Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A07
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: 92880876
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2857347 characters in sequence are not A, C, G, or T
File 113 of 290
Found at i:34955002 original size:51 final size:51
Alignment explanation
Indices: 34954926--34955029 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
34954916 GGGACATAGT
34954926 AAGACAACATGTCCACATTTTGGGGCAACATTGAGGTGATGATGGAATTAA
1 AAGACAACATGTCCACATTTTGGGGCAACATTGAGGTGATGATGGAATTAA
*
34954977 AAGACAACATGTCCACATTTTGGGGCAACATTGAGGTGCTGATGGAATTAA
1 AAGACAACATGTCCACATTTTGGGGCAACATTGAGGTGATGATGGAATTAA
34955028 AA
1 AA
34955030 AAATATTCTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.25
Consensus pattern (51 bp):
AAGACAACATGTCCACATTTTGGGGCAACATTGAGGTGATGATGGAATTAA
Found at i:34956352 original size:46 final size:45
Alignment explanation
Indices: 34956292--34956641 Score: 408
Period size: 46 Copynumber: 8.0 Consensus size: 45
34956282 TTTGACATGA
* * * * *
34956292 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CA-TTTCATATCAGGT
* * * *
34956338 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTA-CCATTTCATATCAGGT
* *
34956384 TGCCATGGTATCTTTCAACCATAGTCTTA-CATATCTCATATTAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACCAT-T-TCATATCAGGT
*
34956430 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CATTTCATATCAGGT
34956476 TGCCATGGTATCTTTCAACCATGGTCTTA-CA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACCATTTCATATCAGGT
34956514 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CATTTCATATCAGGT
34956560 TGCCATGGTATCTTTCAACCATGGTCTTA-CA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACCATTTCATATCAGGT
34956598 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTAC-CATTTCATATCAG
34956642 AGAGCACACT
Statistics
Matches: 267, Mismatches: 15, Indels: 44
0.82 0.05 0.13
Matches are distributed among these distances:
38 67 0.25
39 2 0.01
40 4 0.01
41 2 0.01
43 2 0.01
44 6 0.02
45 7 0.03
46 173 0.65
47 1 0.00
48 3 0.01
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.38
Consensus pattern (45 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACCATTTCATATCAGGT
Found at i:34956525 original size:38 final size:38
Alignment explanation
Indices: 34956474--34956630 Score: 242
Period size: 38 Copynumber: 3.9 Consensus size: 38
34956464 TTCATATCAA
34956474 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
34956512 GTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAG
34956558 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
34956596 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 GTTGCCATGGTATCTTTCAACCATGGTCTTACACA
34956631 TTTCATATCA
Statistics
Matches: 111, Mismatches: 0, Indels: 16
0.87 0.00 0.13
Matches are distributed among these distances:
38 68 0.61
39 1 0.01
40 3 0.03
41 1 0.01
43 1 0.01
44 3 0.03
45 1 0.01
46 33 0.30
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (38 bp):
GTTGCCATGGTATCTTTCAACCATGGTCTTACACACAG
Found at i:34956567 original size:84 final size:84
Alignment explanation
Indices: 34956426--34956641 Score: 423
Period size: 84 Copynumber: 2.6 Consensus size: 84
34956416 ATCTCATATT
*
34956426 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAAGTTGCCATGGTATCTTT
1 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTT
34956491 CAACCATGGTCTTACACAC
66 CAACCATGGTCTTACACAC
34956510 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTT
1 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTT
34956575 CAACCATGGTCTTACACAC
66 CAACCATGGTCTTACACAC
34956594 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
34956642 AGAGCACACT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 131 1.00
ACGTcount: A:0.25, C:0.25, G:0.16, T:0.35
Consensus pattern (84 bp):
AGGTTGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGTTGCCATGGTATCTTT
CAACCATGGTCTTACACAC
Found at i:34959120 original size:30 final size:30
Alignment explanation
Indices: 34959053--34959120 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
34959043 CACCCTTAAA
* *
34959053 ATATTTGCACTATTAGTCCTTCAAATTTTC
1 ATATTTACACTATTAATCCTTCAAATTTTC
*
34959083 ATATTTACACT-TTAATCCTTCAAATTTTG
1 ATATTTACACTATTAATCCTTCAAATTTTC
34959112 AGTATTTAC
1 A-TATTTAC
34959121 TCTTGGGCTA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 17 0.50
30 17 0.50
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (30 bp):
ATATTTACACTATTAATCCTTCAAATTTTC
Found at i:34961175 original size:20 final size:20
Alignment explanation
Indices: 34961150--34961188 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34961140 AACATATAAA
34961150 AATTTAAAAATAATATTAAC
1 AATTTAAAAATAATATTAAC
* *
34961170 AATTTAATAATTATATTAA
1 AATTTAAAAATAATATTAA
34961189 TTAAATAAAA
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:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AATTTAAAAATAATATTAAC
Found at i:34965334 original size:42 final size:42
Alignment explanation
Indices: 34965287--34965369 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
34965277 GACTAATGGG
* *
34965287 TTCCATTGATGCAGAAGGCATCAGTGATGGCATGGCCATTGA
1 TTCCATTGATGCAGAAGACATCAGTGATGGCATGACCATTGA
* * * *
34965329 TTCCATTGATGGAGAAGATATTAGTGATTGCATGACCATTG
1 TTCCATTGATGCAGAAGACATCAGTGATGGCATGACCATTG
34965370 TAGGTTGACT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.30
Consensus pattern (42 bp):
TTCCATTGATGCAGAAGACATCAGTGATGGCATGACCATTGA
Found at i:34980124 original size:21 final size:21
Alignment explanation
Indices: 34980092--34980132 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
34980082 GAACATTTGG
34980092 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
34980113 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
34980133 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:34984768 original size:16 final size:17
Alignment explanation
Indices: 34984707--34984771 Score: 69
Period size: 17 Copynumber: 3.7 Consensus size: 17
34984697 TATTTTAATT
*
34984707 AATAAAACATAAAATAA
1 AATAAAACATAATATAA
**
34984724 AATAAAAGGTTAATATAA
1 AATAAAA-CATAATATAA
34984742 TAATGAAAACATAATA-AA
1 -AAT-AAAACATAATATAA
34984760 AATAAAACATAA
1 AATAAAACATAA
34984772 GTGAATATTC
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
16 9 0.22
17 10 0.25
18 9 0.22
19 8 0.20
20 4 0.10
ACGTcount: A:0.69, C:0.05, G:0.05, T:0.22
Consensus pattern (17 bp):
AATAAAACATAATATAA
Found at i:34985014 original size:16 final size:15
Alignment explanation
Indices: 34984983--34985012 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
34984973 TCTATTGATG
34984983 AATCTAGTGATTTTT
1 AATCTAGTGATTTTT
34984998 AATCTAGTGATTTTT
1 AATCTAGTGATTTTT
34985013 TATGTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (15 bp):
AATCTAGTGATTTTT
Found at i:34986367 original size:67 final size:67
Alignment explanation
Indices: 34986259--34986392 Score: 259
Period size: 67 Copynumber: 2.0 Consensus size: 67
34986249 TCTAGTATAA
34986259 TGGTTATCTATGTTAAGTTCACATGAATTATATTCAATTATGCTAACACGTGTTGTTGTTGGTGC
1 TGGTTATCTATGTTAAGTTCACATGAATTATATTCAATTATGCTAACACGTGTTGTTGTTGGTGC
34986324 TT
66 TT
*
34986326 TGGTTATCTATGTTAAGTTCACATGAATTATATTCAATTATGCTAACATGTGTTGTTGTTGGTGC
1 TGGTTATCTATGTTAAGTTCACATGAATTATATTCAATTATGCTAACACGTGTTGTTGTTGGTGC
34986391 TT
66 TT
34986393 AGGCTTGTGC
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 66 1.00
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (67 bp):
TGGTTATCTATGTTAAGTTCACATGAATTATATTCAATTATGCTAACACGTGTTGTTGTTGGTGC
TT
Found at i:34987760 original size:28 final size:29
Alignment explanation
Indices: 34987709--34987764 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 29
34987699 ACAGGGGTTT
34987709 TCACACGGCCAATCACACGCCCGTGTCCC
1 TCACACGGCCAATCACACGCCCGTGTCCC
* *
34987738 TCACACGGCCTA-GACACGCCCGTGTCC
1 TCACACGGCCAATCACACGCCCGTGTCC
34987765 AAAACCCCGG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.20, C:0.46, G:0.20, T:0.14
Consensus pattern (29 bp):
TCACACGGCCAATCACACGCCCGTGTCCC
Found at i:34990496 original size:23 final size:23
Alignment explanation
