Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000507.1 Hibiscus syriacus cultivar Beakdansim tig00000964_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: 59579
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:6777 original size:215 final size:216
Alignment explanation
Indices: 6362--6837 Score: 699
Period size: 215 Copynumber: 2.2 Consensus size: 216
6352 TTACCAAATA
* * *
6362 GGCACTAAGTGTGCAATTCAC-GAAATTCATCATATATTGATGAATACCCATTTTGGCACTAAGT
1 GGCACTAAGTGTGCAATTCACAG-AATTCATCATATGTTGATGAATAACCATCTTGGCACTAAGT
* *
6426 GTGCAATTCACGAAGTTCATCATATGTTAATGAATAATCGTTTCAACACTAACTGTGCAATTCAC
65 GTGCAATTCACGAAATTCATCATATGTTAATGAATAATAGTTTCAACACTAACTGTGCAATTCAC
* * *
6491 GGAATTCATCTTATGTTGAGGAATAACCGTTTCGGCACTTAGTGTGCAATTCACGGAATTCATCA
130 GGAATTCATCATATGTTGAGGAATAACCGTTTCGGCACTAAGTGTGCAATTCACGAAATTCATCA
6556 TATGTTGATGAATAATC-ATTAC
195 TATGTTGATGAATAA-CAATTAC
*
6578 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTCTTGGCACTAAGTG
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCATCTTGGCACTAAGTG
* * * *
6643 TGCAATTCAC-ATAATTCATTATATGTTGATGAAT-ATAGTTTCGACACTAAGTGTGCAATTCAC
66 TGCAATTCACGA-AATTCATCATATGTTAATGAATAATAGTTTCAACACTAACTGTGCAATTCAC
* *
6706 GGAATTCATCATATGTTGATGAATAATCGTTTCGGCACTAAGTGTGCAATTCACGAAATTCATCA
130 GGAATTCATCATATGTTGAGGAATAACCGTTTCGGCACTAAGTGTGCAATTCACGAAATTCATCA
*
6771 TATGTTGATGAATAACAATTTC
195 TATGTTGATGAATAACAATTAC
* * ** * *
6793 GGCACTATGTGTACAACCCACAGAATTCATAATATGTTTATGAAT
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAAT
6838 GATTGTATAG
Statistics
Matches: 235, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
214 1 0.00
215 145 0.62
216 88 0.37
217 1 0.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (216 bp):
GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCATCTTGGCACTAAGTG
TGCAATTCACGAAATTCATCATATGTTAATGAATAATAGTTTCAACACTAACTGTGCAATTCACG
GAATTCATCATATGTTGAGGAATAACCGTTTCGGCACTAAGTGTGCAATTCACGAAATTCATCAT
ATGTTGATGAATAACAATTAC
Found at i:6851 original size:54 final size:54
Alignment explanation
Indices: 6362--6861 Score: 598
Period size: 54 Copynumber: 9.3 Consensus size: 54
6352 TTACCAAATA
* ** * *
6362 GGCACTAAGTGTGCAATTCAC-GAAATTCATCATATATTGATGAATACCCATTTT
1 GGCACTAAGTGTGCAATTCACAG-AATTCATCATATGTTGATGAATAATCGTTTC
*
6416 GGCACTAAGTGTGCAATTCAC-GAAGTTCATCATATGTTAATGAATAATCGTTTC
1 GGCACTAAGTGTGCAATTCACAGAA-TTCATCATATGTTGATGAATAATCGTTTC
** * * * * *
6470 AACACTAACTGTGCAATTCACGGAATTCATCTTATGTTGAGGAATAACCGTTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTC
* * * *
6524 GGCACTTAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAATCATTAC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTC
*
6578 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAACCGTCTT-
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGT-TTC
* * *
6632 GGCACTAAGTGTGCAATTCACATAATTCATTATATGTTGATGAAT-ATAGTTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTC
* *
6685 GACACTAAGTGTGCAATTCACGGAATTCATCATATGTTGATGAATAATCGTTTC
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTC
*
6739 GGCACTAAGTGTGCAATTCAC-GAAATTCATCATATGTTGATGAATAA-CAATTTC
1 GGCACTAAGTGTGCAATTCACAG-AATTCATCATATGTTGATGAATAATC-GTTTC
* * ** * * * * * *
6793 GGCACTATGTGTACAACCCACAGAATTCATAATATGTTTATGAATGATTGTATA
1 GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTC
*
6847 GGCACTACGTGTGCA
1 GGCACTAAGTGTGCA
6862 TCGTAACGAA
Statistics
Matches: 386, Mismatches: 51, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
52 2 0.01
53 48 0.12
54 331 0.86
55 5 0.01
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (54 bp):
GGCACTAAGTGTGCAATTCACAGAATTCATCATATGTTGATGAATAATCGTTTC
Found at i:9359 original size:4 final size:4
Alignment explanation
Indices: 9352--9845 Score: 953
Period size: 4 Copynumber: 124.8 Consensus size: 4
9342 AATATATATA
9352 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9400 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9448 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9496 TATG TATG TATG TATG TATG TATG TATG TATG --TG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9542 TATG TATG --TG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9588 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9636 TATG T-TG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9683 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9731 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9779 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
