Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008726.1 Hibiscus syriacus cultivar Beakdansim tig00111792_pilon, 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: 1298898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:254548 original size:15 final size:15
Alignment explanation
Indices: 254524--254553 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
254514 TGTATCGATC
*
254524 TATAACAATATAACA
1 TATAAAAATATAACA
254539 TATAAAAATATAACA
1 TATAAAAATATAACA
254554 AAACATGTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (15 bp):
TATAAAAATATAACA
Found at i:257338 original size:12 final size:14
Alignment explanation
Indices: 257289--257347 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 14
257279 GAATGAATAA
*
257289 GAGATGGTTGTAGGGG
1 GAGATGG-TG-AGGCG
257305 GATGATGGTGAGGCG
1 GA-GATGGTGAGGCG
*
257320 GATGATGGTGAGGGG
1 GA-GATGGTGAGGCG
257335 GATGATGGTGAGG
1 GA-GATGGTGAGG
257348 GAAAACAGAG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
15 31 0.77
16 4 0.10
17 5 0.12
ACGTcount: A:0.20, C:0.02, G:0.56, T:0.22
Consensus pattern (14 bp):
GAGATGGTGAGGCG
Found at i:257348 original size:15 final size:15
Alignment explanation
Indices: 257300--257348 Score: 89
Period size: 15 Copynumber: 3.3 Consensus size: 15
257290 AGATGGTTGT
257300 AGGGGGATGATGGTG
1 AGGGGGATGATGGTG
*
257315 AGGCGGATGATGGTG
1 AGGGGGATGATGGTG
257330 AGGGGGATGATGGTG
1 AGGGGGATGATGGTG
257345 AGGG
1 AGGG
257349 AAAACAGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 32 1.00
ACGTcount: A:0.20, C:0.02, G:0.59, T:0.18
Consensus pattern (15 bp):
AGGGGGATGATGGTG
Found at i:257856 original size:3 final size:3
Alignment explanation
Indices: 257829--257873 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
257819 TCAATAAAGA
* * *
257829 GAT GAC GAT GAT GAA GAT GAA GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
257874 CCAAACAAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.38, C:0.02, G:0.33, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:261081 original size:179 final size:179
Alignment explanation
Indices: 260842--261211 Score: 632
Period size: 179 Copynumber: 2.1 Consensus size: 179
260832 TTAATTTGTG
* * *
260842 TCGATACTTTTTGTCCAGAATGAATGACAAAAGAGGTGTATGCGTAAAGTGTCAATACATTTATT
1 TCGATACTTTTTGTCCAGAATGAATGACAAAAGAGGTGCACGCATAAAGTGTCAATACATTTATT
* *
260907 AAAAGTATCGATCCCAAAAATATCGAATCCGATAATTATAATGTAATAGGTAAATTTACAATATA
66 AAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATATA
**
260972 ATGGGTAGAAATATACCGATTTAATTAGAAAATAGGTCAACATAATGTA
131 ACCGGTAGAAATATACCGATTTAATTAGAAAATAGGTCAACATAATGTA
* * *
261021 TCGATACATTTTGTCCAGAATGAATGACAAACGAGGTGCACGCATAAAGTGTCGATACATTTATT
1 TCGATACTTTTTGTCCAGAATGAATGACAAAAGAGGTGCACGCATAAAGTGTCAATACATTTATT
*
261086 AAAAGTATCGATCCCGAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATATA
66 AAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATATA
*
261151 ACCGGTAGAAATATACCGGTTTAATTAGAAAATAGGTCAACATAATGTA
131 ACCGGTAGAAATATACCGATTTAATTAGAAAATAGGTCAACATAATGTA
261200 TCGATACTTTTT
1 TCGATACTTTTT
261212 AAATTATGTC
Statistics
Matches: 178, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
179 178 1.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (179 bp):
TCGATACTTTTTGTCCAGAATGAATGACAAAAGAGGTGCACGCATAAAGTGTCAATACATTTATT
AAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAATAGGTAAATTTACAATATA
ACCGGTAGAAATATACCGATTTAATTAGAAAATAGGTCAACATAATGTA
Found at i:261664 original size:72 final size:72
Alignment explanation
Indices: 261517--261650 Score: 180
Period size: 72 Copynumber: 1.9 Consensus size: 72
261507 GATATTTTTT
* * * * **
261517 AATTTGTGTTGATATTTTTTGTCCATAATGAATGACAAACGAGGTGCACGCATAAAGTGTCGACA
1 AATTTGTGTCGATACTTTTGGTCCAGAATGAATGACAAACGAGGTGCACAAATAAAGTGTCGACA
261582 CCTTACA
66 CCTTACA
* *
261589 AATTTGTGTCGATACTTTTGGTCCAGAATGATTG-CTCAACGAGGTGCACAAATAAAGTGTCG
1 AATTTGTGTCGATACTTTTGGTCCAGAATGAATGAC-AAACGAGGTGCACAAATAAAGTGTCG
261651 CTACATTTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
71 1 0.02
72 52 0.98
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (72 bp):
AATTTGTGTCGATACTTTTGGTCCAGAATGAATGACAAACGAGGTGCACAAATAAAGTGTCGACA
CCTTACA
Found at i:261805 original size:20 final size:21
Alignment explanation
Indices: 261769--261812 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
261759 AGATAAACAT
261769 ATTGTATCGTCA-CTTTTTAA
1 ATTGTATCGTCATCTTTTTAA
*
261789 ATTGTATCGAT-ATTTTTTTAA
1 ATTGTATCG-TCATCTTTTTAA
261810 ATT
1 ATT
261813 ACGCGTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.55
Consensus pattern (21 bp):
ATTGTATCGTCATCTTTTTAA
Found at i:263639 original size:2 final size:2
Alignment explanation
Indices: 263632--263673 Score: 57
Period size: 2 Copynumber: 21.0 Consensus size: 2
263622 CAATGTATCG
* * *
263632 AT AT AT AT AC AC AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
263674 TCATACTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:263915 original size:161 final size:161
Alignment explanation
Indices: 263640--263935 Score: 436
Period size: 161 Copynumber: 1.8 Consensus size: 161
263630 CGATATATAT
*
263640 ACACATACATATATATATATATATATATATATATTCATACTTATAATTCTGAAACATATTACTTT
1 ACACACACATATATATATATATATATATATATATTCATACTTATAATTCTGAAACATATTACTTT
* * * *
263705 TAAGTAATAGGTTAATTGACAATGAAAACGGTTAAATTCATTCGGTATCATGAAAATATAAGTAA
66 AAAGTAATAGATTAATTGACAATGAAAACGGTTAAAGTCAATCGGTATCATGAAAATATAAGTAA
263770 ACAATGTTCTAAGGCCCCATCAGCTTTAACA
131 ACAATGTTCTAAGGCCCCATCAGCTTTAACA
263801 ACACACACAT-TATATATATATATATATATATATTCCATACTTATAATT-TCGAAATC-TATTAC
1 ACACACACATATATATATATATATATATATATATT-CATACTTATAATTCT-GAAA-CATATTAC
** * * * **
263863 TTTAAAGTAATAGATTAATTTCCAATGACAACGGTTAAAGTCAATCGGTATCATTATAATATGCG
63 TTTAAAGTAATAGATTAATTGACAATGAAAACGGTTAAAGTCAATCGGTATCATGAAAATATAAG
263928 TAAACAAT
128 TAAACAAT
263936 TACCATGTTG
Statistics
Matches: 120, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
160 25 0.21
161 94 0.78
162 1 0.01
ACGTcount: A:0.42, C:0.14, G:0.09, T:0.35
Consensus pattern (161 bp):
ACACACACATATATATATATATATATATATATATTCATACTTATAATTCTGAAACATATTACTTT
AAAGTAATAGATTAATTGACAATGAAAACGGTTAAAGTCAATCGGTATCATGAAAATATAAGTAA
ACAATGTTCTAAGGCCCCATCAGCTTTAACA
Found at i:264410 original size:87 final size:87
Alignment explanation
Indices: 264264--264524 Score: 398
Period size: 87 Copynumber: 3.0 Consensus size: 87
264254 TAACAAATTA
* * *
264264 AGTAATTAACCTATTTTATTATATAAACGCTACCTATTACGTTACATAAGTGCTACCTAATATGT
1 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGT
*
264329 TATTATACTTGATAATGTTTCC
66 TATTATGCTTGATAATGTTTCC
*
264351 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATTT
1 AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGT
*
264416 TATTATGTTTGATAATGTTT-C
66 TATTATGCTTGATAATGTTTCC
* * *
264437 TGATAATTAACCTATTTTATTATATAAGCACTACCTATTACGTTATATAAGCGCTACATAATATG
1 AG-TAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATG
* * *
264502 TTATTGTGCTTGATGATATTTCC
65 TTATTATGCTTGATAATGTTTCC
264525 GATTAAATGA
Statistics
Matches: 158, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
86 2 0.01
87 155 0.98
88 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.43
Consensus pattern (87 bp):
AGTAATTAACCTATTTTATTATATAAGCGCTACCTATTACGTTATATAAGCGCTACCTAATATGT
TATTATGCTTGATAATGTTTCC
Found at i:264418 original size:23 final size:23
Alignment explanation
Indices: 264369--264412 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
264359 ACCTATTTTA
*
264369 TTATATAAGCGCTACCTATTACG
1 TTATATAAGCGCTACCTAATACG
264392 TTATATAAGCGCTACCTAATA
1 TTATATAAGCGCTACCTAATA
264413 TTTTATTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.34
Consensus pattern (23 bp):
TTATATAAGCGCTACCTAATACG
Found at i:264421 original size:26 final size:23
Alignment explanation
Indices: 264359--264409 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
264349 CCAGTAATTA
264359 ACCTATTTTATTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
***
264382 ACCTATTACGTTATATAAGCGCT
1 ACCTATTTTATTATATAAGCGCT
264405 ACCTA
1 ACCTA
264410 ATATTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (23 bp):
ACCTATTTTATTATATAAGCGCT
Found at i:264472 original size:23 final size:23
Alignment explanation
Indices: 264446--264493 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
264436 CTGATAATTA
**
264446 ACCTATTTTATTATATAAGCACT
1 ACCTATTACATTATATAAGCACT
* *
264469 ACCTATTACGTTATATAAGCGCT
1 ACCTATTACATTATATAAGCACT
264492 AC
1 AC
264494 ATAATATGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (23 bp):
ACCTATTACATTATATAAGCACT
Found at i:264504 original size:23 final size:23
Alignment explanation
Indices: 264456--264505 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
264446 ACCTATTTTA
* *
264456 TTATATAAGCACTACCTATTACG
1 TTATATAAGCACTACATAATACG
* *
264479 TTATATAAGCGCTACATAATATG
1 TTATATAAGCACTACATAATACG
264502 TTAT
1 TTAT
264506 TGTGCTTGAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.10, T:0.38
Consensus pattern (23 bp):
TTATATAAGCACTACATAATACG
Found at i:266926 original size:61 final size:61
Alignment explanation
Indices: 266838--266952 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 61
266828 GAAGGTGGAT
* * *
266838 ACGACCTTATGTATCATGTCCGGATTAGTACTATAACGTAAGCTTAGTGTAGGTGGTGGGC
1 ACGACCTTATGTATCATGTCCGAATTAGCACTATAACGTAAGCTTAGTGCAGGTGGTGGGC
* **
266899 ACGACCTTATGTGT-ATTGTCCGAATTAGCACTATGGCGTAAGCTTAGTGCAGGT
1 ACGACCTTATGTATCA-TGTCCGAATTAGCACTATAACGTAAGCTTAGTGCAGGT
266953 TTAGCACTAC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
60 1 0.02
61 46 0.98
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.31
Consensus pattern (61 bp):
ACGACCTTATGTATCATGTCCGAATTAGCACTATAACGTAAGCTTAGTGCAGGTGGTGGGC
Found at i:272410 original size:21 final size:21
Alignment explanation
Indices: 272372--272442 Score: 60
Period size: 21 Copynumber: 3.4 Consensus size: 21
272362 CTATTAAATG
*
272372 AAATAATTTTTATT-ATATACT
1 AAATAA-TATTATTAATATACT
272393 AAATAATATTATTAATATA-T
1 AAATAATATTATTAATATACT
272413 GAAATCAATATT-TTAAT-TACCT
1 -AAAT-AATATTATTAATATA-CT
*
272435 CAATAATA
1 AAATAATA
272443 GCGGGAAGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
20 13 0.30
21 23 0.53
22 7 0.16
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.44
Consensus pattern (21 bp):
AAATAATATTATTAATATACT