Indices: 34990470--34990517 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
34990460 TGATGAAATT
*
34990470 TTTACATTTTGGTGCTTAAATGG
1 TTTACATTTTGGTGATTAAATGG
34990493 TTTACATTTTGGTGATTAAATGG
1 TTTACATTTTGGTGATTAAATGG
34990516 TT
1 TT
34990518 AATGTTGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.06, G:0.21, T:0.50
Consensus pattern (23 bp):
TTTACATTTTGGTGATTAAATGG
Found at i:34991234 original size:16 final size:15
Alignment explanation
Indices: 34991213--34991243 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
34991203 AATTATGTGT
34991213 ATTAATTTATAATTTA
1 ATTAATTT-TAATTTA
34991229 ATTAATTTTAATTTA
1 ATTAATTTTAATTTA
34991244 TATCCAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
ATTAATTTTAATTTA
Found at i:34991320 original size:14 final size:14
Alignment explanation
Indices: 34991298--34991328 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
34991288 GAAAAATGGT
*
34991298 CCGATTGAACCGAA
1 CCGAGTGAACCGAA
34991312 CCGAGTGAACCGAA
1 CCGAGTGAACCGAA
34991326 CCG
1 CCG
34991329 TCCAAGGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.32, C:0.32, G:0.26, T:0.10
Consensus pattern (14 bp):
CCGAGTGAACCGAA
Found at i:35003558 original size:49 final size:49
Alignment explanation
Indices: 35003406--35003623 Score: 150
Period size: 49 Copynumber: 4.6 Consensus size: 49
35003396 TGATATGTGT
* * *
35003406 GCTAGTGTAAGACATGTCTGGGACAT-GCATCAGCCTCGC-A-ATAGACAA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCAACCTCACTAGAT-GA-AA
* * * * ***
35003454 GCTAGTGTAAGACTTGTCTGGGACATGGCGTC-AGCT---T-GTTGTGT
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCAACCTCACTAGATGAAA
* * *
35003498 GTTAGTGTAAGACCTGTCCGGGACATGGCATCAACAC-CGA-TAGATGAGA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCAAC-CTC-ACTAGATGAAA
* * * * *
35003547 GCTAGTGTAAGACTTGTTTGGAACATGGCATCAGCCTCACTATATGAAA
1 GCTAGTGTAAGACCTGTCTGGGACATGGCATCAACCTCACTAGATGAAA
*
35003596 GCCAGTGTAAGACCATGTCTGGGACATG
1 GCTAGTGTAAGACC-TGTCTGGGACATG
35003624 ACGTTTGCAT
Statistics
Matches: 130, Mismatches: 28, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
44 28 0.22
45 2 0.02
46 2 0.02
48 30 0.23
49 57 0.44
50 11 0.08
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.25
Consensus pattern (49 bp):
GCTAGTGTAAGACCTGTCTGGGACATGGCATCAACCTCACTAGATGAAA
Found at i:35003573 original size:93 final size:91
Alignment explanation
Indices: 35003401--35003581 Score: 231
Period size: 93 Copynumber: 2.0 Consensus size: 91
35003391 TTGGGTGATA
* *
35003401 TGTGTGCTAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGCAATAGACAAGCTAGTGTAAGA
1 TGTGTGCTAGTGTAAGACATGTCCGGGACATGCATCAACCTCG-AATAGACAAGCTAGTGTAAGA
* *
35003466 CTTGTCTGGGACATGGCGTCAGCTTGT
65 CTTGTCTGGAACATGGCATCAGCTTGT
* * *
35003493 TGTGTGTTAGTGTAAGACCTGTCCGGGACATGGCATCAACAC-CG-ATAGATGAGAGCTAGTGTA
1 TGTGTGCTAGTGTAAGACATGTCCGGGACAT-GCATCAAC-CTCGAATAGA-CA-AGCTAGTGTA
*
35003556 AGACTTGTTTGGAACATGGCATCAGC
62 AGACTTGTCTGGAACATGGCATCAGC
35003582 CTCACTATAT
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
91 5 0.06
92 29 0.38
93 42 0.55
94 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.29, T:0.27
Consensus pattern (91 bp):
TGTGTGCTAGTGTAAGACATGTCCGGGACATGCATCAACCTCGAATAGACAAGCTAGTGTAAGAC
TTGTCTGGAACATGGCATCAGCTTGT
Found at i:35017492 original size:45 final size:45
Alignment explanation
Indices: 35017422--35017508 Score: 120
Period size: 45 Copynumber: 1.9 Consensus size: 45
35017412 GAACTGTGTG
* * *
35017422 ATCTGAACTCATTGAGTTGTTGTCTGAGTTCATGATATATGTGAC
1 ATCTGAACTCATTAAGTTATGGTCTGAGTTCATGATATATGTGAC
* * *
35017467 ATCTGAACTTATTAAGTTATGGTCTGAGTTCATTATGTATGT
1 ATCTGAACTCATTAAGTTATGGTCTGAGTTCATGATATATGT
35017509 AACACATGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 36 1.00
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.43
Consensus pattern (45 bp):
ATCTGAACTCATTAAGTTATGGTCTGAGTTCATGATATATGTGAC
Found at i:35024388 original size:17 final size:17
Alignment explanation
Indices: 35024368--35024422 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
35024358 AAATTTTATA
35024368 ATGATCTCAATTTATGT
1 ATGATCTCAATTTATGT
** *
35024385 ATGAT-AAAATTTGAT-A
1 ATGATCTCAATTT-ATGT
35024401 ATGATCTCAATTTATGT
1 ATGATCTCAATTTATGT
35024418 ATGAT
1 ATGAT
35024423 ACCCATGGTT
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
16 12 0.41
17 17 0.59
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (17 bp):
ATGATCTCAATTTATGT
Found at i:35024395 original size:33 final size:33
Alignment explanation
Indices: 35024358--35024423 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
35024348 GTTTAGAACT
*
35024358 AAATTTTATAATGATCTCAATTTATGTATGATA
1 AAATTTGATAATGATCTCAATTTATGTATGATA
35024391 AAATTTGATAATGATCTCAATTTATGTATGATA
1 AAATTTGATAATGATCTCAATTTATGTATGATA
35024424 CCCATGGTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.39, C:0.06, G:0.11, T:0.44
Consensus pattern (33 bp):
AAATTTGATAATGATCTCAATTTATGTATGATA
Found at i:35025234 original size:20 final size:21
Alignment explanation
Indices: 35025182--35025295 Score: 58
Period size: 20 Copynumber: 5.2 Consensus size: 21
35025172 CAAAATAAAA
35025182 ATTAAATTAAATTAAATTTAAT
1 ATTAAATT-AATTAAATTTAAT
* *
35025204 ATTAAGA-TAATT-ACTTTGAT
1 ATTAA-ATTAATTAAATTTAAT
*
35025224 ATTAAATTAATAAAATACTATTAAT
1 ATTAAATTAAT-TAA-A-T-TTAAT
*
35025249 A-TAATTATTAAATTAAATTTAAT
1 ATTAA--ATTAAT-TAAATTTAAT
*
35025272 ATTAAATCT-ATTAAA-ATAAT
1 ATTAAAT-TAATTAAATTTAAT
35025292 ATTA
1 ATTA
35025296 TTTTTTGGAA
Statistics
Matches: 71, Mismatches: 10, Indels: 24
0.68 0.10 0.23
Matches are distributed among these distances:
19 1 0.01
20 23 0.32
21 8 0.11
22 10 0.14
23 8 0.11
24 8 0.11
25 6 0.08
26 7 0.10
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.44
Consensus pattern (21 bp):
ATTAAATTAATTAAATTTAAT
Found at i:35033284 original size:23 final size:23
Alignment explanation
Indices: 35033257--35033300 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
35033247 TACGTTCTTT
*
35033257 ACATATGCTCAAACCA-AAATCAC
1 ACATATGCAC-AACCATAAATCAC
35033280 ACATATGCACAACCATAAATC
1 ACATATGCACAACCATAAATC
35033301 TCATGAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.48, C:0.30, G:0.05, T:0.18
Consensus pattern (23 bp):
ACATATGCACAACCATAAATCAC
Found at i:35036949 original size:46 final size:49
Alignment explanation
Indices: 35036807--35037121 Score: 225
Period size: 47 Copynumber: 6.7 Consensus size: 49
35036797 GTTAAGTGCC
* *
35036807 GATGCCATGTCCCAAACATGGTCTTACACTGGCTCATA-G-CTCAAGTC-
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT-ATACGTCTCAAGGCT
* * * *
35036854 GATGCCATGTCCCAGACATGGTCTTACAGTGACTATCACCTCT-TA-GCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTAT-ACGTCTCAAGGCT
*
35036902 GATG-CATGTCCCAGACAT-GTCTTACATTGGCT-TACGTCTCAAGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATACGTCTCAAGGCT
* **
35036948 GATG-CATGTCCCAGACAT-GTCTTACACTAGC-ACT-CGTCTCATTG-T
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTA-TACGTCTCAAGGCT
* * * * * * **
35036993 CGATGCCATGTCCTAGACATGGTTTTACACTAGCTCT-CATAAT-GTGGCT
1 -GATGCCATGTCCCAGACATGGTCTTACACTGGCTATACGT-CTCAAGGCT
* * ** * * *
35037042 GTTG-CATGTCCCAGACAT-GTCTTACACTAGCCCT-CATCTCAATGTT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCTATACGTCTCAAGGCT
*
35037088 GATGCCATGTCCCGGACATGGTCTTACACTGGCT
1 GATGCCATGTCCCAGACATGGTCTTACACTGGCT
35037122 TACACGAGTG
Statistics
Matches: 217, Mismatches: 34, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
44 5 0.02
45 4 0.02
46 80 0.37
47 87 0.40
48 37 0.17
49 4 0.02
ACGTcount: A:0.22, C:0.28, G:0.20, T:0.30
Consensus pattern (49 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGGCTATACGTCTCAAGGCT
Found at i:35037059 original size:94 final size:94
Alignment explanation
Indices: 35036944--35037117 Score: 276
Period size: 94 Copynumber: 1.9 Consensus size: 94
35036934 TACGTCTCAA
* * *
35036944 GGCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCGTCTCATTGTCGATGCCATGTCCTAG
1 GGCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCAATGTCGATGCCATGTCCCAG
*
35037009 ACATGGTTTTACACTAGCTCTCATAATGT
66 ACATGGTCTTACACTAGCTCTCATAATGT
