Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015039.1 Kokia drynarioides strain JFW-HI SEQ_130083, 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: 570965
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Warning! 437 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:374707 original size:30 final size:29
Alignment explanation
Indices: 374671--374747 Score: 101
Period size: 24 Copynumber: 2.8 Consensus size: 29
374661 CCTTCTCTTT
374671 CTTCTCTTTCTCTTTTCGTTCACGTGCCTC
1 CTTCTCTTTCTC-TTTCGTTCACGTGCCTC
374701 CTTCTC--T-TC--TCGTTCACGTGCCTC
1 CTTCTCTTTCTCTTTCGTTCACGTGCCTC
374725 CTTCTCTTTCTCTTCTCGTTCAC
1 CTTCTCTTTCTCTT-TCGTTCAC
374748 AAGCTTCCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
24 21 0.51
26 1 0.02
27 4 0.10
28 1 0.02
30 14 0.34
ACGTcount: A:0.04, C:0.39, G:0.09, T:0.48
Consensus pattern (29 bp):
CTTCTCTTTCTCTTTCGTTCACGTGCCTC
Found at i:374757 original size:30 final size:28
Alignment explanation
Indices: 374671--374757 Score: 83
Period size: 30 Copynumber: 3.1 Consensus size: 28
374661 CCTTCTCTTT
* *
374671 CTTCTCTTTCTCTTTTCGTTCACG-TGC
1 CTTCTCTTTCTCTTCTCGTTCACGCTTC
*
374698 C-TC-C-TTCTCTTCTCGTTCACGTGCCTC
1 CTTCTCTTTCTCTTCTCGTTCAC--GCTTC
374725 CTTCTCTTTCTCTTCTCGTTCACAAGCTTC
1 CTTCTCTTTCTCTTCTCGTTCAC--GCTTC
374755 CTT
1 CTT
374758 TAATCTCTTC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
24 15 0.31
25 1 0.02
26 3 0.06
27 3 0.06
28 2 0.04
29 1 0.02
30 23 0.48
ACGTcount: A:0.06, C:0.38, G:0.09, T:0.47
Consensus pattern (28 bp):
CTTCTCTTTCTCTTCTCGTTCACGCTTC
Found at i:374769 original size:39 final size:39
Alignment explanation
Indices: 374725--375360 Score: 689
Period size: 39 Copynumber: 16.4 Consensus size: 39
374715 CACGTGCCTC
* *
374725 CTTCTCTTTCTCTTCTCGTTCACAAGCTTCCTTTAATCT
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* * *
374764 CTTCTCATTCTCTTCTCGTTCACAAGCTTCCTTTAATCT
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* * *
374803 CTTCTCATTCTCTTCTCGTTCACAAGCTTCCTTCAATTT
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* * *
374842 CTTCTCTTTCTCTTCTCGTTCATGTGCCTCCTTC--TCTT
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATC-T
374880 CCTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTC--TCTT
1 -CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATC-T
** * **
374919 CCTTCTCAATCTCTTCTCGTTCACCAATTTCCTTCAATCT
1 -CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* **
374959 CTTCTCATTCTCTTCTCGTTCACGAATTTCCTTCAATCT
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* * *
374998 CCTCTCATTCTCTTCTCTTTCACGAGCTTCCTTCAAT-T
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* * * ** *
375036 CCTTCTCTTTCTCTTCTCGTTCATGTGCCTCCTTCTCTTT
1 -CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* * * *
375076 CTTCTCTTTCTCTTCTTGCTCACGAGCCTCCCTCAATCT
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* *
375115 CTTCTCATTATCTTCTCGTTCACGAGCTTCCTTCAAGT-T
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAA-TCT
* * *
375154 CTTCTCTTTCTCTTCTCGTTCTCGAGCCTCCATCAATCT
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* * *
375193 CTTCTCATTCTCTTCTCGTTCACGAGCCTCCCTCAATCT
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* * *
375232 CTTCTCATTCTCTTCCCGTTCACGAGCTTCCTTCAATTT
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* * * *
375271 CTTCTCTTTCTCTTCTAGTTCACGTGCCTCC-TC--TTT
1 CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
* *
375307 CTTC-CTTCTCTCTTCTCGTTCATGAGCTTCCTTCAATTT
1 CTTCTCTT-TCTCTTCTCGTTCACGAGCTTCCTTCAATCT
*
375346 TTTCTCTTTCTCTTC
1 CTTCTCTTTCTCTTC
375361 CTGCTCAACA
Statistics
Matches: 517, Mismatches: 67, Indels: 26
0.85 0.11 0.04
Matches are distributed among these distances:
35 3 0.01
36 26 0.05
37 3 0.01
38 5 0.01
39 472 0.91
40 6 0.01
41 2 0.00
ACGTcount: A:0.11, C:0.36, G:0.07, T:0.47
Consensus pattern (39 bp):
CTTCTCTTTCTCTTCTCGTTCACGAGCTTCCTTCAATCT
Found at i:378274 original size:6 final size:6
Alignment explanation
Indices: 378263--378290 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
378253 ACTGAGAGAG
378263 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
378291 CAAAATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:378419 original size:2 final size:2
Alignment explanation
Indices: 378412--378445 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
378402 AAAGAAAGAA
* *
378412 AG AG AG AG AG AG AG CG AG AG CG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
378446 TCAGAGGAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.44, C:0.06, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:378796 original size:27 final size:27
Alignment explanation
Indices: 378757--378811 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
378747 CCTACAATTT
* *
378757 TAAAAAATTATA-TCAATTCTTAAAAA
1 TAAAAAATTATATTAAATTATTAAAAA
378783 TAAAAAATATATATTAAATTATTAAAAA
1 TAAAAAAT-TATATTAAATTATTAAAAA
378811 T
1 T
378812 CATGAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 8 0.32
27 4 0.16
28 13 0.52
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (27 bp):
