Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008206.1 Hibiscus syriacus cultivar Beakdansim tig00110828_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: 1504526
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 9
Found at i:511901 original size:60 final size:60
Alignment explanation
Indices: 511819--511948 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 60
511809 GTTAAATTAT
511819 AAAATGGTCCTTCAACTATAGAGTACTACATTATTAAGTCCATCAACTATTAAAAGTTAC
1 AAAATGGTCCTTCAACTATAGAGTACTACATTATTAAGTCCATCAACTATTAAAAGTTAC
** * * * * * * ** *
511879 AAAATGGTGTTTCGACTATAGAGTTCTACTTTGTTGAGTCCCTTGATTATTAAAAGTTAC
1 AAAATGGTCCTTCAACTATAGAGTACTACATTATTAAGTCCATCAACTATTAAAAGTTAC
511939 AAAATGGTCC
1 AAAATGGTCC
511949 CCGACTATTT
Statistics
Matches: 57, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (60 bp):
AAAATGGTCCTTCAACTATAGAGTACTACATTATTAAGTCCATCAACTATTAAAAGTTAC
Found at i:514300 original size:35 final size:35
Alignment explanation
Indices: 514261--514355 Score: 163
Period size: 35 Copynumber: 2.7 Consensus size: 35
514251 CGTCAAGTCC
* *
514261 AGTAAGGCCCTGAGCATACAGCCGAGGCACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
*
514296 AGTAAGGCCCTGAGCACACAGCTGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
514331 AGTAAGGCCCTGAGCACACAGCCGA
1 AGTAAGGCCCTGAGCACACAGCCGA
514356 TGAGTCTCCA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 56 1.00
ACGTcount: A:0.31, C:0.28, G:0.31, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
Found at i:514459 original size:24 final size:24
Alignment explanation
Indices: 514432--514482 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
514422 TAAATCAAAA
* * *
514432 ATCAAAACATAGTCCAGGTCTAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* *
514456 ATCAGATCAAAATCCAGGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
514480 ATC
1 ATC
514483 TGTTCAGAAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:522793 original size:37 final size:37
Alignment explanation
Indices: 522743--522816 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
522733 TTTACCATCT
522743 TATATGGTAAAGTCTAAGGAGAGACAACCTAATTCAA
1 TATATGGTAAAGTCTAAGGAGAGACAACCTAATTCAA
522780 TATATGGTAAAGTCTAAGGAGAGACAACCTAATTCAA
1 TATATGGTAAAGTCTAAGGAGAGACAACCTAATTCAA
522817 GGTTAAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (37 bp):
TATATGGTAAAGTCTAAGGAGAGACAACCTAATTCAA
Found at i:531395 original size:48 final size:48
Alignment explanation
Indices: 531342--531550 Score: 238
Period size: 48 Copynumber: 4.4 Consensus size: 48
531332 CTGCGATTGA
* * * * *
531342 TGTACCTGATGTTGCAGCAGGTGCACCAGGACACGCTTAGCCTATAGG
1 TGTACCTGATGTTGCAGCCGGTGCACCAGGACATGATGATCCTATAGG
* * **
531390 TGTACCTGTTGTTGCAGCCGTTGCACCAGGAGGTGATGATCCTATAGG
1 TGTACCTGATGTTGCAGCCGGTGCACCAGGACATGATGATCCTATAGG
* * * **
531438 TTTGCCTGATGTTGCAGCCGTTGCACCAGGAGGTGATGATCCTATAGG
1 TGTACCTGATGTTGCAGCCGGTGCACCAGGACATGATGATCCTATAGG
* * * * * *
531486 TTTGCCTGATGTTGCAGTCGGTGCACCAGGACATGGTGCTCCTATTGG
1 TGTACCTGATGTTGCAGCCGGTGCACCAGGACATGATGATCCTATAGG
531534 TGTACCTGATGTTGCAG
1 TGTACCTGATGTTGCAG
531551 TTGATGCATC
Statistics
Matches: 140, Mismatches: 21, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 140 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.29
Consensus pattern (48 bp):
TGTACCTGATGTTGCAGCCGGTGCACCAGGACATGATGATCCTATAGG
Found at i:531574 original size:48 final size:48
Alignment explanation
Indices: 531342--531599 Score: 219
Period size: 48 Copynumber: 5.4 Consensus size: 48
531332 CTGCGATTGA
* * * * * ***
531342 TGTACCTGATGTTGCAGCAGGTGCACCAGGACACGCTTAGCCTATAGG
1 TGTACCTGATGTTGCAGCCGATGCACCAGGAGATGATGCTCCTATAGG
* * * *
531390 TGTACCTGTTGTTGCAGCCGTTGCACCAGGAGGTGATGATCCTATAGG
1 TGTACCTGATGTTGCAGCCGATGCACCAGGAGATGATGCTCCTATAGG
* * * * *
531438 TTTGCCTGATGTTGCAGCCGTTGCACCAGGAGGTGATGATCCTATAGG
1 TGTACCTGATGTTGCAGCCGATGCACCAGGAGATGATGCTCCTATAGG
* * * * * * *
531486 TTTGCCTGATGTTGCAGTCGGTGCACCAGGACATGGTGCTCCTATTGG
1 TGTACCTGATGTTGCAGCCGATGCACCAGGAGATGATGCTCCTATAGG
** * * *
531534 TGTACCTGATGTTGCAGTTGATGCATCGGGAGATGATGCTCCAATAGG
1 TGTACCTGATGTTGCAGCCGATGCACCAGGAGATGATGCTCCTATAGG
** * *
531582 CATTCCTGGTGTTGCAGC
1 TGTACCTGATGTTGCAGC
531600 TGGTGCATTG
Statistics
Matches: 176, Mismatches: 34, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
48 176 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.29
Consensus pattern (48 bp):
TGTACCTGATGTTGCAGCCGATGCACCAGGAGATGATGCTCCTATAGG
Found at i:531626 original size:144 final size:144
Alignment explanation
Indices: 531346--531606 Score: 319
Period size: 144 Copynumber: 1.8 Consensus size: 144
531336 GATTGATGTA
* * *
531346 CCTGATGTTGCAGCAGGTGCACCAGGACACGCTTAGCCTATAGGTGTACCTGTTGTTGCAGCCGT
1 CCTGATGTTGCAGCAGGTGCACCAGGACACGCTGAGCCTATAGGTGTACCTGATGTTGCAGCCGA
* * * *
531411 TGCACCAGGAGGTGATGATCCTATAGGTTTGCCTGATGTTGCAGCCGTTGCACCAGGAGGTGATG
66 TGCACCAGGAGATGATGATCCAATAGGATTGCCTGATGTTGCAGCCGGTGCACCAGGAGGTGATG
531476 ATCCTATAGGTTTG
131 ATCCTATAGGTTTG
* * ** * **
531490 CCTGATGTTGCAGTC-GGTGCACCAGGACATGGTGCTCCTATTGGTGTACCTGATGTTGCAGTTG
1 CCTGATGTTGCAG-CAGGTGCACCAGGACACGCTGAGCCTATAGGTGTACCTGATGTTGCAGCCG
* * * * *
531554 ATGCATCGGGAGATGATGCTCCAATAGGCATT-CCTGGTGTTGCAGCTGGTGCA
65 ATGCACCAGGAGATGATGATCCAATAGG-ATTGCCTGATGTTGCAGCCGGTGCA
531607 TTGAGAGGTG
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
144 93 0.97
145 3 0.03
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (144 bp):
CCTGATGTTGCAGCAGGTGCACCAGGACACGCTGAGCCTATAGGTGTACCTGATGTTGCAGCCGA
TGCACCAGGAGATGATGATCCAATAGGATTGCCTGATGTTGCAGCCGGTGCACCAGGAGGTGATG
ATCCTATAGGTTTG
Found at i:531636 original size:144 final size:144
Alignment explanation
Indices: 531346--531637 Score: 302
Period size: 144 Copynumber: 2.0 Consensus size: 144
531336 GATTGATGTA
* * *
531346 CCTGATGTTGCAGCAGGTGCACCAGGACACGCTTAGCCTATAGGTGTACCTGTTGTTGCAGCCGT
1 CCTGATGTTGCAGCAGGTGCACCAGGACACGCTGAGCCTATAGGTGTACCTGATGTTGCAGCCGA
* * * *
531411 TGCACCAGGAGGTGATGATCCTATAGGTTTGCCTGATGTTGCAGCCGTTGCACCAGGAGGTGATG
66 TGCACCAGGAGATGATGATCCAATAGGATTGCCTGATGTTGCAGCCGGTGCACCAGGAGGTGATG
**
531476 ATCCTATAGGTTTG
131 ATCCTATAGGCGTG
* * ** * **
531490 CCTGATGTTGCAGTC-GGTGCACCAGGACATGGTGCTCCTATTGGTGTACCTGATGTTGCAGTTG
1 CCTGATGTTGCAG-CAGGTGCACCAGGACACGCTGAGCCTATAGGTGTACCTGATGTTGCAGCCG
* * * * * **
531554 ATGCATCGGGAGATGATGCTCCAATAGGCATT-CCTGGTGTTGCAGCTGGTGCA-TTGAGAGGTG
65 ATGCACCAGGAGATGATGATCCAATAGG-ATTGCCTGATGTTGCAGCCGGTGCACCAG-GAGGTG
* **
531617 ATGTTCCTATTTGCGTG
128 ATGATCCTATAGGCGTG
531634 CCTG
1 CCTG
531638 GTGATGCATC
Statistics
Matches: 119, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
143 1 0.01
144 115 0.97
145 3 0.03
ACGTcount: A:0.18, C:0.21, G:0.31, T:0.29
Consensus pattern (144 bp):
CCTGATGTTGCAGCAGGTGCACCAGGACACGCTGAGCCTATAGGTGTACCTGATGTTGCAGCCGA
TGCACCAGGAGATGATGATCCAATAGGATTGCCTGATGTTGCAGCCGGTGCACCAGGAGGTGATG
ATCCTATAGGCGTG
Found at i:532466 original size:35 final size:36
Alignment explanation
Indices: 532427--532507 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 36
532417 CTGCTCCTAT
532427 TGGTGTTTCTGGTGTAGCAACCGGTGCACC-AGAAA
1 TGGTGTTTCTGGTGTAGCAACCGGTGCACCAAGAAA
** * * *
532462 TGGTGTGCCAGGTGTAGCAGCCGGTGCACCAAGAAC
1 TGGTGTTTCTGGTGTAGCAACCGGTGCACCAAGAAA
*
532498 TGGTGGTTCT
1 TGGTGTTTCT
532508 ATTGGTGTGC
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
35 26 0.72
36 10 0.28
ACGTcount: A:0.20, C:0.21, G:0.35, T:0.25
Consensus pattern (36 bp):
TGGTGTTTCTGGTGTAGCAACCGGTGCACCAAGAAA
Found at i:532632 original size:19 final size:19
Alignment explanation
Indices: 532608--532650 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
532598 GCCAATGGTT
532608 TGTTGGACTGGGAAGTCTG
1 TGTTGGACTGGGAAGTCTG
532627 TGTTGGACTGGGAAGTCTG
1 TGTTGGACTGGGAAGTCTG
532646 TGTTG
1 TGTTG
532651 TCAGAAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.14, C:0.09, G:0.42, T:0.35
Consensus pattern (19 bp):
TGTTGGACTGGGAAGTCTG
Found at i:535414 original size:19 final size:19
Alignment explanation
Indices: 535390--535427 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
535380 CAGACAGCAA
535390 GAAATGGAGCCTTCTGAAT
1 GAAATGGAGCCTTCTGAAT
535409 GAAATGGAGCCTTCTGAAT
1 GAAATGGAGCCTTCTGAAT
535428 AGCTTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (19 bp):
GAAATGGAGCCTTCTGAAT
Found at i:539627 original size:30 final size:29
Alignment explanation
Indices: 539572--539631 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
539562 GTCCCGAAGG
*
539572 ACCTATCCATATTCTCGAAGAACATAGGT
1 ACCTATCCATATTCCCGAAGAACATAGGT
* *
539601 ACCTGTCCATATGTCCCGAAGGACATAGGT
1 ACCTATCCATAT-TCCCGAAGAACATAGGT
539631 A
1 A
539632 ACCCTCGACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 11 0.41
30 16 0.59
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (29 bp):
ACCTATCCATATTCCCGAAGAACATAGGT
Found at i:543783 original size:120 final size:122
Alignment explanation
Indices: 543571--543806 Score: 320
Period size: 121 Copynumber: 2.0 Consensus size: 122
543561 AAACTACCCA
* * * * * *
543571 TTTAGTATCTAAACTATTATTTTTAGTCTGTTTTTGTATCTAAACTTTCATTTTCTTCAAAATCA
1 TTTAGTACCTAAACTATCAATTTTAGTCTATTTTAGTATCTAAACTTTCATTCTCTTCAAAATCA
*
543636 TACCTAACATTTAGTTTTTTTCCCATTTTAGTACCC-ACCATTAAAAACTTAACTCG
66 TACATAACATTTAGTTTTTTTCCCATTTTAGTACCCTACCATTAAAAACTTAACTCG
*
543692 TTTAGTACCTAAACTATCAATTTTGGTCTATTTTAGTA-CTTAAACTTTCATTCT-TTCAAAATC
1 TTTAGTACCTAAACTATCAATTTTAGTCTATTTTAGTATC-TAAACTTTCATTCTCTTCAAAATC
* *
543755 ATACATAA-AGTTTAGTTTTTGTT-TCATTTTATTACCCTACCATTAAAAACTT
65 ATACATAACA-TTTAGTTTTT-TTCCCATTTTAGTACCCTACCATTAAAAACTT
543807 TAGTTTTTGT
Statistics
Matches: 101, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
119 1 0.01
120 39 0.39
121 61 0.60
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.46
Consensus pattern (122 bp):
TTTAGTACCTAAACTATCAATTTTAGTCTATTTTAGTATCTAAACTTTCATTCTCTTCAAAATCA
TACATAACATTTAGTTTTTTTCCCATTTTAGTACCCTACCATTAAAAACTTAACTCG
Found at i:544190 original size:31 final size:32
Alignment explanation
Indices: 544148--544237 Score: 89
Period size: 31 Copynumber: 2.9 Consensus size: 32
544138 TGAATCTATC
*
544148 AAACTATTACAAAA-TAGTTATTAAATTTTATT
1 AAACTATTACAAAATTA-TAATTAAATTTTATT
*
544180 AAACTA-TACAAAATTATAATTAATTTTTATT
1 AAACTATTACAAAATTATAATTAAATTTTATT
* * *
544211 GAAA-TGTT-CAAAATGATCATTAAATTT
1 -AAACTATTACAAAATTATAATTAAATTT
544238 ATCAAACATT
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
31 37 0.76
32 12 0.24
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (32 bp):
AAACTATTACAAAATTATAATTAAATTTTATT
Found at i:546860 original size:18 final size:18
Alignment explanation
Indices: 546839--546885 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
546829 TAAAAATATG
* *
546839 AATGATAATCATACTAAT
1 AATGATAATAATAATAAT
*
546857 AATGATAAGAATAATAAT
1 AATGATAATAATAATAAT
*
546875 AAGGATAATAA
1 AATGATAATAA
546886 GATTATATGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.28
Consensus pattern (18 bp):
AATGATAATAATAATAAT
Found at i:548154 original size:29 final size:29
Alignment explanation
Indices: 548109--548218 Score: 91
Period size: 29 Copynumber: 3.7 Consensus size: 29
548099 GAGGCCATAA