* * * *
35037038 GGCTGTTGCATGTCCCAGACATGTCTTACACTAGCCCTCATCTCAATGTTGATGCCATGTCCCGG
1 GGCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCAATGTCGATGCCATGTCCCAG
35037103 ACATGGTCTTACACT
66 ACATGGTCTTACACT
35037118 GGCTTACACG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
94 72 1.00
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.31
Consensus pattern (94 bp):
GGCTGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCAATGTCGATGCCATGTCCCAG
ACATGGTCTTACACTAGCTCTCATAATGT
Found at i:35040031 original size:17 final size:18
Alignment explanation
Indices: 35039998--35040037 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
35039988 ACTTATTGCC
*
35039998 TATTTTTTTTATATTATA
1 TATTTTTATTATATTATA
*
35040016 TATTTTTATTAT-TTATT
1 TATTTTTATTATATTATA
35040033 TATTT
1 TATTT
35040038 ATTAACCCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (18 bp):
TATTTTTATTATATTATA
Found at i:35046963 original size:14 final size:14
Alignment explanation
Indices: 35046944--35046972 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
35046934 ATATTATAAT
35046944 ATTATTAAAACTTA
1 ATTATTAAAACTTA
35046958 ATTATTAAAACTTA
1 ATTATTAAAACTTA
35046972 A
1 A
35046973 AAGTTAAGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTATTAAAACTTA
Found at i:35047036 original size:11 final size:11
Alignment explanation
Indices: 35047022--35047060 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
35047012 GCATAAAATA
35047022 AAAAGAGAAAG
1 AAAAGAGAAAG
35047033 AAAAG-GAAAG
1 AAAAGAGAAAG
35047043 AAAAAGAGAAAG
1 -AAAAGAGAAAG
35047055 AAAAGA
1 AAAAGA
35047061 AGGAGAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 5 0.19
11 16 0.62
12 5 0.19
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:35047048 original size:16 final size:17
Alignment explanation
Indices: 35047022--35047061 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
35047012 GCATAAAATA
*
35047022 AAAAGAGAAAGA-AAAG
1 AAAAGAAAAAGAGAAAG
*
35047038 GAAAGAAAAAGAGAAAG
1 AAAAGAAAAAGAGAAAG
35047055 AAAAGAA
1 AAAAGAA
35047062 GGAGAATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 10 0.50
17 10 0.50
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAAGAGAAAG
Found at i:35047343 original size:30 final size:28
Alignment explanation
Indices: 35047289--35047345 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
35047279 AATTGTAAGA
*
35047289 TAAATTGTAAATTTTGAGTATTAGGGAC
1 TAAATTGTAAATTTTGAATATTAGGGAC
35047317 TAAATTGTGAAAATTTTGAA-ATTTAGGGA
1 TAAATTGT--AAATTTTGAATA-TTAGGGA
35047346 TTTAAGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 8 0.32
29 1 0.04
30 16 0.64
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.39
Consensus pattern (28 bp):
TAAATTGTAAATTTTGAATATTAGGGAC
Found at i:35051502 original size:46 final size:46
Alignment explanation
Indices: 35051371--35051588 Score: 153
Period size: 46 Copynumber: 4.7 Consensus size: 46
35051361 ATATCTGTGT
*
35051371 CGATGCCATGTCCCAGACATGGTCTTACACT-G-ACACATCTCGTA-GC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCATCTCG-AGGC
* * * *
35051417 CAATGCATGTCCCAAACATGTCTTACAC-A-AACTTACGTCTCGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGCAC-T-CATCTCGAGGC
* * * * *
35051463 CGATGCATGCCCCAGACATGTTTTACACTAGCACTCGTCTC-ATTGT
1 CGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCGA-GGC
* * * * *
35051509 CGATGCCATGTCCTAGACATGGTTTTACACTAGCTCTCATAAT-GTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCACTCAT-CTCGAGGC
* *
35051557 CGTTGCATCTCCCAGACATGTCTTACACTAGC
1 CGATGCATGTCCCAGACATGTCTTACACTAGC
35051589 TCACAATAGC
Statistics
Matches: 137, Mismatches: 23, Indels: 24
0.74 0.12 0.13
Matches are distributed among these distances:
44 11 0.08
45 15 0.11
46 60 0.44
47 26 0.19
48 24 0.18
49 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTAGCACTCATCTCGAGGC
Found at i:35064214 original size:49 final size:48
Alignment explanation
Indices: 35064132--35064381 Score: 149
Period size: 49 Copynumber: 5.2 Consensus size: 48
35064122 TTCTAAACAT
* * * * *
35064132 GGTCTTACACTAGCT-CTCACATCTAGGTCGATGCCATGTCCAAGACA
1 GGTCTTACACTAACTCCACACATCAATGCCGATGCCATGTCCAAGACA
*
35064179 GGTCTTACACTAACTTCCACACATCAATGCCGATGCCATGTCCCAGACA
1 GGTCTTACACTAAC-TCCACACATCAATGCCGATGCCATGTCCAAGACA
* * * * * *
35064228 GGTCTTACACCAA---CACACCTCAA-GCCGATGCCGTGTCCCATATA
1 GGTCTTACACTAACTCCACACATCAATGCCGATGCCATGTCCAAGACA
* * * * * * * * *
35064272 GGTCTTACCATTAGCTTGCATATC-TTAAGGTCGATGCGATGT-CTAGACA
1 GGTCTTA-CACTAAC-TCCACA-CATCAATGCCGATGCCATGTCCAAGACA
** * *
35064321 GGTCTTACACTGGCTCTCATC-TATCAGTGCCGATGCCATGTCCCAA-ACA
1 GGTCTTACACTAACTC-CA-CACATCAATGCCGATGCCATGT-CCAAGACA
35064370 GGTCTTACACTA
1 GGTCTTACACTA
35064382 GCACACACAT
Statistics
Matches: 155, Mismatches: 34, Indels: 26
0.72 0.16 0.12
Matches are distributed among these distances:
44 25 0.16
45 12 0.08
47 14 0.09
48 21 0.14
49 70 0.45
50 13 0.08
ACGTcount: A:0.26, C:0.30, G:0.18, T:0.26
Consensus pattern (48 bp):
GGTCTTACACTAACTCCACACATCAATGCCGATGCCATGTCCAAGACA
Found at i:35071948 original size:49 final size:46
Alignment explanation
Indices: 35071847--35072014 Score: 171
Period size: 49 Copynumber: 3.6 Consensus size: 46
35071837 CAATGCCAAC
* * **
35071847 GCCATGTTCCAAACATGGTCTTACACTGACTCTCACATCGAAGTTGAT
1 GCCATG-TCCAAACA-GGTCTTACACTAACTCACACATCGAAGCCGAT
*
35071895 GCCATGTCCAAGACAGGTCTTACACTAACTTCCACACATCGAGGCCGAT
1 GCCATGTCCAA-ACAGGTCTTACACTAAC-T-CACACATCGAAGCCGAT
* *
35071944 GCCATGTCCCAAACAGGTCTTACACTGA--CACACCTC-AAGCCGAT
1 GCCATGT-CCAAACAGGTCTTACACTAACTCACACATCGAAGCCGAT
* *
35071988 GCCATGTCTCATACAAGTCTTACACTA
1 GCCATGTC-CAAACAGGTCTTACACTA
35072015 GCTGGCATAT
Statistics
Matches: 104, Mismatches: 11, Indels: 14
0.81 0.09 0.11
Matches are distributed among these distances:
43 1 0.01
44 29 0.28
45 7 0.07
47 18 0.17
48 10 0.10
49 35 0.34
50 4 0.04
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.24
Consensus pattern (46 bp):
GCCATGTCCAAACAGGTCTTACACTAACTCACACATCGAAGCCGAT
Found at i:35072010 original size:93 final size:95
Alignment explanation
Indices: 35071847--35072063 Score: 226
Period size: 93 Copynumber: 2.3 Consensus size: 95
35071837 CAATGCCAAC
* * ** *
35071847 GCCATGTTCCAAACATGGTCTTACACTGACTCTCACATCGAAGTTGATGCCATGTCCAAGACAGG
1 GCCATGTCCCAAACA-GGTCTTACACTGAC-CACACATCGAAGCCGATGCCATGTCCAAGACAAG
*
35071912 TCTTACACTAACTTCCACA-CATCGAGGCCGAT
64 TCTTACACTAACTGCCACATC-TCGAGGCCGAT
* *
35071944 GCCATGTCCCAAACAGGTCTTACACTGA-CACACCTC-AAGCCGATGCCATGTCTC-ATACAAGT
1 GCCATGTCCCAAACAGGTCTTACACTGACCACACATCGAAGCCGATGCCATGTC-CAAGACAAGT
* * * * *
35072006 CTTACACTAGCTGGCATATCTTGAGGTCGAT
65 CTTACACTAACTGCCACATCTCGAGGCCGAT
* * *
35072037 GCGATGTCCCAGATAGGTCTTACACTG
1 GCCATGTCCCAAACAGGTCTTACACTG
35072064 GCTCTCATCT
Statistics
Matches: 102, Mismatches: 16, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
93 67 0.66
94 8 0.08
96 13 0.13
97 14 0.14
ACGTcount: A:0.27, C:0.29, G:0.19, T:0.25
Consensus pattern (95 bp):
GCCATGTCCCAAACAGGTCTTACACTGACCACACATCGAAGCCGATGCCATGTCCAAGACAAGTC
TTACACTAACTGCCACATCTCGAGGCCGAT
Found at i:35074827 original size:20 final size:21
Alignment explanation
Indices: 35074802--35074841 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
35074792 TGGGCGTATG
35074802 TGAAA-GGGAAGAGAAAACCA
1 TGAAAGGGGAAGAGAAAACCA
35074822 TGAAAGGGGAAGAGAAAACC
1 TGAAAGGGGAAGAGAAAACC
35074842 CAACAACATG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.53, C:0.10, G:0.33, T:0.05
Consensus pattern (21 bp):
TGAAAGGGGAAGAGAAAACCA
Found at i:35075745 original size:20 final size:20
Alignment explanation
Indices: 35075720--35075765 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
35075710 AGGGACTAAA
*
35075720 ATGAAAAGTTGTAAAATTTG
1 ATGAAAAATTGTAAAATTTG
* *
35075740 ATGAAAAATTTTAAAATTTT
1 ATGAAAAATTGTAAAATTTG
35075760 ATGAAA
1 ATGAAA
35075766 GCATGTGTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
ATGAAAAATTGTAAAATTTG
Found at i:35087970 original size:21 final size:18
Alignment explanation
Indices: 35087930--35087973 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 18
35087920 TAATAATTGT