Found at i:273436 original size:17 final size:17
Alignment explanation
Indices: 273416--273473 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 17
273406 AATTTGACCA
*
273416 GGTTTGATCTTTGAGAG
1 GGTTTGAGCTTTGAGAG
*
273433 GG-TTGGGCTTTGAGAG
1 GGTTTGAGCTTTGAGAG
*
273449 GGTTTGGGCTTTGAGAG
1 GGTTTGAGCTTTGAGAG
273466 GGTTTGAG
1 GGTTTGAG
273474 GATTTGAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
16 14 0.38
17 23 0.62
ACGTcount: A:0.14, C:0.05, G:0.45, T:0.36
Consensus pattern (17 bp):
GGTTTGAGCTTTGAGAG
Found at i:273445 original size:16 final size:16
Alignment explanation
Indices: 273424--273469 Score: 83
Period size: 17 Copynumber: 2.8 Consensus size: 16
273414 CAGGTTTGAT
273424 CTTTGAGAGGGTTGGG
1 CTTTGAGAGGGTTGGG
273440 CTTTGAGAGGGTTTGGG
1 CTTTGAGAGGG-TTGGG
273457 CTTTGAGAGGGTT
1 CTTTGAGAGGGTT
273470 TGAGGATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.45
17 16 0.55
ACGTcount: A:0.13, C:0.07, G:0.46, T:0.35
Consensus pattern (16 bp):
CTTTGAGAGGGTTGGG
Found at i:273488 original size:33 final size:32
Alignment explanation
Indices: 273424--273488 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 32
273414 CAGGTTTGAT
* *
273424 CTTTGAGAGGGTTGGGCTTTGAGAGGGTTTGGG
1 CTTTGAGAGGGTTGGGATTTGAGA-GATTTGGG
273457 CTTTGAGAGGGTTTGAGGATTTGAGA-ATTTGG
1 CTTTGAGAGGG-TTG-GGATTTGAGAGATTTGG
273489 TGTGTGTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 16 0.57
34 3 0.11
35 9 0.32
ACGTcount: A:0.17, C:0.05, G:0.43, T:0.35
Consensus pattern (32 bp):
CTTTGAGAGGGTTGGGATTTGAGAGATTTGGG
Found at i:274424 original size:222 final size:223
Alignment explanation
Indices: 274033--274484 Score: 816
Period size: 222 Copynumber: 2.0 Consensus size: 223
274023 AACTTGGGTC
*
274033 ATAGACGTGGTTGTGGCTACGTTGATAACATCTTTTGGTGTAAAAGTTATTTTTTTGTCTTGGTA
1 ATAGACGTGGTTGTGGCTACGTTGATAACATCTTTTGGTGTAAAAGTTATTTTTTTGTCTTGGGA
274098 TCAAATTAGTTATTGGATAGTCAAAATCGTAATAGACATTCCGAAAACTTTTTCGAAGAGTTTCT
66 TCAAATTAGTTATTGGATAGTCAAAATCGTAATAGACATTCCGAAAACTTTTTCGAAGAGTTTCT
*
274163 CTTTCCCCCTTCCTTTTAGATAGTTTTAAGAT-TATATATATATATCGATTAAGATAAATTTTAC
131 CTTTCCCCCTTCCTTTTAGATAGTTTTAAGATGAATATATATATATCGATTAAGATAAATTTTAC
274227 AAAATTAATTTATATTTATCAATATAAG
196 AAAATTAATTTATATTTATCAATATAAG
274255 ATAGACGTGGTTGTGGCTACGTTGATAACATCTTTTGGTGTAAAAGTTATTTTTTTGTCTTGGGA
1 ATAGACGTGGTTGTGGCTACGTTGATAACATCTTTTGGTGTAAAAGTTATTTTTTTGTCTTGGGA
274320 TCAAATTAGTTATTGGATAGTCAAAATCGTAATAGACATTCCGAAAACTTTTTCGAAGAGTTTCT
66 TCAAATTAGTTATTGGATAGTCAAAATCGTAATAGACATTCCGAAAACTTTTTCGAAGAGTTTCT
*
274385 CTTTCCCCCTTCCTTTTAGATAGTTTTAAGATGATATATATATATATATATCGATTAAGATAATT
131 CTTTCCCCCTTCCTTTTAGATAGTTTTAAGATG----A-ATATATATATATCGATTAAGATAAAT
*
274450 TTTACTAAATTAATTTATATTTATCAATATAAG
191 TTTACAAAATTAATTTATATTTATCAATATAAG
274483 AT
1 AT
274485 TATAGATGAA
Statistics
Matches: 220, Mismatches: 4, Indels: 6
0.96 0.02 0.03
Matches are distributed among these distances:
222 161 0.73
228 59 0.27
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (223 bp):
ATAGACGTGGTTGTGGCTACGTTGATAACATCTTTTGGTGTAAAAGTTATTTTTTTGTCTTGGGA
TCAAATTAGTTATTGGATAGTCAAAATCGTAATAGACATTCCGAAAACTTTTTCGAAGAGTTTCT
CTTTCCCCCTTCCTTTTAGATAGTTTTAAGATGAATATATATATATCGATTAAGATAAATTTTAC
AAAATTAATTTATATTTATCAATATAAG
Found at i:282411 original size:20 final size:21
Alignment explanation
Indices: 282386--282426 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
282376 ACTTTGTATA
282386 ATAGTATCGATACCAT-AGGC
1 ATAGTATCGATACCATCAGGC
282406 ATAGTATCGATACCATCAGGC
1 ATAGTATCGATACCATCAGGC
282427 CCCAACTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (21 bp):
ATAGTATCGATACCATCAGGC
Found at i:288946 original size:40 final size:39
Alignment explanation
Indices: 288902--288982 Score: 126
Period size: 40 Copynumber: 2.1 Consensus size: 39
288892 CTTTCTGTCG
* *
288902 CCCCACCCCTCAACCCTCTCCCTTTTTACTATACTGTGGA
1 CCCCACCCCTCAACCCTCTACC-TTTTACTATACTGTAGA
*
288942 CCCCATCCCTCAACCCTCTACCTTTTACTATACTGTAGA
1 CCCCACCCCTCAACCCTCTACCTTTTACTATACTGTAGA
288981 CC
1 CC
288983 TTACCCCTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
39 18 0.47
40 20 0.53
ACGTcount: A:0.20, C:0.44, G:0.06, T:0.30
Consensus pattern (39 bp):
CCCCACCCCTCAACCCTCTACCTTTTACTATACTGTAGA
Found at i:291583 original size:10 final size:9
Alignment explanation
Indices: 291556--291582 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
291546 ACAGCAGTTT
291556 GAAAAAAAA
1 GAAAAAAAA
291565 GAAAAAAAA
1 GAAAAAAAA
291574 GAAAAAAAA
1 GAAAAAAAA
291583 AAGATATTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:292696 original size:25 final size:26
Alignment explanation
Indices: 292657--292705 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
292647 AGCTTTCTCT
292657 TTTTACTTTTCAAGTTTTCTTTTTTC
1 TTTTACTTTTCAAGTTTTCTTTTTTC
*
292683 TTTTA-TTTTCAAGTTTTGTTTTT
1 TTTTACTTTTCAAGTTTTCTTTTT
292706 AATATGCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.12, C:0.10, G:0.06, T:0.71
Consensus pattern (26 bp):
TTTTACTTTTCAAGTTTTCTTTTTTC
Found at i:297604 original size:14 final size:14
Alignment explanation
Indices: 297587--297647 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
297577 AAAATAAAAA
297587 CCTAAACCATAATC
1 CCTAAACCATAATC
297601 CCTAATACC-TAATC
1 CCTAA-ACCATAATC
* * * *
297615 TCTAAATCTTAAAC
1 CCTAAACCATAATC
297629 CCTAAA-CATTAATC
1 CCTAAACCA-TAATC
297643 CCTAA
1 CCTAA
297648 TCCCTAATTC
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
13 3 0.08
14 32 0.84
15 3 0.08
ACGTcount: A:0.41, C:0.31, G:0.00, T:0.28
Consensus pattern (14 bp):
CCTAAACCATAATC
Found at i:297647 original size:35 final size:34
Alignment explanation
Indices: 297603--297710 Score: 101
Period size: 35 Copynumber: 3.1 Consensus size: 34
297593 CCATAATCCC
*
297603 TAATACCTAATCTCTAAATCTTAAACCCTAAACA
1 TAATCCCTAATCTCTAAATCTTAAACCCTAAACA
* * * *
297637 TTAATCCCTAATCCCTAATTCATAAACACTAAAACA
1 -TAATCCCTAATCTCTAAATCTTAAACCCT-AAACA
* * *
297673 TAAACCCTAATTTCT-AAGCATTAAACCCTAAACCA
1 TAATCCCTAATCTCTAAATC-TTAAACCCTAAA-CA
297708 TAA
1 TAA
297711 ATACTAAACC
Statistics
Matches: 58, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
34 5 0.09
35 48 0.83
36 5 0.09
ACGTcount: A:0.44, C:0.27, G:0.01, T:0.28
Consensus pattern (34 bp):
TAATCCCTAATCTCTAAATCTTAAACCCTAAACA
Found at i:297677 original size:42 final size:41
Alignment explanation
Indices: 297583--297677 Score: 104
Period size: 42 Copynumber: 2.3 Consensus size: 41
297573 CTCTAAAATA
*
297583 AAAACCTAAACCATAATCCCTAATACCTAATCTCTAAATCTT
1 AAAACCTAAA-CATAATCCCTAATACCTAATCTCTAAATCCT
* *
297625 AAACCCTAAACATTAATCCCTAATCCCTAAT-TCATAAA-CACT
1 AAAACCTAAACA-TAATCCCTAATACCTAATCTC-TAAATC-CT
*
297667 AAAACATAAAC
1 AAAACCTAAAC
297678 CCTAATTTCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
41 5 0.11
42 40 0.89
ACGTcount: A:0.46, C:0.28, G:0.00, T:0.25
Consensus pattern (41 bp):
AAAACCTAAACATAATCCCTAATACCTAATCTCTAAATCCT
Found at i:297704 original size:7 final size:7
Alignment explanation
Indices: 297694--297745 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
297684 TTCTAAGCAT
297694 TAAACCC
1 TAAACCC
*
297701 TAAACCA
1 TAAACCC
**
297708 TAAATAC
1 TAAACCC
297715 TAAACCC
1 TAAACCC
*
297722 TAAACCA
1 TAAACCC
**
297729 TAAATAC
1 TAAACCC
297736 TAAACCC
1 TAAACCC
297743 TAA
1 TAA
297746 TCCTTAAGCC
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:297704 original size:28 final size:27
Alignment explanation
Indices: 297630--297706 Score: 82
Period size: 28 Copynumber: 2.8 Consensus size: 27
297620 ATCTTAAACC
* *
297630 CTAAACATTAATCCCTAATCCCTAATT
1 CTAAACATTAAACCCTAAACCCTAATT
* * *
297657 CATAAACACTAAAACATAAACCCTAATTT
1 C-TAAACATTAAACCCTAAACCCTAA-TT
*
297686 CTAAGCATTAAACCCTAAACC
1 CTAAACATTAAACCCTAAACC
297707 ATAAATACTA
Statistics
Matches: 39, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
27 1 0.03
28 35 0.90
29 3 0.08
ACGTcount: A:0.44, C:0.29, G:0.01, T:0.26
Consensus pattern (27 bp):
CTAAACATTAAACCCTAAACCCTAATT
Found at i:297718 original size:21 final size:21
Alignment explanation
Indices: 297694--297745 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
297684 TTCTAAGCAT
297694 TAAACCCTAAACCATAAATAC
1 TAAACCCTAAACCATAAATAC
297715 TAAACCCTAAACCATAAATAC
1 TAAACCCTAAACCATAAATAC
297736 TAAACCCTAA
1 TAAACCCTAA
297746 TCCTTAAGCC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (21 bp):
TAAACCCTAAACCATAAATAC
Found at i:299833 original size:13 final size:11
Alignment explanation
Indices: 299802--299840 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
299792 CATTAACCCG
299802 TCGAGCTTGAA
1 TCGAGCTTGAA
299813 TCGAGCTTGAA
1 TCGAGCTTGAA
*
299824 TTCTGAGCTTCAA
1 -TC-GAGCTTGAA
299837 TCGA
1 TCGA
299841 ACTTTTGAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 13 0.52
12 4 0.16
13 8 0.32
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.31
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:307962 original size:22 final size:22
Alignment explanation
Indices: 307936--307982 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
307926 TCAGAACGTT
* *
307936 TTACCCCATTAACTTTAAATCG
1 TTACCCCATTAACTTCAAACCG
* *
307958 TTACCCTATTTACTTCAAACCG
1 TTACCCCATTAACTTCAAACCG
307980 TTA
1 TTA
307983 ACATCGTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.30, C:0.28, G:0.04, T:0.38
Consensus pattern (22 bp):
TTACCCCATTAACTTCAAACCG
Found at i:314902 original size:12 final size:12
Alignment explanation
Indices: 314885--314909 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
314875 TACTGTTTAT
314885 TGCTACAGTAAC
1 TGCTACAGTAAC
314897 TGCTACAGTAAC
1 TGCTACAGTAAC
314909 T
1 T
314910 TCCGAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.28
Consensus pattern (12 bp):
TGCTACAGTAAC
Found at i:315352 original size:47 final size:44
Alignment explanation
Indices: 315286--315410 Score: 171
Period size: 47 Copynumber: 2.8 Consensus size: 44
315276 TATAAAATCT
*
315286 CTTACCACTTATACCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
315331 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCA-TT--ATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
*
315378 CTTGCCATTATT-CATAAGCTCGTAAGCTTATTT
1 CTTACCATTATTCCATAAGCTCGTAAGCTTATTT
315411 GCATACTTAC
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
43 21 0.29
44 3 0.04
45 9 0.12
46 2 0.03
47 38 0.52
