Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008059.1 Corchorus capsularis cultivar CVL-1 contig08080, 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: 81047
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:691 original size:322 final size:322
Alignment explanation
Indices: 1--1377 Score: 1520
Period size: 322 Copynumber: 4.3 Consensus size: 322
* * ***
1 TTTTTTGCCACAATATTCAAGAAAAAATATATTATTCAA-GCCAAAAAGATTGGTGGG-TTTTCC
1 TTTTTTGCCACAATACTC-AGAAAAAATATATAATTCAACGCCAAAAAGATTAACGGGCTTTT-C
* * * * *
64 ACACTTCTAATATCGTTTTTCC-A-TTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGA-TT
64 ACGCTTCTAATACCGGTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTT
* * ** * * *
126 -GA-GAT-G------C---TCCTTATATCAAATATGGCTGAAATTTGGTTCGATGAATATAGATA
129 AGATGCTCGTAAAAACAAATCCTTATATCCAACGTGGGTGACATTTGCTTCGATGAATATAGATA
** * **
179 CTTCAATAAGTCTTTATGCCAAAAATCATGCAAAATTGAGGTAGAGCTCCGGAACGCGTTTTTAG
194 CTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGACAGAGCTCCGGAACGCGTTTTTAG
*
244 CCAAAAACTATGA-GAGTTAGTACACGATTTCGGCTAAAA-ACTTACCCGAAAAGTTTTTTTCTC
259 CCAAAAACTGTGATG-GTTAGTACACGATTTCGGCTAAAATA-TTACCCGAAAAG-TTTTTTCTC
307 AA
321 AA
* * * *
309 -TTTTTGCCACAATACTCGGAAAAAATGTATAATTCAACTTCC-AAAAGATTAATC-GGCTTTTT
1 TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAC-GCCAAAAAGATTAA-CGGGCTTTTC
*
371 ACGCTTCTAATCCCGGTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTT
64 ACGCTTCTAATACCGGTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTT
* *
436 AGATGCTCGTAAAAACAAATCCTTATATCCAACGTGGGTGACATTTACTTCGATGAATTTAGATA
129 AGATGCTCGTAAAAACAAATCCTTATATCCAACGTGGGTGACATTTGCTTCGATGAATATAGATA
* * * * * *
501 TTTCAAGGAGTATTTGCGCCAAAATTCTTGCAAAATTGA-ACACGGGCTCCGGAACGCGTTTTTA
194 CTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGACA-GAGCTCCGGAACGCGTTTTTA
* * *
565 GCCAAAAACTGTGATGGTTAATACACGATTTCGGCTAAAATCTTACTCGAAAAGTTTTTTCTCAA
258 GCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATATTACCCGAAAAGTTTTTTCTCAA
* * * * **
630 TTTTTTGCCACAGTACTCAGAAAAAATATTTAATTAAACGCCAACAAGATTGGCGGGCTTTTCAC
1 TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAC
* * * *
695 GCTTCTAATATCGTTTTTCCAACTTTTTTTCCGAATTAATTTCTAATTTAATCGAAACAAGA-TT
66 GCTTCTAATACCGGTTTTCCAA--TTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTT
* * ** * * *
759 -GA-GAT-G------C---TCCTTATATCCCATATGGCTGAAATTTGGTTCGATGAATATAGATA
129 AGATGCTCGTAAAAACAAATCCTTATATCCAACGTGGGTGACATTTGCTTCGATGAATATAGATA
* * * *
812 CTTCAAAGAGTCTTTATGCCAAAAATCATGCAAAATTTGAGGCAGAGCTCCGGAACGCATTTTTA
194 CTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAA-TTGAGACAGAGCTCCGGAACGCGTTTTTA
*
877 GCCAAAAACTGTGATAGTTAGTACACGATTTCGGCTAAAATATTACCCGAAAAGTTTTTT-TCAC
258 GCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATATTACCCGAAAAGTTTTTTCTCA-
941 A
322 A
* * * * *
942 ATTTTTGCCACAATACTCAGAAAAAATATTTAATTCAACGTCAAAAATG-TTAACCGGCTTTTTA
1 TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAA-GATTAACGGGCTTTTCA
*
1006 CGCTTCTAATCCCGGTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTA
65 CGCTTCTAATACCGGTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTA
* *
1071 GATGCTCGTAAAAACAAATCCTTATATCCAACGTGGGTGACATTTGCTTCGATGAATTTAGATAT
130 GATGCTCGTAAAAACAAATCCTTATATCCAACGTGGGTGACATTTGCTTCGATGAATATAGATAC
* * * * *
1136 TTCAAGGAGTCTTTGCGCCAAAATTCATGCAAAGTTGA-ACCCG-GACTCCGGTACGCGTTTTTA
195 TTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGA-CAGAG-CTCCGGAACGCGTTTTTA
* * *
1199 GCCAAAAACTGTGATGGTTAGTACACGGTTTCAGCTAAAATATTACTCGAAAAGTTTTTTCTCAA
258 GCCAAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATATTACCCGAAAAGTTTTTTCTCAA
* ** * * *
1264 TTTTTTGCCACAGTACTCAGATGAAATATATAATTCAATGCCAAAAAAATTGACGGGCTTTTCAC