35087930 TATAAGTTTTTATATTTA
1 TATAAGTTTTTATATTTA
35087948 TATAAGTTATTTATATGTTTA
1 TATAAGTT-TTTATA--TTTA
35087969 TATAA
1 TATAA
35087974 AAATTTAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
21 9 0.39
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (18 bp):
TATAAGTTTTTATATTTA
Found at i:35088007 original size:20 final size:20
Alignment explanation
Indices: 35087979--35088026 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
35087969 TATAAAAATT
* *
35087979 TAATATTTTTATCATACTTA
1 TAATTTTTTTATAATACTTA
**
35087999 TAATTTTTTTATAATTTTTA
1 TAATTTTTTTATAATACTTA
35088019 TAATTTTT
1 TAATTTTT
35088027 ATTAGAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (20 bp):
TAATTTTTTTATAATACTTA
Found at i:35088025 original size:8 final size:9
Alignment explanation
Indices: 35087883--35088028 Score: 57
Period size: 9 Copynumber: 15.2 Consensus size: 9
35087873 GAGTTTTATA
35087883 ATAATTTTT
1 ATAATTTTT
*
35087892 AT-ATTTAT
1 ATAATTTTT
* *
35087900 GTATTTTTAT
1 ATAATTTT-T
35087910 ATAAAATTTTT
1 AT--AATTTTT
*
35087921 AATAATTGTT
1 -ATAATTTTT
35087931 ATAAGTTTTT
1 ATAA-TTTTT
*
35087941 AT-ATTTAT
1 ATAATTTTT
35087949 ATAAGTTATTT
1 ATAA-TT-TTT
35087960 AT-ATGTTTAT
1 ATAAT-TTT-T
**
35087970 ATAAAAATTT
1 AT-AATTTTT
35087980 A-ATATTTTT
1 ATA-ATTTTT
* **
35087989 ATCATACTT
1 ATAATTTTT
35087998 ATAATTTTTTT
1 ATAA--TTTTT
35088009 ATAATTTTT
1 ATAATTTTT
35088018 ATAATTTTT
1 ATAATTTTT
35088027 AT
1 AT
35088029 TAGAAATGAA
Statistics
Matches: 100, Mismatches: 20, Indels: 34
0.65 0.13 0.22
Matches are distributed among these distances:
8 13 0.13
9 42 0.42
10 23 0.23
11 14 0.14
12 8 0.08
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (9 bp):
ATAATTTTT
Found at i:35095060 original size:13 final size:13
Alignment explanation
Indices: 35095044--35095070 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35095034 ATTTCTTGGA
35095044 GAAATGTCGGTCT
1 GAAATGTCGGTCT
35095057 GAAATGTCGGTCT
1 GAAATGTCGGTCT
35095070 G
1 G
35095071 GTTCTTAACT
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:0.22, C:0.15, G:0.33, T:0.30
Consensus pattern (13 bp):
GAAATGTCGGTCT
Found at i:35109322 original size:55 final size:55
Alignment explanation
Indices: 35109238--35109346 Score: 200
Period size: 55 Copynumber: 2.0 Consensus size: 55
35109228 GGTATCCCAT
* *
35109238 TTACCATCAAATTGTGTAAGTGGCCATTTTAAGTATGCACTCCTGTGAACCTCGG
1 TTACCATAAAATTGTGTAAGTGACCATTTTAAGTATGCACTCCTGTGAACCTCGG
35109293 TTACCATAAAATTGTGTAAGTGACCATTTTAAGTATGCACTCCTGTGAACCTCG
1 TTACCATAAAATTGTGTAAGTGACCATTTTAAGTATGCACTCCTGTGAACCTCG
35109347 CTCTTACGGC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (55 bp):
TTACCATAAAATTGTGTAAGTGACCATTTTAAGTATGCACTCCTGTGAACCTCGG
Found at i:35113847 original size:24 final size:24
Alignment explanation
Indices: 35113815--35113868 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
35113805 TTGCAAATTT
*
35113815 TGCCTTAAACCCTAGTATGTGACA
1 TGCCTTAAACCCTAGTATATGACA
35113839 TGCCTTAAACCCTAGTATATGACA
1 TGCCTTAAACCCTAGTATATGACA
*
35113863 TACCTT
1 TGCCTT
35113869 GTTTTAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (24 bp):
TGCCTTAAACCCTAGTATATGACA
Found at i:35122873 original size:6 final size:6
Alignment explanation
Indices: 35122862--35123029 Score: 336
Period size: 6 Copynumber: 28.0 Consensus size: 6
35122852 TTCATCCTTA
35122862 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35122910 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35122958 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT ACATAT
35123006 ACATAT ACATAT ACATAT ACATAT
1 ACATAT ACATAT ACATAT ACATAT
35123030 GACTCATTTC
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 162 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ACATAT
Found at i:35123983 original size:47 final size:47
Alignment explanation
Indices: 35123900--35124009 Score: 139
Period size: 47 Copynumber: 2.3 Consensus size: 47
35123890 TCTGAACAAA
* * * * * *
35123900 GACATATTAAAATGCTGTACTAAGTAAGACATAATTATTAGACTTAG
1 GACACATTAAAATGTTGTACTAAATAAGACACAATTAGTAAACTTAG
* *
35123947 GACACATTAAAATGTTGTACTAAATAGGACACAATTAGTAAACTTAT
1 GACACATTAAAATGTTGTACTAAATAAGACACAATTAGTAAACTTAG
35123994 GACACATTAAAGATGT
1 GACACATTAAA-ATGT
35124010 ATATATTAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
47 50 0.93
48 4 0.07
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.30
Consensus pattern (47 bp):
GACACATTAAAATGTTGTACTAAATAAGACACAATTAGTAAACTTAG
Found at i:35127251 original size:16 final size:15
Alignment explanation
Indices: 35127224--35127257 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
35127214 ATAACTAGTA
*
35127224 TATAATTATATTTAT
1 TATAATTATATTAAT
35127239 TATAATGTATATTAAT
1 TATAAT-TATATTAAT
35127255 TAT
1 TAT
35127258 TATAAACTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (15 bp):
TATAATTATATTAAT
Found at i:35135506 original size:25 final size:25
Alignment explanation
Indices: 35135478--35135554 Score: 70
Period size: 25 Copynumber: 3.2 Consensus size: 25
35135468 CCAAAATACC
35135478 CTTAATGCATTTCCTTCAAAATTTT
1 CTTAATGCATTTCCTTCAAAATTTT
* ** ***
35135503 CTT-ATACATGTGAC--CAAAATACC
1 CTTAATGCAT-TTCCTTCAAAATTTT
35135526 CTTAATGCATTTCCTTCAAAATTTT
1 CTTAATGCATTTCCTTCAAAATTTT
35135551 CTTA
1 CTTA
35135555 TACATGTCCA
Statistics
Matches: 36, Mismatches: 12, Indels: 8
0.64 0.21 0.14
Matches are distributed among these distances:
23 11 0.31
24 10 0.28
25 15 0.42
ACGTcount: A:0.31, C:0.22, G:0.05, T:0.42
Consensus pattern (25 bp):
CTTAATGCATTTCCTTCAAAATTTT
Found at i:35135521 original size:48 final size:48
Alignment explanation
Indices: 35135465--35135561 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
35135455 ATTTACCAAA
35135465 TGACCAAAATACCCTTAATGCATTTCCTTCAAAATTTTCTTATACATG
1 TGACCAAAATACCCTTAATGCATTTCCTTCAAAATTTTCTTATACATG
35135513 TGACCAAAATACCCTTAATGCATTTCCTTCAAAATTTTCTTATACATG
1 TGACCAAAATACCCTTAATGCATTTCCTTCAAAATTTTCTTATACATG
35135561 T
1 T
35135562 CCATTTTTGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (48 bp):
TGACCAAAATACCCTTAATGCATTTCCTTCAAAATTTTCTTATACATG
Found at i:35142525 original size:42 final size:42
Alignment explanation
Indices: 35142466--35142558 Score: 177
Period size: 42 Copynumber: 2.2 Consensus size: 42
35142456 CCCCAAAATA
*
35142466 TCACACGGCCATGGCACACACCCGTGTGCTAGGCCGTGTCCC
1 TCACACGGCCATGGCACACACCCGTGTGCTAGGCCATGTCCC
35142508 TCACACGGCCATGGCACACACCCGTGTGCTAGGCCATGTCCC
1 TCACACGGCCATGGCACACACCCGTGTGCTAGGCCATGTCCC
35142550 TCACACGGC
1 TCACACGGC
35142559 GGAGACACAC
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.18, C:0.41, G:0.25, T:0.16
Consensus pattern (42 bp):
TCACACGGCCATGGCACACACCCGTGTGCTAGGCCATGTCCC
Found at i:35143562 original size:48 final size:46
Alignment explanation
Indices: 35143438--35143608 Score: 184
Period size: 47 Copynumber: 3.6 Consensus size: 46
35143428 TTTCTCAAGT
* *
35143438 CGATGCCATGTCCCAGACATGGTCTTACACTGACTA-TCATCTCGTAGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGC-ACTCATCTTGTAGC
* *
35143486 CGATGCTTGTCCTAGACATGTCTTACACTGGCACTCATCTTG-ATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTTGTA-GC
* * * ** *
35143532 TGATGACATGTCCCAAACATGGTCTTACACTGGCTCTCATAATGTGGC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCACTCATCTTGTAGC
35143580 CGATGCATGTCCCAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
35143609 AGCTCACAAT
Statistics
Matches: 104, Mismatches: 14, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
45 2 0.02
46 35 0.34
47 36 0.35
48 31 0.30
ACGTcount: A:0.23, C:0.29, G:0.19, T:0.29
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCACTCATCTTGTAGC
Found at i:35147576 original size:49 final size:49
Alignment explanation
Indices: 35147516--35147643 Score: 136
Period size: 49 Copynumber: 2.6 Consensus size: 49
35147506 GCACATTGAA
** *
35147516 GTCGATGCCATGTCCCAGGCAAGTCTTACACTGACTTTCATATATCGAG-
1 GTCGATGCCATGTCCCAGAAAAGTCTTACACTGACTCTCATATATCG-GT
** * *
35147565 G-CTGATGCCATGTCTTAGAAAAGTCTTACACTGGCTCTCATTTATCGGT
1 GTC-GATGCCATGTCCCAGAAAAGTCTTACACTGACTCTCATATATCGGT
*
35147614 GTCGATGCCATGTCCCA-AACAGGTCTTACA