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (44 bp):
CTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:315418 original size:38 final size:41
Alignment explanation
Indices: 315286--315424 Score: 131
Period size: 47 Copynumber: 3.2 Consensus size: 41
315276 TATAAAATCT
* *
315286 CTTACCACTTATACCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCA-TTAT-TCATAAGCTCGTAAGCTTATTTTAGC--AATA
*
315331 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCA-TT--ATT-CATAAGCTCGTAAGCTTATTTTAGC-A-ATA
*
315378 CTTGCCATTATTCATAAGCTCGTAAGCTTA-TTT-GC-ATA
1 CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
315416 CTTACCATT
1 CTTACCATT
315425 TATTAACCAA
Statistics
Matches: 84, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
38 11 0.13
41 1 0.01
42 3 0.04
43 18 0.21
44 3 0.04
45 9 0.11
46 4 0.05
47 35 0.42
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (41 bp):
CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
Found at i:318039 original size:11 final size:12
Alignment explanation
Indices: 318010--318062 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
318000 TTATTTAAAT
318010 GGGTATTGGGCC
1 GGGTATTGGGCC
*
318022 GGGTATTGGGTC
1 GGGTATTGGGCC
318034 -GGTATTGGGCC
1 GGGTATTGGGCC
* *
318045 GGGAATCGGGCC
1 GGGTATTGGGCC
*
318057 AGGTAT
1 GGGTAT
318063 ATATATATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 10 0.29
12 24 0.71
ACGTcount: A:0.13, C:0.15, G:0.47, T:0.25
Consensus pattern (12 bp):
GGGTATTGGGCC
Found at i:318120 original size:24 final size:25
Alignment explanation
Indices: 318060--318120 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
318050 TCGGGCCAGG
318060 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
318083 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
318107 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
318121 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:318210 original size:13 final size:13
Alignment explanation
Indices: 318154--318197 Score: 63
Period size: 13 Copynumber: 3.5 Consensus size: 13
318144 TTTAATATTT
*
318154 ATCGGGTCGGGT-
1 ATCGGGGCGGGTA
318166 ATCGGGGCGGGTA
1 ATCGGGGCGGGTA
*
318179 ATCGGGGCAGGTA
1 ATCGGGGCGGGTA
318192 ATCGGG
1 ATCGGG
318198 TAATCGGGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.16, C:0.16, G:0.50, T:0.18
Consensus pattern (13 bp):
ATCGGGGCGGGTA
Found at i:320394 original size:19 final size:19
Alignment explanation
Indices: 320357--320394 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
320347 TGCTGCAGGT
*
320357 ATTATTATAGAGATTAAGC
1 ATTATTATAGAGATAAAGC
320376 ATTATTA-AGACGATAAAGC
1 ATTATTATAGA-GATAAAGC
320395 CATATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.45, C:0.08, G:0.16, T:0.32
Consensus pattern (19 bp):
ATTATTATAGAGATAAAGC
Found at i:321565 original size:22 final size:22
Alignment explanation
Indices: 321535--321591 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
321525 TGATCACATA
* *
321535 TTCAAATTTCATAATCCATAAT
1 TTCACATTTCATAATCAATAAT
** *
321557 TTCACATTTCATGTTCAATACT
1 TTCACATTTCATAATCAATAAT
*
321579 TTCACTTTTCATA
1 TTCACATTTCATA
321592 TGAATATGAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.32, C:0.21, G:0.02, T:0.46
Consensus pattern (22 bp):
TTCACATTTCATAATCAATAAT
Found at i:321598 original size:6 final size:6
Alignment explanation
Indices: 321589--323042 Score: 2822
Period size: 6 Copynumber: 244.0 Consensus size: 6
321579 TTCACTTTTC
321589 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
321637 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
321685 ATATGA ATATGA ATATGA ATATGA ATATG- ATATG- A-ATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
321730 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
321778 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
321826 ATATGA ATATGA ATATGA ATATG- A-ATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
321872 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATG-
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
321919 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
321967 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322015 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322063 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322111 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322159 ATATGA ATATGA ATATGA ATATG- ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322206 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322254 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322302 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322350 ATATGA ATATGAA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATG-A ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322399 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322447 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322495 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322543 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322591 ATATGA ATATGA ATATGA ATATGA ATATG- A-ATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322637 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322685 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322733 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322781 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATG-
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322828 A-ATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322875 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322923 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
322971 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA ATATGA
323019 ATATGA ATATGA ATATGA ATATGA
1 ATATGA ATATGA ATATGA ATATGA
323043 CCCAAAGGTG
Statistics
Matches: 1437, Mismatches: 0, Indels: 22
0.98 0.00 0.02
Matches are distributed among these distances:
4 12 0.01
5 23 0.02
6 1396 0.97
7 6 0.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
ATATGA
Found at i:323802 original size:20 final size:20
Alignment explanation
Indices: 323777--323814 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
323767 GAATGCTAGA
*
323777 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
323797 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
323815 AAAAAAGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:324797 original size:103 final size:103
Alignment explanation
Indices: 324572--324797 Score: 389
Period size: 103 Copynumber: 2.2 Consensus size: 103
324562 GTCGAGGGTC
* *
324572 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCTGGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
324637 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
324675 TATGTGGTCCTTCTAGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCTGGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
324740 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
*
324778 TATGTGGTCCTTATGGACAT
1 TATGTGGTCCTTCTGGACAT
324798 TATTATATGG
Statistics
Matches: 115, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 115 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCTGGACATATATGCATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:324845 original size:23 final size:23
Alignment explanation
Indices: 324829--324872 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
324819 AATTCTACGC
324829 GGCACTCCGGTGCAATTATATAG
1 GGCACTCCGGTGCAATTATATAG
*
324852 GGCACTTCGGTGCAATTATAT
1 GGCACTCCGGTGCAATTATAT
324873 GAGCTGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (23 bp):
GGCACTCCGGTGCAATTATATAG
Found at i:329785 original size:46 final size:46
Alignment explanation
Indices: 329735--330084 Score: 495
Period size: 46 Copynumber: 7.6 Consensus size: 46
329725 TAAGATCTCT
* * * *
329735 TTTCAT-CCATTAATGCATCCTTTCATCCATTTTAATCATGACATCC
1 TTTCATGCC-TTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
*
329781 TTTCATGCCTTGATGCATCCGTTCATGCATTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* * *
329827 TTTCTTGCCTTAATGTATCCGTTCATGCATTTTAATCATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
** * *
329873 TTTCATGTCGATAATGCATCTGTTCATGCATTTTAATTATGGCACCC
1 TTTCATG-CCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
*
329920 TTTCATGCCTTAATGCATACGTTCATGCATTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
*
329966 TTTCATGCCTTAATGCATCTGTTCATGCATTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
* *
330012 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCC
1 TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
** * *
330058 TTTCATTACGTAATGCATTCGTTCATG
1 TTTCATGCCTTAATGCATCCGTTCATG
330085 TCGTAATGCA
Statistics
Matches: 272, Mismatches: 30, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
46 230 0.85
47 42 0.15
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGGCATCC
Found at i:329990 original size:20 final size:20
Alignment explanation
Indices: 329967--330039 Score: 58
Period size: 20 Copynumber: 3.4 Consensus size: 20
329957 ATGGCATCCT
329967 TTCATGCCTTAATGCATCTG
1 TTCATGCCTTAATGCATCTG
*
329987 TTCATGCATTTTAATTATGGCATCCT-
1 TTCATGC--CTT-A--AT-GCAT-CTG
*
330013 TTCATGCCTTAATGCATCCG
1 TTCATGCCTTAATGCATCTG
330033 TTCATGC
1 TTCATGC
330040 ATTTTAGTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 16
0.69 0.05 0.26
Matches are distributed among these distances:
19 1 0.02
20 18 0.43
21 2 0.05
22 2 0.05
23 2 0.05
24 2 0.05
25 2 0.05
26 11 0.26
27 2 0.05
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.41
Consensus pattern (20 bp):
TTCATGCCTTAATGCATCTG
Found at i:330059 original size:185 final size:184
Alignment explanation
Indices: 329735--330084 Score: 535
Period size: 185 Copynumber: 1.9 Consensus size: 184
329725 TAAGATCTCT
* * *
329735 TTTCATCCATTAATGCATCCTTTCATCCATTTTAATCATGACATCCTTTCATGCCTTGATGCATC
1 TTTCATCCATTAATGCATACGTTCATCCATTTTAATCATGACATCCTTTCATGCCTTAATGCATC
* *
329800 CGTTCATGCATTTTAATTATGGCATCCTTTCTTGCCTTAATGTATCCGTTCATGCATTTTAATCA
66 CGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAATCA
*
329865 TGGCATCCTTTCATGT-CGATAATGCA-TCTGTTCATGCATTTTAATTATGGCACCC
131 TGACATCCTTTCAT-TACG-TAATGCATTC-GTTCATGCATTTTAATTATGGCACCC
* * *
329920 TTTCATGCC-TTAATGCATACGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCAT
1 TTTCAT-CCATTAATGCATACGTTCATCCATTTTAATCATGACATCCTTTCATGCCTTAATGCAT
* * *