9827 TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TAT
9846 ATATATATAT
Statistics
Matches: 485, Mismatches: 0, Indels: 10
0.98 0.00 0.02
Matches are distributed among these distances:
2 4 0.01
3 3 0.01
4 478 0.99
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:15208 original size:3 final size:3
Alignment explanation
Indices: 15200--15249 Score: 91
Period size: 3 Copynumber: 16.3 Consensus size: 3
15190 AATGTAATTA
15200 AAT AAT AAT AAT AAT AAT AAT AAT AATT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT
15246 AAT A
1 AAT A
15250 TATTAATATT
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 43 0.93
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:17306 original size:18 final size:19
Alignment explanation
Indices: 17285--17326 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
17275 ACATCTTTAC
17285 TTAAATTCACATATTAA-A
1 TTAAATTCACATATTAACA
* *
17303 TTAATTTCACATCTTAACA
1 TTAAATTCACATATTAACA
17322 TTAAA
1 TTAAA
17327 AAATATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAAATTCACATATTAACA
Found at i:17355 original size:25 final size:26
Alignment explanation
Indices: 17313--17362 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
17303 TTAATTTCAC
*
17313 ATCTTAACATTAAAAAATATTTTTTT
1 ATCTTAACATTAAAAAATATATTTTT
**
17339 ATCTTAAC-TTATTAAATATATTTT
1 ATCTTAACATTAAAAAATATATTTT
17363 ATTCTTCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (26 bp):
ATCTTAACATTAAAAAATATATTTTT
Found at i:17391 original size:29 final size:29
Alignment explanation
Indices: 17352--17459 Score: 101
Period size: 30 Copynumber: 3.7 Consensus size: 29
17342 TTAACTTATT
*
17352 AAATATATTTTATTCTTCTCGTAAC-CTAA
1 AAATATATTTTATTCTTATCGTAACTC-AA
* *
17381 AAATATATTTTATTTTTATCTTAACTGCAA
1 AAATATATTTTATTCTTATCGTAACT-CAA
* * * * *
17411 AAATATATTTTAATCTTATATGAAATTAAA
1 AAATATATTTTATTCTTAT-CGTAACTCAA
*
17441 AAATATAATTTATTCTTAT
1 AAATATATTTTATTCTTAT
17460 ATTAACTTAA
Statistics
Matches: 64, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
29 22 0.34
30 38 0.59
31 4 0.06
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (29 bp):
AAATATATTTTATTCTTATCGTAACTCAA
Found at i:17415 original size:30 final size:29
Alignment explanation
Indices: 17334--17487 Score: 100
Period size: 30 Copynumber: 5.3 Consensus size: 29
17324 AAAAAATATT
* *
17334 TTTTTATCTTAACTTATTAAATATATTTTA
1 TTTTTATCTTAACTCA-AAAATATATTTTA
* * *
17364 TTCTTCTCGTAAC-CTAAAAATATATTTTA
1 TTTTTATCTTAACTC-AAAAATATATTTTA
17393 TTTTTATCTTAACTGCAAAAATATATTTTA
1 TTTTTATCTTAACT-CAAAAATATATTTTA
* * * * * * *
17423 ATCTTATATGAAATTAAAAAATATAATTTA
1 TTTTTATCT-TAACTCAAAAATATATTTTA
* * *
17453 TTCTTATATTAACT--TAAATAT-TTTTA
1 TTTTTATCTTAACTCAAAAATATATTTTA
*
17479 TTTTAATCT
1 TTTTTATCT
17488 AATAATATTT
Statistics
Matches: 97, Mismatches: 23, Indels: 12
0.73 0.17 0.09
Matches are distributed among these distances:
26 10 0.10
27 6 0.06
29 25 0.26
30 52 0.54
31 4 0.04
ACGTcount: A:0.38, C:0.09, G:0.02, T:0.51
Consensus pattern (29 bp):
TTTTTATCTTAACTCAAAAATATATTTTA
Found at i:17516 original size:22 final size:22
Alignment explanation
Indices: 17468--17516 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
17458 ATATTAACTT
* * **
17468 AAATATTTTTATTTTAATCTAA
1 AAATATTTATAATTTAAGATAA
*
17490 TAATATTTATAATTTAAGATAA
1 AAATATTTATAATTTAAGATAA
17512 AAATA
1 AAATA
17517 ATATATTTTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
AAATATTTATAATTTAAGATAA
Found at i:17537 original size:29 final size:28
Alignment explanation
Indices: 17503--17834 Score: 118
Period size: 30 Copynumber: 11.5 Consensus size: 28
17493 TATTTATAAT
17503 TTAAGATAAAAATAATATATTTTTTCTAG
1 TTAAGATAAAAATAATATATTTTTT-TAG
* *
17532 TTAAGATAAAAATAAAATATATTTTT-G
1 TTAAGATAAAAATAATATATTTTTTTAG
* * *
17559 GTAA-A-ATAAA-AATATA-TTTTTAAG
1 TTAAGATAAAAATAATATATTTTTTTAG
* * *
17583 TTAAGATAAAAATAAAAGATATGTTTTAAG
1 TTAAGATAAAAAT--AATATATTTTTTTAG
