Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008926.1 Hibiscus syriacus cultivar Beakdansim tig00112231_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: 4069050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 20
Found at i:2784261 original size:24 final size:22
Alignment explanation
Indices: 2784233--2784297 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 22
2784223 CATTGATGCA
2784233 TAAGGAGTGCATCGATGCACATG
1 TAAGGAGTGCATCGATGCAC-TG
*
2784256 TTAAGG-GATGCATCGATACACTG
1 -TAAGGAG-TGCATCGATGCACTG
*
2784279 T-AGCA-TGCATCGATGCACT
1 TAAGGAGTGCATCGATGCACT
2784298 TCAAGGGGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 13 0.36
21 2 0.06
22 1 0.03
23 3 0.08
24 17 0.47
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.25
Consensus pattern (22 bp):
TAAGGAGTGCATCGATGCACTG
Found at i:2784546 original size:20 final size:17
Alignment explanation
Indices: 2784499--2784545 Score: 85
Period size: 17 Copynumber: 2.8 Consensus size: 17
2784489 GTTAAGGTGA
2784499 GTGCATATTATTAGATT
1 GTGCATATTATTAGATT
*
2784516 GTTCATATTATTAGATT
1 GTGCATATTATTAGATT
2784533 GTGCATATTATTA
1 GTGCATATTATTA
2784546 TATGGAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.30, C:0.06, G:0.15, T:0.49
Consensus pattern (17 bp):
GTGCATATTATTAGATT
Found at i:2790431 original size:2 final size:2
Alignment explanation
Indices: 2790424--2790491 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
2790414 ATTAGAAGCA
2790424 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2790465 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2790492 GTTCTTTTGT
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2791254 original size:29 final size:31
Alignment explanation
Indices: 2791218--2791282 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2791208 TTTGTAATCT
*
2791218 TAAAATGTTGTAATAT-ATA-A-GTATAATAA
1 TAAAATGTT-CAATATAATACATGTATAATAA
*
2791247 TAAAATGTTCAATGTAATACATGTATAATAA
1 TAAAATGTTCAATATAATACATGTATAATAA
2791278 TAAAA
1 TAAAA
2791283 ATGATTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 4 0.13
29 12 0.39
30 1 0.03
31 14 0.45
ACGTcount: A:0.52, C:0.03, G:0.09, T:0.35
Consensus pattern (31 bp):
TAAAATGTTCAATATAATACATGTATAATAA
Found at i:2791348 original size:19 final size:17
Alignment explanation
Indices: 2791309--2791351 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
2791299 AAAAAAAATA
2791309 ATTTAA-TATATATAAT
1 ATTTAATTATATATAAT
2791325 ATTTAATTATATATAGAT
1 ATTTAATTATATATA-AT
2791343 ATTTTAATT
1 A-TTTAATT
2791352 TAATCTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.25
17 8 0.33
18 3 0.12
19 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTAATTATATATAAT
Found at i:2792368 original size:37 final size:33
Alignment explanation
Indices: 2792274--2792369 Score: 92
Period size: 32 Copynumber: 2.9 Consensus size: 33
2792264 TAATAAAATT
* *
2792274 AAATATATATTTTATTCTTACATTAACTAAAGAA
1 AAATATATATTTTATTTTTAC-TTAACTAAAAAA
* * *
2792308 AAA-A-ATATTTTAGTTTTTTCTAAACT--TAAA
1 AAATATATATTTTA-TTTTTACTTAACTAAAAAA
2792338 AAATATATATTTTATTTTTACCTTAACTAAAA
1 AAATATATATTTTATTTTTA-CTTAACTAAAA
2792370 TTTTTAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
30 5 0.10
31 6 0.12
32 27 0.56
33 6 0.12
34 4 0.08
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (33 bp):
AAATATATATTTTATTTTTACTTAACTAAAAAA
Found at i:2792487 original size:31 final size:28
Alignment explanation
Indices: 2792397--2792491 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 28
2792387 TATAATACGA
*
2792397 TAAAATAAAGATAAAA-ATATTTTGTTAAT
1 TAAAATAAAAATAAAATATA-TTT-TTAAT
* *
2792426 TAAGATAAAAATAAAATATATTTCCTAAT
1 TAAAATAAAAATAAAATATATTT-TTAAT
*
2792455 TAAAATAAGAATAAAATATGTATTTTTAAAT
1 TAAAATAAAAATAAAATA--TATTTTT-AAT
2792486 TAAAAT
1 TAAAAT
2792492 GAAATATATA
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
29 37 0.67
30 4 0.07
31 14 0.25
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (28 bp):
TAAAATAAAAATAAAATATATTTTTAAT
Found at i:2792677 original size:32 final size:33
Alignment explanation
Indices: 2792595--2792722 Score: 124
Period size: 31 Copynumber: 4.1 Consensus size: 33
2792585 AATATATGCA
*
2792595 AAAAGTTAAGATAAAAATAAAA-A-ATATTTTT
1 AAAAGTTAAGATAAGAATAAAATATATATTTTT
*
2792626 AAAAGTTAAGATAATAATAAAATATATATTTTT
1 AAAAGTTAAGATAAGAATAAAATATATATTTTT
* * *
2792659 -TAAGTTAAGGTAGGAAT-AAA-ATATA-TTTT
1 AAAAGTTAAGATAAGAATAAAATATATATTTTT
* * * * *
2792688 ATAAGCTAAGATAAGATTAAACTATATGTTTTT
1 AAAAGTTAAGATAAGAATAAAATATATATTTTT
2792721 AA
1 AA
2792723 CTAATATATG
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
29 4 0.05
30 18 0.23
31 26 0.33
32 18 0.23
33 13 0.16
ACGTcount: A:0.52, C:0.02, G:0.10, T:0.37
Consensus pattern (33 bp):
AAAAGTTAAGATAAGAATAAAATATATATTTTT
Found at i:2792685 original size:30 final size:30
Alignment explanation
Indices: 2792407--2792776 Score: 176
Period size: 30 Copynumber: 12.5 Consensus size: 30
2792397 TAAAATAAAG
*
2792407 ATAAAA-ATATTTTGTTAA-TTAAGATAAAA
1 ATAAAATATATTTT-TTAAGTTAAGATAAGA
** *
2792436 ATAAAATATATTTCCTAA-TTAAAATAAGA
1 ATAAAATATATTTTTTAAGTTAAGATAAGA
* * *
2792465 ATAAAATATGTATTTTTAAATTAA-A-ATG-
1 ATAAAATATAT-TTTTTAAGTTAAGATAAGA
* * *
2792493 A-AATATATA-ATTTGAAGTTAAGATAAGA
1 ATAAAATATATTTTTTAAGTTAAGATAAGA
* ** **
2792521 AT-AAATA-ATATTAAATAGTTTAAGGCAAGA
1 ATAAAATATATTTTTTA-AG-TTAAGATAAGA
* ** * *
2792551 ATATAATATATTTAATAATTTAA-ATTAATA
1 ATAAAATATATTTTTTAAGTTAAGA-TAAGA
* ***** *
2792581 ATATAATATATGCAAAAAGTTAAGATAAAA
1 ATAAAATATATTTTTTAAGTTAAGATAAGA
* * *
2792611 ATAAAAAATATTTTTAAAAGTTAAGATAATA
1 ATAAAATATATTTTT-TAAGTTAAGATAAGA
* *
2792642 ATAAAATATATATTTTTTAAGTTAAGGTAGGA
1 AT-AAA-ATATATTTTTTAAGTTAAGATAAGA
* *
2792674 ATAAAATATATTTTATAAGCTAAGATAAGA
1 ATAAAATATATTTTTTAAGTTAAGATAAGA
* * * * *
2792704 TTAAACTATATGTTTTTAA-CTAATATATGA
1 ATAAAATATAT-TTTTTAAGTTAAGATAAGA
**
2792734 ATAAAATATATTTAATAAGTTAAGGA-AA-A
1 ATAAAATATATTTTTTAAGTTAA-GATAAGA
2792763 AT-AAATATATTTTT
1 ATAAAATATATTTTT
2792777 AAATATTAAG
Statistics
Matches: 259, Mismatches: 62, Indels: 41
0.72 0.17 0.11
Matches are distributed among these distances:
25 9 0.03
26 1 0.00
27 9 0.03
28 20 0.08
29 40 0.15
30 114 0.44
31 36 0.14
32 21 0.08
33 9 0.03
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.37
Consensus pattern (30 bp):
ATAAAATATATTTTTTAAGTTAAGATAAGA
Found at i:2794090 original size:12 final size:13
Alignment explanation
Indices: 2794060--2794097 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2794050 GTAAACTAAA
2794060 ATAATTTTTATTC
1 ATAATTTTTATTC
*
2794073 ATAATTTTTTTTC
1 ATAATTTTTATTC
2794086 A-AATTTGTTATT
1 ATAATTT-TTATT
2794098 TTATATTTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 5 0.23
13 17 0.77
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (13 bp):
ATAATTTTTATTC
Found at i:2798059 original size:23 final size:23
Alignment explanation
Indices: 2798014--2798063 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
2798004 TGGTGACTAA
*
2798014 CAACATCAACCGACAGTGCTTGG
1 CAACATCAACCGACAGTGATTGG
* **
2798037 CAACATCAACTGATGGTGATTGG
1 CAACATCAACCGACAGTGATTGG
2798060 CAAC
1 CAAC
2798064 GATGATGAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.20
Consensus pattern (23 bp):
CAACATCAACCGACAGTGATTGG
Found at i:2798135 original size:23 final size:23
Alignment explanation
Indices: 2798109--2798185 Score: 55
Period size: 23 Copynumber: 3.0 Consensus size: 23
2798099 ATGATTGGAT
2798109 GGTTAAATTAATATTTTATCTAA
1 GGTTAAATTAATATTTTATCTAA
* *
2798132 GGTTCAAGGATTAAATCAATATTTTATTTAG
1 GGTT-AA--A-T---T-AATATTTTATCTAA
*
2798163 GGTCAAATTAATATTTTATCTAA
1 GGTTAAATTAATATTTTATCTAA
2798186 AATTTAGGGG
Statistics
Matches: 41, Mismatches: 5, Indels: 16
0.66 0.08 0.26
Matches are distributed among these distances:
23 16 0.39
24 3 0.07
26 1 0.02
27 2 0.05
28 1 0.02
30 3 0.07
31 15 0.37
ACGTcount: A:0.38, C:0.06, G:0.12, T:0.44
Consensus pattern (23 bp):
GGTTAAATTAATATTTTATCTAA
Found at i:2799030 original size:13 final size:13
Alignment explanation
Indices: 2799012--2799037 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2799002 TTTTCTTTTA
2799012 GTTATTTTTTTCT
1 GTTATTTTTTTCT
2799025 GTTATTTTTTTCT
1 GTTATTTTTTTCT
2799038 TCTCTTAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.77
Consensus pattern (13 bp):
GTTATTTTTTTCT
Found at i:2799416 original size:28 final size:28
Alignment explanation
Indices: 2799384--2799617 Score: 167
Period size: 28 Copynumber: 8.3 Consensus size: 28
2799374 CATAATTTGG
*
2799384 AAAAGTTTGATCTTTATTATAATTTATA
1 AAAAGTTTGGTCTTTATTATAATTTATA
* * *
2799412 AAAAGTTTGGGT-TGGTGTT-TAATTTGTA
1 AAAAGTTT-GGTCT-TTATTATAATTTATA
* *
2799440 AAAAGTTTGG-CTTTATTATAATTTTTG
1 AAAAGTTTGGTCTTTATTATAATTTATA
* * *
2799467 AAAAGTTTTGGT-ATTATTGTAATTTATG
1 AAAAG-TTTGGTCTTTATTATAATTTATA
* * *
2799495 GAAAGTTTGGGCATTTATTATGATTTATA
1 AAAAGTTTGGTC-TTTATTATAATTTATA
*
2799524 AAAAGTTTGGGT-TATTATTATAATTTATG
1 AAAAGTTT-GGTCT-TTATTATAATTTATA
* * * *
2799553 AAAACTTTGGGCTTTAATGTAATTTATAA
1 AAAAGTTTGGTCTTTATTATAATTTAT-A
**
2799582 AAAAGTTTGGGT-TTTATTGCAATTT-TA
1 AAAAGTTT-GGTCTTTATTATAATTTATA
*
2799609 TAAAGTTTG
1 AAAAGTTTG
2799618 TTACTATAGT
Statistics
Matches: 162, Mismatches: 31, Indels: 28
0.73 0.14 0.13
Matches are distributed among these distances:
26 4 0.02
27 28 0.17
28 63 0.39
29 63 0.39
30 4 0.02
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (28 bp):
AAAAGTTTGGTCTTTATTATAATTTATA
Found at i:2799460 original size:55 final size:57
Alignment explanation
Indices: 2799342--2799599 Score: 265
Period size: 55 Copynumber: 4.6 Consensus size: 57
2799332 GTTGGGTTGA
* * * * * **
2799342 TATTATAATTTGTAAACATTTTGGGTTGTTATCATAATTT-GGAAAAGTTTGATCTT
1 TATTATAATTTATAAAAAGTTTGGGTTGTTATTATAATTTATGAAAAGTTTGGGCTT
* * * *
2799398 TATTATAATTTATAAAAAGTTTGGGTTGGTGTT-TAATTTGTAAAAAGTTT-GGCTT
1 TATTATAATTTATAAAAAGTTTGGGTTGTTATTATAATTTATGAAAAGTTTGGGCTT
* * * * * *
2799453 TATTATAATTTTTGAAAAGTTTTGG-TATTATTGTAATTTATGGAAAGTTTGGGCATT
1 TATTATAATTTATAAAAAGTTTGGGTTGTTATTATAATTTATGAAAAGTTTGGGC-TT
* * *
2799510 TATTATGATTTATAAAAAGTTTGGGTTATTATTATAATTTATGAAAACTTTGGGCTT
1 TATTATAATTTATAAAAAGTTTGGGTTGTTATTATAATTTATGAAAAGTTTGGGCTT
* *
2799567 TAATGTAATTTATAAAAAAGTTTGGGTT-TTATT
1 TATTATAATTTAT-AAAAAGTTTGGGTTGTTATT
2799600 GCAATTTTAT
Statistics
Matches: 167, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
54 4 0.02
55 45 0.27
56 38 0.23
57 40 0.24
58 40 0.24
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (57 bp):
TATTATAATTTATAAAAAGTTTGGGTTGTTATTATAATTTATGAAAAGTTTGGGCTT
Found at i:2799605 original size:29 final size:28
Alignment explanation
Indices: 2799327--2799617 Score: 216
Period size: 29 Copynumber: 10.4 Consensus size: 28
2799317 AATTTGTAGA
* *
2799327 AAAAAG-TTGGGTTGATATTATAATTTGT
1 AAAAAGTTTGGGTT-TTATTATAATTTAT
* * * *
2799355 AAACATTTTGGGTTGTTATCATAATTT-G
1 AAAAAGTTTGGGTT-TTATTATAATTTAT
* *
2799383 GAAAAGTTT-GATCTTTATTATAATTTAT
1 AAAAAGTTTGGGT-TTTATTATAATTTAT
* * *
2799411 AAAAAGTTTGGGTTGGTGTT-TAATTTGT
1 AAAAAGTTTGGGTT-TTATTATAATTTAT
* *
2799439 AAAAAGTTT-GGCTTTATTATAATTTTT
1 AAAAAGTTTGGGTTTTATTATAATTTAT
* * * *
2799466 GAAAAGTTTTGGTATTATTGTAATTTAT
1 AAAAAGTTTGGGTTTTATTATAATTTAT
** * *
2799494 GGAAAGTTTGGGCATTTATTATGATTTAT
1 AAAAAGTTTGGG-TTTTATTATAATTTAT
2799523 AAAAAGTTTGGGTTATTATTATAATTTAT
1 AAAAAGTTTGGGTT-TTATTATAATTTAT
* * * * *
2799552 GAAAACTTTGGGCTTTAATGTAATTTAT
1 AAAAAGTTTGGGTTTTATTATAATTTAT
**
2799580 AAAAAAGTTTGGGTTTTATTGCAATTT-T
1 -AAAAAGTTTGGGTTTTATTATAATTTAT
*
2799608 ATAAAGTTTG
1 AAAAAGTTTG
2799618 TTACTATAGT
Statistics
Matches: 207, Mismatches: 46, Indels: 21
0.76 0.17 0.08
Matches are distributed among these distances:
26 3 0.01
27 40 0.19
28 74 0.36
29 90 0.43
ACGTcount: A:0.32, C:0.03, G:0.18, T:0.47
Consensus pattern (28 bp):
AAAAAGTTTGGGTTTTATTATAATTTAT
Found at i:2799609 original size:58 final size:57
Alignment explanation
Indices: 2799396--2799606 Score: 205
Period size: 57 Copynumber: 3.7 Consensus size: 57
2799386 AAGTTTGATC
* * * * * *
2799396 TTTATTATAATTTATAAAAAGTTTGGGTTGGTGTT-TAATTTGTAAAAAGTTT-GGC-
1 TTTAATATAATTTATAAAAAGTTTGGGTT-TTATTGTAATTTATGAAAACTTTGGGCA