1 TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAC
* * * * *
1329 ACTTCTAATATCGTTTTTCCATTTTTTTTTTCGGAATTAATTTCTAATT
66 GCTTCTAATACCGGTTTTCCA---ATTTTTTCTGAATTAATTTCTAATT
1378 CACAACATAT
Statistics
Matches: 888, Mismatches: 130, Indels: 85
0.81 0.12 0.08
Matches are distributed among these distances:
306 17 0.02
307 44 0.05
308 7 0.01
309 35 0.04
310 38 0.04
311 73 0.08
312 157 0.18
313 6 0.01
314 2 0.00
319 1 0.00
320 2 0.00
321 18 0.02
322 355 0.40
323 74 0.08
324 36 0.04
325 23 0.03
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (322 bp):
TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTAACGGGCTTTTCAC
GCTTCTAATACCGGTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAG
ATGCTCGTAAAAACAAATCCTTATATCCAACGTGGGTGACATTTGCTTCGATGAATATAGATACT
TCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGACAGAGCTCCGGAACGCGTTTTTAGCC
AAAAACTGTGATGGTTAGTACACGATTTCGGCTAAAATATTACCCGAAAAGTTTTTTCTCAA
Found at i:1323 original size:634 final size:631
Alignment explanation
Indices: 1--1377 Score: 2246
Period size: 634 Copynumber: 2.2 Consensus size: 631
* * * *
1 TTTTTTGCCACAATATTCAAGAAAAAATATATTATTCAAGCCAAAAAGATTGGTGGG-TTTTCCA
1 TTTTTTGCCACAGTACTC-AGAAAAAATATATAATTCAAGCCAAAAAGATTGGCGGGCTTTT-CA
*
65 CACTTCTAATATCGTTTTTCC-A--TTTTTCCGAATTAATTTCTAATTAAATTGAAACAAGATTG
64 CACTTCTAATATCGTTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTG
127 AGATGCTCCTTATATCAAATATGGCTGAAATTTGGTTCGATGAATATAGATACTTCAATAAGTCT
129 AGATGCTCCTTATATCAAATATGGCTGAAATTTGGTTCGATGAATATAGATACTTCAATAAGTCT
* *
192 TTATGCCAAAAATCATGCAAAATTGAGGTAGAGCTCCGGAACGCGTTTTTAGCCAAAAACTATGA
194 TTATGCCAAAAATCATGCAAAATTGAGGCAGAGCTCCGGAACGCATTTTTAGCCAAAAACTATGA
*
257 GAGTTAGTACACGATTTCGGCTAAAAACTTACCCGAAAAGTTTTTTTCTCAATTTTTGCCACAAT
259 GAGTTAGTACACGATTTCGGCTAAAAACTTACCCGAAAAGTTTTTTTCACAATTTTTGCCACAAT
* * * * *
322 ACTCGGAAAAAATGTATAATTCAACTTCCAAAAGATTAATCGGCTTTTTACGCTTCTAATCCCGG
324 ACTCAGAAAAAATATATAATTCAACGTCAAAAAGATTAACCGGCTTTTTACGCTTCTAATCCCGG
387 TTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAC
389 TTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAAC
452 AAATCCTTATATCCAACGTGGGTGACATTTACTTCGATGAATTTAGATATTTCAAGGAGTATTTG
454 AAATCCTTATATCCAACGTGGGTGACATTTACTTCGATGAATTTAGATATTTCAAGGAGTATTTG
* *
517 CGCCAAAATTCTTGCAAAATTGAACACGGGCTCCGGAACGCGTTTTTAGCCAAAAACTGTGATGG
519 CGCCAAAATTCATGCAAAATTGAACACGGACTCCGGAACGCGTTTTTAGCCAAAAACTGTGATGG
* *
582 TTAATACACGATTTCGGCTAAAATCTTACTCGAAAAGTTTTTTCTCAA
584 TTAATACACGATTTCAGCTAAAATATTACTCGAAAAGTTTTTTCTCAA
* * *
630 TTTTTTGCCACAGTACTCAGAAAAAATATTTAATTAAACGCCAACAAGATTGGCGGGCTTTTCAC
1 TTTTTTGCCACAGTACTCAGAAAAAATATATAATTCAA-GCCAAAAAGATTGGCGGGCTTTTCAC
* *
695 GCTTCTAATATCGTTTTTCCAACTTTTTTTCCGAATTAATTTCTAATTTAATCGAAACAAGATTG
65 ACTTCTAATATCGTTTTTCCAA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTG
**
760 AGATGCTCCTTATATCCCATATGGCTGAAATTTGGTTCGATGAATATAGATACTTCAA-AGAGTC
129 AGATGCTCCTTATATCAAATATGGCTGAAATTTGGTTCGATGAATATAGATACTTCAATA-AGTC
*
824 TTTATGCCAAAAATCATGCAAAATTTGAGGCAGAGCTCCGGAACGCATTTTTAGCCAAAAACTGT
193 TTTATGCCAAAAATCATGCAAAA-TTGAGGCAGAGCTCCGGAACGCATTTTTAGCCAAAAACTAT
*
889 GATAGTTAGTACACGATTTCGGCTAAAATA-TTACCCGAAAAGTTTTTTTCACAATTTTTGCCAC
257 GAGAGTTAGTACACGATTTCGGCTAAAA-ACTTACCCGAAAAGTTTTTTTCACAATTTTTGCCAC
*
953 AATACTCAGAAAAAATATTTAATTCAACGTCAAAAATG-TTAACCGGCTTTTTACGCTTCTAATC
321 AATACTCAGAAAAAATATATAATTCAACGTCAAAAA-GATTAACCGGCTTTTTACGCTTCTAATC
1017 CCGGTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAA
385 CCGGTTTTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAA
* *
1082 AAACAAATCCTTATATCCAACGTGGGTGACATTTGCTTCGATGAATTTAGATATTTCAAGGAGTC
450 AAACAAATCCTTATATCCAACGTGGGTGACATTTACTTCGATGAATTTAGATATTTCAAGGAGTA
* * *
1147 TTTGCGCCAAAATTCATGCAAAGTTGAACCCGGACTCCGGTACGCGTTTTTAGCCAAAAACTGTG