* * ** * *
17613 TTAAAATAAGAATTAATTATATTTAATAAT
1 TTAAGATAA-AAATAA-TATATTTTTTTAG
* ** * *
17643 TTAAGGTAAGAATATAATATATTTAATAAT
1 TTAAGATAA-AA-ATAATATATTTTTTTAG
* * ** *
17673 TTAAGTTAAGAATATAA-ATTATATAATAAG
1 TTAAGATAA-AA-ATAATA-TATTTTTTTAG
* *
17703 TTAAGATAAGAATAAAATATATTTTTTAAG
1 TTAAGATAA-AA-ATAATATATTTTTTTAG
* * *
17733 TTAAGATAAATACTAAAAATATATTTTTAAG
1 TTAAGATAAA-AAT-AATATAT-TTTTTTAG
* * *
17764 TTAAAATAAGAATAAAATATTTTTTTAG
1 TTAAGATAAAAATAATATATTTTTTTAG
* * * ** *
17792 TAAAGACAAGAATAAAATATATTTAATAAG
1 TTAAGATAA-AA-ATAATATATTTTTTTAG
*
17822 TTAATATAAAAAT
1 TTAAGATAAAAAT
17835 GAAATACATT
Statistics
Matches: 237, Mismatches: 49, Indels: 35
0.74 0.15 0.11
Matches are distributed among these distances:
23 4 0.02
24 9 0.04
25 5 0.02
26 5 0.02
27 4 0.02
28 15 0.06
29 42 0.18
30 130 0.55
31 23 0.10
ACGTcount: A:0.52, C:0.01, G:0.08, T:0.39
Consensus pattern (28 bp):
TTAAGATAAAAATAATATATTTTTTTAG
Found at i:17597 original size:30 final size:29
Alignment explanation
Indices: 17567--17858 Score: 257
Period size: 30 Copynumber: 9.8 Consensus size: 29
17557 TGGTAAAATA
*
17567 AAAATATATTTTTAAGTTAAGATAAAAAT
1 AAAATATATTTTTAAGTTAAGATAAGAAT
* *
17596 AAAAGATATGTTTTAAGTTAAAATAAGAAT
1 AAAATATAT-TTTTAAGTTAAGATAAGAAT
* * * * *
17626 TAATTATATTTAATAATTTAAGGTAAGAAT
1 AAAATATATTT-TTAAGTTAAGATAAGAAT
* * * *
17656 ATAATATATTTAATAATTTAAGTTAAGAAT
1 AAAATATATTT-TTAAGTTAAGATAAGAAT
**
17686 ATAAAT-TATATAATAAGTTAAGATAAGAAT
1 A-AAATATAT-TTTTAAGTTAAGATAAGAAT
17716 AAAATATATTTTTTAAGTTAAGATAA-ATACT
1 AAAATATA-TTTTTAAGTTAAGATAAGA-A-T
*
17747 AAAAATATATTTTTAAGTTAAAATAAGAAT
1 -AAAATATATTTTTAAGTTAAGATAAGAAT
* * *
17777 AAAATAT-TTTTTTAGTAAAGACAAGAAT
1 AAAATATATTTTTAAGTTAAGATAAGAAT
* * *
17805 AAAATATATTTAATAAGTTAATATAAAAAT
1 AAAATATATTT-TTAAGTTAAGATAAGAAT
* *
17835 GAAATACATTTTTAATGTTAAGAT
1 AAAATATATTTTTAA-GTTAAGAT
17859 GTAAAATTAA
Statistics
Matches: 215, Mismatches: 35, Indels: 25
0.78 0.13 0.09
Matches are distributed among these distances:
28 24 0.11
29 28 0.13
30 131 0.61
31 23 0.11
32 9 0.04
ACGTcount: A:0.52, C:0.01, G:0.09, T:0.38
Consensus pattern (29 bp):
AAAATATATTTTTAAGTTAAGATAAGAAT
Found at i:17858 original size:149 final size:148
Alignment explanation
Indices: 17567--17834 Score: 346
Period size: 149 Copynumber: 1.8 Consensus size: 148
17557 TGGTAAAATA
*
17567 AAAATATATTTTTAAGTTAAGATAAAAATAAAAGATATGTTTTAAGTTAAAATAAGAATTAATTA
1 AAAATATATTTTTAAGTTAAGATAAAAATAAAAGATATGTTTTAAGTTAAAATAAGAATTAATAA
* * ** * * *
17632 TATTTAATAATTTAAGGTAAGAATATAATATATTTAATAATTTAAGTTAAGAATATAAATTATAT
66 TATTTAATAAGTAAAGACAAGAATAAAATATATTTAATAAGTTAAGTTAAAAATATAAATTATAT
17697 AATAAGTTAAGATAAGAAT
131 AAT-AGTTAAGATAAGAAT
* *
17716 AAAATATATTTTTTAAGTTAAGATAAATACTAAAA-ATATATTTTTAAGTTAAAATAAGAA-TAA
1 AAAATATA-TTTTTAAGTTAAGATAAA-AATAAAAGATAT-GTTTTAAGTTAAAATAAGAATTAA
** *
17779 -AATATTTTTTTAGTAAAGACAAGAATAAAATATATTTAATAAGTTAA-TATAAAAAT
63 TAATATTTAATAAGTAAAGACAAGAATAAAATATATTTAATAAGTTAAGT-TAAAAAT
17835 GAAATACATT
Statistics
Matches: 102, Mismatches: 13, Indels: 8
0.83 0.11 0.07
Matches are distributed among these distances:
148 1 0.01
149 51 0.50
150 25 0.25
151 25 0.25
ACGTcount: A:0.53, C:0.01, G:0.08, T:0.38
Consensus pattern (148 bp):
AAAATATATTTTTAAGTTAAGATAAAAATAAAAGATATGTTTTAAGTTAAAATAAGAATTAATAA
TATTTAATAAGTAAAGACAAGAATAAAATATATTTAATAAGTTAAGTTAAAAATATAAATTATAT
AATAGTTAAGATAAGAAT
Found at i:18666 original size:50 final size:53
Alignment explanation
Indices: 18605--18707 Score: 149
Period size: 50 Copynumber: 2.0 Consensus size: 53
18595 TTATTTGTAC
*
18605 TTTTTATAATTTTTTATAGCTTAAATTGATATAATTCATATATA-ATA-ATAT
1 TTTTTATAATTTATTATAGCTTAAATTGATATAATTCATATATATATATATAT
** *
18656 TTTTTA-AATTTATTATATTTTAAATTGATATGATTCATATATATATATATAT
1 TTTTTATAATTTATTATAGCTTAAATTGATATAATTCATATATATATATATAT
18708 ATATATAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
50 33 0.72
51 9 0.20
52 4 0.09
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (53 bp):
TTTTTATAATTTATTATAGCTTAAATTGATATAATTCATATATATATATATAT
Found at i:20207 original size:2 final size:2
Alignment explanation
Indices: 20202--20230 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20192 TTTTTTTTAA