* * * * * * *
2799451 TTTATTATAATTTTTGAAAAGTTTTGGTATTATTGTAATTTATGGAAAGTTTGGGCA
1 TTTAATATAATTTATAAAAAGTTTGGGTTTTATTGTAATTTATGAAAACTTTGGGCA
* * *
2799508 TTTATTATGATTTATAAAAAGTTTGGGTTATTATTATAATTTATGAAAACTTTGGGC-
1 TTTAATATAATTTATAAAAAGTTTGGGTT-TTATTGTAATTTATGAAAACTTTGGGCA
* *
2799565 TTTAATGTAATTTATAAAAAAGTTTGGGTTTTATTGCAATTT
1 TTTAATATAATTTAT-AAAAAGTTTGGGTTTTATTGTAATTT
2799607 TATAAAGTTT
Statistics
Matches: 129, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
54 3 0.02
55 39 0.30
56 3 0.02
57 46 0.36
58 38 0.29
ACGTcount: A:0.32, C:0.02, G:0.18, T:0.48
Consensus pattern (57 bp):
TTTAATATAATTTATAAAAAGTTTGGGTTTTATTGTAATTTATGAAAACTTTGGGCA
Found at i:2801671 original size:30 final size:30
Alignment explanation
Indices: 2801598--2801673 Score: 109
Period size: 30 Copynumber: 2.5 Consensus size: 30
2801588 AAGTTAAAGA
*
2801598 TAAGAATA-AATAATATTTAATAATTCAAGT
1 TAAGAATATAAT-ATATTTAATAATTCAAAT
*
2801628 TAAGAATATAATATATTTAATAATTTAAAT
1 TAAGAATATAATATATTTAATAATTCAAAT
*
2801658 TAATAATATAATATAT
1 TAAGAATATAATATAT
2801674 GTAAAAAGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
30 39 0.93
31 3 0.07
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (30 bp):
TAAGAATATAATATATTTAATAATTCAAAT
Found at i:2801733 original size:31 final size:30
Alignment explanation
Indices: 2801677--2801740 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 30
2801667 AATATATGTA
2801677 AAAAGTTAAGATAAAAATGAAATATAGTTTT
1 AAAAGTTAAGATAAAAA-GAAATATAGTTTT
*
2801708 AAAAGTTAAGATAAATAA-AATATATATTTTT
1 AAAAGTTAAGATAAA-AAGAA-ATATAGTTTT
2801739 AA
1 AA
2801741 GTTATGTAGG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 2 0.07
31 26 0.87
32 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.34
Consensus pattern (30 bp):
AAAAGTTAAGATAAAAAGAAATATAGTTTT
Found at i:2801742 original size:29 final size:28
Alignment explanation
Indices: 2801679--2801865 Score: 137
Period size: 29 Copynumber: 6.4 Consensus size: 28
2801669 TATATGTAAA
* **
2801679 AAGTTAAGATAAAAATGAAATATAGTTTTAA
1 AAGTTAAGAT--AAATAAAATATA-TTTTTT
2801710 AAGTTAAGATAAATAAAATATATATTTTT
1 AAGTTAAGATAAATAAAATATAT-TTTTT
* *
2801739 AAGTTATG-TAGGAATAAAATATATTTTAT
1 AAGTTAAGATA--AATAAAATATATTTTTT
*
2801768 AAGCTAAGATAAGATTAAAATATATTTTTT
1 AAGTTAAGATAA-A-TAAAATATATTTTTT
* **
2801798 AA-CTAAGATAGGAATAAAATATATTTACT
1 AAGTTAAGATA--AATAAAATATATTTTTT
* * *
2801827 ATGTTCAGAAAAAT-AAATATATTTTTT
1 AAGTTAAGATAAATAAAATATATTTTTT
*
2801854 AATATTAAGATA
1 AA-GTTAAGATA
2801866 TGATTTTAAG
Statistics
Matches: 126, Mismatches: 20, Indels: 23
0.75 0.12 0.14
Matches are distributed among these distances:
27 12 0.10
28 13 0.10
29 54 0.43
30 36 0.29
31 11 0.09
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (28 bp):
AAGTTAAGATAAATAAAATATATTTTTT
Found at i:2801757 original size:30 final size:30
Alignment explanation
Indices: 2801696--2801823 Score: 138
Period size: 29 Copynumber: 4.3 Consensus size: 30
2801686 GATAAAAATG
** *
2801696 AAATATAGTTTTAAAAGTTAAGATA--AATA
1 AAATATA-TTTTTTAAGCTAAGATAGGAATA
* *
2801725 AAATATATATTTTTAAGTTATG-TAGGAATA
1 AAATATAT-TTTTTAAGCTAAGATAGGAATA
* * *
2801755 AAATATATTTTATAAGCTAAGATAAGATTA
1 AAATATATTTTTTAAGCTAAGATAGGAATA
2801785 AAATATATTTTTTAA-CTAAGATAGGAATA
1 AAATATATTTTTTAAGCTAAGATAGGAATA
2801814 AAATATATTT
1 AAATATATTT
2801824 ACTATGTTCA
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
28 3 0.04
29 49 0.58
30 32 0.38
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (30 bp):
AAATATATTTTTTAAGCTAAGATAGGAATA
Found at i:2801759 original size:59 final size:59
Alignment explanation
Indices: 2801696--2801823 Score: 172
Period size: 59 Copynumber: 2.2 Consensus size: 59
2801686 GATAAAAATG
* * *
2801696 AAATATAGTTTTAAAAGTTAAGATAA-A-TAAAATATATATTTTTAAGTTATG-TAGGAATA
1 AAATATA-TTTTAAAAGCTAAGATAAGATTAAAATATAT-TTTTTAA-CTAAGATAGGAATA
*
2801755 AAATATATTTTATAAGCTAAGATAAGATTAAAATATATTTTTTAACTAAGATAGGAATA
1 AAATATATTTTAAAAGCTAAGATAAGATTAAAATATATTTTTTAACTAAGATAGGAATA
2801814 AAATATATTT
1 AAATATATTT
2801824 ACTATGTTCA
Statistics
Matches: 62, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
58 19 0.31
59 33 0.53
60 10 0.16
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.39
Consensus pattern (59 bp):
AAATATATTTTAAAAGCTAAGATAAGATTAAAATATATTTTTTAACTAAGATAGGAATA
Found at i:2803570 original size:38 final size:38
Alignment explanation
Indices: 2803516--2803588 Score: 119
Period size: 38 Copynumber: 1.9 Consensus size: 38
2803506 ATATGAAAAT
* *
2803516 ATTATTTTACAGTAAAAGTTAAGAATGGAAAACTTAAA
1 ATTATTTCACAATAAAAGTTAAGAATGGAAAACTTAAA
*
2803554 ATTATTTCACAATAAAAGTTAAGAATGGCAAACTT
1 ATTATTTCACAATAAAAGTTAAGAATGGAAAACTT
2803589 TTGAAAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (38 bp):
ATTATTTCACAATAAAAGTTAAGAATGGAAAACTTAAA
Found at i:2806245 original size:21 final size:21
Alignment explanation
Indices: 2806221--2806261 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
2806211 ATGTTTAATG
2806221 AAAAAGATATCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
2806242 AAAAGGATATCAATTGTTAA
1 AAAAAGATATCAATTGTTAA
2806262 AAAGATACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.29
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:2806268 original size:18 final size:18
Alignment explanation
Indices: 2806221--2806278 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 18
2806211 ATGTTTAATG
2806221 AAAAAGATATCAATTGTT
1 AAAAAGATATCAATTGTT
2806239 AACAAAAGGATATCAATTGTT
1 -A-AAAA-GATATCAATTGTT
* *
2806260 AAAAAGATACCTATTGTT
1 AAAAAGATATCAATTGTT
2806278 A
1 A
2806279 CCAATTGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
18 12 0.34
19 5 0.14
20 5 0.14
21 13 0.37
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (18 bp):
AAAAAGATATCAATTGTT
Found at i:2808390 original size:34 final size:33
Alignment explanation
Indices: 2808329--2808399 Score: 90
Period size: 34 Copynumber: 2.1 Consensus size: 33
2808319 CTTTTATAAC
* *
2808329 TCCCTAGTTTTTCATGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTTCATGGGATAAACTAGAACATT
*
2808362 TCCCTAGATTTTAT-ATGGGATAAGCTAGAACATT
1 TCCCTAG-TTTT-TCATGGGATAAACTAGAACATT
2808396 TCCC
1 TCCC
2808400 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 7 0.21
34 25 0.76
35 1 0.03
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (33 bp):
TCCCTAGTTTTTCATGGGATAAACTAGAACATT
Found at i:2814967 original size:6 final size:6
Alignment explanation
Indices: 2814951--2814989 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
2814941 TGAATGACAC
*
2814951 CATTTG TATTTG CATTTAG CATTTG CATTTG CA-TTG CAT
1 CATTTG CATTTG CATTT-G CATTTG CATTTG CATTTG CAT
2814990 GTATTTATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 18 0.62
7 6 0.21
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (6 bp):
CATTTG
Found at i:2814976 original size:13 final size:12
Alignment explanation
Indices: 2814951--2814989 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
2814941 TGAATGACAC
*
2814951 CATTTGTATTTG
1 CATTTGCATTTG
2814963 CATTTAGCATTTG
1 CATTT-GCATTTG
2814976 CATTTGCA-TTG
1 CATTTGCATTTG
2814987 CAT
1 CAT
2814990 GTATTTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 6 0.24
12 8 0.32
13 11 0.44
ACGTcount: A:0.21, C:0.15, G:0.15, T:0.49
Consensus pattern (12 bp):
CATTTGCATTTG
Found at i:2819947 original size:37 final size:37
Alignment explanation
Indices: 2819886--2819957 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
2819876 TGAATATTTT
* * * *
2819886 AAGCCTTCACCGAAGAGCAGTGAAGCAAATTCATCCC
1 AAGCCTTCACCAAAGAACAATGAAGCAAATCCATCCC
*
2819923 AAGCCTTCACCAAAGAATAATGAAGCAAATCCATC
1 AAGCCTTCACCAAAGAACAATGAAGCAAATCCATC
2819958 TGTAAGTCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.40, C:0.28, G:0.15, T:0.17
Consensus pattern (37 bp):
AAGCCTTCACCAAAGAACAATGAAGCAAATCCATCCC
Found at i:2820349 original size:217 final size:216
Alignment explanation
Indices: 2819958--2820401 Score: 511
Period size: 217 Copynumber: 2.0 Consensus size: 216
2819948 CAAATCCATC
* * *
2819958 TGTAAGTCTTTAGAACAAGATGATAAGTCCGTCGGGCCATCCATAAGACCTTCGGATAGGATGTT
1 TGTAAGCCTTTAGAACAAGATGATAAGTACGTCGGGCCATCCATAAGACATTCGGATAGGATGTT
* * * * *
2820023 TTGACATGAATTTTTAAAAAAAATGAAGTAATGCTTTAAGATAATGAAATCTTTGAAAACTAAGA
66 TTCACATCAATTTTGAAAAAAAATGAAGTAATGCTTTAAGAAAATGAAATCTTTAAAAACTAAGA
* * * * *
2820088 AGGCGATTTCTAAAATTTTGCATTTGGTAAGTCCTTTGGGCCATCAATAAGACTTTCGATCATGA
131 AGGCGATTCCCAAAATTTTGCA-TTAGTAAGTCCTTTAGGCCATCAATAAGACTTTCGAGCATGA
* * * *
2820153 TGCTTAAATCCTTTGGGTCATT
195 TGATTAAATCCATCGGGTAATT
* * *
2820175 TGTAAGCCTTTAGAGCAAGATGATAAGTACTTTGGGCCATCCATAAGACATTCAGG-TAGGATGT
1 TGTAAGCCTTTAGAACAAGATGATAAGTACGTCGGGCCATCCATAAGACATTC-GGATAGGATGT
** * * * *
2820239 TTTCACATCAA-TTTGAGAAAATCA-GAAAGTGATGTTTTAAGAAAATGAAATTTTTAAAAATTA
65 TTTCACATCAATTTTGA-AAAAAAATG-AAGTAATGCTTTAAGAAAATGAAATCTTTAAAAACTA
* * * *
2820302 AGAAGGCGATTCCCAAACTTTCGTGC-TTAGTAAGT-CTTTCAGGCCATCAGTAAGTCTTTTGAG
128 AGAAGGCGATTCCCAAAATTT--TGCATTAGTAAGTCCTTT-AGGCCATCAATAAGACTTTCGAG
*
2820365 CATGCTGATTAAATCCATCGGGTAATT
190 CATGATGATTAAATCCATCGGGTAATT
2820392 TGTAAGCCTT
1 TGTAAGCCTT
2820402 CACATAAGAG
Statistics
Matches: 190, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
216 9 0.05
217 176 0.93
218 2 0.01
219 3 0.02
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.33
Consensus pattern (216 bp):
TGTAAGCCTTTAGAACAAGATGATAAGTACGTCGGGCCATCCATAAGACATTCGGATAGGATGTT
TTCACATCAATTTTGAAAAAAAATGAAGTAATGCTTTAAGAAAATGAAATCTTTAAAAACTAAGA
AGGCGATTCCCAAAATTTTGCATTAGTAAGTCCTTTAGGCCATCAATAAGACTTTCGAGCATGAT
GATTAAATCCATCGGGTAATT
Found at i:2820505 original size:93 final size:93
Alignment explanation
Indices: 2820344--2820568 Score: 317
Period size: 93 Copynumber: 2.4 Consensus size: 93
2820334 AGTCTTTCAG
* * * *
2820344 GCCATCAGTAAGTCTTTTGAGCATGCTGATTAAATCCATCGGGTAATTTGTAAGCCTTCACATAA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAA
*
2820409 GAGTAGTGAAGCAAACTCATCAGAAAAT
66 GAGTAGTGAAGCAAACTCATCACAAAAT
* * *
2820437 GTCATCAGTAAGTCTTTCGATCATGATGATTAAATCCTTCGGGTAATTTGTAAGCTTTCACAGAA
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAA
* *
2820502 GAGTAGTGAAGCAAACTCATCACTAAGT
66 GAGTAGTGAAGCAAACTCATCACAAAAT
* * *
2820530 GCCATCAGTAAGAT-TTTCGAGCATAATGATGAAGTCCTT
1 GCCATCAGTAAG-TCTTTCGAGCATGATGATTAAATCCTT
2820569 TGGTACATCA
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
93 115 0.99
94 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (93 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAA
GAGTAGTGAAGCAAACTCATCACAAAAT
Found at i:2820610 original size:135 final size:135
Alignment explanation
Indices: 2820439--2820895 Score: 711
Period size: 135 Copynumber: 3.4 Consensus size: 135
2820429 CAGAAAATGT
* *
2820439 CATCAGTAAGTCTTTCGATCATGATGATTAAATCCTTCGGGTAATTTGTAAGCTTTCACAGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAAGA
* *
2820504 GTAGTGAAGCAAACTCATCACTAAGTGCCATCAGTAAGAT-TTTCGAGCATAATGATGAAGTCCT
66 GTAGTGAAGCAAACTCATCAGTAAGTGCCATCAGTAAG-TCTTTCGAGCATGATGATGAAGTCCT
*
2820568 TTGGTA
130 TTGGTC
*
2820574 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACATAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAAGA
2820639 GTAGTGAAGCAAACTCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTT
66 GTAGTGAAGCAAACTCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTT
2820704 TGGTC
131 TGGTC
* * * *
2820709 CATCAGTAAGACTTTCGAGCATGATGATTAAATCCTTCGAGTAAATTGTAAGCCTTCACGGAAGA
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAAGA
* * * *
2820774 GTAATGAAGCAAA-TCCATTAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATAATGAAATCCT
66 GTAGTGAAGCAAACT-CATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCT
*
2820838 TTGGGC
130 TTGGTC
* * * *
2820844 CATCAGTAAGTCTTTCTAGCATGATGATTAAATCTTTTGGGTAATTTCTAAG
1 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAG
2820896 TCTTTCGAGC
Statistics
Matches: 297, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
134 2 0.01
135 295 0.99
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (135 bp):
CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACAGAAGA
GTAGTGAAGCAAACTCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTT
TGGTC
Found at i:2820625 original size:42 final size:42
Alignment explanation
Indices: 2820532--2820926 Score: 122
Period size: 42 Copynumber: 9.0 Consensus size: 42
2820522 CACTAAGTGC
* *
2820532 CATCAGTAAGAT-TTTCGAGCATAATGATGAAGTCCTTTGGTA
1 CATCAGTAAG-TCTTTCGAGCATAATGATGAAATCCTTGGGTA
* *
2820574 CATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTA
1 CATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTT-GGGTA
** * * * * * * ** *
2820617 -ATTTGTAAGCCTTCACATAAG-AGTAGTGAAGCAAACTCATCAGTAAGTGC
1 CATCAGTAAGTCTT-TC--GAGCA-TAATGATG-AAA-TC--C-TTGGGT-A
* * * *
2820667 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTTGGTC
1 CATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTTGGGTA
* * * *
2820709 CATCAGTAAGACTTTCGAGCATGATGATTAAATCCTTCGAGTA
1 CATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTT-GGGTA
* * * * * * *
2820752 AAT-TGTAAGCCTTCACGGAAG-AGTAATGAAGCAAATCCATTAGTAAGTGC
1 CATCAGTAAGTCTT-TC-G-AGCA-TAATGATG-AAATCC-TT-G--GGT-A
* * *
2820802 CATCAGTAAGTCTTTCGAGCATGATAATGAAATCCTTTGGG-C
1 CATCAGTAAGTCTTTCGAGCATAATGATGAAATCC-TTGGGTA
* * * *
2820844 CATCAGTAAGTCTTTCTAGCATGATGATTAAATCTTTTGGGTA
1 CATCAGTAAGTCTTTCGAGCATAATGATGAAATC-CTTGGGTA
*** * *
2820887 -ATTTCTAAGTCTTTCGAGCAAAATAAT-AAATCCTTCGGGT
1 CATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTT-GGGT
2820927 CATTCATAAG
Statistics
Matches: 258, Mismatches: 66, Indels: 59
0.67 0.17 0.15
Matches are distributed among these distances:
40 2 0.01
41 10 0.04
42 142 0.55
43 13 0.05
44 5 0.02
45 13 0.05
46 12 0.05
47 15 0.06
48 14 0.05
49 9 0.03
50 5 0.02
51 18 0.07
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (42 bp):
CATCAGTAAGTCTTTCGAGCATAATGATGAAATCCTTGGGTA
Found at i:2832099 original size:23 final size:23
Alignment explanation
Indices: 2832069--2832131 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
2832059 ATTCCCCTAC
*
2832069 AGGGGGAATCGGTTCCCCTTTAA
1 AGGGGGAATCGGTTCCCCTTCAA
2832092 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
* * *
2832115 GGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
2832132 TCTGCACTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.19, C:0.24, G:0.33, T:0.24
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:2832132 original size:22 final size:21
Alignment explanation
Indices: 2832050--2832131 Score: 76
Period size: 23 Copynumber: 3.7 Consensus size: 21
2832040 GAACCCCAGA
*
2832050 GGGGTATCGATTCCCC-TACAG
1 GGGGAATCGATTCCCCTTA-AG
*
2832071 GGGGAATCGGTTCCCCTTTAAAG
1 GGGGAATCGATTCCCC-TT-AAG
*
2832094 GGGGAATCGGTTCCCCTTCAAGG
1 GGGGAATCGATTCCCCTT-AA-G
*
2832117 GGGGTATCGATTCCC
1 GGGGAATCGATTCCC
2832132 TCTGCACTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
21 14 0.27
22 4 0.08
23 33 0.63
24 1 0.02
ACGTcount: A:0.18, C:0.26, G:0.32, T:0.24
Consensus pattern (21 bp):
GGGGAATCGATTCCCCTTAAG
Found at i:2839625 original size:45 final size:43
Alignment explanation
Indices: 2839590--2839964 Score: 430
Period size: 45 Copynumber: 8.4 Consensus size: 43
2839580 TAAGTATTCA
* *
2839590 TTAT-TTTCATTTATGGCATCCTTTCATGCCTTTAATTCA-CAA
1 TTATATTTCATTTATGGCATCCTTTCATGCCTTTAATGCATC-G
*
2839632 TTGTGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCATCG
1 TTAT--ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCATCG
* *
2839677 TTATGCATTTCCTTTATGGCATCCTTTCATACCTTTAATGCATCG
1 TTAT--ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCATCG
*
2839722 TTATACATTTCATTTATGGCATCCTTCCATGCCTTTAATGCATCG
1 TTAT--ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCATCG
*
2839767 TTATGCATTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCG
1 TTAT--ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCATCG
* * * *
2839812 TTATGCATTTCATTTATGTCATCATTCCATGCCTTTAATGCATCA
1 TTAT--ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCATCG
* * * *
2839857 TTATGCATTTCATTTCTGGCATCTTTTCATGCCTTTAATGCACCA
1 TTAT--ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCATCG
* *
2839902 TTATGCATTTCATTTTTGGCATCCTTTCATGCCTTTAATGCACCG
1 TTAT--ATTTCATTTATGGCATCCTTTCATGCCTTTAATGCATCG
2839947 TTATGCATTTCATTTATG
1 TTAT--ATTTCATTTATG
2839965 TAATGTAAAT
Statistics
Matches: 302, Mismatches: 27, Indels: 5
0.90 0.08 0.01
Matches are distributed among these distances:
42 3 0.01
45 298 0.99
46 1 0.00
ACGTcount: A:0.21, C:0.23, G:0.11, T:0.45
Consensus pattern (43 bp):
TTATATTTCATTTATGGCATCCTTTCATGCCTTTAATGCATCG
Found at i:2839731 original size:90 final size:90
Alignment explanation
Indices: 2839594--2839964 Score: 580
Period size: 90 Copynumber: 4.1 Consensus size: 90
2839584 TATTCATTAT
* * * *
2839594 TTTCATTTATGGCATCCTTTCATGCCTTTAATTCACAATTGTGCATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTC
2839659 CATGCCTTTAATGCATCGTTATGCA
66 CATGCCTTTAATGCATCGTTATGCA
* * * * *
2839684 TTTCCTTTATGGCATCCTTTCATACCTTTAATGCATCGTTATACATTTCATTTATGGCATCCTTC
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTC
2839749 CATGCCTTTAATGCATCGTTATGCA
66 CATGCCTTTAATGCATCGTTATGCA
* * *
2839774 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCGTTATGCATTTCATTTATGTCATCATTC
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTC
*
2839839 CATGCCTTTAATGCATCATTATGCA
66 CATGCCTTTAATGCATCGTTATGCA
* * * *
2839864 TTTCATTTCTGGCATCTTTTCATGCCTTTAATGCACCATTATGCATTTCATTTTTGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTC
*
2839929 CATGCCTTTAATGCACCGTTATGCA
66 CATGCCTTTAATGCATCGTTATGCA
2839954 TTTCATTTATG
1 TTTCATTTATG
2839965 TAATGTAAAT
Statistics
Matches: 255, Mismatches: 26, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 255 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.44
Consensus pattern (90 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTC
CATGCCTTTAATGCATCGTTATGCA
Found at i:2839965 original size:135 final size:135
Alignment explanation
Indices: 2839594--2839965 Score: 591
Period size: 135 Copynumber: 2.8 Consensus size: 135
2839584 TATTCATTAT
* * *
2839594 TTTCATTTATGGCATCCTTTCATGCCTTTAATTCACAATTGTGCATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTT
* * * * * *
2839659 CATGCCTTTAATGCATCGTTATGCATTTCCTTTATGGCATCCTTTCATACCTTTAATGCATCGTT
66 CATGCCTTTAATGCACCGTTATGCATTTCATTTATGTCATCATTCCATACCTTTAATGCATCATT
2839724 ATACA
131 ATACA
* * *
2839729 TTTCATTTATGGCATCCTTCCATGCCTTTAATGCATCGTTATGCATTTCATTTATGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTT
*
2839794 CATGCCTTTAATGCACCGTTATGCATTTCATTTATGTCATCATTCCATGCCTTTAATGCATCATT
66 CATGCCTTTAATGCACCGTTATGCATTTCATTTATGTCATCATTCCATACCTTTAATGCATCATT
*
2839859 ATGCA
131 ATACA
* * *
2839864 TTTCATTTCTGGCATCTTTTCATGCCTTTAATGCACCATTATGCATTTCATTTTTGGCATCCTTT
1 TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTT
2839929 CATGCCTTTAATGCACCGTTATGCATTTCATTTATGT
66 CATGCCTTTAATGCACCGTTATGCATTTCATTTATGT
2839966 AATGTAAATA
Statistics
Matches: 217, Mismatches: 20, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
135 217 1.00
ACGTcount: A:0.21, C:0.23, G:0.12, T:0.45
Consensus pattern (135 bp):
TTTCATTTATGGCATCCTTTCATGCCTTTAATGCACCATTATGCATTTCATTTATGGCATCCTTT
CATGCCTTTAATGCACCGTTATGCATTTCATTTATGTCATCATTCCATACCTTTAATGCATCATT
ATACA
Found at i:2840473 original size:95 final size:96
Alignment explanation
Indices: 2840328--2840517 Score: 253
Period size: 95 Copynumber: 2.0 Consensus size: 96
2840318 CCTACCATGG
* * * *
2840328 TATCGATACTTCTATACTATGGTATCGATATGCCTTTCTAGTATCGATACCATTTCTACATTCT-
1 TATCGATACTTCTATACTATGGTACCGATATGCCTTTCTAGTATCAATACCATTTCAAAATTCTA
*
2840392 GTAATTC-ATGGTATCAATATCTTTCTCTTAC
66 G-AATTCTATGGTATCAATACCTTTCTCTTAC
*
2840423 TATCGATACTTCTATATTATGGTACCGATACT-CCTTT-TCAGTATCAATACCATTTCAAAATTC
1 TATCGATACTTCTATACTATGGTACCGATA-TGCCTTTCT-AGTATCAATACCATTTCAAAATTC
* *
2840486 TAGAATTCTCTGGTATCGATACCTTTCTCTTA
64 TAGAATTCTATGGTATCAATACCTTTCTCTTA
2840518 GAATTGATTG
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
94 1 0.01
95 60 0.72
96 22 0.27
ACGTcount: A:0.26, C:0.22, G:0.10, T:0.42
Consensus pattern (96 bp):
TATCGATACTTCTATACTATGGTACCGATATGCCTTTCTAGTATCAATACCATTTCAAAATTCTA
GAATTCTATGGTATCAATACCTTTCTCTTAC
Found at i:2842031 original size:33 final size:31
Alignment explanation
Indices: 2841984--2842052 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 31
2841974 TTTGTAATCT
*
2841984 TAAAATGTCGAATGTAATATATAAGTATAATAA
1 TAAAATGTCGAATGTAATACAT--GTATAATAA
*
2842017 TAAAATGTTC-AATGTAATGCATGTATAATAA
1 TAAAATG-TCGAATGTAATACATGTATAATAA
2842048 TAAAA
1 TAAAA
2842053 ATGATTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 14 0.42
33 17 0.52
34 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.12, T:0.33
Consensus pattern (31 bp):
TAAAATGTCGAATGTAATACATGTATAATAA
Found at i:2842098 original size:15 final size:16
Alignment explanation
Indices: 2842080--2842111 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
2842070 AAAAATAAAA
2842080 AATTATTTAA-TATAT
1 AATTATTTAATTATAT
2842095 AATTATTTAATTATAT
1 AATTATTTAATTATAT
2842111 A
1 A
2842112 TAGATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AATTATTTAATTATAT
Found at i:2842185 original size:2 final size:2
Alignment explanation
Indices: 2842178--2842221 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2842168 TATTAGATTA
2842178 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2842220 AT
1 AT
2842222 TCAATATTAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2842957 original size:30 final size:29
Alignment explanation
Indices: 2842893--2842987 Score: 104
Period size: 30 Copynumber: 3.2 Consensus size: 29
2842883 TATAATACGA
* *
2842893 TAAAATAAAGATAAAA-ATATTTTTATAA-
1 TAAAATAAAAATAAAATATATTTCTA-AAT
2842921 TAAAATAAAAATAAAATATATTTCCTAAAT
1 TAAAATAAAAATAAAATATATTT-CTAAAT
* *
2842951 TAAAATAAGAATAAAATATGTATTTGTAAAT
1 TAAAATAAAAATAAAATA--TATTTCTAAAT
2842982 TAAAAT
1 TAAAAT
2842988 GAAATATATA
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
28 15 0.26
29 8 0.14
30 19 0.33
31 11 0.19
32 5 0.09
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (29 bp):
TAAAATAAAAATAAAATATATTTCTAAAT
Found at i:2843047 original size:30 final size:30
Alignment explanation
Indices: 2843013--2843268 Score: 110
Period size: 30 Copynumber: 8.6 Consensus size: 30
2843003 AAGTTAACAT
2843013 AAGAATA-AATAATATTTAATAATTTAAGGC
1 AAGAATATAAT-ATATTTAATAATTTAAGGC
***
2843043 AAGAATATAATATATTTAATAATTTAATTT
1 AAGAATATAATATATTTAATAATTTAAGGC
* * * **
2843073 AAGAATATAATATATGTAAAAAGTTAAGAT
1 AAGAATATAATATATTTAATAATTTAAGGC
* * * ***
2843103 AAAAATAAAATATACTTTTAA-AAGTTAAAAT
1 AAGAATATAATATA--TTTAATAATTTAAGGC
* * ** * *
2843134 AATAACA-ATATATATTTTTTAAGTTAAGGT
1 AAGAATATA-ATATATTTAATAATTTAAGGC
* * * * **
2843164 AGGAATAAAATATATTTTATAAGTTAAGAT
1 AAGAATATAATATATTTAATAATTTAAGGC
* * ** * **
2843194 AAGATTAGAATATATTTTTTTAA-CTAAGTT
1 AAGAATATAATATA-TTTAATAATTTAAGGC
*
2843224 AAGAATAAAATATATTTAATAATTTAAGG-
1 AAGAATATAATATATTTAATAATTTAAGGC
*
2843253 AAAAATA-AATATATTT
1 AAGAATATAATATATTT
2843269 TTTAATATTA
Statistics
Matches: 182, Mismatches: 36, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
28 9 0.05
29 15 0.08
30 124 0.68
31 30 0.16
32 4 0.02
ACGTcount: A:0.52, C:0.02, G:0.09, T:0.38
Consensus pattern (30 bp):
AAGAATATAATATATTTAATAATTTAAGGC
Found at i:2843129 original size:31 final size:30
Alignment explanation
Indices: 2843076--2843283 Score: 127
Period size: 30 Copynumber: 6.9 Consensus size: 30
2843066 TTAATTTAAG
* * *
2843076 AATATAATATATGTAAAAAGTTAAGATAAA
1 AATAAAATATATTTTAAAAGTTAAGATAAA
* *
2843106 AATAAAATATACTTTTAAAAGTTAAAATAAT
1 AATAAAATATA-TTTTAAAAGTTAAGATAAA
* * ** * **
2843137 AACAATATATATTTTTTAAGTTAAGGTAGG
1 AATAAAATATATTTTAAAAGTTAAGATAAA
* *
2843167 AATAAAATATATTTTATAAGTTAAGATAAG
1 AATAAAATATATTTTAAAAGTTAAGATAAA
* * ** * * *
2843197 ATTAGAATATATTTTTTTAA-CTAAGTTAAG
1 AATAAAATATA-TTTTAAAAGTTAAGATAAA
* *
2843227 AATAAAATATA-TTTAATAATTTAAG-GAAA
1 AATAAAATATATTTTAA-AAGTTAAGATAAA
* *
2843256 AATAAATATATTTTTTAATA-TTAAGATA
1 AATAAA-ATATATTTTAAAAGTTAAGATA
2843284 TGATTTTAAT
Statistics
Matches: 138, Mismatches: 33, Indels: 14
0.75 0.18 0.08
Matches are distributed among these distances:
28 3 0.02
29 15 0.11
30 84 0.61
31 36 0.26
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (30 bp):
