Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014568.1 Corchorus capsularis cultivar CVL-1 contig14589, 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: 72670
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1138 original size:35 final size:35
Alignment explanation
Indices: 1092--1165 Score: 148
Period size: 35 Copynumber: 2.1 Consensus size: 35
1082 GTGACATGGC
1092 TGGACCTCTCCACTAATAGCCAATTTGTTTTAGGT
1 TGGACCTCTCCACTAATAGCCAATTTGTTTTAGGT
1127 TGGACCTCTCCACTAATAGCCAATTTGTTTTAGGT
1 TGGACCTCTCCACTAATAGCCAATTTGTTTTAGGT
1162 TGGA
1 TGGA
1166 TGCTTAGCAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (35 bp):
TGGACCTCTCCACTAATAGCCAATTTGTTTTAGGT
Found at i:1570 original size:197 final size:197
Alignment explanation
Indices: 1197--1651 Score: 634
Period size: 197 Copynumber: 2.3 Consensus size: 197
1187 CATGTCAACC
* * *
1197 CTAATTAATTAAATATTCAATATTAATAAATATTCCCTAAGGGATACATGTCAACCCTTAAACCC
1 CTAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGACACATGTCAACCCTTAAACCC
* * *
1262 CGCACGTGAAGTCTGCTAAACTCCAACGACTGTGTATTGCATAATTTTTCTTATAGGATTATTAT
66 CGCACGTGAAGTCTCCTAAAATCCAACGACTGGGTATTGCATAATTTTTCTTATAGGATTATTAT
* *
1327 ACAATACACTATCAGTATAAATTTTGGACTCCATAAGCGAGTTAAGAAGTTGACACATACCTCAT
131 ACAATACACTATCAGTATAAATTTTGGACACCATAAGCGAGTTAAGAAGTTGACACATACCCCAT
1392 TT
196 TT
* *
1394 CATAATTAATTAAATATTTAATATTAATACATATTCACTAAGGGACACATGTCAACCCTTAAATC
1 C-TAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGACACATGTCAACCCTTAAACC
* * **
1459 CTGCACGTGTAGTCTCCTAAAATCC-ACTGA-TGGGTATTGTTTAATTTTTCTTATAGGATTATT
65 CCGCACGTGAAGTCTCCTAAAATCCAAC-GACTGGGTATTGCATAATTTTTCTTATAGGATTATT
* * * *
1522 ATATAATACACTATCAGTGTAAATTTTGGACACCGTGAA-CGGGTTAAGAAGTTGACACATACCC
129 ATACAATACACTATCAGTATAAATTTTGGACACCAT-AAGCGAGTTAAGAAGTTGACACATACCC
1586 CATTT
193 CATTT
* * * *
1591 C--A-TAATTAAATAATTAAAATTAAGACGTATTCCCTAAGGGTACACATGTCAACCCTTAAAC
1 CTAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGG-ACACATGTCAACCCTTAAAC
1652 TTAAACTCCG
Statistics
Matches: 230, Mismatches: 24, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
193 33 0.14
194 20 0.09
197 94 0.41
198 83 0.36
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (197 bp):
CTAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGACACATGTCAACCCTTAAACCC
CGCACGTGAAGTCTCCTAAAATCCAACGACTGGGTATTGCATAATTTTTCTTATAGGATTATTAT
ACAATACACTATCAGTATAAATTTTGGACACCATAAGCGAGTTAAGAAGTTGACACATACCCCAT
TT
Found at i:3913 original size:35 final size:35
Alignment explanation
Indices: 3861--3952 Score: 139
Period size: 35 Copynumber: 2.6 Consensus size: 35
3851 TGTATAAAAC
*
3861 TAGGAGTAGGATTAATATTATGAGACTTGCTCGTG
1 TAGGACTAGGATTAATATTATGAGACTTGCTCGTG
* *
3896 TAGTACTAGGATTAATATCATGAGACTTGCTCGTG
1 TAGGACTAGGATTAATATTATGAGACTTGCTCGTG
* *
3931 TAGGACTAGGAATAGTATTATG
1 TAGGACTAGGATTAATATTATG
3953 TTTGTAGTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.30, C:0.10, G:0.26, T:0.34
Consensus pattern (35 bp):
TAGGACTAGGATTAATATTATGAGACTTGCTCGTG
Found at i:4863 original size:20 final size:19
Alignment explanation
Indices: 4840--4879 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
4830 GGGGTTTCCC
4840 TTTTCTGCTTGTAGTTTTTT
1 TTTTCTGCTTGTA-TTTTTT
4860 TTTTCTGCTTGTATTTTTT
1 TTTTCTGCTTGTATTTTTT
4879 T
1 T
4880 CATACAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.05, C:0.10, G:0.12, T:0.72
Consensus pattern (19 bp):
TTTTCTGCTTGTATTTTTT
Found at i:16267 original size:5 final size:5
Alignment explanation
Indices: 16257--16314 Score: 70
Period size: 5 Copynumber: 12.0 Consensus size: 5
16247 CTTGTGCACA