548109 TTTGAGGATGGAA-TTAGAATGTTCAAAAG
1 TTTGAGGAT-GAATTTAGAATGTTCAAAAG
* *
548138 TTTGAGGATTAATTTAGAATGTGAGTC-ATAG
1 TTTGAGGATGAATTTAGAATGT---TCAAAAG
* * *
548169 TTT-AGGGATGAAATTAGAATATCCAAAAG
1 TTTGA-GGATGAATTTAGAATGTTCAAAAG
* *
548198 TTTAAGGATTAATTTAGAATG
1 TTTGAGGATGAATTTAGAATG
548219 AGAGTTGTAG
Statistics
Matches: 64, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
28 3 0.05
29 37 0.58
30 2 0.03
31 20 0.31
32 2 0.03
ACGTcount: A:0.38, C:0.04, G:0.24, T:0.35
Consensus pattern (29 bp):
TTTGAGGATGAATTTAGAATGTTCAAAAG
Found at i:548207 original size:60 final size:60
Alignment explanation
Indices: 548114--548232 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
548104 CATAATTTGA
* * * * *
548114 GGATGGAATTAGAATGTTCAAAAGTTTGAGGATTAATTTAGAATGTGAGTCATAGTTTAG
1 GGATGAAATTAGAATATCCAAAAGTTTAAGGATTAATTTAGAATGAGAGTCATAGTTTAG
**
548174 GGATGAAATTAGAATATCCAAAAGTTTAAGGATTAATTTAGAATGAGAGTTGTAGTTTA
1 GGATGAAATTAGAATATCCAAAAGTTTAAGGATTAATTTAGAATGAGAGTCATAGTTTA
548233 TGGACGTGTG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.34
Consensus pattern (60 bp):
GGATGAAATTAGAATATCCAAAAGTTTAAGGATTAATTTAGAATGAGAGTCATAGTTTAG
Found at i:551867 original size:22 final size:21
Alignment explanation
Indices: 551842--551889 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 21
551832 TTATTTTATT
*
551842 TTTTAATTTATGTTGTTTTTTC
1 TTTTAATTTATGTT-TTTTTTA
*
551864 TTTTATTTTATGTTTTTTTTA
1 TTTTAATTTATGTTTTTTTTA
551885 TTTTA
1 TTTTA
551890 TTAAGTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.15, C:0.02, G:0.06, T:0.77
Consensus pattern (21 bp):
TTTTAATTTATGTTTTTTTTA
Found at i:551879 original size:17 final size:16
Alignment explanation
Indices: 551831--551891 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 16
551821 TAAATGTAGG
*
551831 TTTATTTTATTTTTTAA
1 TTTATTTTATTTTTT-T
* *
551848 TTTATGTTGTTTTTTCT
1 TTTATTTTATTTTTT-T
*
551865 TTTATTTTATGTTTTT
1 TTTATTTTATTTTTTT
551881 TTTATTTTATT
1 TTTATTTTATT
551892 AAGTTTATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
16 11 0.31
17 25 0.69
ACGTcount: A:0.15, C:0.02, G:0.05, T:0.79
Consensus pattern (16 bp):
TTTATTTTATTTTTTT
Found at i:554366 original size:108 final size:108
Alignment explanation
Indices: 554252--554468 Score: 434
Period size: 108 Copynumber: 2.0 Consensus size: 108
554242 TGGTTTCTAG
554252 TTAGTTGAATAGAGCTTGAAAATTTTAAGTTTGCGAGTTTTCAAGTCGAGTCAAACTTCATTTTA
1 TTAGTTGAATAGAGCTTGAAAATTTTAAGTTTGCGAGTTTTCAAGTCGAGTCAAACTTCATTTTA
554317 GAGTTTTCGAGTCGAGCTCAACAATACTTGAGCTAGACTCGGC
66 GAGTTTTCGAGTCGAGCTCAACAATACTTGAGCTAGACTCGGC
554360 TTAGTTGAATAGAGCTTGAAAATTTTAAGTTTGCGAGTTTTCAAGTCGAGTCAAACTTCATTTTA
1 TTAGTTGAATAGAGCTTGAAAATTTTAAGTTTGCGAGTTTTCAAGTCGAGTCAAACTTCATTTTA
554425 GAGTTTTCGAGTCGAGCTCAACAATACTTGAGCTAGACTCGGC
66 GAGTTTTCGAGTCGAGCTCAACAATACTTGAGCTAGACTCGGC
554468 T
1 T
554469 CATTTACAGC
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.35
Consensus pattern (108 bp):
TTAGTTGAATAGAGCTTGAAAATTTTAAGTTTGCGAGTTTTCAAGTCGAGTCAAACTTCATTTTA
GAGTTTTCGAGTCGAGCTCAACAATACTTGAGCTAGACTCGGC
Found at i:555446 original size:9 final size:9
Alignment explanation
Indices: 555432--555457 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
555422 TTTAACTATT
555432 TAAATTATG
1 TAAATTATG
555441 TAAATTATG
1 TAAATTATG
555450 TAAATTAT
1 TAAATTAT
555458 ACCACCTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (9 bp):
TAAATTATG
Found at i:555963 original size:39 final size:35
Alignment explanation
Indices: 555876--556107 Score: 177
Period size: 30 Copynumber: 6.7 Consensus size: 35
555866 TATGGGTAAC
*
555876 ATATAGTTTTAAAATCATTTT-AAAAACTTATATA-
1 ATATAGTTTTAAAAACATTTTGAAAAA-TTATATAT
555910 ATAT-GTTTTAAAAAACATTTTTGAATAAATTATATAAT
1 ATATAGTTTT-AAAAACA-TTTTGAA-AAATTATAT-AT
555948 ATATAGTTTTAAAAAAACATTTTGAATAAATTATATAT
1 ATATAGTTTT--AAAAACATTTTGAA-AAATTATATAT
* * *
555986 ATATAGTTTTAAAAACGTTTTTTTAAAACTTATATA-
1 ATATAGTTTTAAAAAC--ATTTTGAAAAATTATATAT
*
556022 ATAT--TTTT-AAAACATTTTG-AAAACTATATA-
1 ATATAGTTTTAAAAACATTTTGAAAAATTATATAT
* **
556052 ATATAGTTTT-GAAAC-TTTT-TTAAA-TATA-AT
1 ATATAGTTTTAAAAACATTTTGAAAAATTATATAT
* *
556082 ATATAGTTTAAAAAATATTTTTGAAA
1 ATATAGTTTTAAAAACA-TTTTGAAA
556108 TATGTATTAT
Statistics
Matches: 165, Mismatches: 15, Indels: 36
0.76 0.07 0.17
Matches are distributed among these distances:
29 1 0.01
30 26 0.16
31 14 0.08
32 8 0.05
33 14 0.08
34 15 0.09
35 4 0.02
36 18 0.11
37 13 0.08
38 22 0.13
39 22 0.13
40 8 0.05
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (35 bp):
ATATAGTTTTAAAAACATTTTGAAAAATTATATAT
Found at i:555988 original size:38 final size:37
Alignment explanation
Indices: 555876--556000 Score: 170
Period size: 39 Copynumber: 3.4 Consensus size: 37
555866 TATGGGTAAC
*
555876 ATATAGTTTT-AAAATCATTTT-AA-AAACTTATATA-
1 ATATAGTTTTAAAAAACATTTTGAATAAA-TTATATAT
555910 ATAT-GTTTTAAAAAACATTTTTGAATAAATTATATAAT
1 ATATAGTTTTAAAAAACA-TTTTGAATAAATTATAT-AT
555948 ATATAGTTTTAAAAAAACATTTTGAATAAATTATATAT
1 ATATAGTTTT-AAAAAACATTTTGAATAAATTATATAT
555986 ATATAGTTTTAAAAA
1 ATATAGTTTTAAAAA
556001 CGTTTTTTTA
Statistics
Matches: 82, Mismatches: 1, Indels: 13
0.85 0.01 0.14
Matches are distributed among these distances:
33 5 0.06
34 10 0.12
35 4 0.05
36 8 0.10
37 9 0.11
38 16 0.20
39 22 0.27
40 8 0.10
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (37 bp):
ATATAGTTTTAAAAAACATTTTGAATAAATTATATAT
Found at i:555994 original size:110 final size:110
Alignment explanation
Indices: 555812--556056 Score: 281
Period size: 110 Copynumber: 2.2 Consensus size: 110
555802 TTGCAAACGG
*
555812 TTTTTGAAAATATATATATAATATATAGTTTTTAAAAAGAAAACATTTTGAAAATATGGGTAACA
1 TTTTTGAAAA-AT-TATATAATATATAGTTTTT-AAAAGAAAACATTTTGAAAATATGGATAACA
*
555877 TATAGTTTTAAAATC-ATTTTAAAAACTTATATAATATGTTTTAAAAAACA
63 TATAGTTTTAAAAACGATTTTAAAAACTTATATAATAT-TTTT--AAAACA
* *
555927 TTTTTGAATAAATTATATAATATATAG-TTTT-AAA-AAAACATTTTGAATAA-AT-TATATATA
1 TTTTTGAA-AAATTATATAATATATAGTTTTTAAAAGAAAACATTTTGAA-AATATGGATA-ACA
* *
555987 TATAGTTTTAAAAACGTTTTTTTAAAACTTATATAATATTTTTAAAACA
63 TATAGTTTTAAAAACG-ATTTTAAAAACTTATATAATATTTTTAAAACA
*
556036 -TTTTG-AAAACTATATAATATA
1 TTTTTGAAAAATTATATAATATA
556057 GTTTTGAAAC
Statistics
Matches: 118, Mismatches: 7, Indels: 19
0.82 0.05 0.13
Matches are distributed among these distances:
106 14 0.12
107 1 0.01
108 5 0.04
109 8 0.07
110 31 0.26
111 9 0.08
112 20 0.17
113 4 0.03
114 14 0.12
115 10 0.08
116 2 0.02
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (110 bp):
TTTTTGAAAAATTATATAATATATAGTTTTTAAAAGAAAACATTTTGAAAATATGGATAACATAT
AGTTTTAAAAACGATTTTAAAAACTTATATAATATTTTTAAAACA
Found at i:556681 original size:127 final size:126
Alignment explanation
Indices: 556453--556708 Score: 455
Period size: 127 Copynumber: 2.0 Consensus size: 126
556443 GGGGGGACAG
556453 CCACGCAAATCTCAGAAGCATAAACACAGTAAACCAAATAACCAAAACAGATCAAGGAGAACCCA
1 CCACGCAAATCTCAGAAGCATAAACACAGTAAACCAAATAACCAAAACAGATCAAGGAGAACCCA
556518 CAACGGATCACAGTAAACCAGAGTTCAAACCAACAACAAGTAAAAACAGAACCAACCATAAA
66 CAACGGATCACAGTAAACCAGAGTTCAAACCAACAACAAGTAAAAACAGAACCAA-CATAAA
556580 CCACGCAAATCTCAGAAGCATAAACACAGTAAACCAAATAACCAAAACAAGATCAAGGAGAA-CC
1 CCACGCAAATCTCAGAAGCATAAACACAGTAAACCAAATAACCAAAAC-AGATCAAGGAGAACCC
556644 ACAACGGATCAACAGT-AACCAAGAGTTCAAACC-ACAACAAGTAAAAACAGAACCAACATAAA
65 ACAACGGATC-ACAGTAAACC-AGAGTTCAAACCAACAACAAGTAAAAACAGAACCAACATAAA
556706 CCA
1 CCA
556709 TCGACCAACA
Statistics
Matches: 126, Mismatches: 0, Indels: 7
0.95 0.00 0.05
Matches are distributed among these distances:
126 9 0.07
127 87 0.69
128 30 0.24
ACGTcount: A:0.52, C:0.27, G:0.12, T:0.09
Consensus pattern (126 bp):
CCACGCAAATCTCAGAAGCATAAACACAGTAAACCAAATAACCAAAACAGATCAAGGAGAACCCA
CAACGGATCACAGTAAACCAGAGTTCAAACCAACAACAAGTAAAAACAGAACCAACATAAA
Found at i:556750 original size:32 final size:31
Alignment explanation
Indices: 556687--556751 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
556677 ACAACAAGTA
* *
556687 AAAACAGAACCAACATAAACCATCGACCAAC
1 AAAACAGAACCAACATAAACCAACGAACAAC
*
556718 AAAACAGAAACC-ACATCAAACCAAGGAACAAC
1 AAAACAG-AACCAACAT-AAACCAACGAACAAC
556750 AA
1 AA
556752 CAAACCAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 11 0.38
32 18 0.62
ACGTcount: A:0.58, C:0.29, G:0.08, T:0.05
Consensus pattern (31 bp):
AAAACAGAACCAACATAAACCAACGAACAAC
Found at i:562594 original size:84 final size:83
Alignment explanation
Indices: 562506--563267 Score: 932
Period size: 84 Copynumber: 9.2 Consensus size: 83
562496 GCTCAAGGCC
*
562506 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
562571 TGCAGAATAGCTTAAGTCG
65 TGCAGCATAACTTAAGTCG
* ** * * * *
562590 AGAAGGGCTATCT---ACCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
1 AGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
*
562652 TGTAGCATAACTTAAGTCG
65 TGCAGCATAACTTAAGTCG
* *
562671 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
562736 TGCAGCATAGCTTAAGTCG
65 TGCAGCATAACTTAAGTCG
* ** * * * *
562755 AGAAGGGCTATCTG---CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
1 AGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
*
562817 TGCAGCATAACCTAAGTCG
65 TGCAGCATAACTTAAGTCG
* *
562836 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
562901 TGCAGCATAGCTTAAGTCG
65 TGCAGCATAACTTAAGTCG
* * * * * * *
562920 AGAAGGGCTATCTG---CCAAAGACCCTCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATT
1 AGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATT
*
562982 TGTAGCATAACTTAAGTCG
65 TGCAGCATAACTTAAGTCG
*
563001 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
563066 TGCAGCACAACTTAAGTCT
65 TGCAGCATAACTTAAGTCG
* * * *
563085 AGAAGGGTTGTCTGGCAACAAAAGACCTTTGAGTTTGACTACGCTCAGCT-CAACGGCACATCAT
1 AGAAGGGTTATCT-GCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCAT
* * * *
563149 TTACAGCATAACTCAAGGCT
64 TTGCAGCATAACTTAAGTCG
** *
563169 AGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCAACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
*
563234 TGCAGCATAACTTAAGTCA
65 TGCAGCATAACTTAAGTCG
563253 AGAAGGGTTATCTGC
1 AGAAGGGTTATCTGC
563268 TAAAGACCTT
Statistics
Matches: 576, Mismatches: 83, Indels: 38
0.83 0.12 0.05
Matches are distributed among these distances:
80 79 0.14
81 130 0.23
83 6 0.01
84 277 0.48
85 84 0.15
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.24
Consensus pattern (83 bp):
AGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
GCAGCATAACTTAAGTCG
Found at i:562778 original size:165 final size:165
Alignment explanation
Indices: 562506--563275 Score: 1157
Period size: 165 Copynumber: 4.6 Consensus size: 165
562496 GCTCAAGGCC
562506 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
562571 TGCAGAATAGCTTAAGTCGAGAAGGGCTATCTACCAAAGACCCCCGAGTTCGATTACACTCAGCT
66 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
*
562636 TCGAGGGCACATCATTTGTAGCATAACTTAAGTCG
131 TCGAGGGCACATCATTTGCAGCATAACTTAAGTCG
*
562671 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
562736 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
66 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
*
562801 TCGAGGGCACATCATTTGCAGCATAACCTAAGTCG
131 TCGAGGGCACATCATTTGCAGCATAACTTAAGTCG
*