AATAAAATATATTTTAAAAGTTAAGATAAA
Found at i:2843209 original size:60 final size:59
Alignment explanation
Indices: 2843003--2843273 Score: 226
Period size: 60 Copynumber: 4.5 Consensus size: 59
2842993 ATATAATTTG
* ** * * *
2843003 AAGTTAACATAAGAATAAATAATATTTAATAATTTAAGGCAAGAATATAATATATTTAAT
1 AAGTTAAGATAAGAATAAAT-ATATTTTTTAAGTTAAGGTAAGAATAAAATATATTTAAT
* ** * *** * *
2843063 AATTTAATTTAAGAATATAATATATGTAAAAAGTTAAGATAAAAATAAAATATACTTTTAA-
1 AAGTTAAGATAAGAATA-AATATATTTTTTAAGTTAAGGTAAGAATAAAATATA--TTTAAT
* * * * *
2843124 AAGTTAAAATAATAACAATATATATTTTTTAAGTTAAGGTAGGAATAAAATATATTTTAT
1 AAGTTAAGATAAGAATAA-ATATATTTTTTAAGTTAAGGTAAGAATAAAATATATTTAAT
* * *
2843184 AAGTTAAGATAAGATTAGAATATATTTTTTTAA-CTAAGTTAAGAATAAAATATATTTAAT
1 AAGTTAAGATAAGAATA-AATATA-TTTTTTAAGTTAAGGTAAGAATAAAATATATTTAAT
*
2843244 AATTTAAGGA-AA-AATAAATATATTTTTTAA
1 AAGTTAA-GATAAGAATAAATATATTTTTTAA
2843274 TATTAAGATA
Statistics
Matches: 170, Mismatches: 33, Indels: 19
0.77 0.15 0.09
Matches are distributed among these distances:
57 8 0.05
58 6 0.04
59 7 0.04
60 90 0.53
61 54 0.32
62 5 0.03
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (59 bp):
AAGTTAAGATAAGAATAAATATATTTTTTAAGTTAAGGTAAGAATAAAATATATTTAAT
Found at i:2843250 original size:25 final size:25
Alignment explanation
Indices: 2843212--2843259 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
2843202 AATATATTTT
2843212 TTTAACTAAGTTAAGAATAAAATATA
1 TTTAACTAAGTTAAGAA-AAAATATA
* *
2843238 TTTAA-TAATTTAAGGAAAAATA
1 TTTAACTAAGTTAAGAAAAAATA
2843260 AATATATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 6 0.30
25 9 0.45
26 5 0.25
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.35
Consensus pattern (25 bp):
TTTAACTAAGTTAAGAAAAAATATA
Found at i:2843284 original size:20 final size:18
Alignment explanation
Indices: 2843261--2843304 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 18
2843251 GGAAAAATAA
2843261 ATATATTTTTTAATATTAAG
1 ATATA-TTTTTAAT-TTAAG
2843281 ATATGA-TTTTAATTTAAG
1 ATAT-ATTTTTAATTTAAG
2843299 ATATAT
1 ATATAT
2843305 ATAATATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 1 0.05
18 9 0.41
19 7 0.32
20 4 0.18
21 1 0.05
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
ATATATTTTTAATTTAAG
Found at i:2846485 original size:16 final size:16
Alignment explanation
Indices: 2846454--2846495 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
2846444 AGCAATAAGC
* *
2846454 TGAGCAACGGGTTTAA
1 TGAGCAACGAGCTTAA
2846470 TGAGCAACGAGCTTAA
1 TGAGCAACGAGCTTAA
*
2846486 CGAGC-ACGAG
1 TGAGCAACGAG
2846496 TCGAGCAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 5 0.22
16 18 0.78
ACGTcount: A:0.33, C:0.19, G:0.31, T:0.17
Consensus pattern (16 bp):
TGAGCAACGAGCTTAA
Found at i:2848773 original size:31 final size:29
Alignment explanation
Indices: 2848679--2848780 Score: 96
Period size: 31 Copynumber: 3.3 Consensus size: 29
2848669 TATAATACGA
* **
2848679 TAAAATAAAGATAAAAAAATATTTTTATAAT
1 TAAAATAAAAAT-AAAATGTATTTTTA-AAT
* *
2848710 TAAGATAAAAATAAAATGTATTTCCTAAAT
1 TAAAATAAAAATAAAATGTATTT-TTAAAT
*
2848740 TAAAATAAGAATAAAATATGTATTTTTAAAT
1 TAAAATAAAAAT-AAA-ATGTATTTTTAAAT
*
2848771 TAAAAGAAAA
1 TAAAATAAAA
2848781 TATATAATTT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
30 22 0.38
31 28 0.48
32 8 0.14
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (29 bp):
TAAAATAAAAATAAAATGTATTTTTAAAT
Found at i:2848829 original size:30 final size:30
Alignment explanation
Indices: 2848795--2849037 Score: 140
Period size: 30 Copynumber: 8.2 Consensus size: 30
2848785 TAATTTGAAG
2848795 TTAAGATAAGAATA-AATAATATTTAATAAT
1 TTAAGATAAGAATATAAT-ATATTTAATAAT
2848825 TTAAGGA-AAGAATATAATATATTTAATAAT
1 TTAA-GATAAGAATATAATATATTTAATAAT
* * * *
2848855 TTAA-ATTAAGAATGTAATATATGTAAAAAG
1 TTAAGA-TAAGAATATAATATATTTAATAAT
* * * *
2848885 GTCAGATAA-AATAAAATATATTTTTAA-AAG
1 TTAAGATAAGAATATAATATA--TTTAATAAT
* * * * ** * *
2848915 TTAAAATAATAATAAAATATTTTTTTTGAG
1 TTAAGATAAGAATATAATATATTTAATAAT
* * * * *
2848945 TTAAGGTAGGAATAAAATATATTTTATAAG
1 TTAAGATAAGAATATAATATATTTAATAAT
* * * *
2848975 CTAAGATAAGATTAAAATATATTT-TTAA-
1 TTAAGATAAGAATATAATATATTTAATAAT
* * *
2849003 CTAAGATAAGAATAAAATATATTTAATAAG
1 TTAAGATAAGAATATAATATATTTAATAAT
2849033 TTAAG
1 TTAAG
2849038 GAAAAATACA
Statistics
Matches: 171, Mismatches: 31, Indels: 22
0.76 0.14 0.10
Matches are distributed among these distances:
28 24 0.14
29 18 0.11
30 109 0.64
31 20 0.12
ACGTcount: A:0.52, C:0.01, G:0.10, T:0.37
Consensus pattern (30 bp):
TTAAGATAAGAATATAATATATTTAATAAT
Found at i:2848994 original size:28 final size:29
Alignment explanation
Indices: 2848694--2849037 Score: 134
Period size: 30 Copynumber: 11.7 Consensus size: 29
2848684 TAAAGATAAA
* * *
2848694 AAAATATTTTTATAA-TTAAGATAAAAAT
1 AAAATATATTTATAAGCTAAGATAAGAAT
* * ** *
2848722 AAAATGTATTTCCTAAATTAAAATAAGAAT
1 AAAATATATTT-ATAAGCTAAGATAAGAAT
* * *
2848752 AAAATATGTATTTTTAA-ATTA-A-AAGAA-
1 AAAATA--TATTTATAAGCTAAGATAAGAAT
* * *
2848779 AATATATAATTT-GAAGTTAAGATAAGAAT
1 AAAATAT-ATTTATAAGCTAAGATAAGAAT
**
2848808 -AAATAATATTTAATAATTTAAGGA-AAGAAT
1 AAAAT-ATATTT-ATAAGCTAA-GATAAGAAT
* **
2848838 ATAATATATTTAATAATTTAA-ATTAAGAAT
1 AAAATATATTT-ATAAGCTAAGA-TAAGAAT
** * * * *
2848868 GTAATATATGTAAAAAGGTCAGATAA-AAT
1 AAAATATAT-TTATAAGCTAAGATAAGAAT
* * * *
2848897 AAAATATATTTTTAAAAGTTAAAATAATAAT
1 AAAATATA--TTTATAAGCTAAGATAAGAAT
* * * * * *
2848928 AAAATATTTTTTTTGAGTTAAGGTAGGAAT
1 AAAATA-TATTTATAAGCTAAGATAAGAAT
*
2848958 AAAATATATTTTATAAGCTAAGATAAGATT
1 AAAATATA-TTTATAAGCTAAGATAAGAAT
*
2848988 AAAATATATTTTTAA-CTAAGATAAGAAT
1 AAAATATATTTATAAGCTAAGATAAGAAT
*
2849016 AAAATATATTTAATAAGTTAAG
1 AAAATATATTT-ATAAGCTAAG
2849038 GAAAAATACA
Statistics
Matches: 243, Mismatches: 48, Indels: 48
0.72 0.14 0.14
Matches are distributed among these distances:
25 3 0.01
26 6 0.02
27 6 0.02
28 50 0.21
29 25 0.10
30 127 0.52
31 20 0.08
32 6 0.02
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (29 bp):
AAAATATATTTATAAGCTAAGATAAGAAT
Found at i:2849508 original size:36 final size:38
Alignment explanation
Indices: 2849439--2849509 Score: 110
Period size: 36 Copynumber: 1.9 Consensus size: 38
2849429 ATATAGTTTG
* *
2849439 AAATCATTTTGAAAATTATATAATATATGGTTTTTATA
1 AAATCATTTTGAAAATTAAATAATATATAGTTTTTATA
2849477 AAAT-ATTTTGAAAA-TAAATAATATATAGTTTTT
1 AAATCATTTTGAAAATTAAATAATATATAGTTTTT
2849510 GAATTTTTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
36 17 0.55
37 10 0.32
38 4 0.13
ACGTcount: A:0.45, C:0.01, G:0.07, T:0.46
Consensus pattern (38 bp):
AAATCATTTTGAAAATTAAATAATATATAGTTTTTATA
Found at i:2849635 original size:48 final size:50
Alignment explanation
Indices: 2849579--2849686 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 50
2849569 TATTATATAA
*
2849579 TTTTGAAAATTA-GTTTCT-AAATATATATTATATAGTTTTGAAAATTAG
1 TTTTGAAAATTATGTTTCTAAAATATATATTATATAGTTTTGAAAAGTAG
* * *
2849627 TTTTGAAAATTATTTTTTTAAAATATATGTTATATAGTTTTGAAAAGTAG
1 TTTTGAAAATTATGTTTCTAAAATATATATTATATAGTTTTGAAAAGTAG
*
2849677 TTTTTAAAAT
1 TTTTGAAAAT
2849687 ATATATATTA
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
48 12 0.23
49 4 0.08
50 37 0.70
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.50
Consensus pattern (50 bp):
TTTTGAAAATTATGTTTCTAAAATATATATTATATAGTTTTGAAAAGTAG
Found at i:2849650 original size:14 final size:13
Alignment explanation
Indices: 2849611--2849642 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
2849601 ATATATTATA
2849611 TAGTTTTGAAAAT
1 TAGTTTTGAAAAT
2849624 TAGTTTTGAAAAT
1 TAGTTTTGAAAAT
2849637 TA-TTTT
1 TAGTTTT
2849643 TTTAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (13 bp):
TAGTTTTGAAAAT
Found at i:2849660 original size:85 final size:84
Alignment explanation
Indices: 2849564--2849724 Score: 227
Period size: 85 Copynumber: 1.9 Consensus size: 84
2849554 TTTGAAAAAC
* *
2849564 ATATATATTATATAATTTTGAAAATTAGTTTCT-AA-ATATATATTATATAGTTTTGAAAATTAG
1 ATATATATTATATAATTTTGAAAAGTAGTTTCTAAATATATATATTATATAG-TTTG-AAATCA-
2849627 TTTTGAAAATTATTTTTTTAAA
63 TTTTGAAAATTATTTTTTTAAA
* * *
2849649 ATATATGTTATATAGTTTTGAAAAGTAGTTTTTAAAATATATATATTATATAGTTTGAAATCATT
1 ATATATATTATATAATTTTGAAAAGTAGTTTCT-AAATATATATATTATATAGTTTGAAATCATT
2849714 TTGAAAATTAT
65 TTGAAAATTAT
2849725 ATAATATATG
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
85 42 0.62
86 5 0.07
87 6 0.09
88 15 0.22
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (84 bp):
ATATATATTATATAATTTTGAAAAGTAGTTTCTAAATATATATATTATATAGTTTGAAATCATTT
TGAAAATTATTTTTTTAAA
Found at i:2849688 original size:36 final size:39
Alignment explanation
Indices: 2849624--2849783 Score: 117
Period size: 37 Copynumber: 4.3 Consensus size: 39
2849614 TTTTGAAAAT
* * *
2849624 TAGTTTTGAAAATTAT-TTTTTTAAA-ATATATGTTATA
1 TAGTTTTGAAAAGTATGTTTTTAAAATATATATATTATA
2849661 TAGTTTTGAAAAGTA-GTTTTTAAAATATATATATTATA
1 TAGTTTTGAAAAGTATGTTTTTAAAATATATATATTATA
* *
2849699 TAG-TTTG-AAA-TCA--TTTTGAAAAT-TATATAATATA
1 TAGTTTTGAAAAGT-ATGTTTTTAAAATATATATATTATA
* * * * *
2849733 TGGTTTTTATAAA--ATATTTTGAAAATATATATAATATA
1 TAGTTTTGA-AAAGTATGTTTTTAAAATATATATATTATA
*
2849771 TAAGTTTTTAAAA
1 T-AGTTTTGAAAA
2849784 CAATTTTTGA
Statistics
Matches: 105, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
34 12 0.11
35 14 0.13
36 4 0.04
37 39 0.37
38 29 0.28
39 7 0.07
ACGTcount: A:0.42, C:0.01, G:0.09, T:0.48
Consensus pattern (39 bp):
TAGTTTTGAAAAGTATGTTTTTAAAATATATATATTATA
Found at i:2849691 original size:38 final size:36
Alignment explanation
Indices: 2849624--2849805 Score: 158
Period size: 38 Copynumber: 4.9 Consensus size: 36
2849614 TTTTGAAAAT
*
2849624 TAGTTTTGAAAATTATTTTTTTAAAATATATGT--TATA
1 TAGTTTTGAAAA-TA--TTTTTAAAATATATATAATATA
*
2849661 TAGTTTTGAAAAGTAGTTTTTAAAATATATATATTATA
1 TAGTTTTGAAAA-TA-TTTTTAAAATATATATAATATA
*
2849699 TAG-TTTG-AAATCATTTTGAAAAT-TATATAATATA
1 TAGTTTTGAAAAT-ATTTTTAAAATATATATAATATA
* * *
2849733 TGGTTTTTATAAAATATTTTGAAAATATATATAATATA
1 TAG-TTTT-GAAAATATTTTTAAAATATATATAATATA
* * *
2849771 TAAGTTTTTAAAACAATTTTTGAAATATATATAAT
1 T-AGTTTTGAAAA-TATTTTTAAAATATATATAAT
2849806 TTTGAAAATT
Statistics
Matches: 124, Mismatches: 11, Indels: 19
0.81 0.07 0.12
Matches are distributed among these distances:
34 12 0.10
35 10 0.08
36 22 0.18
37 34 0.27
38 45 0.36
39 1 0.01
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (36 bp):
TAGTTTTGAAAATATTTTTAAAATATATATAATATA
Found at i:2849836 original size:32 final size:31
Alignment explanation
Indices: 2849761--2849853 Score: 100
Period size: 32 Copynumber: 2.9 Consensus size: 31
2849751 TTGAAAATAT
* *
2849761 ATATAATATATAAGTTTTTAAAACA-ATTTTTGA
1 ATAT-ATATATAA--TTTTAAAAAATATTTTTAA
* *
2849794 A-ATATATATAATTTTGAAAATTATTTTTAA
1 ATATATATATAATTTTAAAAAATATTTTTAA
2849824 CATATATATATAATTTTAAAAAATATTTTT
1 -ATATATATATAATTTTAAAAAATATTTTT
2849854 TTATTATTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
29 7 0.14
30 7 0.14
31 9 0.18
32 27 0.53
33 1 0.02
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (31 bp):
ATATATATATAATTTTAAAAAATATTTTTAA
Found at i:2849860 original size:3 final size:3
Alignment explanation
Indices: 2849854--2849915 Score: 56
Period size: 3 Copynumber: 19.7 Consensus size: 3
2849844 AAATATTTTT
2849854 TTA TTA TTAA TTA TTA TTA TTTA TTA TTA TTTA TT- TTA TT- TTA TTTA
1 TTA TTA TT-A TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA TTA -TTA
*
2849901 TTA CTTA TTT TTA TT
1 TTA -TTA TTA TTA TT
2849916 TTTTTTCTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
2 4 0.08
3 31 0.62
4 15 0.30
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (3 bp):
TTA
Found at i:2849869 original size:10 final size:10
Alignment explanation
Indices: 2849854--2849909 Score: 55
Period size: 10 Copynumber: 5.8 Consensus size: 10
2849844 AAATATTTTT
2849854 TTATTATTAA
1 TTATTATTAA
*
2849864 TTATTATTAT
1 TTATTATTAA
*
2849874 TTATTATTAT
1 TTATTATTAA
2849884 TTATT-TT-A
1 TTATTATTAA
*
2849892 TT-TTATTTA
1 TTATTATTAA
2849901 TTACTTATT
1 TTA-TTATT
2849910 TTTATTTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
7 2 0.05
8 4 0.10
9 5 0.12
10 24 0.60
11 5 0.12
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.70
