-AGGTAGTTATCAAAATTTCATAAT-G
*
111269 AGTTT
61 AGGTT
* * * ** * * * *
111274 GTCAACATATCATAGTGTTGGTTATCAAAATCTCATTGGGAAGTTATCAAAATTTCATATTGAGG
1 ATCAAAATTTCATAG-GGAGGTTATCAAAATTTCA-TAGGTAGTTATCAAAATTTCATAATGAGG
111339 TCT
64 T-T
* * *
111342 -TCAAAATTCCTTAGGGAGGTTAACAAAATTTCATA
1 ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATA
111377 AGAAGGTTAA
Statistics
Matches: 319, Mismatches: 80, Indels: 61
0.69 0.17 0.13
Matches are distributed among these distances:
59 1 0.00
60 36 0.11
61 12 0.04
62 2 0.01
63 1 0.00
64 12 0.04
65 15 0.05
66 115 0.36
67 68 0.21
68 38 0.12
69 19 0.06
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (65 bp):
ATCAAAATTTCATAGGGAGGTTATCAAAATTTCATAGGTAGTTATCAAAATTTCATAATGAGGTT
Found at i:111064 original size:38 final size:38
Alignment explanation
Indices: 111010--111082 Score: 101
Period size: 38 Copynumber: 1.9 Consensus size: 38
111000 TCATAATGAG
* * *
111010 GTTATCAAAATATCATAGGGAGGTTATCAAAATTTGTA
1 GTTATCAAAATATCATAAGAAAGTTATCAAAATTTGTA
* *
111048 GTTATCAAGATTTCATAAGAAAGTTATCAAAATTT
1 GTTATCAAAATATCATAAGAAAGTTATCAAAATTT
111083 TATAGGAAGG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.41, C:0.08, G:0.15, T:0.36
Consensus pattern (38 bp):
GTTATCAAAATATCATAAGAAAGTTATCAAAATTTGTA
Found at i:111099 original size:23 final size:23
Alignment explanation
Indices: 111049--111151 Score: 145
Period size: 23 Copynumber: 4.5 Consensus size: 23
111039 AAATTTGTAG
* * * *
111049 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTTATAGGAAGGT
111071 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAGGT
111094 TTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTTATAGGAAGGT
* *
111117 TTATCAAAATTTTATAGAAAGAT
1 TTATCAAAATTTTATAGGAAGGT
111140 TTATCAAAATTT
1 TTATCAAAATTT
111152 CATAACGAGG
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
22 18 0.24
23 56 0.76
ACGTcount: A:0.43, C:0.06, G:0.13, T:0.39
Consensus pattern (23 bp):
TTATCAAAATTTTATAGGAAGGT
Found at i:111123 original size:46 final size:45
Alignment explanation
Indices: 111049--111195 Score: 163
Period size: 46 Copynumber: 3.3 Consensus size: 45
111039 AAATTTGTAG
* * *
111049 TTATCAAGATTTCATAAGAAAGTTATCAAAATTTTATAGGAAGGT
1 TTATCAAAATTTCATAAGAAAGTTATCAAAATTTTATAGAAAGAT
* * *
111094 TTATCAAAATTTTATAGGAAGGTTTATCAAAATTTTATAGAAAGAT
1 TTATCAAAATTTCATAAGAAAG-TTATCAAAATTTTATAGAAAGAT
* * * * *
111140 TTATCAAAATTTCATAACG-AGGTTATCACAATTTCATAGCATGA-
1 TTATCAAAATTTCATAA-GAAAGTTATCAAAATTTTATAGAAAGAT
111184 TTATCAAAATTT
1 TTATCAAAATTT
111196 TAGAGTGTGA
Statistics
Matches: 88, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