TAAAAAATTATATTAAATTATTAAAAA
Found at i:386363 original size:28 final size:29
Alignment explanation
Indices: 386319--386373 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
386309 AAGTTCAATA
*
386319 TTAACTGCTTATTTAATT-TAATTTAATT
1 TTAACTGCTTATATAATTGTAATTTAATT
386347 TTAACTG-TTAATATAATTGTAATTTAA
1 TTAACTGCTT-ATATAATTGTAATTTAA
386374 AATATTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 2 0.08
28 14 0.58
29 8 0.33
ACGTcount: A:0.36, C:0.05, G:0.05, T:0.53
Consensus pattern (29 bp):
TTAACTGCTTATATAATTGTAATTTAATT
Found at i:387464 original size:14 final size:14
Alignment explanation
Indices: 387445--387471 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
387435 TATATTTATT
387445 TCTTTGCCAGTTTG
1 TCTTTGCCAGTTTG
387459 TCTTTGCCAGTTT
1 TCTTTGCCAGTTT
387472 AGCAACTATG
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:0.07, C:0.22, G:0.19, T:0.52
Consensus pattern (14 bp):
TCTTTGCCAGTTTG
Found at i:389915 original size:358 final size:354
Alignment explanation
Indices: 389260--389959 Score: 994
Period size: 358 Copynumber: 2.0 Consensus size: 354
389250 ATACAAAACT
*
389260 GGGAACTTTTACATCAATATCATTTCCAATAGGAACAACAAAAATGGATGGATAAAGGTTCGGTC
1 GGGAACTTTTACATCAATATCATTTCCAATAGGAACAACAAAAATGAATGGATAAAGGTTCGGTC
* * *
389325 ATGAATTTCTGAAGTCTTGTGTCAATTTGAGAGCTAGATAATAACTAACCTACGAGATTCATATT
66 ATGAATTTCTAAAGTCTTGTATCAATTCGAGAGCTAGATAATAACTAA-C-ACGAGATTCATATT
* * *
389390 TTCATTCGTCATGAAAGCAACATGATCCAACATGTAGTGAATTATAGCTTGTGTTAAATGAACAT
129 TTCATTCATCATGAAAGCAACATGATCCAACACGTAGTGAATTATAGCTTATGTTAAATGAACAT
* ** * * * *
389455 ACCAGTTTTGGTCATTAATCATACACAATTTAGTTTCATTATAAGTTTCTAGCGAATTCCAGTAC
194 ACCAGTTTGGGTCATTAATCATACACAAGATAGTTTCATCATAAGTTTCTAGCAAACTCCAGCAC
* *
389520 CGTCACTCAAAAATTCTTAATTCTGAACTTGCACAGAAAATTCAATTTAACTTCCTAACACACAT
259 CATCACTCAAAAATTCTTAATTCTGAACTTACACAGAAAATTCAATTTAACTTCCTAACACACAT
389585 ATATGATG-GAACAAAGGGAAGTGTCGAAGCC
324 ATATGA-GAGAACAAAGGGAAGTGTCGAAGCC
* ** *
389616 GGGAACTTTTACATCAATCTCATTTTTAATAGGAACAACAAAAATGAATGGATCAAGGTTCATCC
1 GGGAACTTTTACATCAATATCATTTCCAATAGGAACAACAAAAATGAATGGATAAAGG-T--T-C
* * * *
389681 GGTCATGAATTTCTAAAGTCTCT-TATTACTTCGAGAGCTAGATAATTACTAGA-ATGAGATTCA
62 GGTCATGAATTTCTAAAGTCT-TGTATCAATTCGAGAGCTAGATAATAACTA-ACACGAGATTCA
* * *
389744 TATTTTTATTCATCATGAGAGCAACATGATCCAACACGTTGTGAATTATAGCTTATGTTAAATGA
125 TATTTTCATTCATCATGAAAGCAACATGATCCAACACGTAGTGAATTATAGCTTATGTTAAATGA
*
389809 ACATACC-GCTTTGGGTCATTAATCATACACAAGATAGTTTGATCATAAGTTTCTAGCAAACTCC
190 ACATACCAG-TTTGGGTCATTAATCATACACAAGATAGTTTCATCATAAGTTTCTAGCAAACTCC
* * * *
389873 AGCCCCATCACTCAAAAATTCTTAATTCTGAATTTACACAGAAAATTCAATTTAACTTGCTAACG
254 AGCACCATCACTCAAAAATTCTTAATTCTGAACTTACACAGAAAATTCAATTTAACTTCCTAACA
389938 CACATATATGAGAGAACAAAGG
319 CACATATATGAGAGAACAAAGG
389960 AAGAGACAAA
Statistics
Matches: 304, Mismatches: 32, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
356 53 0.17
357 3 0.01
358 201 0.66
359 1 0.00
360 44 0.14
361 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.31
Consensus pattern (354 bp):
GGGAACTTTTACATCAATATCATTTCCAATAGGAACAACAAAAATGAATGGATAAAGGTTCGGTC
ATGAATTTCTAAAGTCTTGTATCAATTCGAGAGCTAGATAATAACTAACACGAGATTCATATTTT
CATTCATCATGAAAGCAACATGATCCAACACGTAGTGAATTATAGCTTATGTTAAATGAACATAC
CAGTTTGGGTCATTAATCATACACAAGATAGTTTCATCATAAGTTTCTAGCAAACTCCAGCACCA
TCACTCAAAAATTCTTAATTCTGAACTTACACAGAAAATTCAATTTAACTTCCTAACACACATAT
ATGAGAGAACAAAGGGAAGTGTCGAAGCC
Found at i:405633 original size:204 final size:199
Alignment explanation
Indices: 405250--405765 Score: 551
Period size: 204 Copynumber: 2.6 Consensus size: 199
405240 TTCTATATTT
** * * * *
405250 CCAAAATGCAGCTTAG-GTACAATCTTAACTCTAGACTGCCCTATGTGAAACAAAACCTAGTTCA
1 CCAAAATGCAGCTTAGACAACAATCTCAACTATAGACTGTCCTATGTG-AACAAAACCGAGTT-A
* * * *
405314 --A-CAATAGTTTTGTCTTAAACTAAGATAGAACACAATTTCTCAGCTAAAGATGCCCTATGTAT
64 TGATCCA-A--TTGGCCTTAAACTAAGACAGAACACAATTTCTCAGCTAAAGATGCCCTATGTAT
* * * **
405376 TTGCCGACCGTGCCACGGCCAGATATTGTATCCGTTCGGCTTGAACGGTAATCTCTCCCCAGAAT
126 TTGCCGACCGCGCCACGGCCAGATATTGTATCCGTCCGGCTTGAACAGTAATCTCTCCAAAGAAT
*
405441 TCTACATTC
191 TCCACATTC
* * *
405450 CCAACATGCAGCTTAAGTACAACAATCTCAACTCTAGACTGTCCTATGTGAACAAAGCCGAGTTA
1 CCAAAATGCAGCTT-AG-ACAACAATCTCAACTATAGACTGTCCTATGTGAACAAAACCGAGTTA
* *
405515 TGATCCAATTGGCCTTAATCTAAGACAGAACACACAATTTCTTAGCTAAAGACTGCCCTATGTAT
64 TGATCCAATTGGCCTTAAACTAAGACAG-A-ACACAATTTCTCAGCTAAAGA-TGCCCTATGTAT
* * * *
405580 TTTCCGACCGCGCCATGTCCAGATATTGTATCTGTCCGGCTTGAACAGTAATCTCTCCAAAGAAT
126 TTGCCGACCGCGCCACGGCCAGATATTGTATCCGTCCGGCTTGAACAGTAATCTCTCCAAAGAAT
*
405645 TCCATATTC
191 TCCACATTC
* * * *
405654 CCAAAATGCAGCTTAGGCAACAATCTCAACTATAGACTGTTCTATGTGAATAAAACCTAGTTATG
1 CCAAAATGCAGCTTAGACAACAATCTCAACTATAGACTGTCCTATGTGAACAAAACCGAGTTAT-
* * ** * *
405719 GA-CCAACTGGTCTTACTCTATGAC--ATCACAATTTTCTCAGCTAAAGA
65 GATCCAATTGGCCTTAAACTAAGACAGAACACAA-TTTCTCAGCTAAAGA
405766 ACTACTACTT
Statistics
Matches: 268, Mismatches: 37, Indels: 23
0.82 0.11 0.07
Matches are distributed among these distances:
198 5 0.02
199 15 0.06
200 13 0.05
201 19 0.07
202 73 0.27