515 TTTGCGCCAAAATTCATGCAAAATTGAACACGGACTCCGGAACGCGTTTTTAGCCAAAAACTGTG
* *
1212 ATGGTTAGTACACGGTTTCAGCTAAAATATTACTCGAAAAGTTTTTTCTCAA
580 ATGGTTAATACACGATTTCAGCTAAAATATTACTCGAAAAGTTTTTTCTCAA
** * *
1264 TTTTTTGCCACAGTACTCAGATGAAATATATAATTCAATGCCAAAAAAATTGACGGGCTTTTCAC
1 TTTTTTGCCACAGTACTCAGAAAAAATATATAATTCAA-GCCAAAAAGATTGGCGGGCTTTTCAC
* *
1329 ACTTCTAATATCGTTTTTCCATTTTTTTTTTCGGAATTAATTTCTAATT
65 ACTTCTAATATCGTTTTTCCA--ATTTTTTTCCGAATTAATTTCTAATT
1378 CACAACATAT
Statistics
Matches: 691, Mismatches: 45, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
628 17 0.02
629 54 0.08
630 5 0.01
632 1 0.00
633 121 0.18
634 467 0.68
635 26 0.04
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.35
Consensus pattern (631 bp):
TTTTTTGCCACAGTACTCAGAAAAAATATATAATTCAAGCCAAAAAGATTGGCGGGCTTTTCACA
CTTCTAATATCGTTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTGAG
ATGCTCCTTATATCAAATATGGCTGAAATTTGGTTCGATGAATATAGATACTTCAATAAGTCTTT
ATGCCAAAAATCATGCAAAATTGAGGCAGAGCTCCGGAACGCATTTTTAGCCAAAAACTATGAGA
GTTAGTACACGATTTCGGCTAAAAACTTACCCGAAAAGTTTTTTTCACAATTTTTGCCACAATAC
TCAGAAAAAATATATAATTCAACGTCAAAAAGATTAACCGGCTTTTTACGCTTCTAATCCCGGTT
TTCCAATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAA
ATCCTTATATCCAACGTGGGTGACATTTACTTCGATGAATTTAGATATTTCAAGGAGTATTTGCG
CCAAAATTCATGCAAAATTGAACACGGACTCCGGAACGCGTTTTTAGCCAAAAACTGTGATGGTT
AATACACGATTTCAGCTAAAATATTACTCGAAAAGTTTTTTCTCAA
Found at i:1401 original size:12 final size:12
Alignment explanation
Indices: 1384--1409 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1374 AATTCACAAC
1384 ATATTTAATAGA
1 ATATTTAATAGA
1396 ATATTTAATAGA
1 ATATTTAATAGA
1408 AT
1 AT
1410 TTCCCATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
ATATTTAATAGA
Found at i:2199 original size:22 final size:22
Alignment explanation
Indices: 2171--2214 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2161 ATAAATCGAC
2171 CAATTCTCAATTTGGCTAAAAT
1 CAATTCTCAATTTGGCTAAAAT
2193 CAATTCTCAATTTGGCTAAAAT
1 CAATTCTCAATTTGGCTAAAAT
2215 TGCAACCCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
CAATTCTCAATTTGGCTAAAAT
Found at i:3237 original size:21 final size:20
Alignment explanation
Indices: 3189--3273 Score: 63
Period size: 20 Copynumber: 4.4 Consensus size: 20
3179 CACGCGGCAC
* *
3189 ATTCACATTTAACTTTCCCA
1 ATTCACATTGAACTTGCCCA
* *
3209 ATTGACATTGAACTTGCCTTA
1 ATTCACATTGAACTTGCC-CA
3230 ATTCACATT----TT-CCCA
1 ATTCACATTGAACTTGCCCA
* *
3245 ATTGACATTGAACTTGCCTTA
1 ATTCACATTGAACTTGCC-CA
3266 ATTCACAT
1 ATTCACAT
3274 CCAAATGACA
Statistics
Matches: 49, Mismatches: 9, Indels: 13
0.69 0.13 0.18
Matches are distributed among these distances:
15 9 0.18
16 2 0.04
17 2 0.04
19 2 0.04
20 17 0.35
21 17 0.35
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.39
Consensus pattern (20 bp):
ATTCACATTGAACTTGCCCA
Found at i:3288 original size:32 final size:32
Alignment explanation
Indices: 3206--3469 Score: 429
Period size: 32 Copynumber: 8.1 Consensus size: 32
3196 TTTAACTTTC
*
3206 CCAATTGACATTGAACTTGCCTTAATTCACATTTT
1 CCAAATGACATTGAACTTGCCTTAATTCACA---T
*
3241 CCCAATTGACATTGAACTTGCCTTAATTCACAT
1 -CCAAATGACATTGAACTTGCCTTAATTCACAT
*
3274 CCAAATGACATTGAACTTGCCTTAATTCATAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
3306 CCAAATGACATTGAACTTGCCTTAGTTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
3338 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
* * *
3370 CCAAATAACATTGAACTTGCCTGAATTCATAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
3402 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
3434 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
3466 CCAA
1 CCAA
3470 CTTTCCCAAA
Statistics
Matches: 217, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
32 185 0.85