44 12 0.14
45 36 0.41
46 39 0.44
47 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.37
Consensus pattern (45 bp):
TTATCAAAATTTCATAAGAAAGTTATCAAAATTTTATAGAAAGAT
Found at i:111264 original size:22 final size:22
Alignment explanation
Indices: 111239--111301 Score: 56
Period size: 22 Copynumber: 2.8 Consensus size: 22
111229 TTTTAAATCT
*
111239 TCATAATGTTGTTATCAATATA
1 TCATAATGTTGTTATCAACATA
** *
111261 TCAT-ATGGAGTTTGTCAACATA
1 TCATAATGTTG-TTATCAACATA
*
111283 TCATAGTGTTGGTTATCAA
1 TCATAATGTT-GTTATCAA
111302 AATCTCATTG
Statistics
Matches: 30, Mismatches: 8, Indels: 5
0.70 0.19 0.12
Matches are distributed among these distances:
21 4 0.13
22 17 0.57
23 8 0.27
24 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.41
Consensus pattern (22 bp):
TCATAATGTTGTTATCAACATA
Found at i:111383 original size:22 final size:22
Alignment explanation
Indices: 111358--111406 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
111348 TTCCTTAGGG
* *
111358 AGGTT-AACAAAATTTCATAAGA
1 AGGTTAAAAAAAATTT-ATAAAA
111380 AGGTTAAAAAAAATTTATAAAA
1 AGGTTAAAAAAAATTTATAAAA
111402 AGGTT
1 AGGTT
111407 CTCTAAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 15 0.62
23 9 0.38
ACGTcount: A:0.53, C:0.04, G:0.14, T:0.29
Consensus pattern (22 bp):
AGGTTAAAAAAAATTTATAAAA
Found at i:111596 original size:22 final size:22
Alignment explanation
Indices: 111568--111741 Score: 120
Period size: 22 Copynumber: 7.9 Consensus size: 22
111558 TGGTAATCAC
111568 TATAAAATTTTGATAACCTCCA
1 TATAAAATTTTGATAACCTCCA
* *
111590 TATAAAATTTTGATAA-TTACA
1 TATAAAATTTTGATAACCTCCA
* * * * *
111611 CTATAAAGTTTTTATGACGATAC-
1 -TATAAAATTTTGATAAC-CTCCA
* * *
111634 TATAGAATTTCGAGAACCTCCA
1 TATAAAATTTTGATAACCTCCA
* * * *
111656 TATGAAATTTTGTTAACTTCCC
1 TATAAAATTTTGATAACCTCCA
* *
111678 TATAAAATTTTG-TCACACTCCC
1 TATAAAATTTTGATAAC-CTCCA
* * *
111700 TATGAAATTTTGATAACCACCC
1 TATAAAATTTTGATAACCTCCA
*
111722 TATGAAATTTTGATAACCTC
1 TATAAAATTTTGATAACCTC
111742 TTGTTGGTAA
Statistics
Matches: 118, Mismatches: 28, Indels: 12
0.75 0.18 0.08
Matches are distributed among these distances:
21 8 0.07
22 104 0.88
23 3 0.03
24 3 0.03
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.37
Consensus pattern (22 bp):
TATAAAATTTTGATAACCTCCA
Found at i:111833 original size:22 final size:21
Alignment explanation
Indices: 111808--112169 Score: 161
Period size: 22 Copynumber: 16.6 Consensus size: 21
111798 TCACATTTTA
*
111808 AAATTTTGATAATCATACCATG
1 AAATTTTGATAACCAT-CCATG
111830 AAATTTTGAT-ACC-TCACTATG
1 AAATTTTGATAACCATC-C-ATG
* * *
111851 AAATTTTTATAAACATCCCTATT
1 AAATTTTGATAACCAT-CC-ATG
* *
