Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015834.1 Corchorus olitorius cultivar O-4 contig15867, 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: 66770
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:4801 original size:21 final size:21
Alignment explanation
Indices: 4775--4817 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4765 CTAGTATCCT
*
4775 TCCTACCAAACAATAAAAGGG
1 TCCTACCAAACAACAAAAGGG
4796 TCCTACCAAACAACAAAAGGG
1 TCCTACCAAACAACAAAAGGG
4817 T
1 T
4818 AGTGTAGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.26, G:0.14, T:0.14
Consensus pattern (21 bp):
TCCTACCAAACAACAAAAGGG
Found at i:9189 original size:31 final size:30
Alignment explanation
Indices: 9151--9255 Score: 99
Period size: 31 Copynumber: 3.5 Consensus size: 30
9141 AACTGATGCA
9151 AGGCCCTTATTTGAGCATTTTCGATACTGTT
1 AGGCCCTTATTTGAGCATTTTCGATA-TGTT
** * *
9182 AGGCCCTTATTTG-GCCAAATTC-A-AAGAT
1 AGGCCCTTATTTGAG-CATTTTCGATATGTT
*
9210 CGAGCCCTTATTTGAGCATTTTCGATAATGTT
1 AG-GCCCTTATTTGAGCATTTTCGAT-ATGTT
*
9242 AGGCCCTAATTTGA
1 AGGCCCTTATTTGA
9256 CTAAATTAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 3 0.05
29 17 0.30
30 4 0.07
31 29 0.51
32 4 0.07
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (30 bp):
AGGCCCTTATTTGAGCATTTTCGATATGTT
Found at i:9229 original size:60 final size:60
Alignment explanation
Indices: 9151--9308 Score: 194
Period size: 60 Copynumber: 2.6 Consensus size: 60
9141 AACTGATGCA
* * * *
9151 AGGCCCTTATTTGAGCATTTTCGATACTGTTAGGCCCTTATTTGGCCAAATTCAAAGATCG
1 AGGCCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTAATTTGACCAAATTAAAAGAT-G
* *
9212 A-GCCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTAATTTGACTAAATTAAAAGATT
1 AGGCCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTAATTTGACCAAATTAAAAGATG
* * * *
9271 AGGTCCTTATTTGAGTATTTT-GACAAATATTAGGCCCT
1 AGGCCCTTATTTGAGCATTTTCGA-TAATGTTAGGCCCT
9309 TATTGAACAA
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
59 3 0.04
60 81 0.95
61 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (60 bp):
AGGCCCTTATTTGAGCATTTTCGATAATGTTAGGCCCTAATTTGACCAAATTAAAAGATG
Found at i:9753 original size:2 final size:2
Alignment explanation
Indices: 9746--9771 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9736 TTTCGGCCAA
9746 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
9772 CTATTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10337 original size:10 final size:11
Alignment explanation
Indices: 10322--10350 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
10312 ACCTGTTCAT
10322 GGGCCGGG-TC
1 GGGCCGGGTTC
10332 GGGCCGGGTTC
1 GGGCCGGGTTC
10343 GGGCCGGG
1 GGGCCGGG
10351 CCTAGCCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 8 0.44
11 10 0.56
ACGTcount: A:0.00, C:0.28, G:0.62, T:0.10
Consensus pattern (11 bp):
GGGCCGGGTTC
Found at i:10440 original size:41 final size:41
Alignment explanation
Indices: 10383--10488 Score: 185
Period size: 41 Copynumber: 2.6 Consensus size: 41
10373 TTAGTGTTGC
*
10383 CCAAGCCCGGCCCATTTATAAAATGGGTCTCAAACTTTTGT
1 CCAAGCCCGGCCCATTTATAAAATGGGCCTCAAACTTTTGT
*
10424 CCAAGCCCGGCCCATTTATAAAACGGGCCTCAAACTTTTGT
1 CCAAGCCCGGCCCATTTATAAAATGGGCCTCAAACTTTTGT
*
10465 CCAAGCCCGGCCCATTTATCAAAT
1 CCAAGCCCGGCCCATTTATAAAAT
10489 ACTTAGACCA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 61 1.00
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.25
Consensus pattern (41 bp):
CCAAGCCCGGCCCATTTATAAAATGGGCCTCAAACTTTTGT
Found at i:12248 original size:25 final size:26
Alignment explanation
Indices: 12198--12253 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
12188 TTTTAATAAG
*
12198 TATTCTTTTTAGTCATTTAACTTTTT
1 TATTCTTTTTAGTCATTCAACTTTTT
*
12224 TATT-TTTTTAGATGATTCAACTTTTT
1 TATTCTTTTTAG-TCATTCAACTTTTT
12250 TATT
1 TATT
12254 AATTATGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.64
Consensus pattern (26 bp):
TATTCTTTTTAGTCATTCAACTTTTT
Found at i:15046 original size:332 final size:331
Alignment explanation
Indices: 14397--18303 Score: 2691
Period size: 332 Copynumber: 11.9 Consensus size: 331
14387 TTTTTTTTCG
* * * * * *
14397 AAATTTTAACTGAAATAGTGCACTAACTATCACGGTTTTTTTGGGCTAAAAACACGTTTC-GAG-
1 AAATTTTAGCCGAAATCGTGTACTAACCATCACGG--TTTTT-GGCTAAAAACGCGTTTCGGAGT
* * * * * * *
14460 GCCCCGGCTTAGTTTTGCATGATTTTAGGTAGAAAGATTCCTTGAAATATCTATATTCATCTAAT
63 G--CCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAAC
* * * ** *
14525 TAAATTTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCAAGTTTCGATTTG
126 CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
* *
14590 ATTAGAAATAAATTCGGGAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATGT
191 ATTAGAAATTAATTC--GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATAT
* * * **
14654 TTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTGGCAAAAAATTGAGGAAAAACTTTTTTG
254 TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCAG
14719 GTTAATTTTTGCA
319 GTTAATTTTTGCA
14732 AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGTGCC
1 AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGTGCC
* *
14797 GGCTCAATTTTGCAAGATTTTTGGCACAAAGACTCCTT-AAAGTATCTATATTCATCGAACCAAA
66 GGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA-TATCTATATTCATCGAACCAAA
* * * * * * *
14861 TGTCAGCCACATTGGATATAAGGATTTCTATTTACGAGAATCTCAATCTTGTTTTGATTTAATTA
130 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* * * *
14926 GAAATTAATTCGAAAACAAATGGAAAAACGATATTAGAAGCGCGAAAAACCCGTCAATCTTTGTG
195 GAAATTAATTCGAAAA-AAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTG
* * * * **
14991 GCATTCAATTATATATTTTTTCTAAATATT-TCACAAAAAAATTGAGAAAAAACTTTTC-GG---
259 GCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGAGAAAAAACTTTTCAGGTTA
15051 A----T-C-
323 ATTTTTGCA
** *
15054 AGTTTTTAGCCGAAATCG-GTACTAACCATCACGGTTTTCGGCTAAAAACGCGTTTCGG-G-GCC
1 AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGTG-C
* * * *
15116 ACGACT-AAGTTTTGCATGATTTTTGGCAGAAGGACTCCTTGAAAAATCTATATTCATCTAACCA
65 -CGGCTCAA-TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCA
* *
15180 AATCTAAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCAT-TCGAATCTTGTTTCGATTTAA
128 AATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCT-GAATCTTGTTTCGATTTAA
* ** *
15244 TTAACTAGAAATAAATTCAGAAAAAAAAAGAAAAACGATATTAGAAGTGTGAAAAACCCGTT-AA
192 -T---TAGAAATTAATTC-GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCC-TTCAA
* * *
15308 TTTTTTTGGTGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAGAATTGAGGAAAAAA-TTT
251 TATTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAAAAAACTTT
* * *
15372 TCAGATCAGTTTTTGCA
315 TCAGGTTAATTTTTGCA
** ** * * * * *
15389 AAATTTTAGTTGAAATCGT-T--T-ACTTTCAAGTTTTTTGGATAAAAACGCGTTCCGG-GTCCC
1 AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGTGCC
* * *
15449 GGCTTAGTTTTGCATGATTTTTGGC-GTAAAGACTCCTTGAAATATCTATATTCATCGAACTAAA
66 GGCTCAATTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTCATCGAACCAAA
* ** *
15513 TCCCAGCCACATTGGATTTAACTATTTGTTTTTACGAG---CT---TC-----T-GA-TT-CTT-
130 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA
* *
15563 G----T--TTCGAAAAAAATGGAAAAACGATATTAGAGGCGTGAAAAACCCTTCAATCTTTTTGG
195 GAAATTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGG
* * * * * *
15622 CGTTGAATTATATATTTTTTATGAGTATTGTGGCAAAAAAATGAGAAAAAAAATTTTCACGTCAG
260 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAG-AAAAAACTTTTCAGGTTAA
15687 TTTTT---
324 TTTTTGCA
* * * *
15692 --A----A-CCGAAATCATGTAC--ATCATCACGTTTTTTTGGCTAAAAACGCGTTT-TGA-TGC
1 AAATTTTAGCCGAAATCGTGTACTAACCATCACG-GTTTTTGGCTAAAAACGCGTTTCGGAGTG-
* * * * * * * ** * *
15746 CTCGACTCAATTTTGCATGGTTTTTGTCATAAAAACTCCTCGAAATATATATACCCATCTAACCG
64 C-CGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCA
* * * * *
15811 AATATCAGCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTCGTTTCCATTTTAT
128 AATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
* * * * * *
15876 TAGAAATAAATTCGGAAAAAAAAACGAAAAAACGATATTGGAATCGTGAAAAAACCCTTCAATGT
193 TAGAAATTAATTC-G--AAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAAACCCTTCAATAT
* * *
15941 TTTTGGCGTTAAATTATATATATATATATTTTTTGAGTATTGCCGGCAAAAAATTGAGAAAAAA-
254 TTTTGGCGTT-GA--AT-TATATAT-T-TTTTCTGAGTATTG-TGGCAAAAAATTGAGAAAAAAC
** ** * *
16005 TTTTTGGGGCAGTTTTTACA
312 TTTTCAGGTTAATTTTTGCA
* * ** ** * *
16025 AAATTTTTGCCGAAATTGTGTACTATTCAAAATCGGTTTTTCGCTAAAAACGCG-TTCCGAG-GA
1 AAATTTTAGCCGAAATCGTGTACTAACCATCA-CGGTTTTTGGCTAAAAACGCGTTTCGGAGTG-
** * **** * *
16088 CCCACCTCAATTTTGCATGATTTTTGACTCCGAGACTACTTGAAATATCTATACTT-ATCAAACC
64 -CCGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATA-TTCATCGAACC
** * *
16152 AAATCTCAGCCACATTGGACATATGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTCAA
127 AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
* ** *
16217 TTAGAAATTAATCCGGAAAAAATAATGGAAAAACGATATTAGAAGCGTGAAAAGGCCGTCAATAT
192 TTAGAAATTAATTC-G-AAAAA-AATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATAT
* * * * * *
16282 TTTTGGTGTTGAATTTTATATTTTTTATGAATATT-TTGCAAAAAATTGAGAAGAAACTTTTC--
254 TTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCAG
16344 GTGTAAGTTTTT---
319 GT-TAA-TTTTTGCA
* * * * * * *
16356 --A---T--CCGAAATCGTGTAGTCA-C-T-A--TTTTTTGGCTAAAAACACGTTTCGGGGCGTC
1 AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGTGCC
* ** * *
16409 GACTCTGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTACATTCATCTAACCAAAT
66 GGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
* * * * *
16474 CTCAGCGATATTGG-TATATGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCAATTTAATTA
131 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC-TTGTTTCGATTTAATTA
* * *
16538 G-ATTTAAATTCGGAAAAAA-GGAAAAACG-TATTAGAAGTGTGAAAAACCCTTCAAT-TTTATT
195 GAAATT-AATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTT-TT
* * * *
16599 GGCGTTGAAGTATATA-TTTTTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCA
258 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCAGGTTA
16663 A-TTTTGCA