329984 CTGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTT
65 CCGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAATC
330049 ATGACATCCTTTCATTACGTAATGCATTCGTTCATG
130 ATGACATCCTTTCATTACGTAATGCATTCGTTCATG
330085 TCGTAATGCA
Statistics
Matches: 150, Mismatches: 12, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
184 15 0.10
185 133 0.89
186 2 0.01
ACGTcount: A:0.22, C:0.23, G:0.13, T:0.42
Consensus pattern (184 bp):
TTTCATCCATTAATGCATACGTTCATCCATTTTAATCATGACATCCTTTCATGCCTTAATGCATC
CGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAATCA
TGACATCCTTTCATTACGTAATGCATTCGTTCATGCATTTTAATTATGGCACCC
Found at i:330083 original size:66 final size:66
Alignment explanation
Indices: 330006--330151 Score: 211
Period size: 66 Copynumber: 2.2 Consensus size: 66
329996 TTTAATTATG
* * * *
330006 GCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCCTTTCATTACGTAA
1 GCATCCGTTCATGCCGTAATGCATCCGTTCATGCATTTTAGTTATGACATCATTTCATGACGTAA
330071 T
66 T
* * * * *
330072 GCATTCGTTCATGTCGTAATGCATTCGTTCATGCATTTTAGTTATGACATCATTTCATGCCTTAA
1 GCATCCGTTCATGCCGTAATGCATCCGTTCATGCATTTTAGTTATGACATCATTTCATGACGTAA
330137 T
66 T
330138 GCATCCGTTCATGC
1 GCATCCGTTCATGC
330152 ATTTTAATTA
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.22, C:0.23, G:0.14, T:0.40
Consensus pattern (66 bp):
GCATCCGTTCATGCCGTAATGCATCCGTTCATGCATTTTAGTTATGACATCATTTCATGACGTAA
T
Found at i:330089 original size:20 final size:20
Alignment explanation
Indices: 330066--330104 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
330056 CCTTTCATTA
330066 CGTAATGCATTCGTTCATGT
1 CGTAATGCATTCGTTCATGT
330086 CGTAATGCATTCGTTCATG
1 CGTAATGCATTCGTTCATG
330105 CATTTTAGTT
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:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
CGTAATGCATTCGTTCATGT
Found at i:330092 original size:112 final size:112
Alignment explanation
Indices: 329967--330197 Score: 347
Period size: 112 Copynumber: 2.1 Consensus size: 112
329957 ATGGCATCCT
* * *
329967 TTCATGCCTTAATGCA-TCTGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATC
1 TTCATGCCGTAATGCATTC-GTTCATGCATTTTAATTATGACATCATTTCATGCCTTAATGCATC
* * * *
330031 CGTTCATGCATTTTAGTTATGACATCCTTTCATTACGTAATGCATTCG
65 CGTTCATGCATTTTAATTATAAAATCCTTTCATGACGTAATGCATTCG
* *
330079 TTCATGTCGTAATGCATTCGTTCATGCATTTTAGTTATGACATCATTTCATGCCTTAATGCATCC
1 TTCATGCCGTAATGCATTCGTTCATGCATTTTAATTATGACATCATTTCATGCCTTAATGCATCC
* *
330144 GTTCATGCATTTTAATTATAAAATCCTTTCATGCCTTAATGCATTCG
66 GTTCATGCATTTTAATTATAAAATCCTTTCATGACGTAATGCATTCG
330191 TTCATGC
1 TTCATGC
330198 ATTTTAGTTA
Statistics
Matches: 106, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
112 104 0.98
113 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (112 bp):
TTCATGCCGTAATGCATTCGTTCATGCATTTTAATTATGACATCATTTCATGCCTTAATGCATCC
GTTCATGCATTTTAATTATAAAATCCTTTCATGACGTAATGCATTCG
Found at i:330108 original size:204 final size:205
Alignment explanation
Indices: 329867--330288 Score: 643
Period size: 204 Copynumber: 2.1 Consensus size: 205
329857 TTTAATCATG
* * *
329867 GCATCCTTTCATGTCGATAATGCATCTGTTCATGCATTTTAATTATGGCACCCTTTCATGCCTTA
1 GCATCCGTTCATGTCGATAATGCATCTGTTCATGCATTTTAATTATGACACCATTTCATGCCTTA
***
329932 ATGCATACGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCA-TCTGTTCATGCAT
66 ATGCATACGTTCATGCATTTTAATTATAAAATCCTTTCATGCCTTAATGCATTC-GTTCATGCAT
* * *
329996 TTTAATTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGACATCCTTT
130 TTTAATTATGGCATCCTTTCATGCCTTAATACATCAGTTCATGCATTTTAATTATGACATCCTTT
*
330061 CATTACGTAAT
195 CATGACGTAAT
* * *
330072 GCATTCGTTCATGTCG-TAATGCAT-TCGTTCATGCATTTTAGTTATGACATCATTTCATGCCTT
1 GCATCCGTTCATGTCGATAATGCATCT-GTTCATGCATTTTAATTATGACACCATTTCATGCCTT
*
330135 AATGCATCCGTTCATGCATTTTAATTATAAAATCCTTTCATGCCTTAATGCATTCGTTCATGCAT
65 AATGCATACGTTCATGCATTTTAATTATAAAATCCTTTCATGCCTTAATGCATTCGTTCATGCAT
* *
330200 TTTAGTTATGGCATCCTTTCATGCCTTAATACATCAGTTCATGCATTTTAATTATGGCATCCTTT
130 TTTAATTATGGCATCCTTTCATGCCTTAATACATCAGTTCATGCATTTTAATTATGACATCCTTT
* *
330265 CATGCCTTAAT
195 CATGACGTAAT
330276 GCATCCGTTCATG
1 GCATCCGTTCATG
330289 CATTTTAGTT
Statistics
Matches: 196, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
203 1 0.01
204 179 0.91
205 16 0.08
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.41
Consensus pattern (205 bp):
GCATCCGTTCATGTCGATAATGCATCTGTTCATGCATTTTAATTATGACACCATTTCATGCCTTA
ATGCATACGTTCATGCATTTTAATTATAAAATCCTTTCATGCCTTAATGCATTCGTTCATGCATT
TTAATTATGGCATCCTTTCATGCCTTAATACATCAGTTCATGCATTTTAATTATGACATCCTTTC
ATGACGTAAT
Found at i:330128 original size:158 final size:158
Alignment explanation
Indices: 329921--330221 Score: 494
Period size: 158 Copynumber: 1.9 Consensus size: 158
329911 ATGGCACCCT
* * * *
329921 TTCATGCCTTAATGCATACGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCT
1 TTCATGCCGTAATGCATACGTTCATGCATTTTAATTATGACATCATTTCATGCCTTAATGCATCC
***
329986 GTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTAT
66 GTTCATGCATTTTAATTATAAAATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTAT
330051 GACATCCTTTCATTACGTAATGCATTCG
131 GACATCCTTTCATTACGTAATGCATTCG
* * *
330079 TTCATGTCGTAATGCATTCGTTCATGCATTTTAGTTATGACATCATTTCATGCCTTAATGCATCC
1 TTCATGCCGTAATGCATACGTTCATGCATTTTAATTATGACATCATTTCATGCCTTAATGCATCC
*
330144 GTTCATGCATTTTAATTATAAAATCCTTTCATGCCTTAATGCATTCGTTCATGCATTTTAGTTAT
66 GTTCATGCATTTTAATTATAAAATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTAT
*
330209 GGCATCCTTTCAT
131 GACATCCTTTCAT
330222 GCCTTAATAC
Statistics
Matches: 131, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
158 131 1.00
ACGTcount: A:0.23, C:0.21, G:0.13, T:0.43
Consensus pattern (158 bp):
TTCATGCCGTAATGCATACGTTCATGCATTTTAATTATGACATCATTTCATGCCTTAATGCATCC
GTTCATGCATTTTAATTATAAAATCCTTTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTAT
GACATCCTTTCATTACGTAATGCATTCG
Found at i:330129 original size:46 final size:46
Alignment explanation
Indices: 330079--330510 Score: 552
Period size: 46 Copynumber: 9.4 Consensus size: 46
330069 AATGCATTCG
* * * * *
330079 TTCATGTCGTAATGCATTCGTTCATGCATTTTAGTTATGACATCAT
1 TTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
* ***
330125 TTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATAAAATCCT
1 TTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
*
330171 TTCATGCCTTAATGCATTCGTTCATGCATTTTAGTTATGGCATCCT
1 TTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
* * *
330217 TTCATGCCTTAATACATCAGTTCATGCATTTTAATTATGGCATCCT
1 TTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
330263 TTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
1 TTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
* *
330309 TTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCTTCTT
1 TTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
* *
330355 TTCATGCCTTAATGCATCCGTTCATGCATTTTAATTATGACATCCT
1 TTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
* ** *
330401 TTCATGCCAATAATGCA-CCCAT-ATGCATTATTA-TTTTGGCATCCT
1 TTCATGCC-TTAATGCATCCGTTCATGCATT-TTAGTTATGGCATCCT
** * *
330446 TTCATGCCTATAATGCA-CC-CACATGAATTATTA-TTTTGGCATCCT
1 TTCATGCCT-TAATGCATCCGTTCATGCATT-TTAGTTATGGCATCCT
330491 TTCATGCCTATAATGCATCC
1 TTCATGCCT-TAATGCATCC
330511 ATATGCATTA
Statistics
Matches: 347, Mismatches: 34, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
45 73 0.21
46 267 0.77
47 7 0.02
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (46 bp):
TTCATGCCTTAATGCATCCGTTCATGCATTTTAGTTATGGCATCCT
Found at i:330224 original size:250 final size:251
Alignment explanation
Indices: 329837--330334 Score: 791
Period size: 250 Copynumber: 2.0 Consensus size: 251
329827 TTTCTTGCCT
* * * * *
329837 TAATGTATCCGTTCATGCATTTTAATCATGGCATCCTTTCATGTCGATAATGCATCTGTTCATGC
1 TAATGCATCCGTTCATGCATTTTAATCATGACATCATTTCATGTCCATAATGCATCCGTTCATGC
***
329902 ATTTTAATTATGGCACCCTTTCATGCCTTAATGCATACGTTCATGCATTTTAATTATGGCATCCT
66 ATTTTAATTATAAAACCCTTTCATGCCTTAATGCATACGTTCATGCATTTTAATTATGGCATCCT
* *
329967 TTCATGCCTTAATGCATCTGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCC
131 TTCATGCCTTAATACATCAGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCC
* *
330032 GTTCATGCATTTTAGTTATGACATCCTTTCATTACGTAATGCATTCGTTCATGTCG
196 GTTCATGCATTTTAGTTATGACATCCTTTCATGACGTAATGCATCCGTTCATGTCG
* * * *
330088 TAATGCATTCGTTCATGCATTTTAGTTATGACATCATTTCATG-CCTTAATGCATCCGTTCATGC
1 TAATGCATCCGTTCATGCATTTTAATCATGACATCATTTCATGTCCATAATGCATCCGTTCATGC
* * *
330152 ATTTTAATTATAAAATCCTTTCATGCCTTAATGCATTCGTTCATGCATTTTAGTTATGGCATCCT
66 ATTTTAATTATAAAACCCTTTCATGCCTTAATGCATACGTTCATGCATTTTAATTATGGCATCCT
330217 TTCATGCCTTAATACATCAGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCC
131 TTCATGCCTTAATACATCAGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCC
* * *
330282 GTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATG
196 GTTCATGCATTTTAGTTATGACATCCTTTCATGACGTAATGCATCCGTTCATG
330335 CATTTTAGTT
Statistics
Matches: 225, Mismatches: 22, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
250 188 0.84
251 37 0.16
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.42
Consensus pattern (251 bp):
TAATGCATCCGTTCATGCATTTTAATCATGACATCATTTCATGTCCATAATGCATCCGTTCATGC
ATTTTAATTATAAAACCCTTTCATGCCTTAATGCATACGTTCATGCATTTTAATTATGGCATCCT
TTCATGCCTTAATACATCAGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCC
GTTCATGCATTTTAGTTATGACATCCTTTCATGACGTAATGCATCCGTTCATGTCG
Found at i:330241 original size:112 final size:109
Alignment explanation
Indices: 329976--330243 Score: 254
Period size: 112 Copynumber: 2.4 Consensus size: 109
329966 TTTCATGCCT
* * * **
329976 TAATGCATCTGTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATGCATCCGTTCATGCA
1 TAATGCATCCGTTCATGCA-CTT-A-TATGACATCAGTTCATGCCTTAATGCATCCGTTCATGCA
* * * * *
330041 TTTTAGTTATGACATCCTTTCATTACGTAATGCATTCGTTCATGTCG
63 TTTTAATTATAAAATCCTTTCATGACGTAATGCATTCGTTCATGTAG
* * *
330088 TAATGCATTCGTTCATGCATTTTAGTTATGACATCATTTCATGCCTTAATGCATCCGTTCATGCA
1 TAATGCATCCGTTCATGCA-CTTA--TATGACATCAGTTCATGCCTTAATGCATCCGTTCATGCA
* *
330153 TTTTAATTATAAAATCCTTTCATGCCTTAATGCATTCGTTCATGCATTTTAG
63 TTTTAATTATAAAATCCTTTCATGACGTAATGCATTCGTTCATG-----TAG
* *
330205 TTATGGCATCCTTTCATGC-CTTA-AT-ACATCAGTTCATGC
1 TAAT-GCATCCGTTCATGCACTTATATGACATCAGTTCATGC
330244 ATTTTAATTA
Statistics
Matches: 133, Mismatches: 16, Indels: 14
0.82 0.10 0.09