562836 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCTAAGGCACATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* *
562901 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCAAGTTCGATTACACTCAGCT
66 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
*
562966 TCGAGGGCACATCATTTGTAGCATAACTTAAGTCG
131 TCGAGGGCACATCATTTGCAGCATAACTTAAGTCG
* *
563001 AGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATT
1 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
* * * * * *** * * *
563066 TGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGGCAACAAAAGACCTTTGAGTTTGACTACGCTC
66 TGCAGCATAGCTTAAGTCGAGAAGGGCTATCT-GC--C-AAAGACCCCCGAGTTCGATTACACTC
* * * * * *
563131 AGC-TCAACGGCACATCATTTACAGCATAACTCAAGGCT
127 AGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCG
** * *
563169 AGAAGGGTTATCTG-TGACCAAAAGACCTTCGAGTTCGACTCCGCTCAGCTCCAAGGCACATCAT
1 AGAAGGGTTATCTGCCAACC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCAT
* * * *
563233 TTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCTAAAGACC
65 TTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
563276 TTTGAGTTCG
Statistics
Matches: 562, Mismatches: 38, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
164 7 0.01
165 410 0.73
166 2 0.00
167 5 0.01
168 115 0.20
169 23 0.04
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (165 bp):
AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATT
TGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAGCT
TCGAGGGCACATCATTTGCAGCATAACTTAAGTCG
Found at i:564111 original size:39 final size:37
Alignment explanation
Indices: 564011--564246 Score: 227
Period size: 39 Copynumber: 6.7 Consensus size: 37
564001 TATGGGTAAC
*
564011 ATATAGTTTTAAAATCA-TTTT-AAAAACTTATATAAT
1 ATATAGTTTTAAAAACATTTTTGAAAAA-TTATATAAT
564047 ATATAGTTTTAAAAACATTTTTGAATAAATTATATAAT
1 ATATAGTTTTAAAAACATTTTTGAA-AAATTATATAAT
564085 ATATAGTTTTAAAAAACATTTTTGAATAAATTATATAAT
1 ATATAGTTTT-AAAAACATTTTTGAA-AAATTATATAAT
* * *
564124 ATATAGTTTTAAAAACGTTTTTTTAAAACTTATAT-A-
1 ATATAGTTTTAAAAAC-ATTTTTGAAAAATTATATAAT
*
564160 ATAT--TTTT-AAAACA-TTTTG-AAAACTATAT-A-
1 ATATAGTTTTAAAAACATTTTTGAAAAATTATATAAT
* *
564190 ATATAGTTTTGAAAAC-TTTTT---TAA--ATATAAT
1 ATATAGTTTTAAAAACATTTTTGAAAAATTATATAAT
* *
564221 ATATAGTTTAAAAAATATTTTTGAAA
1 ATATAGTTTTAAAAACATTTTTGAAA
564247 TATATGTATT
Statistics
Matches: 172, Mismatches: 13, Indels: 31
0.80 0.06 0.14
Matches are distributed among these distances:
29 4 0.02
30 14 0.08
31 19 0.11
32 9 0.05
33 14 0.08
34 4 0.02
36 20 0.12
37 5 0.03
38 35 0.20
39 48 0.28
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (37 bp):
ATATAGTTTTAAAAACATTTTTGAAAAATTATATAAT
Found at i:564125 original size:77 final size:72
Alignment explanation
Indices: 564011--564246 Score: 223
Period size: 77 Copynumber: 3.3 Consensus size: 72
564001 TATGGGTAAC
*
564011 ATATAGTTTTAAAATCATTTT-AAAAACTTATATAATATATAGTTTTAAAAACATTTTTGAATAA
1 ATATAGTTTTAAAAACATTTTGAAAAA-TTATATAATATATAGTTTTAAAAAC-TTTTT-AATAA
564075 ATTATATAAT
63 ATTATATAAT
564085 ATATAGTTTTAAAAAACATTTTTGAATAAATTATATAATATATAGTTTTAAAAACGTTTTTTTAA
1 ATATAGTTTT-AAAAACA-TTTTGAA-AAATTATATAATATATAGTTTTAAAAAC---TTTTTAA
*
564150 -AACTTATAT-A-
60 TAAATTATATAAT
* *
564160 ATAT--TTTT-AAAACATTTTG-AAAACTATAT-A-ATATAGTTTTGAAAACTTTTT--T-AA--
1 ATATAGTTTTAAAAACATTTTGAAAAATTATATAATATATAGTTTTAAAAACTTTTTAATAAATT
564214 ATATAAT
66 ATATAAT
* *
564221 ATATAGTTTAAAAAATATTTTTGAAA
1 ATATAGTTTTAAAAACA-TTTTGAAA
564247 TATATGTATT
Statistics
Matches: 140, Mismatches: 8, Indels: 36
0.76 0.04 0.20
Matches are distributed among these distances:
59 4 0.03
60 1 0.01
61 5 0.04
63 8 0.06
64 5 0.04
65 5 0.04
66 17 0.12
67 1 0.01
68 8 0.06
69 1 0.01
70 5 0.04
71 6 0.04
73 4 0.03
74 10 0.07
75 10 0.07
76 5 0.04
77 35 0.25
78 5 0.04
79 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.45
Consensus pattern (72 bp):
ATATAGTTTTAAAAACATTTTGAAAAATTATATAATATATAGTTTTAAAAACTTTTTAATAAATT
ATATAAT
Found at i:564172 original size:33 final size:31
Alignment explanation
Indices: 564122--564211 Score: 85
Period size: 33 Copynumber: 2.8 Consensus size: 31
564112 AAATTATATA
* *
564122 ATAT-ATAGTTTTAAAAACGTTTTTTTAAAACTT
1 ATATAATA-TTTTTAAAAC-TTTTTTGAAAAC-T
*
564155 ATATAATATTTTTAAAAC-ATTTTGAAAACT
1 ATATAATATTTTTAAAACTTTTTTGAAAACT
564185 ATATAATATAGTTTTGAAAACTTTTTT
1 ATATAATAT--TTTT-AAAACTTTTTT
564212 AAATATAATA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
30 10 0.21
31 9 0.19
32 4 0.08
33 18 0.38
34 7 0.15
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.48
Consensus pattern (31 bp):
ATATAATATTTTTAAAACTTTTTTGAAAACT
Found at i:566506 original size:29 final size:29
Alignment explanation
Indices: 566436--566499 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
566426 TATTTGCATC
*
566436 ATTATTAAAAATTATAAAATTATCATTTG
1 ATTATTAAAAATTATAAAATGATCATTTG
566465 ATTATTAAAAATTATAAAATGATCATTTG
1 ATTATTAAAAATTATAAAATGATCATTTG
566494 ATTATT
1 ATTATT
566500 CTAAATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (29 bp):
ATTATTAAAAATTATAAAATGATCATTTG
Found at i:568865 original size:19 final size:21
Alignment explanation
Indices: 568843--568884 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
568833 ATTAAATAAA
568843 TTAAATA-A-ATTTAAAGTTT
1 TTAAATATATATTTAAAGTTT
*
568862 TTAAATATATATTTTAAGTTT
1 TTAAATATATATTTAAAGTTT
568883 TT
1 TT
568885 TTAAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (21 bp):
TTAAATATATATTTAAAGTTT
Found at i:570523 original size:25 final size:28
Alignment explanation
Indices: 570467--570519 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
570457 TCTAAATTAT
* * *
570467 TTTATTATTATTTTTGTATGATATAACA
1 TTTATTATTATTTATGTATAAAATAACA
570495 TTTATTATTATTTAT-TATAAAATAA
1 TTTATTATTATTTATGTATAAAATAA
570520 TTTAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 8 0.36
28 14 0.64
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.57
Consensus pattern (28 bp):
TTTATTATTATTTATGTATAAAATAACA
Found at i:570836 original size:17 final size:17
Alignment explanation
Indices: 570814--570859 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
570804 TCTTTTGCTT
570814 TTATTTTATATTTTAAA
1 TTATTTTATATTTTAAA
*
570831 TTATTTTATATTTTATA
1 TTATTTTATATTTTAAA
570848 TTATTTTATATT
1 TTATTTTATATT
570860 AAATAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTATTTTATATTTTAAA
Found at i:576596 original size:10 final size:10
Alignment explanation
Indices: 576583--576651 Score: 50
Period size: 10 Copynumber: 6.5 Consensus size: 10
576573 GAGAACGGTA
*
576583 GAGAGCGAGC
1 GAGAGAGAGC
576593 GAGAGAGAGC
1 GAGAGAGAGC
576603 GGTAGAGAGCGAGC
1 -G-AGAGA--GAGC
576617 GAGAGAGAGC
1 GAGAGAGAGC
*
576627 G-GTAGAGAGG
1 GAG-AGAGAGC
* *
576637 GAGCGAGAGG
1 GAGAGAGAGC
576647 GAGAG
1 GAGAG
576652 GTAGAGAGGG
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
9 1 0.02
10 31 0.63
11 2 0.04
12 10 0.20
13 1 0.02
14 4 0.08
ACGTcount: A:0.33, C:0.10, G:0.54, T:0.03
Consensus pattern (10 bp):
GAGAGAGAGC
Found at i:576605 original size:24 final size:24
Alignment explanation
Indices: 576569--576672 Score: 154
Period size: 24 Copynumber: 4.3 Consensus size: 24
576559 AACGACACAT
*
576569 GAGAGAGAACGGTAGAGAGCGAGC
1 GAGAGAGAGCGGTAGAGAGCGAGC
576593 GAGAGAGAGCGGTAGAGAGCGAGC
1 GAGAGAGAGCGGTAGAGAGCGAGC
*
576617 GAGAGAGAGCGGTAGAGAGGGAGC
1 GAGAGAGAGCGGTAGAGAGCGAGC
* * * *
576641 GAGAGGGAGAGGTAGAGAGGGAGG
1 GAGAGAGAGCGGTAGAGAGCGAGC
576665 GAGAGAGA
1 GAGAGAGA
576673 ATTTGAAAAG
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.36, C:0.08, G:0.53, T:0.04
Consensus pattern (24 bp):
GAGAGAGAGCGGTAGAGAGCGAGC
Found at i:576634 original size:14 final size:13
Alignment explanation
Indices: 576582--576672 Score: 59
Period size: 14 Copynumber: 7.2 Consensus size: 13
576572 AGAGAACGGT
*
576582 AGAGAGCGAGCGAG
1 AGAGAGCG-GAGAG
576596 AGAGAGCGGTAGAG
1 AGAGAGCGG-AGAG
*
576610 AGCGAGC---GAG
1 AGAGAGCGGAGAG
576620 AGAGAGCGGTAGAG
1 AGAGAGCGG-AGAG
*
576634 AGGGAGC-GAGAG
1 AGAGAGCGGAGAG
* *
576646 GGAGAG-GTAGAG
1 AGAGAGCGGAGAG
*
576658 AGGGAG-GGAGAG
1 AGAGAGCGGAGAG
576670 AGA
1 AGA
576673 ATTTGAAAAG
Statistics
Matches: 60, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 9 0.15
12 23 0.38
13 2 0.03
14 26 0.43
ACGTcount: A:0.35, C:0.08, G:0.54, T:0.03
Consensus pattern (13 bp):
AGAGAGCGGAGAG
Found at i:578428 original size:29 final size:29
Alignment explanation
Indices: 578393--578474 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
578383 AAACTAAATT
* *
578393 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
578422 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
578451 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
578475 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:580785 original size:60 final size:58
Alignment explanation
Indices: 580633--580800 Score: 162
Period size: 60 Copynumber: 2.8 Consensus size: 58
580623 GTATATACGT
* *
580633 ATAGTTTGGGATGAAATTAGAACGTTAAAAAAGTTTAAGGACTAATTTAGAATATATGCC
1 ATAGTTTGGGATGAAATTAGAACATT-TAAAAGTTTAAGGACTAATTTAGAATATAT-CC
* * * *
580693 GTAGTTTGGGGATGGAATT-GAA-ATCTTCAAAAGTTTGAGGAGTAATTTAGAATGATAAT-C
1 ATAGTTT-GGGATGAAATTAGAACAT-TT-AAAAGTTTAAGGACTAATTTAGAAT-AT-ATCC
* * *
580753 ATAGTTTAGGAATGAAATTAGAACATTTAAAAGTTCAGGGACTAATTT
1 ATAGTTT-GGGATGAAATTAGAACATTTAAAAGTTTAAGGACTAATTT
580801 TAAATGACTC
Statistics
Matches: 87, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
59 1 0.01
60 65 0.75
61 17 0.20
62 4 0.05
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.33
Consensus pattern (58 bp):
ATAGTTTGGGATGAAATTAGAACATTTAAAAGTTTAAGGACTAATTTAGAATATATCC
Found at i:584361 original size:59 final size:59
Alignment explanation
Indices: 584217--584361 Score: 145
Period size: 59 Copynumber: 2.5 Consensus size: 59
584207 ATTTTAGTCT
* * * *
584217 CTAAACTTTTGAACATTCTAACA-TCGTTCTTAAACTATGAATTCCATTTTAAATTGGTC
1 CTAAACATTTGAACATTCTAA-ATTCATTCTTAAACTATGAATCCCATTTTAAATTGATC
* * *
584276 CTACACTTTTAAACATT-TCAAATTCATTCTTAAACTATG-ATCCCATTCTT-AATTGATCC
1 CTAAACATTTGAACATTCT-AAATTCATTCTTAAACTATGAATCCCATT-TTAAATTGAT-C
* *
584335 CTAAAGATTTGAACATTCTAATTTCAT
1 CTAAACATTTGAACATTCTAAATTCAT
584362 CCTCAGACTA
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
58 15 0.21
59 55 0.77
60 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.41
Consensus pattern (59 bp):
CTAAACATTTGAACATTCTAAATTCATTCTTAAACTATGAATCCCATTTTAAATTGATC
Found at i:584915 original size:20 final size:21
Alignment explanation
Indices: 584881--584922 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
584871 TTGTTTTTAT
*
584881 GAAAGAAAGATGGAACGTGAG
1 GAAAGAAAGATGGAACGAGAG
584902 GAAAGAAA-ATGGAACGAGAG
1 GAAAGAAAGATGGAACGAGAG
584922 G
1 G
584923 TACCAACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.50, C:0.05, G:0.38, T:0.07
Consensus pattern (21 bp):
GAAAGAAAGATGGAACGAGAG
Found at i:593411 original size:48 final size:48
Alignment explanation
Indices: 593355--593450 Score: 192
Period size: 48 Copynumber: 2.0 Consensus size: 48
593345 ATCCCTGACC
593355 GGAACTAACATTTAAATGATACAGCATTCCAGTTTAGTACCTTAACCA
1 GGAACTAACATTTAAATGATACAGCATTCCAGTTTAGTACCTTAACCA
593403 GGAACTAACATTTAAATGATACAGCATTCCAGTTTAGTACCTTAACCA