323 ATTTTTGCA
* *** * *
16671 AAATTTTAGTCGAAATC--GT-CT-A-C-T--TTTTTTTTTGCCAACGAAAC-CG--T----GT-
1 AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA--AAACGCGTTTCGGAGTG
* ** * * * * * * * * **
16720 ---ACT-AATCAT-CATGGTGTTTTGCCTA-AAA-ACGCGTTCCAGA-GTCTA-AGCTCAAT-TT
64 CCGGCTCAATTTTGCATGAT-TTTTGGC-AGAAAGACTCCTT-GAAATATCTATA-TTC-ATCGA
** * * ** * * ** ** * *
16775 TGCATTATTTTTGGCGCA-AAGACTTTTTGAAATATCTATATTCATTGAATCAAATCTCAGCCAC
124 ACCA-AATCTCAGCCACATTGGA---TTT-AAGGAT-T-TGTT--TT---T---A-C-GAG-CA-
* * * * * *
16839 ACTGTATATAAAAATTTGTTTTTACTAGCATGTGAATCTTGTTTCAATTTAATTAGAAATTAATT
170 TCTG-A-AT-----CTTG--TTT-C--G-AT-TTAAT-TAG----AAATTAATTCG-AA------
* * * ** * *
16904 CAGAAAAAATAATGAAAAATGATATTAGAAGCGTCAAAAGGCCGTCAATATTTTTGGCATTGAAT
209 ----AAAAAT--GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGCGTTGAAT
* * *
16969 TATAT-TTTTTT-T-AATATT-TTGCAAAAAATTGAG-AAAAGCTTTTC-GAGTT-A-----G--
268 TATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCAG-GTTAATTTTTGCA
* * * * * * **
17020 --TTTTTAGTCGTAATAGTGTACTAACCATCACGGTTTTTGGCTAAAAACGAGTTTCATG-GCCC
1 AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGAGTGC
* * * *
17082 CGACTCAGTTTTGAATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAA
65 CGGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAA
* *
17147 TCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTCCGATTTAATT
130 TCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC-TTGTTTCGATTTAATT
* * *
17212 AGAAATAAATTCGGAAAAAAA-GGAAAAACGATATT-GAAAGCGTGAAAACCCCTTCAATTTTTT
194 AGAAATTAATTC-GAAAAAAATGGAAAAACGATATTAG-AAGCGTGAAAAACCCTTCAATATTTT
** * *
17275 TGGCGTTGAATTATATA-TTTTTCTGAGTATTGTGTTAAAAAAATTGAGGAAAGACTTTTCAGGT
257 TGGCGTTGAATTATATATTTTTTCTGAGTATTGTG-GCAAAAAATTGAGAAAAAACTTTTCAGGT
* *
17339 CAATATTTGCA
321 TAATTTTTGCA
* * * * *
17350 AAATTTTAGCCGAAATCGTGAACTAACTATCACGGTTTTTGGCCAAAAACACG-TTCTGAAGT-C
1 AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGAGTGC
17413 TCGGCTCAATTTTGCATGATTTTTGG-AGTAAAGAC-CCATTGAAATATCTATATTCATCGAACC
65 -CGGCTCAATTTTGCATGATTTTTGGCAG-AAAGACTCC-TTGAAATATCTATATTCATCGAACC
* * * * * * *
17476 CAATCTCAACCACATTGTATATAAGGATTTGTTTTAACGAGCACCCGAATCTTGTTTCGATTTAA
127 AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAA
* * ** * *
17541 TTAGAAATTAATTC-AGAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGGCCGTCAATCTTTT
192 TTAGAAATTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTT
* * * * *
17605 TGGAGTTGAATTATATATTTTTACTGAATATT-TTGCAAAAAATTGAG-AAAAACTTTTCGGGTT
257 TGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCAGGTT
17668 -A-----G--
322 AATTTTTGCA
* * *
17670 --TTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTTCGGA-TCCC
1 AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGTGCC
* ** * * *
17732 GGCTCAGTTTTAAATGATTTTTGGCAGAAAGGCTCCTTGAAATATCTATATTCATCTAACGAAAT
66 GGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
* * * * *
17797 CTCAGCCACAATGGATTTAAGAATTTATTTTTACGAGTATCTCAATCTTTGTTTCGATTTAATTA
131 CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC-TTGTTTCGATTTAATTA
* ** *
17862 GAAATAAATTCGGGAAAAAAATGTTAAAACGATATTAAAAGCGTGAAAAACCCTTCAAT-TTTTT
195 GAAATTAATTC--GAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTT
* * *
17926 GGGCGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAAATTGAGGAAAAACTTTTCAAGT
258 -GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAAATTGAGAAAAAACTTTTCAGGT
* *
17991 CAGTTTTTGCA
321 TAATTTTTGCA
** * * **
18002 AAATTTTAGCCGAAATCGTGTACTAACCATCACTATTTTTGGCTAAAAACGCGTTCCGAAGCCCC
1 AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGTGCC
* * * * * *
18067 GTCTCAATTTTGCATGATTTTTTG-TGTAAAGACTCATTGAAATAT-TCAAATTCATTGAACCAA
66 GGCTCAATTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCT-ATATTCATCGAACCAA
* * * *
18130 ATGTCAGCCACATTGGATATAAGGATTTGTTTTTCCGAGCATCTGAATCTTGTTTCGATTTAATC
129 ATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* * * ** *
18195 AGAAATTAATTC-ATAAATAATGGAAAAATGATATTAGAAACGTGAAAAGGCCGTCAATATTTTT
194 AGAAATTAATTCGA-AAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTT
*
18259 GACGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG
258 GGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG
18304 GGAATATAAC
Statistics
Matches: 2808, Mismatches: 499, Indels: 534
0.73 0.13 0.14
Matches are distributed among these distances:
296 7 0.00
297 2 0.00
298 7 0.00
299 21 0.01
300 83 0.03
301 1 0.00
303 2 0.00
304 3 0.00
305 92 0.03
306 20 0.01
307 1 0.00
308 20 0.01
309 20 0.01
310 4 0.00
311 1 0.00
312 23 0.01
313 68 0.02
314 15 0.01
315 8 0.00
316 6 0.00
317 183 0.07
318 185 0.07
319 27 0.01
320 24 0.01
321 225 0.08
322 43 0.02
323 16 0.01
324 54 0.02
325 119 0.04
326 20 0.01
327 4 0.00
328 18 0.01
329 28 0.01
330 82 0.03
331 175 0.06
332 469 0.17
333 37 0.01
334 95 0.03
335 155 0.06
336 4 0.00
337 7 0.00
338 2 0.00
339 3 0.00
340 19 0.01
341 31 0.01
342 164 0.06
343 4 0.00
345 5 0.00
346 7 0.00
347 13 0.00
348 3 0.00