Matches are distributed among these distances:
111 1 0.01
112 110 0.83
113 2 0.02
116 3 0.02
117 5 0.04
118 12 0.09
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (109 bp):
TAATGCATCCGTTCATGCACTTATATGACATCAGTTCATGCCTTAATGCATCCGTTCATGCATTT
TAATTATAAAATCCTTTCATGACGTAATGCATTCGTTCATGTAG
Found at i:330462 original size:35 final size:35
Alignment explanation
Indices: 330423--330508 Score: 82
Period size: 45 Copynumber: 2.2 Consensus size: 35
330413 ATGCACCCAT
330423 ATGCATTATTATTTTGGCATCCTTTCATGCCTATA
1 ATGCATTATTATTTTGGCATCCTTTCATGCCTATA
330458 ATGCACCCACATGAATTATTATTTTGGCATCCTTTCATGCCTATA
1 ATG------C----ATTATTATTTTGGCATCCTTTCATGCCTATA
330503 ATGCAT
1 ATGCAT
330509 CCATATGCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 20
0.67 0.00 0.33
Matches are distributed among these distances:
35 5 0.12
39 1 0.02
41 1 0.02
45 34 0.83
ACGTcount: A:0.26, C:0.22, G:0.12, T:0.41
Consensus pattern (35 bp):
ATGCATTATTATTTTGGCATCCTTTCATGCCTATA
Found at i:330963 original size:19 final size:19
Alignment explanation
Indices: 330939--330980 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
330929 CGGCTCCTCA
330939 GATACTATACTATGGTACC
1 GATACTATACTATGGTACC
* *
330958 GATACTCTACTATGGTATC
1 GATACTATACTATGGTACC
330977 GATA
1 GATA
330981 TCATTTTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (19 bp):
GATACTATACTATGGTACC
Found at i:331030 original size:20 final size:20
Alignment explanation
Indices: 331005--331056 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
330995 TGTTTCAAAT
*
331005 GGTATCGATACAT-TCCCTTC
1 GGTATCGATAC-TCCCCCTTC
331025 GGTATCGATACTCCCCCTTC
1 GGTATCGATACTCCCCCTTC
*
331045 GGTATCAATACT
1 GGTATCGATACT
331057 GATTGCATCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.21, C:0.31, G:0.15, T:0.33
Consensus pattern (20 bp):
GGTATCGATACTCCCCCTTC
Found at i:331180 original size:12 final size:12
Alignment explanation
Indices: 331163--331188 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
331153 CATTTTTCAA
331163 CCTGAAATATAC
1 CCTGAAATATAC
331175 CCTGAAATATAC
1 CCTGAAATATAC
331187 CC
1 CC
331189 AAATTTGGTC
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:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (12 bp):
CCTGAAATATAC
Found at i:332791 original size:11 final size:11
Alignment explanation
Indices: 332775--332808 Score: 59
Period size: 11 Copynumber: 3.1 Consensus size: 11
332765 TGGATTAGGA
332775 TATTATTTTAT
1 TATTATTTTAT
332786 TATTATTTTAT
1 TATTATTTTAT
*
332797 TGTTATTTTAT
1 TATTATTTTAT
332808 T
1 T
332809 CCTTAATCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:342072 original size:24 final size:24
Alignment explanation
Indices: 342040--342085 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
342030 GCATGATATG
342040 GTACATAGATATTTTATACATCGT
1 GTACATAGATATTTTATACATCGT
*
342064 GTACATAGATGTTTTATACATC
1 GTACATAGATATTTTATACATC
342086 ACATGGAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (24 bp):
GTACATAGATATTTTATACATCGT
Found at i:343460 original size:43 final size:43
Alignment explanation
Indices: 343378--343469 Score: 107
Period size: 43 Copynumber: 2.1 Consensus size: 43
343368 GAATGCATCG
* * *
343378 ATGCATATTCAAGAGTGCATTGGTGCACCTTCATGGTGTATCA
1 ATGCATATTCAAGAGTGCATCGATGCACCTTCATAGTGTATCA
* *
343421 ATGCATATTCAAGGGATGCATCGATGCA-CTGTC-TAGTGTATCG
1 ATGCATATTCAAGAG-TGCATCGATGCACCT-TCATAGTGTATCA
343464 ATGCAT
1 ATGCAT
343470 TATGCACAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 30 0.71
44 12 0.29
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (43 bp):
ATGCATATTCAAGAGTGCATCGATGCACCTTCATAGTGTATCA
Found at i:349735 original size:25 final size:26
Alignment explanation
Indices: 349695--349750 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 26
349685 ACAAATTATG
349695 AAAA-TGAAATGAGAAAGTGA-ATAT
1 AAAAGTGAAATGAGAAAGTGAGATAT
*
349719 AAAAGTGAAA-GATGAAATTGAGATAT
1 AAAAGTGAAATGA-GAAAGTGAGATAT
*
349745 GAAAGT
1 AAAAGT
349751 TTTGTATTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 6 0.22
25 12 0.44
26 9 0.33
ACGTcount: A:0.55, C:0.00, G:0.23, T:0.21
Consensus pattern (26 bp):
AAAAGTGAAATGAGAAAGTGAGATAT
Found at i:350907 original size:26 final size:26
Alignment explanation
Indices: 350871--350921 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
350861 ATAAATACAC
*
350871 GAACATAAACA-AACACGAACATAAAT
1 GAACACAAACATAA-ACGAACATAAAT
*
350897 GAACACAAACATAAATGAACATAAA
1 GAACACAAACATAAACGAACATAAA
350922 CGTTGGAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 20 0.91
27 2 0.09
ACGTcount: A:0.63, C:0.18, G:0.08, T:0.12
Consensus pattern (26 bp):
GAACACAAACATAAACGAACATAAAT
Found at i:350912 original size:16 final size:16
Alignment explanation
Indices: 350867--350922 Score: 67
Period size: 16 Copynumber: 3.5 Consensus size: 16
350857 TTTAATAAAT
* **
350867 ACACGAACATAAACAA
1 ACACAAACATAAATGA
*
350883 ACACGAACATAAATGA
1 ACACAAACATAAATGA
350899 ACACAAACATAAATGA
1 ACACAAACATAAATGA
*
350915 ACATAAAC
1 ACACAAAC
350923 GTTGGAGACT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.61, C:0.21, G:0.07, T:0.11
Consensus pattern (16 bp):
ACACAAACATAAATGA
Found at i:352014 original size:14 final size:14
Alignment explanation
Indices: 351997--352071 Score: 67
Period size: 14 Copynumber: 5.9 Consensus size: 14
351987 GATTGGGTTA
*
351997 AACATAAATGAACG
1 AACATAAACGAACG
352011 AACAT--A--AACG
1 AACATAAACGAACG
*
352021 AACATAACCGAACG
1 AACATAAACGAACG
352035 AACAT--A--AACG
1 AACATAAACGAACG
*
352045 AACATAACCGAACG
1 AACATAAACGAACG
352059 AACATAAACGAAC
1 AACATAAACGAAC
352072 ATAACCGAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
10 18 0.37
12 1 0.02
14 30 0.61
ACGTcount: A:0.56, C:0.23, G:0.12, T:0.09
Consensus pattern (14 bp):
AACATAAACGAACG
Found at i:352022 original size:10 final size:10
Alignment explanation
Indices: 352007--352081 Score: 69
Period size: 10 Copynumber: 6.7 Consensus size: 10
351997 AACATAAATG
352007 AACGAACATA
1 AACGAACATA
352017 AACGAACATAA
1 AACGAACAT-A
352028 CCGAACGAACATA
1 ---AACGAACATA
352041 AACGAACATAA
1 AACGAACAT-A
352052 CCGAACGAACATA
1 ---AACGAACATA
352065 AACGAACATA
1 AACGAACATA
*
352075 ACCGAAC
1 AACGAAC
352082 GTTCACGAAC
Statistics
Matches: 56, Mismatches: 1, Indels: 16
0.77 0.01 0.22
Matches are distributed among these distances:
10 34 0.61
11 2 0.04
13 2 0.04
14 18 0.32
ACGTcount: A:0.55, C:0.25, G:0.12, T:0.08
Consensus pattern (10 bp):
AACGAACATA
Found at i:352082 original size:14 final size:14
Alignment explanation
Indices: 352017--352082 Score: 76
Period size: 14 Copynumber: 5.3 Consensus size: 14
352007 AACGAACATA
352017 AACGAACATAACCG
1 AACGAACATAACCG
352031 AACGAACAT-A---
1 AACGAACATAACCG
352041 AACGAACATAACCG
1 AACGAACATAACCG
352055 AACGAACAT-A---
1 AACGAACATAACCG
352065 AACGAACATAACCG
1 AACGAACATAACCG
352079 AACG
1 AACG
352083 TTCACGAACG
Statistics
Matches: 44, Mismatches: 0, Indels: 16
0.73 0.00 0.27
Matches are distributed among these distances:
10 18 0.41
11 2 0.05
13 2 0.05
14 22 0.50
ACGTcount: A:0.53, C:0.26, G:0.14, T:0.08
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:352091 original size:34 final size:34
Alignment explanation
Indices: 352007--352105 Score: 85
Period size: 34 Copynumber: 2.9 Consensus size: 34
351997 AACATAAATG
* * ***
352007 AACGAACATAAACGAACATAACCGAACGAACATA
1 AACGAACATAACCGAACGTAAATAAACGAACATA
352041 AACGAACATAACCGAACG-AACATAAACGAACATA
1 AACGAACATAACCGAACGTAA-ATAAACGAACATA
* * * *
352075 ACCGAACGT-TCACGAACGTAAATGAACGAAC
1 AACGAACATAAC-CGAACGTAAATAAACGAAC
352106 GAGACCTATG
Statistics
Matches: 53, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
33 3 0.06
34 48 0.91
35 2 0.04
ACGTcount: A:0.52, C:0.24, G:0.14, T:0.10
Consensus pattern (34 bp):
AACGAACATAACCGAACGTAAATAAACGAACATA
Found at i:352092 original size:24 final size:24
Alignment explanation
Indices: 351997--352082 Score: 154
Period size: 24 Copynumber: 3.6 Consensus size: 24
351987 GATTGGGTTA
**
351997 AACATAAATGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
352021 AACATAACCGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
352045 AACATAACCGAACGAACATAAACG
1 AACATAACCGAACGAACATAAACG
352069 AACATAACCGAACG
1 AACATAACCGAACG
352083 TTCACGAACG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.55, C:0.23, G:0.13, T:0.09
Consensus pattern (24 bp):
AACATAACCGAACGAACATAAACG
Found at i:356640 original size:110 final size:106
Alignment explanation
Indices: 356452--356864 Score: 547
Period size: 106 Copynumber: 3.9 Consensus size: 106
356442 ATCCTCCGCC
** * * * * *
356452 GTGAAGTTGAAATTGGTTTTGGAACTAGGAATTTTTTTGTTGACAACCAGTCGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGACTCTGAAACTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGT
356517 GAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCATTCGCT
66 GAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCATTCGCT
** * * * *
356558 GTGAAGTTGAAATTGACTCTGAATGAGACTGAAAAATTGTTTGCTGATAGCCAGTCGCCCCTTCG
1 GTGAAGTTGAAATTGACTCTG-A--A-ACTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCG
* * * *
356623 CTGTGAAGTTGAGCTTGTGCTATCTCGAGTCTAATATCATTCGCT
62 TTGTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCATTCGCT
* *
356668 GTGAAGTTGAAATTGACTCTGAAACTGGGAAATTGTTGGTTGACAACCAGCCGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGACTCTGAAACTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGT
* * *
356733 GAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCTTTCGTT
66 GAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCATTCGCT
* * * *
356774 GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAACCAGTCGTCCCTTCGTTAT
1 GTGAAGTTGAAATTGACTCTGAAACTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGT
*
356839 GAAGTTGAACTTGTGTTGTCTTGAGT
66 GAAGTTGAACTTGTGTTGTCTCGAGT
356865 GGCACGATAT
Statistics
Matches: 264, Mismatches: 39, Indels: 8
0.85 0.13 0.03
Matches are distributed among these distances:
106 170 0.64
107 1 0.00
109 2 0.01
110 91 0.34
ACGTcount: A:0.23, C:0.16, G:0.24, T:0.36
Consensus pattern (106 bp):
GTGAAGTTGAAATTGACTCTGAAACTGGGAAATTGTTTGTTGACAACCAGTCGTCCCTTCGTTGT
GAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCATTCGCT
Found at i:357009 original size:262 final size:264
Alignment explanation
Indices: 356668--357149 Score: 815
Period size: 262 Copynumber: 1.8 Consensus size: 264
