Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007636.1 Corchorus capsularis cultivar CVL-1 contig07657, 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: 46631
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:840 original size:336 final size:330
Alignment explanation
Indices: 147--2992 Score: 2658
Period size: 336 Copynumber: 8.5 Consensus size: 330
137 TTGTAAAACA
*
147 AGCATCTAAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAGGAAAAACGATATTA
1 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATAGGAAAAACGATATTA
* * * * ** * * * *
212 GAAACATAAAAAACTTTTTAA-TCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTGTGGC
65 GAAGCGTGAAAAGCCCTTCAATTTTTTTTGACGTTGAATTATATA-TTTTTATGAGTATTTTAGC
* *
276 TAAAAATTGA-GAAAATAACTTTTGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTAATAA
129 TAAAAATTGAGGAAAAT--CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAA
* * * * * * * * *
340 TCATCATGATTTTTGGCTAAAAACGCATTCCGGGGTCCCAGTTAAGTTTTGCACGATTTTTGGCA
192 CCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGG-CCCGGCTCAGTTTTGCATGATTTTTGGCG
* * * * * *
405 CCAACACTCCTTG-AGATATCCATATTCATCTAATAAAATTTCAGCTACATTGGATTTAAGAATT
256 CCAAGACTCCTTGAAGATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATT
469 TGTTTTTTA-G
321 TG-TTTTTACG
* * * * * * * *
479 AGTATCTGAATCTTGTTTTGATTTAATTAGAATTTAATTTAGAAAAATAAGAAATACGATA-TAA
1 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGGAAAAACGATATTAG
* * * * *
543 AAACATGAAAAGCCCTCCAATTTTTTTTGACGTTGAATTATATATTTTTATAAGTATTTTAGCCA
66 AAGCGTGAAAAGCCCTTCAATTTTTTTTGACGTTGAATTATATATTTTTATGAGTATTTTAGCTA
* * **
608 AAAATTGAGGAGAAATCTTTCGTGTCAATTTTTACAAAATTTTAGCCGAAAAAGTGTACTAACTA
131 AAAATTGAGGA-AAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TAA-TA
* * *
673 ACCATCACGGTTTTTGACTAAAAATGCGTTCCGGGGACCCGGCTCAATTTTGCATGATTTCTTTG
191 ACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGG-CCCGGCTCAGTTTTGCATGA-TT-TTTG
**** * * * *
738 GCTTTGAGACTACTTGTA-ATATCTATATTCATCTAATCAAATCTCAACCACATTAGATTTAAGG
253 GCGCCAAGACTCCTTGAAGATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGG
* **
802 ATTTGTTTTCAAA
318 ATTTGTTTTTACG
* * *
815 AGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACGATATTAG
1 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGGAAAAACGATATTAG
* * * *
880 AAACGTCAAAAGCCCTTCAA-TCTTTTTGGCGTTGAATTATATATATATATATATTTGAGTATTT
66 AAGCGTGAAAAGCCCTTCAATTTTTTTTGACGTTGAATTATATAT-T-T-T-TA--TGAGTATTT
* * * * * *
944 TATCCAAAAATTGAGTAAATATCTTTTGGGTCAATTTTTACAAAATTTTAACCGAAATCGTGTAA
125 TAGCTAAAAATTGAGGAAA-ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA
* * * * * *
1009 TAATCATCACAGTTTTTGGCTAAAAAAGCGTTCCCGAGCCCCAGCTCAGTTTTGCATGATTTTTG
189 TAACCATCACGGTTTTTGGCTAAAAACGCGTT-CCGGGGCCCGGCTCAGTTTTGCATGATTTTTG
* * * * *
1074 ACGCCAAGACTCCTTG-AGATATCCATATTCATCTAATCAAATCTTAGCTACATTGGACTTAAGG
253 GCGCCAAGACTCCTTGAAGATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGG
*
1138 GTTTGTTTTTACG
318 ATTTGTTTTTACG
* *
1151 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATACAAAAAAAATAAGAGGAAAAAACGAT