16257 GTTTT GTTTT GTTTT GTTTT GTTTT G-TTT GTTTT -TGTTT GTTTT -TGTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GT-TTT GTTTT GT-TTT
16306 GTTTT -TTTT
1 GTTTT GTTTT
16315 ATGCTTTAGA
Statistics
Matches: 48, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
4 10 0.21
5 36 0.75
6 2 0.04
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (5 bp):
GTTTT
Found at i:16282 original size:20 final size:19
Alignment explanation
Indices: 16257--16314 Score: 75
Period size: 19 Copynumber: 3.0 Consensus size: 19
16247 CTTGTGCACA
16257 GTTTTGTTTTGTTTTGTTTT
1 GTTTTGTTTTGTTTT-TTTT
16277 GTTTTG-TTTGTTTTTGTTT
1 GTTTTGTTTTGTTTTT-TTT
16296 GTTTT-TGTTTGTTTTTTTT
1 GTTTTGT-TTTGTTTTTTTT
16315 ATGCTTTAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 1 0.03
19 19 0.54
20 15 0.43
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (19 bp):
GTTTTGTTTTGTTTTTTTT
Found at i:20301 original size:325 final size:322
Alignment explanation
Indices: 18517--20870 Score: 3567
Period size: 325 Copynumber: 7.4 Consensus size: 322
18507 ATATTGATTG
* * * *
18517 AACGATATTAGAAGCGTGTAAAACTCGTCAATCTTTTTGGCCTTCAATTAAATATTTTTTCTAAG
1 AACGATATTAGAAGCGTGTAAAGCCCGTCAATCTTTTTGGCCTTGAATTAAATATTTTTTCTGAG
* *
18582 TACTATAGG-AAAAAATTAAGAAAAAC-TTTTCGGGTCAGTTTTTAGTCGAAATCGTGTACTAAC
66 TACTGT-GGCAAAAAATTAAGAAAAACTTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAC
* * * *
18645 CATCACGGTTTTCGGCTAAAAACGCGTTCCGCAGCCCCGGCTCAATTTTGAATGATTTTTGGCAC
130 CATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGC
* *
18710 AAAAACTCCTTGAAATATCTATATTCATCGAGCCAAATGTCAGCCATATTGAATATAAGAATTTG
195 AAAAACTCCTTGAAATATCTATATTCATCGAGTCAAATGTCAGCCACATTGAATATAAGAATTTG
18775 TTTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTCGGAAAAAATATGAAAA
260 TTTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTCGGAAAAAA-ATGAAAA
* *
18840 AACGATACTAGAAGCGTGTAAAGCCCGTCAATCTTTTTGGCCTTGACTTAAATA-TTTTTCTGAG
1 AACGATATTAGAAGCGTGTAAAGCCCGTCAATCTTTTTGGCCTTGAATTAAATATTTTTTCTGAG
*
18904 TACTGTGGCAAAAAATTAAGAAAAACTTTTTCGGGTTAGTTTTTAGCCGAAATCGTGTACTAACC
66 TACTGTGGCAAAAAATTAAGAAAAACTTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
* *
18969 ATCATGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATAATTTTTGGCGCA
131 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCA
* *
19034 AAGACTCCTTCAAATATCTATA-T--TC-A-TC----G--AGCCACATTGAATATAAGAATTTGT
196 AAAACTCCTTGAAATATCTATATTCATCGAGTCAAATGTCAGCCACATTGAATATAAGAATTTGT
*
19088 TTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGAAAAAATGAAAA
261 TTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAAAA
* * *
19150 AACGATATTAGAAGAGTGTAAAGTCCGTC-ATACTTTTTGACCTTGAATTAAATATTTTTTCTGA
1 AACGATATTAGAAGCGTGTAAAGCCCGTCAAT-CTTTTTGGCCTTGAATTAAATATTTTTTCTGA
*
19214 GTACTGTGGCAAAAAATTAAGCAAAACTTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAC
65 GTACTGTGGCAAAAAATTAAGAAAAACTTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAC
* * *
19279 CATCACGGTTTTTGGCTAAAAACGCATTCCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCGG
130 CATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGC
* * *
19344 AAAAATTCATTGAAATATCTATATTCATCGAGCCAAATGTCAGCCACATTGAATATAAGAATTTG
195 AAAAACTCCTTGAAATATCTATATTCATCGAGTCAAATGTCAGCCACATTGAATATAAGAATTTG
19409 TTTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAAAA
260 TTTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAAAA
*
19472 AACGATATTAAAAGCGTGTAAAGCCCGTCAATCTTTTTGGCCTTGAATTAAATATTTTTT-TGAG
1 AACGATATTAGAAGCGTGTAAAGCCCGTCAATCTTTTTGGCCTTGAATTAAATATTTTTTCTGAG
* * * * *
19536 TACTATGGGAAAAAATTAAGAAAAACTTTTTTGGGTCAGTTTTTAGCCGAAATCGTATAGTAACC