349 4 0.00
350 4 0.00
351 3 0.00
352 2 0.00
353 5 0.00
354 1 0.00
355 12 0.00
356 18 0.01
357 14 0.00
358 7 0.00
359 8 0.00
360 46 0.02
361 4 0.00
362 4 0.00
363 3 0.00
364 4 0.00
365 23 0.01
366 20 0.01
367 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (331 bp):
AAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGAGTGCC
GGCTCAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
CTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
AAATTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATATTTTTGGC
GTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTTTCAGGTTAATT
TTTGCA
Found at i:18158 original size:652 final size:646
Alignment explanation
Indices: 15571--18303 Score: 2948
Period size: 650 Copynumber: 4.1 Consensus size: 646
15561 TTGTTTCGAA
* * ** * * *
15571 AAAAATGGAAAAACGATATTAGAGGCGTGAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATA
1 AAAAATGGAAAAATGATATTAGAAGCGTGAAAAGGCCGTCAATATTTTTGGAGTTGAATTATATA
* * * * * *
15636 TTTTTTATGAGTATTGTGGCAAAAAAATGAGAAAAAAAATTTTC-ACGTCAGTTTTTAACCGAAA
66 -TTTTTATGAATATT-TTGCAAAAAATTGAG--AAAAACTTTTCGA-GTTAGTTTTTAGCCGAAA
* * * * *
15700 TCATGTAC--ATCATCACGTTTTTTTGGCTAAAAACGCGTTT-TGATGCCTCGACTCAATTTTGC
126 TCGTGTACTAACCATCACG-TTTTTTGGCTAAAAACGCGTTTCGGAT-CC-CGACTCAGTTTTGA
* * * * * * ** * * **
15762 ATGGTTTTTGTCATAAAAACTCCTCGAAATATATATACCCATCTAACCGAATATCAGCCACTTTG
188 ATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATG
* * *
15827 GATTTAAGGATTTGTTTTTACGAGCATCTGAATC-TCGTTTCCATTTTATTAGAAATAAATTCGG
253 GATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGG
* ** *
15891 AAAAAAAAACGAAAAAACGATATTGGAATCGTGAAAAAACCCTTCAATGTTTTTGGCGTTAAATT
318 --AAAAAAA-GGAAAAACGATATTAAAAGCGTG-AAAAACCCTTCAAT-TTTTTGGCGTT--A--
* * * ** *
15956 ATATATATATATATTTTTTGAGTATTGCCGGCAAAAAATTGA-GAAAAAATTTTTGGGGCAGTTT
374 A-AT-TATATAT-TTTTCTGAGTATTG-TGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAGTTT
* * * ** ** *
16020 TTACAAAATTTTTGCCGAAATTGTGTACTATTCAAAATCGGTTTTTCGCTAAAAACGCGTTCCGA
435 TTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATCGGTTTTTGGCTAAAAACGCGTTCCGA
* * ** *
16085 GGACCCAC-CTCAATTTTGCATGATTTTT-GACTCCGAGACT-ACTTGAAATATCTATACTT-AT
500 AG-CCC-CGCTCAATTTTGCATGATTTTTGGAGT-AAAGACTCA-TTGAAATATCTA-AATTCAT
* * *
16146 CAAACCAAATCTCAGCCACATTGGACATATGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
560 CGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
* * *
16211 ATTCAATTAGAAATTAATCCGGAAA
625 ATTTAATTAGAAATTAATTC---AG
* * *
16236 AAATAATGGAAAAACGATATTAGAAGCGTGAAAAGGCCGTCAATATTTTTGGTGTTGAATTTTAT
1 AAA-AATGGAAAAATGATATTAGAAGCGTGAAAAGGCCGTCAATATTTTTGGAGTTGAATTATAT
* * *
16301 ATTTTTTATGAATATTTTGCAAAAAATTGAGAAGAAACTTTTCGTGTAAGTTTTTATCCGAAATC
65 A-TTTTTATGAATATTTTGCAAAAAATTGAGAA-AAACTTTTCGAGTTAGTTTTTAGCCGAAATC
* * * ** * * *
16366 GTGTAGTCA-C-T-A--TTTTTTGGCTAAAAACACGTTTCGGGGCGTCGACTCTGTTTTGCATGA
128 GTGTACTAACCATCACGTTTTTTGGCTAAAAACGCGTTTCGGATC-CCGACTCAGTTTTGAATGA
* * * * *
16426 TTTTTGGCAGAAAGACTCCTTGAAATATCTACATTCATCTAACCAAATCTCAGCGATATTGG-TA
192 TTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATT
* * **
16490 TATGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCAATTTAATTAGATTTAAATTCGG-AAA
257 TAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAA
* * * *
16554 AAAGGAAAAACG-TATTAGAAGTGTGAAAAACCCTTCAATTTTATTGGCGTTGAAGTATATATTT
322 AAAGGAAAAACGATATTAAAAGCGTGAAAAACCCTTCAATTTT-TTGGCGTTAAATTATATATTT
* * *
16618 TTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCGGGTCA-ATTTTGCAAAATTTTAGTC
386 TTCTGAGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAGTTTTTGCAAAATTTTAGCC
* *
16682 GAAATCGTCTACTTTTTTTTTTGCCAACGAAACCGTGTACTAATCATCATGGTGTTTTGCCTAAA
451 GAAATCGTGTAC---------T--------AA-C-----C--ATCATC--GGT-TTTTGGCTAAA
*** * * * **
16747 AACGCGTTCC-AGAGTCTAAGCTCAATTTTGCATTATTTTTGGCGCAAAGACTTTTTGAAATATC
488 AACGCGTTCCGA-AG-CCCCGCTCAATTTTGCATGATTTTTGGAGTAAAGACTCATTGAAATATC
* * * * * ** * *
16811 TATATTCATTGAATCAAATCTCAGCCACACTGTATATAAAAATTTGTTTTTACTAGCATGTGAAT
551 TAAATTCATCGAACCAAATCTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAAT
*
16876 CTTGTTTCAATTTAATTAGAAATTAATTCAG
616 CTTGTTTCGATTTAATTAGAAATTAATTCAG
* *
16907 AAAAAATAATGAAAAATGATATTAGAAGCGTCAAAAGGCCGTCAATATTTTTGGCA-TTGAATTA
1 -AAAAAT--GGAAAAATGATATTAGAAGCGTGAAAAGGCCGTCAATATTTTTGG-AGTTGAATTA
* * * *
16971 TAT-TTTTT-TTAATATTTTGCAAAAAATTGAGAAAAGCTTTTCGAGTTAGTTTTTAGTCGTAAT
62 TATATTTTTATGAATATTTTGCAAAAAATTGAGAAAAACTTTTCGAGTTAGTTTTTAGCCGAAAT
* * * *
17034 AGTGTACTAACCATCACGGTTTTTGGCTAAAAACGAGTTTCATGG-CCCCGACTCAGTTTTGAAT
127 CGTGTACTAACCATCACGTTTTTTGGCTAAAAACGCGTTTC--GGATCCCGACTCAGTTTTGAAT
17098 GATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGA
190 GATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGA
*
17163 TTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTCCGATTTAATTAGAAATAAATTCGGAA
255 TTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAA
* * *
17228 AAAAAGGAAAAACGATATTGAAAGCGTGAAAACCCCTTCAATTTTTTTGGCGTTGAATTATATAT