1 GTCGATGCCATGTCCCAGAA-AAGTCTTACA
35147644 ATAGCTTGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
48 4 0.06
49 60 0.92
50 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (49 bp):
GTCGATGCCATGTCCCAGAAAAGTCTTACACTGACTCTCATATATCGGT
Found at i:35147728 original size:46 final size:46
Alignment explanation
Indices: 35147662--35147790 Score: 154
Period size: 46 Copynumber: 2.8 Consensus size: 46
35147652 TATATCCTGA
* * *
35147662 GGCCGATGAATGTCCTAGACATGTCTTACACTAGCTCTCATC-TCAAT
1 GGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCAT--AT
* * * *
35147709 -GCCGATGCATGTCCCAGACATGTGTTACACTGGCACTCATGATGT
1 GGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCATAT
*
35147754 GGCAGATGCATGTCCCAGACATGTCTTACACTGGCTC
1 GGCCGATGCATGTCCCAGACATGTCTTACACTGGCTC
35147791 ACATACCACC
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
45 1 0.01
46 68 0.97
47 1 0.01
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (46 bp):
GGCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCATAT
Found at i:35164919 original size:50 final size:48
Alignment explanation
Indices: 35164806--35164927 Score: 140
Period size: 50 Copynumber: 2.5 Consensus size: 48
35164796 ATTTATGTGT
* *
35164806 TAGTGCAAGA-CATGTCTGGGACAT-GCATCAGCCACATTATGAGAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGACAGC
* * * * *
35164852 CAATGTAAGACCATGTCTGGGACATGGCATCGGCACAGATATGTGACAGC
1 TAGTGTAAGACCATGTCTGGGACATGGCATCAGC-CACAT-TATGACAGC
*
35164902 TAGTGTAAGACCATGTCTAGGACATG
1 TAGTGTAAGACCATGTCTGGGACATG
35164928 TCATTGACTT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 7 0.11
47 14 0.23
48 7 0.11
49 4 0.06
50 30 0.48
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.22
Consensus pattern (48 bp):
TAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACATTATGACAGC
Found at i:35166609 original size:11 final size:11
Alignment explanation
Indices: 35166593--35166623 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
35166583 GTTTAGGTGA
*
35166593 ATTACCGGTCT
1 ATTACCGGCCT
35166604 ATTACCGGCCT
1 ATTACCGGCCT
35166615 ATTACCGGC
1 ATTACCGGC
35166624 ATTGACTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.19, C:0.32, G:0.19, T:0.29
Consensus pattern (11 bp):
ATTACCGGCCT
Found at i:35167797 original size:30 final size:29
Alignment explanation
Indices: 35167763--35167823 Score: 104
Period size: 30 Copynumber: 2.1 Consensus size: 29
35167753 CTTAACAAGT
35167763 AAATGCCTCTAAAATAATAAAAAAATTAAC
1 AAATGCCTCTAAAATAAT-AAAAAATTAAC
*
35167793 AAATGCCTTTAAAATAATAAAAAATTAAC
1 AAATGCCTCTAAAATAATAAAAAATTAAC
35167822 AA
1 AA
35167824 GAAAATAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.61, C:0.11, G:0.03, T:0.25
Consensus pattern (29 bp):
AAATGCCTCTAAAATAATAAAAAATTAAC
Found at i:35168601 original size:16 final size:16
Alignment explanation
Indices: 35168569--35168608 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 16
35168559 AGTAATAATT
35168569 TATATTATATAAAAAAA
1 TATATT-TATAAAAAAA
35168586 TATATTTATAATAAAAA
1 TATATTTATAA-AAAAA
35168603 -ATATTT
1 TATATTT
35168609 CATTAATAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 11 0.50
17 11 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TATATTTATAAAAAAA
Found at i:35168601 original size:19 final size:17
Alignment explanation
Indices: 35168569--35168607 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
35168559 AGTAATAATT
35168569 TATATTATATAAAAAAA
1 TATATTATATAAAAAAA
35168586 TATATT-TATAATAAAAA
1 TATATTATATAA-AAAAA
35168603 -ATATT
1 TATATT
35168608 TCATTAATAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATATTATATAAAAAAA
Found at i:35176434 original size:14 final size:14
Alignment explanation
Indices: 35176415--35176449 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
35176405 CAAAAATTGA
35176415 GTTAGTAGAACCAG
1 GTTAGTAGAACCAG
*
35176429 GTTAGTAGAATCAG
1 GTTAGTAGAACCAG
35176443 GTTAGTA
1 GTTAGTA
35176450 AATCAAACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.29, T:0.29
Consensus pattern (14 bp):
GTTAGTAGAACCAG
Found at i:35186261 original size:22 final size:22
Alignment explanation
Indices: 35186233--35186274 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
35186223 GTTAAAGAAG
*
35186233 GTTTAGCATAATCTTACATAAA
1 GTTTAGCATAATCATACATAAA
35186255 GTTTAGCATAATCATACATA
1 GTTTAGCATAATCATACATA
35186275 GTACGTGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.36
Consensus pattern (22 bp):
GTTTAGCATAATCATACATAAA
Found at i:35187806 original size:40 final size:40
Alignment explanation
Indices: 35187751--35187968 Score: 305
Period size: 40 Copynumber: 5.5 Consensus size: 40
35187741 CGGATGATAA
* * *
35187751 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
35187791 CCGGGCTAAGTCCCGAAGGCATTTGTGCAAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
35187831 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTCACTGTAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
35187871 CAGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
35187911 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
35187951 -CTGGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
35187969 TACCTAGCTT
Statistics
Matches: 163, Mismatches: 14, Indels: 3
0.91 0.08 0.02
Matches are distributed among these distances:
39 16 0.10
40 147 0.90
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:35195090 original size:40 final size:40
Alignment explanation
Indices: 35195033--35195250 Score: 278
Period size: 40 Copynumber: 5.5 Consensus size: 40
35195023 CGGATGATAA
* * *
35195033 CCGGGCTAAGTCCCGAAGGCATTTGCGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
* *
35195073 CTGGGCTAAGTCCCGAAGGTATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * * * *
35195113 CCAGGCTAAGTCCCGAAGGCAATTGTGCGAGTCACTGTAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
35195153 CCGGGCTAAGTCCCGAAAGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
35195193 CCGGGCTAAGTCCCGAAGGCATTGGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* *
35195233 CC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
35195251 TACCTGGCTT
Statistics
Matches: 155, Mismatches: 22, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
39 15 0.10
40 140 0.90
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:35199177 original size:21 final size:21
Alignment explanation
Indices: 35199153--35199196 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
35199143 TCGAGAACTT
35199153 GAGAAGTTTCAAGAAAAATTA
1 GAGAAGTTTCAAGAAAAATTA
35199174 GAGAAGTTTCAAGAAAAATTA
1 GAGAAGTTTCAAGAAAAATTA
35199195 GA
1 GA
35199197 AAATTTTCCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.05, G:0.20, T:0.23
Consensus pattern (21 bp):
GAGAAGTTTCAAGAAAAATTA
Found at i:35199204 original size:21 final size:21
Alignment explanation
Indices: 35199156--35199204 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
35199146 AGAACTTGAG
*
35199156 AAGTTTCAAGAAAAATTAGAG
1 AAGTTTCAAGAAAAATTAGAA
35199177 AAGTTTCAAGAAAAATTAGAA
1 AAGTTTCAAGAAAAATTAGAA
*
35199198 AATTTTC
1 AAGTTTC
35199205 CCCTAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (21 bp):
AAGTTTCAAGAAAAATTAGAA
Found at i:35201340 original size:48 final size:46
Alignment explanation
Indices: 35201280--35201400 Score: 154
Period size: 46 Copynumber: 2.6 Consensus size: 46
35201270 AAGCTGGTGC
* * *
35201280 CATGTCCCAGACAGGTCTTACACTAGCT-TGTATATCTCGAGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCT-CATA-AT-GAGGCCGATG
* *
35201328 CATGTCCCAGACATGTCTTACACTGGCTCTCATAATGTGGCCGATG
1 CATGTCCCAGACATGTCTTACACTAGCTCTCATAATGAGGCCGATG
*
35201374 CATTTCCCAGACATGTCTTACACTAGC
1 CATGTCCCAGACATGTCTTACACTAGC
35201401 ACACATATCA
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
46 34 0.52
47 1 0.02
48 29 0.45
49 1 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTAGCTCTCATAATGAGGCCGATG
Found at i:35209034 original size:47 final size:46
Alignment explanation
Indices: 35208924--35209044 Score: 138
Period size: 47 Copynumber: 2.6 Consensus size: 46
35208914 TTATTTGTGT
* *
35208924 GCTAGTGTAAGACATGTCTGGGACATGCAATGACCATATTATGAGA