1 GGAACTAACATTTAAATGATACAGCATTCCAGTTTAGTACCTTAACCA
593451 TTCCCGTTCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (48 bp):
GGAACTAACATTTAAATGATACAGCATTCCAGTTTAGTACCTTAACCA
Found at i:599945 original size:22 final size:22
Alignment explanation
Indices: 599864--599939 Score: 129
Period size: 22 Copynumber: 3.5 Consensus size: 22
599854 TGGGCAAGGA
599864 GAATCGGTACCCATTCAA--GG
1 GAATCGGTACCCATTCAATGGG
599884 GAATCGGTACCCATTCAATGGG
1 GAATCGGTACCCATTCAATGGG
599906 GAATCGGTACCCATTCAATGGG
1 GAATCGGTACCCATTCAATGGG
*
599928 GAATCGATACCC
1 GAATCGGTACCC
599940 CCTCAAACGA
Statistics
Matches: 53, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
20 18 0.34
22 35 0.66
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.21
Consensus pattern (22 bp):
GAATCGGTACCCATTCAATGGG
Found at i:600018 original size:23 final size:22
Alignment explanation
Indices: 599974--600018 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
599964 AATCTCATAG
* *
599974 GGGAATCGATTCCCCCACAGGA
1 GGGAACCGATTCCCCCAAAGGA
599996 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATTCCCCC-AAAGGA
600019 AAATTGTGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (22 bp):
GGGAACCGATTCCCCCAAAGGA
Found at i:601513 original size:103 final size:103
Alignment explanation
Indices: 601293--601505 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
601283 GGGTCTACGC
601293 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
601358 CATTGGCATATGTATATGATTATTAAGGAATGATATGT
66 CACTAGCATATGTATATGATTATTAAGGAATGATATGT
601396 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* * *
601461 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CACTAGCATATGTATATGATTATTAAGGAATGATATGT
601499 GGTCCTT
1 GGTCCTT
601506 ATGGACATTA
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.27, C:0.13, G:0.24, T:0.36
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CACTAGCATATGTATATGATTATTAAGGAATGATATGT
Found at i:601556 original size:23 final size:23
Alignment explanation
Indices: 601522--601589 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
601512 ATTATTATAT
601522 GGCAC-TACGGTGCAATTCTACGC
1 GGCACTTA-GGTGCAATTCTACGC
* *
601545 GGCACTTTGGTGCAATTCTACGT
1 GGCACTTAGGTGCAATTCTACGC
*
601568 GGCACTTAGGTGCAATTATACG
1 GGCACTTAGGTGCAATTCTACG
601590 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 39 0.98
24 1 0.03
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
GGCACTTAGGTGCAATTCTACGC
Found at i:603271 original size:31 final size:29
Alignment explanation
Indices: 603227--603289 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 29
603217 GAAATAAATG
* *
603227 AAAAATATTTTAATAAAAAACTTTAATAATA
1 AAAAAGATCTTAAT-AAAAACTTTAATAA-A
603258 AAAAAGATCTTAATAAAAACTTTAATAAA
1 AAAAAGATCTTAATAAAAACTTTAATAAA
603287 AAA
1 AAA
603290 TAAAAAGATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 14 0.47
31 12 0.40
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (29 bp):
AAAAAGATCTTAATAAAAACTTTAATAAA
Found at i:607119 original size:12 final size:12
Alignment explanation
Indices: 607102--607127 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
607092 TTAGAAATAT
607102 AATAATAATAAA
1 AATAATAATAAA
607114 AATAATAATAAA
1 AATAATAATAAA
607126 AA
1 AA
607128 ATGTTCAAAA
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:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:607215 original size:38 final size:37
Alignment explanation
Indices: 607172--607525 Score: 153
Period size: 38 Copynumber: 9.5 Consensus size: 37
607162 ATATTTTATT
*
607172 AAAACTATATATTATACGTATTTTCAAAAATGTTTCAA
1 AAAACTATATATTATATGTATTTTCAAAAATGTTT-AA
* ** *
607210 AAAACTATATAATATATGTATTTTTTAAAATGTTTTA
1 AAAACTATATATTATATGTATTTTCAAAAATGTTTAA
** *
607247 AAAGTTATATATTATATATATTTTCAAAAATGTTTTTTTTTAA
1 AAAACTATATATTATATGTATTTTCAAAAATG------TTTAA
* * ** * **
607290 AAAACCATATAACATATAAATGTTTTC-AAAATGTTTTC
1 AAAACTATAT-A-TTATATGTATTTTCAAAAATGTTTAA
**
607328 AAAACTATATA-T-TA--TA---T--AAAATGTTTTC
1 AAAACTATATATTATATGTATTTTCAAAAATGTTTAA
* *
607356 AAAATTATATATTATATAAG-A-TTTCAAAAATGATTTTA
1 AAAACTATATATTATAT--GTATTTTCAAAAATG-TTTAA
* * * * * *
607394 AAAATTATATATTATCTATATTTTCTAAAACGTTTTTTTA
1 AAAACTATATATTATATGTATTTTC-AAAA--ATGTTTAA
* *
607434 AAAACTGTATATTATA--TAGTTTTCAAAAATGTTTTA
1 AAAACTATATATTATATGTA-TTTTCAAAAATGTTTAA
* *
607470 AAAACTATATATTATATACGTATTTTCAAAGATCGTTT-G
1 AAAACTATATATTATAT--GTATTTTCAAAAAT-GTTTAA
* *
607509 CAAACTATATAATATAT
1 AAAACTATATATTATAT
607526 ATATATGTAT
Statistics
Matches: 248, Mismatches: 38, Indels: 59
0.72 0.11 0.17
Matches are distributed among these distances:
28 21 0.08
29 2 0.01
30 2 0.01
32 1 0.00
33 1 0.00
34 2 0.01
35 2 0.01
36 21 0.08
37 35 0.14
38 73 0.29
39 34 0.14
40 24 0.10
41 1 0.00
43 11 0.04
44 7 0.03
45 11 0.04
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.44
Consensus pattern (37 bp):
AAAACTATATATTATATGTATTTTCAAAAATGTTTAA
Found at i:607323 original size:11 final size:11
Alignment explanation
Indices: 607307--607331 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
607297 TATAACATAT
607307 AAATGTTTTCA
1 AAATGTTTTCA
607318 AAATGTTTTCA
1 AAATGTTTTCA
607329 AAA
1 AAA
607332 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:607371 original size:26 final size:28
Alignment explanation
Indices: 607317--607374 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
607307 AAATGTTTTC
607317 AAAATGTTTTCAAAACTATATATTATAT
1 AAAATGTTTTCAAAACTATATATTATAT
*
607345 AAAATGTTTTCAAAATTATATATTATAT
1 AAAATGTTTTCAAAACTATATATTATAT
607373 AA
1 AA
607375 GATTTCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (28 bp):
AAAATGTTTTCAAAACTATATATTATAT
Found at i:607386 original size:26 final size:27
Alignment explanation
Indices: 607318--607384 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
607308 AATGTTTTCA
* *
607318 AAATGTTTTCAAAACTATATATTATAT
1 AAATGATTTCAAAATTATATATTATAT
*
607345 AAAATGTTTTCAAAATTATATATTATAT
1 -AAATGATTTCAAAATTATATATTATAT
607373 -AA-GATTTCAAAA
1 AAATGATTTCAAAA
607385 ATGATTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 9 0.24
26 2 0.05
28 26 0.70
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (27 bp):
AAATGATTTCAAAATTATATATTATAT
Found at i:607496 original size:39 final size:37
Alignment explanation
Indices: 607345--607526 Score: 163
Period size: 39 Copynumber: 4.8 Consensus size: 37
607335 TATATTATAT
* *
607345 AAAATGTTTTCAAAATTATATATTATATAAGA-TTTCA
1 AAAATGTTTTAAAAACTATATATTATAT-AGATTTTCA
* * *
607382 AAAATGATTTTAAAAATTATATATTATCTATATTTTCTA
1 AAAATG-TTTTAAAAACTATATATTATATAGATTTTC-A
* * *
607421 AAACGTTTTTTTAAAAACTGTATATTATATAG-TTTTCA
1 AAA--ATGTTTTAAAAACTATATATTATATAGATTTTCA
607459 AAAATGTTTTAAAAACTATATATTATATACGTATTTTCA
1 AAAATGTTTTAAAAACTATATATTATATA-G-ATTTTCA
* ** *
607498 AAGATCG-TTTGCAAACTATATAATATATA
1 AAAAT-GTTTTAAAAACTATATATTATATA
607527 TATATGTATA
Statistics
Matches: 120, Mismatches: 16, Indels: 16
0.79 0.11 0.11
Matches are distributed among these distances:
36 23 0.19
37 9 0.08
38 28 0.23
39 38 0.32
40 21 0.17
41 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATATTATATAGATTTTCA
Found at i:608274 original size:84 final size:82
Alignment explanation
Indices: 608100--608873 Score: 762
Period size: 84 Copynumber: 9.4 Consensus size: 82
608090 TTATCGACAA
* * * * * * * * * * *
608100 ATAGCCCTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
**
608165 CGGGGGTC-T-TTGGCAG
65 CGAAGGTCTTGTTGGCAG
* *
608181 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTT-GAGCTGATCGTAGTCAAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACT
*
608245 CAAAGGTCTTTTGTTGGCAG
65 CGAAGGTC--TTGTTGGCAG
* * * * * * *
608265 ACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
608330 GAAGGTCTTTGGTTGGCAG
66 GAAGGTC-TT-GTTGGCAG
* * *
608349 ATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
608414 AAAGGTCTT-TTGGTCACAG
66 GAAGGTCTTGTTGG---CAG
* * * * * * * *
608433 ATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGTGACCTCGAAGCTGAGTGTAATCGAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
* *
608498 CG-GGGTC--CTTGGCAG
65 CGAAGGTCTTGTTGGCAG
* * * * *
608513 ATAGCCCTTCTCGACTTAGGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
**
608578 CGGGGGTC-T-TTGGCAG
65 CGAAGGTCTTGTTGGCAG
608594 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
608659 GAAGGTCTT-TTGGTCACAG
66 GAAGGTCTTGTTGG---CAG
* * * * * * * * * * *
608678 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAACGAAATCGAACT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
**
608743 CGGGGGTC-T-TTGGCAG
65 CGAAGGTCTTGTTGGCAG
*
608759 ATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
*
608824 GAAGGTCTTGGTGGCAG
66 GAAGGTCTTGTTGGCAG
* * * *
608841 ATAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 ATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
608874 AGTTTGTTTA
Statistics
Matches: 587, Mismatches: 85, Indels: 41
0.82 0.12 0.06
Matches are distributed among these distances:
80 138 0.24
81 129 0.22
82 34 0.06
83 12 0.02
84 226 0.39
85 48 0.08
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (82 bp):
ATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTC
GAAGGTCTTGTTGGCAG
Found at i:608632 original size:245 final size:245
Alignment explanation
Indices: 608258--608873 Score: 883
Period size: 245 Copynumber: 2.5 Consensus size: 245
608248 AGGTCTTTTG
* * * * * * *
608258 TTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTAGAGCTGAGCGTAGT
* * *
608323 CGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG
66 CGAACTCGAAGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
608388 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAG
127 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAG
** *
608453 TTATGCTGTAAATGATGTGACCTCGAAGCTGAGTGTAATCGAACTC-GGGGTCC
192 TTATGCTGTAAATGATGTGACCTCGAAGCTGAACGAAATCGAACTCGGGGGTCC
* * * *
608506 TTGGCAGATAGCCCTTCTCGACTTAGGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTAG-AGCTGAGCGTAG
**
608571 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
65 TCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
* * *
608636 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTA
130 TGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTA
* *
608701 TGCTGTAAATGATGTGCCCTCGAAGCTGAACGAAATCGAACTCGGGGGTCT
195 TGCTGTAAATGATGTGACCTCGAAGCTGAACGAAATCGAACTCGGGGGTCC
* * *
608752 TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTAGAGCTGAGCGTAGT
* * * *
608817 CGAACTCGAAGGTCTTGGTGGCAGATAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
66 CGAACTCGAAGGTCTT--TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAT
608874 AGTTTGTTTA
Statistics
Matches: 328, Mismatches: 36, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
245 172 0.52
246 54 0.16
247 36 0.11
248 43 0.13
249 23 0.07
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.28
Consensus pattern (245 bp):
TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCCTAGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTT
GGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTAT
GCTGTAAATGATGTGACCTCGAAGCTGAACGAAATCGAACTCGGGGGTCC
