Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold28
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: 2815568
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.30
Warning! 166732 characters in sequence are not A, C, G, or T
File 8 of 16
Found at i:1234273 original size:130 final size:129
Alignment explanation
Indices: 1234134--1234537 Score: 481
Period size: 130 Copynumber: 3.1 Consensus size: 129
1234124 GAAATAACAA
* * *
1234134 GGTTGGAGTATCCTCGATTGTGGAAAATTAGTGTTTTAGAAATAAAATCGAGATTGGAGTATCCC
1 GGTTAGAGTATCCTCGATTGTGGAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
** * **
1234199 CTTGA-AAATAATGGGGTTAGAGTATCCTCGATTATAAAAAATTGATGTTTTGAAAATAAAACTA
66 CTT-ACAAATAACAGGGTTGGAGTATCC-CGATTATGGAAAATTGATGTTTTGAAAATAAAACTA
1234263 G
129 G
* * * *
1234264 GGTTAGAGTATCCTCGATTGTGAAAAATTGGTGTTTTAAAAATAAAATCGGGGTCGGAGTATCCC
1 GGTTAGAGTATCCTCGATTGTGGAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
* * * * *
1234329 TTTACAACTAACAGGGTTGGAGTATCCCCGATTATGGAAAATCGATGTTTTGAAAAAAAAACTGG
66 CTTACAAATAACAGGGTTGGAGTAT-CCCGATTATGGAAAATTGATGTTTTGAAAATAAAACT-A
1234394 G
129 G
* * * * * *
1234395 GGTTGGAGTATCCTCGATTAT-GAAAAATCGATGTTTTGGAAATAAAACCGGGGTTGGAGTATCC
1 GGTTAGAGTATCCTCGATTGTGGAAAATTAG-TGTTTTAGAAATAAAATCGGGGTTGGAGTATCC
* * * *
1234459 CCTTAGAAATAACAAGGTTGGAGTATCCCTGATTATGGAAAATTGGTGTTTT-AGAAATAAAACC
65 CCTTACAAATAACAGGGTTGGAGTATCCC-GATTATGGAAAATTGATGTTTTGA-AAATAAAACT
1234523 AG
128 AG
1234525 GGTTAGAGTATCC
1 GGTTAGAGTATCC
1234538 CCTCGGAAAT
Statistics
Matches: 232, Mismatches: 36, Indels: 12
0.83 0.13 0.04
Matches are distributed among these distances:
129 1 0.00
130 130 0.56
131 101 0.44
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (129 bp):
GGTTAGAGTATCCTCGATTGTGGAAAATTAGTGTTTTAGAAATAAAATCGGGGTTGGAGTATCCC
CTTACAAATAACAGGGTTGGAGTATCCCGATTATGGAAAATTGATGTTTTGAAAATAAAACTAG
Found at i:1234275 original size:209 final size:211
Alignment explanation
Indices: 1233923--1234388 Score: 541
Period size: 209 Copynumber: 2.2 Consensus size: 211
1233913 AATAAAATTG
* * * * *
1233923 AGGTTGAAGTATCCTCGATTGT-GAAAAATCGATGTTTTGGAAATAAAACCAGGGTTGGAGTATC
1 AGGTTGGAGTATCCTCGATTGTGGAAAATTAGATGTTTTAGAAATAAAACCAGGATTGGAGTATC
* * ** *
1233987 TCCTTGGAAAATAACGAGGTTGGAGTATCCCCAATTATGGAAAATTGATGTTTTGGAAATAAAAC
66 CCCTTGGAAAATAACGAGGTTAGAGTATCCCCAATTATAAAAAATTGATGTTTTGAAAATAAAAC
* * * *
1234052 TGGGGTTGGAGTATCGC-CGATTATGAAAAATTGCTATTTTAGAAATAAAACCAGAGTTGGACAA
131 TAGGGTTAGAGTATC-CTCGATTATGAAAAATTGCTATTTTAAAAATAAAACCAGAGTCGGACAA
*
1234116 TCCCCTCAGAAATAACA
195 TCCCCTCACAAATAACA
*
1234133 AGGTTGGAGTATCCTCGATTGTGGAAAATTAG-TGTTTTAGAAATAAAATC-GAGATTGGAGTAT
1 AGGTTGGAGTATCCTCGATTGTGGAAAATTAGATGTTTTAGAAATAAAACCAG-GATTGGAGTAT
* * * *
1234196 CCCCTT-GAAAATAATGGGGTTAGAGTATCCTCGATTATAAAAAATTGATGTTTTGAAAATAAAA
65 CCCCTTGGAAAATAACGAGGTTAGAGTATCCCCAATTATAAAAAATTGATGTTTTGAAAATAAAA
* * * * * * **
1234260 CTAGGGTTAGAGTATCCTCGATTGTGAAAAATTGGTGTTTTAAAAATAAAATCGGGGTCGGAGTA
130 CTAGGGTTAGAGTATCCTCGATTATGAAAAATTGCTATTTTAAAAATAAAACCAGAGTCGGACAA
* * *
1234325 TCCCTTTACAACTAACA
195 TCCCCTCACAAATAACA
* * * * *
1234342 GGGTTGGAGTATCCCCGATTATGGAAAA-TCGATGTTTT-GAAAAAAAA
1 AGGTTGGAGTATCCTCGATTGTGGAAAATTAGATGTTTTAGAAATAAAA
1234389 ACTGGGGGTT
Statistics
Matches: 216, Mismatches: 36, Indels: 10
0.82 0.14 0.04
Matches are distributed among these distances:
208 11 0.05
209 146 0.68
210 52 0.24
211 7 0.03
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (211 bp):
AGGTTGGAGTATCCTCGATTGTGGAAAATTAGATGTTTTAGAAATAAAACCAGGATTGGAGTATC
CCCTTGGAAAATAACGAGGTTAGAGTATCCCCAATTATAAAAAATTGATGTTTTGAAAATAAAAC
TAGGGTTAGAGTATCCTCGATTATGAAAAATTGCTATTTTAAAAATAAAACCAGAGTCGGACAAT
CCCCTCACAAATAACA
Found at i:1234324 original size:51 final size:51
Alignment explanation
Indices: 1234212--1234327 Score: 144
Period size: 51 Copynumber: 2.3 Consensus size: 51
1234202 GAAAATAATG
* *
1234212 GGGTTAGAGTATCCTCGATTATAAAAAATTGATGTTTTGAAAATAAAACTA
1 GGGTCAGAGTATCCTCGATTATAAAAAATTGATGTTTTAAAAATAAAACTA
* * * * *
1234263 GGGTTAGAGTATCCTCGATTGTGAAAAATTGGTGTTTTAAAAATAAAA-TCG
1 GGGTCAGAGTATCCTCGATTATAAAAAATTGATGTTTTAAAAATAAAACT-A
*
1234314 GGGTCGGAGTATCC
1 GGGTCAGAGTATCC
1234328 CTTTACAACT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 1 0.02
51 56 0.98
ACGTcount: A:0.35, C:0.09, G:0.23, T:0.32
Consensus pattern (51 bp):
GGGTCAGAGTATCCTCGATTATAAAAAATTGATGTTTTAAAAATAAAACTA
Found at i:1234453 original size:51 final size:52
Alignment explanation
Indices: 1234342--1234460 Score: 186
Period size: 52 Copynumber: 2.3 Consensus size: 52
1234332 ACAACTAACA
* *
1234342 GGGTTGGAGTATCCCCGATTATGGAAAATCGATGTTTTGAAAAAAAAACTGG
1 GGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAAAAAAACTCG
* * *
1234394 GGGTTGGAGTATCCTCGATTATGAAAAATCGATGTTTTGGAAATAAAAC-CG
1 GGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAAAAAAACTCG
1234445 GGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
1234461 TTAGAAATAA
Statistics
Matches: 61, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
51 16 0.26
52 45 0.74
ACGTcount: A:0.31, C:0.13, G:0.28, T:0.28
Consensus pattern (52 bp):
GGGTTGGAGTATCCCCGATTATGAAAAATCGATGTTTTGAAAAAAAAACTCG
Found at i:1234509 original size:210 final size:209
Alignment explanation
Indices: 1234264--1234812 Score: 692
Period size: 210 Copynumber: 2.6 Consensus size: 209
1234254 ATAAAACTAG
* * * * *
1234264 GGTTAGAGTAT-CCTCGATTGTGAAAAATTGGTGTTTTAAAAATAAAATCGGGGTCGGAGTATCC
1 GGTTGGAGTATCCCT-GATTGTGGAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCC
* * * *
1234328 CTTTACAACTAACAGGGTTGGAGTATCCCCGATTATGGAAAATCGA-TGTTTTGAAAAAAAAACT
65 CTTCAAAAATAAC-GGGTTGGAGTATCCCCGATTATGGAAAAT-GAGTGTTTTGAAAAAAAAACC
** * *
1234392 GGGGGTTGGAGTATCCTCGATTATGAAAAATC-GATGTTTTGGAAATAAAACCGGGGTTGGAGTA
128 GGGGGTTAAAGTATCCTCGATTATGAAAAATCAG-TGTTTTGAAAATAAAACCGGGATTGGAGTA
1234456 TCCCCTTAGAAATAACAA
192 TCCCCTTAGAAATAACAA
* * *
1234474 GGTTGGAGTATCCCTGATTATGGAAAATTGGTGTTTTAGAAATAAAACCAGGGTTAGAGTATCCC
1 GGTTGGAGTATCCCTGATTGTGGAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
* ** * * * * * *
1234539 CTCGGAAATAACGGGATTGGAGTGTCCTCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGG
66 TTCAAAAATAACGGG-TTGGAGTATCCCCGATTATGGAAAATGAGTGTTTTGAAAAAAAAACCGG
* * *
1234604 GGGTTAAAGTATCGTCGATTATGAAAAATCAGTGTTTTGAAAATTAAATCGGGATTGGAGTATCC
130 GGGTTAAAGTATCCTCGATTATGAAAAATCAGTGTTTTGAAAATAAAACCGGGATTGGAGTATCC
* *
1234669 CCTTGGAAATAACGA
195 CCTTAGAAATAACAA
* *
1234684 GGTTGGAGTATCCCTGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCCC
1 GGTTGGAGTATCCCTGATTGTGGAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
* * *
1234749 TTCAAAAATTACGGGGTTGGAGTATCCCCGATTATGGAAAATTAGTG-TTTCAAAAATAAAACCG
66 TTCAAAAATAAC-GGGTTGGAGTATCCCCGATTATGGAAAATGAGTGTTTTGAAAAA-AAAACCG
1234813 AGGTTGGAGT
Statistics
Matches: 289, Mismatches: 44, Indels: 12
0.84 0.13 0.03
Matches are distributed among these distances:
209 10 0.03
210 272 0.94
211 7 0.02
ACGTcount: A:0.34, C:0.13, G:0.25, T:0.29
Consensus pattern (209 bp):
GGTTGGAGTATCCCTGATTGTGGAAAATTGGTGTTTTAGAAATAAAACCGGGGTTGGAGTATCCC
TTCAAAAATAACGGGTTGGAGTATCCCCGATTATGGAAAATGAGTGTTTTGAAAAAAAAACCGGG
GGTTAAAGTATCCTCGATTATGAAAAATCAGTGTTTTGAAAATAAAACCGGGATTGGAGTATCCC
CTTAGAAATAACAA
Found at i:1234528 original size:79 final size:78
Alignment explanation
Indices: 1234395--1234616 Score: 284
Period size: 79 Copynumber: 2.8 Consensus size: 78
1234385 AAAAACTGGG
* * * *
1234395 GGTTGGAGTATCCTCGATTATGAAAAATCGATGTTTTGGAAATAAAACCGGGGTTGGAGTATCCC
1 GGTTGGAGTATCCTCGATTATGAAAAATTGGTGTTTTGGAAATAAAACCAGGGTTAGAGTATCCC
*
1234460 CTTAGAAATAACAA
66 CTCAGAAATAAC-A
* *
1234474 GGTTGGAGTATCC-CTGATTATGGAAAATTGGTGTTTTAGAAATAAAACCAGGGTTAGAGTATCC
1 GGTTGGAGTATCCTC-GATTATGAAAAATTGGTGTTTTGGAAATAAAACCAGGGTTAGAGTATCC
* *
1234538 CCTCGGAAATAACG
65 CCTCAGAAATAACA
* * * *
1234552 GGATTGGAGTGTCCTCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGGGGGTTAAAGTATC
1 GG-TTGGAGTATCCTCGATTATGAAAAATTGGTGTTTTGGAAATAAAACC-AGGGTTAGAGTATC
1234617 GTCGATTATG
Statistics
Matches: 124, Mismatches: 15, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
78 3 0.02
79 108 0.87
80 13 0.10
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.29
Consensus pattern (78 bp):
GGTTGGAGTATCCTCGATTATGAAAAATTGGTGTTTTGGAAATAAAACCAGGGTTAGAGTATCCC
CTCAGAAATAACA
Found at i:1234615 original size:131 final size:131
Alignment explanation
Indices: 1234480--1234733 Score: 320
Period size: 131 Copynumber: 1.9 Consensus size: 131
1234470 ACAAGGTTGG
* **
1234480 AGTATCC-CTGATTATGGAAAATTGGTGTTTT-AGAAATAAAACCAGGG-TTAGAGTATCCCCTC
1 AGTATCCTC-GATTATGAAAAATCAGTGTTTTGA-AAATAAAACC-GGGATTAGAGTATCCCCTC
* *
1234542 GGAAATAACG-GGATTGGAGTGT-CCTCGATTATGAAAAATTAGTGTTTTGGAAATAAAACCGGG
63 GGAAATAACGAGG-TTGGAGTATCCCT-GATTATGAAAAATTAGTGTTTTAGAAATAAAACCGGG
1234605 GGTTAA
126 GGTTAA
* * * * *
1234611 AGTATCGTCGATTATGAAAAATCAGTGTTTTGAAAATTAAATCGGGATTGGAGTATCCCCTTGGA
1 AGTATCCTCGATTATGAAAAATCAGTGTTTTGAAAATAAAACCGGGATTAGAGTATCCCCTCGGA
* *
1234676 AATAACGAGGTTGGAGTATCCCTGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCG
66 AATAACGAGGTTGGAGTATCCCTGATTATGAAAAATTAGTGTTTTAGAAATAAAACCG
1234734 AGGTTGGAGT
Statistics
Matches: 106, Mismatches: 12, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
130 3 0.03
131 96 0.91
132 7 0.07
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (131 bp):
AGTATCCTCGATTATGAAAAATCAGTGTTTTGAAAATAAAACCGGGATTAGAGTATCCCCTCGGA
AATAACGAGGTTGGAGTATCCCTGATTATGAAAAATTAGTGTTTTAGAAATAAAACCGGGGGTTA
A
Found at i:1234741 original size:79 final size:78
Alignment explanation
Indices: 1234619--1234838 Score: 264
Period size: 79 Copynumber: 2.8 Consensus size: 78
1234609 AAAGTATCGT
* * * *
1234619 CGATTATGAAAAATCAGTGTTTT-GAAAATTAAATCG-GGATTGGAGTATCCCCTTGGAAATAAC
1 CGATTATGGAAAATTAGTGTTTTAG-AAATAAAACCGAGG-TTGGAGTAT-CCCTTGGAAATAAC
1234682 GAGGTTGGAGTATCCC
63 GAGGTTGGAGTATCCC
* * ** * *
1234698 TGATTGTGGAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCTTCAAAAATTACGG
1 CGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCTT-GGAAATAACGA
1234763 GGTTGGAGTATCCC
65 GGTTGGAGTATCCC
* * *
1234777 CGATTATGGAAAATTAGTGTTTCAAAAATAAAACCGAGGTTGGAGTATTCCCTCGGAAATAA
1 CGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTA-TCCCTTGGAAATAA
1234839 AAACATAAAT
Statistics
Matches: 119, Mismatches: 18, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
78 5 0.04
79 106 0.89
80 8 0.07
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (78 bp):
CGATTATGGAAAATTAGTGTTTTAGAAATAAAACCGAGGTTGGAGTATCCCTTGGAAATAACGAG
GTTGGAGTATCCC
Found at i:1235474 original size:16 final size:15
Alignment explanation
Indices: 1235450--1235481 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
1235440 AGTCTAGACA
1235450 AAGCTGGGGGCAAAC
1 AAGCTGGGGGCAAAC
1235465 AAGCTGGGGGCAAAC
1 AAGCTGGGGGCAAAC
1235480 AA
1 AA
1235482 TCTGTTAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.38, T:0.06
Consensus pattern (15 bp):
AAGCTGGGGGCAAAC
Found at i:1236976 original size:50 final size:50
Alignment explanation
Indices: 1236922--1237037 Score: 144
Period size: 50 Copynumber: 2.3 Consensus size: 50
1236912 AAAAATGCTT
* * *
1236922 GAATGTATCGATACATTGAGA-AATGTATTGATACATCTGGGTAAAACCCA
1 GAATGTATCGATACAATGA-ATAATGTATCGATACATCTAGGTAAAACCCA
* * * *
1236972 GAATGTAACGATACAATGAATGATGTATCGATAGATCTAGGTAAAAGCCA
1 GAATGTATCGATACAATGAATAATGTATCGATACATCTAGGTAAAACCCA
*
1237022 AAATGTATCGATACAA
1 GAATGTATCGATACAA
1237038 ATTGTGAAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
49 1 0.02
50 55 0.98
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (50 bp):
GAATGTATCGATACAATGAATAATGTATCGATACATCTAGGTAAAACCCA
Found at i:1244698 original size:33 final size:33
Alignment explanation
Indices: 1244656--1244720 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
1244646 TTGGAAGCAA
* * *
1244656 TGTATCGATACAATTCATCATGTGTCGATACAT
1 TGTATCGATACAATGCACCATGTATCGATACAT