Consensus pattern (10 bp):
TTATTATTAA
Found at i:2849879 original size:17 final size:16
Alignment explanation
Indices: 2849854--2849916 Score: 69
Period size: 17 Copynumber: 3.9 Consensus size: 16
2849844 AAATATTTTT
2849854 TTATTATTAATTA-TTA
1 TTATTATT-ATTATTTA
2849870 TTATTTATTATTATTTA
1 TTA-TTATTATTATTTA
2849887 TT-TTATT-TTATTTA
1 TTATTATTATTATTTA
*
2849901 TTACTTATTTTTATTT
1 TTA-TTATTATTATTT
2849917 TTTTTCTTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
14 9 0.21
15 5 0.12
16 12 0.29
17 16 0.38
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTATTATTATTTA
Found at i:2849909 original size:31 final size:31
Alignment explanation
Indices: 2849867--2849926 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2849857 TTATTAATTA
*
2849867 TTATTATTTATTATTATTTATTTTATTTTAT
1 TTATTACTTATTATTATTTATTTTATTTTAT
* * *
2849898 TTATTACTTATTTTTATTTTTTTTCTTTT
1 TTATTACTTATTATTATTTATTTTATTTT
2849927 CTCATTTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (31 bp):
TTATTACTTATTATTATTTATTTTATTTTAT
Found at i:2849915 original size:13 final size:12
Alignment explanation
Indices: 2849847--2849915 Score: 58
Period size: 13 Copynumber: 5.8 Consensus size: 12
2849837 TTTTAAAAAA
2849847 TATTTTT-TTAT
1 TATTTTTATTAT
*
2849858 TA--TTAATTAT
1 TATTTTTATTAT
2849868 TATTATTTATTAT
1 TATT-TTTATTAT
2849881 TATTTATT-TTAT
1 TATTT-TTATTAT
2849893 T-TTATTTATTACT
1 TATT-TTTATTA-T
2849906 TATTTTTATT
1 TATTTTTATT
2849916 TTTTTTCTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
9 2 0.04
10 6 0.13
11 6 0.13
12 10 0.21
13 21 0.45
14 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTTTTATTAT
Found at i:2851182 original size:2 final size:2
Alignment explanation
Indices: 2851175--2851199 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2851165 TATTTTTATT
2851175 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2851200 TTGACTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2851359 original size:12 final size:13
Alignment explanation
Indices: 2851342--2851371 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2851332 TCGAATCGAG
2851342 TAATTTAAA-TTT
1 TAATTTAAATTTT
2851354 TAATTTAAATTTT
1 TAATTTAAATTTT
2851367 TAATT
1 TAATT
2851372 CTTCGCAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TAATTTAAATTTT
Found at i:2856797 original size:165 final size:164
Alignment explanation
Indices: 2856350--2857035 Score: 933
Period size: 165 Copynumber: 4.2 Consensus size: 164
2856340 TAAACAAACT
* * * * * *
2856350 ATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTACCTGCCACC-AAGACCTTCGAGTTCGACTACGC
1 ATTTACAGCATAGCTCAAGGCTAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGC
* *
2856414 TCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCGAAGACCCT
66 TCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCC
* * *
2856479 TAAGTTCGATTACACTCAGCTTCAAGGGCATAAC
131 CAAGTTCGATTACACTCAGCTTCAAGGGCACATC
* * ** * *
2856513 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTTAGCAAAGACCTTTGAGTTCGACTACGC
1 ATTTACAGCATAGCTCAAGGCTAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGC
* *
2856578 TCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTTAAGAAGGGCTATCTGCCAAAGAGCCC
66 TCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCC
*
2856643 CGAGTTCGATTACACTCAGCTTCAAGGGCACATC
131 CAAGTTCGATTACACTCAGCTTCAAGGGCACATC
** * *
2856677 ATTTACAGCATAGCTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCCTCGAGTGCGACTACG
1 ATTTACAGCATAGCTCAAGGCTAGAAGGGTTATCTGCAACC-AAAGACCTTCGAGTTCGACTACG
* *
2856742 CTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
65 CTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCC
*
2856807 CCAAGTTCGATTACACTCAGCTTCGAGGGCACATC
130 CCAAGTTCGATTACACTCAGCTTCAAGGGCACATC
* * * * * * * *
2856842 ATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGATTACA
1 ATTTACAGCATAGCTCAAGGCTAGAAGGGTTATCTG-CAACCAAAGACCTTCGAGTTCGACTACG
* * *
2856907 CTCAGCTCCAAGGCACATCATTTACAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCC
65 CTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCC
* * * * *
2856972 CCGAGTTCGATTACACTCAACTTCGAGGTCATATC
130 CCAAGTTCGATTACACTCAGCTTCAAGGGCACATC
* **
2857007 ATTTACAACATAGCTCAAGGAAAGAAGGG
1 ATTTACAGCATAGCTCAAGGCTAGAAGGG
2857036 CTATTTGTCG
Statistics
Matches: 464, Mismatches: 56, Indels: 4
0.89 0.11 0.01
Matches are distributed among these distances:
163 31 0.07
164 150 0.32
165 280 0.60
166 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.23
Consensus pattern (164 bp):
ATTTACAGCATAGCTCAAGGCTAGAAGGGTTATCTGCAACCAAAGACCTTCGAGTTCGACTACGC
TCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCAAGAAGGGCTATCTGCCAAAGACCCC
CAAGTTCGATTACACTCAGCTTCAAGGGCACATC
Found at i:2857037 original size:81 final size:80
Alignment explanation
Indices: 2856372--2857039 Score: 663
Period size: 81 Copynumber: 8.1 Consensus size: 80
2856362 GCTCAAGGCC
* * * * *
2856372 AGAAGGGCTACCTGCCACCAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTG
1 AGAAGGGCTATCTGCCA--AAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTA
*
2856437 CAGAATAGCTTAAGTCA
64 CAGCATAGCTTAAGTCA
* ** * * *
2856454 AGAAGGGCTATCTGCCGAAGACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTAC
1 AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTCCAA-GGCACATCATTTAC
* * * *
2856519 AGCATAACTCAAGGCT
65 AGCATAGCTTAAGTCA
* * * * * * *
2856535 AGAAGGGTTATATGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTT
1 AGAAGGGCTATCTG---CCAAAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTT
* * *
2856600 GCAGAATAGCTTAAGTTA
63 ACAGCATAGCTTAAGTCA
*
2856618 AGAAGGGCTATCTGCCAAAGAGCCC-CGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTA
1 AGAAGGGCTATCTGCCAAAGA-CCCTCGAGTTCGATTACACTCAGCTCCAA-GGCACATCATTTA
* * *
2856682 CAGCATAGCTCAAGGCT
64 CAGCATAGCTTAAGTCA
* * * *
2856699 AGAAGGGTTATCTGTGACCAAAAGACCCTCGAGTGCGACTACGCTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATC--TG-CC-AAAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATT
* *
2856764 TGCAGCATAGCTTAAGTCG
62 TACAGCATAGCTTAAGTCA
* * * * *
2856783 AGAAGGGCTATCTGCCAAAGACCCCCAAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTGC
1 AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGC-TCCAAGGCACATCATTTAC
* *
2856848 AGCATAACTTAAGTCG
65 AGCATAGCTTAAGTCA
* * *
2856864 AGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGATTACACTCAGCTCCAAGGCACATCATT
1 AGAAGGGCTATCTG----CCAAAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATT
*
2856929 TACAGCATAGCTTAAGTCG
62 TACAGCATAGCTTAAGTCA
* * * * *
2856948 AGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACACTCAACTTCGAGGTCATATCATTTAC
1 AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTCCAAGG-CACATCATTTAC
* * **
2857013 AACATAGCTCAAGGAA
65 AGCATAGCTTAAGTCA
2857029 AGAAGGGCTAT
1 AGAAGGGCTAT
2857040 TTGTCGATAA
Statistics
Matches: 481, Mismatches: 88, Indels: 35
0.80 0.15 0.06
Matches are distributed among these distances:
80 110 0.23
81 151 0.31
82 17 0.04
83 35 0.07
84 115 0.24
85 53 0.11
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (80 bp):
AGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCACATCATTTACA
GCATAGCTTAAGTCA
Found at i:2857758 original size:37 final size:35
Alignment explanation
Indices: 2857610--2858065 Score: 125
Period size: 35 Copynumber: 12.9 Consensus size: 35
2857600 ATTTTTTTAT
* * *
2857610 ATATATATTATATAGTTTGA-AATCA-TTTTGAAAA
1 ATATATAATATATAGTTTTATAA-AATTTTTGAAAA
* *
2857644 TTATATAATATATGGTTTTTATAAAATATTTTG-AAA
1 ATATATAATATATAG-TTTTATAAAAT-TTTTGAAAA
* * * *
2857680 ATATATAATATATAGTTTT-TGAATTTTTTCTAAAT
1 ATATATAATATATAGTTTTATAAAATTTTT-GAAAA
*
2857715 ATATATAATATATAGCTTTTAAAAACATTTTTGAAAAA
1 ATATATAATATATAG-TTTTATAAA-ATTTTTG-AAAA
* * * **
2857753 CATATATATTATATAATTTT-GAAAATTAGTTT-CTAA
1 -ATATATAATATATAGTTTTATAAAATT--TTTGAAAA
* *
2857789 ATATATATTATATAGTTTT-GAAAATTAGTTT-----
1 ATATATAATATATAGTTTTATAAAATT--TTTGAAAA
* **
2857820 -T-GA-AA-AT-TAGTTTTGA-AAATTATTTTTTTAAA
1 ATATATAATATATAGTTTT-ATAAA--ATTTTTGAAAA
** *
2857852 ATATATGTTATATAGTTTTGA-AAATTAGTTTTT-AAGAT
1 ATATATAATATATAGTTTT-ATAAA--A-TTTTTGAA-AA
* * * *
2857890 ATATATATTATATTGTTTGA-AATCA-TTTTGAAAA
1 ATATATAATATATAGTTTTATAA-AATTTTTGAAAA
* *
2857924 TTATATAATATATGGTTTTTATAAAATATTTTGAAAA
1 ATATATAATATATAG-TTTTATAAAAT-TTTTGAAAA
*
2857961 TATATATAATATATAAGTTTTTAAAACAATTTTTG-AAA
1 -ATATATAATATAT-AG-TTTTATAA-AATTTTTGAAAA
* * * *
2857999 ATATATATTATATAATTTTGA-AAATTATTTTT-TAAC
1 ATATATAATATATAGTTTT-ATAAA--ATTTTTGAAAA
* * *
2858035 ATATATATTATATAATTTTAAAAAATATTTT
1 ATATATAATATATAGTTTTATAAAAT-TTTT
2858066 TTTATTATAT
Statistics
Matches: 333, Mismatches: 45, Indels: 87
0.72 0.10 0.19
Matches are distributed among these distances:
26 7 0.02
27 8 0.02
28 1 0.00
29 4 0.01
30 1 0.00
33 5 0.02
34 37 0.11
35 74 0.22
36 64 0.19
37 50 0.15
38 52 0.16
39 27 0.08
40 3 0.01
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.48
Consensus pattern (35 bp):
ATATATAATATATAGTTTTATAAAATTTTTGAAAA
Found at i:2857819 original size:13 final size:13
Alignment explanation
Indices: 2857801--2857883 Score: 84
Period size: 13 Copynumber: 6.5 Consensus size: 13
2857791 ATATATTATA
2857801 TAGTTTTGAAAAT
1 TAGTTTTGAAAAT
2857814 TAGTTTTGAAAAT
1 TAGTTTTGAAAAT
2857827 TAGTTTTGAAAAT
1 TAGTTTTGAAAAT
* *
2857840 TATTTTTTTAAAAT
1 TA-GTTTTGAAAAT
* *
2857854 ATA-TGTT--ATA-
1 -TAGTTTTGAAAAT
2857864 TAGTTTTGAAAAT
1 TAGTTTTGAAAAT
2857877 TAGTTTT
1 TAGTTTT
2857884 TAAGATATAT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
9 2 0.03
10 3 0.05
11 2 0.03
12 2 0.03
13 38 0.66
14 9 0.16
15 2 0.03
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (13 bp):
TAGTTTTGAAAAT
Found at i:2858039 original size:36 final size:36
Alignment explanation
Indices: 2857830--2858067 Score: 198
Period size: 36 Copynumber: 6.5 Consensus size: 36
2857820 TGAAAATTAG
* *
2857830 TTTTGAAAATTATTTTTTTAAAATATATGTTATATAG
1 TTTTGAAAATTA-TTTTTTAAAATATATATTATATAA
*
2857867 TTTTGAAAATTAGTTTTTAAGATATATATATTATAT--
1 TTTTGAAAATTATTTTTTAA-A-ATATATATTATATAA
* * * **
2857903 TGTTTG-AAATCA-TTTTGAAAATTATATAATATATGG
1 T-TTTGAAAATTATTTTTTAAAA-TATATATTATATAA
* * *
2857939 TTTTTATAAAATA-TTTTGAAAATATATATAATATATAA
1 TTTTGA-AAATTATTTTTTAAAATATATAT--TATATAA
* ** *
2857977 GTTTTTAAAACAATTTTTGAAAATATATATTATATAA
1 -TTTTGAAAATTATTTTTTAAAATATATATTATATAA
*
2858014 TTTTGAAAATTATTTTTTAACATATATATTATATAA
1 TTTTGAAAATTATTTTTTAAAATATATATTATATAA
* *
2858050 TTTTAAAAAATATTTTTT
1 TTTTGAAAATTATTTTTT
2858068 TATTATATTA
Statistics
Matches: 169, Mismatches: 20, Indels: 25
0.79 0.09 0.12
Matches are distributed among these distances:
33 1 0.01
34 12 0.07
35 9 0.05
36 67 0.40
37 37 0.22
38 21 0.12
39 22 0.13
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.50
Consensus pattern (36 bp):
TTTTGAAAATTATTTTTTAAAATATATATTATATAA
Found at i:2858073 original size:3 final size:3
Alignment explanation
Indices: 2858067--2858133 Score: 50
Period size: 3 Copynumber: 21.7 Consensus size: 3
2858057 AAATATTTTT
*
2858067 TTA TTA -TA TTAA TTA TTA TTA TTA TTTA TTA TTA TTTA TT- TTG TT-
1 TTA TTA TTA TT-A TTA TTA TTA TTA -TTA TTA TTA -TTA TTA TTA TTA
*
2858112 TTA TTTA TTA CTTA TTT TTA TT
1 TTA -TTA TTA -TTA TTA TTA TT
2858134 TTTTTTCTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 16
0.75 0.03 0.22
Matches are distributed among these distances:
2 6 0.11
3 33 0.61
4 15 0.28
ACGTcount: A:0.27, C:0.01, G:0.01, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:2858095 original size:10 final size:10
Alignment explanation
Indices: 2858067--2858134 Score: 59
Period size: 10 Copynumber: 6.6 Consensus size: 10
2858057 AAATATTTTT
2858067 TTATTATATTAA
1 TTATT-TATT-A
2858079 TTA-TTATTA
1 TTATTTATTA
2858088 TTATTTATTA
1 TTATTTATTA
2858098 TTATTTATT-
1 TTATTTATTA
*
2858107 TTGTTTTATTTA
1 TT-ATTTA-TTA
* *
2858119 TTACTTATTT
1 TTATTTATTA
2858129 TTATTT
1 TTATTT
2858135 TTTTTCTTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
9 6 0.13
10 30 0.64
11 6 0.13
12 5 0.11
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (10 bp):
TTATTTATTA
Found at i:2858120 original size:31 final size:31
Alignment explanation