20202 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20231 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20236 original size:3 final size:3
Alignment explanation
Indices: 20228--20258 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
20218 ATATATATAT
20228 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
20259 CGGAATTGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:21515 original size:21 final size:21
Alignment explanation
Indices: 21494--21546 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
21484 ATAATCCCTT
*
21494 AACCTTTAAACCCTAAATCTTA
1 AACC-TTAAACACTAAATCTTA
21516 AACCTTAAACACT-AA-CTTAA
1 AACCTTAAACACTAAATCTT-A
*
21536 AACCGTAAACA
1 AACCTTAAACA
21547 ATAGTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 3 0.11
20 13 0.46
21 8 0.29
22 4 0.14
ACGTcount: A:0.47, C:0.26, G:0.02, T:0.25
Consensus pattern (21 bp):
AACCTTAAACACTAAATCTTA
Found at i:23143 original size:14 final size:14
Alignment explanation
Indices: 23103--23153 Score: 57
Period size: 15 Copynumber: 3.5 Consensus size: 14
23093 TAACCGGTTT
23103 CGTTTTAAAAAAAC
1 CGTTTTAAAAAAAC
**
23117 CGGTTTTTTAAAAAC
1 C-GTTTTAAAAAAAC
*
23132 CGTTATAAAAAAAC
1 CGTTTTAAAAAAAC
23146 CGATTTTA
1 CG-TTTTA
23154 TATTCCAGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
14 13 0.45
15 16 0.55
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (14 bp):
CGTTTTAAAAAAAC
Found at i:23562 original size:13 final size:13
Alignment explanation
Indices: 23544--23591 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
23534 CGATAAATTC
23544 AATACTTAATTGA
1 AATACTTAATTGA
23557 AATACTTAATT-A
1 AATACTTAATTGA
* *
23569 ACTCACATAATTGA
1 AAT-ACTTAATTGA
23583 AATACTTAA
1 AATACTTAA
23592 ATACTTCCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
12 3 0.10
13 23 0.79
14 3 0.10
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.35
Consensus pattern (13 bp):
AATACTTAATTGA
Found at i:23622 original size:33 final size:33
Alignment explanation
Indices: 23577--23676 Score: 157
Period size: 33 Copynumber: 3.0 Consensus size: 33
23567 TAACTCACAT
* * *
23577 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
23610 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
23643 AATTCAAATACTTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATAC-TTAAAAACTTCCAAGTTCGATA
23676 A
1 A
23677 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
33 53 0.84
34 10 0.16
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:23695 original size:21 final size:21
Alignment explanation
Indices: 23671--23710 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
23661 ACTTCAAGTT
23671 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
23692 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
23711 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:25304 original size:92 final size:92
Alignment explanation
Indices: 25147--25331 Score: 370
Period size: 92 Copynumber: 2.0 Consensus size: 92
25137 TGAATTGTTT
25147 CGTGAAATCTTCATCATCAAAGTGGTCGAACGGCAATGCTTTTGTAATCACGAACTTTGTAAACG
1 CGTGAAATCTTCATCATCAAAGTGGTCGAACGGCAATGCTTTTGTAATCACGAACTTTGTAAACG
25212 CTTCTCGTAATTTTTCGTTGTCGTAAA
66 CTTCTCGTAATTTTTCGTTGTCGTAAA
25239 CGTGAAATCTTCATCATCAAAGTGGTCGAACGGCAATGCTTTTGTAATCACGAACTTTGTAAACG
1 CGTGAAATCTTCATCATCAAAGTGGTCGAACGGCAATGCTTTTGTAATCACGAACTTTGTAAACG
25304 CTTCTCGTAATTTTTCGTTGTCGTAAA
66 CTTCTCGTAATTTTTCGTTGTCGTAAA
25331 C
1 C
25332 AAAAACACCT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 93 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (92 bp):
CGTGAAATCTTCATCATCAAAGTGGTCGAACGGCAATGCTTTTGTAATCACGAACTTTGTAAACG
CTTCTCGTAATTTTTCGTTGTCGTAAA
Found at i:25824 original size:11 final size:12
Alignment explanation
Indices: 25803--25848 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
25793 TCCGGATAAA
25803 AACCGGTTTTTT
1 AACCGGTTTTTT
25815 AACCGGTTTTTTT
1 AACCGG-TTTTTT
25828 CAAACCGGTTTTTT
1 --AACCGGTTTTTT
*
25842 ATCCGGT
1 AACCGGT
25849 AAAAAAACCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 12 0.40
13 6 0.20
14 6 0.20
15 6 0.20
ACGTcount: A:0.17, C:0.20, G:0.17, T:0.46
Consensus pattern (12 bp):
AACCGGTTTTTT