66 TACTGTGGCAAAAAATTAAGAAAAACTTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
* * *
19601 ATCACAGTTTTTGG-TTAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCCCA
131 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCA
* * ** ** * *
19665 AAAACTTCTTGAAATATCTATATTTATCGAACCAAATCCCAACCACATTCG-ATTTAACG-ATTT
196 AAAACTCCTTGAAATATCTATATTCATCGAGTCAAATGTCAGCCACATT-GAATATAA-GAATTT
* * * * * *
19728 GTTTTTCCT-AGCATGC-AAATCTTGTTTTGATTTAATTAGAAATTAATGCGGAAAAAAA-GGAA
259 GTTTTT-ATGAGTAT-CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAAA
19790 A
322 A
* * * *
19791 AACGATATTAGAAGCGTGAAAAGCTCGTCAATTTTTTTGGCCTTGAATTAAATA-TTTTTCTAAG
1 AACGATATTAGAAGCGTGTAAAGCCCGTCAATCTTTTTGGCCTTGAATTAAATATTTTTTCTGAG
* * * *
19855 TACTGTGGCAAAAAATTAAGCACAACTTTTTCGGGTTAGTTTTTAGCCGAAATCGTGTACTAAAC
66 TACTGTGGCAAAAAATTAAGAAAAACTTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
19920 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCA
131 ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCA
* * * *
19985 AAAACTCCGTAAAATATCTATATTCATCAAGTCAAATGTTAGCCACATTGAATATAAGAATTTGT
196 AAAACTCCTTGAAATATCTATATTCATCGAGTCAAATGTCAGCCACATTGAATATAAGAATTTGT
*
20050 TTTTATGAGTATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAATGAAAA
261 TTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG--AAAAAAATGAAAA
*
20114 AACGATATTAGAAGCGTGTAAAGCCCGTCAATCTTTTTGGCCTTCAATTAAATATTTTTTCTGAG
1 AACGATATTAGAAGCGTGTAAAGCCCGTCAATCTTTTTGGCCTTGAATTAAATATTTTTTCTGAG
* * *
20179 TACTGTGGGAAAAAAATTAAGAAAAACTTTTTCAGGTCAGTTTTTAGCCGAAATCGTGTATTAAC
66 TACTGT-GGCAAAAAATTAAGAAAAACTTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAC
* * *
20244 CATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAGTTTTGCATGATTTTTGGCGG
130 CATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGC
20309 AAAAACTCCTTGAAATATCTATATTCATCGAGTCAAATGTCAGCCACATTGAATATAAGAATTTG
195 AAAAACTCCTTGAAATATCTATATTCATCGAGTCAAATGTCAGCCACATTGAATATAAGAATTTG
20374 TTTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAATGAAAA
260 TTTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG--AAAAAAATGAAAA
20439 AACGATATTAGAAGCGTGTAAAGCCCGTCAATCTTTTTTGGCCTTGAATTAAATATTTTTTCTGA
1 AACGATATTAGAAGCGTGTAAAGCCCGTCAATC-TTTTTGGCCTTGAATTAAATATTTTTTCTGA
* *
20504 GTACTGTGGCAAAAAATTAAGAAAAACTTTTTCGGGTTAGTTTTTTGCCGAAATCGTGTACTAAC
65 GTACTGTGGCAAAAAATTAAGAAAAACTTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAAC
* * *
20569 CATCATGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGACTCAATTTTGCATAATTTTTGGCGC
130 CATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGC
* *
20634 AAAGACTCCTTCAAATATCTATA-T--TC-A-TC-AA-GT----CACATTGAATATAAGAATTTG
195 AAAAACTCCTTGAAATATCTATATTCATCGAGTCAAATGTCAGCCACATTGAATATAAGAATTTG
*
20688 TTTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATG--AG
260 TTTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAAAA
* *
20749 AACGATATTAGAAGCGTGTAAAGTCCGTC-ATACTTTTTGACCTTGAATTAAATATTTTTTCTGA
1 AACGATATTAGAAGCGTGTAAAGCCCGTCAAT-CTTTTTGGCCTTGAATTAAATATTTTTTCTGA
20813 GTACTGTGGCAAAAAATTAAGAAAAACTTTTTCGGGTCAGTTTTTAGCCGAAATCGTG
65 GTACTGTGGCAAAAAATTAAGAAAAACTTTTTCGGGTCAGTTTTTAGCCGAAATCGTG
20871 AGCCCCGGCT
Statistics
Matches: 1854, Mismatches: 144, Indels: 80
0.89 0.07 0.04
Matches are distributed among these distances:
309 90 0.05
310 83 0.04
311 161 0.09
312 78 0.04
314 74 0.04
315 1 0.00
316 1 0.00
318 8 0.00
319 133 0.07
320 285 0.15
321 83 0.04
322 180 0.10
323 220 0.12
324 16 0.01
325 404 0.22
326 37 0.02
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (322 bp):
AACGATATTAGAAGCGTGTAAAGCCCGTCAATCTTTTTGGCCTTGAATTAAATATTTTTTCTGAG