Indices: 2858085--2858144 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2858075 TTAATTATTA
* *
2858085 TTATTATTTATTATTATTTATTTTGTTTTAT
1 TTATTACTTATTATTATTTATTTTCTTTTAT
* *
2858116 TTATTACTTATTTTTATTTTTTTTCTTTT
1 TTATTACTTATTATTATTTATTTTCTTTT
2858145 CTCATTTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.18, C:0.03, G:0.02, T:0.77
Consensus pattern (31 bp):
TTATTACTTATTATTATTTATTTTCTTTTAT
Found at i:2858121 original size:21 final size:20
Alignment explanation
Indices: 2858091--2858129 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
2858081 ATTATTATTA
*
2858091 TTTATTATTATTTATTTTGT
1 TTTATTATTACTTATTTTGT
2858111 TTTATTTATTACTTATTTT
1 TTTA-TTATTACTTATTTT
2858130 TATTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTATTATTACTTATTTTGT
Found at i:2858130 original size:17 final size:16
Alignment explanation
Indices: 2858062--2858134 Score: 55
Period size: 17 Copynumber: 4.5 Consensus size: 16
2858052 TTAAAAAATA
2858062 TTTT-TTTATTA-TAT
1 TTTTATTTATTATTAT
*
2858076 TAATTA-TTATTATTAT
1 T-TTTATTTATTATTAT
*
2858092 TTATTA-TTATTTATTTT
1 TT-TTATTTA-TTATTAT
2858109 GTTTTATTTATTACTTAT
1 -TTTTATTTATTA-TTAT
2858127 TTTTATTT
1 TTTTATTT
2858135 TTTTTCTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 13
0.73 0.06 0.20
Matches are distributed among these distances:
14 1 0.02
15 8 0.17
16 10 0.21
17 20 0.43
18 8 0.17
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.73
Consensus pattern (16 bp):
TTTTATTTATTATTAT
Found at i:2858133 original size:13 final size:13
Alignment explanation
Indices: 2858066--2858133 Score: 65
Period size: 13 Copynumber: 5.5 Consensus size: 13
2858056 AAAATATTTT
2858066 TTTATTA-TATTA
1 TTTATTATTATTA
*
2858078 ATTATTATTATTA
1 TTTATTATTATTA
2858091 TTTATTATTATT-
1 TTTATTATTATTA
*
2858103 TATT-TTGTT-TTA
1 T-TTATTATTATTA
2858115 TTTATTACTTATT-
1 TTTATTA-TTATTA
2858128 TTTATT
1 TTTATT
2858134 TTTTTTCTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
11 4 0.09
12 14 0.30
13 26 0.57
14 2 0.04
ACGTcount: A:0.26, C:0.01, G:0.01, T:0.71
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:2859399 original size:2 final size:2
Alignment explanation
Indices: 2859392--2859426 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2859382 TTTTTATTTT
2859392 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2859427 TGACTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2863403 original size:29 final size:30
Alignment explanation
Indices: 2863157--2863437 Score: 180
Period size: 30 Copynumber: 9.4 Consensus size: 30
2863147 GGGGGAAATG
*
2863157 AAATATATAATTTTAAGTTAAAGATAAGAAT-
1 AAATATAT-TTTTTAAGTT-AAGATAAGAATA
** * *
2863188 AAATAATATTTAATAATTTAAGTTAAGAATA
1 AAAT-ATATTTTTTAAGTTAAGATAAGAATA
* ** * *
2863219 TAATATATTTAATAATTTAA-ATTAATAATA
1 AAATATATTTTTTAAGTTAAGA-TAAGAATA
* * *** * *
2863249 TAATATATGTAAAAAGTTAAGATAAAAATG
1 AAATATATTTTTTAAGTTAAGATAAGAATA
* ** *
2863279 AATTATAGTTTTAAAAGTTAAGATGAGAATA
1 AAATATA-TTTTTTAAGTTAAGATAAGAATA
* *
2863310 AAATATATATTTTTAAGTTATG-TAGGAATA
1 AAATATAT-TTTTTAAGTTAAGATAAGAATA
* * *
2863340 AAATATATTTTATAAGTTAAAATAAGATTA
1 AAATATATTTTTTAAGTTAAGATAAGAATA
* *
2863370 AAATATATTTTTTAA-CTAAGATAAGAAAA
1 AAATATATTTTTTAAGTTAAGATAAGAATA
** *
2863399 AAATATATTTAATATGTTAAGA-AA-AAT-
1 AAATATATTTTTTAAGTTAAGATAAGAATA
2863426 AAATATATTTTT
1 AAATATATTTTT
2863438 AAATATTAAT
Statistics
Matches: 199, Mismatches: 43, Indels: 20
0.76 0.16 0.08
Matches are distributed among these distances:
27 10 0.05
28 2 0.01
29 34 0.17
30 101 0.51
31 48 0.24
32 4 0.02
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (30 bp):
AAATATATTTTTTAAGTTAAGATAAGAATA
Found at i:2863418 original size:59 final size:57
Alignment explanation
Indices: 2863288--2863437 Score: 146
Period size: 59 Copynumber: 2.6 Consensus size: 57
2863278 GAATTATAGT
* * * * *
2863288 TTTAA-AAGTTAAGATGAGAATAAAATATATATTTTTAAGTTATGTAGGAATAAAATATA
1 TTTAATAAGTTAAGA--AAAATAAAATATAT-TTTTTAAGCTAAGTAAGAAAAAAATATA
*
2863347 TTTTATAAGTTAA-AATAAGATTAAAATATATTTTTTAA-CTAAGATAAGAAAAAAATATA
1 TTTAATAAGTTAAGAA-AA-A-TAAAATATATTTTTTAAGCTAAG-TAAGAAAAAAATATA
*
2863406 TTTAATATGTTAAGAAAAAT-AAATATATTTTT
1 TTTAATAAGTTAAGAAAAATAAAATATATTTTT
2863438 AAATATTAAT
Statistics
Matches: 77, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
56 12 0.16
57 2 0.03
58 5 0.06
59 39 0.51
60 19 0.25
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.39
Consensus pattern (57 bp):
TTTAATAAGTTAAGAAAAATAAAATATATTTTTTAAGCTAAGTAAGAAAAAAATATA
Found at i:2867112 original size:33 final size:31
Alignment explanation
Indices: 2867065--2867133 Score: 86
Period size: 33 Copynumber: 2.2 Consensus size: 31
2867055 TTTGTAATCT
* *
2867065 TAAAATGTCGAATGTAATATATAATTATAATAA
1 TAAAATGTCGAATGTAATACAT--GTATAATAA
2867098 TAAAATGTTC-AATGTAATACATGTATAATAA
1 TAAAATG-TCGAATGTAATACATGTATAATAA
2867129 TAAAA
1 TAAAA
2867134 ATGATTTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 13 0.39
33 18 0.55
34 2 0.06
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (31 bp):
TAAAATGTCGAATGTAATACATGTATAATAA
Found at i:2868075 original size:63 final size:63
Alignment explanation
Indices: 2868002--2868128 Score: 236
Period size: 63 Copynumber: 2.0 Consensus size: 63
2867992 AACATTGAGT
2868002 ATGATCTAAAATAAATAAAAATTGAGTGGTCAAAACAGAAACTAAATAATTTATGGGTGACTG
1 ATGATCTAAAATAAATAAAAATTGAGTGGTCAAAACAGAAACTAAATAATTTATGGGTGACTG
* *
2868065 ATGATCTAAAATAAATAAAAATTGAGTGGTCAAAACATAAACTAAATTATTTATGGGTGACTG
1 ATGATCTAAAATAAATAAAAATTGAGTGGTCAAAACAGAAACTAAATAATTTATGGGTGACTG
2868128 A
1 A
2868129 ATAAATAATT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (63 bp):
ATGATCTAAAATAAATAAAAATTGAGTGGTCAAAACAGAAACTAAATAATTTATGGGTGACTG
Found at i:2871538 original size:21 final size:20
Alignment explanation
Indices: 2871494--2871544 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
2871484 TATCTCAAGT
*
2871494 AAAAC-TATCATATGATATTC
1 AAAACATAT-ATATGATATTA
2871514 AAAACATATATATGTATATTA
1 AAAACATATATATG-ATATTA
*
2871535 AAAATATATA
1 AAAACATATA
2871545 CTCAAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 10 0.37
21 17 0.63
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.35
Consensus pattern (20 bp):
AAAACATATATATGATATTA
Found at i:2871543 original size:19 final size:18
Alignment explanation
Indices: 2871493--2871544 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
2871483 TTATCTCAAG
*
2871493 TAAAACTATCATATGATAT
1 TAAAAATAT-ATATGATAT
2871512 TCAAAACATATATATGTATAT
1 T-AAAA-ATATATATG-ATAT
2871533 TAAAAATATATA
1 TAAAAATATATA
2871545 CTCAAAATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 8 0.28
20 13 0.45
21 8 0.28
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.37
Consensus pattern (18 bp):
TAAAAATATATATGATAT
Found at i:2872063 original size:26 final size:25
Alignment explanation
Indices: 2872027--2872082 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 25
2872017 ACCGTAGTGC
2872027 TACACATAAGGTCGTGCCCAGCATAA
1 TACACATAAGGTCGTGCCCAGCAT-A
*
2872053 TACACATAAGGTCGTGCCCATCATA
1 TACACATAAGGTCGTGCCCAGCATA
2872078 TACAC
1 TACAC
2872083 TTAGTGTCCT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.34, C:0.29, G:0.16, T:0.21
Consensus pattern (25 bp):
TACACATAAGGTCGTGCCCAGCATA
Found at i:2876596 original size:23 final size:23
Alignment explanation
Indices: 2876568--2876617 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
2876558 ATGGAAGGAC
2876568 CACTACAAGCAACCATAAAAGAT
1 CACTACAAGCAACCATAAAAGAT
*
2876591 CACTACATGCAACCATAAAAGAT
1 CACTACAAGCAACCATAAAAGAT
2876614 CACT
1 CACT
2876618 TAGAATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.48, C:0.28, G:0.08, T:0.16
Consensus pattern (23 bp):
CACTACAAGCAACCATAAAAGAT
Found at i:2878212 original size:41 final size:41
Alignment explanation
Indices: 2878167--2878276 Score: 170
Period size: 41 Copynumber: 2.7 Consensus size: 41
2878157 ATTCACGTTG
* **
2878167 CATTTCGCATTGCGATAGTTGAGAATCGCGTTGCGTTTTTC
1 CATTTCGCGTTGCGATAGTTGAGAATCGCGTTGCAATTTTC
2878208 CATTTCGCGTTGCGATAGTTG-GAGATCGCGTTGCAATTTTC
1 CATTTCGCGTTGCGATAGTTGAGA-ATCGCGTTGCAATTTTC
2878249 CATTTCGCGTTGCGATAGTTGA-AATCGC
1 CATTTCGCGTTGCGATAGTTGAGAATCGC
2878277 AACGCGATCT
Statistics
Matches: 64, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
40 7 0.11
41 57 0.89
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.36
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAGAATCGCGTTGCAATTTTC
Found at i:2878217 original size:20 final size:20
Alignment explanation
Indices: 2878192--2878262 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
2878182 TAGTTGAGAA
2878192 TCGCGTTGCGTTTTTCCATT
1 TCGCGTTGCGTTTTTCCATT
** ** **
2878212 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCG-TTTTTCCATT
**
2878233 TCGCGTTGCAATTTTCCATT
1 TCGCGTTGCGTTTTTCCATT
2878253 TCGCGTTGCG
1 TCGCGTTGCG
2878263 ATAGTTGAAA
Statistics
Matches: 35, Mismatches: 15, Indels: 2
0.67 0.29 0.04
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.11, C:0.23, G:0.27, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGTTTTTCCATT
Found at i:2878276 original size:20 final size:21
Alignment explanation
Indices: 2878171--2878276 Score: 58
Period size: 20 Copynumber: 5.2 Consensus size: 21
2878161 ACGTTGCATT
*
2878171 TCGCATTGCGATAGTT-GAGAA
1 TCGCGTTGCGATAGTTCGA-AA
** * **
2878192 TCGCGTTGCG-TTTTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
* *
2878212 TCGCGTTGCGATAGTTGGAGA
1 TCGCGTTGCGATAGTTCGAAA
* * * **
2878233 TCGCGTTGCAAT-TTTCCATT
1 TCGCGTTGCGATAGTTCGAAA
2878253 TCGCGTTGCGATAGTT-GAAA
1 TCGCGTTGCGATAGTTCGAAA
2878273 TCGC
1 TCGC
2878277 AACGCGATCT
Statistics
Matches: 59, Mismatches: 23, Indels: 7
0.66 0.26 0.08
Matches are distributed among these distances:
20 32 0.54
21 27 0.46
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCGAAA
Found at i:2878339 original size:21 final size:21
Alignment explanation
Indices: 2878313--2878386 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
2878303 GCGTTGCATT
2878313 TCGCGTTGCGATAGTTTAAAA
1 TCGCGTTGCGATAGTTTAAAA
* * **
2878334 TCGCGTTGTGAT--TTTCCATT
1 TCGCGTTGCGATAGTTT-AAAA
*
2878354 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTTAAAA
2878375 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2878387 TTTCCATTTC
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
19 3 0.07
20 12 0.29
21 24 0.59
22 2 0.05
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTTAAAA
Found at i:2878354 original size:41 final size:41
Alignment explanation
Indices: 2878309--2878409 Score: 184
Period size: 41 Copynumber: 2.5 Consensus size: 41
2878299 ATTCGCGTTG
* *
2878309 CATTTCGCGTTGCGATAGTTTAAAATCGCGTTGTGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
2878350 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
2878391 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGT
2878410 CTACAGTTGT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.39
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:2878359 original size:20 final size:20
Alignment explanation
Indices: 2878334--2878406 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
2878324 TAGTTTAAAA
*
2878334 TCGCGTTGTGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
2878354 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
2878375 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
2878395 TCGCGTTGCGAT
1 TCGCGTTGCGAT
2878407 AGTCTACAGT
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.15, C:0.21, G:0.25, T:0.40
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:2878389 original size:142 final size:142
Alignment explanation
Indices: 2878138--2878409 Score: 447
Period size: 142 Copynumber: 1.9 Consensus size: 142
2878128 AATTCGCATT
* *
2878138 GCGATCTCCACTATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAGAATCGCGTTGCGT
1 GCGATCTCCACTATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGA
* *
2878203 TTTTCCATTTCGCGTTGCGATAGTTGGAGATCGCGTTGCAATTTTCCATTTCGCGTTGCGATAGT
66 TTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATTTCGCGTTGCGATAGT
2878268 TGAAATCGCAAC
131 TGAAATCGCAAC
* * * *
2878280 GCGATCTCCA-TCATCGCAAATTCGCGTTGCATTTCGCGTTGCGATAGTTTAAAATCGCGTTGTG