356658 ATCATTCGCT
*
356668 GTGAAGTTGAAATTGACTCTGAAACTGGGAAATTGTTGGTTGACAACCAGCCGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGACTCTGAAACTGGGAAATTGTTGGTTGACAACCAACCGTCCCTTCGTTGT
* * * *
356733 GAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAA
66 GAAGTTGAACTTGTGTTATCTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA
* * *
356798 TTGGGAAATTATTTGTTGACAACCAGTCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTTGA
131 TTGGGAAATGATTTATTGACAACCAGTCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTCGA
356863 GTGGCACGATATCCTCCGTCGTGGAGTTGAAATCGCGGATGACCCATTCCGAGTCCAATATCCTC
196 GTGGCACGATATCCTCCGTCGTGGAGTTGAAATCGCGGATGACCCATTCCGAGTCCAATATCCTC
356928 CGTC
261 CGTC
* * ** *
356932 GTGAAGTTGAAATTG-GT-TGGAACTGGGAGTTTGTTTGTTGACAACCAACCGTCCCTTCGTTGT
1 GTGAAGTTGAAATTGACTCTGAAACTGGGAAATTGTTGGTTGACAACCAACCGTCCCTTCGTTGT
356995 GAAGTTGAACTTGTGTTATCTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA
66 GAAGTTGAACTTGTGTTATCTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA
* *
357060 TTGGGAAATGGTTTATTGACAACCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGA
131 TTGGGAAATGATTTATTGACAACCAGTCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTCGA
357125 GTGGCACGATATCCTCCGTCGTGGA
196 GTGGCACGATATCCTCCGTCGTGGA
357150 TGGCCCCTTC
Statistics
Matches: 203, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
262 187 0.92
263 1 0.00
264 15 0.07
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.33
Consensus pattern (264 bp):
GTGAAGTTGAAATTGACTCTGAAACTGGGAAATTGTTGGTTGACAACCAACCGTCCCTTCGTTGT
GAAGTTGAACTTGTGTTATCTCAAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA
TTGGGAAATGATTTATTGACAACCAGTCGTCCCTTCGTTATGAAGTTGAACTTGTGTTGTCTCGA
GTGGCACGATATCCTCCGTCGTGGAGTTGAAATCGCGGATGACCCATTCCGAGTCCAATATCCTC
CGTC
Found at i:357100 original size:106 final size:104
Alignment explanation
Indices: 356914--357147 Score: 299
Period size: 106 Copynumber: 2.2 Consensus size: 104
356904 ACCCATTCCG
* ** * *
356914 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTGGAACTGGGAGTTTGTTTGTTGACAACCA
1 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTGAAACTGGGAAATGGTTTATTGACAACCA
356979 ACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCA
66 ACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCA
* *
357018 AGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGGTTTATTGACAA
1 AGTCCAATATCCTCCGTC-GTGAAGTTGAAATTGG-T-TGAAACTGGGAAATGGTTTATTGACAA
** * *
357082 CCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
63 CCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCA
*
357124 AGTGGCACGATATCCTCCGTCGTG
1 AGT--C-CAATATCCTCCGTCGTG
357148 GATGGCCCCT
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
103 1 0.01
104 31 0.28
105 1 0.01
106 62 0.56
108 1 0.01
109 13 0.12
110 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (104 bp):
AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTGAAACTGGGAAATGGTTTATTGACAACCA
ACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTATCTCA
Found at i:357494 original size:36 final size:36
Alignment explanation
Indices: 357445--357514 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
357435 CAAAGTTTAT
* *
357445 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTC
1 GTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTC
* *
357481 GTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 GTTTCAAGAGAAACTATCTCAAGCGAGACAAAAT
357515 CTTCTAGTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
GTTTCAAGAGAAACTATCTCAAGCGAGACAAAATTC
Found at i:358462 original size:22 final size:22
Alignment explanation
Indices: 358437--358487 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
358427 GTTTGGTCAG
358437 AGGTTTGGCATTTGATGCTCAA
1 AGGTTTGGCATTTGATGCTCAA
358459 AGGTTTGGCATTTGATGCTCAA
1 AGGTTTGGCATTTGATGCTCAA
358481 AGGTTTG
1 AGGTTTG
358488 ATGGGGTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.12, G:0.29, T:0.37
Consensus pattern (22 bp):
AGGTTTGGCATTTGATGCTCAA
Found at i:364798 original size:20 final size:21
Alignment explanation
Indices: 364773--364811 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
364763 TTGTCCCTTT
364773 TTCTTTTTGAT-TTTTGTTCA
1 TTCTTTTTGATCTTTTGTTCA
*
364793 TTCTTTTTGTTCTTTTGTT
1 TTCTTTTTGATCTTTTGTT
364812 TTTTTCTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.05, C:0.10, G:0.10, T:0.74
Consensus pattern (21 bp):
TTCTTTTTGATCTTTTGTTCA
Found at i:364829 original size:14 final size:13
Alignment explanation
Indices: 364796--364851 Score: 60
Period size: 13 Copynumber: 4.2 Consensus size: 13
364786 TTGTTCATTC
*
364796 TTTTTGTTCT-TT
1 TTTTTTTTCTCTT
364808 TGTTTTTTTCTCTT
1 T-TTTTTTTCTCTT
*
364822 TTTATTTTCTCTT
1 TTTTTTTTCTCTT
*
364835 TGCTTTTTTCTCTT
1 T-TTTTTTTCTCTT
364849 TTT
1 TTT
364852 GTTCTTGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
12 1 0.03
13 21 0.58
14 14 0.39
ACGTcount: A:0.02, C:0.14, G:0.05, T:0.79
Consensus pattern (13 bp):
TTTTTTTTCTCTT
Found at i:372173 original size:21 final size:22
Alignment explanation
Indices: 372149--372193 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 22
372139 ATATCAAATT
*
372149 ATATGACAAAAT-TAATAGAAA
1 ATATGAAAAAATATAATAGAAA
* *
372170 ATATTAAAAAATATAATATAAA
1 ATATGAAAAAATATAATAGAAA
372192 AT
1 AT
372194 CCTTTTATGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.29
Consensus pattern (22 bp):
ATATGAAAAAATATAATAGAAA
Found at i:372932 original size:13 final size:13
Alignment explanation
Indices: 372916--372997 Score: 51
Period size: 15 Copynumber: 6.2 Consensus size: 13
372906 TAAAAATAAT
372916 TAATTTATATATA
1 TAATTTATATATA
* *
372929 TAATATTAATAAATT
1 TAAT-TT-ATATATA
*
372944 TAATTTAAAT-TA
1 TAATTTATATATA
**
372956 -AAAATATATATA
1 TAATTTATATATA
*
372968 TAATATTTATATATT
1 T-A-ATTTATATATA
*
372983 TAATTTAAATATA
1 TAATTTATATATA
372996 TA
1 TA
372998 TACCCGGCCC
Statistics
Matches: 50, Mismatches: 13, Indels: 12
0.67 0.17 0.16
Matches are distributed among these distances:
11 6 0.12
12 3 0.06
13 17 0.34
14 6 0.12
15 18 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
TAATTTATATATA
Found at i:373014 original size:12 final size:12
Alignment explanation
Indices: 372997--373027 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
372987 TTAAATATAT
372997 ATACCCGGCCCG
1 ATACCCGGCCCG
*
373009 ATACCCGGTCCG
1 ATACCCGGCCCG
373021 ATACCCG
1 ATACCCG
373028 TTTAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (12 bp):
ATACCCGGCCCG
Found at i:375054 original size:19 final size:19
Alignment explanation
Indices: 375017--375054 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
375007 GACTTTGTTA
375017 AATGATATTAAACTGCTTT
1 AATGATATTAAACTGCTTT
*
375036 AATGA-ATTTAACTGTCTTT
1 AATGATATTAAACTG-CTTT
375055 CAACTTTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.45
Consensus pattern (19 bp):
AATGATATTAAACTGCTTT
Found at i:379785 original size:16 final size:17
Alignment explanation
Indices: 379759--379790 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
379749 CAATATAGAA
379759 ATACTAGAATAGGTAGG
1 ATACTAGAATAGGTAGG
379776 ATACTA-AATAGGTAG
1 ATACTAGAATAGGTAG
379791 ATTATTCATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.44, C:0.06, G:0.25, T:0.25
Consensus pattern (17 bp):
ATACTAGAATAGGTAGG
Found at i:380295 original size:3 final size:3
Alignment explanation
Indices: 380287--380312 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
380277 ACTTCTCCGG
380287 CCT CCT CCT CCT CCT CCT CCT CCT CC
1 CCT CCT CCT CCT CCT CCT CCT CCT CC
380313 CCCAATCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.69, G:0.00, T:0.31
Consensus pattern (3 bp):
CCT
Found at i:389110 original size:32 final size:32
Alignment explanation
Indices: 389074--389141 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 32
389064 CTACCTCTAC
389074 TGTGCATTATCTGAATGTC-ATACGAACTATGT
1 TGTGCATTATCTGAATG-CAATACGAACTATGT
* *
389106 TGTGCATTATCTGAATGCAATACTAACTCTGT
1 TGTGCATTATCTGAATGCAATACGAACTATGT
389138 TGTG
1 TGTG
389142 ACTAATACAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
31 1 0.03
32 32 0.97
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.38
Consensus pattern (32 bp):
TGTGCATTATCTGAATGCAATACGAACTATGT
Found at i:389562 original size:22 final size:22
Alignment explanation
Indices: 389523--389565 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
389513 GTTGTAGCCA
* *
389523 TTTTTAGCTGCTATTACTACTG
1 TTTTTAACTGCTACTACTACTG
*
389545 TTTTTAACTGTTACTACTACT
1 TTTTTAACTGCTACTACTACT
389566 ATTTCTGTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.19, G:0.09, T:0.51
Consensus pattern (22 bp):
TTTTTAACTGCTACTACTACTG
Found at i:393276 original size:20 final size:23
Alignment explanation
Indices: 393237--393277 Score: 61
Period size: 20 Copynumber: 1.9 Consensus size: 23
393227 ATTAGGCATT
393237 TATTTGTCATTTTAGGACTTTTA
1 TATTTGTCATTTTAGGACTTTTA
393260 TATTT-TCA-TTT-GGACTTT
1 TATTTGTCATTTTAGGACTTT
393278 ATGCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 3 0.17
23 5 0.28
ACGTcount: A:0.20, C:0.10, G:0.12, T:0.59
Consensus pattern (23 bp):
TATTTGTCATTTTAGGACTTTTA
Found at i:393763 original size:14 final size:14
Alignment explanation
Indices: 393742--393776 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
393732 TTTACATTTC
393742 ACAATTTTT-ATAA
1 ACAATTTTTCATAA
*
393755 ATAATTTTTCATAA
1 ACAATTTTTCATAA
393769 ACAATTTT
1 ACAATTTT
393777 AAAGTATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 8 0.42
14 11 0.58
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (14 bp):
ACAATTTTTCATAA
Found at i:394705 original size:21 final size:21
Alignment explanation
Indices: 394661--394705 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
394651 ATTTAACTCG
* *
394661 TTTAGTACCTAAACTATCAGT
1 TTTAGTAACTAAACTATCAAT
* *
394682 TTTAGTAACTAAACTTTTAAT
1 TTTAGTAACTAAACTATCAAT
394703 TTT
1 TTT
394706 TTTAAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTAGTAACTAAACTATCAAT
Found at i:411797 original size:2 final size:2
Alignment explanation
Indices: 411790--411822 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
411780 AATGGATTGC
411790 AT AT AT AT A- AT AT GAT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT A
411823 ATTTACGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:412001 original size:13 final size:13