Found at i:608705 original size:165 final size:164
Alignment explanation
Indices: 608175--608873 Score: 775
Period size: 165 Copynumber: 4.2 Consensus size: 164
608165 CGGGGGTCTT
* * * * * *
608175 TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGATCGTAGT
1 TGGCAGATAACCCTTCTCGACTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAAT
* *** * * * *
608239 CAAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATG
66 CGAACTCGGGGGTC---T-TTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTG
*
608304 CCTTAGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
127 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * * * *
608342 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATGTG-CCTTGGAGCTGAGCGTAG
1 -TGGCAGATAACCCTTCTCGACTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAA
*** * *
608406 TCGAACTCAAAGGTCTTTTGGTCACAGATAACCCTTCTAGACTTAAGTTATGCTGTAAATGATGT
65 TCGAACTCGGGGGTC-TTTGG---CAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGT
* * * * * *
608471 GACCTCGAAGCTGAGTGTAATCGAACTCG-GGGTC-CT--
126 G-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* *
608507 TGGCAGATAGCCCTTCTCGACTT-AGGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAA
1 TGGCAGATAACCCTTCTCGACTTGA-GCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAA
* *
608571 TCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCT
65 TCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCT
608636 TGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG
130 TGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGG
** * * * * * *
608672 TCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAACGAAAT
1 TGGCAGATAACCCTTCTCGACTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAAT
* * *
608737 CGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTT
66 CGAACTCGGGGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTT
608802 GGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTGG
131 GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* * * *
608835 TGGCAGATAGCCCTTCTGGCCTTGAGCTAAGCTGCAAAT
1 TGGCAGATAACCCTTCTCGACTTGAGCTATGCTGCAAAT
608874 AGTTTGTTTA
Statistics
Matches: 463, Mismatches: 55, Indels: 31
0.84 0.10 0.06
Matches are distributed among these distances:
160 23 0.05
161 42 0.09
163 38 0.08
164 45 0.10
165 176 0.38
166 3 0.01
167 5 0.01
168 109 0.24
169 22 0.05
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.29
Consensus pattern (164 bp):
TGGCAGATAACCCTTCTCGACTTGAGCTATGCTGCAAATGATGTGCCCTCGAAGCTGAGCGTAAT
CGAACTCGGGGGTCTTTGGCAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATGTGCCTT
GGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:612211 original size:19 final size:19
Alignment explanation
Indices: 612187--612232 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
612177 AGTTAATGTG
612187 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
612206 AATGCAAAGAAAATAACGA
1 AATGCAAAGAAAATAACAA
612225 AATGCAAA
1 AATGCAAA
612233 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.65, C:0.11, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:614967 original size:12 final size:12
Alignment explanation
Indices: 614950--614980 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
614940 CGATTTTGTG
614950 TACCTCCGATGA
1 TACCTCCGATGA
614962 TACCTCCGATGA
1 TACCTCCGATGA
614974 TACCTCC
1 TACCTCC
614981 CCCTTCGTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.23, C:0.39, G:0.13, T:0.26
Consensus pattern (12 bp):
TACCTCCGATGA
Found at i:615286 original size:11 final size:11
Alignment explanation
Indices: 615270--615294 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
615260 TATAACATAT
615270 AAATGTTTTCA
1 AAATGTTTTCA
615281 AAATGTTTTCA
1 AAATGTTTTCA
615292 AAA
1 AAA
615295 CTATATATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (11 bp):
AAATGTTTTCA
Found at i:615301 original size:38 final size:39
Alignment explanation
Indices: 615248--615323 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 39
615238 AAATGTTTTT
615248 TTTTAAAAACCATATAACATAT-AAATGTTTTCAAAATG
1 TTTTAAAAACCATATAACATATAAAATGTTTTCAAAATG
* * **
615286 TTTTCAAAACTATATATTATATAAAATGTTTTCAAAAT
1 TTTTAAAAACCATATAACATATAAAATGTTTTCAAAAT
615324 TATATATTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
38 18 0.55
39 15 0.45
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (39 bp):
TTTTAAAAACCATATAACATATAAAATGTTTTCAAAATG
Found at i:615334 original size:26 final size:28
Alignment explanation
Indices: 615280--615337 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
615270 AAATGTTTTC
615280 AAAATGTTTTCAAAACTATATATTATAT
1 AAAATGTTTTCAAAACTATATATTATAT
*
615308 AAAATGTTTTCAAAATTATATATTATAT
1 AAAATGTTTTCAAAACTATATATTATAT
615336 AA
1 AA
615338 GATTTCAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (28 bp):
AAAATGTTTTCAAAACTATATATTATAT
Found at i:615349 original size:26 final size:27
Alignment explanation
Indices: 615281--615347 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 27
615271 AATGTTTTCA
* *
615281 AAATGTTTTCAAAACTATATATTATAT
1 AAATGATTTCAAAATTATATATTATAT
*
615308 AAAATGTTTTCAAAATTATATATTATAT
1 -AAATGATTTCAAAATTATATATTATAT
615336 -AA-GATTTCAAAA
1 AAATGATTTCAAAA
615348 ATGATTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
25 9 0.24
26 2 0.05
28 26 0.70
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (27 bp):
AAATGATTTCAAAATTATATATTATAT
Found at i:615362 original size:38 final size:37
Alignment explanation
Indices: 615308--615450 Score: 155
Period size: 38 Copynumber: 3.8 Consensus size: 37
615298 TATATTATAT
* * *
615308 AAAATGTTTTCAAAATTATATATTATATAAGATTTCA
1 AAAATGTTTTAAAAACTATATATTATATAAGTTTTCA
* *
615345 AAAATGATTTTAAAAATTATATATTATCTATA-TTTTCTA
1 AAAATG-TTTTAAAAACTATATATTATATA-AGTTTTC-A
* * *
615384 AAACGTTTTTTTAAAAACTGTATATTATAT-AGTTTTCA
1 AAA--ATGTTTTAAAAACTATATATTATATAAGTTTTCA
615422 AAAATGTTTTAAAAACTATATATTATATA
1 AAAATGTTTTAAAAACTATATATTATATA
615451 CGTATTTTCA
Statistics
Matches: 88, Mismatches: 11, Indels: 14
0.78 0.10 0.12
Matches are distributed among these distances:
36 22 0.25
37 6 0.07
38 30 0.34
39 10 0.11
40 19 0.22
41 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATATTATATAAGTTTTCA
Found at i:615459 original size:39 final size:37
Alignment explanation
Indices: 615308--615489 Score: 163
Period size: 39 Copynumber: 4.8 Consensus size: 37
615298 TATATTATAT
* *
615308 AAAATGTTTTCAAAATTATATATTATATAAGA-TTTCA
1 AAAATGTTTTAAAAACTATATATTATAT-AGATTTTCA
* * *
615345 AAAATGATTTTAAAAATTATATATTATCTATATTTTCTA
1 AAAATG-TTTTAAAAACTATATATTATATAGATTTTC-A
* * *
615384 AAACGTTTTTTTAAAAACTGTATATTATATAG-TTTTCA
1 AAA--ATGTTTTAAAAACTATATATTATATAGATTTTCA
615422 AAAATGTTTTAAAAACTATATATTATATACGTATTTTCA
1 AAAATGTTTTAAAAACTATATATTATATA-G-ATTTTCA
* ** *
615461 AAGATCG-TTTGCAAACTATATAATATATA
1 AAAAT-GTTTTAAAAACTATATATTATATA
615490 TATATGTATA
Statistics
Matches: 120, Mismatches: 16, Indels: 16
0.79 0.11 0.11
Matches are distributed among these distances:
36 23 0.19
37 9 0.08
38 28 0.23
39 38 0.32
40 21 0.17
41 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (37 bp):
AAAATGTTTTAAAAACTATATATTATATAGATTTTCA
Found at i:616260 original size:12 final size:12
Alignment explanation
Indices: 616243--616267 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
616233 CGAAAATTGA
616243 AAAATTTAAATT
1 AAAATTTAAATT
616255 AAAATTTAAATT
1 AAAATTTAAATT
616267 A
1 A
616268 CCCGATTCGA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTTAAATT
Found at i:616404 original size:11 final size:12
Alignment explanation
Indices: 616383--616408 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
616373 TAAATCAAAG
616383 GAGGAAAAAAAT
1 GAGGAAAAAAAT
616395 GAGGAAAAAAAT
1 GAGGAAAAAAAT
616407 GA
1 GA
616409 ATAAAGAGGA
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:0.65, C:0.00, G:0.27, T:0.08
Consensus pattern (12 bp):
GAGGAAAAAAAT
Found at i:616431 original size:20 final size:19
Alignment explanation
Indices: 616395--616433 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
616385 GGAAAAAAAT
*
616395 GAGGAAAAAAATGAATAAA
1 GAGGAAAAAAATAAATAAA
*
616414 GAGGAAAAATATTAAATAAA
1 GAGGAAAAA-AATAAATAAA
616434 TAAAAAACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (19 bp):
GAGGAAAAAAATAAATAAA
Found at i:617269 original size:14 final size:14
Alignment explanation
Indices: 617244--617278 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
617234 TCCTCGGTCT
617244 TTGTTG-GTTGATG
1 TTGTTGTGTTGATG
617257 TTGTTGTGTTGATG
1 TTGTTGTGTTGATG
*
617271 GTGTTGTG
1 TTGTTGTG
617279 ATGTTCGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 6 0.30
14 14 0.70
ACGTcount: A:0.06, C:0.00, G:0.40, T:0.54
Consensus pattern (14 bp):
TTGTTGTGTTGATG
Found at i:617742 original size:5 final size:5
Alignment explanation
Indices: 617728--617779 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
617718 AAAAATAAGG
* *
617728 AATAA AATAA CATAA AATAA AATAA TAATAA TAAT-A AATAA TA-AA AATAA
1 AATAA AATAA AATAA AATAA AATAA -AATAA -AATAA AATAA AATAA AATAA
617778 AA
1 AA
617780 ATATTTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 6 0.15
5 25 0.62
6 9 0.22
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (5 bp):
AATAA
Found at i:617766 original size:16 final size:15
Alignment explanation
Indices: 617731--617782 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
617721 AATAAGGAAT
*
617731 AAAATAACATAAAAT-
1 AAAATAATA-AAAATA
*
617746 AAAATAATAATAATA
1 AAAATAATAAAAATA
617761 ATAAATAATAAAAATA
1 A-AAATAATAAAAATA
617777 AAAATA
1 AAAATA
617783 TTTTCAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 4 0.12
15 14 0.44
16 14 0.44
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATAATAAAAATA
Found at i:618781 original size:84 final size:83
Alignment explanation
Indices: 618665--619617 Score: 959
Period size: 84 Copynumber: 11.4 Consensus size: 83
618655 GGTCTTTGGC
* * * * *
618665 AGATAGCCCTTCTCGACTTAGGCTATGCTGCAAATGATGTGCCGTT-GAGATGAGCGTAGTCGAA
1 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAA
*
618729 CTCAAAGGTCTTTTGGTCAG
65 CTCAAAGGTC-TTTGGTTAG
* * * * * * * *
618749 AGATAACCCTTCTAGTCTTGAGTTACGTTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAA
1 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAA
* *
618814 CTCAAAGGTCTTTTGTTGG
65 CTCAAAGGTCTTTGGTTAG
* * *
618833 CAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAA
1 -AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
* * *
618898 CTCGAAGGTCTTTGGTCAC
65 CTCAAAGGTCTTTGGTTAG
* * * * * *
618917 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAA
1 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAA
** *
618982 CTC-GGGGTCCTTTGGTTGG
65 CTCAAAGGT-CTTTGGTTAG
* *
619001 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAACGTAGTCGAA
1 -AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
619066 CTCAAAGGTCTTTTGTTAG
65 CTCAAAGGTCTTTGGTTAG
* * * *
619085 CAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGA
1 -AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTCGA
* * *
619150 ACTCGAGGGTCTTTGG---C
64 ACTCAAAGGTCTTTGGTTAG
* * * * *
619167 AGATAACCCTTCTCGACTTAAGCTATTCTGCAGATGTTGTGCCTTGGAGCTGAGCGTAGTCGAAC