203 53 0.20
204 90 0.34
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (199 bp):
CCAAAATGCAGCTTAGACAACAATCTCAACTATAGACTGTCCTATGTGAACAAAACCGAGTTATG
ATCCAATTGGCCTTAAACTAAGACAGAACACAATTTCTCAGCTAAAGATGCCCTATGTATTTGCC
GACCGCGCCACGGCCAGATATTGTATCCGTCCGGCTTGAACAGTAATCTCTCCAAAGAATTCCAC
ATTC
Found at i:407175 original size:24 final size:24
Alignment explanation
Indices: 407104--407164 Score: 115
Period size: 24 Copynumber: 2.6 Consensus size: 24
407094 AGTTTAGCTA
407104 CCAAAATGGAAAAAAATTTAAATT
1 CCAAAATGGAAAAAAATTTAAATT
407128 CCAAAATGGAAAAAAATTTAAATT
1 CCAAAATGGAAAAAAATTTAAATT
407152 CCAAAAT-GAAAAA
1 CCAAAATGGAAAAA
407165 TAAATATAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 6 0.16
24 31 0.84
ACGTcount: A:0.61, C:0.10, G:0.08, T:0.21
Consensus pattern (24 bp):
CCAAAATGGAAAAAAATTTAAATT
Found at i:420436 original size:59 final size:61
Alignment explanation
Indices: 420317--420446 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 61
420307 TATAATATTC
* * * *
420317 GGTACCTGAACTTGACACTTTTTTTTTAGTTTGGTACCTAAACTTTTTTTGGACCCAATTT
1 GGTACCTAAACTTGACACTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGACCCAATTT
* * * *
420378 GGTATCTAAACTTGACA-TTTTTTTCCTAATTT-GTACCTAAGCTTTTTTTATA-TCAATTT
1 GGTACCTAAACTTGACACTTTTTTT-CTAATTTGGTACCTAAACTTTTTTTAGACCCAATTT
420437 GGTACCTAAA
1 GGTACCTAAA
420447 TTTATTAAAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 15 0.25
60 24 0.41
61 20 0.34
ACGTcount: A:0.25, C:0.17, G:0.12, T:0.46
Consensus pattern (61 bp):
GGTACCTAAACTTGACACTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGACCCAATTT
Found at i:420702 original size:27 final size:27
Alignment explanation
Indices: 420664--420717 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
420654 AAAAATTGTC
420664 AAGTTTGAGTACCAAATT-GAACAAAAA
1 AAGTTTGAGTACCAAATTAGAA-AAAAA
420691 AAGTTT-AGGTACCAAATTAGAAAAAAA
1 AAGTTTGA-GTACCAAATTAGAAAAAAA
420718 GTGTAAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 1 0.04
27 21 0.84
28 3 0.12
ACGTcount: A:0.54, C:0.09, G:0.15, T:0.22
Consensus pattern (27 bp):
AAGTTTGAGTACCAAATTAGAAAAAAA
Found at i:420715 original size:89 final size:90
Alignment explanation
Indices: 420553--420724 Score: 224
Period size: 89 Copynumber: 1.9 Consensus size: 90
420543 TAAAAATAAG
* ** *
420553 TACCAAATTAGGAAAAATAGTCAAGTTCAGGTACCAAATTGGACCCCAGAAAGTTTAAGTACCAA
1 TACCAAATTAGGAAAAATAGTCAAGTTCAGGTACCAAATTGGAACAAAAAAAGTTTAAGTACCAA
* *
420618 CTT-TAAAAAAGTGTAAACTTTAGA
66 ATTGAAAAAAAGTGTAAACTTTAGA
* * *
420642 TACCAAATTAGGAAAAATTGTCAAGTT-TGAGTACCAAATT-GAACAAAAAAAGTTTAGGTACCA
1 TACCAAATTAGGAAAAATAGTCAAGTTCAG-GTACCAAATTGGAACAAAAAAAGTTTAAGTACCA
420705 AATTAGAAAAAAAGTGTAAA
65 AATT-GAAAAAAAGTGTAAA
420725 GTTCAAGTAC
Statistics
Matches: 71, Mismatches: 9, Indels: 5
0.84 0.11 0.06
Matches are distributed among these distances:
88 22 0.31
89 36 0.51
90 13 0.18
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (90 bp):
TACCAAATTAGGAAAAATAGTCAAGTTCAGGTACCAAATTGGAACAAAAAAAGTTTAAGTACCAA
ATTGAAAAAAAGTGTAAACTTTAGA
Found at i:420726 original size:32 final size:32
Alignment explanation
Indices: 420622--420739 Score: 106
Period size: 31 Copynumber: 3.9 Consensus size: 32
420612 TACCAACTTT
* *
420622 AAAAAAGTGTAAACTTTAGATACCAAATTAG-
1 AAAAAAGTGTAAAGTTTAGGTACCAAATTAGA
* * *
420653 GAAAAATTGTCAAGTTT-GAGTACCAAATT-GA
1 AAAAAAGTGTAAAGTTTAG-GTACCAAATTAGA
*
420684 ACAAAA----AAAGTTTAGGTACCAAATTAGA
1 AAAAAAGTGTAAAGTTTAGGTACCAAATTAGA
* *
420712 AAAAAAGTGTAAAGTTCAAGTACCAAAT
1 AAAAAAGTGTAAAGTTTAGGTACCAAAT
420740 GTTATATTAA
Statistics
Matches: 68, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
27 16 0.24
28 8 0.12
30 2 0.03
31 26 0.38
32 16 0.24
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (32 bp):
AAAAAAGTGTAAAGTTTAGGTACCAAATTAGA
Found at i:421105 original size:28 final size:28
Alignment explanation
Indices: 421060--421134 Score: 107
Period size: 29 Copynumber: 2.7 Consensus size: 28
421050 TTAAATTTTG
421060 AAAAAA-AAAAATTAAATTATATAAATA
1 AAAAAACAAAAATTAAATTATATAAATA
* *
421087 AAAATACAAAAATTTAATTTATATAAATA
1 AAAAAACAAAAA-TTAAATTATATAAATA
*
421116 AAAAAACAAAGATTAAATT
1 AAAAAACAAAAATTAAATT
421135 TCAAAATTTG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
27 5 0.12
28 11 0.27
29 25 0.61
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (28 bp):
AAAAAACAAAAATTAAATTATATAAATA
Found at i:422685 original size:34 final size:34
Alignment explanation
Indices: 422647--422722 Score: 134
Period size: 34 Copynumber: 2.2 Consensus size: 34
422637 AGTAAACATC
*
422647 ATTTGGGTAAGGTAAAAGGTAAAAAACTAAAAAT
1 ATTTGGGTAAGATAAAAGGTAAAAAACTAAAAAT
*
422681 ATTTGGGTAAGATAAAAGGTAAAAAATTAAAAAT
1 ATTTGGGTAAGATAAAAGGTAAAAAACTAAAAAT
422715 ATTTGGGT
1 ATTTGGGT
422723 TTAATTTATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 40 1.00
ACGTcount: A:0.50, C:0.01, G:0.21, T:0.28
Consensus pattern (34 bp):
ATTTGGGTAAGATAAAAGGTAAAAAACTAAAAAT
Found at i:423374 original size:59 final size:59
Alignment explanation
Indices: 423292--423403 Score: 152
Period size: 59 Copynumber: 1.9 Consensus size: 59