TACTGTGGCAAAAAATTAAGAAAAACTTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACC
ATCACGGTTTTTGGCTAAAAACGCGTTCCGGAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCA
AAAACTCCTTGAAATATCTATATTCATCGAGTCAAATGTCAGCCACATTGAATATAAGAATTTGT
TTTTATGAGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATGAAAA
Found at i:21603 original size:309 final size:312
Alignment explanation
Indices: 20870--21688 Score: 1039
Period size: 309 Copynumber: 2.6 Consensus size: 312
20860 CCGAAATCGT
*
20870 GAGCCCCGGCTCTAATTTTGCATGATTTTTGGCACAAAGTACTCCTTGAAATATCTATATTCATC
1 GAGCCCCGGCTC-AATTTTGCATGATTTTTGGCGCAAAG-ACTCCTTGAAATATCTATATTCATC
* *
20935 GAGCCAAATGTCAGCCACATTGAATATAAGAATTTGTTTTTATGAGTATCTAAATCTTGTTTCGA
64 GAGTCAAATGTCAGCCACATTAAATATAAGAATTTGTTTTTATGAGTATCTAAATCTTGTTTCGA
* * *
21000 TTTAATTAGAATTTAATTCGGAAAAAAAATGAAAAAACGATATTAGAAGCGTGTAAAACCCGTCA
129 TTTAATTAGAAATTAATGCGG---AAAAA-GAAAAAACGATATTAGAAGCGTGAAAAACCCGTCA
* * * *
21065 ATCTTTTTGGCCTTGAATTAAATATTTTTTCTGAGTATTGTGTCAAAAAATTAAGAAAAACTTTT
190 ATCTTTTTGGCCATGAATTAAATATTTTTTCAGAGTACTGTGGCAAAAAATTAAGAAAAACTTTT
*
21130 TCGGGTAAGTTTTTAGCCGAAATCTTGTAGTAACCATCACGGTTTTTGGTTAAAACGCGTTCCG
255 TCGGGTAAGTTTTTAGCCGAAATC-TGTAG-----ATCACGGTTTTTGGTAAAAACGCGTTCCG
* *
21194 GAGCCTCGGCTCAATTTTGCATGATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTCATCGA
1 GAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGA
* ** * ** * *
21259 ATCAAATCCCAACCACATTCGATTTAACG-ATTTGTTTTTACT-AGCATGC-AAATCTTGTTTCG
66 GTCAAATGTCAGCCACATTAAATATAA-GAATTTGTTTTTA-TGAGTAT-CTAAATCTTGTTTCG
* * * *
21321 ATTTAATTAGAAATTAATGCGG-GAAA-AAAAAACGATATTAGAAGCGTGAAAAACTCGTTAATG
128 ATTTAATTAGAAATTAATGCGGAAAAAGAAAAAACGATATTAGAAGCGTGAAAAACCCGTCAATC
21384 TTTTTGGCCATGAATTAAATATTTTTTTCAGAGTACTGTGGCAAAAAA-T-AGTTAAAAACTTTT
193 TTTTTGGCCATGAATTAAATA-TTTTTTCAGAGTACTGTGGCAAAAAATTAAG--AAAAACTTTT
* *
21447 TCGGGTGAGTTTTTAGCCGAAATC-GT-G-TCACGGTTTTTGGCTAAAAACGTGTTCCG
255 TCGGGTAAGTTTTTAGCCGAAATCTGTAGATCACGGTTTTTGG-TAAAAACGCGTTCCG
* *
21503 GAGCCCCGGCTCAATTTTGCATTATTTTTGGCGCAAAGACTCCTTTAAATATCTATATTCATCGA
1 GAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGA
*
21568 GTCAAATGTCAGCCGCATTAAATATAAGAATTTGTTTTTATGAGTATCTAAATCTTGTTTCGATT
66 GTCAAATGTCAGCCACATTAAATATAAGAATTTGTTTTTATGAGTATCTAAATCTTGTTTCGATT
* * ** * *
21633 TAATAAGAAATAAATTTGGAAAAAATGGAAAAACTATAGTT-GAAGCGTGAAAAACC
131 TAATTAGAAATTAATGCGG-AAAAA-GAAAAAACGATA-TTAGAAGCGTGAAAAACC
21689 TTTAAATTTT
Statistics
Matches: 433, Mismatches: 47, Indels: 41
0.83 0.09 0.08
Matches are distributed among these distances:
308 16 0.04
309 139 0.32
311 3 0.01
313 23 0.05
314 3 0.01
315 4 0.01
316 54 0.12
317 56 0.13
318 3 0.01
322 94 0.22
323 27 0.06
324 11 0.03
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (312 bp):
GAGCCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGA
GTCAAATGTCAGCCACATTAAATATAAGAATTTGTTTTTATGAGTATCTAAATCTTGTTTCGATT
TAATTAGAAATTAATGCGGAAAAAGAAAAAACGATATTAGAAGCGTGAAAAACCCGTCAATCTTT
TTGGCCATGAATTAAATATTTTTTCAGAGTACTGTGGCAAAAAATTAAGAAAAACTTTTTCGGGT
AAGTTTTTAGCCGAAATCTGTAGATCACGGTTTTTGGTAAAAACGCGTTCCG
Found at i:22417 original size:56 final size:56
Alignment explanation
Indices: 22295--23391 Score: 931
Period size: 56 Copynumber: 19.3 Consensus size: 56
22285 ACTATATGTC
*
22295 CCCTACTGAATATGCAACTATATGAGTGAGCCCTACT-AATATGCAACTATATGAGTGAA
1 CCCTACTGAATATGCAAC--TAT-A-TGAGCCCTACTGAATATGCAACTATATGAGTGAG
* * *
22354 CCCTACTGAATATGCAACTATATGAGCCCCACCGAACATGCAACTATATGAGTGAG
1 CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGTGAG
*
22410 CCCTACTGAATATGCAATTATATGAGTGAGCCCTACTGAATATGCAACTATATGA-T---