1 GCTAGTGTAAGACATGTCTGGGACATGCAATGACCATATGACGAGA
* * * *
35208970 GCCAGTGTAAGACCATGTTTGGGACATGCCATTG-GCAT-TGAGACGAGA
1 GCTAGTGTAAGA-CATGTCTGGGACATG-CAATGACCATAT--GACGAGA
35209018 GCTAGTGTAAGACATGTCTGGGACATG
1 GCTAGTGTAAGACATGTCTGGGACATG
35209045 TATCAGCCTC
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
46 12 0.19
47 31 0.49
48 20 0.32
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.25
Consensus pattern (46 bp):
GCTAGTGTAAGACATGTCTGGGACATGCAATGACCATATGACGAGA
Found at i:35209090 original size:46 final size:46
Alignment explanation
Indices: 35209020--35209107 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
35209010 AGACGAGAGC
* * *
35209020 TAGTGTAAGACATGTCTGGGACATGTATCAGCCT-CGAGATGTAAAA
1 TAGTGTAAGACATGTCTAGAACATGCATC-GCCTACGAGATGTAAAA
* *
35209066 TAGTGTAAGACATGTTTAGAACATGCATCGGCTACGAGATGT
1 TAGTGTAAGACATGTCTAGAACATGCATCGCCTACGAGATGT
35209108 GTCAGTGTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
45 3 0.08
46 33 0.92
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (46 bp):
TAGTGTAAGACATGTCTAGAACATGCATCGCCTACGAGATGTAAAA
Found at i:35212454 original size:38 final size:38
Alignment explanation
Indices: 35212320--35212454 Score: 119
Period size: 38 Copynumber: 3.4 Consensus size: 38
35212310 TTCCAACATG
* * *
35212320 TATTATCTTCAATTTAATTTCTCTTTAAAATAATCAAA
1 TATTATCTTCAATTTAATTTCTATTCAAAATAATAAAA
* * * *
35212358 TATAATCTTCAATTCAATTTCTGTCCAAAATAATCCCCAATAA
1 TATTATCTTCAATTTAATTTCTATTCAAAATAAT----AA-AA
* *
35212401 -ACTTTATTTTCAATTTAATTACTATTCAAAATAATAAAA
1 TA--TTATCTTCAATTTAATTTCTATTCAAAATAATAAAA
35212440 TATTATCTTCAATTT
1 TATTATCTTCAATTT
35212455 CATTCCTTTA
Statistics
Matches: 76, Mismatches: 13, Indels: 16
0.72 0.12 0.15
Matches are distributed among these distances:
38 41 0.54
39 2 0.03
40 3 0.04
42 2 0.03
43 2 0.03
44 26 0.34
ACGTcount: A:0.40, C:0.16, G:0.01, T:0.44
Consensus pattern (38 bp):
TATTATCTTCAATTTAATTTCTATTCAAAATAATAAAA
Found at i:35215656 original size:21 final size:22
Alignment explanation
Indices: 35215631--35215672 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35215621 TAAAGAAAAT
35215631 AGAAAATAT-AAATACAAATAA
1 AGAAAATATAAAATACAAATAA
*
35215652 AGAAAATATAAAATATAAATA
1 AGAAAATATAAAATACAAATA
35215673 TAAATAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (22 bp):
AGAAAATATAAAATACAAATAA
Found at i:35215658 original size:28 final size:28
Alignment explanation
Indices: 35215618--35215680 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 28
35215608 ACATGCAAGA
35215618 AAATAAAGAAAATAGAAAATATAAATAC
1 AAATAAAGAAAATAGAAAATATAAATAC
* *
35215646 AAATAAAGAAAATATAAAATATAAATAT
1 AAATAAAGAAAATAGAAAATATAAATAC
35215674 AAATAAA
1 AAATAAA
35215681 AAATACAAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.73, C:0.02, G:0.05, T:0.21
Consensus pattern (28 bp):
AAATAAAGAAAATAGAAAATATAAATAC
Found at i:35215683 original size:19 final size:19
Alignment explanation
Indices: 35215655--35215699 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
35215645 CAAATAAAGA
* *
35215655 AAATATAAAATATAAATAT
1 AAATAAAAAATACAAATAT
35215674 AAATAAAAAATACAAATAT
1 AAATAAAAAATACAAATAT
35215693 -AATAAAA
1 AAATAAAA
35215700 TTGGGTTGCC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAAAAATACAAATAT
Found at i:35215698 original size:28 final size:28
Alignment explanation
Indices: 35215618--35215694 Score: 106
Period size: 28 Copynumber: 2.9 Consensus size: 28
35215608 ACATGCAAGA
*
35215618 AAATAAAGAAAATAGAAAATATAAATAC
1 AAATAAAGAAAATACAAAATATAAATAC
* *
35215646 AAATAAAGAAAATATAAAATATAAATAT
1 AAATAAAGAAAATACAAAATATAAATAC
35215674 AAAT-AA-AAAATAC-AAATATAA
1 AAATAAAGAAAATACAAAATATAA
35215695 TAAAATTGGG
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 8 0.17
26 6 0.13
27 2 0.04
28 30 0.65
ACGTcount: A:0.73, C:0.03, G:0.04, T:0.21
Consensus pattern (28 bp):
AAATAAAGAAAATACAAAATATAAATAC
Found at i:35220284 original size:27 final size:29
Alignment explanation
Indices: 35220223--35220286 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 29
35220213 ATATTTTGGT
*
35220223 GATATTTTTAATTAATTAATTAATTAGTTA
1 GATATTTTTAATTAATTAATT-ATTACTTA
*
35220253 AATATTATTTAATTAA-T-ATT-TTACTTA
1 GATATT-TTTAATTAATTAATTATTACTTA
35220280 GATATTT
1 GATATTT
35220287 ATTATTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 1 0.03
27 11 0.37
29 3 0.10
30 6 0.20
31 9 0.30
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.55
Consensus pattern (29 bp):
GATATTTTTAATTAATTAATTATTACTTA
Found at i:35220290 original size:23 final size:24
Alignment explanation
Indices: 35220258--35220304 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
35220248 AGTTAAATAT
35220258 TATTTAATTAATATTTTACTTAGA
1 TATTTAATTAATATTTTACTTAGA
* *
35220282 TATTT-ATTATTATTTTATTTAGA
1 TATTTAATTAATATTTTACTTAGA
35220305 AAATAGTAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.60
Consensus pattern (24 bp):
TATTTAATTAATATTTTACTTAGA
Found at i:35221010 original size:12 final size:12
Alignment explanation
Indices: 35220995--35221021 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
35220985 TAAATTAGAG
35220995 ATTGAATTAAAT
1 ATTGAATTAAAT
35221007 ATTGAATTAAAT
1 ATTGAATTAAAT
35221019 ATT
1 ATT
35221022 AATGAGTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (12 bp):
ATTGAATTAAAT
Found at i:35223762 original size:22 final size:21
Alignment explanation
Indices: 35223723--35223768 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
35223713 TAAAAACTAC
**
35223723 AAAAATTTATAATTTTTACAA
1 AAAAATTTATAAAATTTACAA
*
35223744 AAAAATTATATAAAATTTATAA
1 AAAAATT-TATAAAATTTACAA
35223766 AAA
1 AAA
35223769 TATAATAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AAAAATTTATAAAATTTACAA
Found at i:35224005 original size:10 final size:10
Alignment explanation
Indices: 35223982--35224061 Score: 55
Period size: 9 Copynumber: 8.5 Consensus size: 10
35223972 TTTTACATAA
35223982 TTTTAA-ATT
1 TTTTAATATT
*
35223991 CTTTAATATT
1 TTTTAATATT
35224001 TTTT-AT-TT
1 TTTTAATATT
*
35224009 TTTTATTA-T
1 TTTTAATATT
**
35224018 TTTTAATAAG
1 TTTTAATATT
*
35224028 GTTTAATATT
1 TTTTAATATT
*
35224038 TTTATAAT-TA
1 TTT-TAATATT
35224048 TTTTAA-ATT
1 TTTTAATATT
35224057 TTTTA
1 TTTTA
35224062 TTTTTAAAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
8 6 0.11
9 25 0.46
10 19 0.35
11 4 0.07
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (10 bp):
TTTTAATATT
Found at i:35224076 original size:26 final size:28
Alignment explanation
Indices: 35224033--35224095 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
35224023 ATAAGGTTTA
* *
35224033 ATATTTTTATAATTATTTTAAATT-TTT
1 ATATTTTTAAAATAATTTTAAATTATTT
**
35224060 -TATTTTTAAAATAATTTTCTATTATTT
1 ATATTTTTAAAATAATTTTAAATTATTT
35224087 ATATTTTTA
1 ATATTTTTA
35224096 CAAGGTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 19 0.63
27 3 0.10
28 8 0.27
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (28 bp):
ATATTTTTAAAATAATTTTAAATTATTT
Found at i:35224146 original size:16 final size:18
Alignment explanation
Indices: 35224127--35224165 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
35224117 AATAGTGCTG
35224127 TTTTAAT-TTTTTTAT-A
1 TTTTAATATTTTTTATAA
35224143 TTTT-ATATTTTTTATAA
1 TTTTAATATTTTTTATAA
35224160 TTTTAA
1 TTTTAA
35224166 AAAATTAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.10
16 12 0.60
17 5 0.25
18 1 0.05
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTAATATTTTTTATAA
Found at i:35228225 original size:9 final size:9
Alignment explanation
Indices: 35228196--35228225 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
35228186 TGAATTTTAC
35228196 AATTCGAAT
1 AATTCGAAT
*
35228205 AACTCGAAT
1 AATTCGAAT
35228214 AATTCGAAT
1 AATTCGAAT
35228223 AAT
1 AAT
35228226 GGATTGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:35228544 original size:16 final size:16
Alignment explanation
Indices: 35228525--35228555 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35228515 TTGAAAAATT
35228525 TTTCAAATATATATGA
1 TTTCAAATATATATGA
*
35228541 TTTCAAATTTATATG
1 TTTCAAATATATATG
35228556 CTCTAATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGA
Found at i:35238011 original size:40 final size:40
Alignment explanation
Indices: 35237955--35238031 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
35237945 ATGATTTAGT
*
35237955 TGAGGAATAATATTGCTGATCAGGCTTGGCTAAGTGGAAC
1 TGAGGAATAATATTGCTGACCAGGCTTGGCTAAGTGGAAC
* *
35237995 TGAGGAATAATCTTGCTGACCAGGCTTGGCTAGGTGG
1 TGAGGAATAATATTGCTGACCAGGCTTGGCTAAGTGG
35238032 CTAAGTAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.26, C:0.14, G:0.32, T:0.27
Consensus pattern (40 bp):
TGAGGAATAATATTGCTGACCAGGCTTGGCTAAGTGGAAC
Found at i:35240819 original size:17 final size:18
Alignment explanation
Indices: 35240788--35240822 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
35240778 CACAACTCAG
35240788 TAAATATTCAATAACAAA
1 TAAATATTCAATAACAAA
*
35240806 TAAA-ATTCATTAACAAA
1 TAAATATTCAATAACAAA
35240823 CACAATGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.60, C:0.11, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAATATTCAATAACAAA
Found at i:35241006 original size:43 final size:43
Alignment explanation
Indices: 35240943--35241053 Score: 143
Period size: 43 Copynumber: 2.6 Consensus size: 43
35240933 TTCAGGTGTC
* *
35240943 ACACGCCCGTGTGAACAGGTCATGTGCCTCACACAGCCACCAG
1 ACACGCCCATGTAAACAGGTCATGTGCCTCACACAGCCACCAG
* * *
35240986 ACACGCCCATGTAAATAGGTCGTGTGCCTCACACTGCCACCAG
1 ACACGCCCATGTAAACAGGTCATGTGCCTCACACAGCCACCAG
* * *
35241029 ACACGCCCGTGT-CACAGGTCGTGTG
1 ACACGCCCATGTAAACAGGTCATGTG
35241054 AAAATAGGGC
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
42 11 0.18
43 49 0.82
ACGTcount: A:0.23, C:0.35, G:0.24, T:0.17
Consensus pattern (43 bp):
ACACGCCCATGTAAACAGGTCATGTGCCTCACACAGCCACCAG
Found at i:35242366 original size:41 final size:41
Alignment explanation
Indices: 35242237--35242460 Score: 217
Period size: 42 Copynumber: 5.5 Consensus size: 41
35242227 ATACTCGGAT
* * **
35242237 TCTCGCACACTAAGTGCCAAAGCATAGTTGAAGCTATTACAA
1 TCTCGCACACTAAGTGCCATATCATAGCCGAAGCTATT-CAA
* * *
35242279 TCTCGCACACTAAGTGCCAAAGCATAGCTGAAGCTATTACAA
1 TCTCGCACACTAAGTGCCATATCATAGCCGAAGCTATT-CAA
* *
35242321 TCTCGCACACTAAGTGCC-TTTCATAGCCGAAGCTATCTCAG
1 TCTCGCACACTAAGTGCCATATCATAGCCGAAGCTAT-TCAA
*
35242362 TCTCGCACACTAAGTGCCATAT-ATAGTCGAAGCTATTCCGAA
1 TCTCGCACACTAAGTGCCATATCATAGCCGAAGCTATT-C-AA
* ** *
35242404 --TCACACACTAAGTGCTTTAT-ATAGCCAAAGCTATCTCAA
1 TCTCGCACACTAAGTGCCATATCATAGCCGAAGCTAT-TCAA
*
35242443 T-ACGCACACTAAGTGCCA
1 TCTCGCACACTAAGTGCCA
35242461 AACTTAATCA
Statistics
Matches: 158, Mismatches: 18, Indels: 14
0.83 0.09 0.07
Matches are distributed among these distances:
39 2 0.01
40 44 0.28
41 49 0.31
42 63 0.40
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.25
Consensus pattern (41 bp):
TCTCGCACACTAAGTGCCATATCATAGCCGAAGCTATTCAA
Found at i:35242425 original size:40 final size:40
Alignment explanation
Indices: 35242323--35242458 Score: 134
Period size: 40 Copynumber: 3.4 Consensus size: 40
35242313 TATTACAATC
* * **
35242323 TCGCACACTAAGTGCCTTT-CATAGCCGAAGCTATCTCAGTC
1 TCGCACACTAAGTG-CTTTATATAGCCGAAGCTAT-TCCGAA
** *
35242364 TCGCACACTAAGTGCCATATATAGTCGAAGCTATTCCGAA
1 TCGCACACTAAGTGCTTTATATAGCCGAAGCTATTCCGAA
* *
35242404 TCACACACTAAGTGCTTTATATAGCCAAAGCTA-TCTC-AA
1 TCGCACACTAAGTGCTTTATATAGCCGAAGCTATTC-CGAA
35242443 TACGCACACTAAGTGC
1 T-CGCACACTAAGTGC
35242459 CAAACTTAAT
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
39 5 0.06
40 47 0.59
41 27 0.34
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (40 bp):
TCGCACACTAAGTGCTTTATATAGCCGAAGCTATTCCGAA
Found at i:35242439 original size:81 final size:82
Alignment explanation
Indices: 35242267--35242462 Score: 233
Period size: 81 Copynumber: 2.4 Consensus size: 82
35242257 AGCATAGTTG
*
35242267 AAGCTAT-TACAATCTCGCACACTAAGTGCCAAAGCATAGCTGAAGCTATTACAATCTCGCACAC
1 AAGCTATCT-CAATCTCGCACACTAAGTGCCAAAGCATAGCTGAAGCTATTACAA-CTCACACAC
*
35242331 TAAGTGCCTTTCATAGCCG
64 TAAGTGCCTTTCATAGCCA
* * * *
35242350 AAGCTATCTCAGTCTCGCACACTAAGTGCCATA-TATAG-TCGAAGCTATTCCGAA-TCACACAC
1 AAGCTATCTCAATCTCGCACACTAAGTGCCAAAGCATAGCT-GAAGCTATTAC-AACTCACACAC
*
35242412 TAAGTG-CTTTATATAGCCA
64 TAAGTGCCTTT-CATAGCCA
*
35242431 AAGCTATCTCAAT-ACGCACACTAAGTGCCAAA
1 AAGCTATCTCAATCTCGCACACTAAGTGCCAAA
35242463 CTTAATCAAT
Statistics
Matches: 99, Mismatches: 10, Indels: 11
0.82 0.08 0.09
Matches are distributed among these distances:
80 21 0.21
81 32 0.32
82 14 0.14
83 31 0.31
84 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (82 bp):
AAGCTATCTCAATCTCGCACACTAAGTGCCAAAGCATAGCTGAAGCTATTACAACTCACACACTA
AGTGCCTTTCATAGCCA
Found at i:35243547 original size:12 final size:12
Alignment explanation
Indices: 35243532--35243557 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35243522 AAATAATTCA
35243532 CACATATATAAT
1 CACATATATAAT
35243544 CACATATATAAT
1 CACATATATAAT
35243556 CA
1 CA
35243558 ACCCGTGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.19, G:0.00, T:0.31
Consensus pattern (12 bp):
CACATATATAAT
Found at i:35245495 original size:39 final size:40
Alignment explanation
Indices: 35245450--35245674 Score: 242
Period size: 40 Copynumber: 5.7 Consensus size: 40
35245440 GCTCCTCGTT
* * * *
35245450 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
35245490 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
35245529 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
35245569 CAAAGGCCTTCGGGACTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
35245609 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
35245650 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
35245675 CAGCATTCAA
Statistics
Matches: 159, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
39 39 0.25
40 106 0.67
41 14 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:35245683 original size:41 final size:41
Alignment explanation
Indices: 35245606--35245683 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
35245596 CTTGTATCTC
* * *
35245606 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
35245647 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
35245684 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:35253423 original size:39 final size:40
Alignment explanation
Indices: 35253378--35253602 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
35253368 GCTCCTCGTT
* * * *
35253378 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
35253418 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
35253457 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
35253497 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
35253537 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
35253578 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
35253603 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:35253611 original size:41 final size:41
Alignment explanation
Indices: 35253534--35253611 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
35253524 CTTGTATCTC
* * *
35253534 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
35253575 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
35253612 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:35262255 original size:46 final size:46
Alignment explanation
Indices: 35262188--35262363 Score: 191
Period size: 46 Copynumber: 3.8 Consensus size: 46
35262178 TATTTGGGCA
35262188 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* *
35262234 TCCGAACTCGTTGAGTTGAGTCCGAGTT---C-GTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATG-GATGCGAA-T--G
* * *
35262279 CATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
* * *
35262327 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGG
35262364 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 10, Indels: 22
0.77 0.07 0.16
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
45 1 0.01
46 62 0.57
47 27 0.25
48 1 0.01
50 4 0.04
51 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATG
Found at i:35262343 original size:93 final size:93
Alignment explanation
Indices: 35262184--35262355 Score: 299
Period size: 93 Copynumber: 1.8 Consensus size: 93
35262174 AGGATATTTG
* *