33 1 0.00
36 31 0.14
ACGTcount: A:0.33, C:0.25, G:0.09, T:0.33
Consensus pattern (32 bp):
CCAAATGACATTGAACTTGCCTTAATTCACAT
Found at i:3471 original size:21 final size:21
Alignment explanation
Indices: 3447--3506 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 21
3437 AATGACATTG
3447 AACTTGCCTTAATTCACATCC
1 AACTTGCCTTAATTCACATCC
* * * * **
3468 AACTTTCC-CAAATGACATTG
1 AACTTGCCTTAATTCACATCC
3488 AACTTGCCTTAATTCACAT
1 AACTTGCCTTAATTCACAT
3507 TGGCCCTCAA
Statistics
Matches: 28, Mismatches: 10, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.32, C:0.28, G:0.07, T:0.33
Consensus pattern (21 bp):
AACTTGCCTTAATTCACATCC
Found at i:3491 original size:20 final size:20
Alignment explanation
Indices: 3434--3495 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
3424 TAATTCACAT
3434 CCAAATGACATTGAACTTGC
1 CCAAATGACATTGAACTTGC
* * * ** *
3454 CTTAATTCACATCCAACTTTC
1 C-CAAATGACATTGAACTTGC
3475 CCAAATGACATTGAACTTGC
1 CCAAATGACATTGAACTTGC
3495 C
1 C
3496 TTAATTCACA
Statistics
Matches: 29, Mismatches: 12, Indels: 2
0.67 0.28 0.05
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29
Consensus pattern (20 bp):
CCAAATGACATTGAACTTGC
Found at i:3507 original size:21 final size:21
Alignment explanation
Indices: 3441--3508 Score: 75
Period size: 21 Copynumber: 3.3 Consensus size: 21
3431 CATCCAAATG
3441 ACATTGAACTTGCCTTAATTC
1 ACATTGAACTTGCCTTAATTC
** * * * *
3462 ACATCCAACTTTCC-CAAATG
1 ACATTGAACTTGCCTTAATTC
3482 ACATTGAACTTGCCTTAATTC
1 ACATTGAACTTGCCTTAATTC
3503 ACATTG
1 ACATTG
3509 GCCCTCAATG
Statistics
Matches: 34, Mismatches: 12, Indels: 2
0.71 0.25 0.04
Matches are distributed among these distances:
20 14 0.41
21 20 0.59
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (21 bp):
ACATTGAACTTGCCTTAATTC
Found at i:4743 original size:297 final size:297
Alignment explanation
Indices: 4209--4806 Score: 1196
Period size: 297 Copynumber: 2.0 Consensus size: 297
4199 CATAAATTCT
4209 GAACCTGCACACAGCTGCACGAGTGAGAAGAGATGCGATATAACCAAAACAGTTTTGATGCGCGA
1 GAACCTGCACACAGCTGCACGAGTGAGAAGAGATGCGATATAACCAAAACAGTTTTGATGCGCGA
4274 GTAAGAAGAGATGCAATATATCAAAAAAGCCAGAACATTAAGAGAGACATACATGTGTGGCTCCA
66 GTAAGAAGAGATGCAATATATCAAAAAAGCCAGAACATTAAGAGAGACATACATGTGTGGCTCCA
4339 ACTAAGCCCATAAGCAGGAGAAAGGCAATTGTAGTTCCTTGAAGATCACTGCGTAGAAAAGGAAA
131 ACTAAGCCCATAAGCAGGAGAAAGGCAATTGTAGTTCCTTGAAGATCACTGCGTAGAAAAGGAAA
4404 AATACTTCTATTAAACAAAACTAACAAAAGGTTCCAACATTGAAACACATAAATCAGTGCACTTC
196 AATACTTCTATTAAACAAAACTAACAAAAGGTTCCAACATTGAAACACATAAATCAGTGCACTTC
4469 TTGTTCTTACATGACCATAAGTTAAAGGTAGCTTCAA
261 TTGTTCTTACATGACCATAAGTTAAAGGTAGCTTCAA
4506 GAACCTGCACACAGCTGCACGAGTGAGAAGAGATGCGATATAACCAAAACAGTTTTGATGCGCGA
1 GAACCTGCACACAGCTGCACGAGTGAGAAGAGATGCGATATAACCAAAACAGTTTTGATGCGCGA
4571 GTAAGAAGAGATGCAATATATCAAAAAAGCCAGAACATTAAGAGAGACATACATGTGTGGCTCCA
66 GTAAGAAGAGATGCAATATATCAAAAAAGCCAGAACATTAAGAGAGACATACATGTGTGGCTCCA
4636 ACTAAGCCCATAAGCAGGAGAAAGGCAATTGTAGTTCCTTGAAGATCACTGCGTAGAAAAGGAAA
131 ACTAAGCCCATAAGCAGGAGAAAGGCAATTGTAGTTCCTTGAAGATCACTGCGTAGAAAAGGAAA
4701 AATACTTCTATTAAACAAAACTAACAAAAGGTTCCAACATTGAAACACATAAATCAGTGCACTTC
196 AATACTTCTATTAAACAAAACTAACAAAAGGTTCCAACATTGAAACACATAAATCAGTGCACTTC
4766 TTGTTCTTACATGACCATAAGTTAAAGGTAGCTTCAA
261 TTGTTCTTACATGACCATAAGTTAAAGGTAGCTTCAA
4803 GAAC
1 GAAC
4807 GGAGCTGGAA
Statistics
Matches: 301, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
297 301 1.00
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (297 bp):
GAACCTGCACACAGCTGCACGAGTGAGAAGAGATGCGATATAACCAAAACAGTTTTGATGCGCGA
GTAAGAAGAGATGCAATATATCAAAAAAGCCAGAACATTAAGAGAGACATACATGTGTGGCTCCA
ACTAAGCCCATAAGCAGGAGAAAGGCAATTGTAGTTCCTTGAAGATCACTGCGTAGAAAAGGAAA
AATACTTCTATTAAACAAAACTAACAAAAGGTTCCAACATTGAAACACATAAATCAGTGCACTTC