Found at i:25833 original size:15 final size:14
Alignment explanation
Indices: 25802--25841 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
25792 TTCCGGATAA
25802 AAACCGG-TTTTTT
1 AAACCGGTTTTTTT
25815 -AACCGGTTTTTTT
1 AAACCGGTTTTTTT
25828 CAAACCGGTTTTTT
1 -AAACCGGTTTTTT
25842 ATCCGGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.25
13 6 0.25
15 12 0.50
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (14 bp):
AAACCGGTTTTTTT
Found at i:26186 original size:18 final size:18
Alignment explanation
Indices: 26163--26199 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
26153 AAGAAGTCCC
26163 ACCTAACATTAGACTAAA
1 ACCTAACATTAGACTAAA
26181 ACCTAACATTAGACTAAA
1 ACCTAACATTAGACTAAA
26199 A
1 A
26200 ATCGTCACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.22, G:0.05, T:0.22
Consensus pattern (18 bp):
ACCTAACATTAGACTAAA
Found at i:27574 original size:16 final size:17
Alignment explanation
Indices: 27553--27584 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
27543 AATGGGCAGT
27553 AATCCCTGC-AAAAAAA
1 AATCCCTGCGAAAAAAA
27569 AATCCCTGCGAAAAAA
1 AATCCCTGCGAAAAAA
27585 TCTCTGTATA
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:0.53, C:0.25, G:0.09, T:0.12
Consensus pattern (17 bp):
AATCCCTGCGAAAAAAA
Found at i:29623 original size:17 final size:15
Alignment explanation
Indices: 29593--29626 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 15
29583 GAGAAAAATA
29593 AATTTTAAAATTTTT
1 AATTTTAAAATTTTT
29608 AATTGTTAATAATTTTT
1 AATT-TTAA-AATTTTT
29625 AA
1 AA
29627 AATATGAGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 4 0.24
17 9 0.53
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
AATTTTAAAATTTTT
Found at i:30466 original size:6 final size:6
Alignment explanation
Indices: 30455--30519 Score: 76
Period size: 6 Copynumber: 10.8 Consensus size: 6
30445 GTCTTTTATA
* * * * *
30455 ACACAC ACACAC GCACAC GCACAC GCACAC GCACAC GCACAC ACACAC
1 ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC ACACAC
*
30503 ACACAC ATACAC ACACA
1 ACACAC ACACAC ACACA
30520 TACAGACATA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.43, C:0.48, G:0.08, T:0.02
Consensus pattern (6 bp):
ACACAC
Found at i:30483 original size:18 final size:18
Alignment explanation
Indices: 30456--30519 Score: 92
Period size: 18 Copynumber: 3.6 Consensus size: 18
30446 TCTTTTATAA
30456 CACACACACACGCACACG
1 CACACACACACGCACACG
*
30474 CACACGCACACGCACACG
1 CACACACACACGCACACG
* *
30492 CACACACACACACACACA
1 CACACACACACGCACACG
*
30510 TACACACACA
1 CACACACACA
30520 TACAGACATA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 41 1.00
ACGTcount: A:0.42, C:0.48, G:0.08, T:0.02
Consensus pattern (18 bp):
CACACACACACGCACACG
Found at i:30520 original size:10 final size:10
Alignment explanation
Indices: 30492--30523 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
30482 CACGCACACG
*
30492 CACACACACA
1 CACACACATA
30502 CACACACATA
1 CACACACATA
30512 CACACACATA
1 CACACACATA
30522 CA
1 CA
30524 GACATACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.44, G:0.00, T:0.06
Consensus pattern (10 bp):
CACACACATA
Found at i:30532 original size:4 final size:4
Alignment explanation
Indices: 30517--31233 Score: 1292
Period size: 4 Copynumber: 181.8 Consensus size: 4
30507 ACATACACAC
* *
30517 ACAT ACAG ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ATAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30565 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30613 ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30659 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30707 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30755 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30803 ACAT ACAT ACAT ACAT AC-- ACAT ACAT ACAT ACAT --AT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30847 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30895 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30943 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
30991 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* *
31039 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAC ACAT AC-- ACAC