423282 TTAATATAAC
* * * * * *
423292 ATTTGGTATCTAAATTTGACATTTTTTCTTAATTTGGTACCTAAACTTTTTTTGACCCA
1 ATTTAGTACCTAAACTTGACATTTTTGCCTAATTTAGTACCTAAACTTTTTTTGACCCA
* *
423351 ATTTAGTACCTAAACTTGACATTTTTGCCTAATTTAGTGCCTAAGCTTTTTTT
1 ATTTAGTACCTAAACTTGACATTTTTGCCTAATTTAGTACCTAAACTTTTTTT
423404 AGATTCAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
59 45 1.00
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (59 bp):
ATTTAGTACCTAAACTTGACATTTTTGCCTAATTTAGTACCTAAACTTTTTTTGACCCA
Found at i:423388 original size:31 final size:31
Alignment explanation
Indices: 423292--423394 Score: 97
Period size: 31 Copynumber: 3.4 Consensus size: 31
423282 TTAATATAAC
* * * * *
423292 ATTTGGTATCTAAATTTGACATTTTTTCTTA
1 ATTTAGTACCTAAACTTGACATTTTTGCCTA
* *
423323 ATTTGGTACCTAAACTT----TTTTTGACCCA
1 ATTTAGTACCTAAACTTGACATTTTTG-CCTA
423351 ATTTAGTACCTAAACTTGACATTTTTGCCTA
1 ATTTAGTACCTAAACTTGACATTTTTGCCTA
*
423382 ATTTAGTGCCTAA
1 ATTTAGTACCTAA
423395 GCTTTTTTTA
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
27 5 0.08
28 18 0.31
31 30 0.51
32 6 0.10
ACGTcount: A:0.27, C:0.17, G:0.11, T:0.46
Consensus pattern (31 bp):
ATTTAGTACCTAAACTTGACATTTTTGCCTA
Found at i:431698 original size:5 final size:4
Alignment explanation
Indices: 431645--431688 Score: 54
Period size: 4 Copynumber: 11.0 Consensus size: 4
431635 CGGGCCAAAA
**
431645 AAAT AAAT AAAT AAAT AAAT AAA- ACCT AAAT AAAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT
431689 TTAAATTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
3 1 0.03
4 29 0.85
5 4 0.12
ACGTcount: A:0.73, C:0.05, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:436388 original size:18 final size:19
Alignment explanation
Indices: 436365--436400 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
436355 TTAACTTTCA
*
436365 TCAAATC-AACCCTAAAAC
1 TCAAATCGAACACTAAAAC
436383 TCAAATCGAACACTAAAA
1 TCAAATCGAACACTAAAA
436401 AGATAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.53, C:0.28, G:0.03, T:0.17
Consensus pattern (19 bp):
TCAAATCGAACACTAAAAC
Found at i:437245 original size:2 final size:2
Alignment explanation
Indices: 437238--437265 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
437228 ATAGTGATTC
437238 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
437266 TGTTAATCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:445336 original size:15 final size:16
Alignment explanation
Indices: 445307--445336 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
445297 GCTTAAGATA
445307 TAAGATTATGAAAAAT
1 TAAGATTATGAAAAAT
445323 TAAGATTA-GAAAAA
1 TAAGATTATGAAAAA
445337 GAAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (16 bp):
TAAGATTATGAAAAAT
Found at i:448716 original size:33 final size:33
Alignment explanation
Indices: 448678--448807 Score: 88
Period size: 33 Copynumber: 3.9 Consensus size: 33
448668 CGCAACATCC
* *
448678 AAACAACCAAAATAACAATCAAAATAGCAACAA
1 AAACAACCAAAACAACAATCAAAATAGCAAAAA
* *
448711 AAACAA-CAACAACAAC-ACCAAAATAGTAAAAAAA
1 AAACAACCAA-AACAACAATCAAAATAG--CAAAAA
* * * * * *
448745 AAATAGCACCAAAATAGCAATTAAAACAGTAAAAA
1 AAACA--ACCAAAACAACAATCAAAATAGCAAAAA
*
448780 AAAAAACCAAAACAACAA--AAAATAGCAA
1 AAACAACCAAAACAACAATCAAAATAGCAA
448808 CCAAAATAGT
Statistics
Matches: 74, Mismatches: 16, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
31 8 0.11
32 12 0.16
33 22 0.30
34 8 0.11
35 9 0.12
36 5 0.07
37 10 0.14
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.08
Consensus pattern (33 bp):
AAACAACCAAAACAACAATCAAAATAGCAAAAA
Found at i:451024 original size:13 final size:13
Alignment explanation
Indices: 451006--451033 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
450996 TATATCATAT
451006 AAAAAAATTTAAC
1 AAAAAAATTTAAC
451019 AAAAAAATTTAAC
1 AAAAAAATTTAAC
451032 AA
1 AA
451034 TATCAGTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (13 bp):
AAAAAAATTTAAC
Found at i:461601 original size:20 final size:20
Alignment explanation
Indices: 461562--461601 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
461552 AAATTCATAT
* *
461562 TTAAAACTTTAAATATTTAA
1 TTAAAACTTTAAAAAATTAA
*
461582 TTAAATCTTTAAAAAATTAA
1 TTAAAACTTTAAAAAATTAA
461602 ATTATGAGCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAAAACTTTAAAAAATTAA
Found at i:466786 original size:6 final size:6
Alignment explanation
Indices: 466777--466805 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
466767 ATGTATATGT
466777 ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATA
466806 TACCTTTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:470681 original size:23 final size:23
Alignment explanation
Indices: 470651--470704 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
470641 ACGCTAGCGC
470651 GCTTACTG-TTCAGCACTAT-GTGT
1 GCTTACTGTTTC-GCACT-TCGTGT
470674 GCTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
470697 GCTTACTG
1 GCTTACTG
470705 ATTTGCGCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 1 0.03
23 25 0.86
24 3 0.10
ACGTcount: A:0.13, C:0.24, G:0.22, T:0.41
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:470726 original size:23 final size:23