1244689 TGTATCGATACAATGCACCATGTATCGATACA
1 TGTATCGATACAATGCACCATGTATCGATACA
1244721 AACAGTGGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.32
Consensus pattern (33 bp):
TGTATCGATACAATGCACCATGTATCGATACAT
Found at i:1244775 original size:20 final size:20
Alignment explanation
Indices: 1244750--1244809 Score: 86
Period size: 19 Copynumber: 3.0 Consensus size: 20
1244740 CTGCCAGTTT
1244750 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGTC
**
1244770 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGTC
1244789 CATGTATCGATACAATGTGTC
1 CATGTATCGATACAAT-TGTC
1244810 GATACAAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.50
20 15 0.44
21 2 0.06
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGTC
Found at i:1245370 original size:30 final size:32
Alignment explanation
Indices: 1245326--1245398 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 32
1245316 TTTCTTGTTT
* *
1245326 CATGCA-TGCATATGTTCATTTCA-TGCA-TA
1 CATGCATTTCATATGTTCATCTCATTGCATTA
1245355 CATGCATTTCATATGTTCATCTCATTGCATTA
1 CATGCATTTCATATGTTCATCTCATTGCATTA
* *
1245387 CTTTCATTTCAT
1 CATGCATTTCAT
1245399 GCATTCATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 6 0.16
30 15 0.41
31 4 0.11
32 12 0.32
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.44
Consensus pattern (32 bp):
CATGCATTTCATATGTTCATCTCATTGCATTA
Found at i:1245711 original size:45 final size:45
Alignment explanation
Indices: 1245603--1245725 Score: 156
Period size: 45 Copynumber: 2.7 Consensus size: 45
1245593 AGCAATAATG
* * * *
1245603 AAGACAAAGCAACATGGAACAACAAAGCACCAATGAAGAAAGTGG
1 AAGACAAAGCAACATGGAACAGCAAAGCAACAAAGAAGAAAGTGA
*
1245648 AAGAGAAAGCAACATGGAACAGCAAAGCAACAAAGAAGAAAGTGA
1 AAGACAAAGCAACATGGAACAGCAAAGCAACAAAGAAGAAAGTGA
* *** *
1245693 AAGACAAAGTAGTGTGGAACAGTAAAGCAACAA
1 AAGACAAAGCAACATGGAACAGCAAAGCAACAA
1245726 GTTGAAAAAT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.54, C:0.15, G:0.24, T:0.07
Consensus pattern (45 bp):
AAGACAAAGCAACATGGAACAGCAAAGCAACAAAGAAGAAAGTGA
Found at i:1247715 original size:20 final size:21
Alignment explanation
Indices: 1247690--1247742 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1247680 TACAAGCCAA
* *
1247690 TGTATCGATACAAT-TTTTTG
1 TGTATCGATACAATACTTTGG
1247710 TGTATCGATAC-ATACTTTGG
1 TGTATCGATACAATACTTTGG
1247730 TGTATCGATACAA
1 TGTATCGATACAA
1247743 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.90
21 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (21 bp):
TGTATCGATACAATACTTTGG
Found at i:1247747 original size:19 final size:19
Alignment explanation
Indices: 1247690--1247748 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 19
1247680 TACAAGCCAA
* *
1247690 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA-CTTTGG
1247710 TGTATCGATACATACTTTGG
1 TGTATCGATACA-ACTTTGG
*
1247730 TGTATCGATACAAGTTTGG
1 TGTATCGATACAACTTTGG
1247749 CTACTGCCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
19 6 0.17
20 28 0.80
21 1 0.03
ACGTcount: A:0.25, C:0.12, G:0.20, T:0.42
Consensus pattern (19 bp):
TGTATCGATACAACTTTGG
Found at i:1249849 original size:21 final size:20
Alignment explanation
Indices: 1249820--1249862 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1249810 GGCTAGTATG
*
1249820 GGGACTGCCCGGTTGCGACCT
1 GGGACTG-CCGGTCGCGACCT
*
1249841 GGGAGTGCCGGTCGCGACCT
1 GGGACTGCCGGTCGCGACCT
1249861 GG
1 GG
1249863 TGGTGCTGCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.09, C:0.30, G:0.44, T:0.16
Consensus pattern (20 bp):
GGGACTGCCGGTCGCGACCT
Found at i:1250319 original size:13 final size:13
Alignment explanation
Indices: 1250301--1250336 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1250291 ATAATCCCCC
*
1250301 TGTATCGATACAG
1 TGTATCGATACAA
1250314 TGTATCGATACAA
1 TGTATCGATACAA
1250327 TGTATCGATA
1 TGTATCGATA
1250337 TAAAGAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.14, G:0.19, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1256049 original size:13 final size:13
Alignment explanation
Indices: 1256031--1256056 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1256021 CAATTTTTTG
1256031 TGTATCGATACAT
1 TGTATCGATACAT
1256044 TGTATCGATACAT
1 TGTATCGATACAT
1256057 ACTTTGGTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1256053 original size:33 final size:33
Alignment explanation
Indices: 1256011--1256075 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1256001 TACAAGCCAA
* *
1256011 TGTATCGATACA-ATTTTTTGTGTATCGATACAT
1 TGTATCGATACATA-CTTTGGTGTATCGATACAT
1256044 TGTATCGATACATACTTTGGTGTATCGATACA
1 TGTATCGATACATACTTTGGTGTATCGATACA
1256076 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATACTTTGGTGTATCGATACAT
Found at i:1269553 original size:84 final size:84
Alignment explanation
Indices: 1269459--1269904 Score: 389
Period size: 84 Copynumber: 5.3 Consensus size: 84
1269449 TTTTTGTTTG
* * * * * * *
1269459 CCTGTTGGCTTTGACCCTGGAGATTTTCCTACCCTTCAGTTTGCCTATCGACTTT-ACCCTAAAG
1 CCTGTCGGCTTTGACCCTAGAGACTTTCCTACCCTT-AGTCTGCCTGTCGGCTTTGACCCTAGAG
1269523 ACTGCCTCATCTAAAGTCTA
65 ACTGCCTCATCTAAAGTCTA
* * * * * *
1269543 CCCGTCGGCTTTGA-CCTCAGAGACTTTCCTACCCTCAGTCTGCCTATCGGCATCGACTCTAGAG
1 CCTGTCGGCTTTGACCCT-AGAGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAG
*
1269607 ATTGCCTCATCTAAAGTCTA
65 ACTGCCTCATCTAAAGTCTA
* * * * * * *
1269627 CCTGTCGACTTTGACCCTGGAGACGTTT-CTACCCCTAATCTGCCTGTTGGCTTTGACCTTGGAG
1 CCTGTCGGCTTTGACCCTAGAGAC-TTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAG
* *
1269691 ACTGCCTCATCTAAAATCTG
65 ACTGCCTCATCTAAAGTCTA
* ** * * * *
1269711 CTTGTTAGCTTTAACCCTAGAGACTTTCCTACCCTTAGTCTGCCTGTTGGCTTTGACCTTAAAGA
1 CCTGTCGGCTTTGACCCTAGAGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGA
* *
1269776 CTACCTCATCTAAAGTCTG
66 CTGCCTCATCTAAAGTCTA
* * ** * * *
1269795 CCTATCGGCTTTGACCTTAGAGACTTTTCC-ATCTTTTAGTTTGCATGTCGACTTTGACCCTAGA
1 CCTGTCGGCTTTGACCCTAGAGAC-TTTCCTA-CCCTTAGTCTGCCTGTCGGCTTTGACCCTAGA
* * *** *
1269859 GACTTTCCT-ACCCCCAGTCTG
64 GAC-TGCCTCATCTAAAGTCTA
*
1269880 CATGTCGGCTTTGACCCTAGAGACT
1 CCTGTCGGCTTTGACCCTAGAGACT
1269905 GCTTCATCTA
Statistics
Matches: 292, Mismatches: 62, Indels: 16
0.79 0.17 0.04
Matches are distributed among these distances:
83 20 0.07
84 201 0.69
85 67 0.23
86 4 0.01
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (84 bp):
CCTGTCGGCTTTGACCCTAGAGACTTTCCTACCCTTAGTCTGCCTGTCGGCTTTGACCCTAGAGA
CTGCCTCATCTAAAGTCTA
Found at i:1269593 original size:42 final size:43
Alignment explanation
Indices: 1269457--1269988 Score: 229
Period size: 42 Copynumber: 12.7 Consensus size: 43
1269447 TCTTTTTGTT
* * * * *
1269457 TGCCTGTTGGCTTTGACC-CTGGAGATTTTCCTACCCTTCAGTT
1 TGCCTGTCGGCTTTGACCTCTAGAGACTTTCCTACCC-TAAGTC
* * * * *
1269500 TGCCTATCGACTTT-ACC-CTAAAGAC-TGCCT-CATCTAAAGTC
1 TGCCTGTCGGCTTTGACCTCTAGAGACTTTCCTAC-CCT-AAGTC
* * *
1269541 TACCCGTCGGCTTTGACCTC-AGAGACTTTCCTACCCTCAGTC
1 TGCCTGTCGGCTTTGACCTCTAGAGACTTTCCTACCCTAAGTC
* * * * *
1269583 TGCCTATCGGCATCGA-CTCTAGAGA-TTGCCT-CATCTAAAGTC
1 TGCCTGTCGGCTTTGACCTCTAGAGACTTTCCTAC-CCT-AAGTC
* * *
1269625 TACCTGTCGACTTTGACC-CTGGAGACGTTT-CTACCCCTAA-TC
1 TGCCTGTCGGCTTTGACCTCTAGAGAC-TTTCCTA-CCCTAAGTC
* * * * *
1269667 TGCCTGTTGGCTTTGACCT-TGGAGAC-TGCCT-CATCTAAAATC
1 TGCCTGTCGGCTTTGACCTCTAGAGACTTTCCTAC-CCT-AAGTC
* ** * *
1269709 TGCTTGTTAGCTTTAACC-CTAGAGACTTTCCTACCCTTAGTC
1 TGCCTGTCGGCTTTGACCTCTAGAGACTTTCCTACCCTAAGTC
* * * *
1269751 TGCCTGTTGGCTTTGACCT-TAAAGAC-TACCT-CATCTAAAGTC
1 TGCCTGTCGGCTTTGACCTCTAGAGACTTTCCTAC-CCT-AAGTC
* ** * *
1269793 TGCCTATCGGCTTTGACCT-TAGAGACTTTTCC-ATCTTTTAGTT
1 TGCCTGTCGGCTTTGACCTCTAGAGAC-TTTCCTA-CCCTAAGTC
* * **
1269836 TGCATGTCGACTTTGACC-CTAGAGACTTTCCTACCCCCAGTC
1 TGCCTGTCGGCTTTGACCTCTAGAGACTTTCCTACCCTAAGTC
* *
1269878 TGCATGTCGGCTTTGACC-CTAGAGACTGCTT-C-A-TCTAAAGTC
1 TGCCTGTCGGCTTTGACCTCTAGAGACT--TTCCTACCCT-AAGTC
* * * * * *
1269920 TACCTATCAGTTTTGACCT-TGGAGACTTTCCTACCCTCAGTC
1 TGCCTGTCGGCTTTGACCTCTAGAGACTTTCCTACCCTAAGTC
* * *
1269962 TACCTGTCAGCTTTGACCT-TGGAGACT
1 TGCCTGTCGGCTTTGACCTCTAGAGACT
1269989 GCCTCATCTA
Statistics
Matches: 368, Mismatches: 83, Indels: 77
0.70 0.16 0.15
Matches are distributed among these distances:
39 1 0.00
40 9 0.02
41 40 0.11
42 245 0.67
43 58 0.16
44 13 0.04
45 2 0.01
ACGTcount: A:0.20, C:0.30, G:0.17, T:0.33
Consensus pattern (43 bp):
TGCCTGTCGGCTTTGACCTCTAGAGACTTTCCTACCCTAAGTC
Found at i:1269894 original size:127 final size:127
Alignment explanation
Indices: 1269719--1269948 Score: 343
Period size: 127 Copynumber: 1.8 Consensus size: 127
1269709 TGCTTGTTAG
** * * *
1269719 CTTTAACCCTAGAGACTTTCCTACCCTTAGTCTGCCTGTTGGCTTTGACCTTAAAGACTACCTCA
1 CTTTAACCCTAGAGACTTTCCTACCCCCAGTCTGCATGTCGGCTTTGACCCTAAAGACTACCTCA
* *
1269784 TCTAAAGTCTGCCTATCGGCTTTGACCTTAGAGACTTTTCCATCTTTTAGTTTGCATGTCGA
66 TCTAAAGTCTACCTATCAGCTTTGACCTTAGAGACTTTTCCATCTTTTAGTTTGCATGTCGA
* * * *
1269846 CTTTGACCCTAGAGACTTTCCTACCCCCAGTCTGCATGTCGGCTTTGACCCTAGAGACTGCTTCA
1 CTTTAACCCTAGAGACTTTCCTACCCCCAGTCTGCATGTCGGCTTTGACCCTAAAGACTACCTCA
* *
1269911 TCTAAAGTCTACCTATCAGTTTTGACCTTGGAGACTTT
66 TCTAAAGTCTACCTATCAGCTTTGACCTTAGAGACTTT
1269949 CCTACCCTCA
Statistics
Matches: 90, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
127 90 1.00
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (127 bp):
CTTTAACCCTAGAGACTTTCCTACCCCCAGTCTGCATGTCGGCTTTGACCCTAAAGACTACCTCA
TCTAAAGTCTACCTATCAGCTTTGACCTTAGAGACTTTTCCATCTTTTAGTTTGCATGTCGA
Found at i:1269913 original size:85 final size:85
Alignment explanation
Indices: 1269789--1270032 Score: 226
Period size: 84 Copynumber: 2.9 Consensus size: 85
1269779 CCTCATCTAA
* * ** * * *
1269789 AGTCTGCCTATCGGCTTTGACCTTAGAGACT-TTTCCATCTTTTAGTTTGCATGTC-GACTTTGA
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCTT-CATCTTAAAGTCTACATATCAG-CTTTGA
1269852 CCCTAGAGACTTTCCTACCCCC
64 CCCTAGAGACTTTCCTACCCCC
* * * *
1269874 AGTCTGCATGTCGGCTTTGACCCTAGAGACTGCTTCATC-TAAAGTCTACCTATCAGTTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCTTCATCTTAAAGTCTACATATCAGCTTTGACC
* * *
1269938 TTGGAGACTTTCCTACCCTC
66 CTAGAGACTTTCCTACCCCC
* * * * * * * *
1269958 AGTCTACCTGTCAGCTTTGACCTTGGAGACTGCCTCATC-TAAAGTTTGCCTATCCGCTTTGACC
1 AGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCTTCATCTTAAAGTCTACATATCAGCTTTGACC
* *
1270022 TTGGAGACTTT
66 CTAGAGACTTT
1270033 TCCATCTTTT
Statistics
Matches: 133, Mismatches: 24, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
84 98 0.74
85 33 0.25
86 2 0.02
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (85 bp):
AGTCTGCCTGTCGGCTTTGACCTTAGAGACTGCTTCATCTTAAAGTCTACATATCAGCTTTGACC
CTAGAGACTTTCCTACCCCC
Found at i:1269914 original size:211 final size:211
Alignment explanation
Indices: 1269629--1270081 Score: 602
Period size: 211 Copynumber: 2.1 Consensus size: 211
1269619 AAAGTCTACC
* * * * * *
1269629 TGTCGACTTTGACCCTGGAGACGTTT-CTACCCCTAATCTGCCTGTTGGCTTTGACCTTGGAGAC
1 TGTCGACTTTGACCCTAGAGAC-TTTCCTACCCCCAATCTGCATGTCGGCTTTGACCCTAGAGAC
* * * * * *
1269693 TGCCTCATCTAAAATCTGCTTGTTAGCTTTAACCCTAGAGACTTTCCTACCCTTAGTCTGCCTGT
65 TGCCTCATCTAAAATCTACCTATCAGCTTTAACCCTAGAGACTTTCCTACCCTCAGTCTACCTGT
** *
1269758 TGGCTTTGACCTTAAAGACTACCTCATCTAAAGTCTGCCTATCGGCTTTGACCTTAGAGACTTTT
130 CAGCTTTGACCTTAAAGACTACCTCATCTAAAGTCTGCCTATCCGCTTTGACCTTAGAGACTTTT
*
1269823 CCATCTTTTAGTTTGCA
195 CCATCTTTTAGTCTGCA
*
1269840 TGTCGACTTTGACCCTAGAGACTTTCCTACCCCCAGTCTGCATGTCGGCTTTGACCCTAGAGACT
1 TGTCGACTTTGACCCTAGAGACTTTCCTACCCCCAATCTGCATGTCGGCTTTGACCCTAGAGACT
* * * * * *
1269905 GCTTCATCTAAAGTCTACCTATCAGTTTTGACCTTGGAGACTTTCCTACCCTCAGTCTACCTGTC
66 GCCTCATCTAAAATCTACCTATCAGCTTTAACCCTAGAGACTTTCCTACCCTCAGTCTACCTGTC
** * * *
1269970 AGCTTTGACCTTGGAGACTGCCTCATCTAAAGTTTGCCTATCCGCTTTGACCTTGGAGACTTTTC
131 AGCTTTGACCTTAAAGACTACCTCATCTAAAGTCTGCCTATCCGCTTTGACCTTAGAGACTTTTC
* *
1270035 CATCTTTTTGTCTGCT
196 CATCTTTTAGTCTGCA
* *
1270051 TGTAGACTTTGACCCTAGAGACTTTCTTACC
1 TGTCGACTTTGACCCTAGAGACTTTCCTACC
1270082 TTCAGTTTGC
Statistics