320 AAAAAGGAAAAACGATATTAAAAGCGTGAAAAACCCTTCAA-TTTTTTGGCGTTAAATTATATAT
** * * *
17293 TTTTCTGAGTATTGTGTTAAAAAAATTGAGGAAAGACTTTTCAGGTCAATATTTGCAAAATTTTA
384 TTTTCTGAGTATTGTG-GCAAAAAATTGAGGAAAAACTTTTCAGGTCAGTTTTTGCAAAATTTTA
* * * * * * *
17358 GCCGAAATCGTGAACTAACTATCA-CGGTTTTTGGCCAAAAACACGTTCTGAAGTCTCGGCTCAA
448 GCCGAAATCGTGTACTAACCATCATCGGTTTTTGGCTAAAAACGCGTTCCGAAG-CCCCGCTCAA
* * * *
17422 TTTTGCATGATTTTTGGAGTAAAGACCCATTGAAATATCTATATTCATCGAACCCAATCTCAACC
512 TTTTGCATGATTTTTGGAGTAAAGACTCATTGAAATATCTAAATTCATCGAACCAAATCTCAGCC
* * * *
17487 ACATTGTATATAAGGATTTGTTTTAACGAGCACCCGAATCTTGTTTCGATTTAATTAGAAATTAA
577 ACATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
17552 TTCAG
642 TTCAG
*
17557 AAAAATGGAAAAATGATATTAGAAGCGTGAAAAGGCCGTCAATCTTTTTGGAGTTGAATTATATA
1 AAAAATGGAAAAATGATATTAGAAGCGTGAAAAGGCCGTCAATATTTTTGGAGTTGAATTATATA
*
17622 TTTTTACTGAATATTTTGCAAAAAATTGAGAAAAACTTTTCGGGTTAGTTTTTAGCCGAAATCGT
66 TTTTTA-TGAATATTTTGCAAAAAATTGAGAAAAACTTTTCGAGTTAGTTTTTAGCCGAAATCGT
* * *
17687 GTACTAACCATCACGATTTTTGGCTAAAAACGCGTTTCGGATCCCGGCTCAGTTTTAAATGATTT
130 GTACTAACCATCACGTTTTTTGGCTAAAAACGCGTTTCGGATCCCGACTCAGTTTTGAATGATTT
* *
17752 TTGGCAGAAAGGCTCCTTGAAATATCTATATTCATCTAACGAAATCTCAGCCACAATGGATTTAA
195 TTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAA
* * * *
17817 GAATTTATTTTTACGAGTATCTCAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGGAAAAAA
260 GGATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTC-GGAAAAAA
**
17882 ATGTTAAAACGATATTAAAAGCGTGAAAAACCCTTCAATTTTTTGGGCGTTAAATTATATATTTT
324 A-GGAAAAACGATATTAAAAGCGTGAAAAACCCTTCAATTTTTT-GGCGTTAAATTATATA-TTT
*
17947 TTCTGAGTATTGTGGCAAAAAAATTGAGGAAAAACTTTTCAAGTCAGTTTTTGCAAAATTTTAGC
386 TTCTGAGTATTGTGGC-AAAAAATTGAGGAAAAACTTTTCAGGTCAGTTTTTGCAAAATTTTAGC
**
18012 CGAAATCGTGTACTAACCATCA-CTATTTTTGGCTAAAAACGCGTTCCGAAGCCCCGTCTCAATT
450 CGAAATCGTGTACTAACCATCATCGGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCG-CTCAATT
* * * *
18076 TTGCATGATTTTTTGTGTAAAGACTCATTGAAATAT-TCAAATTCATTGAACCAAATGTCAGCCA
514 TTGCATGATTTTTGGAGTAAAGACTCATTGAAATATCT-AAATTCATCGAACCAAATCTCAGCCA
* *
18140 CATTGGATATAAGGATTTGTTTTTCCGAGCATCTGAATCTTGTTTCGATTTAATCAGAAATTAAT
578 CATTGGATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT
*
18205 TCAT
643 TCAG
*
18209 AAATAATGGAAAAATGATATTAGAAACGTGAAAAGGCCGTCAATATTTTT-GACGTTGAATTATA
1 AAA-AATGGAAAAATGATATTAGAAGCGTGAAAAGGCCGTCAATATTTTTGGA-GTTGAATTATA
* * *
18273 TATTTTTTCTGAGTATTGTGGCAAAAAATTG
64 TA-TTTTTATGAATATT-TTGCAAAAAATTG
18304 GGAATATAAC
Statistics
Matches: 1762, Mismatches: 229, Indels: 165
0.82 0.11 0.08
Matches are distributed among these distances:
646 39 0.02
647 81 0.05
648 14 0.01
649 142 0.08
650 248 0.14
651 55 0.03
652 233 0.13
653 68 0.04
654 43 0.02
655 11 0.01
656 8 0.00
657 6 0.00
659 30 0.02
660 111 0.06
661 2 0.00
662 2 0.00
663 4 0.00
664 31 0.02
665 17 0.01
666 70 0.04
669 32 0.02
670 26 0.01
671 14 0.01
672 4 0.00
673 58 0.03
674 224 0.13
675 59 0.03
676 17 0.01
677 56 0.03
678 31 0.02
679 26 0.01
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (646 bp):
AAAAATGGAAAAATGATATTAGAAGCGTGAAAAGGCCGTCAATATTTTTGGAGTTGAATTATATA
TTTTTATGAATATTTTGCAAAAAATTGAGAAAAACTTTTCGAGTTAGTTTTTAGCCGAAATCGTG
TACTAACCATCACGTTTTTTGGCTAAAAACGCGTTTCGGATCCCGACTCAGTTTTGAATGATTTT
TGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAG
GATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAG
GAAAAACGATATTAAAAGCGTGAAAAACCCTTCAATTTTTTGGCGTTAAATTATATATTTTTCTG
AGTATTGTGGCAAAAAATTGAGGAAAAACTTTTCAGGTCAGTTTTTGCAAAATTTTAGCCGAAAT
CGTGTACTAACCATCATCGGTTTTTGGCTAAAAACGCGTTCCGAAGCCCCGCTCAATTTTGCATG
ATTTTTGGAGTAAAGACTCATTGAAATATCTAAATTCATCGAACCAAATCTCAGCCACATTGGAT
ATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG
Found at i:19207 original size:17 final size:18
Alignment explanation
Indices: 19185--19218 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
19175 GGTTATAAAA
*
19185 AATCATTGGAA-GTTTAC
1 AATCATAGGAAGGTTTAC
19202 AATCATAGGAAGGTTTA
1 AATCATAGGAAGGTTTA
19219 TTAAAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (18 bp):
AATCATAGGAAGGTTTAC
Found at i:19246 original size:22 final size:23
Alignment explanation
Indices: 19216--19341 Score: 93
Period size: 22 Copynumber: 5.7 Consensus size: 23
19206 ATAGGAAGGT
* *
19216 TTATTAAAATTTTATAGT-TAGG
1 TTATCAAAATTTCATAGTGTAGG
* *
19238 TTATCAAAATTTCATA-TGGAGT
1 TTATCAAAATTTCATAGTGTAGG
* * **
19260 TTATCACAATTTCATA-AGTAAA
1 TTATCAAAATTTCATAGTGTAGG
19282 TTATCAAAATTTCATAGTGT-GG
1 TTATCAAAATTTCATAGTGTAGG
* * *
19304 TTATCAAATTTTAATTG-GATA-G
1 TTATCAAAATTTCATAGTG-TAGG
*
19326 CTATCAAAATTTCATA
1 TTATCAAAATTTCATA
19342 AAAATATTCA
Statistics
Matches: 80, Mismatches: 20, Indels: 8
0.74 0.19 0.07
Matches are distributed among these distances:
21 2 0.03
22 76 0.95
23 2 0.03
ACGTcount: A:0.38, C:0.09, G:0.11, T:0.42
Consensus pattern (23 bp):
TTATCAAAATTTCATAGTGTAGG
Found at i:19664 original size:30 final size:30
Alignment explanation