Alignment explanation
Indices: 470700--470753 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
470690 TTCGTGTGCT
470700 TACTGATTTGCGCTATGTGCGCC
1 TACTGATTTGCGCTATGTGCGCC
470723 TACTGATTTGCGCTATGTGCGCC
1 TACTGATTTGCGCTATGTGCGCC
470746 TACTGATT
1 TACTGATT
470754 CCCCAGCAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (23 bp):
TACTGATTTGCGCTATGTGCGCC
Found at i:484313 original size:40 final size:40
Alignment explanation
Indices: 484260--484342 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
484250 ATTATTTGAT
*
484260 TAATAACTAACAAGCACGTGTATCTGAGAAAGAAATACAA
1 TAATAACTAACAAGCACGTGCATCTGAGAAAGAAATACAA
*
484300 TAATAACTAACAAGGACGTGCATCTGAGAAAGAAATACAA
1 TAATAACTAACAAGCACGTGCATCTGAGAAAGAAATACAA
484340 TAA
1 TAA
484343 CAGGTTTGTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.51, C:0.14, G:0.16, T:0.19
Consensus pattern (40 bp):
TAATAACTAACAAGCACGTGCATCTGAGAAAGAAATACAA
Found at i:486030 original size:125 final size:123
Alignment explanation
Indices: 485810--486062 Score: 398
Period size: 125 Copynumber: 2.0 Consensus size: 123
485800 ATCTTTCATA
* * *
485810 CTAAGCACGCCAATGAAAAGAGAAGTATTTTTTTCTATCTTTCTATTTTTCTCCCCCTTTAATTT
1 CTAAGCACGCCAATGAAAAAAAAAGAATTTTTTTCTATCTTTCTATTTTTCTCCCCCTTTAATTT
* * *
485875 TTCGTTTTTCCAATTTTCTTTTCACCTTACCAAGCAAAGCCTTATAGTTAATATGCCT
66 TCCATTTTTCCAATTTTCTTTTCACCTTACCAAGCAAAGCCTTAAAGTTAATATGCCT
* * *
485933 CTAAGCATGCCAATGAAAATAAAAAGAAATTTTTTTCTATGTTTCTATTTTTCTCCCCCTTTAGT
1 CTAAGCACGCCAATGAAAA-AAAAAG-AATTTTTTTCTATCTTTCTATTTTTCTCCCCCTTTAAT
*
485998 TTTCCATTTTTCCAATTTTCTTTTTACCTTACCAAGCAAAGCCTTAAAGTTAATATGCCT
64 TTTCCATTTTTCCAATTTTCTTTTCACCTTACCAAGCAAAGCCTTAAAGTTAATATGCCT
486058 CTAAG
1 CTAAG
486063 AGATTCTTTG
Statistics
Matches: 118, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
123 18 0.15
124 4 0.03
125 96 0.81
ACGTcount: A:0.27, C:0.22, G:0.09, T:0.42
Consensus pattern (123 bp):
CTAAGCACGCCAATGAAAAAAAAAGAATTTTTTTCTATCTTTCTATTTTTCTCCCCCTTTAATTT
TCCATTTTTCCAATTTTCTTTTCACCTTACCAAGCAAAGCCTTAAAGTTAATATGCCT
Found at i:486208 original size:4 final size:4
Alignment explanation
Indices: 486201--486225 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
486191 ATATATATGT
486201 ATGG ATGG ATGG ATGG ATGG ATGG A
1 ATGG ATGG ATGG ATGG ATGG ATGG A
486226 GAGGGAGAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.48, T:0.24
Consensus pattern (4 bp):
ATGG
Found at i:489387 original size:30 final size:29
Alignment explanation
Indices: 489313--489391 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
489303 TTGGGAAGGT
* * * *
489313 CCCCCAAAGTTTCTAAAATTTTAATTATA
1 CCCCCAAAATTTTTAAAAATTTAATTAGA
**
489342 CCCTTAAAATATTTTAAAAATTTAATTAGA
1 CCCCCAAAAT-TTTTAAAAATTTAATTAGA
489372 CCACCCAAAATTTTTAAAAA
1 CC-CCCAAAATTTTTAAAAA
489392 AATTATTATT
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 7 0.17
30 27 0.68
31 6 0.15
ACGTcount: A:0.44, C:0.18, G:0.03, T:0.35
Consensus pattern (29 bp):
CCCCCAAAATTTTTAAAAATTTAATTAGA
Found at i:490738 original size:2 final size:2
Alignment explanation
Indices: 490731--490770 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
490721 TTTTGAACTA
490731 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
490771 TTGAGAGTAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:493220 original size:16 final size:16
Alignment explanation
Indices: 493199--493237 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
493189 ACCTACTTGT
493199 AAAAGAACAAA-AAAAA
1 AAAAGAA-AAAGAAAAA
493215 AAAAGAAAAAGAAAAA
1 AAAAGAAAAAGAAAAA
*
493231 AGAAGAA
1 AAAAGAA
493238 GGTGAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAGAAAAA
Found at i:500682 original size:12 final size:12
Alignment explanation
Indices: 500665--500694 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
500655 ATTGTTAAAA
500665 AATTAATATTTT
1 AATTAATATTTT
500677 AATTAATATTTT
1 AATTAATATTTT
*
500689 TATTAA
1 AATTAA
500695 AAATGATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (12 bp):
AATTAATATTTT
Found at i:500746 original size:2 final size:2
Alignment explanation
Indices: 500739--500768 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
500729 TAATTTAACC
500739 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
500769 AACATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:500794 original size:21 final size:21
Alignment explanation
Indices: 500770--500813 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
500760 ATATATATAA
* *
500770 ACATTATATGCTATTTTAAAT
1 ACATAATATGATATTTTAAAT
* *
500791 ACATAATTTTATATTTTAAAT
1 ACATAATATGATATTTTAAAT
500812 AC
1 AC
500814 GTGATTTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (21 bp):
ACATAATATGATATTTTAAAT
Found at i:503568 original size:31 final size:31
Alignment explanation
Indices: 503533--503591 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
503523 TTTTTAATTA
503533 AATTTAAATT-TCAACCTTTT-AAAAAGAGTCG
1 AATTT-AATTATC-ACCTTTTCAAAAAGAGTCG
*
503564 AATTTAATTATCATCTTTTCAAAAAGAG
1 AATTTAATTATCACCTTTTCAAAAAGAG