Matches: 209, Mismatches: 32, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
210 3 0.01
211 206 0.99
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (211 bp):
TGTCGACTTTGACCCTAGAGACTTTCCTACCCCCAATCTGCATGTCGGCTTTGACCCTAGAGACT
GCCTCATCTAAAATCTACCTATCAGCTTTAACCCTAGAGACTTTCCTACCCTCAGTCTACCTGTC
AGCTTTGACCTTAAAGACTACCTCATCTAAAGTCTGCCTATCCGCTTTGACCTTAGAGACTTTTC
CATCTTTTAGTCTGCA
Found at i:1269975 original size:84 final size:84
Alignment explanation
Indices: 1269846--1270032 Score: 257
Period size: 84 Copynumber: 2.2 Consensus size: 84
1269836 TGCATGTCGA
* * * * *
1269846 CTTTGACCCTAGAGACTTTCCTACCCCCAGTCTGCATGTCGGCTTTGACCCTAGAGACTGCTTCA
1 CTTTGACCTTGGAGACTTTCCTACCCCCAGTCTACATGTCAGCTTTGACCCTAGAGACTGCCTCA
1269911 TCTAAAGTCTACCTATCAG
66 TCTAAAGTCTACCTATCAG
* * * * *
1269930 TTTTGACCTTGGAGACTTTCCTACCCTCAGTCTACCTGTCAGCTTTGACCTTGGAGACTGCCTCA
1 CTTTGACCTTGGAGACTTTCCTACCCCCAGTCTACATGTCAGCTTTGACCCTAGAGACTGCCTCA
* * *
1269995 TCTAAAGTTTGCCTATCCG
66 TCTAAAGTCTACCTATCAG
1270014 CTTTGACCTTGGAGACTTT
1 CTTTGACCTTGGAGACTTT
1270033 TCCATCTTTT
Statistics
Matches: 89, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
84 89 1.00
ACGTcount: A:0.19, C:0.30, G:0.18, T:0.33
Consensus pattern (84 bp):
CTTTGACCTTGGAGACTTTCCTACCCCCAGTCTACATGTCAGCTTTGACCCTAGAGACTGCCTCA
TCTAAAGTCTACCTATCAG
Found at i:1270039 original size:42 final size:41
Alignment explanation
Indices: 1269676--1270039 Score: 169
Period size: 42 Copynumber: 8.6 Consensus size: 41
1269666 CTGCCTGTTG
* ** * * * *
1269676 GCTTTGACCTTGGAGACTGCCTCATCTAAAATCTGCTTGTTA
1 GCTTTGACCTTAGAGACTTTC-CATCTAAAGTCTGCCTATCA
* * * * * **
1269718 GCTTTAACCCTAGAGACTTTCCTACCCT-TAGTCTGCCTGTTG
1 GCTTTGACCTTAGAGACTTTCC-A-TCTAAAGTCTGCCTATCA
* ** *
1269760 GCTTTGACCTTAAAGACTACCTCATCTAAAGTCTGCCTATCG
1 GCTTTGACCTTAGAGACTTTC-CATCTAAAGTCTGCCTATCA
** * * *
1269802 GCTTTGACCTTAGAGACTTTTCCATCTTTTAGTTTGCATGTC-
1 GCTTTGACCTTAGAGAC-TTTCCATC-TAAAGTCTGCCTATCA
* * *** * * *
1269844 GACTTTGACCCTAGAGACTTTCCTACCCCCAGTCTGCATGTCG
1 G-CTTTGACCTTAGAGACTTTCC-ATCTAAAGTCTGCCTATCA
* *
1269887 GCTTTGACCCTAGAGACTGCTT-CATCTAAAGTCTACCTATCA
1 GCTTTGACCTTAGAGACT--TTCCATCTAAAGTCTGCCTATCA
* * * * * *
1269929 GTTTTGACCTTGGAGACTTTCCTACCCT-CAGTCTACCTGTCA
1 GCTTTGACCTTAGAGACTTTCC-A-TCTAAAGTCTGCCTATCA
* ** * *
1269971 GCTTTGACCTTGGAGACTGCCTCATCTAAAGTTTGCCTATCC
1 GCTTTGACCTTAGAGACTTTC-CATCTAAAGTCTGCCTATCA
*
1270013 GCTTTGACCTTGGAGACTTTTCCATCT
1 GCTTTGACCTTAGAGAC-TTTCCATCT
1270040 TTTTGTCTGC
Statistics
Matches: 247, Mismatches: 58, Indels: 34
0.73 0.17 0.10
Matches are distributed among these distances:
40 2 0.01
41 6 0.02
42 198 0.80
43 39 0.16
44 2 0.01
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (41 bp):
GCTTTGACCTTAGAGACTTTCCATCTAAAGTCTGCCTATCA
Found at i:1270320 original size:42 final size:42
Alignment explanation
Indices: 1270279--1270719 Score: 209
Period size: 42 Copynumber: 10.5 Consensus size: 42
1270269 TCCGTCTATT
* * * * *
1270279 GGCTTTGACCTTGGAGACTTTCCTACCCTTAGTCTACCTATT
1 GGCTTTGACCTTAGAGACTTTCCTACCCTCAGTCTGCCTGTC
* * *
1270321 GGTTTTGACCCTAGAGACTTTCCTACCCTCATTCTGCCTGTC
1 GGCTTTGACCTTAGAGACTTTCCTACCCTCAGTCTGCCTGTC
* * ** ** * *
1270363 AGCTTTGACCCTAGAGACTTTTCC-ATCATTTTGTCTACCTATC
1 GGCTTTGACCTTAGAGAC-TTTCCTA-CCCTCAGTCTGCCTGTC
* * *
1270406 GACTTTGACCATAGAGACTTTCCTACCCTCAGTCTGCCTCTC
1 GGCTTTGACCTTAGAGACTTTCCTACCCTCAGTCTGCCTGTC
* * * *
1270448 GACTTTGACTTTAGAGACTTTCCTACCATCAGTCTACCTGTC
1 GGCTTTGACCTTAGAGACTTTCCTACCCTCAGTCTGCCTGTC
** * * * * * ** * *
1270490 GTTTTTGACCTTGGA-AATTGCCT-CATCTAAAACCTGCTTGTT
1 GGCTTTGACCTTAGAGACTTTCCTAC-CCT-CAGTCTGCCTGTC
* * *
1270532 GGCTTTGACC-TAGGAGACTTTCCAACCCTCAATCTGCCTGTT
1 GGCTTTGACCTTA-GAGACTTTCCTACCCTCAGTCTGCCTGTC
* * * * *
1270574 GGCTTTGACCCTGGAGACTACTT-C-A-TCTAAAGTCTGCCTGTT
1 GGCTTTGACCTTAGAGACT--TTCCTACCCT-CAGTCTGCCTGTC
* ** * * *
1270616 GCCTTTGACAC-TAGAGACTTTTCC-ATCTTTTTA-TCTGCTTGTT
1 GGCTTTGAC-CTTAGAGAC-TTTCCTA-C-CCTCAGTCTGCCTGTC
* * * * *
1270659 GGCTTTGACCCTAGAGACTTTCTTACCTTTAGTCTGCTTGTC
1 GGCTTTGACCTTAGAGACTTTCCTACCCTCAGTCTGCCTGTC
* *
1270701 GACTTTGACCCTAGAGACT
1 GGCTTTGACCTTAGAGACT
1270720 GCCTCATCTA
Statistics
Matches: 309, Mismatches: 69, Indels: 42
0.74 0.16 0.10
Matches are distributed among these distances:
40 1 0.00
41 16 0.05
42 219 0.71
43 67 0.22
44 4 0.01
45 2 0.01
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.37
Consensus pattern (42 bp):
GGCTTTGACCTTAGAGACTTTCCTACCCTCAGTCTGCCTGTC
Found at i:1270328 original size:84 final size:84
Alignment explanation
Indices: 1270113--1270677 Score: 263
Period size: 84 Copynumber: 6.7 Consensus size: 84
1270103 AACCTATCGA
* * * *
1270113 CTTTGACCTTAGAGACTTTCCTACCCTTACTATGCTTGTTGGCTTTGACCTTGGAGACTACCTCA
1 CTTTGACCTTAGAGACTTTCCTACCCTTAATCTGCCTGTTGGCTTTGACCCTGGAGACTACCTCA
*
1270178 TCTAAAGTCTGCCTATTAG
66 TCTAAAGTCCGCCTATTAG
* * * * * * * **
1270197 TTTTGACGC-TAAAGACTTTTCTACCCTCAATCTGCCTGTCGACTTTGACCCTGGAGATTGTCTC
1 CTTTGAC-CTTAGAGACTTTCCTACCCTTAATCTGCCTGTTGGCTTTGACCCTGGAGACTACCTC
* * *
1270261 ATGTAAAGTCCGTCTATTGG
65 ATCTAAAGTCCGCCTATTAG
* * * * * * *
1270281 CTTTGACCTTGGAGACTTTCCTACCCTTAGTCTACCTATTGGTTTTGACCCTAGAGACTTTCCT-
1 CTTTGACCTTAGAGACTTTCCTACCCTTAATCTGCCTGTTGGCTTTGACCCTGGAGAC-TACCTC
* * * * * *
1270345 ACCCT-CATTCTGCCTGTCAG
65 A-TCTAAAGTCCGCCTATTAG
* ** ** * * * * * * *
1270365 CTTTGACCCTAGAGACTTTTCC-ATCATTTTGTCTACCTATCGACTTTGACCATAGAGACTTTCC
1 CTTTGACCTTAGAGAC-TTTCCTA-CCCTTAATCTGCCTGTTGGCTTTGACCCTGGAGAC-TACC
* * * * *
1270429 T-ACCCT-CAGTCTGCCT-CTCG
63 TCA-TCTAAAGTCCGCCTATTAG
* * * * * * ** * * * *
1270449 ACTTTGACTTTAGAGACTTTCCTACCATCAGTCTACCTGTCGTTTTTGACCTTGGAAATTGCCTC
1 -CTTTGACCTTAGAGACTTTCCTACCCTTAATCTGCCTGTTGGCTTTGACCCTGGAGACTACCTC
* * * *
1270514 ATCTAAA-ACCTGCTTGTTGG
65 ATCTAAAGTCC-GCCTATTAG
* * *
1270534 CTTTGACC-TAGGAGACTTTCCAACCCTCAATCTGCCTGTTGGCTTTGACCCTGGAGACTACTTC
1 CTTTGACCTTA-GAGACTTTCCTACCCTTAATCTGCCTGTTGGCTTTGACCCTGGAGACTACCTC
* *
1270598 ATCTAAAGTCTGCCTGTT-G
65 ATCTAAAGTCCGCCTATTAG
** * * *
1270617 CCTTTGACAC-TAGAGACTTTTCC-ATCTTTTTATCTGCTTGTTGGCTTTGACCCTAGAGACT
1 -CTTTGAC-CTTAGAGAC-TTTCCTA-CCCTTAATCTGCCTGTTGGCTTTGACCCTGGAGACT
1270678 TTCTTACCTT
Statistics
Matches: 366, Mismatches: 97, Indels: 35
0.73 0.19 0.07
Matches are distributed among these distances:
83 11 0.03
84 241 0.66
85 114 0.31
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (84 bp):
CTTTGACCTTAGAGACTTTCCTACCCTTAATCTGCCTGTTGGCTTTGACCCTGGAGACTACCTCA
TCTAAAGTCCGCCTATTAG
Found at i:1270339 original size:126 final size:124
Alignment explanation
Indices: 1270151--1270592 Score: 365
Period size: 126 Copynumber: 3.5 Consensus size: 124
1270141 ACTATGCTTG
* * * * * * *
1270151 TTGGCTTTGACCTTGGAGAC-TACCT-CATCTAAAGTCTGCCTATTAGTTTTGACGCTAAAGACT
1 TTGGCTTTGACCTTGGAGACTTTCCTAC-CCT-CAGTCTGCCTATTGGCTTTGACCCTAGAGACT
*
1270214 TTTCTACCCTCAATCTGCCTGTCGACTTTGACCCTGGAGATTGTCTCATGTAAAGTCCGTCTA
64 TTCCTACCCTCAATCTGCCTGTCGACTTTGACCCTGGAGATTGTCTCAT-TAAAGTCC-TCTA
* * *
1270277 TTGGCTTTGACCTTGGAGACTTTCCTACCCTTAGTCTACCTATTGGTTTTGACCCTAGAGACTTT
1 TTGGCTTTGACCTTGGAGACTTTCCTACCCTCAGTCTGCCTATTGGCTTTGACCCTAGAGACTTT
* * * **
1270342 CCTACCCTCATTCTGCCTGTC-AGCTTTGACCCTAGAGACTTTTCCATCATT-TTGT-CTACCTA
66 CCTACCCTCAATCTGCCTGTCGA-CTTTGACCCTGGAGA-TTGT-C-TCATTAAAGTCCT--CTA
* * * * * * * **
1270404 TCGACTTTGACCATAGAGACTTTCCTACCCTCAGTCTGCCTCTCGACTTTGACTTTAGAGACTTT
1 TTGGCTTTGACCTTGGAGACTTTCCTACCCTCAGTCTGCCTATTGGCTTTGACCCTAGAGACTTT
* * * ** * * * * *
1270469 CCTACCATCAGTCTACCTGTCGTTTTTGACCTTGGAAATTGCCTCATCTAAA-ACCTGCTTG
66 CCTACCCTCAATCTGCCTGTCGACTTTGACCCTGGAGATTGTCTCAT-TAAAGTCCT-C-TA
* * * * *
1270530 TTGGCTTTGACCTAGGAGACTTTCCAACCCTCAATCTGCCTGTTGGCTTTGACCCTGGAGACT
1 TTGGCTTTGACCTTGGAGACTTTCCTACCCTCAGTCTGCCTATTGGCTTTGACCCTAGAGACT
1270593 ACTTCATCTA
Statistics
Matches: 250, Mismatches: 53, Indels: 26
0.76 0.16 0.08
Matches are distributed among these distances:
124 4 0.02
125 5 0.02
126 138 0.55
127 96 0.38
128 3 0.01
129 4 0.02
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (124 bp):
TTGGCTTTGACCTTGGAGACTTTCCTACCCTCAGTCTGCCTATTGGCTTTGACCCTAGAGACTTT
CCTACCCTCAATCTGCCTGTCGACTTTGACCCTGGAGATTGTCTCATTAAAGTCCTCTA
Found at i:1270422 original size:85 final size:85
Alignment explanation
Indices: 1270310--1270468 Score: 230
Period size: 85 Copynumber: 1.9 Consensus size: 85
1270300 CCTACCCTTA
* ** * * *
1270310 GTCTACCTATTGGTTTTGACCCTAGAGACTTTCCTACCCTCATTCTGCCTGTC-AGCTTTGACCC
1 GTCTACCTATCGACTTTGACCATAGAGACTTTCCTACCCTCAGTCTGCCTCTCGA-CTTTGACCC
1270374 TAGAGACTTTTCCATCATTTT
65 TAGAGACTTTTCCATCATTTT
**
1270395 GTCTACCTATCGACTTTGACCATAGAGACTTTCCTACCCTCAGTCTGCCTCTCGACTTTGACTTT
1 GTCTACCTATCGACTTTGACCATAGAGACTTTCCTACCCTCAGTCTGCCTCTCGACTTTGACCCT
1270460 AGAGACTTT
66 AGAGACTTT
1270469 CCTACCATCA
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
85 64 0.98
86 1 0.02
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.37
Consensus pattern (85 bp):
GTCTACCTATCGACTTTGACCATAGAGACTTTCCTACCCTCAGTCTGCCTCTCGACTTTGACCCT
AGAGACTTTTCCATCATTTT
Found at i:1270693 original size:85 final size:85
Alignment explanation
Indices: 1270563--1270719 Score: 208
Period size: 85 Copynumber: 1.8 Consensus size: 85
1270553 CCAACCCTCA
* * * *
1270563 ATCTGCCTGTTGGCTTTGACCCTGGAGACTACTTCATCTAAAGTCTGCCTGTTGCCTTTGACACT
1 ATCTGCCTGTTGGCTTTGACCCTAGAGACTACTTCACCTAAAGTCTGCCTGTCGACTTTGACACT
1270628 AGAGACTTTTCCATCTTTTT
66 AGAGACTTTTCCATCTTTTT
* * ** * *
1270648 ATCTGCTTGTTGGCTTTGACCCTAGAGACTTTCTT-ACCTTTAGTCTGCTTGTCGACTTTGACCC
1 ATCTGCCTGTTGGCTTTGACCCTAGAGAC-TACTTCACCTAAAGTCTGCCTGTCGACTTTGACAC
1270712 TAGAGACT
65 TAGAGACT
1270720 GCCTCATCTA
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
85 57 0.93
86 4 0.07
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.39
Consensus pattern (85 bp):
ATCTGCCTGTTGGCTTTGACCCTAGAGACTACTTCACCTAAAGTCTGCCTGTCGACTTTGACACT
AGAGACTTTTCCATCTTTTT
Found at i:1270750 original size:42 final size:42
Alignment explanation
Indices: 1270149--1270762 Score: 170
Period size: 42 Copynumber: 14.6 Consensus size: 42
1270139 TTACTATGCT
* * *
1270149 TGTTGGCTTTGACCTTGGAGACTACCTCATCTAAAGTCTGCC
1 TGTTGGCTTTGACCCTAGAGACTTCCTCATCTAAAGTCTGCC
* * * * * * * *
1270191 TATTAGTTTTGACGCTAAAGACTT-TTCTACCCTCAA-TCTGCC
1 TGTTGGCTTTGACCCTAGAGACTTCCTC-A-TCTAAAGTCTGCC
* * * * * * *
1270233 TGTCGACTTTGACCCTGGAGA-TTGTCTCATGTAAAGTCCGTC
1 TGTTGGCTTTGACCCTAGAGACTT-CCTCATCTAAAGTCTGCC
* * * * * *
1270275 TATTGGCTTTGACCTTGGAGACTTTCCT-ACCCT-TAGTCTACC
1 TGTTGGCTTTGACCCTAGAGAC-TTCCTCA-TCTAAAGTCTGCC
* * * * *
1270317 TATTGGTTTTGACCCTAGAGACTTTCCT-ACCCT-CATTCTGCC
1 TGTTGGCTTTGACCCTAGAGAC-TTCCTCA-TCTAAAGTCTGCC
** ** *
1270359 TGTCAGCTTTGACCCTAGAGACTTTTCCATCAT-T-TTGTCTACC
1 TGTTGGCTTTGACCCTAGAGAC--TTCC-TCATCTAAAGTCTGCC
* * * * * *
1270402 TATCGACTTTGACCATAGAGACTTTCCT-ACCCT-CAGTCTGCC
1 TGTTGGCTTTGACCCTAGAGAC-TTCCTCA-TCTAAAGTCTGCC
* * * ** *
1270444 TCTCGACTTTGACTTTAGAGACTTTCCTACCATC---AGTCTACC
1 TGTTGGCTTTGACCCTAGAGAC-TTCCT--CATCTAAAGTCTGCC
* ** * * * ** *
1270486 TGTCGTTTTTGACCTTGGA-AATTGCCTCATCTAAAACCTGCT
1 TGTTGGCTTTGACCCTAGAGACTT-CCTCATCTAAAGTCTGCC
* * *
1270528 TGTTGGCTTTGA-CCTAGGAGACTTTCC-AACCCTCAA-TCTGCC
1 TGTTGGCTTTGACCCTA-GAGAC-TTCCTCA-TCTAAAGTCTGCC
* * *
1270570 TGTTGGCTTTGACCCTGGAGACTACTTCATCTAAAGTCTGCC
1 TGTTGGCTTTGACCCTAGAGACTTCCTCATCTAAAGTCTGCC
* * * ** *
1270612 TGTTGCCTTTGACACTAGAGACTTTTCCATC-TTTTTA-TCTGCT
1 TGTTGGCTTTGACCCTAGAGAC--TTCC-TCATCTAAAGTCTGCC
* * * ** *
1270655 TGTTGGCTTTGACCCTAGAGACTTTCTTACCTTTAGTCTGCT
1 TGTTGGCTTTGACCCTAGAGACTTCCTCATCTAAAGTCTGCC
* * *
1270697 TGTCGACTTTGACCCTAGAGACTGCCTCATCTAAAGTCTGCC
1 TGTTGGCTTTGACCCTAGAGACTTCCTCATCTAAAGTCTGCC
* * * *
1270739 TGTTAGTTTTGACCTTGGAGACTT
1 TGTTGGCTTTGACCCTAGAGACTT
1270763 TTCTATCGAC
Statistics
Matches: 418, Mismatches: 122, Indels: 64
0.69 0.20 0.11
Matches are distributed among these distances:
39 4 0.01
40 4 0.01
41 27 0.06
42 295 0.71
43 73 0.17
44 11 0.03
45 4 0.01
ACGTcount: A:0.19, C:0.27, G:0.17, T:0.37