TTGTTCTTACATGACCATAAGTTAAAGGTAGCTTCAA
Found at i:8743 original size:14 final size:14
Alignment explanation
Indices: 8724--8750 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8714 AAACTGGAAA
8724 AAAAATAAATAAAT
1 AAAAATAAATAAAT
8738 AAAAATAAATAAA
1 AAAAATAAATAAA
8751 AATCTCATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (14 bp):
AAAAATAAATAAAT
Found at i:9018 original size:211 final size:213
Alignment explanation
Indices: 8651--9074 Score: 642
Period size: 211 Copynumber: 2.0 Consensus size: 213
8641 AACAAAGCTA
8651 ATATCATAGCCCTGAAGCTAGACCAAGTTAGATCTATTCCATCACTTAGGGAGCAGAGAGAGGAA
1 ATATCATAGCCCTGAAGCTAGACCAAGTTAGATCTATTCCATCACTTAGGGAGCAGAGAGAGGAA
8716 ACTGGAAAAAAAATAAATAAATAAAAATAAATAAAAATCTCATTATAATTTTGCATGTTTGGTTA
66 ACTGGAAAAAAAATAAAT-AATAAAAATAAATAAAAATCTCATTATAATTTTGCATGTTTGGTTA
8781 CTTTGGTATCTAAGCCAAATAATAATACCAAAAAAATGATATACAGTAGCATACCTCAAGGCCAA
130 CTTTGGTATCTAAGCCAAATAATAATACCAAAAAAATGATATACAGTAGCATACCTCAAGGCCAA
8846 ACATGCTAGCCCAGGGGTT
195 ACATGCTAGCCCAGGGGTT
8865 ATATCATAGCCCTGAAGCTAGACCAAGTTAGATCTATTCCATCACTTTAGGGAGCAGAGAGAGGA
1 ATATCATAGCCCTGAAGCTAGACCAAGTTAGATCTATTCCATCAC-TTAGGGAGCAGAGAGAGGA
*** * * *** ** ***
8930 AACTGG-GGGAAAA-AAAT-CTCATTCT-TCTTGCAATCTTC-TCTATAATTTTGCATGTTTGGT
65 AACTGGAAAAAAAATAAATAATAAAAATAAATAAAAATC-TCAT-TATAATTTTGCATGTTTGGT
**
8990 TACTTTGGTATCTAAGCCAAATAATAATACCAAAAAAATGATATGTAGTAGCATACCTCAAGGCC
128 TACTTTGGTATCTAAGCCAAATAATAATACCAAAAAAATGATATACAGTAGCATACCTCAAGGCC
9055 AAACATGCTAGCCCAGGGGT
193 AAACATGCTAGCCCAGGGGT
9075 ATAACAACCT
Statistics
Matches: 192, Mismatches: 15, Indels: 9
0.89 0.07 0.04
Matches are distributed among these distances:
210 6 0.03
211 108 0.56
213 4 0.02
214 49 0.26
215 25 0.13
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.27
Consensus pattern (213 bp):
ATATCATAGCCCTGAAGCTAGACCAAGTTAGATCTATTCCATCACTTAGGGAGCAGAGAGAGGAA
ACTGGAAAAAAAATAAATAATAAAAATAAATAAAAATCTCATTATAATTTTGCATGTTTGGTTAC
TTTGGTATCTAAGCCAAATAATAATACCAAAAAAATGATATACAGTAGCATACCTCAAGGCCAAA
CATGCTAGCCCAGGGGTT
Found at i:9259 original size:30 final size:30
Alignment explanation
Indices: 9223--9331 Score: 200
Period size: 30 Copynumber: 3.6 Consensus size: 30
9213 ATAATGCTTC
9223 GGTTGACATGGTTCCAATGTATGATTCTTT
1 GGTTGACATGGTTCCAATGTATGATTCTTT
9253 GGTTGACATGGTTCCAATGTATGATTCTTT
1 GGTTGACATGGTTCCAATGTATGATTCTTT
*
9283 GGTTGACATGGTTCCAATGCATGATTCTTT
1 GGTTGACATGGTTCCAATGTATGATTCTTT
*
9313 GATTGACATGGTTCCAATG
1 GGTTGACATGGTTCCAATG
9332 AGTATGTGTT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 77 1.00
ACGTcount: A:0.21, C:0.15, G:0.24, T:0.40
Consensus pattern (30 bp):
GGTTGACATGGTTCCAATGTATGATTCTTT
Found at i:10326 original size:51 final size:51
Alignment explanation
Indices: 10150--10403 Score: 205
Period size: 51 Copynumber: 5.0 Consensus size: 51
10140 GAATCAGTTC
* * * * *
10150 CCTGTTCCAAATTTCTTCC--A-ATTCCAGCTTCTTTTCTAGATTCAGCAG
1 CCTGTTCCAAACTTCTCCCAGATATTCCAACTTCTCTTCTTGATTCAGCAG
* * ** *
10198 -CTGGTTCCAAAC-TCATTCCAGCTATTCCAACTTCTCTTCTTGATTTGGCTG
1 CCT-GTTCCAAACTTC-TCCCAGATATTCCAACTTCTCTTCTTGATTCAGCAG
* * * * * *
10249 CCGGCTCCTAACTCCTCCCAGCTATTCCAACTTCTCTTCTCGATTCAGCAG
1 CCTGTTCCAAACTTCTCCCAGATATTCCAACTTCTCTTCTTGATTCAGCAG
* * * * *
10300 CCTGTTCCAAGCTTCTCACAGATATTCTAGCTTCTCTTCTGGATTCAGCAG
1 CCTGTTCCAAACTTCTCCCAGATATTCCAACTTCTCTTCTTGATTCAGCAG
* * * * *
10351 CATGTTTCAAACTTCTCCCTGACATTCCAACTTC-CTTTCTTGATCCAGCAG
1 CCTGTTCCAAACTTCTCCCAGATATTCCAACTTCTC-TTCTTGATTCAGCAG
10402 CC
1 CC
10404 CGCTCCAGCC
Statistics
Matches: 160, Mismatches: 38, Indels: 13
0.76 0.18 0.06
Matches are distributed among these distances:
47 4 0.03
48 12 0.08
50 1 0.01
51 141 0.88
52 2 0.01
ACGTcount: A:0.19, C:0.33, G:0.12, T:0.35
Consensus pattern (51 bp):