503592 ACGAGTTGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.42, C:0.12, G:0.08, T:0.37
Consensus pattern (31 bp):
AATTTAATTATCACCTTTTCAAAAAGAGTCG
Found at i:508408 original size:26 final size:27
Alignment explanation
Indices: 508372--508422 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
508362 ATAACATTGA
*
508372 ATTTAACTTTTTTTATATTTAAAAATG
1 ATTTAACTTTTTTAATATTTAAAAATG
*
508399 ATTTAA-TTTTTTAATTTTTAAAAA
1 ATTTAACTTTTTTAATATTTAAAAA
508423 CTTTTAATTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.73
27 6 0.27
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (27 bp):
ATTTAACTTTTTTAATATTTAAAAATG
Found at i:508428 original size:25 final size:25
Alignment explanation
Indices: 508372--508440 Score: 68
Period size: 26 Copynumber: 2.7 Consensus size: 25
508362 ATAACATTGA
* *
508372 ATTTAACTTTTTTTATATTTAAAAAT
1 ATTTAA-TTTTTTAATTTTTAAAAAT
508398 GATTTAATTTTTTAATTTTTAAAAACT
1 -ATTTAATTTTTTAATTTTTAAAAA-T
* *
508425 -TTTAATTCTTTCATTT
1 ATTTAATTTTTTAATTT
508441 CTTTTAAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 14 0.38
26 16 0.43
27 7 0.19
ACGTcount: A:0.33, C:0.06, G:0.01, T:0.59
Consensus pattern (25 bp):
ATTTAATTTTTTAATTTTTAAAAAT
Found at i:511817 original size:110 final size:110
Alignment explanation
Indices: 511621--511843 Score: 385
Period size: 110 Copynumber: 2.0 Consensus size: 110
511611 TTATAGAATA
* *
511621 CAGCTTTAGCCTTTCTTCAATAACCTCACTCCAAAATGTTTCTCTTAGGACATACAGAAGGCCCA
1 CAGCTTTAGCATTTCTTCAATAACCCCACTCCAAAATGTTTCTCTTAGGACATACAGAAGGCCCA
511686 TTAAACTTTGTTTCCACTGTAACAGATAAAAGAAATTAATCTGAT
66 TTAAACTTTGTTTCCACTGTAACAGATAAAAGAAATTAATCTGAT
*
511731 CAGCTTTAGCATTTCTTCAATAACCCCACTCCAAAATGTTTTTCTTAGGACATACAGAAGGCCCA
1 CAGCTTTAGCATTTCTTCAATAACCCCACTCCAAAATGTTTCTCTTAGGACATACAGAAGGCCCA
**
511796 TTAAACTTTGTTTCC-CATGTAATGGATAAAAGAAATTAATCTGAT
66 TTAAACTTTGTTTCCAC-TGTAACAGATAAAAGAAATTAATCTGAT
511841 CAG
1 CAG
511844 TAGGCAGGTT
Statistics
Matches: 107, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
109 1 0.01
110 106 0.99
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.32
Consensus pattern (110 bp):
CAGCTTTAGCATTTCTTCAATAACCCCACTCCAAAATGTTTCTCTTAGGACATACAGAAGGCCCA
TTAAACTTTGTTTCCACTGTAACAGATAAAAGAAATTAATCTGAT
Found at i:519793 original size:6 final size:6
Alignment explanation
Indices: 519777--519806 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
519767 AAGGCAACAA
519777 GCAGA- GCAGAG GCAGAG GCAGAG GCAGAG G
1 GCAGAG GCAGAG GCAGAG GCAGAG GCAGAG G
519807 TAGCGACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.33, C:0.17, G:0.50, T:0.00
Consensus pattern (6 bp):
GCAGAG
Found at i:519900 original size:3 final size:3
Alignment explanation
Indices: 519892--519924 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
519882 TTTGATGGTT
519892 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
519925 CCTTTCTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:520084 original size:31 final size:30
Alignment explanation
Indices: 520046--520114 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
520036 AGTGAATGAT
*
520046 TGATTTGTCACTTTTTAATAACGTT-AGTGAC
1 TGATTTGTCA-TTTTT-ATAAAGTTGAGTGAC
* *
520077 TGATTTGTTATTTTTCTAAAGTTGAGTGAC
1 TGATTTGTCATTTTTATAAAGTTGAGTGAC
*
520107 TGTTTTGT
1 TGATTTGT
520115 TATTGAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 6 0.18
30 18 0.55
31 9 0.27
ACGTcount: A:0.22, C:0.09, G:0.19, T:0.51
Consensus pattern (30 bp):
TGATTTGTCATTTTTATAAAGTTGAGTGAC
Found at i:528694 original size:16 final size:16
Alignment explanation
Indices: 528654--528704 Score: 66
Period size: 16 Copynumber: 3.2 Consensus size: 16
528644 AGTTAGGGTG
*
528654 AATGAAATAAAACTGT
1 AATGAAATAAAATTGT
*
528670 AATAAAATAAAATTGT
1 AATGAAATAAAATTGT
* *
528686 AATGGAATAAAGTTGT
1 AATGAAATAAAATTGT
528702 AAT
1 AAT
528705 CACTAATTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.55, C:0.02, G:0.14, T:0.29
Consensus pattern (16 bp):
AATGAAATAAAATTGT
Found at i:530355 original size:7 final size:7
Alignment explanation
Indices: 530343--530384 Score: 68
Period size: 7 Copynumber: 6.1 Consensus size: 7
530333 AAACTCTCTT
530343 TTTTTTC
1 TTTTTTC
530350 TTTTTTC
1 TTTTTTC
*
530357 TTTTTTT
1 TTTTTTC
530364 TTTTTTC
1 TTTTTTC
530371 -TTTTTC
1 TTTTTTC
530377 TTTTTTC
1 TTTTTTC
530384 T
1 T
530385 CTGCGAGAAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
6 6 0.19
7 26 0.81
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:530367 original size:21 final size:20
Alignment explanation
Indices: 530341--530382 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 20
530331 GAAAACTCTC
530341 TTTTTTTTCTTTTTTCTTTTT
1 TTTTTTTTC-TTTTTCTTTTT
530362 TTTTTTTTCTTTTTCTTTTT
1 TTTTTTTTCTTTTTCTTTTT
530382 T
1 T
530383 CTCTGCGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (20 bp):
TTTTTTTTCTTTTTCTTTTT
Found at i:530941 original size:21 final size:21
Alignment explanation
Indices: 530915--530986 Score: 76
Period size: 21 Copynumber: 3.4 Consensus size: 21
530905 GGAAGGGATG
530915 GAGCAGTGGAAGGA-TCAATTA
1 GAGCAGTGGAA-GATTCAATTA
* *
530936 GAGCAGTTGAAGATTCAATTC