1 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTC-AGAAAAAT---AGG-AAAAACGAT
* * ** * * * * *
1216 TTTATAAGAATGAAATGCCCTTCAATATTTTTGGA-ATT-AAGTTATATAATTTTTATAAGTATT
61 ATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTTGACGTTGAA-TTATAT-ATTTTTATGAGTATT
* * * *
1279 GTAGCTAAAAATTGAGGAAATAACTTTCGAGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTA
124 TTAGCTAAAAATTGAGGAAA-ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA
* * * * * * *
1344 ATAATCAACACGGTTTTTGGCTAAAAACACGTTCTTGGGCCCCGACTAAGTTTTGCATGATTTTT
188 ATAACCATCACGGTTTTTGGCTAAAAACGCGTTC-CGGGGCCCGGCTCAGTTTTGCATGATTTTT
* * * *
1409 TGCGCCAAGATTCTCTTTG-AGATATCCATATTCATCTAATCAAATCTCAGCTACATTGGATTTA
252 GGCGCCAAGA--CTCCTTGAAGATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTA
*
1473 AGAATTTGTTTTTACG
315 AGGATTTGTTTTTACG
* *
1489 AGCATCGATCTAAATCTTGTTTCGA-TTAATTAGAAATTAATTCAGAAAAATATGAAAAATGATA
1 AG---C-ATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGGAAAAACGATA
* * * * ** *
1553 TTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCGTTAATATATATATATATATATATATATATA
62 TTAGAAGCGTGAAAAGCCCTTCAAT-TTTTT----TT--GACGT-T-GA-AT-TATATAT-T-T-
* * * * *
1618 TTATGAGTATTTTA--TAAAAAATTAAGGAAAAATTTTTTGGGTCATTTTTTACAAAATTTTAGC
113 TTATGAGTATTTTAGCT-AAAAATTGAGG-AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
* * * * * * *
1681 CGAAATCATGTATTAACCATCACGGTTTTTGGCTAAAAATGCGTTTCGGGGCCATGACTTAGTTT
176 CGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCC-CGGCTCAGTTT
* * * * * *
1746 TGCATGACTTTTGACGCCGAGACTCTTTGAA-ATATCTATATTAATCTAAACAAATCTCAGCCAC
240 TGCATGATTTTTGGCGCCAAGACTCCTTGAAGATATCTATATTCATCTAATCAAATCTCAGCCAC
* *
1810 ATTGAATTTAAGGATTTGTTCTTACG
305 ATTGGATTTAAGGATTTGTTTTTACG
* *
1836 AGCATCCAAA--TTGTAATTCAATTTAATTAGAAATTAATT-AGGAAAACAATAGGAAAAACGAT
1 AGCATCTAAATCTTGT--TTCGATTTAATTAGAAATTAATTCA-G-AAA-AATAGGAAAAACGAT
* * * * * * * *
1898 ATTAGTAGCGTGAAAAGTCATCCAATCTTTTTGGA-GTTGAATTATATATAATTTATGAGTATTG
61 ATTAGAAGCGTGAAAAGCCCTTCAATTTTTTTTGACGTTGAATTATATAT-TTTTATGAGTATTT
* * * * *
1962 TGGCTAAAAATTGAGTAATAATATTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATAGTG---
125 TAGCTAAAAATTGAGGAA-AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA
** * * * *
2024 T-ACCATCATTGTTTTGTGGCTAAAAACGCGTTCCCGTGCCGGGGTCAGTTTTGCATGATTTTTG
189 TAACCATCACGGTTTT-TGGCTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTG
* * * *
2088 GCGCCAAGACTCCTTAAAATATATCTATATTCATCTAACCAAATCTCAGCCACATTGTATTTAAG
253 GCGCCAAGACTCCTT-GAAGATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAG
*
2153 GATTTTTTTTTACG
317 GATTTGTTTTTACG
** * *
2167 ATTATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAGATAAAATAGGAAAAACGATAT
1 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAA-TT-CAGA-AAAATAGGAAAAACGATAT
* * * ** *
2232 TAGAAGCGTGAAAAAGGCTTTCGA-TTTTTTTGGTGTTGAATTGTATATTTTTTATGAGTATTTT
63 TAGAAGCGTG-AAAAGCCCTTCAATTTTTTTTGACGTTGAATTATATA-TTTTTATGAGTATTTT
* * *
2296 CGCTAAAAATTGAGGAAAAATCTTTCAGTTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAT
126 AGCTAAAAATTGAGG-AAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAAT
** * * * *
2361 AACCATCACGGTTTTCAGCTAAAAACGCGTTCCGAGACCCAGCTCAGTTTTGCATGATTTTTGGT
190 AACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGC
* * * * *
2426 GTCAAGAATCCTTGAA-ATATCTATATTCATCTAACCAAATCTCAGTCATATTGGATTTAAGGAT
255 GCCAAGACTCCTTGAAGATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGAT
2490 TTGTTTTTACG
320 TTGTTTTTACG
* * * * *
2501 ATGTATCTGAATCATTGATTCGATTTAATTAGAAATTATTTC-GAAAAAATAGGAAAAACAATAT
1 A-GCATCTAAATC-TTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATAGGAAAAACGATAT
* * * *
2565 TAGAAGCGTTAAAAGCCCTTCAATCTTTTTTGATGTCGAATTATATATTTTTTATGAGTATTTTA
63 TAGAAGCGTGAAAAGCCCTTCAATTTTTTTTGACGTTGAATTATATA-TTTTTATGAGTATTTTA
* * * *
2630 GCTAAAAATTGAGGAAATATCTTTCAGGTCAATGTTTGCAAAATTTTAGCCGAAAACGTGTACGT
127 GCTAAAAATTGAGGAAA-ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA-AT
** * * * *
2695 -TGCATCACGATTTTTGGCTAAAAACGCATTCCGGGGCCATGGCTCTGTTTTGCATGATTTTTGG
190 AACCATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGCC-CGGCTCAGTTTTGCATGATTTTTGG
* ** * * * *
2759 TGCTGAG-GTGCCTTGAA-ATATCTTTATTCATCTAATCAAGTCTCAGTCACATTGGATTTAAGG
254 CGCCAAGACT-CCTTGAAGATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGG
2822 ATTTGTTTTTACG
318 ATTTGTTTTTACG
* * * * * *
2835 TGCATCTGAATCTTGTATGGATTTAATTAGAGATTAATTCAGAAAAAATATGAAAAAACGATATT
1 AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAATA-GGAAAAACGATATT
* * * * * * *
2900 AAAAGTGTGAAAAGTCCTCCAATCTTTTTTGGCGTTGAATTATATA-TATTATGAGTACTTTT-G
64 AGAAGCGTGAAAAGCCCTTCAATTTTTTTTGACGTTGAATTATATATTTTTATGAGTA-TTTTAG
* * *
2963 CCAAAAATTGAGAAAAAATATTTCGGGTCA
128 CTAAAAATTGAG-GAAAATCTTTCGGGTCA
2993 TTCTTACCAT
Statistics
Matches: 2084, Mismatches: 336, Indels: 188
0.80 0.13 0.07
Matches are distributed among these distances:
329 43 0.02
330 98 0.05
331 121 0.06
332 158 0.08
333 317 0.15
334 256 0.12
335 24 0.01
336 459 0.22
337 48 0.02
338 115 0.06
339 10 0.00
340 15 0.01
341 62 0.03
342 85 0.04
343 12 0.01
344 21 0.01
345 8 0.00
346 36 0.02
347 65 0.03
348 14 0.01
349 102 0.05
350 15 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.37
Consensus pattern (330 bp):
AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGGAAAAACGATATTAG
AAGCGTGAAAAGCCCTTCAATTTTTTTTGACGTTGAATTATATATTTTTATGAGTATTTTAGCTA
AAAATTGAGGAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCAT
CACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAG
ACTCCTTGAAGATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
TTACG
Found at i:1598 original size:2 final size:2
Alignment explanation
Indices: 1591--1618 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1581 TTTGGCGTTA
1591 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
1619 TATGAGTATT
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:8451 original size:3 final size:3
Alignment explanation
Indices: 8443--8502 Score: 93
Period size: 3 Copynumber: 20.0 Consensus size: 3
8433 GAGGCGGAGC
* *
8443 TGG TGG TGG TGG TGG TGG TGG TGG TTG TGG TGG TTG TGG TGG TGG TGG
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG TGG