Consensus pattern (42 bp):
TGTTGGCTTTGACCCTAGAGACTTCCTCATCTAAAGTCTGCC
Found at i:1270750 original size:127 final size:127
Alignment explanation
Indices: 1270523--1270765 Score: 321
Period size: 127 Copynumber: 1.9 Consensus size: 127
1270513 CATCTAAAAC
* * *
1270523 CTGCTTGTTGGCTTTGACCTAGGAGACTTTCCAACCCTCAATCTGCCTGTTGGCTTTGACCCTGG
1 CTGCTTGTTGGCTTTGACCTAGGAGACTTTCCAACCCTCAATCTGCCTGTCGACTTTGACCCTAG
*
1270588 AGACTACTTCATCTAAAGTCTGCCTGTTGCCTTTGACAC-TAGAGACTTTTCCATCTTTTTAT
66 AGACTACCTCATCTAAAGTCTGCCTGTTGCCTTTGAC-CTTAGAGACTTTTCCATCTTTTTAT
** * * * *
1270650 CTGCTTGTTGGCTTTGACCCTA-GAGACTTTCTTACCTTTAGTCTGCTTGTCGACTTTGACCCTA
1 CTGCTTGTTGGCTTTGA-CCTAGGAGACTTTCCAACCCTCAATCTGCCTGTCGACTTTGACCCTA
* * *
1270714 GAGACTGCCTCATCTAAAGTCTGCCTGTTAG-TTTTGACCTTGGAGACTTTTC
65 GAGACTACCTCATCTAAAGTCTGCCTGTT-GCCTTTGACCTTAGAGACTTTTC
1270766 TATCGACTTA
Statistics
Matches: 100, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
126 1 0.01
127 94 0.94
128 5 0.05
ACGTcount: A:0.17, C:0.26, G:0.19, T:0.38
Consensus pattern (127 bp):
CTGCTTGTTGGCTTTGACCTAGGAGACTTTCCAACCCTCAATCTGCCTGTCGACTTTGACCCTAG
AGACTACCTCATCTAAAGTCTGCCTGTTGCCTTTGACCTTAGAGACTTTTCCATCTTTTTAT
Found at i:1270751 original size:253 final size:252
Alignment explanation
Indices: 1270277--1270757 Score: 553
Period size: 253 Copynumber: 1.9 Consensus size: 252
1270267 AGTCCGTCTA
* * * * *
1270277 TTGGCTTTGACCTTGGAGACTTTCCTACCCTTAGTCTACCTATTGGTTTTGACCCTAGAGACTTT
1 TTGGCTTTGACCTAGGAGACTTTCCAACCCTCAATCTACCTATTGGCTTTGACCCTAGAGACTTT
* * * *
1270342 CCTACCCTCATTCTGCCTGTCAGCTTTGACCCTAGAGACTTTTCCATCATTTTGTCTACCTATCG
66 CCTACCCTAAGTCTGCCTGTCAGCTTTGACACTAGAGACTTTTCCATCATTTTATCTACCTATCG
** *
1270407 ACTTTGACCATAGAGACTTTCCTACCCTCAGTCTGCCTCTCGACTTTGACTTTAGAGACTTTCCT
131 ACTTTGACCATAGAGACTTTCCTACCCTCAGTCTGCCTCTCGACTTTGACCCTAGAGACTTGCCT
*
1270472 ACCATCAGTCTACCTGTCGTTTTTGACCTTGGAAATTGCCTCATCTAAAACCTGCTTG
196 A-CATCAGTCTACCTGTAGTTTTTGACCTTGGAAATTGCCTCATCTAAAACCTGCTTG
* * *
1270530 TTGGCTTTGACCTAGGAGACTTTCCAACCCTCAATCTGCCTGTTGGCTTTGACCCTGGAGACTAC
1 TTGGCTTTGACCTAGGAGACTTTCCAACCCTCAATCTACCTATTGGCTTTGACCCTAGAGACT--
* * * * *
1270595 TT-C-A-TCTAAAGTCTGCCTGT-TGCCTTTGACACTAGAGACTTTTCCATCTTTTTATCTGCTT
64 TTCCTACCCT-AAGTCTGCCTGTCAG-CTTTGACACTAGAGACTTTTCCATCATTTTATCTACCT
* * * * * * * * *
1270656 GTTGGCTTTGACCCTAGAGACTTTCTTACCTTTAGTCTGCTTGTCGACTTTGACCCTAGAGAC-T
127 ATCGACTTTGACCATAGAGACTTTCCTACCCTCAGTCTGCCTCTCGACTTTGACCCTAGAGACTT
*
1270720 GCCT-CATCTAAAGTCTGCCTGTTAG-TTTTGACCTTGGA
192 GCCTACATC---AGTCTACCTG-TAGTTTTTGACCTTGGA
1270758 GACTTTTCTA
Statistics
Matches: 189, Mismatches: 31, Indels: 16
0.80 0.13 0.07
Matches are distributed among these distances:
250 4 0.02
252 7 0.04
253 173 0.92
254 3 0.02
255 2 0.01
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.37
Consensus pattern (252 bp):
TTGGCTTTGACCTAGGAGACTTTCCAACCCTCAATCTACCTATTGGCTTTGACCCTAGAGACTTT
CCTACCCTAAGTCTGCCTGTCAGCTTTGACACTAGAGACTTTTCCATCATTTTATCTACCTATCG
ACTTTGACCATAGAGACTTTCCTACCCTCAGTCTGCCTCTCGACTTTGACCCTAGAGACTTGCCT
ACATCAGTCTACCTGTAGTTTTTGACCTTGGAAATTGCCTCATCTAAAACCTGCTTG
Found at i:1271256 original size:11 final size:12
Alignment explanation
Indices: 1271228--1271257 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
1271218 AAGAAGAAAT
1271228 AAAAAATTATTA
1 AAAAAATTATTA
1271240 AAAAAATT-TTA
1 AAAAAATTATTA
1271251 AAAAAAT
1 AAAAAAT
1271258 CCAAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAAAATTATTA
Found at i:1271275 original size:20 final size:20
Alignment explanation
Indices: 1271252--1271290 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1271242 AAAATTTTAA
*
1271252 AAAAATCCAAAAATAAAATC
1 AAAAATCCAAAAAAAAAATC
*
1271272 AAAAATTCAAAAAAAAAAT
1 AAAAATCCAAAAAAAAAAT
1271291 GTGAAAGAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.10, G:0.00, T:0.15
Consensus pattern (20 bp):
AAAAATCCAAAAAAAAAATC
Found at i:1271771 original size:45 final size:45
Alignment explanation
Indices: 1271705--1271915 Score: 352
Period size: 45 Copynumber: 4.7 Consensus size: 45
1271695 AATGATGAAC
* * *
1271705 ACAAAGCAACA-TGGAATAGCAAAGCAATAATGAAGAAAGTGGAAG
1 ACAAAGCAA-AGTGGAACAGCAAAGCAACAAGGAAGAAAGTGGAAG
1271750 ACAAAGCAAAGTGGAACAGCAAAGCAACAAGGAAGAAAGTGGAAG
1 ACAAAGCAAAGTGGAACAGCAAAGCAACAAGGAAGAAAGTGGAAG
*
1271795 ACAAAGCAAAGTGGAACAGCAAAGCAACAATGAAGAAAGTGGAAG
1 ACAAAGCAAAGTGGAACAGCAAAGCAACAAGGAAGAAAGTGGAAG
* *
1271840 ACAAAGCAACGTGGAACAGCAAAGCAATAAGGAAGAAAGTGGAAG
1 ACAAAGCAAAGTGGAACAGCAAAGCAACAAGGAAGAAAGTGGAAG
1271885 ACAAAGCAAAGTGGAACAGCAAAGCAACAAG
1 ACAAAGCAAAGTGGAACAGCAAAGCAACAAG
1271916 TTGAAAAATG
Statistics
Matches: 156, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
44 1 0.01
45 155 0.99
ACGTcount: A:0.53, C:0.14, G:0.27, T:0.07
Consensus pattern (45 bp):
ACAAAGCAAAGTGGAACAGCAAAGCAACAAGGAAGAAAGTGGAAG
Found at i:1271774 original size:18 final size:17
Alignment explanation
Indices: 1271740--1271776 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1271730 AATAATGAAG
*
1271740 AAAGTGGAAGACAAAGC
1 AAAGTGGAACACAAAGC
1271757 AAAGTGGAACAGCAAAGC
1 AAAGTGGAACA-CAAAGC
1271775 AA
1 AA
1271777 CAAGGAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.54, C:0.14, G:0.27, T:0.05
Consensus pattern (17 bp):
AAAGTGGAACACAAAGC
Found at i:1271819 original size:18 final size:17
Alignment explanation
Indices: 1271785--1271821 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1271775 AACAAGGAAG
*
1271785 AAAGTGGAAGACAAAGC
1 AAAGTGGAACACAAAGC
1271802 AAAGTGGAACAGCAAAGC
1 AAAGTGGAACA-CAAAGC
1271820 AA
1 AA
1271822 CAATGAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.54, C:0.14, G:0.27, T:0.05
Consensus pattern (17 bp):
AAAGTGGAACACAAAGC
Found at i:1271909 original size:18 final size:17
Alignment explanation
Indices: 1271875--1271911 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1271865 AATAAGGAAG
*
1271875 AAAGTGGAAGACAAAGC
1 AAAGTGGAACACAAAGC
1271892 AAAGTGGAACAGCAAAGC
1 AAAGTGGAACA-CAAAGC
1271910 AA
1 AA
1271912 CAAGTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.54, C:0.14, G:0.27, T:0.05
Consensus pattern (17 bp):
AAAGTGGAACACAAAGC
Found at i:1272229 original size:40 final size:40
Alignment explanation
Indices: 1272144--1272269 Score: 126
Period size: 40 Copynumber: 3.1 Consensus size: 40
1272134 ACAACTCCAA
* * * * * *
1272144 TAGCTCCAATGGTAGCCTCCAGCAGCTTAACAACCACTAA
1 TAGCTCCCACGGTAGCCTCTAGCAGCTTAGCAACCACGAG
* * *
1272184 CAGCTCCCACGGTAACCTCTAGCAGCTTAGCAACTACGAG
1 TAGCTCCCACGGTAGCCTCTAGCAGCTTAGCAACCACGAG
* * * * *
1272224 TAGCTCCCACAGTAGCTTTTAGCAGCTCAGCAACCATGAG
1 TAGCTCCCACGGTAGCCTCTAGCAGCTTAGCAACCACGAG
1272264 TAGCTC
1 TAGCTC
1272270 TTGTAGCATC
Statistics
Matches: 69, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
40 69 1.00
ACGTcount: A:0.29, C:0.33, G:0.18, T:0.21
Consensus pattern (40 bp):
TAGCTCCCACGGTAGCCTCTAGCAGCTTAGCAACCACGAG
Found at i:1272435 original size:26 final size:24
Alignment explanation
Indices: 1272405--1272454 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
1272395 TCGGGCAAGG
*
1272405 AAGAAAAATAGCAAATAGCTAGCAGC
1 AAGAAAAATAAC-AATAG-TAGCAGC
*
1272431 AAGAACAATAACAATAGTAGCAGC
1 AAGAAAAATAACAATAGTAGCAGC
1272455 TGCTGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 7 0.32
25 5 0.23
26 10 0.45
ACGTcount: A:0.54, C:0.16, G:0.18, T:0.12
Consensus pattern (24 bp):
AAGAAAAATAACAATAGTAGCAGC
Found at i:1274510 original size:100 final size:99
Alignment explanation
Indices: 1274337--1274535 Score: 371
Period size: 100 Copynumber: 2.0 Consensus size: 99
1274327 TTCACGACAT
*
1274337 AATAAATTTCTTTTAGGGGAATTGTGATTAAATACTACATATTGAATAATTAACACTTAAATTGA
1 AATAAATTTCTTTTAGGGGAATTGTGATTAAATACTACATATTGAATAATTAAAACTTAAATTGA
1274402 TGCGTGATCAATAAGGTACCAATTTTTGGGCACAA
66 TGCGTGATCAATAAGGTA-CAATTTTTGGGCACAA
*
1274437 AATAAATTTCTTTTGGGGGAATTGTGATTAAATACTACATATTGAATAATTAAAACTTAAATTGA
1 AATAAATTTCTTTTAGGGGAATTGTGATTAAATACTACATATTGAATAATTAAAACTTAAATTGA
1274502 TGCGTGATCAATAAGGTACAATTTTTGGGCACAA
66 TGCGTGATCAATAAGGTACAATTTTTGGGCACAA
1274536 CGAGAGGGTC
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
99 16 0.16
100 81 0.84
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (99 bp):
AATAAATTTCTTTTAGGGGAATTGTGATTAAATACTACATATTGAATAATTAAAACTTAAATTGA
TGCGTGATCAATAAGGTACAATTTTTGGGCACAA
Found at i:1278033 original size:21 final size:20
Alignment explanation
Indices: 1278004--1278046 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1277994 GGCTAGTGTG
**
1278004 GGGACTGCCCGGTTGTGACCT
1 GGGACTG-CCGGTCATGACCT
*
1278025 GGGAGTGCCGGTCATGACCT
1 GGGACTGCCGGTCATGACCT
1278045 GG
1 GG
1278047 TGATGCTGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.12, C:0.26, G:0.42, T:0.21
Consensus pattern (20 bp):
GGGACTGCCGGTCATGACCT
Found at i:1278501 original size:13 final size:13
Alignment explanation
Indices: 1278485--1278520 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
1278475 AATCCCCCTA
1278485 TATCGATACAGTG
1 TATCGATACAGTG
*
1278498 TATCGATACATTG
1 TATCGATACAGTG
1278511 TATCGATACA
1 TATCGATACA
1278521 AAGAAAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (13 bp):
TATCGATACAGTG
Found at i:1282464 original size:21 final size:21
Alignment explanation
Indices: 1282435--1282479 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1282425 AAGTTTTTAT
*
1282435 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1282455 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1282477 TTT
1 TTT
1282480 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1282637 original size:15 final size:16
Alignment explanation
Indices: 1282613--1282645 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1282603 CAATCTTTTG
1282613 TTCAAGA-TTTTCAAT
1 TTCAAGATTTTTCAAT
*
1282628 TTCAATATTTTTCAAT
1 TTCAAGATTTTTCAAT
1282644 TT
1 TT
1282646 ATTATCTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.30, C:0.12, G:0.03, T:0.55
Consensus pattern (16 bp):
TTCAAGATTTTTCAAT
Found at i:1284704 original size:20 final size:20
Alignment explanation
Indices: 1284679--1284730 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1284669 TACAAGCCAA
** *
1284679 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTGG
1284699 TGTATCGATAC-ATACTTGG
1 TGTATCGATACAATACTTGG
1284718 TGTATCGATACAA
1 TGTATCGATACAA
1284731 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.40
Consensus pattern (20 bp):
TGTATCGATACAATACTTGG
Found at i:1284736 original size:19 final size:18
Alignment explanation
Indices: 1284679--1284736 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 18
1284669 TACAAGCCAA
*
1284679 TGTATCGATACAATTTTTTG
1 TGTATCGATACAA--TTTGG
*
1284699 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
1284718 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
1284737 CTACTGCCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
18 1 0.03
19 19 0.58
20 12 0.36
21 1 0.03
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:1285489 original size:52 final size:51
Alignment explanation
Indices: 1285411--1285547 Score: 177
Period size: 51 Copynumber: 2.7 Consensus size: 51
1285401 TTGCCTGCAA
* * * * *
1285411 GTATCGATACATTGAAGAATTTATCGATTCATTT-GGTTCAAAAACCCAGAAT
1 GTATCAATACAATGAAGAATGTATCGATACATTTAGG-TC-AAAACCCAAAAT
*
1285463 GTATCAATACAATGAAGAATGTATCGATACCTTTAGGTCAAAACCCAAAAT
1 GTATCAATACAATGAAGAATGTATCGATACATTTAGGTCAAAACCCAAAAT
* *
1285514 GGATCAATACAATGAAAAATGTATCGATACATTT
1 GTATCAATACAATGAAGAATGTATCGATACATTT
1285548 TCATTCCAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
51 42 0.56
52 31 0.41
53 2 0.03
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (51 bp):
GTATCAATACAATGAAGAATGTATCGATACATTTAGGTCAAAACCCAAAAT
Found at i:1285628 original size:20 final size:20
Alignment explanation
Indices: 1285583--1285654 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
1285573 GACATGGTCT
***
1285583 TGTATCGATACATTTCAAACA
1 TGTATCGATACATTT-ACTTA
1285604 TGTATCGATACATTTACTTA
1 TGTATCGATACATTTACTTA