1 CCCTACTGAATATGCAA--CTAT-A-TGAGCCCTACTGAATATGCAACTATATGAGTGAG
* * * ** * ** *
22466 CCCTACTGAACATGCAACTACACGAGTTCAGTACCT-ATATGATCCCTACAGAACATGCAACTAC
1 CCCTACTGAATATGCAACTATATGAG--CCCTA-CTGA-AT-AT-GC-A-ACTATATG-----A-
*
22530 ATGAG
52 GTGAG
* * **
22535 CCATACTGAACATGCAACTATATGTCCCCTACTGAATATGCAACTATATGAGTGAG
1 CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGTGAG
*
22591 CCCTACTGAATATGCAACTATATG-TCTCCTACTGAATATGCAACTATATGA---A-
1 CCCTACTGAATATGCAACTATATGAGC-CCTACTGAATATGCAACTATATGAGTGAG
* *
22643 CCCTACTCAATATGCAACTATATGAGTGAGCCCTACTGAATATGCAACTATAT--GT--C
1 CCCTACTGAATATGCAAC--TAT-A-TGAGCCCTACTGAATATGCAACTATATGAGTGAG
* * * *
22699 CCCTACTGAATTTACAACTATATGAGCCCCACTGAATATGCAACGATATGAGTGAG
1 CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGTGAG
* * *
22755 CCCTACTGAATATGCAACAATATGAGCCCTACTGAATATGCAACTCTATGAGCGAG
1 CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGTGAG
* ** * *
22811 TCCTACTGAATATGCAACTATATGTCCCCTACTGAACATGCAACTATAT--GT--C
1 CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGTGAG
22863 CCCTACTGAATATGCAACTATATGAGTGAGCCATACTGAATATGCAACTGAATATGCAACTATAT
1 CCCTACTGAATATGCAAC--TAT-A-TGAGCC---C------T---ACTGAATATGCAACTATAT
*
22928 GAATGAG
50 GAGTGAG
* *
22935 CCCTACTGAATATGCAACTATATGAGTGAGTCCTACTGAATATGCAACTAT-T---TTAG
1 CCCTACTGAATATGCAAC--TAT-A-TGAGCCCTACTGAATATGCAACTATATGAGTGAG
* * **
22991 CCCTACTGAATATGCAACTATGTGAACCCTACTGAATATGCAA--ATAT-A-TGTC
1 CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGTGAG
**
23043 CCCTACTGAATATGCAACTATATGCCCCCTACTGAATATGCAACTATATGAGTGAG
1 CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGTGAG
* * * *
23099 CCCTACTGAATATGCAACTATATGAACCATACTGAATAAGCAACTATAT--GT--C
1 CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGTGAG
23151 CCCTACTGAATATGCAACTATATGAGTGAGCCCTACTGAATATGCAACTATATGAGTGAG
1 CCCTACTGAATATGCAAC--TAT-A-TGAGCCCTACTGAATATGCAACTATATGAGTGAG
* ** *
23211 CCCTACTAAATATGCAACTATATGTCCCCTACTGAATTTGCAAC--TAT-A-TGAG
1 CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGTGAG
**
23263 CCCTACTGAATATAAAACTATATGAGTGAGCCCTACTGAATATGCAACTATATGAGTGAG
1 CCCTACTGAATATGCAAC--TAT-A-TGAGCCCTACTGAATATGCAACTATATGAGTGAG
* *
23323 TCATACTGAATATGCAACTATATGAGCCCTACTGAATATGCAAC--TAT-A-TGAG
1 CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGTGAG
23375 CCCTACTGAATATGCAA
1 CCCTACTGAATATGCAA
23392 ATTCTTTCAA
Statistics
Matches: 859, Mismatches: 100, Indels: 165
0.76 0.09 0.15
Matches are distributed among these distances:
50 2 0.00
51 1 0.00
52 178 0.21
53 5 0.01
54 39 0.05
55 19 0.02
56 393 0.46
57 8 0.01
58 15 0.02
59 28 0.03
60 78 0.09
62 5 0.01
63 2 0.00
64 2 0.00
65 3 0.00
66 5 0.01
67 4 0.00
68 18 0.02
69 22 0.03
70 1 0.00
72 31 0.04
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (56 bp):
CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGTGAG
Found at i:22647 original size:82 final size:81
Alignment explanation
Indices: 22509--23391 Score: 844
Period size: 82 Copynumber: 10.5 Consensus size: 81
22499 CCTATATGAT
* * * * * * **
22509 CCCTACAGAACATGCAACTACATGAGCCATACTGAACATGCAACTATATGTCCCCTACTGAATAT
1 CCCTACTGAATATGCAACTATATG-TCCCTACTGAATATGCAACTATATGAACCCTACTGAATAT
22574 GCAACTATATGAGTGAG
65 GCAACTATATGAGTGAG
*
22591 CCCTACTGAATATGCAACTATATGTCTCCTACTGAATATGCAACTATATGAACCCTACTCAATAT
1 CCCTACTGAATATGCAACTATATGTC-CCTACTGAATATGCAACTATATGAACCCTACTGAATAT
22656 GCAACTATATGAGTGAG
65 GCAACTATATGAGTGAG
* * * *
22673 CCCTACTGAATATGCAACTATATGTCCCCTACTGAATTTACAACTATATGAGCCCCACTGAATAT
1 CCCTACTGAATATGCAACTATATGT-CCCTACTGAATATGCAACTATATGAACCCTACTGAATAT
*
22738 GCAACGATATGAGTGAG
65 GCAACTATATGAGTGAG
* * * *