Indices: 19628--19703 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 30
19618 GTGTTGAAGG
19628 AAGAAAATCAAAATTC-CTTTTTT-GCACAAC
1 AAGAAAATCAAAATTCGCTTTTTTGGC-C-AC
* *
19658 AAGAAAATCAAAATTCGTTTTTTTGGCCAG
1 AAGAAAATCAAAATTCGCTTTTTTGGCCAC
19688 AAGAAAATCAAAATTC
1 AAGAAAATCAAAATTC
19704 AATATATGTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
30 33 0.79
31 7 0.17
32 2 0.05
ACGTcount: A:0.45, C:0.16, G:0.11, T:0.29
Consensus pattern (30 bp):
AAGAAAATCAAAATTCGCTTTTTTGGCCAC
Found at i:19862 original size:18 final size:19
Alignment explanation
Indices: 19839--19877 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
19829 TATTATATAC
19839 AATTTATA-AT-GAAGAAAA
1 AATTTATATATGGAA-AAAA
19857 AATTTATATATGGAAAAAA
1 AATTTATATATGGAAAAAA
19876 AA
1 AA
19878 AAGATGCTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.42
19 8 0.42
20 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (19 bp):
AATTTATATATGGAAAAAA
Found at i:19876 original size:20 final size:18
Alignment explanation
Indices: 19839--19878 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
19829 TATTATATAC
*
19839 AATTTATAATGAAGAAAA
1 AATTTATAATGAAAAAAA
19857 AATTTATATATGGAAAAAAA
1 AATTTATA-AT-GAAAAAAA
19877 AA
1 AA
19879 AGATGCTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 2 0.11
20 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (18 bp):
AATTTATAATGAAAAAAA
Found at i:20691 original size:2 final size:2
Alignment explanation
Indices: 20684--20732 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
20674 TAATTTTTGA
* * * * *
20684 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT GT TT GT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20726 AT AT AT A
1 AT AT AT A
20733 AGATAATTGG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (2 bp):
AT
Found at i:32474 original size:17 final size:18
Alignment explanation
Indices: 32452--32487 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
32442 AGTAAAAAAG
32452 AACC-TTGATTTCCCCTT
1 AACCTTTGATTTCCCCTT
32469 AACCTTTTGATTTCCCCTT
1 AACC-TTTGATTTCCCCTT
32488 GACCATGAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
19 13 0.76
ACGTcount: A:0.17, C:0.33, G:0.06, T:0.44
Consensus pattern (18 bp):
AACCTTTGATTTCCCCTT
Found at i:33812 original size:30 final size:30
Alignment explanation
Indices: 33778--33835 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
33768 TTATCTTGAC
33778 TTTTCTCTTACACCCTCAAATTTTAATGAT
1 TTTTCTCTTACACCCTCAAATTTTAATGAT
*
33808 TTTTCTCTTATACCCTCAAATTTTAATG
1 TTTTCTCTTACACCCTCAAATTTTAATG
33836 GCTTATTAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.26, C:0.22, G:0.03, T:0.48
Consensus pattern (30 bp):
TTTTCTCTTACACCCTCAAATTTTAATGAT
Found at i:39194 original size:7 final size:7
Alignment explanation
Indices: 39182--39214 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
39172 CTTAATATGA
39182 TCCTTTT
1 TCCTTTT
39189 TCCTTTT
1 TCCTTTT
39196 TCCTTTT
1 TCCTTTT
39203 TCCTTTT
1 TCCTTTT
39210 TCCTT
1 TCCTT
39215 CTATAATAAT
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:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (7 bp):
TCCTTTT
Found at i:39954 original size:32 final size:31
Alignment explanation
Indices: 39891--40026 Score: 137
Period size: 31 Copynumber: 4.3 Consensus size: 31
39881 TTTGTGCACG
*
39891 TGGCATGCCACGTGTCACTTTTTGAACACACA
1 TGGCATGCCACGTGTCACTTTTTG-ATACACA
*
39923 TGGCATGCCACGTGTCACTTTTTTGGTACACA
1 TGGCATGCCACGTGTCAC-TTTTTGATACACA
* ** * *
39955 TGGCGTGATATGTGTCACTTTTTGATACACG
1 TGGCATGCCACGTGTCACTTTTTGATACACA
* * * * * *
39986 TGGCGTGCGACATGTCGCTTTTTGGTACACG
1 TGGCATGCCACGTGTCACTTTTTGATACACA
40017 TGGCATGCCA
1 TGGCATGCCA
40027 TCGTCGGATA
Statistics
Matches: 87, Mismatches: 16, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
31 44 0.51
32 37 0.43
33 6 0.07
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (31 bp):
TGGCATGCCACGTGTCACTTTTTGATACACA
Found at i:44408 original size:11 final size:11
Alignment explanation
Indices: 44384--44425 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
44374 TTGACAGCGC
44384 AACAAAAACAA
1 AACAAAAACAA
* *
44395 AACGAAAACGA
1 AACAAAAACAA
44406 AACAAAAACAAA
1 AACAAAAAC-AA
44418 AACAAAAA
1 AACAAAAA
44426 ACAGAATAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
11 17 0.65
12 9 0.35
ACGTcount: A:0.79, C:0.17, G:0.05, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:44428 original size:7 final size:6
Alignment explanation
Indices: 44384--44425 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
44374 TTGACAGCGC
* *
44384 AACAAA AAC-AA AACGAA AAC-GA AACAAA AACAAA AACAAA AA
1 AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AACAAA AA
44426 ACAGAATAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 9 0.28
6 23 0.72
ACGTcount: A:0.79, C:0.17, G:0.05, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:46294 original size:41 final size:41
Alignment explanation
Indices: 46249--46363 Score: 230
Period size: 41 Copynumber: 2.8 Consensus size: 41