111874 AAATTTTGATAACCTTCCGATA
1 AAATTTTGATAACCATCC-ATG
* * * * *
111896 AAATATCGGTAATCACAT-TATA
1 AAATTTTGATAA-C-CATCCATG
111918 AAATTTTGATAACCATACCATG
1 AAATTTTGATAACCAT-CCATG
* * *
111940 AAATTGTGATACCTCAT-TATG
1 AAATTTTGATAAC-CATCCATG
*
111961 AAATTTTTATAAACC-TCCCTATG
1 AAATTTTGAT-AACCAT-CC-ATG
* *
111984 AAATTTTGAAAACCATCTCACG
1 AAATTTTGATAACCATC-CATG
* *
112006 AAATTTTGAAAACCATCTTATG
1 AAATTTTGATAACCATC-CATG
*
112028 AAATTTTGATAACCATCTTATG
1 AAATTTTGATAACCATC-CATG
*
112050 AAATTTTGATAA-CATCCCTATA
1 AAATTTTGATAACCAT-CC-ATG
*
112072 AACATTTT-ATAACC-TCCTCATA
1 AA-ATTTTGATAACCAT-C-CATG
* *
112094 AAATTTTGTTAACC-TCCTACG
1 AAATTTTGATAACCATCC-ATG
* * * * *
112115 AATTTTTTATAAGAACA-CTATT
1 AAATTTTGAT-A-ACCATCCATG
112137 AAATTTTGATAACC-TCCAATG
1 AAATTTTGATAACCATCC-ATG
112158 AAATTTTGATAA
1 AAATTTTGATAA
112170 TTAACTACAC
Statistics
Matches: 263, Mismatches: 49, Indels: 57
0.71 0.13 0.15
Matches are distributed among these distances:
19 1 0.00
20 10 0.04
21 59 0.22
22 145 0.55
23 45 0.17
24 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.37
Consensus pattern (21 bp):
AAATTTTGATAACCATCCATG
Found at i:111899 original size:110 final size:110
Alignment explanation
Indices: 111760--111997 Score: 404
Period size: 110 Copynumber: 2.2 Consensus size: 110
111750 AAGCGCACAT
* *
111760 TATGAAATTTTGATAACCTTCCGATAAAATATCAGTAATCACATTTTAAAATTTTGATAATCATA
1 TATGAAATTTTGATAACCTTCCGATAAAATATCAGTAATCACATTATAAAATTTTGATAACCATA
*
111825 CCATGAAATTTTGATACCTCACTATGAAATTTTTATAAACATCCC
66 CCATGAAATTGTGATACCTCACTATGAAATTTTTATAAACATCCC
* *
111870 TATTAAATTTTGATAACCTTCCGATAAAATATCGGTAATCACATTATAAAATTTTGATAACCATA
1 TATGAAATTTTGATAACCTTCCGATAAAATATCAGTAATCACATTATAAAATTTTGATAACCATA
* *
111935 CCATGAAATTGTGATACCTCATTATGAAATTTTTATAAACCTCCC
66 CCATGAAATTGTGATACCTCACTATGAAATTTTTATAAACATCCC
*
111980 TATGAAATTTTGAAAACC
1 TATGAAATTTTGATAACC
111998 ATCTCACGAA
Statistics
Matches: 119, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
110 119 1.00
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (110 bp):
TATGAAATTTTGATAACCTTCCGATAAAATATCAGTAATCACATTATAAAATTTTGATAACCATA
CCATGAAATTGTGATACCTCACTATGAAATTTTTATAAACATCCC
Found at i:112032 original size:110 final size:110
Alignment explanation
Indices: 111760--112060 Score: 340
Period size: 110 Copynumber: 2.7 Consensus size: 110
111750 AAGCGCACAT
* * * * * * *
111760 TATGAAATTTTGATAACCTTCCGATAAAATATC-AGTAATCACATTTTAAAATTTTGATAATCAT
1 TATGAAATTTTGAAAACCATCCGACAAAATATCGA-AAACCACATTATAAAATTTTGATAACCAT
111824 ACCATGAAATTTTGATACCTCACTATGAAATTTTTATAAACATCCC
65 ACCATGAAATTTTGATACCTCACTATGAAATTTTTATAAACATCCC