*
8491 TGG TGT TGG TGG
1 TGG TGG TGG TGG
8503 CAGAGTTTGG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.62, T:0.38
Consensus pattern (3 bp):
TGG
Found at i:22115 original size:1 final size:1
Alignment explanation
Indices: 22109--22133 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
22099 TCATATAGCC
22109 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
22134 TGCCCAAGGA
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:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:28503 original size:36 final size:36
Alignment explanation
Indices: 28463--28532 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
28453 AACTAGACAT
* *
28463 AGAGATGCATCAAATACACCCAAATCATAATCAAGG
1 AGAGATGCATCAAATACACACAAAGCATAATCAAGG
*
28499 AGAGATGCATCAAATATACACAAAGCATAATCAA
1 AGAGATGCATCAAATACACACAAAGCATAATCAA
28533 AGAGGAGCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.50, C:0.20, G:0.13, T:0.17
Consensus pattern (36 bp):
AGAGATGCATCAAATACACACAAAGCATAATCAAGG
Found at i:30944 original size:11 final size:11
Alignment explanation
Indices: 30928--30954 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
30918 AGTTTAAGAG
30928 GTGTCACGGTA
1 GTGTCACGGTA
30939 GTGTCACGGTA
1 GTGTCACGGTA
30950 GTGTC
1 GTGTC
30955 GCGGGCGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.30
Consensus pattern (11 bp):
GTGTCACGGTA
Found at i:33590 original size:30 final size:29
Alignment explanation
Indices: 33521--33600 Score: 97
Period size: 29 Copynumber: 2.7 Consensus size: 29
33511 GTAACTTTTA
** *
33521 GACGTTTTGCCCCCCGAACTTTAATCTTG
1 GACGTTTTGCCCCCTAAACTTCAATCTTG
* *
33550 GACATTTTGCCCCCTAAACTTCAATTTTGG
1 GACGTTTTGCCCCCTAAACTTCAATCTT-G
*
33580 GACGTTTTGCCCCCTCAACTT
1 GACGTTTTGCCCCCTAAACTT
33601 AACGGATCCG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 23 0.53
30 20 0.47
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.35
Consensus pattern (29 bp):
GACGTTTTGCCCCCTAAACTTCAATCTTG
Found at i:33671 original size:29 final size:30
Alignment explanation
Indices: 33613--33692 Score: 108
Period size: 29 Copynumber: 2.7 Consensus size: 30
33603 CGGATCCGTT
*
33613 AAGTTGAGGGGGCAAAACGTCCCAAAATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
* * *
33643 AAGTTCAGGGGGTAAAATGT-CCAAGATTG
1 AAGTTCAGGGGGCAAAACGTCCCAAAATTG
*
33672 AAGTTCGGGGGGCAAAACGTC
1 AAGTTCAGGGGGCAAAACGTC
33693 TAAACGCTAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
29 25 0.60
30 17 0.40
ACGTcount: A:0.34, C:0.15, G:0.33, T:0.19
Consensus pattern (30 bp):
AAGTTCAGGGGGCAAAACGTCCCAAAATTG
Found at i:34203 original size:20 final size:21
Alignment explanation
Indices: 34166--34205 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
34156 AACCCGTTAA
*
34166 TTAAAGCGTGTCACTCGTGTT
1 TTAAAGCGTGTCAATCGTGTT
*
34187 TTAAA-CGTGTTAATCGTGT
1 TTAAAGCGTGTCAATCGTGT
34206 CTTGACACGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.40
Consensus pattern (21 bp):
TTAAAGCGTGTCAATCGTGTT
Found at i:34278 original size:42 final size:43
Alignment explanation
Indices: 34196--34278 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 43