46239 GACTTGTAAC
46249 ATATTTTTGTGAAAGATATATCATATATGTTTTTGTGAAAG
1 ATATTTTTGTGAAAGATATATCATATATGTTTTTGTGAAAG
46290 ATATTTTTGTGAAAGATATATCATATATGTTTTTGTGAAAG
1 ATATTTTTGTGAAAGATATATCATATATGTTTTTGTGAAAG
46331 ATATTTTTGTGAAAGATATATCATATATGTTTT
1 ATATTTTTGTGAAAGATATATCATATATGTTTT
46364 AGTTATGCAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.34, C:0.03, G:0.16, T:0.48
Consensus pattern (41 bp):
ATATTTTTGTGAAAGATATATCATATATGTTTTTGTGAAAG
Found at i:46298 original size:15 final size:15
Alignment explanation
Indices: 46278--46349 Score: 71
Period size: 15 Copynumber: 5.1 Consensus size: 15
46268 ATCATATATG
46278 TTTTTGTGAAAGATA
1 TTTTTGTGAAAGATA
46293 TTTTTGTGAAAGATA
1 TTTTTGTGAAAGATA
* * * * *
46308 ----TATCATATATG
1 TTTTTGTGAAAGATA
46319 TTTTTGTGAAAGATA
1 TTTTTGTGAAAGATA
46334 TTTTTGTGAAAGATA
1 TTTTTGTGAAAGATA
46349 T
1 T
46350 ATCATATATG
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
11 6 0.14
15 37 0.86
ACGTcount: A:0.33, C:0.01, G:0.18, T:0.47
Consensus pattern (15 bp):
TTTTTGTGAAAGATA
Found at i:46310 original size:17 final size:17
Alignment explanation
Indices: 46273--46310 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 17
46263 GATATATCAT
*
46273 ATATGTTTTTGTGAAAG
1 ATATATTTTTGTGAAAG
46290 --ATATTTTTGTGAAAG
1 ATATATTTTTGTGAAAG
46305 ATATAT
1 ATATAT
46311 CATATATGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 4
0.78 0.04 0.17
Matches are distributed among these distances:
15 14 0.78
17 4 0.22
ACGTcount: A:0.34, C:0.00, G:0.18, T:0.47
Consensus pattern (17 bp):
ATATATTTTTGTGAAAG
Found at i:59084 original size:102 final size:102
Alignment explanation
Indices: 58908--59161 Score: 409
Period size: 102 Copynumber: 2.5 Consensus size: 102
58898 AACTGGTGGC
* **
58908 TTCTTTGGAGGTTCATAGACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGGAGGTTTATAAAC
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGGAGGAGTATAAAC
58973 TGGTGGCTTTGGTGGCTTAGGTTCGTAGGTTGGGGGT
66 TGGTGGCTTTGGTGGCTTAGGTTCGTAGGTTGGGGGT
*
59010 TTCTTTGGAGGTTCATACACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGGAGGAGTATAAAC
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGGAGGAGTATAAAC
* *
59075 TGGTGGCTTTGGTGGCTTAGGTTCGTATGTTGGTGGT
66 TGGTGGCTTTGGTGGCTTAGGTTCGTAGGTTGGGGGT
* * * * *
59112 TTCTTTGGTGGTTCATAAACTGGTGGTTTGGGCTTTGGCTTCTCCTTCTT
1 TTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTT
59162 CGGGGGCTCG
Statistics
Matches: 141, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
102 141 1.00
ACGTcount: A:0.11, C:0.14, G:0.33, T:0.43
Consensus pattern (102 bp):
TTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGGAGGAGTATAAAC
TGGTGGCTTTGGTGGCTTAGGTTCGTAGGTTGGGGGT
Found at i:59176 original size:102 final size:100
Alignment explanation
Indices: 58901--59186 Score: 394
Period size: 102 Copynumber: 2.8 Consensus size: 100
58891 GCTCATAAAC
* * *
58901 TGGTGGCTTCTTTGGAGGTTCATAGACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGGAGGTT
1 TGGTGGTTTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGG-GG-G
58966 TATAAACTGGTGGCTTTGGTGGCTTAGGTTCGTAGGT
64 TATAAACTGGTGGCTTTGGTGGCTTAGGTTCGTAGGT
* *
59003 TGGGGGTTTCTTTGGAGGTTCATACACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGGAGGAG
1 TGGTGGTTTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGG-GG-G
*
59068 TATAAACTGGTGGCTTTGGTGGCTTAGGTTCGTATGT
64 TATAAACTGGTGGCTTTGGTGGCTTAGGTTCGTAGGT
* * * * * *
59105 TGGTGGTTTCTTTGGTGGTTCATAAACTGGTGGTTTGGGCTTTGGCTTCTCCTTCTTCGGGGGCT
1 TGGTGGTTTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGGGGG-T
*
59170 CGTAAACTGGTGG-TTTG
65 -ATAAACTGGTGGCTTTG
59187 TCCTTTGGCT
Statistics
Matches: 167, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
100 1 0.01
101 7 0.04
102 159 0.95
ACGTcount: A:0.10, C:0.14, G:0.34, T:0.41
Consensus pattern (100 bp):
TGGTGGTTTCTTTGGAGGTTCATAAACTGGTGGCTTGGGTTTTGGCTCCTCTTTCTTTGGGGGTA
TAAACTGGTGGCTTTGGTGGCTTAGGTTCGTAGGT
Found at i:59271 original size:135 final size:135
Alignment explanation
Indices: 59112--59547 Score: 590
Period size: 135 Copynumber: 3.2 Consensus size: 135
59102 TGTTGGTGGT
* * * * *
59112 TTCTTTGGTGGTTCATAAACTGGTGGTTTGGGCTTTGGCTTCTCCTTCTTCGGGGGCTCGTAAAC
1 TTCTTTGGGGGTTCATAAACTGGTGGCTTGGGCTTCGGCTTCTCCTTCTTTGGGGGTTCGTAAAC
* ** * * * *
59177 TGGTGG-TT-TGTCCTTTGGCTTCTCCTTCTTTGGTGGTTCATAAACTGGTGGCTTAGGTTCAGG
66 TGGTGGCTTAGGT--TCAGGCTTTTCCTTCTTTGGTGGTTCATAAACTGGAGGCTTGGGTTCGGG
*
59240 CTTTTCC
129 TTTTTCC
* * * **
59247 TTCTTTGGGGGCTCGTAAACTGGTGGTTTGTCCTTCGGCTTCTCCTTCTTTGGGGGTTCGTAAAC
1 TTCTTTGGGGGTTCATAAACTGGTGGCTTGGGCTTCGGCTTCTCCTTCTTTGGGGGTTCGTAAAC
59312 TGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGTGGTTCATAAACTGGAGGCTTGGGTTCGGGTT
66 TGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGTGGTTCATAAACTGGAGGCTTGGGTTCGGGTT
59377 TTTCC
131 TTTCC
* * * * *
59382 TTCTTTGGTGGTTCATAAACTGGAGGCTTGGG-TTCGGGCTTTTCCTTCTTTGGTGGTTCATAAA
1 TTCTTTGGGGGTTCATAAACTGGTGGCTTGGGCTTC-GGCTTCTCCTTCTTTGGGGGTTCGTAAA
* * *