* *
1285624 TGTATCAATACATTCACTTA
1 TGTATCGATACATTTACTTA
*
1285644 T-TGTCGATACA
1 TGTATCGATACA
1285655 AATTGTTGAA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 8 0.18
20 21 0.48
21 15 0.34
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATTTACTTA
Found at i:1288555 original size:21 final size:21
Alignment explanation
Indices: 1288531--1288583 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
1288521 TTTTATGATT
1288531 TGTATCGATACAATTA-GTGAA
1 TGTATCGATACAA-TAGGTGAA
1288552 TGTATCGATAC-ATAGGTGAA
1 TGTATCGATACAATAGGTGAA
1288572 TGTATCGATACA
1 TGTATCGATACA
1288584 CATCTCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
19 2 0.07
20 17 0.57
21 11 0.37
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.32
Consensus pattern (21 bp):
TGTATCGATACAATAGGTGAA
Found at i:1296829 original size:13 final size:13
Alignment explanation
Indices: 1296811--1296849 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1296801 TACACAAAGT
1296811 ATGTATCGATACA
1 ATGTATCGATACA
1296824 ATGTATCGATACA
1 ATGTATCGATACA
1296837 ATGTATCGATACA
1 ATGTATCGATACA
1296850 CAAAAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1300904 original size:15 final size:15
Alignment explanation
Indices: 1300884--1300914 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1300874 TAAAAATGTC
*
1300884 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1300899 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1300914 C
1 C
1300915 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1304700 original size:23 final size:21
Alignment explanation
Indices: 1304658--1304700 Score: 50
Period size: 23 Copynumber: 2.0 Consensus size: 21
1304648 GTTTAATGTT
**
1304658 TTTGCTTGACTTTGTGTTTTA
1 TTTGCTTGACTTTGAATTTTA
1304679 TTTGCATTGTACTTTGAATTTT
1 TTTGC-TTG-ACTTTGAATTTT
1304701 TAATCTATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.14, C:0.09, G:0.16, T:0.60
Consensus pattern (21 bp):
TTTGCTTGACTTTGAATTTTA
Found at i:1305615 original size:13 final size:13
Alignment explanation
Indices: 1305597--1305622 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1305587 TACACAAAGT
1305597 ATGTATCGATACA
1 ATGTATCGATACA
1305610 ATGTATCGATACA
1 ATGTATCGATACA
1305623 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1305641 original size:34 final size:32
Alignment explanation
Indices: 1305579--1305643 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1305569 TAGCCAAACT
**
1305579 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
1305611 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
1305644 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:1309087 original size:24 final size:24
Alignment explanation
Indices: 1309055--1309110 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
1309045 GACCTCATAT
*
1309055 TCCCGTGCTATTGGTTAATAGCAC
1 TCCCGTGCTATTGGTCAATAGCAC
*
1309079 TCCCGTGCTATTGGTCGATAGCAC
1 TCCCGTGCTATTGGTCAATAGCAC
1309103 TCCCGTGC
1 TCCCGTGC
1309111 CTAAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.16, C:0.30, G:0.23, T:0.30
Consensus pattern (24 bp):
TCCCGTGCTATTGGTCAATAGCAC
Found at i:1309477 original size:63 final size:63
Alignment explanation
Indices: 1309397--1309519 Score: 228
Period size: 63 Copynumber: 2.0 Consensus size: 63
1309387 TCGTCAACGG
* *
1309397 GCTCAAAGCATTGGGGAAGACATCCCAACAAAAAGATTGTTAAGAAGCTTCTCAAGGATCCAA
1 GCTCAAAGCATTAGGGAAGACATCCCAACAAAAAGATTGTGAAGAAGCTTCTCAAGGATCCAA
1309460 GCTCAAAGCATTAGGGAAGACATCCCAACAAAAAGATTGTGAAGAAGCTTCTCAAGGATC
1 GCTCAAAGCATTAGGGAAGACATCCCAACAAAAAGATTGTGAAGAAGCTTCTCAAGGATC
1309520 TAAGTCTTCC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.40, C:0.20, G:0.21, T:0.19
Consensus pattern (63 bp):
GCTCAAAGCATTAGGGAAGACATCCCAACAAAAAGATTGTGAAGAAGCTTCTCAAGGATCCAA
Found at i:1316455 original size:20 final size:19
Alignment explanation
Indices: 1316409--1316465 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1316399 TTGTATCGAT
* *
1316409 ACATTGTATTGATACATGT
1 ACATTGTATCGATACATGG
*
1316428 TCATTGTATCGATACATGG
1 ACATTGTATCGATACATGG
1316447 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1316466 AAACTGGCAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1326089 original size:8 final size:8
Alignment explanation
Indices: 1326076--1326133 Score: 53
Period size: 8 Copynumber: 6.8 Consensus size: 8
1326066 TTCGTACCAA
1326076 AAAAAAAT
1 AAAAAAAT
1326084 AAAAAAAT
1 AAAAAAAT
*
1326092 AAAAAAAACC
1 -AAAAAAA-T
1326102 AAGAAAAAT
1 AA-AAAAAT
1326111 ATAAAAAAT
1 A-AAAAAAT
* *
1326120 AAACAAAC
1 AAAAAAAT
1326128 AAAAAA
1 AAAAAA
1326134 GGGGTCTAGA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
8 18 0.44
9 17 0.41
10 6 0.15
ACGTcount: A:0.83, C:0.07, G:0.02, T:0.09
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1326089 original size:9 final size:9
Alignment explanation
Indices: 1326075--1326122 Score: 53
Period size: 9 Copynumber: 5.3 Consensus size: 9
1326065 CTTCGTACCA
1326075 AAAAAAAAT
1 AAAAAAAAT
1326084 -AAAAAAAT
1 AAAAAAAAT
*
1326092 AAAAAAAACC
1 AAAAAAAA-T
*
1326102 AAGAAAAAT
1 AAAAAAAAT
*
1326111 ATAAAAAAT
1 AAAAAAAAT
1326120 AAA
1 AAA
1326123 CAAACAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
8 8 0.26
9 16 0.52
10 7 0.23
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.10
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:1326098 original size:19 final size:20
Alignment explanation
Indices: 1326074--1326118 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1326064 CCTTCGTACC
*
1326074 AAAAAAA-AATAAAAAAATA
1 AAAAAAACAAGAAAAAAATA
*
1326093 AAAAAAACCAAGAAAAATATA
1 AAAAAAA-CAAGAAAAAAATA
1326114 AAAAA
1 AAAAA
1326119 TAAACAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
21 15 0.68
ACGTcount: A:0.84, C:0.04, G:0.02, T:0.09
Consensus pattern (20 bp):
AAAAAAACAAGAAAAAAATA
Found at i:1327408 original size:28 final size:28
Alignment explanation
Indices: 1327370--1327777 Score: 466
Period size: 28 Copynumber: 14.5 Consensus size: 28
1327360 CATTCATCTC
*
1327370 TTCAAAGCCCACAGGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1327398 TTCAAAACCCACAAGTCAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
1327426 TTCAAAGCCCACAA-TCAGTGGCA-CCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1327452 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1327480 TTCAAAGCCCACAAGTTAGTGGCATCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
*
1327508 TTCAAAGCCCACAAGTTAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
1327536 TTCAAAGCCTATAAGTCAGTGGTATTCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1327564 TTCAAAGCCTACAAGTTAGTGGCAT-CT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1327591 CTTCAAAAGACCACAAGTTAGTGGCATCCT
1 -TTC-AAAGCCCACAAGTCAGTGGCATCCT
* *
1327621 TTCAAAGCCCACAAGTTAGTGGCACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
* * * *
1327649 TTCAAAGTCCACAAGTTAATAGCATACCCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT---CCT
1327680 TT-AAAGCCCACAAGTCAGTGGCA-CCAT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-T
* *
1327707 TTTAAAGCCCACAAGTCAGTGACATACCCT
1 TTCAAAGCCCACAAGTCAGTGGCAT--CCT
* * *
1327737 TTCAAAGCCCACAAGTCGGTGGTACCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCT
1327765 TTCAAAGCCCACA
1 TTCAAAGCCCACA
1327778 CAAGTTGATG
Statistics
Matches: 332, Mismatches: 35, Indels: 26
0.84 0.09 0.07
Matches are distributed among these distances:
26 18 0.05
27 22 0.07
28 222 0.67
29 23 0.07
30 40 0.12
31 7 0.02
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (28 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:1328911 original size:38 final size:38
Alignment explanation
Indices: 1328869--1328954 Score: 97
Period size: 37 Copynumber: 2.3 Consensus size: 38
1328859 TAGTGTTCAA
*
1328869 TTTAAATTCCTGT-TTTGAACTGTTTCTCT-TTATTTTCT
1 TTTAAATTCCTGTGTTTGAACTG-TTCT-TGTGATTTTCT
* * *
1328907 TTTAAATT-ATGTGTTTGCACTGTTCTTGTGGTTTTCT
1 TTTAAATTCCTGTGTTTGAACTGTTCTTGTGATTTTCT
1328944 TTTAAATTCCT
1 TTTAAATTCCT
1328955 ACGCCTACCC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
36 1 0.03
37 22 0.55
38 17 0.43
ACGTcount: A:0.16, C:0.14, G:0.12, T:0.58
Consensus pattern (38 bp):
TTTAAATTCCTGTGTTTGAACTGTTCTTGTGATTTTCT
Found at i:1334040 original size:18 final size:18
Alignment explanation
Indices: 1334016--1334061 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1334006 AAATAAAGAG
1334016 AGAAGAAGAAAGAAAAAA
1 AGAAGAAGAAAGAAAAAA
*
1334034 GGAAGAAGAAAGAAAAAA
1 AGAAGAAGAAAGAAAAAA
*
1334052 AAAAGAAGAA
1 AGAAGAAGAA
1334062 GGATGGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (18 bp):
AGAAGAAGAAAGAAAAAA
Found at i:1334040 original size:21 final size:21
Alignment explanation
Indices: 1334017--1334079 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
1334007 AATAAAGAGA
*
1334017 GAAG-AAGAAAGAAAAAAGGAA
1 GAAGAAAGAAA-AAAAAAAGAA
1334038 GAAGAAAGAAAAAAAAAAGAA
1 GAAGAAAGAAAAAAAAAAGAA
* * *
1334059 GAAGGATGGAAAAAAAAAGAA
1 GAAGAAAGAAAAAAAAAAGAA
1334080 AAAAAAGGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 31 0.84
22 6 0.16
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (21 bp):
GAAGAAAGAAAAAAAAAAGAA
Found at i:1334976 original size:109 final size:109
Alignment explanation
Indices: 1334786--1335248 Score: 578
Period size: 109 Copynumber: 4.3 Consensus size: 109
1334776 TTAATTTTAT
* *
1334786 CACCAAAAGATTGG-CCCGAAATAAGTCATCATCTAGAGTTATAAAGTGG-AGTACGAATGCCCT
1 CACCAAAAGATTGGCCCCGAAATAGGTCATCATCTAGAGTCATAAAGTGGCA-TACGAATGCCCT
* *
1334849 TTATATAGGATAATTCTTTTTTTGCATTAATTACGTAGATTCGAG
65 TTATATAGGATAATTCTTTTTTTGCATTAATTACATAGATTCGGG
* * *
1334894 CACCAAAAGATCGGCCCCGAAATAGGTCATCGTCTAGAGTCATAAAGTGGCATACGAATGCCTTT
1 CACCAAAAGATTGGCCCCGAAATAGGTCATCATCTAGAGTCATAAAGTGGCATACGAATGCCCTT
* * *
1334959 TATATGGGATAATTCTTTCTTTGCATTAATTATATAGATTCGGG
66 TATATAGGATAATTCTTTTTTTGCATTAATTACATAGATTCGGG
* * * * **
1335003 CACTAAAAGATTGGCTCCGAAATTGGTCATCATCTAGAGTCATAAAATGGTGTACGAATGCCCTT
1 CACCAAAAGATTGGCCCCGAAATAGGTCATCATCTAGAGTCATAAAGTGGCATACGAATGCCCTT
* *
1335068 TAGATAGGATAATTC-TTTTTTGCTTTAATTACATAGATTCGGG
66 TATATAGGATAATTCTTTTTTTGCATTAATTACATAGATTCGGG
* * * * *
1335111 CACTAAAGGATTGGCCTCGAAATAGGTCATCGTCCAGAGTCATAAAGTGGCATACGAATGCCCTT
1 CACCAAAAGATTGGCCCCGAAATAGGTCATCATCTAGAGTCATAAAGTGGCATACGAATGCCCTT
* * *
1335176 TATATAGGATAATTC-ATTTTT-CATGTAAATTACATA-ATACGCAGA
66 TATATAGGATAATTCTTTTTTTGCAT-T-AATTACATAGATTCG--GG
** *
1335221 CACCAAGGGATTGGCCCTGAAATAGGTC
1 CACCAAAAGATTGGCCCCGAAATAGGTC
1335249 TCTCTAACGT
Statistics
Matches: 307, Mismatches: 42, Indels: 10
0.86 0.12 0.03
Matches are distributed among these distances:
107 2 0.01
108 118 0.38
109 161 0.52
110 26 0.08
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (109 bp):
CACCAAAAGATTGGCCCCGAAATAGGTCATCATCTAGAGTCATAAAGTGGCATACGAATGCCCTT
TATATAGGATAATTCTTTTTTTGCATTAATTACATAGATTCGGG
Found at i:1335165 original size:217 final size:209
Alignment explanation
Indices: 1334661--1335195 Score: 671
Period size: 217 Copynumber: 2.5 Consensus size: 209
1334651 TAGAATTTAA
* * * ** * * *
1334661 TTGCATTAATTACGTAGTATTTGAGTATTAAGGGATTGGCCTCAAAATAGATCATCGTCTAGAGT
1 TTGCATTAATTACATAG-ATTCGAGCACCAAAGGATTGGCCTCGAAATAGGTCATCGTCTAGAGT
** * *
1334726 CATAAAGTGGTGTACG-ATGCCCTTTATATAAGATAATTCTTTTTTTTCCATTAATTTTATCACC
65 CATAAAGTGGCATACGAATGCCCTTTATATAGGATAATTCTTTTCTTTCCATTAATTTTATCACC
* * *
1334790 AAAAGATTGGCCCGAAATAAGTCATCATCTAGAGTTATAAAGTGGAGTACGAATGCCCTTTATAT
130 AAAAGATTGGCCCGAAATAAGTCATCATCTAGAGTCATAAAATGGAGTACGAATGCCCTTTAGAT
1334855 AGGATAATTCTTTTT
195 AGGATAATTCTTTTT
* * * *
1334870 TTGCATTAATTACGTAGATTCGAGCACCAAAAGATCGGCCCCGAAATAGGTCATCGTCTAGAGTC
1 TTGCATTAATTACATAGATTCGAGCACCAAAGGATTGGCCTCGAAATAGGTCATCGTCTAGAGTC
* * *
1334935 ATAAAGTGGCATACGAATGCCTTTTATATGGGATAATTC-TTTCTTTGCATTAATTATATAGATT
66 ATAAAGTGGCATACGAATGCCCTTTATATAGGATAATTCTTTTCTTTCCATTAATT-T-T--A-T
* ** *
1334999 CGGGCACTAAAAGATTGGCTCCGAAATTGGTCATCATCTAGAGTCATAAAATGGTGTACGAATGC