1 GAGCAGTGGAAGATTCAATTA
* *
530957 GAGCCA-TGGAAGATTCAAATG
1 GAG-CAGTGGAAGATTCAATTA
530978 GAGCAGTGG
1 GAGCAGTGG
530987 TTGCATCAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
20 4 0.09
21 37 0.86
22 2 0.05
ACGTcount: A:0.35, C:0.12, G:0.32, T:0.21
Consensus pattern (21 bp):
GAGCAGTGGAAGATTCAATTA
Found at i:556226 original size:36 final size:36
Alignment explanation
Indices: 556175--556276 Score: 186
Period size: 36 Copynumber: 2.8 Consensus size: 36
556165 CGCCTCCTTG
556175 TTCTCTTCCTTGTCTGGTAAACTCTTGGGCGCATCT
1 TTCTCTTCCTTGTCTGGTAAACTCTTGGGCGCATCT
* *
556211 TTCTCTTCCTCGTCTGGTAAACTTTTGGGCGCATCT
1 TTCTCTTCCTTGTCTGGTAAACTCTTGGGCGCATCT
556247 TTCTCTTCCTTGTCTGGTAAACTCTTGGGC
1 TTCTCTTCCTTGTCTGGTAAACTCTTGGGC
556277 TGCTGCGCCT
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 62 1.00
ACGTcount: A:0.11, C:0.27, G:0.20, T:0.42
Consensus pattern (36 bp):
TTCTCTTCCTTGTCTGGTAAACTCTTGGGCGCATCT
Found at i:556308 original size:45 final size:45
Alignment explanation
Indices: 556244--556504 Score: 378
Period size: 45 Copynumber: 5.8 Consensus size: 45
556234 TTTGGGCGCA
*
556244 TCTTTCTCTTCCTTGTCTGGTAAACTCTTGGGCTGCTGCGCCTCC
1 TCTTTCTCTTCCTTGTCTGGTAAACTCTCGGGCTGCTGCGCCTCC
* *
556289 TCTTTTTCTTCCTTGTCTGGTAAACTCTTGGGCTGCTGCGCCTCC
1 TCTTTCTCTTCCTTGTCTGGTAAACTCTCGGGCTGCTGCGCCTCC
* * * *
556334 TCTTTTTCTTCCTTGTCTGGTAAACTCTCGGGCTGGTGTGCCTCT
1 TCTTTCTCTTCCTTGTCTGGTAAACTCTCGGGCTGCTGCGCCTCC
556379 TCTTTCTCTTCCTTGTCTGGTAAACTCTCGGGCTGCTGCGCCTCC
1 TCTTTCTCTTCCTTGTCTGGTAAACTCTCGGGCTGCTGCGCCTCC
* * * **
556424 TCTTTCTCTTCCTTGTCTGGTAAACTCTCAGTCTGCTTCGCCTTT
1 TCTTTCTCTTCCTTGTCTGGTAAACTCTCGGGCTGCTGCGCCTCC
* * **
556469 TTTTTCTCTTCCTTGTCTGTTAAGGTCTCGGGCTGC
1 TCTTTCTCTTCCTTGTCTGGTAAACTCTCGGGCTGC
556505 GCTTCCTCTT
Statistics
Matches: 196, Mismatches: 20, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 196 1.00
ACGTcount: A:0.07, C:0.31, G:0.20, T:0.43
Consensus pattern (45 bp):
TCTTTCTCTTCCTTGTCTGGTAAACTCTCGGGCTGCTGCGCCTCC
Found at i:562327 original size:21 final size:20
Alignment explanation
Indices: 562283--562322 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
562273 ATAAATAAAT
562283 TTATATAACACACATTATTA
1 TTATATAACACACATTATTA
562303 TTATATTAACA-ACATT-TTA
1 TTATA-TAACACACATTATTA
562322 T
1 T
562323 ATTATCTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (20 bp):
TTATATAACACACATTATTA
Found at i:562545 original size:16 final size:19
Alignment explanation
Indices: 562524--562569 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
562514 TCTAATTATT
562524 ATCATATTTA-A-AT-AAA
1 ATCATATTTATAGATAAAA
562540 ATCATATTTATAGATAAAA
1 ATCATATTTATAGATAAAA
*
562559 ATTATATTTAT
1 ATCATATTTAT
562570 TTATTATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 10 0.38
17 1 0.04
18 2 0.08
19 13 0.50
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.43
Consensus pattern (19 bp):
ATCATATTTATAGATAAAA
Found at i:562935 original size:15 final size:14
Alignment explanation
Indices: 562903--562940 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
562893 AATGAAAATC
*
562903 AAATAAATTTTCTT
1 AAATAAATTTTATT
562917 -AATAAATATTTATT
1 AAATAAAT-TTTATT
562931 AAATAAATTT
1 AAATAAATTT
562941 AAATAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 7 0.33
14 7 0.33
15 7 0.33
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (14 bp):
AAATAAATTTTATT
Found at i:563371 original size:15 final size:15
Alignment explanation
Indices: 563353--563391 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
563343 ATTATTTCAA
*
563353 TATTTAAAATTTAAT
1 TATTTAAAATTAAAT
*
563368 TATTTAATATTAAAT
1 TATTTAAAATTAAAT
563383 TAATTTAAA
1 T-ATTTAAA
563392 TAATTTAGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 14 0.70
16 6 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTTAAAATTAAAT
Found at i:564582 original size:6 final size:6
Alignment explanation
Indices: 564571--564601 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
564561 CCTATCTATC
564571 TATCCA TATCCA TATCCA TATCCA TATCCA T
1 TATCCA TATCCA TATCCA TATCCA TATCCA T
564602 CCATCTATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (6 bp):
TATCCA
Found at i:565959 original size:30 final size:31
Alignment explanation
Indices: 565905--565965 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
565895 AATTTCAAAT
* *
565905 TTTGAAAAGTACGAGGATTAAAATTGGTCAA
1 TTTGAAAAGTACGAGGACTAAAATTGATCAA
* *
565936 TTTGAAAGGTATG-GGACTAAAATTGATCAA
1 TTTGAAAAGTACGAGGACTAAAATTGATCAA
565966 ATTAAAGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.30
Consensus pattern (31 bp):
TTTGAAAAGTACGAGGACTAAAATTGATCAA
Found at i:566560 original size:31 final size:29
Alignment explanation
Indices: 566543--566601 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
566533 TGTGGTTTAA
566543 TGTGTAATTGTATACATGAACTTTGATTT
1 TGTGTAATTGTATACATGAACTTTGATTT
* * *
566572 TGTTTAATTTTATACATGAAATTTTGATTT
1 TGTGTAATTGTATACATG-AACTTTGATTT
566602 GATCCAATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 16 0.62
30 10 0.38
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.53