1 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* * *
619232 TCAAAGGTCTTTGCTAAC
66 TCAAAGGTCTTTGGTTAG
* * * * * * ** *
619250 AGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTATAATCGAA
1 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAA
* * *
619315 CTTAAGGGTCTTTGGTTGG
65 CTCAAAGGTCTTTGGTTAG
* * *
619334 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTACCTTGGAGCTGAACGTAGTCGAA
1 -AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
*
619399 CTCAAAGGTCTTTTGTTAG
65 CTCAAAGGTCTTTGGTTAG
* * * ** *
619418 CAGATAACCCTTCTTGACTTAAGTTATACTGCAAATGATGCGCCTTCTAAGCTGAACGTAGTCGA
1 -AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTT-GGAGCTGAGCGTAGTCGA
* * *
619483 ACTCGAGGGTCTTTGG---C
64 ACTCAAAGGTCTTTGGTTAG
* * * * * * *
619500 AGATAGCCCTTCTCGACTTAAGCTATTCTGCAGATGTTGTGCCTTAGAGCTGAGCGTAGTCGAAC
1 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
* * *
619565 TCAAAGGTCTTTGCTAAC
66 TCAAAGGTCTTTGGTTAG
* *
619583 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 AGATAACCCTTCTAGACTTAAGTTATGCTGCAAAT
619618 AGTTTGTTTA
Statistics
Matches: 713, Mismatches: 139, Indels: 35
0.80 0.16 0.04
Matches are distributed among these distances:
80 57 0.08
81 78 0.11
83 102 0.14
84 282 0.40
85 194 0.27
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (83 bp):
AGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
TCAAAGGTCTTTGGTTAG
Found at i:618966 original size:168 final size:164
Alignment explanation
Indices: 618590--619617 Score: 1243
Period size: 168 Copynumber: 6.2 Consensus size: 164
618580 TGACAAATAG
* * * * * * * *
618590 CCCTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCC-CGAAGTTGAGTGTAATCGAACCCAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG-CCCTCGAAGCTGAGTGTAATCGAACTCAA
* * *
618654 GGGTCTTTGGCAGATAGCCCTTCTCGACTTAGGCTATGCTGCAAATGATGTGCCGTT-GAGATGA
65 GGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCC-TTGGAGCTGA
* *
618718 GCGTAGTCGAACTCAAAGGTCTTTTGGTCAGAGATAA
129 GCGTAGTCGAACTCAAAGGTC-TTTGGTAACAGATAA
* * * *
618755 CCCTTCTAGTCTTGAGTTACGTTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAA
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAG
* * * * *
618820 GGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCT
66 GGTC---T-TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
* *
618885 GAGCGTAGTCGAACTCGAAGGTCTTTGGTCACAGATAA
127 GAGCGTAGTCGAACTCAAAGGTCTTTGGTAACAGATAA
*
618923 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTC-GG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAG
*
618987 GGTCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGC
66 GGT-C--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGC
* * *
619052 TGAACGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAA
126 TGAGCGTAGTCGAACTCAAAGGTC-TTTGGTAACAGATAA
* * * * * ** * *
619092 CCCTTCTTGACTTAAGTTATACTGCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAG
* * *
619157 GGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATTCTGCAGATGTTGTGCCTTGGAGCTGAGC
66 GGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
619222 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
131 GTAGTCGAACTCAAAGGTCTTTGGTAACAGATAA
* * * * * *
619256 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTATAATCGAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAG
* *
619321 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTACCTTGGAGCT
66 GGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCT
* * *
619386 GAACGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAA
127 GAGCGTAGTCGAACTCAAAGGTC-TTTGGTAACAGATAA
* * * * * * * ** * *
619425 CCCTTCTTGACTTAAGTTATACTGCAAATGATGCGCCTTCTAAGCTGAACGTAGTCGAACTCGAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAG
* * * * *
619490 GGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAGATGTTGTGCCTTAGAGCTGAGC
66 GGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
*
619555 GTAGTCGAACTCAAAGGTCTTTGCTAACAGATAA
131 GTAGTCGAACTCAAAGGTCTTTGGTAACAGATAA
619589 CCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 CCCTTCTAGCCTTGAGTTATGCTGCAAAT
619618 AGTTTGTTTA
Statistics
Matches: 744, Mismatches: 104, Indels: 31
0.85 0.12 0.04
Matches are distributed among these distances:
164 108 0.15
165 200 0.27
166 1 0.00
167 8 0.01
168 224 0.30
169 199 0.27
170 4 0.01
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (164 bp):
CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAG
GGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGC
GTAGTCGAACTCAAAGGTCTTTGGTAACAGATAA
Found at i:619256 original size:333 final size:332
Alignment explanation
Indices: 618590--619617 Score: 1494
Period size: 333 Copynumber: 3.1 Consensus size: 332
618580 TGACAAATAG
* * * * * *
618590 CCCTTCTTGCCTTGAGCTATGTTGTAAATGATATGACCC-CGAAGTTGAGTGTAATCGAACCCAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATATG-CCCTCGAAGCTGAGTGTAATCGAACTC-G
* * *
618654 GGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAGGCTATGCTGCAAATGATGTGCCGTT-GAG
64 GGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCC-TTGGAG
* * * * * * ***
618714 ATGAGCGTAGTCGAACTCAAAGGTCTTTTGGTCAG-AGATAACCCTTCTAGTCTTGAGTTACGTT
128 CTGAACGTAGTCGAACTCAAAGGTCTTTT-GTTAGCAGATAACCCTTCTTGACTTAAGTTATACT
* ** * * * *
618778 GCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCAAAGGTCTTTTGTTGGCAGACAACCC
192 GCAAATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTC---T-TTGGCAGATAACCC
* * * * * * * *
618843 TTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC
253 TTCTCGACTTAAGCTATTCTGCAGATGTTGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC
* *
618908 TTTGGTCACAGATAA
318 TTTGCTAACAGATAA
*
618923 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
618988 GTCCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCT
66 GT-CTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCT
619053 GAACGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCA
130 GAACGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCA
619118 AATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
195 AATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
619183 CTTAAGCTATTCTGCAGATGTTGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTA
260 CTTAAGCTATTCTGCAGATGTTGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTA
619248 ACAGATAA
325 ACAGATAA
* * * * **
619256 CCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTATAATCGAACTTAAG
1 CCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAAC-TCGG
*
619321 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTACCTTGGAGCT
65 GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCT
619386 GAACGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCA
130 GAACGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCA
* * *
619451 AATGATGCGCCTTCTAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGA
195 AATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGA
*
619516 CTTAAGCTATTCTGCAGATGTTGTGCCTTAGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTA
260 CTTAAGCTATTCTGCAGATGTTGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTA
619581 ACAGATAA
325 ACAGATAA
619589 CCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 CCCTTCTAGCCTTGAGTTATGCTGCAAAT
619618 AGTTTGTTTA
Statistics
Matches: 637, Mismatches: 49, Indels: 18
0.90 0.07 0.03
Matches are distributed among these distances:
332 8 0.01
333 478 0.75
334 6 0.01
335 1 0.00
336 6 0.01
337 138 0.22
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (332 bp):
CCCTTCTAGCCTTGAGTTATGCTGCAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGGG
GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTG
AACGTAGTCGAACTCAAAGGTCTTTTGTTAGCAGATAACCCTTCTTGACTTAAGTTATACTGCAA
ATGATGTGCCTTCGAAGCTGAACGTAGTCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGAC
TTAAGCTATTCTGCAGATGTTGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAA
CAGATAA
Found at i:622995 original size:19 final size:19
Alignment explanation
Indices: 622968--623013 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
622958 AGTTAATGTG
*
622968 AATGTAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
622987 AATGCAAAGAAAATAACGA
1 AATGCAAAGAAAATAACAA
623006 AATGCAAA
1 AATGCAAA
623014 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.65, C:0.09, G:0.13, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:624647 original size:12 final size:12
Alignment explanation
Indices: 624630--624654 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
624620 CGAAAATTGA
624630 AAAATTTAAATT
1 AAAATTTAAATT
624642 AAAATTTAAATT
1 AAAATTTAAATT
624654 A
1 A
624655 CCCGATTCGA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAAATTTAAATT
Found at i:624791 original size:11 final size:12
Alignment explanation
Indices: 624770--624795 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
624760 TAAATCAAAG
624770 GAGGAAAAAAAT
1 GAGGAAAAAAAT
624782 GAGGAAAAAAAT
1 GAGGAAAAAAAT
624794 GA
1 GA
624796 ATAAAGAGGA
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:0.65, C:0.00, G:0.27, T:0.08
Consensus pattern (12 bp):
GAGGAAAAAAAT
Found at i:624956 original size:27 final size:28
Alignment explanation
Indices: 624925--624996 Score: 69
Period size: 27 Copynumber: 2.6 Consensus size: 28
624915 AATAATTACA
*
624925 ATTAAAATAAATCAAATAAAATTTAGGG
1 ATTAAAATAAATCAAATAAAATTAAGGG
*
624953 -TT-AAATCGAAA-CAAACAAAATTAAGGG
1 ATTAAAAT--AAATCAAATAAAATTAAGGG
* *
624980 ATTAAATTAAATAAAAT
1 ATTAAAATAAATCAAAT
624997 GAAGGCTGCA
Statistics
Matches: 34, Mismatches: 5, Indels: 10
0.69 0.10 0.20
Matches are distributed among these distances:
26 4 0.12
27 19 0.56
28 8 0.24
29 3 0.09
ACGTcount: A:0.58, C:0.06, G:0.10, T:0.26
Consensus pattern (28 bp):
ATTAAAATAAATCAAATAAAATTAAGGG
Found at i:626036 original size:5 final size:5
Alignment explanation
Indices: 626022--626073 Score: 54
Period size: 5 Copynumber: 10.4 Consensus size: 5
626012 AAAAATAAGG
* *
626022 AATAA AATAA CATAA AATAA AATAA TAATAA TAAT-A AATAA TA-AA AATAA
1 AATAA AATAA AATAA AATAA AATAA -AATAA -AATAA AATAA AATAA AATAA
626072 AA
1 AA
626074 ATATTTTCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
4 6 0.15
5 25 0.62
6 9 0.22
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (5 bp):
AATAA
Found at i:626060 original size:16 final size:15
Alignment explanation
Indices: 626025--626076 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
626015 AATAAGGAAT
*
626025 AAAATAACATAAAAT-
1 AAAATAATA-AAAATA
*
626040 AAAATAATAATAATA
1 AAAATAATAAAAATA
626055 ATAAATAATAAAAATA
1 A-AAATAATAAAAATA
626071 AAAATA
1 AAAATA
626077 TTTTCAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 4 0.12
15 14 0.44
16 14 0.44
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAATAATAAAAATA
Found at i:626126 original size:40 final size:38
Alignment explanation
Indices: 626069--626237 Score: 128
Period size: 37 Copynumber: 4.3 Consensus size: 38
626059 ATAATAAAAA
* *
626069 TAAAAAT-ATTTTCAAAAACATATATAATATATAAATTT
1 TAAAAATGTTTTTAAAAAAC-TATATAATATATAAATTT
* *
626107 CTAAAATATTTTTTTAAAAAACTATAATATATATATATATTT
1 -TAAAA-ATGTTTTTAAAAAACTAT-ATA-ATATATAAATTT
* * * *