CCTGTTCCAAACTTCTCCCAGATATTCCAACTTCTCTTCTTGATTCAGCAG
Found at i:16493 original size:15 final size:15
Alignment explanation
Indices: 16473--16502 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
16463 CATGTAAACT
16473 TAGTTTGCAGTACAA
1 TAGTTTGCAGTACAA
16488 TAGTTTGCAGTACAA
1 TAGTTTGCAGTACAA
16503 CTAATAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
TAGTTTGCAGTACAA
Found at i:19748 original size:16 final size:16
Alignment explanation
Indices: 19727--19760 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19717 AACATCCGTG
* *
19727 TCTCATTTCACTCTTA
1 TCTCATCTCACCCTTA
19743 TCTCATCTCACCCTTA
1 TCTCATCTCACCCTTA
19759 TC
1 TC
19761 ACTTGAGCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.18, C:0.38, G:0.00, T:0.44
Consensus pattern (16 bp):
TCTCATCTCACCCTTA
Found at i:34181 original size:24 final size:24
Alignment explanation
Indices: 34151--34219 Score: 84
Period size: 24 Copynumber: 2.9 Consensus size: 24
34141 GGCTCATTTT
34151 CAGCATTTAAACCAGCATCATTAA
1 CAGCATTTAAACCAGCATCATTAA
* * *
34175 CATCATTCAAACCAACATCATTAA
1 CAGCATTTAAACCAGCATCATTAA
* **
34199 CAGCATCTAAAATAGCATCAT
1 CAGCATTTAAACCAGCATCAT
34220 GTGGATCATC
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.43, C:0.26, G:0.06, T:0.25
Consensus pattern (24 bp):
CAGCATTTAAACCAGCATCATTAA
Found at i:35864 original size:31 final size:29
Alignment explanation
Indices: 35826--35926 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 29
35816 ACGGAATAAA
* **
35826 CTTATTTGAGCTTTTTCGCATAGTTGGGGCC
1 CTTATTTGAGCTTTTT--CAAAGTTCAGGCC
*
35857 CTTATTTGACCTTTTTCAAAGTTCAGGCC
1 CTTATTTGAGCTTTTTCAAAGTTCAGGCC
* * *
35886 CTTATTTGAGATTTATGGCAAAGTTCAAGGAC
1 CTTATTTGAGCTTT-T-TCAAAGTTC-AGGCC
35918 C-TATTTGAG
1 CTTATTTGAG
35927 ATTTCAGCCT
Statistics
Matches: 59, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
29 22 0.37
30 1 0.02
31 31 0.53
32 5 0.08
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.40
Consensus pattern (29 bp):
CTTATTTGAGCTTTTTCAAAGTTCAGGCC
Found at i:35889 original size:29 final size:30
Alignment explanation
Indices: 35826--35894 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
35816 ACGGAATAAA
* * **
35826 CTTATTTGAGCTTTTTCGCATAGTTGGGGCC
1 CTTATTTGACCTTTTTC-CAAAGTTCAGGCC
35857 CTTATTTGACCTTTTT-CAAAGTTCAGGCC
1 CTTATTTGACCTTTTTCCAAAGTTCAGGCC
35886 CTTATTTGA
1 CTTATTTGA
35895 GATTTATGGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.56
31 15 0.44
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.43
Consensus pattern (30 bp):
CTTATTTGACCTTTTTCCAAAGTTCAGGCC
Found at i:36243 original size:20 final size:20
Alignment explanation
Indices: 36218--36256 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
36208 ACCCGCGTCG
36218 CGTATCTAGTTATGGTGGGA
1 CGTATCTAGTTATGGTGGGA
36238 CGTATCTAGTTATGGTGGG
1 CGTATCTAGTTATGGTGGG
36257 TGAGTCTCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.18, C:0.10, G:0.36, T:0.36
Consensus pattern (20 bp):
CGTATCTAGTTATGGTGGGA
Found at i:37442 original size:17 final size:16
Alignment explanation
Indices: 37388--37438 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
37378 ATCACCTCTC
*
37388 AGATCACTAGTGATCTA
1 AGATCACCAGTGATC-A
*
37405 AGAGCACCAGTGATGCA
1 AGATCACCAGTGAT-CA
*
37422 AGATCACCGGTGATCA
1 AGATCACCAGTGATCA
37438 A
1 A
37439 AGATTACATG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 3 0.10
17 25 0.86
18 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (16 bp):
AGATCACCAGTGATCA
Found at i:42547 original size:30 final size:29
Alignment explanation
Indices: 42511--42646 Score: 179
Period size: 30 Copynumber: 4.7 Consensus size: 29
42501 ATGAAGTGAA
42511 AGGGGGCAAAACGTCCAAAATT-ATGAGTTC
1 AGGGGGCAAAACGTCCAAAATTGA--AGTTC
*
42541 AGGGGGCAAAATGTCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCAAAATTGAAGTTC
*
42570 A-GGGACAAAACGTCCAAAATT-ATGAGTTC
1 AGGGGGCAAAACGTCCAAAATTGA--AGTTC
*
42599 AGGGGGCAAAATGTCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCAAAATTGAAGTTC
*
42628 AGGGGACAAAACGTCCAAA
1 AGGGGGCAAAACGTCCAAA
42647 TGCTACAAGT
Statistics
Matches: 94, Mismatches: 7, Indels: 11
0.84 0.06 0.10
Matches are distributed among these distances:
27 1 0.01
28 18 0.19
29 34 0.36
30 39 0.41
31 2 0.02
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18
Consensus pattern (29 bp):
AGGGGGCAAAACGTCCAAAATTGAAGTTC
Found at i:42581 original size:58 final size:59
Alignment explanation
Indices: 42511--42646 Score: 256
Period size: 58 Copynumber: 2.3 Consensus size: 59
42501 ATGAAGTGAA
*
42511 AGGGGGCAAAACGTCCAAAATTATGAGTTCAGGGGGCAAAATGTCCAAAATTGAAGTTC
1 AGGGGACAAAACGTCCAAAATTATGAGTTCAGGGGGCAAAATGTCCAAAATTGAAGTTC
42570 A-GGGACAAAACGTCCAAAATTATGAGTTCAGGGGGCAAAATGTCCAAAATTGAAGTTC
1 AGGGGACAAAACGTCCAAAATTATGAGTTCAGGGGGCAAAATGTCCAAAATTGAAGTTC
42628 AGGGGACAAAACGTCCAAA
1 AGGGGACAAAACGTCCAAA
42647 TGCTACAAGT
Statistics
Matches: 75, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
58 57 0.76
59 18 0.24
ACGTcount: A:0.40, C:0.16, G:0.26, T:0.18
Consensus pattern (59 bp):
AGGGGACAAAACGTCCAAAATTATGAGTTCAGGGGGCAAAATGTCCAAAATTGAAGTTC
Found at i:47961 original size:22 final size:22
Alignment explanation
Indices: 47920--47961 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
47910 AACAAACCCG
**
47920 TAACCCGAATAATCTGAGAAGT
1 TAACCCGAATAATCCAAGAAGT
*
47942 TAACCCGAATGATCCAAGAA
1 TAACCCGAATAATCCAAGAA
47962 CATTATAAAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.21, G:0.17, T:0.19
Consensus pattern (22 bp):
TAACCCGAATAATCCAAGAAGT
Found at i:50122 original size:6 final size:6
Alignment explanation
Indices: 50111--50145 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
50101 AAGAGGATCC
* *
50111 TCTTCG TCTTCG TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
50146 TTCATCCTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.09, C:0.34, G:0.06, T:0.51
Consensus pattern (6 bp):
TCTTCA
Found at i:62829 original size:31 final size:31
Alignment explanation
Indices: 62794--62854 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
62784 TCGAATCTTT
62794 TTAACATCCAAAACATCTTCAATAACATCAC
1 TTAACATCCAAAACATCTTCAATAACATCAC
62825 TTAACATCCAAAACATCTTCAATAACATCA
1 TTAACATCCAAAACATCTTCAATAACATCA
62855 TTTTTTTGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.26
Consensus pattern (31 bp):
TTAACATCCAAAACATCTTCAATAACATCAC
Found at i:63251 original size:25 final size:25
Alignment explanation
Indices: 63223--63300 Score: 63
Period size: 25 Copynumber: 3.2 Consensus size: 25
63213 TAGCATTTAG
63223 AATTGATCTTATCAAGTTATAGATT
1 AATTGATCTTATCAAGTTATAGATT
* ** * **
63248 AATT-AACCGA-CATA-TATGTAGAAA
1 AATTGATCTTATCA-AGT-TATAGATT
63272 AATTGATCTTATCAAGTTATAGATT
1 AATTGATCTTATCAAGTTATAGATT
63297 AATT
1 AATT
63301 AACCGACATA
Statistics
Matches: 36, Mismatches: 12, Indels: 10
0.62 0.21 0.17
Matches are distributed among these distances:
23 3 0.08
24 13 0.36
25 17 0.47
26 3 0.08
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (25 bp):
AATTGATCTTATCAAGTTATAGATT
Found at i:63289 original size:49 final size:49
Alignment explanation
Indices: 63223--63324 Score: 204
Period size: 49 Copynumber: 2.1 Consensus size: 49
63213 TAGCATTTAG
63223 AATTGATCTTATCAAGTTATAGATTAATTAACCGACATATATGTAGAAA
1 AATTGATCTTATCAAGTTATAGATTAATTAACCGACATATATGTAGAAA
63272 AATTGATCTTATCAAGTTATAGATTAATTAACCGACATATATGTAGAAA
1 AATTGATCTTATCAAGTTATAGATTAATTAACCGACATATATGTAGAAA
63321 AATT
1 AATT
63325 AAGTGTAGTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 53 1.00