126 ----CACCAAAAGATTGGC-CCGAAATAAGTCATCATCTAGAGTCATAAAATGGAGTACGAATGC
1335064 CCTTTAGATAGGATAATTC-TTTT
186 CCTTTAGATAGGATAATTCTTTTT
* * * *
1335087 TTGCTTTAATTACATAGATTCGGGCACTAAAGGATTGGCCTCGAAATAGGTCATCGTCCAGAGTC
1 TTGCATTAATTACATAGATTCGAGCACCAAAGGATTGGCCTCGAAATAGGTCATCGTCTAGAGTC
1335152 ATAAAGTGGCATACGAATGCCCTTTATATAGGATAATTCATTTT
66 ATAAAGTGGCATACGAATGCCCTTTATATAGGATAATTC-TTTT
1335196 TCATGTAAAT
Statistics
Matches: 279, Mismatches: 34, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
208 65 0.23
209 38 0.14
210 1 0.00
212 1 0.00
213 1 0.00
217 112 0.40
218 58 0.21
219 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (209 bp):
TTGCATTAATTACATAGATTCGAGCACCAAAGGATTGGCCTCGAAATAGGTCATCGTCTAGAGTC
ATAAAGTGGCATACGAATGCCCTTTATATAGGATAATTCTTTTCTTTCCATTAATTTTATCACCA
AAAGATTGGCCCGAAATAAGTCATCATCTAGAGTCATAAAATGGAGTACGAATGCCCTTTAGATA
GGATAATTCTTTTT
Found at i:1337355 original size:81 final size:80
Alignment explanation
Indices: 1337216--1337471 Score: 306
Period size: 81 Copynumber: 3.2 Consensus size: 80
1337206 ATTTGAGAAG
* * * * *
1337216 AAAA-GAGGTTGGAGTATCCCCTTAGAGATAGTGGGGTTGGAGTGTCCCCGAAGATGGAAATTTT
1 AAAATGAGGTTGGAGTATCCCCTAAGAAATGGTGGGGTT-GAATATCCCCGAAGATGGAAATTTT
1337280 GATATTTTTAGAAGTA
65 GATATTTTTAGAAGTA
* * *
1337296 AAAATGAGGTTGGAGTATCCCCTAAAAAATGGTGGGGTTCGAATATCCCCAAAGATGGAAAATTT
1 AAAATGAGGTTGGAGTATCCCCTAAGAAATGGTGGGGTT-GAATATCCCCGAAGATGGAAATTTT
1337361 -ACTATTTTTAGAAGTA
65 GA-TATTTTTAGAAGTA
* ** * *
1337377 AAAACGAGGTTGGAGTATCCCCTCGGAAATGGT-GGGTTGAAATATCCCTGAAGATGAAAATTTT
1 AAAATGAGGTTGGAGTATCCCCTAAGAAATGGTGGGGTTG-AATATCCCCGAAGATGGAAATTTT
*
1337441 GATATTTTTAGGAGT-
65 GATATTTTTAGAAGTA
1337456 AAAAT-AGTGTTGGAGT
1 AAAATGAG-GTTGGAGT
1337472 TTTCCCTCGA
Statistics
Matches: 152, Mismatches: 19, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
78 2 0.01
79 13 0.09
80 42 0.28
81 95 0.62
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.30
Consensus pattern (80 bp):
AAAATGAGGTTGGAGTATCCCCTAAGAAATGGTGGGGTTGAATATCCCCGAAGATGGAAATTTTG
ATATTTTTAGAAGTA
Found at i:1337511 original size:80 final size:77
Alignment explanation
Indices: 1337266--1337556 Score: 257
Period size: 80 Copynumber: 3.6 Consensus size: 77
1337256 AGTGTCCCCG
* **
1337266 AAGATGGAAATTTTGATATTTTTAGAAGTAAAAATGAGGTTGGAGTATCCCCTAAAAAATGGTGG
1 AAGATGAAAATTTTGATATTTTTAGAAGT-AAAAT-AGGTTGGAGTATCCCCTCGAAAATGGT-G
*
1337331 GGTTCGAATATCCCCA
63 GGTT-GAATATCCCTA
* *
1337347 AAGATGGAAAA-TTT-ACTATTTTTAGAAGTAAAAACGAGGTTGGAGTATCCCCTCGGAAATGGT
1 AAGAT-GAAAATTTTGA-TATTTTTAGAAGT-AAAA-TAGGTTGGAGTATCCCCTCGAAAATGGT
*
1337410 GGGTTGAAATATCCCTG
62 GGGTTG-AATATCCCTA
* * * **
1337427 AAGATGAAAATTTTGATATTTTTAGGAGTAAAATAGTGTTGGAGTTTTCCCTCGAAAATAATAGG
1 AAGATGAAAATTTTGATATTTTTAGAAGTAAAATAG-GTTGGAGTATCCCCTCGAAAATGGT-GG
* *
1337492 GTTGGATCATCCTTA
64 GTTGAAT-ATCCCTA
* ** * *
1337507 AAGATAAAAAAATTGATA-TTTTGGAACTAAAA-AGGGGTTGGAGTATCCCC
1 AAGATGAAAATTTTGATATTTTTAGAAGTAAAATA--GGTTGGAGTATCCCC
1337557 GAAGATGAAA
Statistics
Matches: 174, Mismatches: 25, Indels: 24
0.78 0.11 0.11
Matches are distributed among these distances:
78 3 0.02
79 55 0.32
80 61 0.35
81 51 0.29
82 4 0.02
ACGTcount: A:0.36, C:0.11, G:0.23, T:0.31
Consensus pattern (77 bp):
AAGATGAAAATTTTGATATTTTTAGAAGTAAAATAGGTTGGAGTATCCCCTCGAAAATGGTGGGT
TGAATATCCCTA
Found at i:1337562 original size:51 final size:52
Alignment explanation
Indices: 1337507--1337606 Score: 139
Period size: 51 Copynumber: 1.9 Consensus size: 52
1337497 ATCATCCTTA
* *
1337507 AAGATAAAAAAATTGATATTTTGGAACTAAAAA-GGGGTTGGAGTATCCCCG
1 AAGATAAAAAAATTGATATTTTAGAACTAAAAATGGGGTTAGAGTATCCCCG
* ** *
1337558 AAGATGAAAATTTTGATATTTTAGAAGTAAAAATGGGGTTAGAGTATCC
1 AAGATAAAAAAATTGATATTTTAGAACTAAAAATGGGGTTAGAGTATCC
1337607 TCTCAGAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 28 0.67
52 14 0.33
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (52 bp):
AAGATAAAAAAATTGATATTTTAGAACTAAAAATGGGGTTAGAGTATCCCCG
Found at i:1339931 original size:13 final size:13
Alignment explanation
Indices: 1339913--1339939 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1339903 ACATGCTACC
1339913 TTGTATCGATACA
1 TTGTATCGATACA
1339926 TTGTATCGATACA
1 TTGTATCGATACA
1339939 T
1 T
1339940 GTTCGTTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1339936 original size:33 final size:32
Alignment explanation
Indices: 1339894--1339958 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
1339884 CACACCCAGA
*
1339894 TGTATCGATACATGCTACCTTGTATCGATACAT
1 TGTATCGATACATG-TACCTTGTATCCATACAT
* *
1339927 TGTATCGATACATGTTCGTTGTATCCATACAT
1 TGTATCGATACATGTACCTTGTATCCATACAT
1339959 GGCCAAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.52
33 14 0.48
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATGTACCTTGTATCCATACAT
Found at i:1340048 original size:13 final size:13
Alignment explanation
Indices: 1340030--1340055 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1340020 CATGGTCTAA
1340030 TGTATCGATACAT
1 TGTATCGATACAT
1340043 TGTATCGATACAT
1 TGTATCGATACAT
1340056 GAAGAAATTT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1340069 original size:33 final size:33
Alignment explanation
Indices: 1340009--1340075 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1339999 CTATCACTAT
** *
1340009 TTGTATCGATACATGGTCTAATGTATCGATACA
1 TTGTATCGATACATGAACAAATGTATCGATACA
* *
1340042 TTGTATCGATACATGAAGAAATTTATCGATACA
1 TTGTATCGATACATGAACAAATGTATCGATACA
1340075 T
1 T
1340076 AGCTTGTAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGAACAAATGTATCGATACA
Found at i:1342036 original size:81 final size:80
Alignment explanation
Indices: 1341926--1342122 Score: 207
Period size: 81 Copynumber: 2.5 Consensus size: 80
1341916 GGTTGGGGTG
* * * * * * *
1341926 TCCCCTTGAAAATGACAGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATGA-TTAGGAAAAAAA
1 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAAT-ATTTAGGAAAAAAA
1341990 AAATCGAGATTGGAGTA
65 AAAT-GAGATTGGAGTA
* * * *
1342007 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATATTTTGGGAATAAAA
1 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGGAAAAAAAA
** * *
1342072 GCTGGGGTTGGAGTA
66 AATGAGATTGGAGTA
* **
1342087 TCCCCTCGGAGGTAACGGGGTTGGAGTATCCCCGAT
1 TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGAT
1342123 GAAATAACGA
Statistics
Matches: 96, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
80 43 0.45
81 53 0.55
ACGTcount: A:0.31, C:0.17, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATCAATATTTAGGAAAAAAAA
AATGAGATTGGAGTA
Found at i:1342130 original size:28 final size:28
Alignment explanation
Indices: 1342075--1342150 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 28
1342065 AATAAAAGCT
*** **
1342075 GGGGTTGGAGTATCCCCTCGGAGGTAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
1342103 GGGGTTGGAGTATCCCCGATGAAATAAC
1 GGGGTTGGAGTATCCCCGATGAAATAAC
* *
1342131 GAGGTTGGAGTATCCTCGAT
1 GGGGTTGGAGTATCCCCGAT
1342151 TGTGAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.22, C:0.18, G:0.36, T:0.24
Consensus pattern (28 bp):
GGGGTTGGAGTATCCCCGATGAAATAAC
Found at i:1342204 original size:53 final size:51
Alignment explanation
Indices: 1342133--1342308 Score: 203
Period size: 52 Copynumber: 3.4 Consensus size: 51
1342123 GAAATAACGA
* *
1342133 GGTTGGAGTATCCTCGATTGTGAAAAAATTGGTGTTTTTGGAAATAAAATCG
1 GGTTGGAGTATCCCCGATTGTGAAAAAATTGGTG-TTTTAGAAATAAAATCG
* * * *
1342185 GAGCTAGAGTATCCCCGA-T-TAAAGGAAAATTGGTGTTTTAAAAATAAAATCGG
1 G-GTTGGAGTATCCCCGATTGTGAA--AAAATTGGTGTTTTAGAAATAAAATC-G
* * *
1342238 GGTTGGAGTATCCCCGATTGTGGAAAAATTAGTGTTTTAGCAATAAAATCAG
1 GGTTGGAGTATCCCCGATTGTGAAAAAATTGGTGTTTTAGAAATAAAATC-G
1342290 GGTTGGAGTATCCCCGATT
1 GGTTGGAGTATCCCCGATT
1342309 ATGAGAAATC
Statistics
Matches: 104, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
51 3 0.03
52 73 0.70
53 26 0.25
54 2 0.02
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.31
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTGTGAAAAAATTGGTGTTTTAGAAATAAAATCG
Found at i:1342348 original size:51 final size:52
Alignment explanation
Indices: 1342220--1342355 Score: 161
Period size: 51 Copynumber: 2.6 Consensus size: 52
1342210 AAAATTGGTG
* * * * * *
1342220 TTTTAAAAATAAAATCGGGGTTGGAGTATCCCCGATTGTGGAAAAATTAGTG
1 TTTTAAGAATAAAATAGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATA
*
1342272 TTTT-AGCAATAAAATCA-GGGTTGGAGTATCCCCGATTAT-GAGAAATCAATA
1 TTTTAAG-AATAAAAT-AGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATA
*
1342323 TTTTAAGAATAAAGTAGGGGTTGGAGTATCCCC
1 TTTTAAGAATAAAATAGGGGTTGGAGTATCCCC
1342356 TCGGAAATAA
Statistics
Matches: 72, Mismatches: 8, Indels: 9
0.81 0.09 0.10
Matches are distributed among these distances:
50 1 0.01
51 36 0.50
52 35 0.49
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.30
Consensus pattern (52 bp):
TTTTAAGAATAAAATAGGGGTTGGAGTATCCCCGATTATGGAAAAATCAATA
Found at i:1342373 original size:28 final size:27
Alignment explanation
Indices: 1342339--1342410 Score: 94
Period size: 27 Copynumber: 2.6 Consensus size: 27
1342329 GAATAAAGTA
1342339 GGGGTTGGAGTATCCCCTCG-GAAATAAC
1 GGGGTTGGAGTATCCCCT-GAG-AATAAC
*
1342367 GGGGTTGGAGTAT-CCCTGATGATTAAC
1 GGGGTTGGAGTATCCCCTGA-GAATAAC
1342394 GGGGTTGGAGTATCCCC
1 GGGGTTGGAGTATCCCC
1342411 GATTGTGAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 1 0.03
27 22 0.55
28 17 0.43
ACGTcount: A:0.21, C:0.19, G:0.35, T:0.25
Consensus pattern (27 bp):
GGGGTTGGAGTATCCCCTGAGAATAAC
Found at i:1342483 original size:53 final size:53
Alignment explanation
Indices: 1342134--1342519 Score: 194
Period size: 52 Copynumber: 7.4 Consensus size: 53
1342124 AAATAACGAG
* * * * *
1342134 GTTGGAGTATCCTCGATTGTGAAAAAATTGGTG-TTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTAT-AGAAAATTAGTGTTTTTTGAAAATAAAATCGGA
* * * * * *
1342187 GCTAGAGTATCCCCGATTAAAGGAAAATT-G-GTGTTTTAAAAATAAAATCGGG
1 GTTGGAGTATCCCCGATTATA-GAAAATTAGTGTTTTTTGAAAATAAAATCGGA
* * * *
1342239 GTTGGAGTATCCCCGATTGTGGAAAAATTAGTG-TTTTAG-CAATAAAATCAGG-
1 GTTGGAGTATCCCCGATTATAG-AAAATTAGTGTTTTTTGAAAATAAAATC-GGA
* * * * * *
1342291 GTTGGAGTATCCCCGATTAT-GAGAAATCA--ATATTTT-AAGAATAAAGTAGGG
1 GTTGGAGTATCCCCGATTATAGA-AAATTAGTGTTTTTTGAA-AATAAAATCGGA
* *** * * *** ** * *
1342342 GTTGGAGTATCCCCTCGGA-AATA-ACGGGGTTGGAGTATCCCTGATGAT-TAA-CGGG
1 GTTGGAGTAT-CCC-C-GATTATAGA--AAATTAGTGT-TTTTTGAAAATAAAATCGGA
* *
1342397 GTTGGAGTATCCCCGATTGT-GAAAATTTTGTGTTTTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAA-TTAGTGTTTTTTGAAAATAAAATCGGA
1342450 GTTGGAGTATCCCCGATTATAGAAAATTAGTG--TTTTGAAAATAAAATCGGA
1 GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTTTGAAAATAAAATCGGA
* *
1342501 GATGGAATATCCCCGATTA
1 GTTGGAGTATCCCCGATTA
1342520 CGGAGAATTG
Statistics
Matches: 246, Mismatches: 61, Indels: 54
0.68 0.17 0.15
Matches are distributed among these distances:
50 6 0.02
51 67 0.27
52 80 0.33
53 61 0.25
54 13 0.05
55 13 0.05
56 2 0.01
57 3 0.01
58 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.31
Consensus pattern (53 bp):
GTTGGAGTATCCCCGATTATAGAAAATTAGTGTTTTTTGAAAATAAAATCGGA
Found at i:1342512 original size:51 final size:52
Alignment explanation
Indices: 1342399--1342519 Score: 174
Period size: 51 Copynumber: 2.3 Consensus size: 52
1342389 TTAACGGGGT
* * *
1342399 TGGAGTATCCCCGATTGTGAAAATTTTGTGTTTTTTGAAAATAAAATCGGAGT
1 TGGAGTATCCCCGATTATGAAAATTTAGTG-TTTTTGAAAATAAAATCGGAGA
1342452 TGGAGTATCCCCGATTATAGAAAA-TTAGTG-TTTTGAAAATAAAATCGGAGA
1 TGGAGTATCCCCGATTAT-GAAAATTTAGTGTTTTTGAAAATAAAATCGGAGA
*
1342503 TGGAATATCCCCGATTA
1 TGGAGTATCCCCGATTA
1342520 CGGAGAATTG
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
51 36 0.57
53 22 0.35
54 5 0.08
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (52 bp):
TGGAGTATCCCCGATTATGAAAATTTAGTGTTTTTGAAAATAAAATCGGAGA
Found at i:1344970 original size:19 final size:18
Alignment explanation
Indices: 1344946--1345013 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1344936 AAGTAGCTAA