626149 TCAAAAACG-TTTTCAAAAATTATAT-ATATATAAGTTT
1 T-AAAAATGTTTTTAAAAAACTATATAATATATAAATTT
* * * * *
626186 TCAAAATGATTTTAAAAAATTATATATTATATATATTTT
1 TAAAAATGTTTTTAAAAAACTATATAATATATA-AATTT
*
626225 TTAAAATGTTTTT
1 TAAAAATGTTTTT
626238 TTAAACTATA
Statistics
Matches: 106, Mismatches: 16, Indels: 16
0.77 0.12 0.12
Matches are distributed among these distances:
36 5 0.05
37 26 0.25
38 6 0.06
39 22 0.21
40 17 0.16
41 15 0.14
42 15 0.14
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.46
Consensus pattern (38 bp):
TAAAAATGTTTTTAAAAAACTATATAATATATAAATTT
Found at i:626261 original size:75 final size:73
Alignment explanation
Indices: 626077--626290 Score: 173
Period size: 75 Copynumber: 2.8 Consensus size: 73
626067 AATAAAAATA
* * * *
626077 TTTTCAAAAACATATATAATATATAAATTTCTAAAATATTTTTTTAAAAAACTATAATATATATA
1 TTTTCAAAAAC-TATA-CATATATAAGTTT-TAAAA-A--CTTTTAAAAAATTAT-ATAT-TATA
626142 TATATTTTCAAAAACG
58 TATATTTTCAAAAACG
* *
626158 TTTTCAAAAATTATATATATATAAGTTTTCAAAATGA-TTTTAAAAAATTATATATTATATATAT
1 TTTTCAAAAACTATACATATATAAGTTTT-AAAA--ACTTTTAAAAAATTATATATTATATATAT
** *
626222 TTTTTAAAATG
63 TTTCAAAAACG
*** * *
626233 TTTTTTTAAACTATACAT-TATATGGTTTTAAAAACTATT-AAAAATTATATATTATATA
1 TTTTCAAAAACTATACATATATA-AGTTTTAAAAACTTTTAAAAAATTATATATTATATA
626291 CGTAGTTTTA
Statistics
Matches: 114, Mismatches: 15, Indels: 17
0.78 0.10 0.12
Matches are distributed among these distances:
72 20 0.18
73 3 0.03
74 8 0.07
75 35 0.31
76 4 0.04
77 13 0.11
78 1 0.01
79 15 0.13
80 5 0.04
81 10 0.09
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (73 bp):
TTTTCAAAAACTATACATATATAAGTTTTAAAAACTTTTAAAAAATTATATATTATATATATTTT
CAAAAACG
Found at i:629438 original size:6 final size:6
Alignment explanation
Indices: 629429--629458 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
629419 GCCGCCGTCC
629429 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG
629459 CGTGTCTTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GTCGTG
Found at i:629673 original size:2 final size:2
Alignment explanation
Indices: 629662--629732 Score: 62
Period size: 2 Copynumber: 37.5 Consensus size: 2
629652 TTCTATTATT
* *
629662 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T- TG TG T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
629701 -A AA TA GTT TA -A 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 TA TA T
629733 TATTTTTAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 12
0.80 0.04 0.16
Matches are distributed among these distances:
1 5 0.08
2 54 0.90
3 1 0.02
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:632990 original size:68 final size:68
Alignment explanation
Indices: 632876--633162 Score: 493
Period size: 68 Copynumber: 4.2 Consensus size: 68
632866 AAAGATTAAT
* *
632876 AGGCTTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGACTAAGTGTCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGACTAAGTGCCT
632941 TTG
66 TTG
* *
632944 AGGCCTAACTGTACATTTGACAGAAAGGTGTCATTTTTGCTAGTTAGATGAAAGACTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGACTAAGTGCCT
633009 TTG
66 TTG
633012 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGACTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGACTAAGTGCCT
633077 TTG
66 TTG
* **
633080 AGGCCTAACTGTGCATTTGACAGAAAGGTGTTATTTATGCTAGTTAGATGAAAGGTTAAGTGCCT
1 AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGACTAAGTGCCT
633145 TTG
66 TTG
* *
633148 AGGCGTAATTGTGCA
1 AGGCCTAACTGTGCA
633163 ATTGGCATGA
Statistics
Matches: 208, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
68 208 1.00
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.32
Consensus pattern (68 bp):
AGGCCTAACTGTGCATTTGACAGAAAGGTGTCATTTATGCTAGTTAGATGAAAGACTAAGTGCCT
TTG
Found at i:634573 original size:20 final size:20
Alignment explanation
Indices: 634545--634595 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
634535 GATTTTTTTT
* *
634545 TTGAAAGTTTAGATACTAAA
1 TTGATAGTTTAGACACTAAA
*
634565 TTGATAGTTTAGGCACTAAA
1 TTGATAGTTTAGACACTAAA
**
634585 TACATAGTTTA
1 TTGATAGTTTA
634596 CCCTTTAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.37
Consensus pattern (20 bp):
TTGATAGTTTAGACACTAAA
Found at i:637275 original size:33 final size:33
Alignment explanation
Indices: 637233--637296 Score: 128
Period size: 33 Copynumber: 1.9 Consensus size: 33
637223 ACTAAAAGAG
637233 AGAGTAAATTATACATTTAGTACCTAAACTAAA
1 AGAGTAAATTATACATTTAGTACCTAAACTAAA
637266 AGAGTAAATTATACATTTAGTACCTAAACTA
1 AGAGTAAATTATACATTTAGTACCTAAACTA
637297 TCAGTTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.31
Consensus pattern (33 bp):
AGAGTAAATTATACATTTAGTACCTAAACTAAA
Found at i:640446 original size:60 final size:60
Alignment explanation
Indices: 640334--640458 Score: 144
Period size: 60 Copynumber: 2.1 Consensus size: 60
640324 TCAGGTGATC
* * * * *
640334 ATTTCGTAACTTTTAATAATCGAGGAACTCAACAAAGCAACACTCTATAGTTGGAGGATT
1 ATTTTGTAACATTTAATAATCGAGGAACTCAACAAAACAACACTCTAAAGTTGGAGGACT
* * * * *
640394 ATTTTGTAACATTTAATAGTCGAGGAACTCAATAAAATAATA-TCCTAAAGTTGGGGGACT
1 ATTTTGTAACATTTAATAATCGAGGAACTCAACAAAACAACACT-CTAAAGTTGGAGGACT
640454 ATTTT
1 ATTTT
640459 TGTACTTTAC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.33
Consensus pattern (60 bp):
ATTTTGTAACATTTAATAATCGAGGAACTCAACAAAACAACACTCTAAAGTTGGAGGACT
Found at i:643957 original size:51 final size:51
Alignment explanation
Indices: 643875--643989 Score: 133
Period size: 51 Copynumber: 2.3 Consensus size: 51
643865 GTAACCATTG
* * * *
643875 AATAAAATAACAATAAATTAAAGATAATGTTTT-GATTTTAACATAATTCTT
1 AATAAAATAATAATAAACTAAAAATAATGTTTTAG-TTATAACATAATTCTT
* * * * *
643926 AATAAAATAATATTAAACTAAAAATAGTGTTTTAGTTATATCTTAATTGTT
1 AATAAAATAATAATAAACTAAAAATAATGTTTTAGTTATAACATAATTCTT
643977 AATAAAATAATAA
1 AATAAAATAATAA
643990 ATTTAATCCT
Statistics
Matches: 53, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
51 52 0.98
52 1 0.02
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.39
Consensus pattern (51 bp):
AATAAAATAATAATAAACTAAAAATAATGTTTTAGTTATAACATAATTCTT
Found at i:644564 original size:19 final size:19
Alignment explanation
Indices: 644533--644577 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
644523 TATATATATA
644533 TAATA-TTATTTTAATTATT
1 TAATATTTATTTT-ATTATT
*
644552 TAATATTTA-TTTATTTTT
1 TAATATTTATTTTATTATT
644570 TAAT-TTTA
1 TAATATTTA
644578 AAAAATTAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 4 0.17
18 9 0.38
19 8 0.33
20 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TAATATTTATTTTATTATT
Found at i:646711 original size:18 final size:18
Alignment explanation
Indices: 646690--646737 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
646680 TTTTTAATAA
646690 AAAATATTTAAAAAATTT
1 AAAATATTTAAAAAATTT
* * * *
646708 AAAATATATGATAATTTT
1 AAAATATTTAAAAAATTT
646726 AAAAT-TTTAAAA
1 AAAATATTTAAAA
646738 TACGATTATG
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAAATATTTAAAAAATTT
Found at i:648447 original size:2 final size:2
Alignment explanation
Indices: 648401--648428 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
648391 AGTAATAATT
648401 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
648429 ATTATATTTT
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):
TA
Found at i:649076 original size:3 final size:3
Alignment explanation
Indices: 649068--649131 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
649058 TCTTCGGGAC
649068 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
649116 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
649132 GTAACATTTA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:653484 original size:44 final size:46
Alignment explanation
Indices: 653431--653534 Score: 115
Period size: 46 Copynumber: 2.3 Consensus size: 46
653421 CACATTGAAT
* * *
653431 GTGCATCGATGCA-CTCTTTAAAGAA-G-AAACATCGAATGCAATTG
1 GTGCATCGATGCATCCCTTTAAA-AATGAAAACATCAAAGGCAATTG
* * *
653475 GTGCATCGATACATCCCTTTAAAAATGAAAACATCAAAGGTAATTT
1 GTGCATCGATGCATCCCTTTAAAAATGAAAACATCAAAGGCAATTG
*
653521 GTGTATCGATGCAT
1 GTGCATCGATGCAT
653535 GTGTAGTGCA
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
44 14 0.29
45 9 0.18
46 26 0.53
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.28
Consensus pattern (46 bp):
GTGCATCGATGCATCCCTTTAAAAATGAAAACATCAAAGGCAATTG
Found at i:653586 original size:20 final size:20
Alignment explanation
Indices: 653561--653598 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
653551 CACAGGTTAA
*
653561 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATACACTGT
653581 AGAATGCATCGATACACT
1 AGAATGCATCGATACACT
653599 TCAAGGGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATACACTGT
Found at i:654418 original size:18 final size:18
Alignment explanation
Indices: 654371--654422 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
654361 AGGTCTACGC
* *
654371 GGTCATTCGGGATATAGT
1 GGTCTTTCGGGACATAGT
654389 GGTCCTTT-GGGACATAGT
1 GGT-CTTTCGGGACATAGT
654407 GGTCTTTCGGGACATA
1 GGTCTTTCGGGACATA
654423 TGTGTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 4 0.13
18 23 0.77
19 3 0.10
ACGTcount: A:0.19, C:0.15, G:0.33, T:0.33
Consensus pattern (18 bp):
GGTCTTTCGGGACATAGT
Found at i:657524 original size:65 final size:63
Alignment explanation
Indices: 657404--657545 Score: 180
Period size: 65 Copynumber: 2.2 Consensus size: 63
657394 GATGCACATT
* *
657404 GTGCATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCAT-AGGTA
* * * *
657467 GTGCATCGATGCATCCCTTTAAA-AATGAAAACATCGAAGGTAATTTGTGTATTGATGCATAGGT
1 GTGCATCGATGCA-CCCTTTAAAGAA-G-AAACATCGAAGGCAATTGGTGCATCGATGCATAGGT
657531 A
63 A
657532 GTGCATCGATGCAC
1 GTGCATCGATGCAC
657546 AGGTTAAAGA
Statistics
Matches: 69, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
63 15 0.22
64 13 0.19
65 41 0.59
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (63 bp):
GTGCATCGATGCACCCTTTAAAGAAGAAACATCGAAGGCAATTGGTGCATCGATGCATAGGTA
Found at i:657565 original size:24 final size:20
Alignment explanation
Indices: 657533--657589 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 20
657523 GCATAGGTAG
657533 TGCATCGATGCACAGGTTAAAGAA
1 TGCATCGATGCAC-GG-T--AGAA
*
657557 TGCATCGATGCACTGTAGAA
1 TGCATCGATGCACGGTAGAA
657577 TGCATCGATGCAC
1 TGCATCGATGCAC
657590 TTTAAGGGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 17 0.53
22 1 0.03
23 1 0.03
24 13 0.41
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.23
Consensus pattern (20 bp):
TGCATCGATGCACGGTAGAA
Found at i:657578 original size:20 final size:20
Alignment explanation
Indices: 657553--657590 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
657543 CACAGGTTAA
657553 AGAATGCATCGATGCACTGT
1 AGAATGCATCGATGCACTGT
657573 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
657591 TTAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTGT
Found at i:658265 original size:18 final size:18
Alignment explanation
Indices: 658236--658287 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
658226 AGGTCAACGC
* *
658236 GGTCATTCGGGACATAGT
1 GGTCTTTCGGGACATAGA
658254 GGTCCTTT-GGGACATAGA
1 GGT-CTTTCGGGACATAGA
658272 GGTCTTTCGGGACATA
1 GGTCTTTCGGGACATA