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
* * * *
31085 ACAT ACAT AC-- ACAC ACAC ACAC ACAC ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
31131 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
31179 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
31227 ACAT ACA
1 ACAT ACA
31234 CGCACACGCA
Statistics
Matches: 695, Mismatches: 8, Indels: 20
0.96 0.01 0.03
Matches are distributed among these distances:
2 10 0.01
4 685 0.99
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:31246 original size:12 final size:12
Alignment explanation
Indices: 31231--31486 Score: 377
Period size: 12 Copynumber: 21.3 Consensus size: 12
31221 ATACATACAT
31231 ACACGCACACGC
1 ACACGCACACGC
31243 ACACGCACACGC
1 ACACGCACACGC
31255 ACACGCACACGC
1 ACACGCACACGC
31267 ACACGCACACGC
1 ACACGCACACGC
31279 ACACGCACACGC
1 ACACGCACACGC
31291 ACACGCACACGC
1 ACACGCACACGC
31303 ACACGCACACGC
1 ACACGCACACGC
31315 ACACGCACACGC
1 ACACGCACACGC
31327 ACACGCACACGC
1 ACACGCACACGC
31339 ACACGCACACGC
1 ACACGCACACGC
31351 ACACGCACACGC
1 ACACGCACACGC
31363 ACACGCACACGC
1 ACACGCACACGC
31375 ACACGCACACGC
1 ACACGCACACGC
31387 ACACGCACACGC
1 ACACGCACACGC
*
31399 ACACGCACACAC
1 ACACGCACACGC
* * *
31411 ACACACAAACAC
1 ACACGCACACGC
* *
31423 ACACACACACAC
1 ACACGCACACGC
* *
31435 ACACACACACAC
1 ACACGCACACGC
** *
31447 ACAAACACACAC
1 ACACGCACACGC
* *
31459 ACACACACACAC
1 ACACGCACACGC
* *
31471 ACACACACACAC
1 ACACGCACACGC
31483 ACAC
1 ACAC
31487 ACATATATAT
Statistics
Matches: 238, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
12 238 1.00
ACGTcount: A:0.39, C:0.49, G:0.11, T:0.00
Consensus pattern (12 bp):
ACACGCACACGC
Found at i:31254 original size:18 final size:18
Alignment explanation
Indices: 31231--31486 Score: 377
Period size: 18 Copynumber: 14.2 Consensus size: 18
31221 ATACATACAT
31231 ACACGCACACGCACACGC
1 ACACGCACACGCACACGC
31249 ACACGCACACGCACACGC
1 ACACGCACACGCACACGC
31267 ACACGCACACGCACACGC
1 ACACGCACACGCACACGC
31285 ACACGCACACGCACACGC
1 ACACGCACACGCACACGC
31303 ACACGCACACGCACACGC
1 ACACGCACACGCACACGC
31321 ACACGCACACGCACACGC
1 ACACGCACACGCACACGC
31339 ACACGCACACGCACACGC
1 ACACGCACACGCACACGC
31357 ACACGCACACGCACACGC
1 ACACGCACACGCACACGC
31375 ACACGCACACGCACACGC
1 ACACGCACACGCACACGC
*
31393 ACACGCACACGCACACAC
1 ACACGCACACGCACACGC
* * * *
31411 ACACACAAACACACACAC
1 ACACGCACACGCACACGC
* * *
31429 ACACACACACACACACAC
1 ACACGCACACGCACACGC
** * *
31447 ACAAACACACACACACAC
1 ACACGCACACGCACACGC
* * *
31465 ACACACACACACACACAC
1 ACACGCACACGCACACGC
31483 ACAC
1 ACAC
31487 ACATATATAT
Statistics
Matches: 231, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 231 1.00
ACGTcount: A:0.39, C:0.49, G:0.11, T:0.00
Consensus pattern (18 bp):
ACACGCACACGCACACGC
Found at i:31487 original size:12 final size:12
Alignment explanation
Indices: 31071--31489 Score: 262
Period size: 12 Copynumber: 34.9 Consensus size: 12
31061 ATACATACAT
*
31071 ACACACATACAC
1 ACACACACACAC
* *
31083 ACACATACATAC
1 ACACACACACAC
31095 ACACACACACAC
1 ACACACACACAC
* *
31107 ACACACATACAT
1 ACACACACACAC
* * *
31119 ACATACATACAT
1 ACACACACACAC
* * *
31131 ACATACATACAT
1 ACACACACACAC
* * *
31143 ACATACATACAT
1 ACACACACACAC
* * *
31155 ACATACATACAT
1 ACACACACACAC
* * *
31167 ACATACATACAT
1 ACACACACACAC
* * *
31179 ACATACATACAT
1 ACACACACACAC
* * *
31191 ACATACATACAT
1 ACACACACACAC
* * *
31203 ACATACATACAT
1 ACACACACACAC
* * *
31215 ACATACATACAT
1 ACACACACACAC
* *
31227 ACATACACGCAC
1 ACACACACACAC
* *
31239 ACGCACACGCAC
1 ACACACACACAC
* *
31251 ACGCACACGCAC
1 ACACACACACAC
* *
31263 ACGCACACGCAC
1 ACACACACACAC
* *
31275 ACGCACACGCAC
1 ACACACACACAC
* *
31287 ACGCACACGCAC
1 ACACACACACAC
* *
31299 ACGCACACGCAC
1 ACACACACACAC
* *
31311 ACGCACACGCAC
1 ACACACACACAC
* *
31323 ACGCACACGCAC
1 ACACACACACAC
* *
31335 ACGCACACGCAC
1 ACACACACACAC
* *
31347 ACGCACACGCAC
1 ACACACACACAC
* *
31359 ACGCACACGCAC
1 ACACACACACAC
* *
31371 ACGCACACGCAC
1 ACACACACACAC
* *
31383 ACGCACACGCAC
1 ACACACACACAC
* *
31395 ACGCACACGCAC
1 ACACACACACAC
*
31407 ACACACACACAA
1 ACACACACACAC
31419 ACACACACACAC
1 ACACACACACAC
31431 ACACACACACAC
1 ACACACACACAC
*
31443 ACACACAAACAC
1 ACACACACACAC
31455 ACACACACACAC
1 ACACACACACAC