* * * * ** *
111870 TATTAAATTTTGATAACCTTCCGATAAAATATCGGTAATCACATTATAAAATTTTGATAACCATA
1 TATGAAATTTTGAAAACCATCCGACAAAATATCGAAAACCACATTATAAAATTTTGATAACCATA
* * *
111935 CCATGAAATTGTGATACCTCATTATGAAATTTTTATAAACCTCCC
66 CCATGAAATTTTGATACCTCACTATGAAATTTTTATAAACATCCC
* * * *
111980 TATGAAATTTTGAAAACCATCTC-ACGAAATTTTGAAAACCATC-TTATGAAATTTTGATAACCA
1 TATGAAATTTTGAAAACCATC-CGACAAAATATCGAAAACCA-CATTATAAAATTTTGATAACCA
*
112043 T-CTTATGAAATTTTGATA
64 TAC-CATGAAATTTTGATA
112061 ACATCCCTAT
Statistics
Matches: 167, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
109 1 0.01
110 164 0.98
111 2 0.01
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (110 bp):
TATGAAATTTTGAAAACCATCCGACAAAATATCGAAAACCACATTATAAAATTTTGATAACCATA
CCATGAAATTTTGATACCTCACTATGAAATTTTTATAAACATCCC
Found at i:112084 original size:44 final size:44
Alignment explanation
Indices: 111808--112169 Score: 192
Period size: 44 Copynumber: 8.3 Consensus size: 44
111798 TCACATTTTA
* * * *
111808 AAATTTTGATAATCATAC-CATGAAATTTTGAT-ACCTCACTATG
1 AAATTTTGATAACCAT-CTTATGAAATTTTGATAACATCCCTATG
* * * * * * * *
111851 AAATTTTTATAAACATCCCTATTAAATTTTGATAACCTTCCGATA
1 AAATTTTGATAACCAT-CTTATGAAATTTTGATAACATCCCTATG
* * * * * *
111896 AAATATCGGTAATCA-CATTATAAAATTTTGATAACCATACC-ATG
1 AAATTTTGATAACCATC-TTATGAAATTTTGATAA-CATCCCTATG
* * *
111940 AAATTGTGAT-ACC-TCATTATGAAATTTTTATAAACCTCCCTATG
1 AAATTTTGATAACCATC-TTATGAAATTTTGAT-AACATCCCTATG
* * * * *
111984 AAATTTTGAAAACCATCTCACGAAATTTTGAAAACCAT-CTTATG
1 AAATTTTGATAACCATCTTATGAAATTTTGATAA-CATCCCTATG
*
112028 AAATTTTGATAACCATCTTATGAAATTTTGATAACATCCCTATA
1 AAATTTTGATAACCATCTTATGAAATTTTGATAACATCCCTATG
* * * * *
112072 AACATTTT-ATAACC-TCCTCATAAAATTTTGTTAACCT-CCTACG
1 AA-ATTTTGATAACCAT-CTTATGAAATTTTGATAACATCCCTATG
* * * * * *
112115 AATTTTTTATAAGAACA-C-TATTAAATTTTGATAACCT-CCAATG
1 AAATTTTGAT-A-ACCATCTTATGAAATTTTGATAACATCCCTATG
112158 AAATTTTGATAA
1 AAATTTTGATAA
112170 TTAACTACAC
Statistics
Matches: 245, Mismatches: 57, Indels: 36
0.72 0.17 0.11
Matches are distributed among these distances:
41 1 0.00
42 5 0.02
43 77 0.31
44 116 0.47
45 44 0.18
46 2 0.01
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.37
Consensus pattern (44 bp):
AAATTTTGATAACCATCTTATGAAATTTTGATAACATCCCTATG
Found at i:112938 original size:19 final size:18
Alignment explanation
Indices: 112914--112949 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
112904 TGAAGATTTC
112914 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
112933 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
112950 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Done.