22755 CCCTACTGAATATGCAACAATATGAGCCCTACTGAATATGCAACTCTATGAGCGAGTCCTACTGA
1 CCCTACTGAATATGCAACTATATG-TCCCTACTGAATATGCAACTATATGA---A-CCCTACTGA
*
22820 ATATGCAACTATAT--GT--C
61 ATATGCAACTATATGAGTGAG
*
22837 CCCTACTGAACATGCAACTATATGTCCCCTACTGAATATGCAACTATATGAGTGAGCCATACTGA
1 CCCTACTGAATATGCAACTATATGT-CCCTACTGAATATGCAACTATATGA---A-CC---C---
*
22902 ATATGCAACTGAATATGCAACTATATGAATGAG
55 ---T---ACTGAATATGCAACTATATGAGTGAG
* * * *
22935 CCCTACTGAATATGCAACTATATGAGTGAGTCCTACTGAATATGCAACTATTTTAGCCCTACTGA
1 CCCTACTGAATATGCAACTATAT--GT---CCCTACTGAATATGCAACTATATGAACCCTACTGA
*
23000 ATATGCAAC--TAT--GTGAA
61 ATATGCAACTATATGAGTGAG
* **
23017 CCCTACTGAATATGCAAATATATGTCCCCTACTGAATATGCAACTATATGCCCCCTACTGAATAT
1 CCCTACTGAATATGCAACTATATGT-CCCTACTGAATATGCAACTATATGAACCCTACTGAATAT
23082 GCAACTATATGAGTGAG
65 GCAACTATATGAGTGAG
* * * **
23099 CCCTACTGAATATGCAACTATATGAACCATACTGAATAAGCAACTATATGTCCCCTACTGAATAT
1 CCCTACTGAATATGCAACTATATG-TCCCTACTGAATATGCAACTATATGAACCCTACTGAATAT
23164 GCAACTATATGAGTGAG
65 GCAACTATATGAGTGAG
* **
23181 CCCTACTGAATATGCAACTATATGAGTGAGCCCTACTAAATATGCAACTATATGTCCCCTACTGA
1 CCCTACTGAATATGCAACTATAT--GT---CCCTACTGAATATGCAACTATATGAACCCTACTGA
*
23246 ATTTGCAAC--TAT-A-TGAG
61 ATATGCAACTATATGAGTGAG
** * *
23263 CCCTACTGAATATAAAACTATATGAGTGAGCCCTACTGAATATGCAACTATATGAGTGAGTCATA
1 CCCTACTGAATATGCAACTATAT--GT---CCCTACTGAATATGCAACTATATGA---A-CCCTA
23328 CTGAATATGCAAC--TAT-A-TGAG
57 CTGAATATGCAACTATATGAGTGAG
*
23349 CCCTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAA
1 CCCTACTGAATATGCAACTATATG-TCCCTACTGAATATGCAA
23392 ATTCTTTCAA
Statistics
Matches: 688, Mismatches: 70, Indels: 86
0.82 0.08 0.10
Matches are distributed among these distances:
78 39 0.06
80 5 0.01
81 1 0.00
82 441 0.64
83 2 0.00
84 10 0.01
85 1 0.00
86 118 0.17
89 1 0.00
91 1 0.00
94 19 0.03
95 1 0.00
96 1 0.00
98 24 0.03
100 2 0.00
102 22 0.03
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.27
Consensus pattern (81 bp):
CCCTACTGAATATGCAACTATATGTCCCTACTGAATATGCAACTATATGAACCCTACTGAATATG
CAACTATATGAGTGAG
Found at i:22913 original size:42 final size:42
Alignment explanation
Indices: 22867--22953 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
22857 TATGTCCCCT
*
22867 ACTGAATATGCAACTATATGAGTGAGCCATACTGAATATGCA
1 ACTGAATATGCAACTATATGAATGAGCCATACTGAATATGCA
*
22909 ACTGAATATGCAACTATATGAATGAGCCCTACTGAATATGCA
1 ACTGAATATGCAACTATATGAATGAGCCATACTGAATATGCA
22951 ACT
1 ACT
22954 ATATGAGTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.26
Consensus pattern (42 bp):
ACTGAATATGCAACTATATGAATGAGCCATACTGAATATGCA
Found at i:22914 original size:12 final size:12
Alignment explanation
Indices: 22897--22923 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
22887 AGTGAGCCAT
22897 ACTGAATATGCA
1 ACTGAATATGCA
22909 ACTGAATATGCA
1 ACTGAATATGCA
22921 ACT
1 ACT
22924 ATATGAATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (12 bp):
ACTGAATATGCA
Found at i:23002 original size:26 final size:27
Alignment explanation
Indices: 22909--23391 Score: 509
Period size: 26 Copynumber: 17.5 Consensus size: 27
22899 TGAATATGCA
22909 ACTGAATATGCAACTATATGAATGAGCCCT
1 ACTGAATATGCAACTATAT---TGAGCCCT
*
22939 ACTGAATATGCAACTATATGAGTGAGTCCT
1 ACTGAATATGCAACTATAT---TGAGCCCT
*
22969 ACTGAATATGCAACTAT-TTTAGCCCT
1 ACTGAATATGCAACTATATTGAGCCCT
* *
22995 ACTGAATATGCAACTAT-GTGAACCCT
1 ACTGAATATGCAACTATATTGAGCCCT
* **
23021 ACTGAATATGCAAATATA-TGTCCCCT
1 ACTGAATATGCAACTATATTGAGCCCT
**
23047 ACTGAATATGCAACTATA-TGCCCCCT
1 ACTGAATATGCAACTATATTGAGCCCT
23073 ACTGAATATGCAACTATATGAGTGAGCCCT
1 ACTGAATATGCAACTATAT---TGAGCCCT
* *
23103 ACTGAATATGCAACTATA-TGAACCAT