31467 ACACACACACAC
1 ACACACACACAC
31479 ACACACACACA
1 ACACACACACA
31490 TATATATACA
Statistics
Matches: 388, Mismatches: 19, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 388 1.00
ACGTcount: A:0.44, C:0.42, G:0.07, T:0.08
Consensus pattern (12 bp):
ACACACACACAC
Found at i:32407 original size:16 final size:16
Alignment explanation
Indices: 32383--32421 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
32373 GAGAGTTATT
*
32383 TTTGAACAGATAATAC
1 TTTGTACAGATAATAC
32399 TTTGTACAGATAATAC
1 TTTGTACAGATAATAC
32415 TTTGTAC
1 TTTGTAC
32422 TTATCTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (16 bp):
TTTGTACAGATAATAC
Found at i:33154 original size:24 final size:24
Alignment explanation
Indices: 33092--33155 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
33082 ATTTAAAGAC
* *
33092 TCGATTCAAATTACATACTTTTGA
1 TCGATTCAAATTACCTACTTTTAA
33116 TCGATTCAAATTACCTACTTTTAA
1 TCGATTCAAATTACCTACTTTTAA
*
33140 TCGATTGAAATTACCT
1 TCGATTCAAATTACCT
33156 TTAAAAAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.33, C:0.19, G:0.08, T:0.41
Consensus pattern (24 bp):
TCGATTCAAATTACCTACTTTTAA
Found at i:34698 original size:4 final size:4
Alignment explanation
Indices: 34658--34688 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
34648 AAATGAAAAT
34658 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
34689 TAAATAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:34810 original size:33 final size:35
Alignment explanation
Indices: 34753--34839 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 35
34743 CTATACATCG
34753 AACTATATATTATATATATTTTCAAAAACATTTT-AA
1 AACTATATATTATATATA-TTTC-AAAACATTTTCAA
**
34789 AACTATATA-TATATATA-TTCAAAATGTTTTCAA
1 AACTATATATTATATATATTTCAAAACATTTTCAA
34822 AACTATATATTATATATA
1 AACTATATATTATATATA
34840 AAAAATGTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
32 8 0.17
33 14 0.30
34 8 0.17
35 8 0.17
36 9 0.19
ACGTcount: A:0.47, C:0.08, G:0.01, T:0.44
Consensus pattern (35 bp):
AACTATATATTATATATATTTCAAAACATTTTCAA
Found at i:34837 original size:2 final size:2
Alignment explanation
Indices: 34825--34892 Score: 79
Period size: 2 Copynumber: 35.5 Consensus size: 2
34815 TTTTCAAAAC
* * * *
34825 TA TA TA T- TA TA TA TA -A AA AA TG TA T- TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
34864 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
34893 TCAAAATGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
1 3 0.05
2 55 0.95
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (2 bp):
TA
Found at i:34845 original size:32 final size:32
Alignment explanation
Indices: 34783--34875 Score: 107
Period size: 32 Copynumber: 2.8 Consensus size: 32
34773 TTCAAAAACA
**
34783 TTTTAAAACTATATATATATATATTCAAAATG
1 TTTTAAAACTATATATATATATATAAAAAATG
34815 TTTTCAAAACTATATAT-TATATATAAAAAATG
1 TTTT-AAAACTATATATATATATATAAAAAATG
*
34847 TATTATATATAAATATATATATATATATA
1 T-TT-TA-A-AACTATATATATATATATA
34876 TATATATATA
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
32 18 0.35
33 15 0.29
34 2 0.04
35 9 0.17
36 8 0.15
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (32 bp):
TTTTAAAACTATATATATATATATAAAAAATG
Found at i:34938 original size:39 final size:39
Alignment explanation
Indices: 34872--35082 Score: 293
Period size: 39 Copynumber: 5.5 Consensus size: 39
34862 TATATATATA
* *
34872 TATATATATATATATATATATTCAAAATGTTTTCAAAAAC
1 TATATAT-TATATATATTTTTTCAAAATGTTTTCAAAAAC
* *
34912 TATATATTATATATATTTTTTAAAAATATTTTCAAAAAC
1 TATATATTATATATATTTTTTCAAAATGTTTTCAAAAAC
**
34951 TATATATTATATATA--TTTTCAAAA-AATTTCAAAAAC
1 TATATATTATATATATTTTTTCAAAATGTTTTCAAAAAC
* *
34987 TATATATCATATATATTTTTTCAAAATGTTTCCAAAAAC
1 TATATATTATATATATTTTTTCAAAATGTTTTCAAAAAC
** *
35026 TATATATTATATATAAATTTTCAAAGTGTTTTCAAAAAC
1 TATATATTATATATATTTTTTCAAAATGTTTTCAAAAAC
35065 TATATATTATATATATTT
1 TATATATTATATATATTT
35083 CAAAAAAAAT
Statistics
Matches: 151, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
36 25 0.17
37 8 0.05
38 9 0.06
39 102 0.68
40 7 0.05
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (39 bp):
TATATATTATATATATTTTTTCAAAATGTTTTCAAAAAC
Found at i:35090 original size:114 final size:113