1344946 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1344965 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1344980 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1344997 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1345014 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1344986 original size:13 final size:13
Alignment explanation
Indices: 1344968--1344992 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1344958 ACAATACTTA
1344968 TGTATCGATACAT
1 TGTATCGATACAT
1344981 TGTATCGATACA
1 TGTATCGATACA
1344993 AAACTTATGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1344990 original size:32 final size:32
Alignment explanation
Indices: 1344949--1345011 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1344939 TAGCTAATTA
*
1344949 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1344981 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1345012 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1376695 original size:28 final size:28
Alignment explanation
Indices: 1376656--1376725 Score: 131
Period size: 28 Copynumber: 2.5 Consensus size: 28
1376646 CTAACCCAAT
1376656 TTTTGGATTTAAGTGTAATCGAGTAATA
1 TTTTGGATTTAAGTGTAATCGAGTAATA
1376684 TTTTGGATTTAAGTGTAATCGAGTAATA
1 TTTTGGATTTAAGTGTAATCGAGTAATA
*
1376712 TTTTGAATTTAAGT
1 TTTTGGATTTAAGT
1376726 ATCCATTTTA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.31, C:0.03, G:0.20, T:0.46
Consensus pattern (28 bp):
TTTTGGATTTAAGTGTAATCGAGTAATA
Found at i:1378461 original size:81 final size:81
Alignment explanation
Indices: 1378326--1378484 Score: 309
Period size: 81 Copynumber: 2.0 Consensus size: 81
1378316 TTTTTATTAT
1378326 TGATAGTGATTAATGCATACTAAAGTTCAGTATTTTGTTTTATTAAAGCATAAACGCATTTATAC
1 TGATAGTGATTAATGCATACTAAAGTTCAGTATTTTGTTTTATTAAAGCATAAACGCATTTATAC
*
1378391 ATGTGTTAGGTACGTA
66 ATATGTTAGGTACGTA
1378407 TGATAGTGATTAATGCATACTAAAGTTCAGTATTTTGTTTTATTAAAGCATAAACGCATTTATAC
1 TGATAGTGATTAATGCATACTAAAGTTCAGTATTTTGTTTTATTAAAGCATAAACGCATTTATAC
1378472 ATATGTTAGGTAC
66 ATATGTTAGGTAC
1378485 ATATACGAGA
Statistics
Matches: 77, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
81 77 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (81 bp):
TGATAGTGATTAATGCATACTAAAGTTCAGTATTTTGTTTTATTAAAGCATAAACGCATTTATAC
ATATGTTAGGTACGTA
Found at i:1379516 original size:2 final size:2
Alignment explanation
Indices: 1379509--1379542 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1379499 TTGAAGCAAC
1379509 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
1379543 GAAAACTGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1379581 original size:2 final size:2
Alignment explanation
Indices: 1379574--1379616 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
1379564 AAGAATTTAA
* *
1379574 AT AT AT AT AT AT AC AT AT AT AC 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
1379616 A
1 A
1379617 CCGGTAGGGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1381003 original size:13 final size:13
Alignment explanation
Indices: 1380985--1381009 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1380975 GTGAGTAATG
1380985 AAATATTTTTAAA
1 AAATATTTTTAAA
1380998 AAATATTTTTAA
1 AAATATTTTTAA
1381010 CATAATAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAATATTTTTAAA
Found at i:1390592 original size:2 final size:2
Alignment explanation
Indices: 1390585--1390612 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1390575 ATACATATCC
1390585 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
1390613 CATGCTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1391194 original size:16 final size:16
Alignment explanation
Indices: 1391170--1391205 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1391160 TTTAAATTAA
* *
1391170 TTAATTTTGAATTATT
1 TTAAATTTGAATCATT
1391186 TTAAATTTGAATCATT
1 TTAAATTTGAATCATT
1391202 TTAA
1 TTAA
1391206 TTTAATGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.03, G:0.06, T:0.56
Consensus pattern (16 bp):
TTAAATTTGAATCATT
Found at i:1393702 original size:2 final size:2
Alignment explanation
Indices: 1393695--1393720 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1393685 CTATCTATCA
1393695 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
1393721 GTATGTATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1394327 original size:2 final size:2
Alignment explanation
Indices: 1394320--1394388 Score: 58
Period size: 2 Copynumber: 36.0 Consensus size: 2
1394310 ATAATTACTC
* * *
1394320 AT AT AT AT AT AT AT AT AT AT A- AT AA AT -T GAT A- AG AA AGT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT A-T AT
1394360 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1394389 TAGAAGTGTT
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
1 5 0.09
2 50 0.89
3 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (2 bp):
AT
Found at i:1398135 original size:17 final size:18
Alignment explanation
Indices: 1398102--1398139 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
1398092 TAAATATGAC
1398102 TATGACACATGAAAAATA
1 TATGACACATGAAAAATA
*
1398120 TATGAC-CATGATAAATA
1 TATGACACATGAAAAATA
1398137 TAT
1 TAT
1398140 ACAGATTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.50, C:0.11, G:0.11, T:0.29
Consensus pattern (18 bp):
TATGACACATGAAAAATA
Found at i:1399526 original size:36 final size:36
Alignment explanation
Indices: 1399479--1399550 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
1399469 AACAACATAC
*
1399479 ACATTACTAGTTTAAGTAACAAAAAGTTTTCCTTCT
1 ACATTACTAGTTTAAGTAACAAAAACTTTTCCTTCT
1399515 ACATTACTAGTTTAAGTAACAAAAACTTTTCCTTCT
1 ACATTACTAGTTTAAGTAACAAAAACTTTTCCTTCT
1399551 TGTTAGTGGC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (36 bp):
ACATTACTAGTTTAAGTAACAAAAACTTTTCCTTCT
Found at i:1401639 original size:20 final size:21
Alignment explanation
Indices: 1401587--1401639 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
1401577 TTTTACAAAT
1401587 TGTATCGATACAAATAGTAAA
1 TGTATCGATACAAATAGTAAA
* *
1401608 TAG-ATTGATACAAA-AGTGAA
1 T-GTATCGATACAAATAGTAAA
1401628 TGTATCGATACA
1 TGTATCGATACA
1401640 TGCCTAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
19 1 0.04
20 14 0.52
21 11 0.41
22 1 0.04
ACGTcount: A:0.45, C:0.09, G:0.17, T:0.28
Consensus pattern (21 bp):
TGTATCGATACAAATAGTAAA
Found at i:1401766 original size:20 final size:20
Alignment explanation
Indices: 1401741--1401782 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1401731 ATACCAATAT
* *
1401741 ATTTTTCATTGTATCGATAC
1 ATTTTTCAATATATCGATAC
*
1401761 ATTTTTTAATATATCGATAC
1 ATTTTTCAATATATCGATAC
1401781 AT
1 AT
1401783 ACAAGCAATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (20 bp):
ATTTTTCAATATATCGATAC
Found at i:1404225 original size:78 final size:78
Alignment explanation
Indices: 1404117--1404262 Score: 186
Period size: 78 Copynumber: 1.9 Consensus size: 78
1404107 TTTCTCGGGG
* * * ** * * * *
1404117 ATACTTCAACCCCGTTATTTTCGAGGGGATACTCCAGTCCCGTTTTTATTTTCAAAAATTTTAAA
1 ATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCATTTTTATTTCCAAAAATATCAAA
1404182 TTTACCATTGGGA
66 TTTACCATTGGGA
*
1404195 ATACTCCAACCTCATTA-TTTCTGAGAGGATACTCCAACCCCATTTTTATTTCCAAAAATATCAA
1 ATACTCCAACCCCATTATTTTC-GAGAGGATACTCCAACCCCATTTTTATTTCCAAAAATATCAA
1404259 ATTT
65 ATTT
1404263 TTTATCGTGG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
77 4 0.07
78 53 0.93
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (78 bp):
ATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCATTTTTATTTCCAAAAATATCAAA
TTTACCATTGGGA
Found at i:1404307 original size:28 final size:28
Alignment explanation
Indices: 1404274--1404346 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
1404264 TTATCGTGGA
*
1404274 GATACTCTAACCCTGCTATTTTTAAGGG
1 GATACTCCAACCCTGCTATTTTTAAGGG
1404302 GATACTCCAACCCTGCTATTTTTAAGGG
1 GATACTCCAACCCTGCTATTTTTAAGGG
1404330 GATACTCCAACCCTGCT
1 GATACTCCAACCCTGCT
1404347 TTTATTTCCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.25, C:0.27, G:0.16, T:0.32
Consensus pattern (28 bp):
GATACTCCAACCCTGCTATTTTTAAGGG
Found at i:1404322 original size:108 final size:106
Alignment explanation
Indices: 1404210--1404414 Score: 266
Period size: 107 Copynumber: 1.9 Consensus size: 106
1404200 CCAACCTCAT
* *
1404210 TATTTCTGAGAGGATACTCCAACCCCATTTTTATTTCCAAAAATATCAAATTTTTTATCGTGGAG
1 TATTTCTAAGAGGATACTCCAACCCCACTTTTATTTCC-AAAATATCAAATTTTTTATCGTGGAG
* *
1404275 ATACTCTAACCCTGCTATTTTTAAGGGGATACTCCAACCCTGC
65 ATACTCTAACCAT-CTATTTCTAAGGGGATACTCCAACCCTGC
* * ** * ** *
1404318 TATTTTTAAGGGGATACTCCAACCCTGCTTTTATTTCCAAAATATTAAATTTTTTATTTTGGGGA
1 TATTTCTAAGAGGATACTCCAACCCCACTTTTATTTCCAAAATATCAAATTTTTTATCGTGGAGA
* *
1404383 TACTCTAACCATTTATTTCTGAGGGGATACTC
66 TACTCTAACCATCTATTTCTAAGGGGATACTC
1404415 TAACACCATT
Statistics
Matches: 83, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
106 17 0.20
107 34 0.41
108 32 0.39
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (106 bp):
TATTTCTAAGAGGATACTCCAACCCCACTTTTATTTCCAAAATATCAAATTTTTTATCGTGGAGA
TACTCTAACCATCTATTTCTAAGGGGATACTCCAACCCTGC
Found at i:1404396 original size:27 final size:29
Alignment explanation
Indices: 1404366--1404431 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 29
1404356 AAAATATTAA
*
1404366 ATTTTTTATTTTGGGGATACTCT-A-ACC
1 ATTTTTTATTTAGGGGATACTCTAACACC
* *
1404393 ATTTATTT-CTGAGGGGATACTCTAACACC
1 ATTT-TTTATTTAGGGGATACTCTAACACC
1404422 A-TTTTTATTT
1 ATTTTTTATTT
1404432 GCAGAATGTT
Statistics
Matches: 30, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
27 19 0.63
28 7 0.23
29 4 0.13
ACGTcount: A:0.24, C:0.15, G:0.14, T:0.47
Consensus pattern (29 bp):
ATTTTTTATTTAGGGGATACTCTAACACC
Found at i:1405688 original size:36 final size:34
Alignment explanation
Indices: 1405604--1405701 Score: 105
Period size: 36 Copynumber: 2.9 Consensus size: 34
1405594 CCTTACAACA
*
1405604 CTATC-TTTCAAGGATAAGATAGAA-A-C-CTCC
1 CTATCTTTTCAAGGCTAAGATAGAACATCTCTCC
* *
1405634 TTATCTTTTCACGAGCTAAGATAGAACATCTCTCC
1 CTATCTTTTCAAG-GCTAAGATAGAACATCTCTCC
*
1405669 CTATCTTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATC-TTTTC-AAGGCTAAGATAGAACATCTC
1405702 AATCACTTCG
Statistics
Matches: 55, Mismatches: 6, Indels: 8
0.80 0.09 0.12
Matches are distributed among these distances:
30 4 0.07
31 6 0.11
32 11 0.20
33 1 0.02
34 1 0.02
35 8 0.15
36 22 0.40
37 2 0.04
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (34 bp):
CTATCTTTTCAAGGCTAAGATAGAACATCTCTCC
Found at i:1406196 original size:52 final size:52
Alignment explanation
Indices: 1406140--1406246 Score: 178
Period size: 52 Copynumber: 2.1 Consensus size: 52
1406130 GTTGGACTCA
*
1406140 ATGTATTGATACTATTCATAATGTATCAATACATGAACAATGATGAACAGTG
1 ATGTATCGATACTATTCATAATGTATCAATACATGAACAATGATGAACAGTG
* * *
1406192 ATGTATCGATACTATTCATAATGTATCGATACATGAACAGTGATGAATAGTG
1 ATGTATCGATACTATTCATAATGTATCAATACATGAACAATGATGAACAGTG
1406244 ATG
1 ATG
1406247 AACAGTGAAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.33
Consensus pattern (52 bp):
ATGTATCGATACTATTCATAATGTATCAATACATGAACAATGATGAACAGTG
Found at i:1406243 original size:10 final size:10
Alignment explanation
Indices: 1406224--1406254 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1406214 GTATCGATAC
1406224 ATGAACAGTG
1 ATGAACAGTG
*
1406234 ATGAATAGTG
1 ATGAACAGTG
1406244 ATGAACAGTG
1 ATGAACAGTG
1406254 A
1 A
1406255 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:1410201 original size:173 final size:174
Alignment explanation
Indices: 1409966--1410457 Score: 625
Period size: 173 Copynumber: 2.8 Consensus size: 174
1409956 TCCAATTATG
* *
1409966 ATTTTAATTTAATTAAGAAAACTATATTTTCTTACTTAATT-ACATTTATTCTAATTATATTAGA
1 ATTTTAATTTAATTAAGAAAACTAT-TTTTCTTACTTGATTAACATTTATTCTAATCATATTAGA
* * * * *
1410030 ATAAATCCTAATACGATTACGATTAATTAATTAAGTTAAATATTATCCAATTAAACAATTTAACT
65 ATAAATCCTAATACAATTAAGATTAATCAATTAAATTAAATATTATCCAATTAAACAATTTAATT