Alignment explanation
Indices: 411985--412033 Score: 80
Period size: 13 Copynumber: 3.8 Consensus size: 13
411975 GCTCAATGAA
411985 CGTCATAAATGTG
1 CGTCATAAATGTG
411998 CGTCATAAATGTG
1 CGTCATAAATGTG
* *
412011 TGTCATAAATGCG
1 CGTCATAAATGTG
412024 CGTCATAAAT
1 CGTCATAAAT
412034 TTATGACGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 33 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (13 bp):
CGTCATAAATGTG
Found at i:412008 original size:26 final size:26
Alignment explanation
Indices: 411979--412033 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
411969 AATGACGCTC
*
411979 AATGAACGTCATAAATGTGCGTCATA
1 AATGAACGTCATAAATGCGCGTCATA
***
412005 AATGTGTGTCATAAATGCGCGTCATA
1 AATGAACGTCATAAATGCGCGTCATA
412031 AAT
1 AAT
412034 TTATGACGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (26 bp):
AATGAACGTCATAAATGCGCGTCATA
Found at i:414645 original size:12 final size:12
Alignment explanation
Indices: 414628--414668 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
414618 TTATCTCTTG
414628 GAGAAGAAATGA
1 GAGAAGAAATGA
*
414640 GAGAAG-TA-GAA
1 GAGAAGAAATG-A
414651 GAGAAGAAATGA
1 GAGAAGAAATGA
414663 GAGAAG
1 GAGAAG
414669 TAGAAGAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 1 0.04
11 8 0.33
12 14 0.58
13 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (12 bp):
GAGAAGAAATGA
Found at i:414658 original size:23 final size:23
Alignment explanation
Indices: 414628--414682 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
414618 TTATCTCTTG
414628 GAGAAGAAATGAGAGAAGTAGAA
1 GAGAAGAAATGAGAGAAGTAGAA
414651 GAGAAGAAATGAGAGAAGTAGAA
1 GAGAAGAAATGAGAGAAGTAGAA
414674 GAGAAGAAA
1 GAGAAGAAA
414683 AAGACAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.58, C:0.00, G:0.35, T:0.07
Consensus pattern (23 bp):
GAGAAGAAATGAGAGAAGTAGAA
Found at i:423366 original size:244 final size:244
Alignment explanation
Indices: 422934--423423 Score: 885
Period size: 244 Copynumber: 2.0 Consensus size: 244
422924 CTATGGGGCA
*
422934 AGATAAAGCTGCCTCAAAGTCCTTATGGTATCCCTCAACCACTGATTGGTCGAAATCAGATCATC
1 AGATAAAGCTGCCTCAAAGTCCTTATGGTATCCCTCAACCACTGATCGGTCGAAATCAGATCATC
422999 ATCGCCTGAACCGTATAAGTCAACTGTTATACCTACTCAGTCTCTCTACTGGGGTCTCGACTGAA
66 ATCGCCTGAACCGTATAAGTCAACTGTTATACCTACTCAGTCTCTCTACTGGGGTCTCGACTGAA
*
423064 ACTAGCGTACTCTCCATCCTATCCTCAAAACCACACTATAAACTATCGACCATCGCAA-CTCTAC
131 ACTAGCGTACTCTCCATCCTATCCTCAAAACCACACTATAAACTATCGACCATCGCAACCACTAC
*
423128 AACACAGATTAAGAAAGGA-CACCGTCAGAATTCCAGACTAATTCAAGT
196 AACACAGATTAAGAAAGGAGCACCATCAGAATTCCAGACTAATTCAAGT
*
423176 AGATGAAGCTGCCTCAAAGTCCTTATGGTATCCCTCAACCACTGATCGGTCGAAATCAGATCATC
1 AGATAAAGCTGCCTCAAAGTCCTTATGGTATCCCTCAACCACTGATCGGTCGAAATCAGATCATC
423241 ATCGCCTGAACCGTATAAGTCAACTGTCTTATACCTACTCAGTCTCTCTACTGGGGTCTCGACTG
66 ATCGCCTGAACCGTATAAGTCAACTG--TTATACCTACTCAGTCTCTCTACTGGGGTCTCGACTG
*
423306 AAACTAGCGTACTCTCCATCCTATCCTCAAAACCACACTATAAACTATCGGCCATCGCAACGCAC
129 AAACTAGCGTACTCTCCATCCTATCCTCAAAACCACACTATAAACTATCGACCATCGCAAC-CAC
*
423371 TACAACATAGATTAAGAAAGGAGCACCATCAGAATTCCAGACTAATTCAAGT
193 TACAACACAGATTAAGAAAGGAGCACCATCAGAATTCCAGACTAATTCAAGT
423423 A
1 A
423424 CTTTAAGTAC
Statistics
Matches: 237, Mismatches: 6, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
242 89 0.38
244 96 0.41
246 23 0.10
247 29 0.12
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (244 bp):
AGATAAAGCTGCCTCAAAGTCCTTATGGTATCCCTCAACCACTGATCGGTCGAAATCAGATCATC
ATCGCCTGAACCGTATAAGTCAACTGTTATACCTACTCAGTCTCTCTACTGGGGTCTCGACTGAA
ACTAGCGTACTCTCCATCCTATCCTCAAAACCACACTATAAACTATCGACCATCGCAACCACTAC
AACACAGATTAAGAAAGGAGCACCATCAGAATTCCAGACTAATTCAAGT
Found at i:434117 original size:23 final size:22
Alignment explanation
Indices: 434089--434169 Score: 67
Period size: 23 Copynumber: 3.6 Consensus size: 22
434079 GCATGGCCTT
434089 GTGCATCGATGCACATTCAAGA
1 GTGCATCGATGCACATTCAAGA
* * *
434111 CGTGCATCGGTTCATC-TTCATGA
1 -GTGCATCGATGCA-CATTCAAGA
* *
434134 -TGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGA
434156 GATGCATCGATGCA
1 G-TGCATCGATGCA
434170 TTATGCACAA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
20 1 0.02
21 12 0.27
22 2 0.05
23 17 0.39
24 12 0.27
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGA
Found at i:444218 original size:54 final size:54
Alignment explanation
Indices: 444160--444563 Score: 614
Period size: 54 Copynumber: 7.5 Consensus size: 54
444150 TAAACTCATT
* ** **
444160 ATGAATTTTGTGGGTTGCACAGATAGTGCCGAAATGGTTATTCATCAACATATG
1 ATGAATTTCGTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
*
444214 ATGAATTTCGTGAATTGCACACTTAGTGCCGAAACGGTTATTCATCAACATATG
1 ATGAATTTCGTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
* ** *
444268 ATGAATTTCGTGAATTGTACACTTAGTGGTGAAATGGTTATTCATCAACATATA
1 ATGAATTTCGTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
444322 ATGAATTTCGTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
1 ATGAATTTCGTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
** *
444376 ATGAA-TTCTGTGAATTGCACACTTAGTGGTGAAATAGTTATTCATCAACATATG
1 ATGAATTTC-GTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
* *
444430 ATGAATTTCGTGAATTGTACACTTAGTGCCGAAACGGTTATTCATCAACATATG
1 ATGAATTTCGTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
* *
444484 ATGAATTCCGTGAATTACACACTTAGTGCCGAAA-GGTTATTCATCAACATATG
1 ATGAATTTCGTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
* *
444537 ATGAATTCCGTAAATTGCACACTTAGT
1 ATGAATTTCGTGAATTGCACACTTAGT
444564 TCCTATTTGG
Statistics
Matches: 320, Mismatches: 28, Indels: 5
0.91 0.08 0.01
Matches are distributed among these distances:
53 47 0.15
54 270 0.84
55 3 0.01
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (54 bp):
ATGAATTTCGTGAATTGCACACTTAGTGCCGAAATGGTTATTCATCAACATATG
Found at i:444434 original size:26 final size:26
Alignment explanation
Indices: 444352--444434 Score: 62
Period size: 26 Copynumber: 3.1 Consensus size: 26
444342 ACTTAGTGCC
*
444352 GAAATGGTTATTCATCAACATATGAT
1 GAAATAGTTATTCATCAACATATGAT
* * * * *
444378 GAATTCTGTGAATTGCA-C-ACTTAGTGGT
1 GAAAT-AGT-TATT-CATCAACATA-TGAT
444406 GAAATAGTTATTCATCAACATATGAT
1 GAAATAGTTATTCATCAACATATGAT
444432 GAA
1 GAA
444435 TTTCGTGAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 12
0.65 0.16 0.19
Matches are distributed among these distances:
25 2 0.05
26 14 0.34
27 12 0.29
28 11 0.27
29 2 0.05
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (26 bp):
GAAATAGTTATTCATCAACATATGAT
Found at i:444643 original size:15 final size:15
Alignment explanation
Indices: 444623--444652 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
444613 CTAGTATAAC
444623 ATATAGTTACACAAT
1 ATATAGTTACACAAT
444638 ATATAGTTACACAAT
1 ATATAGTTACACAAT
444653 TAAATGCACT
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:0.47, C:0.13, G:0.07, T:0.33
Consensus pattern (15 bp):
ATATAGTTACACAAT
Found at i:444932 original size:20 final size:21
Alignment explanation
Indices: 444904--444960 Score: 71
Period size: 22 Copynumber: 2.7 Consensus size: 21
444894 TGGCTCAATA
*
444904 GTATCGATACTC-CTACCATG
1 GTATCGATACTCTATACCATG
* *
444924 GTATTGATACTACTATACTATG
1 GTATCGATACT-CTATACCATG
444946 GTATCGATACTCTAT
1 GTATCGATACTCTAT
444961 TAGGGTATCG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 10 0.32
21 5 0.16
22 16 0.52
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (21 bp):
GTATCGATACTCTATACCATG
Found at i:444967 original size:19 final size:20
Alignment explanation
Indices: 444904--444974 Score: 72
Period size: 19 Copynumber: 3.5 Consensus size: 20
444894 TGGCTCAATA
* **
444904 GTATCGATACTCCTACCATG
1 GTATCGATACTACTATTATG
*
444924 GTATTGATACTACTATACTATG
1 GTATCGATACTACTAT--TATG
*
444946 GTATCGATACT-CTATTAGG
1 GTATCGATACTACTATTATG
444965 GTATCGATAC
1 GTATCGATAC
444975 CATTTTTACA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 13 0.30
20 13 0.30
21 4 0.09
22 13 0.30
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (20 bp):
GTATCGATACTACTATTATG
Found at i:483028 original size:20 final size:20
Alignment explanation
Indices: 482985--483031 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
482975 AATTGTTTTA
* ***
482985 TGGTTTCGAAACTCCCTTGT
1 TGGTTTCGAAACCCCCTAAC
483005 TGGTTTCGAAACCCCCTAAC
1 TGGTTTCGAAACCCCCTAAC
483025 TGGTTTC
1 TGGTTTC
483032 TAAATCGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.17, C:0.28, G:0.19, T:0.36
Consensus pattern (20 bp):
TGGTTTCGAAACCCCCTAAC
Found at i:492358 original size:40 final size:40
Alignment explanation
Indices: 492285--492364 Score: 99
Period size: 40 Copynumber: 1.9 Consensus size: 40
492275 GGGAAGTTCG
* *
492285 TTTTTGTTCGTTTATTTATTAAACGAACGAACATGAACAATA
1 TTTTTGTTCGTTTA--TATTAAACGAACAAACATAAACAATA
*
492327 TTTTGTGTTCGTTTA-ATTAAATGAACAAACATAAACAA
1 TTTT-TGTTCGTTTATATTAAACGAACAAACATAAACAA
492365 AAGGCTTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 20 0.59
42 4 0.12
43 10 0.29
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (40 bp):
TTTTTGTTCGTTTATATTAAACGAACAAACATAAACAATA
Found at i:492632 original size:20 final size:20
Alignment explanation
Indices: 492595--492632 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
492585 AAAATCTATT
* *
492595 TTCATTTATGTTCGTTTACG
1 TTCATTTATGTCCATTTACG
492615 TTCATTTATGTCCATTTA
1 TTCATTTATGTCCATTTA
492633 TTGTCTTTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.16, G:0.11, T:0.55
Consensus pattern (20 bp):
TTCATTTATGTCCATTTACG
Found at i:492633 original size:10 final size:10
Alignment explanation
Indices: 492595--492633 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
492585 AAAATCTATT
492595 TTCATTTATG
1 TTCATTTATG
* *
492605 TTCGTTTACG
1 TTCATTTATG
492615 TTCATTTATG
1 TTCATTTATG
*
492625 TCCATTTAT
1 TTCATTTAT
492634 TGTCTTTGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.18, C:0.15, G:0.10, T:0.56
Consensus pattern (10 bp):
TTCATTTATG
Found at i:492668 original size:24 final size:23
Alignment explanation
Indices: 492641--492721 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 23
492631 TATTGTCTTT
492641 GTTTATGTTCGTTCATTTGTATTC
1 GTTTATGTTCGTTCATTTGT-TTC
*
492665 GTTTATTATGTTCGTTTACATATG-TTC
1 G--T-TTATGTTCG-TT-CATTTGTTTC
*
492692 GTTTACGTTCGTTCATTTGTGTTC
1 GTTTATGTTCGTTCATTTGT-TTC
492716 GTTTAT
1 GTTTAT
492722 CATTTAAATG
Statistics