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (49 bp):
AATTGATCTTATCAAGTTATAGATTAATTAACCGACATATATGTAGAAA
Found at i:63324 original size:24 final size:24
Alignment explanation
Indices: 63248--63326 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
63238 GTTATAGATT
63248 AATTAACCGACATATATGTAGAAA
1 AATTAACCGACATATATGTAGAAA
* ** * **
63272 AATTGATCTTATCA-AGT-TATAGATT
1 AATT-AACCGA-CATA-TATGTAGAAA
63297 AATTAACCGACATATATGTAGAAA
1 AATTAACCGACATATATGTAGAAA
63321 AATTAA
1 AATTAA
63327 GTGTAGTGGT
Statistics
Matches: 38, Mismatches: 12, Indels: 10
0.63 0.20 0.17
Matches are distributed among these distances:
23 3 0.08
24 19 0.50
25 13 0.34
26 3 0.08
ACGTcount: A:0.47, C:0.10, G:0.11, T:0.32
Consensus pattern (24 bp):
AATTAACCGACATATATGTAGAAA
Found at i:63367 original size:73 final size:73
Alignment explanation
Indices: 63264--63411 Score: 287
Period size: 73 Copynumber: 2.0 Consensus size: 73
63254 CCGACATATA
*
63264 TGTAGAAAAATTGATCTTATCAAGTTATAGATTAATTAACCGACATATATGTAGAAAAATTAAGT
1 TGTAGAAAAATTGATCTTATCAAGTTATAGATTAATTAACCGAAATATATGTAGAAAAATTAAGT
63329 GTAGTGGT
66 GTAGTGGT
63337 TGTAGAAAAATTGATCTTATCAAGTTATAGATTAATTAACCGAAATATATGTAGAAAAATTAAGT
1 TGTAGAAAAATTGATCTTATCAAGTTATAGATTAATTAACCGAAATATATGTAGAAAAATTAAGT
63402 GTAGTGGT
66 GTAGTGGT
63410 TG
1 TG
63412 AGCAAGTGAG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.34
Consensus pattern (73 bp):
TGTAGAAAAATTGATCTTATCAAGTTATAGATTAATTAACCGAAATATATGTAGAAAAATTAAGT
GTAGTGGT
Found at i:68675 original size:109 final size:109
Alignment explanation
Indices: 68439--68733 Score: 423
Period size: 109 Copynumber: 2.7 Consensus size: 109
68429 ACTATTATAG
* *
68439 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTATTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTATTT
*
68504 TATTTTTACC-AAAAGTTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* *
68552 TTTTATTCTACTAAAAACTCTGTTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTATTTTATTT
*
68617 TTACCAAAAAATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* * *
68661 TTTTATTCTACTAAAAATTCTATTTTCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTATTTTA
68725 TTTTTACCA
63 TTTTTACCA
68734 TTTTAATTTA
Statistics
Matches: 167, Mismatches: 11, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
108 42 0.25
109 83 0.50
110 7 0.04
111 15 0.09
113 20 0.12
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.51
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTATTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Found at i:68679 original size:17 final size:18
Alignment explanation
Indices: 68639--68684 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 18
68629 TTGGATATAT
68639 TAAAATTTT-TTCTAATA
1 TAAAATTTTATTCTAATA
* *
68656 TACAATTTTATTCTACTA
1 TAAAATTTTATTCTAATA
*
68674 -AAAATTCTATT
1 TAAAATTTTATT
68685 TTCATTTAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
17 17 0.71
18 7 0.29
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
TAAAATTTTATTCTAATA
Found at i:80980 original size:31 final size:31
Alignment explanation
Indices: 80913--81042 Score: 136
Period size: 31 Copynumber: 4.2 Consensus size: 31
80903 TTTTGTGCAT
* * * **
80913 GTGGCATGCCACGTGCCATTTTTTGAAACATC
1 GTGGCATGACACGTGTCACTTTTTGGTACA-C
*
80945 -TGGCATGCCACGTGTCACTTTTTGGTACAC
1 GTGGCATGACACGTGTCACTTTTTGGTACAC
* * *
80975 GTGGCATGACATGTGTCACATTTCGGTACAC
1 GTGGCATGACACGTGTCACTTTTTGGTACAC
* * *
81006 GTGGCGTGACATGTGTCACTTTTTGGTACAT
1 GTGGCATGACACGTGTCACTTTTTGGTACAC
81037 GTGGCA
1 GTGGCA
81043 CGACT
Statistics
Matches: 84, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
30 1 0.01
31 83 0.99
ACGTcount: A:0.19, C:0.22, G:0.26, T:0.32
Consensus pattern (31 bp):
GTGGCATGACACGTGTCACTTTTTGGTACAC
Done.