* *
1410095 GGAAACAAA-ACATGTCAAATTTATTATCCAATTATGGATCCTAT
130 GGAGACAAATACATGTCAAATTTATTATCCAATTATGAATCCTAT
* * * *
1410139 ATTTTAATTTAATTAAGAAAACTATTTTTCTTATTTGATTAATATTTATTCCAATCATATTAGGA
1 ATTTTAATTTAATTAAGAAAACTATTTTTCTTACTTGATTAACATTTATTCTAATCATATTAGAA
* ** * * * * *
1410204 TAAGTTATTATCCAATTAAGATTAATCAATTAAATAAAATGTTATCCGATTAAACAATTTAATTG
66 TAAATCCTAATACAATTAAGATTAATCAATTAAATTAAATATTATCCAATTAAACAATTTAATTG
* * * * *
1410269 GAGATAAATACTTGTTAATTTTATTATCCAATTATGAATCTTAT
131 GAGACAAATACATGTCAAATTTATTATCCAATTATGAATCCTAT
* * *
1410313 A-TTTAGTTTAATTAAGAAAACTATTTTACTTACTTGATTAACATTTATTCTAATCA-ACTAAGA
1 ATTTTAATTTAATTAAGAAAACTATTTTTCTTACTTGATTAACATTTATTCTAATCATA-TTAGA
* *
1410376 ATAAATCCTAA-ACAAATTTAAGATTAATCAATTAAATTAAATATTATGCAATTAAATAATTTAA
65 ATAAATCCTAATAC-AA-TTAAGATTAATCAATTAAATTAAATATTATCCAATTAAACAATTTAA
*
1410440 TTGGAGACAAATATATGT
128 TTGGAGACAAATACATGT
1410458 TTATCTAATT
Statistics
Matches: 268, Mismatches: 46, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
172 15 0.06
173 165 0.62
174 88 0.33
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (174 bp):
ATTTTAATTTAATTAAGAAAACTATTTTTCTTACTTGATTAACATTTATTCTAATCATATTAGAA
TAAATCCTAATACAATTAAGATTAATCAATTAAATTAAATATTATCCAATTAAACAATTTAATTG
GAGACAAATACATGTCAAATTTATTATCCAATTATGAATCCTAT
Found at i:1410439 original size:174 final size:170
Alignment explanation
Indices: 1409908--1410457 Score: 614
Period size: 173 Copynumber: 3.2 Consensus size: 170
1409898 CATATTAGAA
* * * * * *
1409908 TATCCAATTATACAATTTAACTGAAAATAAA-ACACGTCAATTTTATTATCCAATTATGAT-TT-
1 TATCCAATTAAACAATTTAATTGGAGACAAATACATGTCAATTTTATTATCCAATTATGATCTTA
* *
1409970 TA---ATTTAATTAAGAAAACTATATTTTCTTACTTAATT-ACATTTATTCTAATTATATTAGAA
66 TATTTATTTAATTAAGAAAACTAT-TTTTCTTACTTGATTAACATTTATTCTAATCATATTAGAA
* * * *
1410031 TAAATCCTAATACGATTACGATTAATTAATTAAGTTAAATAT
130 TAAATCCTAA-ACAATTAAGATTAATCAATTAAATTAAATAT
* * * *
1410073 TATCCAATTAAACAATTTAACTGGAAACAAA-ACATGTCAAATTTATTATCCAATTATGGATCCT
1 TATCCAATTAAACAATTTAATTGGAGACAAATACATGTCAATTTTATTATCCAATTAT-GATCTT
* * *
1410137 ATATTTTAATTTAATTAAGAAAACTATTTTTCTTATTTGATTAATATTTATTCCAATCATATTAG
65 ATA-TTT-ATTTAATTAAGAAAACTATTTTTCTTACTTGATTAACATTTATTCTAATCATATTAG
* * ** ** * *
1410202 GATAAGTTATTATCCAATTAAGATTAATCAATTAAATAAAATGT
128 AATAA-ATCCTAAACAATTAAGATTAATCAATTAAATTAAATAT
* * * *
1410246 TATCCGATTAAACAATTTAATTGGAGATAAATACTTGTTAATTTTATTATCCAATTATGAATCTT
1 TATCCAATTAAACAATTTAATTGGAGACAAATACATGTCAATTTTATTATCCAATTATG-ATCTT
* *
1410311 ATATTTAGTTTAATTAAGAAAACTATTTTACTTACTTGATTAACATTTATTCTAATCA-ACTAAG
65 ATATTTA-TTTAATTAAGAAAACTATTTTTCTTACTTGATTAACATTTATTCTAATCATA-TTAG
1410375 AATAAATCCTAAACAAATTTAAGATTAATCAATTAAATTAAATAT
128 AATAAATCCTAAAC-AA-TTAAGATTAATCAATTAAATTAAATAT
* * *
1410420 TATGCAATTAAATAATTTAATTGGAGACAAATATATGT
1 TATCCAATTAAACAATTTAATTGGAGACAAATACATGT
1410458 TTATCTAATT
Statistics
Matches: 319, Mismatches: 50, Indels: 23
0.81 0.13 0.06
Matches are distributed among these distances:
165 52 0.16
166 3 0.01
167 1 0.00
168 2 0.01
172 19 0.06
173 152 0.48
174 90 0.28
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (170 bp):
TATCCAATTAAACAATTTAATTGGAGACAAATACATGTCAATTTTATTATCCAATTATGATCTTA
TATTTATTTAATTAAGAAAACTATTTTTCTTACTTGATTAACATTTATTCTAATCATATTAGAAT
AAATCCTAAACAATTAAGATTAATCAATTAAATTAAATAT
Found at i:1412463 original size:28 final size:28
Alignment explanation
Indices: 1412423--1412478 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
1412413 TCATCTTCAA
*
1412423 TATGCTTTATAATATACCTAAAACTACC
1 TATGCTTTATAATATACCCAAAACTACC
1412451 TATGCTTTATAATATACCCAAAACTACC
1 TATGCTTTATAATATACCCAAAACTACC
1412479 ATCTTTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.23, G:0.04, T:0.34
Consensus pattern (28 bp):
TATGCTTTATAATATACCCAAAACTACC
Found at i:1427274 original size:52 final size:52
Alignment explanation
Indices: 1427212--1427329 Score: 191
Period size: 52 Copynumber: 2.3 Consensus size: 52
1427202 AAAAAGGATG
*
1427212 ATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAATGTATCA
1 ATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGTATCA
* * *
1427264 ATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATTAAATGTATCG
1 ATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGTATCA
*
1427316 ATACATGCAAGCAA
1 ATACATGCAGGCAA
1427330 CTTTTCATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (52 bp):
ATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAATGTATCA
Found at i:1434225 original size:17 final size:18
Alignment explanation
Indices: 1434203--1434237 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
1434193 GGAGTTCCCT
1434203 TAAAAAAAACA-AAAAAA
1 TAAAAAAAACAGAAAAAA
*
1434220 TAAAAAACACAGAAAAAA
1 TAAAAAAAACAGAAAAAA
1434238 GGTGCAACGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.83, C:0.09, G:0.03, T:0.06
Consensus pattern (18 bp):
TAAAAAAAACAGAAAAAA
Found at i:1434506 original size:10 final size:10
Alignment explanation
Indices: 1434493--1434553 Score: 63
Period size: 10 Copynumber: 6.2 Consensus size: 10
1434483 GAAACAAAAC
1434493 AAAAAAGAAA
1 AAAAAAGAAA
*
1434503 AAAAAAGAAG
1 AAAAAAGAAA
*
1434513 AAACAA-AAA
1 AAAAAAGAAA
*
1434522 AAAACA-AAA
1 AAAAAAGAAA
*
1434531 AAAAACGAAA
1 AAAAAAGAAA
1434541 AAAAAACGAAA
1 AAAAAA-GAAA
1434552 AA
1 AA
1434554 CCCCTTTTCA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
9 13 0.32
10 22 0.54
11 6 0.15
ACGTcount: A:0.85, C:0.07, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAGAAA
Found at i:1434507 original size:11 final size:11
Alignment explanation
Indices: 1434476--1434553 Score: 66
Period size: 12 Copynumber: 6.5 Consensus size: 11
1434466 ATTCTTTTCC
*
1434476 AAAAAAAGAAAC
1 AAAAAAA-AAAG
1434488 AAAACAAAAAAG
1 AAAA-AAAAAAG
1434500 AAAAAAAAAGAAG
1 -AAAAAAAA-AAG
*
1434513 AAACAAAAAAAA
1 AAA-AAAAAAAG
1434525 ACAAAAAAAAACG
1 A-AAAAAAAAA-G
*
1434538 AAAAAAAAACG
1 AAAAAAAAAAG
1434549 AAAAA
1 AAAAA
1434554 CCCCTTTTCA
Statistics
Matches: 56, Mismatches: 4, Indels: 13
0.77 0.05 0.18
Matches are distributed among these distances:
11 6 0.11
12 32 0.57
13 18 0.32
ACGTcount: A:0.85, C:0.08, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAG
Found at i:1434543 original size:39 final size:39
Alignment explanation
Indices: 1434477--1434554 Score: 115
Period size: 38 Copynumber: 2.0 Consensus size: 39
1434467 TTCTTTTCCA
1434477 AAAAAAGAAACAAAACAAAAAAGAAAAAAAAAGAAGAAAC
1 AAAAAAGAAACAAAACAAAAAAGAAAAAAAAAGAA-AAAC
*
1434517 AAAAAA-AAACAAAA-AAAAACGAAAAAAAAACGAAAAAC
1 AAAAAAGAAACAAAACAAAAAAGAAAAAAAAA-GAAAAAC
1434555 CCCTTTTCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
38 19 0.53
39 11 0.31
40 6 0.17
ACGTcount: A:0.83, C:0.09, G:0.08, T:0.00
Consensus pattern (39 bp):
AAAAAAGAAACAAAACAAAAAAGAAAAAAAAAGAAAAAC
Found at i:1434553 original size:1 final size:1
Alignment explanation
Indices: 1434476--1434546 Score: 52
Period size: 1 Copynumber: 71.0 Consensus size: 1
1434466 ATTCTTTTCC
* * * * * * * * **
1434476 AAAAAAAGAAACAAAACAAAAAAGAAAAAAAAAGAAGAAACAAAAAAAAACAAAAAAAAACGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1434541 AAAAAA
1 AAAAAA
1434547 CGAAAAACCC
Statistics
Matches: 51, Mismatches: 19, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.86, C:0.07, G:0.07, T:0.00
Consensus pattern (1 bp):
A
Found at i:1435585 original size:30 final size:30
Alignment explanation
Indices: 1435478--1435616 Score: 172
Period size: 31 Copynumber: 4.5 Consensus size: 30
1435468 AATTCTTCAA
* *
1435478 ATCTCTTCTCAAAGCCCACGACTCAGTGGC
1 ATCTTTTCTCAAAGTCCACGACTCAGTGGC
* *
1435508 AATCTCTTCTCAAAGTCCACAACTCAGTGGC
1 -ATCTTTTCTCAAAGTCCACGACTCAGTGGC
1435539 ATCCTTTTCTTCAAAGTCCACGACTCAGTGGC
1 AT-CTTTTC-TCAAAGTCCACGACTCAGTGGC
*
1435571 AT-TTTGTCTCAAAGTCCACGGCTCAGTGGC
1 ATCTTT-TCTCAAAGTCCACGACTCAGTGGC
1435601 ATCCTTTTCTTCAAAG
1 AT-CTTTTC-TCAAAG
1435617 CCCGCAACTC
Statistics
Matches: 97, Mismatches: 5, Indels: 11
0.86 0.04 0.10
Matches are distributed among these distances:
30 28 0.29
31 37 0.38
32 32 0.33
ACGTcount: A:0.24, C:0.31, G:0.16, T:0.29
Consensus pattern (30 bp):
ATCTTTTCTCAAAGTCCACGACTCAGTGGC
Found at i:1435600 original size:62 final size:63
Alignment explanation
Indices: 1435486--1435633 Score: 210
Period size: 62 Copynumber: 2.4 Consensus size: 63
1435476 AAATCTCTTC
1435486 TCAAAGCCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACAACTCAGTGGCATCCTTTTCT
1 TCAAAGCCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACAACTCAGTGGCATCCTTTTCT
* * **
1435549 TCAAAGTCCACGACTCAGTGGC-AT-TTTGTCTCAAAGTCCACGGCTCAGTGGCATCCTTTTCT
1 TCAAAGCCCACGACTCAGTGGCAATCTCT-TCTCAAAGTCCACAACTCAGTGGCATCCTTTTCT
* * *
1435611 TCAAAGCCCGCAACTCCGTGGCA
1 TCAAAGCCCACGACTCAGTGGCA
1435634 CATTTTTCTT
Statistics
Matches: 75, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
61 2 0.03
62 52 0.69
63 21 0.28
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (63 bp):
TCAAAGCCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACAACTCAGTGGCATCCTTTTCT
Found at i:1435659 original size:34 final size:34
Alignment explanation
Indices: 1435613--1436294 Score: 632
Period size: 33 Copynumber: 20.8 Consensus size: 34
1435603 CCTTTTCTTC
* *
1435613 AAAGCCCGCAACTCCGTGGCACATTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
*
1435647 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTT
* * * *
1435683 -AAGTCCACAACTCTGTGGCACCTTGTTCCTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
*
1435716 -AAGTCCACAACTCCGTGGCACC-----C-TTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* * *
1435743 AAAGCCCACAATTCCGTGGCAACCTTTTTCTTCTC
1 AAAGCCCACAACTCCGTGGC-ACCTTTTTCTTTTT
*
1435778 AAAGCCCACCACTCCGTGGCA-CTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
*
1435811 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTC
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTTT
*
1435848 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTT
* * *
1435884 AAAGTCCACGACTCCGTGGCACC---TTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1435915 AAAGCCCACAACTCCGTGGCACC-----C-TTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
1435943 -AAGCCCACAACTCCGTGGCACTTTTTTCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTT
* **
1435977 -AAGTCCACAACTTTGTGGCACC-----C-TTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
1436004 -AAGCCCACAACTCCGTGGCACTTTTTTCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTT
*
1436038 -AAGTCCACAACTCCGTGGCACC-----C-TTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* * *
1436065 -AAGCCCACAACTCCGTGGCACCTTTCTCCTTCT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1436098 -AAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1436131 AAAGCCCACAACTCCGTGGCACCTTTTT-TTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
1436164 AAAGCCCACAACTTCGTGGCACTCTTTTTCCCTTTTC
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTTT
**
1436201 AAAGCCCACAACTTTGTGGCACCTTTTTC-TTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
1436234 AAAGCCCACAACTCCATGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT-CTTTTT
* *
1436270 -AAGTCCACAACTCCGTGGCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTT
1436295 CTCCCTTCCC
Statistics
Matches: 550, Mismatches: 56, Indels: 84
0.80 0.08 0.12
Matches are distributed among these distances:
27 70 0.13
28 21 0.04
29 6 0.01
31 25 0.05
32 5 0.01
33 138 0.25
34 116 0.21
35 70 0.13
36 40 0.07
37 59 0.11
ACGTcount: A:0.21, C:0.34, G:0.13, T:0.33
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
Found at i:1435758 original size:28 final size:27
Alignment explanation
Indices: 1435710--1435770 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
1435700 GCACCTTGTT
* *
1435710 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCGTGGCAA
*
1435737 CCTTTTAAAGCCCACAATTCCGTGGCAA
1 CCTTTT-AAGCCCACAACTCCGTGGCAA
1435765 CCTTTT
1 CCTTTT
1435771 TCTTCTCAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCGTGGCAA
Done.