Matches: 46, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
22 5 0.11
23 2 0.04
24 17 0.37
25 1 0.02
26 1 0.02
27 13 0.28
28 2 0.04
29 5 0.11
ACGTcount: A:0.14, C:0.12, G:0.17, T:0.57
Consensus pattern (23 bp):
GTTTATGTTCGTTCATTTGTTTC
Found at i:492705 original size:14 final size:14
Alignment explanation
Indices: 492662--492697 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
492652 TTCATTTGTA
*
492662 TTCGTTTA-TTATG
1 TTCGTTTACATATG
492675 TTCGTTTACATATG
1 TTCGTTTACATATG
492689 TTCGTTTAC
1 TTCGTTTAC
492698 GTTCGTTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.56
Consensus pattern (14 bp):
TTCGTTTACATATG
Found at i:493397 original size:64 final size:63
Alignment explanation
Indices: 493323--493444 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 63
493313 TCCAAAAAAT
* * * *
493323 TGAATCGAATCGAAACCGACACGAATTCTAGCTAAACCGAAAGTAA-ATCAAACTGAAAATAACC
1 TGAACCGAATCAAAACCAACACGAATTCTAGCCAAACCGAAAGTAACAT-AAACT-AAAATAACC
* *
493387 TGAACCGAATCAAAACCAACCCGAATTTTAGCCAAACCGAAAGTAACATAAACTAAAA
1 TGAACCGAATCAAAACCAACACGAATTCTAGCCAAACCGAAAGTAACATAAACTAAAA
493445 GCAACCCGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
63 4 0.08
64 45 0.88
65 2 0.04
ACGTcount: A:0.48, C:0.23, G:0.12, T:0.16
Consensus pattern (63 bp):
TGAACCGAATCAAAACCAACACGAATTCTAGCCAAACCGAAAGTAACATAAACTAAAATAACC
Found at i:493932 original size:19 final size:20
Alignment explanation
Indices: 493888--493933 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
493878 ATTTTTATTT
493888 TCTATTTTTAATTTAAATAA
1 TCTATTTTTAATTTAAATAA
*
493908 T-AATTTATTAATTT-AAT-A
1 TCTATTT-TTAATTTAAATAA
493926 TCTATTTT
1 TCTATTTT
493934 AGATTTCATT
Statistics
Matches: 22, Mismatches: 2, Indels: 6
0.73 0.07 0.20
Matches are distributed among these distances:
18 3 0.14
19 11 0.50
20 8 0.36
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (20 bp):
TCTATTTTTAATTTAAATAA
Found at i:498321 original size:22 final size:24
Alignment explanation
Indices: 498293--498337 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
498283 TGTTTGTGTG
498293 CTTCATTT-G-ATATATAATATAA
1 CTTCATTTAGTATATATAATATAA
*
498315 CTTCATTTAGTATATATATTATA
1 CTTCATTTAGTATATATAATATA
498338 CCAATAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 1 0.05
24 11 0.55
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (24 bp):
CTTCATTTAGTATATATAATATAA
Found at i:502859 original size:45 final size:45
Alignment explanation
Indices: 502808--502912 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
502798 TAATCCAATG
* * *
502808 CTTTTGATTATTGGGCTATCAAAAGTAAAATCAAATGATTGATTC
1 CTTTTGATTATTGGGCTATCAAAAGTAAAATCAAATAATTAAATC
* * * * *
502853 CTTTTGATTATTGTGTTGTCGAAATTAAAATCAAATAATTAAATC
1 CTTTTGATTATTGGGCTATCAAAAGTAAAATCAAATAATTAAATC
502898 CTTTTGATTATTGGG
1 CTTTTGATTATTGGG
502913 TTGCTAAACT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (45 bp):
CTTTTGATTATTGGGCTATCAAAAGTAAAATCAAATAATTAAATC
Found at i:502926 original size:45 final size:43
Alignment explanation
Indices: 502808--502926 Score: 123
Period size: 45 Copynumber: 2.6 Consensus size: 43
502798 TAATCCAATG
* * * *
502808 CTTTTGATTATTGGGCTAT-CAAAAGTAAAATCAAATGATTGATTC
1 CTTTTGATTATTGGG-T-TGC-AAATTAAAATCAAATAATTAAATC
*
502853 CTTTTGATTATTGTGTTGTCGAAATTAAAATCAAATAATTAAATC
1 CTTTTGATTATTGGGTTG-C-AAATTAAAATCAAATAATTAAATC
502898 CTTTTGATTATTGGGTTGCTAAACTTAAA
1 CTTTTGATTATTGGGTTGC-AAA-TTAAA
502927 GGATTAATTC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 5 0.08
45 57 0.90
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.41
Consensus pattern (43 bp):
CTTTTGATTATTGGGTTGCAAATTAAAATCAAATAATTAAATC
Found at i:503419 original size:58 final size:58
Alignment explanation
Indices: 503091--503496 Score: 349
Period size: 58 Copynumber: 7.0 Consensus size: 58
503081 TCTTGTGTAT
* * * * * *
503091 ATTCTAACTTTGTAAGGGAAATAAATTATTGAATTTATTTTTTTTGAAAATCTTAAAAG
1 ATTCTAACTTTGTAAGGAAAATAAATTATTAAATTTA-TTTTCTTGAGAATCTTGAATG
* * * * * * * *
503150 ATTCTAAATTTGTAAGGAAAATAAATCATTGAATTTCTTTCCTCGAGAATCTAGAACG
1 ATTCTAACTTTGTAAGGAAAATAAATTATTAAATTTATTTTCTTGAGAATCTTGAATG
* * * * * *
503208 ATTATAACTTTATTAA-GAAAATAAATTGTTGAATTTA-TTTCATTGTGAATTTTGAATG
1 ATTCTAACTTT-GTAAGGAAAATAAATTATTAAATTTATTTTC-TTGAGAATCTTGAATG
* * * * * * *
503266 GTTCTAACTTTCTAAGAAAAATAAA-TAGTTAAATTTATTTCCTGGAGATTCTTAAATG
1 ATTCTAACTTTGTAAGGAAAATAAATTA-TTAAATTTATTTTCTTGAGAATCTTGAATG
* *
503324 ATTCTAACTTTGTAATGAAAATAAA-TAGTTAACTTTATTTTCTTGAGAATCTTGAATG
1 ATTCTAACTTTGTAAGGAAAATAAATTA-TTAAATTTATTTTCTTGAGAATCTTGAATG
* * * * *
503382 ATTCTAACTTCGTAAGGAAAATAAATTATCT-AGTTTATTTTCTTGAGGATCGTGGATG
1 ATTCTAACTTTGTAAGGAAAATAAATTAT-TAAATTTATTTTCTTGAGAATCTTGAATG
* * **
503440 ATTTTATCTTT-TAAAAAGAAATAAATTATTAAATTTATTTTCTT-AGGAATCTTGAAT
1 ATTCTAACTTTGTAAGGA-AAATAAATTATTAAATTTATTTTCTTGA-GAATCTTGAAT
503497 TAAAAAAAAA
Statistics
Matches: 278, Mismatches: 59, Indels: 21
0.78 0.16 0.06
Matches are distributed among these distances:
57 13 0.05
58 223 0.80
59 42 0.15
ACGTcount: A:0.37, C:0.08, G:0.13, T:0.42
Consensus pattern (58 bp):
ATTCTAACTTTGTAAGGAAAATAAATTATTAAATTTATTTTCTTGAGAATCTTGAATG
Found at i:503523 original size:44 final size:46
Alignment explanation
Indices: 503450--503536 Score: 133
Period size: 44 Copynumber: 1.9 Consensus size: 46
503440 ATTTTATCTT
* *
503450 TTAAAAAGAAATAAATTATTAAATTTATTTTCTTAGGAATCTTGAA
1 TTAAAAAGAAAAAAAATATTAAATTTATTTTCTTAGGAATCTTGAA
*
503496 TTAAAAA-AAAAAAAAT-TTAAATTTATTTTCTTATGAATCTT
1 TTAAAAAGAAAAAAAATATTAAATTTATTTTCTTAGGAATCTT
503537 TAATGATTCT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 24 0.63
45 7 0.18
46 7 0.18
ACGTcount: A:0.47, C:0.05, G:0.06, T:0.43
Consensus pattern (46 bp):
TTAAAAAGAAAAAAAATATTAAATTTATTTTCTTAGGAATCTTGAA
Found at i:503604 original size:39 final size:39
Alignment explanation
Indices: 503545--503625 Score: 119
Period size: 39 Copynumber: 2.1 Consensus size: 39
503535 TTTAATGATT
*
503545 CTATCTTGTAAAATGAAATAAATCCTTAGATTTATTTTC
1 CTATCTTGTAAAATGAAATAAATCCTTAAATTTATTTTC
* *
503584 CTATTTTGTAAAA-GAAAATAAATCGTTAAATTTATTTTC
1 CTATCTTGTAAAATG-AAATAAATCCTTAAATTTATTTTC
503623 CTA
1 CTA
503626 AGAATCTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.43
Consensus pattern (39 bp):
CTATCTTGTAAAATGAAATAAATCCTTAAATTTATTTTC
Found at i:503654 original size:97 final size:98
Alignment explanation
Indices: 503512--503702 Score: 289
Period size: 97 Copynumber: 2.0 Consensus size: 98
503502 AAAAAAAAAT
* * *
503512 TTAAATTTATTTTCTTATGAATCTTTAATGATTCTATCTTGTAAAATGAAATAAATCCTTA-GAT
1 TTAAATTTATTTTCCTAAGAATCTTTAATGATTCTATCTTGTAAAATGAAATAAAT-CGTAGGAT
*
503576 TTA-TTTTCCTATTTTGTAAAAGAAAATAAATCG
65 TTATTTTTCCTATTTTGAAAAAGAAAATAAATCG
* *
503609 TTAAATTTATTTTCCTAAGAATC-TTATATGATTCTATTTTTTAAAATGAAATAAATCGTAGGAT
1 TTAAATTTATTTTCCTAAGAATCTTTA-ATGATTCTATCTTGTAAAATGAAATAAATCGTAGGAT
503673 TTATTTTTCCTATTTTGAAAAAGAAAATAA
65 TTATTTTTCCTATTTTGAAAAAGAAAATAA
503703 TTTTTTTTTA
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
96 6 0.07
97 54 0.64
98 25 0.29
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (98 bp):
TTAAATTTATTTTCCTAAGAATCTTTAATGATTCTATCTTGTAAAATGAAATAAATCGTAGGATT
TATTTTTCCTATTTTGAAAAAGAAAATAAATCG
Found at i:503826 original size:57 final size:58
Alignment explanation
Indices: 503745--503875 Score: 144
Period size: 59 Copynumber: 2.3 Consensus size: 58
503735 TAAATCGATG
* *
503745 AATTTATTTTCTTGAAGATTAAGTATGA-CTATACT-TAAAAAAGGAAATAAATTATTT
1 AATTTATTTTCTTGAAGATCAAGTATGATCTATACTGTAAAAAA-GAAATAAATTATTA
* ** * *
503802 AATTTATTTTCTT-TAGAATCAAGTATGATTCTATTTTGTAAGAAAGAAATAAATTGTTA
1 AATTTATTTTCTTGAAG-ATCAAGTATGA-TCTATACTGTAAAAAAGAAATAAATTATTA
503861 AATTTA-TTTCTTGAA
1 AATTTATTTTCTTGAA
503876 AATCTCGATA
Statistics
Matches: 61, Mismatches: 8, Indels: 8
0.79 0.10 0.10
Matches are distributed among these distances:
56 2 0.03
57 23 0.38
58 6 0.10
59 24 0.39
60 6 0.10
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (58 bp):
AATTTATTTTCTTGAAGATCAAGTATGATCTATACTGTAAAAAAGAAATAAATTATTA
Found at i:504866 original size:15 final size:15
Alignment explanation
Indices: 504846--504901 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
504836 AACCATGCAG
504846 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
504861 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
504877 TGGGGGAATCTGTTCCC
1 --GGGGAATCTGTACCC
*
504894 GCGGAATC
1 GGGGAATC
504902 GATACCCCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 1 0.03
15 17 0.50
16 3 0.09
17 3 0.09
18 9 0.26
19 1 0.03
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.20
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:504921 original size:20 final size:21
Alignment explanation
Indices: 504896--504950 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
504886 CTGTTCCCGC
504896 GGAATC-GATACCCCCT-GGGG
1 GGAATCTG-TACCCCCTGGGGG
*
504916 GGAATCTGTTCCCCCTGGGGG
1 GGAATCTGTACCCCCTGGGGG
504937 GGAATCTGTACCCC
1 GGAATCTGTACCCC
504951 TTGGACAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 13 0.42
21 18 0.58
ACGTcount: A:0.16, C:0.31, G:0.33, T:0.20
Consensus pattern (21 bp):
GGAATCTGTACCCCCTGGGGG
Found at i:504924 original size:35 final size:33
Alignment explanation
Indices: 504845--504928 Score: 132
Period size: 33 Copynumber: 2.5 Consensus size: 33
504835 AAACCATGCA
* *
504845 GGGGGAATCTGTACCCGGGGAATCGATACCCCT
1 GGGGGAATCTGTTCCCGCGGAATCGATACCCCT
504878 GGGGGAATCTGTTCCCGCGGAATCGATACCCCCT
1 GGGGGAATCTGTTCCCGCGGAATCGATA-CCCCT
504912 GGGGGGAATCTGTTCCC
1 -GGGGGAATCTGTTCCC
504929 CCTGGGGGGG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
33 26 0.55
34 5 0.11
35 16 0.34
ACGTcount: A:0.18, C:0.29, G:0.33, T:0.20
Consensus pattern (33 bp):
GGGGGAATCTGTTCCCGCGGAATCGATACCCCT
Found at i:507912 original size:34 final size:32
Alignment explanation
Indices: 507852--507922 Score: 88
Period size: 34 Copynumber: 2.2 Consensus size: 32
507842 CCTTACAAAC
*
507852 TCCCTAGTTTTTCCGGGATAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGATAAACTAGAACCTT
* *
507884 TCCCTAGCTTTTACACGGGATTAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGGGATAAACTAGAACCTT
*
507918 CCCCT
1 TCCCT
507923 TTACAAATGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.15, T:0.32
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGATAAACTAGAACCTT
Done.