Consensus pattern (29 bp):
TGTGTAATTGTATACATGAACTTTGATTT
Found at i:566821 original size:29 final size:30
Alignment explanation
Indices: 566787--566856 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
566777 CAATTAGAGT
* *
566787 TTTATGTGTATAATT-ATACTAAATTAAAA
1 TTTATGTATACAATTAATACTAAATTAAAA
*
566816 TTTATGTATACAATTACATATTAAATTAAAA
1 TTTATGTATACAATTA-ATACTAAATTAAAA
*
566847 TTCATGTATA
1 TTTATGTATA
566857 ATTTTGAGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 13 0.37
31 22 0.63
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (30 bp):
TTTATGTATACAATTAATACTAAATTAAAA
Found at i:567104 original size:27 final size:26
Alignment explanation
Indices: 567042--567108 Score: 75
Period size: 26 Copynumber: 2.6 Consensus size: 26
567032 CTTCCTTTGA
*
567042 TTTTTGAAAATATTTTCTATTTTCAT
1 TTTTTGAAAATATTATCTATTTTCAT
*
567068 TTTTAGAAAATAATTATC-ATTTTCTAT
1 TTTTTGAAAAT-ATTATCTATTTTC-AT
*
567095 TTTTTTAAAA-ATTA
1 TTTTTGAAAATATTA
567109 AAAAAACATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
25 4 0.11
26 16 0.46
27 15 0.43
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (26 bp):
TTTTTGAAAATATTATCTATTTTCAT
Found at i:568002 original size:6 final size:6
Alignment explanation
Indices: 567991--568060 Score: 51
Period size: 6 Copynumber: 12.2 Consensus size: 6
567981 AATTGAATTT
* * *
567991 ATTTAA ATTTAA GTTT-A TTTTAA ATTTAA ATTT-- ATTTGAA AATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA
*
568037 ATTT-- ATTATAA AATTAA ATTTAA A
1 ATTTAA ATT-TAA ATTTAA ATTTAA A
568061 AAGTCCAATT
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
4 7 0.14
5 5 0.10
6 33 0.66
7 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:568014 original size:17 final size:17
Alignment explanation
Indices: 567980--568058 Score: 97
Period size: 17 Copynumber: 4.7 Consensus size: 17
567970 GACCTATTGG
*
567980 AAATTGAATTTA-TTTA
1 AAATTAAATTTATTTTA
* *
567996 AATTTAAGTTTATTTTA
1 AAATTAAATTTATTTTA
* *
568013 AATTTAAATTTATTTGA
1 AAATTAAATTTATTTTA
*
568030 AAATTAAATTTATTATA
1 AAATTAAATTTATTTTA
568047 AAATTAAATTTA
1 AAATTAAATTTA
568059 AAAAGTCCAA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
16 9 0.17
17 45 0.83
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (17 bp):
AAATTAAATTTATTTTA
Found at i:568075 original size:14 final size:13
Alignment explanation
Indices: 568056--568081 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
568046 AAAATTAAAT
568056 TTAAAAAGTCCAA
1 TTAAAAAGTCCAA
568069 TTAAAAAGTCCAA
1 TTAAAAAGTCCAA
568082 AACAAAGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (13 bp):
TTAAAAAGTCCAA
Found at i:568115 original size:15 final size:15
Alignment explanation
Indices: 568091--568169 Score: 97
Period size: 15 Copynumber: 5.3 Consensus size: 15
568081 AAACAAAGTT
568091 CAATTACAAATGACC
1 CAATTACAAATGACC
* * *
568106 CAACTACAAACGGCC
1 CAATTACAAATGACC
*
568121 CAATTACAAATGGCC
1 CAATTACAAATGACC
*
568136 CAAATACAAAT-AGCC
1 CAATTACAAATGA-CC
568151 CAATTACAAATGACC
1 CAATTACAAATGACC
568166 CAAT
1 CAAT
568170 GACCCAAAGT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
15 53 0.98
16 1 0.02
ACGTcount: A:0.46, C:0.29, G:0.09, T:0.16
Consensus pattern (15 bp):
CAATTACAAATGACC
Found at i:568125 original size:30 final size:30
Alignment explanation
Indices: 568091--568168 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
568081 AAACAAAGTT
* *
568091 CAATTACAAATGACCCAACTACAAACGGCC
1 CAATTACAAATGACCCAAATACAAACAGCC
* *
568121 CAATTACAAATGGCCCAAATACAAATAGCC
1 CAATTACAAATGACCCAAATACAAACAGCC
568151 CAATTACAAATGACCCAA
1 CAATTACAAATGACCCAA
568169 TGACCCAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.46, C:0.29, G:0.09, T:0.15
Consensus pattern (30 bp):
CAATTACAAATGACCCAAATACAAACAGCC
Found at i:568804 original size:19 final size:21
Alignment explanation
Indices: 568780--568829 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 21
568770 TTAATGACTA
*
568780 TTAATAATAATAAAT-A-TTT
1 TTAATAATAATAAATAACGTT
568799 TTAATAATAATAAATAACGTT
1 TTAATAATAATAAATAACGTT
568820 TTAATAATAA
1 TTAATAATAA
568830 AAAGGGAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
19 15 0.54
20 1 0.04
21 12 0.43
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
TTAATAATAATAAATAACGTT
Found at i:569964 original size:23 final size:22
Alignment explanation
Indices: 569933--570079 Score: 86
Period size: 23 Copynumber: 6.5 Consensus size: 22
569923 GCTGGAGAAA
569933 CAGTAAGCACACACAATGCAAT
1 CAGTAAGCACACACAATGCAAT
* *
569955 CTAGTAAGCAGACACAGTGCAAT
1 C-AGTAAGCACACACAATGCAAT
* * * **
569978 CAGTAGGCGCACATAGCGCAAAT
1 CAGTAAGCACACACAATGC-AAT
* *
570001 CAGTAGGCACACGA-AGTGCGAAAT
1 CAGTAAGCACAC-ACAATGC--AAT
* *
570025 -AGTAAGCACACGA-AGTGCGAAA
1 CAGTAAGCACAC-ACAATGC-AAT
570047 CAGTAAGCACACACAATGCTGAA-
1 CAGTAAGCACACACAATGC--AAT
570070 CAGTAAGCAC
1 CAGTAAGCAC
570080 GCTAGCGTTC
Statistics
Matches: 105, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
22 17 0.16
23 80 0.76
24 8 0.08
ACGTcount: A:0.41, C:0.24, G:0.22, T:0.13
Consensus pattern (22 bp):
CAGTAAGCACACACAATGCAAT
Done.