59446 CTGGAGGCTTAGGTTCGGGCTTTTCCTTCTTTGGTGGTTCATACACTGGAGGCTTGGGTTCGGGT
65 CTGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGTGGTTCATAAACTGGAGGCTTGGGTTCGGGT
59511 TTTTCC
130 TTTTCC
59517 TTCTTTGGGGGTTCATAAACTGGTGGCTTGG
1 TTCTTTGGGGGTTCATAAACTGGTGGCTTGG
59548 TTGGAGGTTT
Statistics
Matches: 267, Mismatches: 31, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
134 3 0.01
135 260 0.97
136 2 0.01
137 2 0.01
ACGTcount: A:0.10, C:0.19, G:0.30, T:0.41
Consensus pattern (135 bp):
TTCTTTGGGGGTTCATAAACTGGTGGCTTGGGCTTCGGCTTCTCCTTCTTTGGGGGTTCGTAAAC
TGGTGGCTTAGGTTCAGGCTTTTCCTTCTTTGGTGGTTCATAAACTGGAGGCTTGGGTTCGGGTT
TTTCC
Found at i:59332 original size:45 final size:45
Alignment explanation
Indices: 59112--59547 Score: 518
Period size: 45 Copynumber: 9.7 Consensus size: 45
59102 TGTTGGTGGT
* * *
59112 TTCTTTGGTGGTTCATAAACTGGTGGTTTGGGCTT-TGGCTTCTCC
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTGGG-TTCGGGCTTTTCC
* * * * * ** * *
59157 TTCTTCGGGGGCTCGTAAACTGGTGGTTTGTCCTT-TGGCTTCTCC
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTG-GGTTCGGGCTTTTCC
* *
59202 TTCTTTGGTGGTTCATAAACTGGTGGCTTAGGTTCAGGCTTTTCC
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCGGGCTTTTCC
* * * * ** *
59247 TTCTTTGGGGGCTCGTAAACTGGTGGTTTGTCCTTC-GGCTTCTCC
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTG-GGTTCGGGCTTTTCC
* * * *
59292 TTCTTTGGGGGTTCGTAAACTGGTGGCTTAGGTTCAGGCTTTTCC
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCGGGCTTTTCC
* *
59337 TTCTTTGGTGGTTCATAAACTGGAGGCTTGGGTTCGGGTTTTTCC
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCGGGCTTTTCC
*
59382 TTCTTTGGTGGTTCATAAACTGGAGGCTTGGGTTCGGGCTTTTCC
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCGGGCTTTTCC
* *
59427 TTCTTTGGTGGTTCATAAACTGGAGGCTTAGGTTCGGGCTTTTCC
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCGGGCTTTTCC
* * *
59472 TTCTTTGGTGGTTCATACACTGGAGGCTTGGGTTCGGGTTTTTCC
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCGGGCTTTTCC
*
59517 TTCTTTGGGGGTTCATAAACTGGTGGCTTGG
1 TTCTTTGGTGGTTCATAAACTGGTGGCTTGG
59548 TTGGAGGTTT
Statistics
Matches: 343, Mismatches: 44, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
44 5 0.01
45 335 0.98
46 3 0.01
ACGTcount: A:0.10, C:0.19, G:0.30, T:0.41
Consensus pattern (45 bp):
TTCTTTGGTGGTTCATAAACTGGTGGCTTGGGTTCGGGCTTTTCC
Found at i:64628 original size:51 final size:51
Alignment explanation
Indices: 64573--64779 Score: 276
Period size: 51 Copynumber: 4.3 Consensus size: 51
64563 GGCCATAAGT
* *
64573 TGGCTCGTACGGTGGCTGGTATGGTGGTTCATGTGGAGGAGGCCCATGGGG
1 TGGCTCATAAGGTGGCTGGTATGGTGGTTCATGTGGAGGAGGCCCATGGGG
*
64624 TGGCTCATAAGGTGGCTGGTGTGGTGGTTCATGTGGAGGAGGCCCATGGGG
1 TGGCTCATAAGGTGGCTGGTATGGTGGTTCATGTGGAGGAGGCCCATGGGG
* *
64675 TGGCTCATAAGGTGGCTCGTACGGTGGTTCATGTGGAGGAGGCCCA-----
1 TGGCTCATAAGGTGGCTGGTATGGTGGTTCATGTGGAGGAGGCCCATGGGG
*
64721 TGG-------GGTGGCTGGTAGGGTGGTTCATGTGGAGGAGGCCCATGGGG
1 TGGCTCATAAGGTGGCTGGTATGGTGGTTCATGTGGAGGAGGCCCATGGGG
64765 TGGCTCATAAGGTGG
1 TGGCTCATAAGGTGG
64780 TTCATGTGGA
Statistics
Matches: 136, Mismatches: 8, Indels: 24
0.81 0.05 0.14
Matches are distributed among these distances:
39 34 0.25
44 3 0.02
46 3 0.02
51 96 0.71
ACGTcount: A:0.14, C:0.15, G:0.46, T:0.25
Consensus pattern (51 bp):
TGGCTCATAAGGTGGCTGGTATGGTGGTTCATGTGGAGGAGGCCCATGGGG
Found at i:64689 original size:90 final size:92
Alignment explanation
Indices: 64595--64791 Score: 246
Period size: 90 Copynumber: 2.2 Consensus size: 92
64585 TGGCTGGTAT
* *
64595 GGTGGTTCATGTGGAGGAGGCCCA-TGG-GGTGGCTCATAAGGTGGCTGGT-GTGGTGGTTCATG
1 GGTGGTTCATGTGGAGGAGGCCCAGTGGAGGAGGCCCATAAGGTGGCTGGTAG-GGTGGTTCATG
64657 TGGAGGAGGCCCATGGGGTGGCTCATAA
65 TGGAGGAGGCCCATGGGGTGGCTCATAA
* * ** **
64685 GGTGGCTC--GT--ACGGTGGTTCATGTGGAGGAGGCCCATGGGGTGGCTGGTAGGGTGGTTCAT
1 GGTGGTTCATGTGGA-GGAGGCCCA-GTGGAGGAGGCCCATAAGGTGGCTGGTAGGGTGGTTCAT
64746 GTGGAGGAGGCCCATGGGGTGGCTCATAA
64 GTGGAGGAGGCCCATGGGGTGGCTCATAA
64775 GGTGGTTCATGTGGAGG
1 GGTGGTTCATGTGGAGG
64792 CATTGGTTGC
Statistics
Matches: 89, Mismatches: 9, Indels: 15
0.79 0.08 0.13
Matches are distributed among these distances:
86 1 0.01
87 6 0.07
88 2 0.02
89 3 0.03
90 71 0.80
91 1 0.01
92 2 0.02
93 2 0.02
94 1 0.01
ACGTcount: A:0.15, C:0.14, G:0.47, T:0.24
Consensus pattern (92 bp):
GGTGGTTCATGTGGAGGAGGCCCAGTGGAGGAGGCCCATAAGGTGGCTGGTAGGGTGGTTCATGT
GGAGGAGGCCCATGGGGTGGCTCATAA
Found at i:66674 original size:7 final size:7
Alignment explanation
Indices: 66607--66674 Score: 52
Period size: 7 Copynumber: 9.6 Consensus size: 7
66597 TTTTTGTTTT
*
66607 TAATTAT
1 TAATTAA
66614 TAATTAA
1 TAATTAA
*
66621 TTATT-A
1 TAATTAA
66627 TAATTAA
1 TAATTAA
66634 TAA-TAA
1 TAATTAA
*
66640 CAATTTAAA
1 TAA-TT-AA
66649 TTAA-TAA
1 -TAATTAA
66656 TAATTAAA
1 TAATT-AA
66664 TAATTAA
1 TAATTAA
66671 TAAT
1 TAAT
66675 AATTAAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
6 13 0.27
7 23 0.47
8 9 0.18
9 2 0.04
10 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (7 bp):
TAATTAA
Done.