1 ACTGAATATGCAACTATATTGAGCCCT
* **
23129 ACTGAATAAGCAACTATA-TGTCCCCT
1 ACTGAATATGCAACTATATTGAGCCCT
23155 ACTGAATATGCAACTATATGAGTGAGCCCT
1 ACTGAATATGCAACTATAT---TGAGCCCT
23185 ACTGAATATGCAACTATATGAGTGAGCCCT
1 ACTGAATATGCAACTATAT---TGAGCCCT
* **
23215 ACTAAATATGCAACTATA-TGTCCCCT
1 ACTGAATATGCAACTATATTGAGCCCT
*
23241 ACTGAATTTGCAACTATA-TGAGCCCT
1 ACTGAATATGCAACTATATTGAGCCCT
**
23267 ACTGAATATAAAACTATATGAGTGAGCCCT
1 ACTGAATATGCAACTATAT---TGAGCCCT
* *
23297 ACTGAATATGCAACTATATGAGTGAGTCAT
1 ACTGAATATGCAACTATAT---TGAGCCCT
23327 ACTGAATATGCAACTATA-TGAGCCCT
1 ACTGAATATGCAACTATATTGAGCCCT
23353 ACTGAATATGCAACTATA-TGAGCCCT
1 ACTGAATATGCAACTATATTGAGCCCT
23379 ACTGAATATGCAA
1 ACTGAATATGCAA
23392 ATTCTTTCAA
Statistics
Matches: 401, Mismatches: 39, Indels: 30
0.85 0.08 0.06
Matches are distributed among these distances:
26 226 0.56
29 1 0.00
30 174 0.43
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (27 bp):
ACTGAATATGCAACTATATTGAGCCCT
Found at i:23546 original size:34 final size:33
Alignment explanation
Indices: 23492--23568 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 33
23482 AGTAAAACCA
* * *
23492 GACTAGATGATGCAGATGACCCTACTAAAATTTG
1 GACTAGATGAGGCAGATGACCATACTAAAA-ATG
*
23526 GAGTAGATGAGGCA-AGTGACCATACTAAAAATG
1 GACTAGATGAGGCAGA-TGACCATACTAAAAATG
23559 GACTAGATGA
1 GACTAGATGA
23569 TACAGATGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 12 0.32
34 25 0.68
ACGTcount: A:0.39, C:0.14, G:0.25, T:0.22
Consensus pattern (33 bp):
GACTAGATGAGGCAGATGACCATACTAAAAATG
Found at i:27874 original size:2 final size:2
Alignment explanation
Indices: 27869--27893 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
27859 AGAGAAAAGA
27869 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
27894 ACTTACTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:27881 original size:20 final size:19
Alignment explanation
Indices: 27844--27883 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
27834 CTTAGAAATA
27844 AAAAGAACGAGGAGGAGAG
1 AAAAGAACGAGGAGGAGAG
27863 AAAAGAA-GAGAGAGAGAGAG
1 AAAAGAACGAG-GAG-GAGAG
27883 A
1 A
27884 GAGAGAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 10 0.53
20 6 0.32
ACGTcount: A:0.57, C:0.03, G:0.40, T:0.00
Consensus pattern (19 bp):
AAAAGAACGAGGAGGAGAG
Found at i:30485 original size:50 final size:51
Alignment explanation
Indices: 30261--30511 Score: 329
Period size: 51 Copynumber: 5.1 Consensus size: 51
30251 CTTGGCATTT
* **
30261 CATTTTAAAAAATTTAGTAATTAGGAGACTC-AT-CA--CCAT-CCTCCAAA
1 CATTTTAAAAAATTTAGTAATTAGGAGAC-CGATGAAGGCTGTCCCTCCAAA
* * *
30308 CATTTTAAAAAATTTAGTAATTAGGA-A-CGATGAGGGTTGTCCCTCCAGA
1 CATTTTAAAAAATTTAGTAATTAGGAGACCGATGAAGGCTGTCCCTCCAAA
* * *
30357 CATTTCAAAAAATTTAGTAATTAGGAGATCGATGAGGGCTGTCCCTCCAAA
1 CATTTTAAAAAATTTAGTAATTAGGAGACCGATGAAGGCTGTCCCTCCAAA
* * *
30408 CATTTTAAAAAATTTAGTAATTAGGAGACCGATAAAGGTTGTCACTCCAAA
1 CATTTTAAAAAATTTAGTAATTAGGAGACCGATGAAGGCTGTCCCTCCAAA
30459 C-TTTTAAAAAATTTAGTAATTAGGAGACCGATGAAGGCTGTCCCTCCAAA
1 CATTTTAAAAAATTTAGTAATTAGGAGACCGATGAAGGCTGTCCCTCCAAA
30509 CAT
1 CAT
30512 ATATAACCTA
Statistics
Matches: 178, Mismatches: 18, Indels: 12
0.86 0.09 0.06
Matches are distributed among these distances:
44 1 0.01
45 2 0.01
46 1 0.01
47 26 0.15
48 1 0.01
49 32 0.18
50 48 0.27
51 67 0.38
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (51 bp):
CATTTTAAAAAATTTAGTAATTAGGAGACCGATGAAGGCTGTCCCTCCAAA
Found at i:30499 original size:101 final size:100
Alignment explanation
Indices: 30261--30511 Score: 343
Period size: 101 Copynumber: 2.5 Consensus size: 100
30251 CTTGGCATTT
* **