34186 TTTAAACGTG
* * *
34196 TTAATCGTGTCTTGACACGATTACGACATGAAACATGATAATT
1 TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATT
*
34239 TTAATCGTGTC-CGACACGATT-CAGACACGAGACACGATAA
1 TTAATCGTGTCTCGACACGATTAC-GACACGAAACACGATAA
34279 GCCAAACACG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 1 0.03
42 23 0.66
43 11 0.31
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (43 bp):
TTAATCGTGTCTCGACACGATTACGACACGAAACACGATAATT
Found at i:35503 original size:269 final size:269
Alignment explanation
Indices: 34989--35520 Score: 879
Period size: 270 Copynumber: 2.0 Consensus size: 269
34979 TACCATGAAC
*
34989 GAGAAATTATTAGGTGGGACGGACCCGCCACGTCATCCATGGGACTAACCAATAGAATTTTGCCA
1 GAGAAATTATTAGGTGGGACGGACCCGCCACGTCATCCATGGGACTAACCAATAGAATCTTGCCA
*
35054 TGTCAAATTAACTCCTTAAATTAAGACACGATTTTAGCCCAAGGTTTAGCCCCATTTTAAAACAA
66 TGTCAAATGAACTCCTTAAATTAAGACACGATTTTAGCCCAAGGTTTAGCCCCATTTTAAAACAA
* *
35119 ACCCTATATAAAGGGTAAGTCCCCAAATTTGAGATTTTATTGGGATAGGGTTTTAGAAAATTGAT
131 ACCCTATATAAAGGGTAAGTCCCCAAATTTGAGATATTATTGGGATAGGATTTTAGAAAATTGAT
*
35184 GAGTTGTCTTCATATCACTGGTTGGTCCCATAGATGACGTGGTGGGTCCGTCCCACCTAATAATT
196 GAGTTGTCTTAATATCACTGGTTGGTCCCATAGATGACGTGGTGGGTCCGTCCCACCTAATAATT
35249 TCTACCCAT
261 TCTACCCAT
* *
35258 GAGAAATTATTAGGTGGGACGGACCCGCCACGTCATCCATGGGACTAACCAATGGAATCTTGTCA
1 GAGAAATTATTAGGTGGGACGGACCCGCCACGTCATCCATGGGACTAACCAATAGAATCTTGCCA
* * * * * *
35323 TGTCAAATGACCTCCTTAAATTTAGGCACGATTTTTAGCTCAGGGTTTAGCCCTC-TTTTAAAAT
66 TGTCAAATGAACTCCTTAAATTAAGACACGA-TTTTAGCCCAAGGTTTAGCCC-CATTTTAAAAC
* * *
35387 AAATCCTCTATAAAGGGTAAGTCCCCAAATTTGAGATATTATTGGGATATGATTTTAGAAAATTG
129 AAACCCTATATAAAGGGTAAGTCCCCAAATTTGAGATATTATTGGGATAGGATTTTAGAAAATTG
*
35452 ATGAGTTGTCTTAATATCATTGGTTGGTCCCATAGATGACGTGGT-GGTCCGTCCCACCTAATAA
194 ATGAGTTGTCTTAATATCACTGGTTGGTCCCATAGATGACGTGGTGGGTCCGTCCCACCTAATAA
35516 TTTCT
259 TTTCT
35521 CCTCATTCAA
Statistics
Matches: 244, Mismatches: 17, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
269 113 0.46
270 130 0.53
271 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (269 bp):
GAGAAATTATTAGGTGGGACGGACCCGCCACGTCATCCATGGGACTAACCAATAGAATCTTGCCA
TGTCAAATGAACTCCTTAAATTAAGACACGATTTTAGCCCAAGGTTTAGCCCCATTTTAAAACAA
ACCCTATATAAAGGGTAAGTCCCCAAATTTGAGATATTATTGGGATAGGATTTTAGAAAATTGAT
GAGTTGTCTTAATATCACTGGTTGGTCCCATAGATGACGTGGTGGGTCCGTCCCACCTAATAATT
TCTACCCAT
Found at i:38249 original size:15 final size:15
Alignment explanation
Indices: 38229--38259 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
38219 TTTCACTATC
38229 ATCAGGAACTTGAAT
1 ATCAGGAACTTGAAT
38244 ATCAGGAACTTGAAT
1 ATCAGGAACTTGAAT
38259 A
1 A
38260 GTGATGTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (15 bp):
ATCAGGAACTTGAAT
Found at i:39132 original size:16 final size:15
Alignment explanation
Indices: 39111--39141 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
39101 AAAACTAAAT
39111 TTTAATTTTAATTTAA
1 TTTAATTTT-ATTTAA
39127 TTTAATTTTATTTAA
1 TTTAATTTTATTTAA
39142 AAATTACGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTAATTTTATTTAA
Done.