Alignment explanation
Indices: 34874--35089 Score: 344
Period size: 114 Copynumber: 1.9 Consensus size: 113
34864 TATATATATA
* **
34874 TATATATATATATATATATTCAAAATGTTTTCAAAAACTATATATTATATATATTTTTTAAAAAT
1 TATATATATATATATATATTCAAAATGTTTCCAAAAACTATATATTATATATAAATTTTAAAAAT
34939 ATTTTCAAAAACTATATATTATATATATTTTCAAAAAATTTCAAAAAC
66 ATTTTCAAAAACTATATATTATATATATTTTCAAAAAATTTCAAAAAC
* * * *
34987 TATATATCATATATATTTTTTCAAAATGTTTCCAAAAACTATATATTATATATAAATTTTCAAAG
1 TATATAT-ATATATATATATTCAAAATGTTTCCAAAAACTATATATTATATATAAATTTTAAAAA
*
35052 TGTTTTCAAAAACTATATATTATATATA-TTTCAAAAAA
65 TATTTTCAAAAACTATATATTATATATATTTTCAAAAAA
35090 AATTATATAT
Statistics
Matches: 94, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
113 17 0.18
114 77 0.82
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (113 bp):
TATATATATATATATATATTCAAAATGTTTCCAAAAACTATATATTATATATAAATTTTAAAAAT
ATTTTCAAAAACTATATATTATATATATTTTCAAAAAATTTCAAAAAC
Found at i:41064 original size:64 final size:64
Alignment explanation
Indices: 41011--41173 Score: 229
Period size: 65 Copynumber: 2.5 Consensus size: 64
41001 CGGTGCACCA
*
41011 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTG-AAAATAGCCAGAGTGCATCGATGCATGG
** * **
41075 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAATAGCCAGAGTGCATCGATGCATGG
* *
41140 AGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
41174 CAATTAATTC
Statistics
Matches: 86, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
64 39 0.45
65 47 0.55
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (64 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:41145 original size:19 final size:19
Alignment explanation
Indices: 41121--41157 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
41111 GAAAATATTC
41121 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
41140 AGAGTGCATCGGTGCATG
1 AGAGTGCATCGATGCATG
41158 AAATGCATTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.22
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:41218 original size:65 final size:64
Alignment explanation
Indices: 41015--41215 Score: 225
Period size: 65 Copynumber: 3.1 Consensus size: 64
41005 GCACCAAGTG
* * *
41015 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTGGTGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAAT-TCATGATGCATCGATGCATGGAC-TG
41079 -
64 A
*
41079 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG-TTTGAAAA-ATTCATGA-TGCATCGATGCATGGACT
41141 GA
63 GA
* * *
41143 GTGCATCGGTGCATGAAATGCATTCGATG-TTCAATTAATTCATCGATGCATCGATGCATGGACT
1 -TGCATCGATGCATGAAATGCATTCGATGTTTGAA-AAATTCAT-GATGCATCGATGCATGGACT
41207 GA
63 GA
41209 TGCATCG
1 TGCATCG
41216 GTGTATACCT
Statistics
Matches: 118, Mismatches: 8, Indels: 21
0.80 0.05 0.14
Matches are distributed among these distances:
63 10 0.08
64 45 0.38
65 59 0.50
66 4 0.03
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (64 bp):
TGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:48645 original size:64 final size:65
Alignment explanation
Indices: 48592--48754 Score: 211
Period size: 65 Copynumber: 2.5 Consensus size: 65
48582 CGGTGCACCA
*
48592 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCAGAGTGCATCGATGCATGG
** * * * **
48656 CTTGTGCATCAATGCATCAAATGCATTCGATGTTTTAAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCAGAGTGCATCGATGCATGG
* * * *
48721 AGAGTGCATCGGTACATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
48755 CAATTAATTC
Statistics
Matches: 82, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
64 40 0.49
65 42 0.51
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (65 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTGAAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:48726 original size:19 final size:19
Alignment explanation
Indices: 48702--48752 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
48692 AAAAATATTC
48702 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
* *
48721 AGAGTGCATCGGTACATGG
1 AGAGTGCATCGATGCATGG
48740 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
48753 TTCAATTAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 4 0.15
18 5 0.19
19 18 0.67
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Done.