1 GCGATCTCCACT-ATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCG
*
2878344 ATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTCCATTTCGCGTTGCGATAG
65 ATTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATTTCGCGTTGCGATAG
2878409 T
130 T
2878410 CTACAGTTGT
Statistics
Matches: 120, Mismatches: 9, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
141 1 0.01
142 119 0.99
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (142 bp):
GCGATCTCCACTATCGCAAATTCACGTTGCATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGA
TTTTCCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCAATTTTCCATTTCGCGTTGCGATAGT
TGAAATCGCAAC
Found at i:2878441 original size:22 final size:21
Alignment explanation
Indices: 2878378--2878441 Score: 51
Period size: 22 Copynumber: 3.0 Consensus size: 21
2878368 TTGAAAATCG
2878378 CGTTGCGATTTTCC-ATTTCG-
1 CGTTGCGATTTTCCAATTT-GT
** * *
2878398 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATTTTCCA-ATTTGT
2878420 CGTTGCGATTTTCCAAATTTGT
1 CGTTGCGATTTTCC-AATTTGT
2878442 TGAAAAAAAG
Statistics
Matches: 32, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
20 11 0.34
21 1 0.03
22 19 0.59
23 1 0.03
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (21 bp):
CGTTGCGATTTTCCAATTTGT
Found at i:2878528 original size:6 final size:6
Alignment explanation
Indices: 2878517--2878637 Score: 179
Period size: 6 Copynumber: 21.7 Consensus size: 6
2878507 AGACACGTAT
2878517 GACCAC GACCAC GACCAC GACCAC GACC-C GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
2878564 GACCAC GACC-C GACCAC GACCAC GACC-C GACC-C GACCAC GACC-C
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
2878608 GACC-C GACC-C GACCAC GACC-C GACC-C GACC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACC
2878638 CGAGACGATA
Statistics
Matches: 111, Mismatches: 0, Indels: 9
0.93 0.00 0.08
Matches are distributed among these distances:
5 45 0.41
6 66 0.59
ACGTcount: A:0.28, C:0.54, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:2878550 original size:17 final size:17
Alignment explanation
Indices: 2878517--2878637 Score: 180
Period size: 17 Copynumber: 7.2 Consensus size: 17
2878507 AGACACGTAT
2878517 GACCACGACCACGACCAC
1 GACCACGACC-CGACCAC
2878535 GACCACGACCCGACCAC
1 GACCACGACCCGACCAC
2878552 GACCACGACCACGACCAC
1 GACCACGACC-CGACCAC
2878570 GACC-CGACCACGACCAC
1 GACCACGACC-CGACCAC
2878587 GACC-CGACCCGACCAC
1 GACCACGACCCGACCAC
2878603 GACC-CGACCCGACC-C
1 GACCACGACCCGACCAC
2878618 GACCACGACCCGACC-C
1 GACCACGACCCGACCAC
2878634 GACC
1 GACC
2878638 CGAGACGATA
Statistics
Matches: 101, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.05
16 36 0.36
17 39 0.39
18 21 0.21
ACGTcount: A:0.28, C:0.54, G:0.18, T:0.00
Consensus pattern (17 bp):
GACCACGACCCGACCAC
Found at i:2878551 original size:29 final size:28
Alignment explanation
Indices: 2878517--2878637 Score: 187
Period size: 29 Copynumber: 4.4 Consensus size: 28
2878507 AGACACGTAT
2878517 GACCACGACCACGACCACGACCACGACCC
1 GACCACGACCACGACC-CGACCACGACCC
2878546 GACCACGACCACGACCACGACCACGACCC
1 GACCACGACCACGACC-CGACCACGACCC
2878575 GACCACGACCACGACCCGACC-CGACCAC
1 GACCACGACCACGACCCGACCACGACC-C
2878603 GACC-CGACC-CGACCCGACCACGACCC
1 GACCACGACCACGACCCGACCACGACCC
2878629 GACC-CGACC
1 GACCACGACC
2878638 CGAGACGATA
Statistics
Matches: 90, Mismatches: 0, Indels: 7
0.93 0.00 0.07
Matches are distributed among these distances:
26 20 0.22
27 15 0.17
28 10 0.11
29 45 0.50
ACGTcount: A:0.28, C:0.54, G:0.18, T:0.00
Consensus pattern (28 bp):
GACCACGACCACGACCCGACCACGACCC
Found at i:2879133 original size:5 final size:5
Alignment explanation
Indices: 2879119--2879149 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
2879109 CCGCCGTCGC
2879119 CGTC- CGTCT CGTCT CGTCT CGTCT CGTCT CG
1 CGTCT CGTCT CGTCT CGTCT CGTCT CGTCT CG
2879150 GGTCAGGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.00, C:0.42, G:0.23, T:0.35
Consensus pattern (5 bp):
CGTCT
Found at i:2879311 original size:22 final size:21
Alignment explanation
Indices: 2879285--2879398 Score: 83
Period size: 22 Copynumber: 5.5 Consensus size: 21
2879275 AATTTGGAAA
*
2879285 ATCGCAATGACAACTGTAGACT
1 ATCGCAACG-CAACTGTAGACT
* * **
2879307 ATCGCAACG-AA-TTTGGAAA
1 ATCGCAACGCAACTGTAGACT
2879326 ATCGCAACGACAACTGTAGACT
1 ATCGCAACG-CAACTGTAGACT
* **
2879348 ATCGCAACGCGAAATG--GAAA
1 ATCGCAACGC-AACTGTAGACT
* *
2879368 ATCGCAATGCGACTGTAGACT
1 ATCGCAACGCAACTGTAGACT
2879389 ATCGCAACGC
1 ATCGCAACGC
2879399 GAAATGGAAA
Statistics
Matches: 68, Mismatches: 18, Indels: 13
0.69 0.18 0.13
Matches are distributed among these distances:
19 16 0.24
20 13 0.19
21 14 0.21
22 25 0.37
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (21 bp):
ATCGCAACGCAACTGTAGACT
Found at i:2879320 original size:41 final size:41
Alignment explanation
Indices: 2879263--2879397 Score: 202
Period size: 41 Copynumber: 3.3 Consensus size: 41
2879253 CTTTTTTTTA
*
2879263 ACTATCACAACGAATTTGGAAAATCGCAATGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAATGACAACTGTAG
*
2879304 ACTATCGCAACGAATTTGGAAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGAATTTGGAAAATCGCAATGACAACTGTAG
* *
2879345 ACTATCGCAACGCGAA-ATGGAAAATCGCAATG-CGACTGTAG
1 ACTATCGCAA--CGAATTTGGAAAATCGCAATGACAACTGTAG
2879386 ACTATCGCAACG
1 ACTATCGCAACG
2879398 CGAAATGGAA
Statistics
Matches: 87, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
39 2 0.02
41 67 0.77
42 14 0.16
43 4 0.05
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.19
Consensus pattern (41 bp):
ACTATCGCAACGAATTTGGAAAATCGCAATGACAACTGTAG
Found at i:2879331 original size:19 final size:19
Alignment explanation
Indices: 2879270--2879335 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
2879260 TTAACTATCA
2879270 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
* * * **
2879289 CAATGACAACTGTAGACTATCG
1 CAACG--AA-TTTGGAAAATCG
2879311 CAACGAATTTGGAAAATCG
1 CAACGAATTTGGAAAATCG
2879330 CAACGA
1 CAACGA
2879336 CAACTGTAGA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 18 0.53
20 2 0.06
21 2 0.06
22 12 0.35
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (19 bp):
CAACGAATTTGGAAAATCG
Found at i:2879398 original size:41 final size:40
Alignment explanation
Indices: 2879279--2879516 Score: 221
Period size: 41 Copynumber: 6.0 Consensus size: 40
2879269 ACAACGAATT
* * *
2879279 TGGAAAATCGCAATGACAACTGTAGACTATCGCAA--CGAATT
1 TGGAAAATCGCAACG-CGACTGTA-ACTATCGCAACGCGAA-A
*
2879320 TGGAAAATCGCAACGACAACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACG-CGACTGTA-ACTATCGCAACGCGAAA
*
2879362 TGGAAAATCGCAATGCGACTGTAGACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGTA-ACTATCGCAACGCGAAA
2879403 TGGAAAAT-----CGCG-C----ACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGACTGTAACTATCGCAACGCGAAA
**
2879433 TGGAAAATCGCAACGCGATCTCCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCGA-CTGTAACTATCGCAACGCGAAA
* * * *
2879474 TGGAAAAACGCAACGCGATTTTCAACTATCGCAATGCGAAA
1 TGGAAAATCGCAACGCGACTGT-AACTATCGCAACGCGAAA
2879515 TG
1 TG
2879517 CAACGTGAAT
Statistics
Matches: 173, Mismatches: 10, Indels: 28
0.82 0.05 0.13
Matches are distributed among these distances:
30 25 0.14
35 5 0.03
36 3 0.02
37 1 0.01
40 1 0.01
41 120 0.69
42 14 0.08
43 4 0.02
ACGTcount: A:0.38, C:0.24, G:0.21, T:0.17
Consensus pattern (40 bp):
TGGAAAATCGCAACGCGACTGTAACTATCGCAACGCGAAA
Found at i:2879420 original size:30 final size:30
Alignment explanation
Indices: 2879386--2879443 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
2879376 GCGACTGTAG
2879386 ACTATCGCAACGCGAAATGGAAAATCGCGC
1 ACTATCGCAACGCGAAATGGAAAATCGCGC
2879416 ACTATCGCAACGCGAAATGGAAAATCGC
1 ACTATCGCAACGCGAAATGGAAAATCGC
2879444 AACGCGATCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.26, G:0.22, T:0.14
Consensus pattern (30 bp):
ACTATCGCAACGCGAAATGGAAAATCGCGC
Found at i:2879461 original size:71 final size:71
Alignment explanation
Indices: 2879345--2879480 Score: 229
Period size: 71 Copynumber: 1.9 Consensus size: 71
2879335 ACAACTGTAG
* **
2879345 ACTATCGCAACGCGAAATGGAAAATCGCAATGCGACTGTAGACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTCCAGACTATCGCAACGCGAAATGGAAAA
2879410 TCGCGC
66 TCGCGC
2879416 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCCA-ACTATCGCAACGCGAAATGGAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGA-CTCCAGACTATCGCAACGCGAAATGGAAA
2879480 A
65 A
2879481 ACGCAACGCG
Statistics
Matches: 61, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 58 0.95
72 3 0.05
ACGTcount: A:0.38, C:0.25, G:0.22, T:0.15
Consensus pattern (71 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGACTCCAGACTATCGCAACGCGAAATGGAAAA
TCGCGC
Found at i:2879520 original size:21 final size:21
Alignment explanation
Indices: 2879416--2879520 Score: 88
Period size: 21 Copynumber: 5.1 Consensus size: 21
2879406 AAAATCGCGC
*
2879416 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
2879437 A-AATCGCAACGCGATCTCCA
1 ACTATCGCAACGCGAAATGCA
*
2879457 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * ** *
2879478 A-AAACGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
2879498 ACTATCGCAATGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
2879519 AC
1 AC
2879521 GTGAATTTGC
Statistics
Matches: 60, Mismatches: 22, Indels: 4
0.70 0.26 0.05
Matches are distributed among these distances:
20 29 0.48
21 31 0.52
ACGTcount: A:0.38, C:0.27, G:0.19, T:0.16
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:2879562 original size:19 final size:19
Alignment explanation
Indices: 2879538--2879574 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2879528 TGCGATAGTG
2879538 GAGATCGCAATGCGAATTA
1 GAGATCGCAATGCGAATTA
*
2879557 GAGATCGCATTGCGAATT
1 GAGATCGCAATGCGAATT
2879575 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.27, T:0.24
Consensus pattern (19 bp):
GAGATCGCAATGCGAATTA
Found at i:2881792 original size:17 final size:18
Alignment explanation
Indices: 2881770--2881803 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2881760 AGATGTTCGA
2881770 ACAATCCATGAA-GAAGG
1 ACAATCCATGAATGAAGG
*
2881787 ACAATCGATGAATGAAG
1 ACAATCCATGAATGAAG
2881804 AATCTGAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.47, C:0.15, G:0.24, T:0.15
Consensus pattern (18 bp):
ACAATCCATGAATGAAGG
Found at i:2883891 original size:32 final size:33
Alignment explanation
Indices: 2883830--2883892 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
2883820 TGACACCTTT
*
2883830 TGTATTTGCATTTAGCATTTGTATTTGCATTGAA
1 TGTATTT-CATTTAGCATTTGTATATGCATTGAA
2883864 TGTATTT-ATTTAAGCATTT-TATATGCATT
1 TGTATTTCATTT-AGCATTTGTATATGCATT
2883893 AATTATGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 13 0.48
33 7 0.26
34 7 0.26
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.52
Consensus pattern (33 bp):
TGTATTTCATTTAGCATTTGTATATGCATTGAA
Found at i:2888003 original size:42 final size:42
Alignment explanation
Indices: 2887956--2888099 Score: 234
Period size: 42 Copynumber: 3.4 Consensus size: 42
2887946 CCAAAATTTA
* * *
2887956 TAAATCCTTTGGGTCATCAGTAAGTCTTTCGAGTATGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
* *
2887998 TAAATCTTTCAGGTCATCAGTAAGTCTTCCGAGCATGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
*
2888040 TAAATCCTTCCGGTCATCAGTAAGTCTTCCGAGCATGATGCT
1 TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
2888082 TAAATCCTTCGGGTCATC
1 TAAATCCTTCGGGTCATC
2888100 CATAAGACCT
Statistics
Matches: 94, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 94 1.00
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.34
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
Found at i:2888070 original size:19 final size:19
Alignment explanation
Indices: 2888009--2888070 Score: 54
Period size: 19 Copynumber: 3.1 Consensus size: 19
2887999 AAATCTTTCA
2888009 GGTCATCAGTAAGTCTTCC
1 GGTCATCAGTAAGTCTTCC
* *
2888028 GAG-CATGATGCTTAAATCCTTCC
1 G-GTCATCA-G--TAAGT-CTTCC
2888051 GGTCATCAGTAAGTCTTCC
1 GGTCATCAGTAAGTCTTCC
2888070 G
1 G
2888071 AGCATGATGC
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
19 11 0.33
20 6 0.18
22 6 0.18
23 10 0.30
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (19 bp):