30261 CATTTTAAAAAATTTAGTAATTAGGAGACTC-AT-CA--CCAT-CCTCCAAACATTTTAAAAAAT
1 CATTTTAAAAAATTTAGTAATTAGGAGAC-CGATGAAGGCTGTCCCTCCAAACATTTTAAAAAAT
* * * *
30321 TTAGTAATTAGGAACGATGAGGGTTGTCCCTCCAGA
65 TTAGTAATTAGGAACGATAAAGGTTGTCACTCCAAA
* * *
30357 CATTTCAAAAAATTTAGTAATTAGGAGATCGATGAGGGCTGTCCCTCCAAACATTTTAAAAAATT
1 CATTTTAAAAAATTTAGTAATTAGGAGACCGATGAAGGCTGTCCCTCCAAACATTTTAAAAAATT
30422 TAGTAATTAGGAGACCGATAAAGGTTGTCACTCCAAA
66 TAGTAATTAGGA-A-CGATAAAGGTTGTCACTCCAAA
30459 C-TTTTAAAAAATTTAGTAATTAGGAGACCGATGAAGGCTGTCCCTCCAAACAT
1 CATTTTAAAAAATTTAGTAATTAGGAGACCGATGAAGGCTGTCCCTCCAAACAT
30512 ATATAACCTA
Statistics
Matches: 135, Mismatches: 13, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
95 1 0.01
96 29 0.21
99 2 0.01
100 34 0.25
101 50 0.37
102 19 0.14
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.29
Consensus pattern (100 bp):
CATTTTAAAAAATTTAGTAATTAGGAGACCGATGAAGGCTGTCCCTCCAAACATTTTAAAAAATT
TAGTAATTAGGAACGATAAAGGTTGTCACTCCAAA
Found at i:35011 original size:21 final size:22
Alignment explanation
Indices: 34987--35034 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
34977 CACATCAGGA
* *
34987 AAAGAAGGTTTCTTTGCTG-TG
1 AAAGAACGTTTCTTTGATGATG
*
35008 AAAGATCGTTTCTTTGATGATG
1 AAAGAACGTTTCTTTGATGATG
35030 AAAGA
1 AAAGA
35035 CCCGCCATTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.31, C:0.08, G:0.25, T:0.35
Consensus pattern (22 bp):
AAAGAACGTTTCTTTGATGATG
Found at i:35034 original size:22 final size:21
Alignment explanation
Indices: 34994--35034 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
34984 GGAAAAGAAG
*
34994 GTTTCTTTGCTGTGAAAGATC
1 GTTTCTTTGATGTGAAAGATC
35015 GTTTCTTTGATGATGAAAGA
1 GTTTCTTTGATG-TGAAAGA
35035 CCCGCCATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.41
Consensus pattern (21 bp):
GTTTCTTTGATGTGAAAGATC
Found at i:58247 original size:2 final size:2
Alignment explanation
Indices: 58240--58276 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
58230 TGCATTTTTA
58240 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
58277 TTAATAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:68406 original size:9 final size:9
Alignment explanation
Indices: 68376--68456 Score: 62
Period size: 9 Copynumber: 8.9 Consensus size: 9
68366 GGCCCTTATC
68376 TCTT-TCTT
1 TCTTCTCTT
68384 TCTTCTCCCGTT
1 TCTTCT--C-TT
68396 TCTTCTCTT
1 TCTTCTCTT
68405 TCTTCTCTT
1 TCTTCTCTT
*
68414 TCTTTTCTT
1 TCTTCTCTT
*
68423 TCTTC-CTC
1 TCTTCTCTT
68431 TCTT-TCTT
1 TCTTCTCTT
*
68439 GGCCTTCTC-T
1 --TCTTCTCTT
68449 TCTTCTCT
1 TCTTCTCT
68457 CTGAATCTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 17
0.72 0.07 0.21
Matches are distributed among these distances:
8 18 0.31
9 24 0.41
10 5 0.09
11 3 0.05
12 8 0.14
ACGTcount: A:0.00, C:0.35, G:0.04, T:0.62
Consensus pattern (9 bp):
TCTTCTCTT
Found at i:68434 original size:21 final size:20
Alignment explanation
Indices: 68378--68438 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
68368 CCCTTATCTC
*
68378 TTTCTTTCTTCTCCCGTTTCT
1 TTTCTTTCTTCTCTC-TTTCT
*
68399 TCTCTTTC-T-TCTCTTTCT
1 TTTCTTTCTTCTCTCTTTCT
68417 TTTCTTTCTTCCTCTCTTTCT
1 TTTCTTTCTT-CTCTCTTTCT
68438 T
1 T
68439 GGCCTTCTCT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
18 12 0.35
19 4 0.12
20 1 0.03
21 17 0.50
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTCTTTCTTCTCTCTTTCT
Found at i:70434 original size:2 final size:2
Alignment explanation
Indices: 70427--70453 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
70417 AGAATGATGA
70427 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
70454 CACATACCTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.