658288 TGTGTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 4 0.13
18 23 0.77
19 3 0.10
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (18 bp):
GGTCTTTCGGGACATAGA
Found at i:662179 original size:20 final size:21
Alignment explanation
Indices: 662154--662192 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
662144 ATTCATCCAA
*
662154 GATATTTTAA-TAAATTTAAT
1 GATATTATAATTAAATTTAAT
662174 GATATTATAATTAAATTTA
1 GATATTATAATTAAATTTA
662193 GGGTAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
GATATTATAATTAAATTTAAT
Found at i:662454 original size:35 final size:35
Alignment explanation
Indices: 662415--662528 Score: 147
Period size: 35 Copynumber: 3.3 Consensus size: 35
662405 AAAACAGTCC
* * *
662415 TCAATTTCATTCTAAACCCCAATTTCCAAAATATT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* *
662450 TCAATTTTATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
662485 TCAATTAAATTCTAAATCCCAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
662520 TCAATTTAA
1 TCAATTTAA
662529 GGTTTAGAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:663661 original size:35 final size:35
Alignment explanation
Indices: 663620--663731 Score: 152
Period size: 35 Copynumber: 3.2 Consensus size: 35
663610 TCTAAACCTT
* * *
663620 AAATTGAAGTATTTTAGAATTTAGGGTTTAGAATT
1 AAATTGAAATATTTTGGAATTTAGGGTTTAGAATA
* *
663655 TAATTGAATTATTTTGGAATTTAGGGTTTAGAATA
1 AAATTGAAATATTTTGGAATTTAGGGTTTAGAATA
* * *
663690 AAATTGAAATATTTTGGAAATTGGGGTTTAGAATG
1 AAATTGAAATATTTTGGAATTTAGGGTTTAGAATA
663725 AAATTGA
1 AAATTGA
663732 GGACTGTTTT
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.38, C:0.00, G:0.21, T:0.41
Consensus pattern (35 bp):
AAATTGAAATATTTTGGAATTTAGGGTTTAGAATA
Found at i:667952 original size:38 final size:39
Alignment explanation
Indices: 667900--668004 Score: 135
Period size: 38 Copynumber: 2.7 Consensus size: 39
667890 TCGAGAAATT
*
667900 AAATTCAAATTTGAGTCTAGTTATAAAATTT-GATTCGAA
1 AAATT-AAATTTGAGTCTAGTTATAAAATTTCGATTCAAA
* * *
667939 AAATTAAATTTGAGTAC-AGCTAT-AAATTTCGCTTTAAA
1 AAATTAAATTTGAGT-CTAGTTATAAAATTTCGATTCAAA
667977 AAATTAAATTTGAGTCTAGTTATAAAAT
1 AAATTAAATTTGAGTCTAGTTATAAAAT
668005 AGAGGTTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
37 7 0.12
38 40 0.70
39 10 0.18
ACGTcount: A:0.43, C:0.08, G:0.11, T:0.38
Consensus pattern (39 bp):
AAATTAAATTTGAGTCTAGTTATAAAATTTCGATTCAAA
Found at i:670172 original size:20 final size:20
Alignment explanation
Indices: 670108--670175 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
670098 TTGTAAATTT
670108 TTAAA-TCGCAATATA-ATAG
1 TTAAATTCGCAATATAGA-AG
* *
670127 TAAAATTTGCAATATAGAA-
1 TTAAATTCGCAATATAGAAG
*
670146 TTCAAATTCGCAACATAGAAG
1 TT-AAATTCGCAATATAGAAG
670167 TTAAATTCG
1 TTAAATTCG
670176 TAAAGTGCGT
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
19 5 0.12
20 32 0.80
21 3 0.08
ACGTcount: A:0.46, C:0.12, G:0.12, T:0.31
Consensus pattern (20 bp):
TTAAATTCGCAATATAGAAG
Found at i:670739 original size:19 final size:20
Alignment explanation
Indices: 670715--670761 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
670705 AAATCACGAC
* *
670715 GCGATTTTAGTTTT-GCGTT
1 GCGATTTTAATTTTCGAGTT
*
670734 GCGATTTCAATTTTCGAGTT
1 GCGATTTTAATTTTCGAGTT
670754 GCGATTTT
1 GCGATTTT
670762 TAAGTTTCAG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.15, C:0.13, G:0.23, T:0.49
Consensus pattern (20 bp):
GCGATTTTAATTTTCGAGTT
Found at i:672492 original size:21 final size:21
Alignment explanation
Indices: 672462--672502 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
672452 GAGTTATGTG
* *
672462 ATGAGGTCGGTGCTTTACGTC
1 ATGAGATCGGTACTTTACGTC
672483 ATGAGATCGGTACTTTACGT
1 ATGAGATCGGTACTTTACGT
672503 GAAGACAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.29, T:0.34
Consensus pattern (21 bp):
ATGAGATCGGTACTTTACGTC
Found at i:672969 original size:21 final size:21
Alignment explanation
Indices: 672936--673011 Score: 98
Period size: 21 Copynumber: 3.6 Consensus size: 21
672926 AGCACTTCCT
672936 ATCGTTCAAGAGGCCCCTCTC
1 ATCGTTCAAGAGGCCCCTCTC
* * * *
672957 ATCATTGAAGAGGTCCCTCCC
1 ATCGTTCAAGAGGCCCCTCTC
* *
672978 ACCGTTCAAGAGGCCCCTATC
1 ATCGTTCAAGAGGCCCCTCTC
672999 ATCGTTCAAGAGG
1 ATCGTTCAAGAGG
673012 TTCCGCCCGC
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 44 1.00
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (21 bp):
ATCGTTCAAGAGGCCCCTCTC
Found at i:672984 original size:42 final size:42
Alignment explanation
Indices: 672938--673031 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
672928 CACTTCCTAT
* * *
672938 CGTTCAAGAGGCCCCTCTCATCATTGAAGAGGTCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCATTCAAGAGGTCCCGCCCAC
* * *
672980 CGTTCAAGAGGCCCCTATCATCGTTCAAGAGGTTCCGCCCGC
1 CGTTCAAGAGGCCCCTATCATCATTCAAGAGGTCCCGCCCAC
673022 CGTTCAAGAG
1 CGTTCAAGAG
673032 CCCGATTCAC
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.21, C:0.35, G:0.22, T:0.21
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCATTCAAGAGGTCCCGCCCAC
Found at i:674470 original size:14 final size:14
Alignment explanation
Indices: 674448--674481 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
674438 TTTCTTGTTG
*
674448 ATTTATAAAAGTTA
1 ATTTGTAAAAGTTA
*
674462 ATTTGTAAAAGTTG
1 ATTTGTAAAAGTTA
674476 ATTTGT
1 ATTTGT
674482 TTAATTGATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
ATTTGTAAAAGTTA
Found at i:674672 original size:20 final size:21
Alignment explanation
Indices: 674627--674676 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
674617 GTTGCGATAG
**
674627 TCAAATTCGCAACGTTAAAGT
1 TCAAATTCGCAACGCGAAAGT
674648 T-AAATTCGCAACGCGAAA-T
1 TCAAATTCGCAACGCGAAAGT
674667 TCAAATTCGC
1 TCAAATTCGC
674677 GTTGCGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 23 0.88
21 1 0.04
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (21 bp):
TCAAATTCGCAACGCGAAAGT
Found at i:674717 original size:40 final size:40
Alignment explanation
Indices: 674672--674756 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 40
674662 GAAATTCAAA
* *
674672 TTCGCGTTGCG-ATTTTGATTTTTG-GTTTGCAAATTTGACT
1 TTCGCGTTGCGAATTTT-ACTTTTGCG-TTGCAAATTTAACT
* *
674712 TTCGCGTTGTGAATTTTACTTTTGCGTTGCGAATTTAACT
1 TTCGCGTTGCGAATTTTACTTTTGCGTTGCAAATTTAACT
674752 TTCGC
1 TTCGC
674757 AACAAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
40 33 0.85
41 6 0.15
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.48
Consensus pattern (40 bp):
TTCGCGTTGCGAATTTTACTTTTGCGTTGCAAATTTAACT
Found at i:674726 original size:20 final size:20
Alignment explanation
Indices: 674698--674756 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
674688 GATTTTTGGT
* *
674698 TTGCAAATTTGACTTTCGCG
1 TTGCGAATTTAACTTTCGCG
* * *
674718 TTGTGAATTTTACTTTTGCG
1 TTGCGAATTTAACTTTCGCG
674738 TTGCGAATTTAACTTTCGC
1 TTGCGAATTTAACTTTCGC
674757 AACAAAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.46
Consensus pattern (20 bp):
TTGCGAATTTAACTTTCGCG
Found at i:677308 original size:24 final size:24
Alignment explanation
Indices: 677274--677327 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
677264 CTGAAACATA
677274 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
677298 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
677322 ATCAAA
1 ATCAAA
677328 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:677341 original size:24 final size:24
Alignment explanation
Indices: 677274--677341 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
677264 CTGAAACATA
* * *
677274 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
677298 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
677322 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
677342 TAGTACTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:678306 original size:20 final size:20
Alignment explanation
Indices: 678261--678452 Score: 137
Period size: 20 Copynumber: 9.7 Consensus size: 20
678251 AACTAAAACC
*
678261 TGTTGCGAAATT-AAATTCG
1 TGTTGCGAATTTGAAATTCG
*
678280 TGTTGCGAATTTGAAAATCG
1 TGTTGCGAATTTGAAATTCG
*
678300 AGTTGCGAATTTGAAATTC-
1 TGTTGCGAATTTGAAATTCG
* *
678319 AGTTGCGAATTTGAAATCCAG
1 TGTTGCGAATTTGAAATTC-G
*
678340 TGTTGCGAATTT-AACTTCTG
1 TGTTGCGAATTTGAAATTC-G
* *
678360 TGTTGCGAATTTG-ACTTATG
1 TGTTGCGAATTTGAAATT-CG
* * *
678380 TGTTACGAATTTG-ACTTATG
1 TGTTGCGAATTTGAAATT-CG
*
678400 TGTTGCGAATTTG-ACTTCTG
1 TGTTGCGAATTTGAAATTC-G
* *
678420 TGTTAC-AATTTACAAATTCG
1 TGTTGCGAATTT-GAAATTCG
* *
678440 CGTTGTGAATTTG
1 TGTTGCGAATTTG
678453 GAAAATCGCA
Statistics
Matches: 144, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
19 34 0.24
20 90 0.62
21 20 0.14
ACGTcount: A:0.26, C:0.12, G:0.22, T:0.40
Consensus pattern (20 bp):
TGTTGCGAATTTGAAATTCG
Found at i:678324 original size:39 final size:41
Alignment explanation
Indices: 678262--678373 Score: 142
Period size: 39 Copynumber: 2.8 Consensus size: 41
678252 ACTAAAACCT
*
678262 GTTGCGAAATTAAATTCGTGTTGCGAATTTGAAAAT-C-GA
1 GTTGCGAATTTAAATTCGTGTTGCGAATTTGAAAATCCAGA
* *
678301 GTTGCGAATTTGAAATTC-AGTTGCGAATTTG-AAATCCAGT
1 GTTGCGAATTT-AAATTCGTGTTGCGAATTTGAAAATCCAGA
*
678341 GTTGCGAATTTAACTTCTGTGTTGCGAATTTGA
1 GTTGCGAATTTAAATTC-GTGTTGCGAATTTGA
678374 CTTATGTGTT
Statistics
Matches: 62, Mismatches: 5, Indels: 9
0.82 0.07 0.12
Matches are distributed among these distances:
38 4 0.06
39 28 0.45
40 18 0.29
41 12 0.19
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.37
Consensus pattern (41 bp):
GTTGCGAATTTAAATTCGTGTTGCGAATTTGAAAATCCAGA
Found at i:679867 original size:35 final size:34
Alignment explanation
Indices: 679802--679870 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 34
679792 ATTGTCTTTA
* *
679802 TTATATATTTGTTTTTTAACAAGTTCGAAAATAT
1 TTATATATTTATTTTTTAACAAATTCGAAAATAT
*
679836 TTATATATATTATTTTTTTACAAAATT-GAAAATAT
1 TTATATAT-TTATTTTTTAAC-AAATTCGAAAATAT
679871 AAAAAGGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
34 8 0.27
35 18 0.60
36 4 0.13
ACGTcount: A:0.39, C:0.04, G:0.06, T:0.51
Consensus pattern (34 bp):
TTATATATTTATTTTTTAACAAATTCGAAAATAT
Found at i:682756 original size:23 final size:23
Alignment explanation
Indices: 682726--682770 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
682716 GGAGGGACAA
682726 GGTGTACTGGTACAACTTGGTAT
1 GGTGTACTGGTACAACTTGGTAT
682749 GGTGTACTGGTACAACTTGGTA
1 GGTGTACTGGTACAACTTGGTA
682771 CAATTTCTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.13, G:0.31, T:0.33
Consensus pattern (23 bp):
GGTGTACTGGTACAACTTGGTAT
Found at i:684839 original size:57 final size:57
Alignment explanation
Indices: 684739--684864 Score: 166
Period size: 57 Copynumber: 2.2 Consensus size: 57
684729 TAAATGTAGA
*
684739 TTTGCCCCTAAACTATACTGTTTTTACCGAATTGCTCCCTAAAATACTTTCTAT-ATGT
1 TTTG-CCCTAAACTATACTGTTTTTACCGAATTACTCCCTAAAATACTTT-TATGATGT
* * * *
684797 TTTGCACCTAAACTGTA-TTTTTTTTCCGAATTACTCTCTAAAATACTTTTATGATGT
1 TTTGC-CCTAAACTATACTGTTTTTACCGAATTACTCCCTAAAATACTTTTATGATGT
684854 TTTGCCCTAAA
1 TTTGCCCTAAA
684865 GTTCTCAAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
56 9 0.15
57 38 0.62
58 14 0.23
ACGTcount: A:0.26, C:0.21, G:0.09, T:0.44
Consensus pattern (57 bp):
TTTGCCCTAAACTATACTGTTTTTACCGAATTACTCCCTAAAATACTTTTATGATGT
Done.