GGTCATCAGTAAGTCTTCC
Found at i:2888317 original size:42 final size:42
Alignment explanation
Indices: 2888217--2888318 Score: 141
Period size: 42 Copynumber: 2.4 Consensus size: 42
2888207 CCAAAATTTA
* * *
2888217 TAAATCCTTTGGGTCACCAGTAAGTCTTCTGATCATGATGCT
1 TAAATCCTTTGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
* **
2888259 TAAATACTTTAAGTCATCAGTAAGTCTTCCGAGCATGATGCT
1 TAAATCCTTTGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
*
2888301 TAAATCCTTCGGGTCATC
1 TAAATCCTTTGGGTCATC
2888319 CATAAGACCT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (42 bp):
TAAATCCTTTGGGTCATCAGTAAGTCTTCCGAGCATGATGCT
Found at i:2888394 original size:219 final size:219
Alignment explanation
Indices: 2888009--2888475 Score: 763
Period size: 219 Copynumber: 2.1 Consensus size: 219
2887999 AAATCTTTCA
* * **
2888009 GGTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCCGGTCATCAGTAAGTCTTCCGAGC
1 GGTCACCAGTAAGTCTTCCGAGCATGATGCTTAAATACTTCAAGTCATCAGTAAGTCTTCCGAGC
2888074 ATGATGCTTAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAAGAGGTTTTCACATGAGAAAGG
66 ATGATGCTTAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAAGAGGTTTTCACATGAGAAAGG
*
2888139 TTTCTCATTTAAATCTAAATTTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAATAAACTA
131 TTTCTCATTTAAATCTAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAATAAACTA
2888204 TTTCCAAAATTTATAAATCCTTTG
196 TTTCCAAAATTTATAAATCCTTTG
* * *
2888228 GGTCACCAGTAAGTCTTCTGATCATGATGCTTAAATACTTTAAGTCATCAGTAAGTCTTCCGAGC
1 GGTCACCAGTAAGTCTTCCGAGCATGATGCTTAAATACTTCAAGTCATCAGTAAGTCTTCCGAGC
* *
2888293 ATGATGCTTAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAGGATGTTTTCACATGAGAAAGG
66 ATGATGCTTAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAAGAGGTTTTCACATGAGAAAGG
*
2888358 TTTCTCATTTAAATCTAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAGTAAACTA
131 TTTCTCATTTAAATCTAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAATAAACTA
* * *
2888423 TTTCCAAAATTTATAAGTCATTCG
196 TTTCCAAAATTTATAAATCCTTTG
* * * * *
2888447 GGCCATCAATAAGTCTTTCGAGCAAGATG
1 GGTCACCAGTAAGTCTTCCGAGCATGATG
2888476 ATAAGTCCTC
Statistics
Matches: 227, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
219 227 1.00
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (219 bp):
GGTCACCAGTAAGTCTTCCGAGCATGATGCTTAAATACTTCAAGTCATCAGTAAGTCTTCCGAGC
ATGATGCTTAAATCCTTCGGGTCATCCATAAGACCTTCGGGCAAGAGGTTTTCACATGAGAAAGG
TTTCTCATTTAAATCTAAAATTGAAATTTTTGAAAAGTAAGAAAGGTTTCTTACCTAATAAACTA
TTTCCAAAATTTATAAATCCTTTG
Found at i:2888682 original size:37 final size:37
Alignment explanation
Indices: 2888632--2889207 Score: 363
Period size: 37 Copynumber: 15.2 Consensus size: 37
2888622 GTCCTCTGAG
* * *
2888632 CCATCATAAGCCTTCACGGAAGAGTAGTGAAACAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
*
2888669 CCATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* * * * *
2888706 -TAGTCTAAAGCCTTTACTGAATAGTAGTGAAGCAAAT
1 CCA-TCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* *
2888743 CCATCATAAGCCTTCACCGAATAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* * * * * *** ****
2888780 CCATCAGTAAGTCTTTCGAGCATGATGATTAAGT-CCTCCGGG
1 CCATC-TTAAG-CCTTC-A-C-CGAAGAGT-AGTGAAGCAAAT
* * * *
2888822 CCATCTAAAGCCTTCACTGAAGATTAGTAAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
*
2888859 CCATCATAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* * * * * *** * **
2888896 CCATCAGTAAGTCTTCCAAGCATGACGATTAAGT-CCTCTAGG
1 CCATC-TTAAGCCTT-C-A-C-CGAAGAGT-AGTGAAGCAAAT
* * *
2888938 CCATCTTAAGCCTTCACCAAACATTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* * **
2888975 CAATCTAAAGCCTTCACTAAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
*
2889012 CAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* * * * ***
2889049 CCATCAGTAAGCCTTTCGATC-ATGA-T-GATTAAGTCCTCT
1 CCATC-TTAAGCC-TTC-ACCGAAGAGTAG-TGAAG-CAAAT
2889088 GGGCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
1 ---CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
* * *
2889128 CTATCTTAAGCCTTCACCAAAAAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
** * *
2889165 AAATCTTAAGCATTCACAGAAGAGTAGTGAAGCAAAT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
*
2889202 CGATCT
1 CCATCT
2889208 CGAGTCTGAC
Statistics
Matches: 411, Mismatches: 101, Indels: 54
0.73 0.18 0.10
Matches are distributed among these distances:
36 7 0.02
37 288 0.70
38 25 0.06
39 17 0.04
40 17 0.04
41 23 0.06
42 28 0.07
43 6 0.01
ACGTcount: A:0.36, C:0.22, G:0.18, T:0.24
Consensus pattern (37 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAT
Found at i:2888869 original size:116 final size:116
Alignment explanation
Indices: 2888709--2889012 Score: 439
Period size: 116 Copynumber: 2.6 Consensus size: 116
2888699 AGCAAATTAG
* * * *
2888709 TCTAAAGCCTTTACTGAATAGTAGTGAAGCAAATCCATCATAAGCCTTCACCGAATAGTAGTGAA
1 TCTAAAGCCTTCACTGAACATTAGTGAAGCAAATCCATCATAAGCCTTCACCGAAGAGTAGTGAA
* * * *
2888774 GCAAATCCATCAGTAAGTCTTTCGAGCATGATGATTAAGTCCTCCGGGCCA
66 GCAAATCCATCAGTAAGTCTTCCAAGCATGACGATTAAGTCCTCCAGGCCA
* *
2888825 TCTAAAGCCTTCACTGAAGATTAGTAAAGCAAATCCATCATAAGCCTTCACCGAAGAGTAGTGAA
1 TCTAAAGCCTTCACTGAACATTAGTGAAGCAAATCCATCATAAGCCTTCACCGAAGAGTAGTGAA
*
2888890 GCAAATCCATCAGTAAGTCTTCCAAGCATGACGATTAAGTCCTCTAGGCCA
66 GCAAATCCATCAGTAAGTCTTCCAAGCATGACGATTAAGTCCTCCAGGCCA
* ** * **
2888941 TCTTAAGCCTTCACCAAACATTAGTGAAGCAAATCAATC-TAAAGCCTTCACTAAAGAGTAGTGA
1 TCTAAAGCCTTCACTGAACATTAGTGAAGCAAATCCATCAT-AAGCCTTCACCGAAGAGTAGTGA
2889005 AGCAAATC
65 AGCAAATC
2889013 AATCTTAAGC
Statistics
Matches: 169, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
115 1 0.01
116 168 0.99
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (116 bp):
TCTAAAGCCTTCACTGAACATTAGTGAAGCAAATCCATCATAAGCCTTCACCGAAGAGTAGTGAA
GCAAATCCATCAGTAAGTCTTCCAAGCATGACGATTAAGTCCTCCAGGCCA
Found at i:2888942 original size:79 final size:76
Alignment explanation
Indices: 2888859--2889144 Score: 285
Period size: 79 Copynumber: 3.7 Consensus size: 76
2888849 TAAAGCAAAT
* * *
2888859 CCATCATAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGTCTTCCAAGCATGACGA
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTT-C-A-CATGAAGA
2888924 TTAAGTCCTCTAGG
63 TTAAGTCCTCTAGG
* * * * * *
2888938 CCATCTTAAGCCTTCACCAAACATTAGTGAAGCAAATCAATC--TAAAGCCTTCAC-TAAAGAGT
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGT-AAGCCTTCACATGAAGATT
*** * **
2889000 -AGTGAAGCAAAT
65 AAGT-CCTCTAGG
* *
2889012 CAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTTCGATCATGATGA
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGCC-TTC-A-CATGAAGA
*
2889077 TTAAGTCCTCTGGG
63 TTAAGTCCTCTAGG
* *
2889091 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCTATC-TTAAGCCTTCAC
1 CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCAC
2889145 CAAAAAGTAG
Statistics
Matches: 165, Mismatches: 33, Indels: 22
0.75 0.15 0.10
Matches are distributed among these distances:
73 3 0.02
74 44 0.27
75 7 0.04
76 6 0.04
77 6 0.04
78 13 0.08
79 83 0.50
80 3 0.02
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.24
Consensus pattern (76 bp):
CCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTCACATGAAGATTA
AGTCCTCTAGG
Found at i:2889032 original size:153 final size:153
Alignment explanation
Indices: 2888824--2889202 Score: 569
Period size: 153 Copynumber: 2.5 Consensus size: 153
2888814 CCTCCGGGCC
* * * * *
2888824 ATCTAAAGCCTTCACTGAAGATTAGTAAAGCAAATCCATCATAAGCCTTCACCGAAGAGTAGTGA
1 ATCTAAAGCCTTCACTAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGA
*
2888889 AGCAAATCCATCAGTAAGTCTTCCAAGCATGACGATTAAGTCCTCTAGGCCATCTTAAGCCTTCA
66 AGCAAATCCATCAGTAAGCCTTCCAAGCATGACGATTAAGTCCTCTAGGCCATCTTAAGCCTTCA
*
2888954 CCAAACATTAGTGAAGCAAATCA
131 CCAAACAGTAGTGAAGCAAATCA
2888977 ATCTAAAGCCTTCACTAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGA
1 ATCTAAAGCCTTCACTAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGA
* * * * *
2889042 AGCAAATCCATCAGTAAGCCTTTCGATCATGATGATTAAGTCCTCTGGGCCATCTTAAGCCTTCA
66 AGCAAATCCATCAGTAAGCCTTCCAAGCATGACGATTAAGTCCTCTAGGCCATCTTAAGCCTTCA
* * *
2889107 CCGAAGAGTAGTGAAGCAAATCT
131 CCAAACAGTAGTGAAGCAAATCA
* * * * * *
2889130 ATCTTAAGCCTTCACCAAAAAGTAGTGAAGCAAATAAATCTTAAGCATTCACAGAAGAGTAGTGA
1 ATCTAAAGCCTTCACTAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGA
2889195 AGCAAATC
66 AGCAAATC
2889203 GATCTCGAGT
Statistics
Matches: 205, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
153 205 1.00
ACGTcount: A:0.37, C:0.22, G:0.17, T:0.24
Consensus pattern (153 bp):
ATCTAAAGCCTTCACTAAAGAGTAGTGAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGA
AGCAAATCCATCAGTAAGCCTTCCAAGCATGACGATTAAGTCCTCTAGGCCATCTTAAGCCTTCA
CCAAACAGTAGTGAAGCAAATCA
Found at i:2889156 original size:269 final size:269
Alignment explanation
Indices: 2888669--2889164 Score: 803
Period size: 269 Copynumber: 1.8 Consensus size: 269
2888659 TGAAACAAAT
* * * * * *
2888669 CCATCTTAAGCCTTCACCAAAGAGTAGTGAAGCAAATTAGTCTAAAGCCTTTACTGAATAGTAGT
1 CCATCTTAAGCCTTCACCAAACAGTAGTGAAGCAAATCAATCTAAAGCCTTCACTAAAGAGTAGT
* * *
2888734 GAAGCAAATCCATCATAAGCCTTCACCGAATAGTAGTGAAGCAAATCCATCAGTAAGTCTTTCGA
66 GAAGCAAATCAATCATAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTTCGA
* *
2888799 GCATGATGATTAAGTCCTCCGGGCCATCTAAAGCCTTCACTGAAGATTAGTAAAGCAAATCCATC
131 GCATGATGATTAAGTCCTCCGGGCCATCTAAAGCCTTCACCGAAGAGTAGTAAAGCAAATCCATC
* *
2888864 ATAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGTCTTCCAAGCATGACGATTAAG
196 ATAAGCCTTCACCAAAAAGTAGTGAAGCAAATCCATCAGTAAGTCTTCCAAGCATGACGATTAAG
2888929 TCCTCTAGG
261 TCCTCTAGG
*
2888938 CCATCTTAAGCCTTCACCAAACATTAGTGAAGCAAATCAATCTAAAGCCTTCACTAAAGAGTAGT
1 CCATCTTAAGCCTTCACCAAACAGTAGTGAAGCAAATCAATCTAAAGCCTTCACTAAAGAGTAGT
*
2889003 GAAGCAAATCAATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTTCGA
66 GAAGCAAATCAATCATAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTTCGA
* * * * *
2889068 TCATGATGATTAAGTCCTCTGGGCCATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCTATC
131 GCATGATGATTAAGTCCTCCGGGCCATCTAAAGCCTTCACCGAAGAGTAGTAAAGCAAATCCATC
*
2889133 TTAAGCCTTCACCAAAAAGTAGTGAAGCAAAT
196 ATAAGCCTTCACCAAAAAGTAGTGAAGCAAAT
2889165 AAATCTTAAG
Statistics
Matches: 206, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
269 206 1.00
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (269 bp):
CCATCTTAAGCCTTCACCAAACAGTAGTGAAGCAAATCAATCTAAAGCCTTCACTAAAGAGTAGT
GAAGCAAATCAATCATAAGCCTTCACCGAAGAGTAGTGAAGCAAATCCATCAGTAAGCCTTTCGA
GCATGATGATTAAGTCCTCCGGGCCATCTAAAGCCTTCACCGAAGAGTAGTAAAGCAAATCCATC
ATAAGCCTTCACCAAAAAGTAGTGAAGCAAATCCATCAGTAAGTCTTCCAAGCATGACGATTAAG
TCCTCTAGG
Found at i:2896378 original size:21 final size:20
Alignment explanation
Indices: 2896352--2896391 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2896342 GCATCAAGGT
*
2896352 TTTTGTTGAAGCTATGAAATC
1 TTTTGTCGAAGCTAT-AAATC
*
2896373 TTTTGTCGAGGCTATAAAT
1 TTTTGTCGAAGCTATAAAT
2896392 TCCTGTAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.42
Consensus pattern (20 bp):
TTTTGTCGAAGCTATAAATC
Found at i:2904013 original size:20 final size:21
Alignment explanation
Indices: 2903980--2904029 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
2903970 TTATCTCAAG
2903980 TAAAAC-TATCATATG-ATAT
1 TAAAACATATCATATGTATAT
2903999 TCAAAACATAT-ATATGTATAT
1 T-AAAACATATCATATGTATAT
2904020 TAAATACATA
1 TAAA-ACATA
2904030 AACACAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
19 1 0.04
20 13 0.48
21 13 0.48
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.36
Consensus pattern (21 bp):
TAAAACATATCATATGTATAT
Found at i:2904385 original size:32 final size:30
Alignment explanation
Indices: 2904332--2904398 Score: 73
Period size: 32 Copynumber: 2.1 Consensus size: 30
2904322 TTAACTAAAG
*
2904332 AAAAAAAATATTTTAGTTTTTTTTCTAAACTT
1 AAAAAAAATATTTTAG-TTTTTATCTAAAC-T
*
2904364 AAAAAATATATATTTTA-TTTTTATCTTAACT
1 AAAAAA-A-ATATTTTAGTTTTTATCTAAACT
2904395 AAAA
1 AAAA
2904399 TTTTTAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
31 5 0.16
32 17 0.55
33 1 0.03
34 8 0.26
ACGTcount: A:0.45, C:0.06, G:0.01, T:0.48
Consensus pattern (30 bp):
AAAAAAAATATTTTAGTTTTTATCTAAACT
Done.