35262184 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAG
35262249 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * *
35262277 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAG
35262342 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
35262356 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACCTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:35265334 original size:15 final size:15
Alignment explanation
Indices: 35265314--35265382 Score: 84
Period size: 15 Copynumber: 4.6 Consensus size: 15
35265304 GTATCTTGGG
35265314 TTTCTTTATCCTGGA
1 TTTCTTTATCCTGGA
* *
35265329 TCTCTTTATTCTGGA
1 TTTCTTTATCCTGGA
* *
35265344 TTTCTTTATTCTGGG
1 TTTCTTTATCCTGGA
* *
35265359 TTTCTCTATCTTGGA
1 TTTCTTTATCCTGGA
35265374 TTTCTTTAT
1 TTTCTTTAT
35265383 TCGGTTTTCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 45 1.00
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (15 bp):
TTTCTTTATCCTGGA
Found at i:35265383 original size:30 final size:30
Alignment explanation
Indices: 35265305--35265392 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 30
35265295 CATAGTATCG
* * * *
35265305 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGGATTTCTC
*
35265335 TAT-TCTGGATTTCTTTATTCTGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGATTTCTC
*
35265365 TATCTTGGATTTCTTTATTC-GGTTTTCT
1 TATCTTGGATTTCTTTATTCTGGATTTCT
35265393 TGTTATCTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 8 0.16
30 41 0.82
31 1 0.02
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.57
Consensus pattern (30 bp):
TATCTTGGATTTCTTTATTCTGGATTTCTC
Found at i:35267847 original size:47 final size:47
Alignment explanation
Indices: 35267729--35267902 Score: 188
Period size: 45 Copynumber: 3.8 Consensus size: 47
35267719 AGGATATTTG
35267729 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAAT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTA-GGATGCGAAT
* *
35267777 -G--TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GT-GAGATG-TAACT
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTAG-GATGCGAA-T
35267820 AGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-A-
1 -GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TA-GGATGCGAAT
*
35267868 GCGC--CCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 G-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
35267903 TATGGGCGGG
Statistics
Matches: 109, Mismatches: 5, Indels: 27
0.77 0.04 0.19
Matches are distributed among these distances:
42 3 0.03
43 5 0.05
44 1 0.01
45 31 0.28
46 29 0.27
47 31 0.28
48 2 0.02
49 1 0.01
50 5 0.05
51 1 0.01
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (47 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTAGGATGCGAAT
Found at i:35267898 original size:46 final size:45
Alignment explanation
Indices: 35267734--35267907 Score: 203
Period size: 46 Copynumber: 3.8 Consensus size: 45
35267724 ATTTGGGCAT
* *
35267734 CCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATGT
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCG-AGGC
* * *
35267779 CCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGC
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGAGGC
35267824 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGC
1 --CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAG-GC
*
35267872 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
35267908 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 9, Indels: 19
0.80 0.07 0.14
Matches are distributed among these distances:
43 4 0.04
45 31 0.28
46 36 0.33
47 31 0.28
48 4 0.04
50 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (45 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGGC
Found at i:35284169 original size:14 final size:14
Alignment explanation
Indices: 35284150--35284176 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
35284140 TTTTAATAAC
35284150 TAAGTAAAGATACA
1 TAAGTAAAGATACA
35284164 TAAGTAAAGATAC
1 TAAGTAAAGATAC
35284177 CACACATTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (14 bp):
TAAGTAAAGATACA
Found at i:35300546 original size:40 final size:40
Alignment explanation
Indices: 35300485--35300771 Score: 371
Period size: 40 Copynumber: 7.2 Consensus size: 40
35300475 CGGAATTTAG
* * * *
35300485 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * *
35300525 CCGGGT-ATAGCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* * * *
35300565 CCGGAT-ATATCAACTCGCGCAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
35300605 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
35300645 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
35300685 CCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
35300725 CCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
35300765 CCGGATA
1 CCGGATA
35300772 TCATTCAAAT
Statistics
Matches: 227, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
39 2 0.01
40 221 0.97
41 4 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (40 bp):
CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:35303543 original size:29 final size:30
Alignment explanation
Indices: 35303463--35303553 Score: 94
Period size: 31 Copynumber: 3.0 Consensus size: 30
35303453 TGCATGATTA
* * *
35303463 AAACAAAATTAAAGTTTCAAGTGTACATTT
1 AAACCAAATTAAAGTTTCATGTGTACAATT
* *
35303493 AAACCACAATTAGAGTTTCATGCGTACAATT
1 AAACCA-AATTAAAGTTTCATGTGTACAATT
** *
35303524 GCACCAAATTAAAG-TTCATGTATACAATT
1 AAACCAAATTAAAGTTTCATGTGTACAATT
35303553 A
1 A
35303554 CACATTAAAT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
29 13 0.27
30 12 0.24
31 24 0.49
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (30 bp):
AAACCAAATTAAAGTTTCATGTGTACAATT
Found at i:35305234 original size:20 final size:20
Alignment explanation
Indices: 35305174--35305235 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
35305164 TTCGGTACCG
* *
35305174 CTGAATGCACATTTGTGCCA
1 CTGAATGTACATTTGTGCCC
** * *
35305194 CTGTTTGTAC-TTCGGTACCC
1 CTGAATGTACATT-TGTGCCC
35305214 CTGAATGTACATTTGTGCCC
1 CTGAATGTACATTTGTGCCC
35305234 CT
1 CT
35305236 ATTTGTACTT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 2 0.07
20 26 0.87
21 2 0.07
ACGTcount: A:0.18, C:0.27, G:0.19, T:0.35
Consensus pattern (20 bp):
CTGAATGTACATTTGTGCCC
Found at i:35305390 original size:20 final size:21
Alignment explanation
Indices: 35305330--35305401 Score: 60
Period size: 20 Copynumber: 3.6 Consensus size: 21
35305320 TACTTCGGTA
*
35305330 CCCTAAATGCACATTT-TTGC
1 CCCTAAATGCACATTTGATGC
*** *
35305350 CCCTGTTTGTAC-TTTGATGC
1 CCCTAAATGCACATTTGATGC
*
35305370 CCTTAAATGCACATTTG-TGC
1 CCCTAAATGCACATTTGATGC
*
35305390 CCCTAATTGCAC
1 CCCTAAATGCAC
35305402 TTCGGTGCCC
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
19 3 0.08
20 31 0.82
21 4 0.11
ACGTcount: A:0.21, C:0.29, G:0.14, T:0.36
Consensus pattern (21 bp):
CCCTAAATGCACATTTGATGC
Found at i:35305404 original size:79 final size:78
Alignment explanation
Indices: 35305148--35305424 Score: 322
Period size: 79 Copynumber: 3.5 Consensus size: 78
35305138 AAATAAAGAA
* * *
35305148 GTGCCCTTGTTTGTACTTCGGTACCGCTGAATGCACATTTGTGCCACTGTTTGTACTTCGGTACC
1 GTGCCCCTATTTGTACTTCGGTACC-CTGAATGCACATTTGTGCCCCTGTTTGTACTTCGGTA-C
* *
35305213 CCTGAATGTACATTT
64 CCTAAATGCACATTT
* * *
35305228 GTGCCCCTATTTGTACTTCGATACCCTTGAATGCACATTTGTGCCCATGTTTGTGCTTCGGTACC
1 GTGCCCCTATTTGTACTTCGGTACCC-TGAATGCACATTTGTGCCCCTGTTTGTACTTCGGTACC
*
35305293 CTAAATGCACATCT
65 CTAAATGCACATTT
* * * * * * *
35305307 GTGCCCCTGTTTTTACTTCGGTACCCTAAATGCACATTTTTGCCCCTGTTTGTACTTTGATGCCC
1 GTGCCCCTATTTGTACTTCGGTACCCTGAATGCACATTTGTGCCCCTGTTTGTACTTCGGTACCC
35305372 TTAAATGCACATTT
66 -TAAATGCACATTT
* * *
35305386 GTGCCCCTAATTGCACTTCGGTGCCCCTG-ATCGCACATT
1 GTGCCCCTATTTGTACTTCGGT-ACCCTGAAT-GCACATT
35305425 CATGCTTCTG
Statistics
Matches: 167, Mismatches: 26, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
78 32 0.19
79 69 0.41
80 66 0.40
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.36
Consensus pattern (78 bp):
GTGCCCCTATTTGTACTTCGGTACCCTGAATGCACATTTGTGCCCCTGTTTGTACTTCGGTACCC
TAAATGCACATTT
Found at i:35305411 original size:40 final size:39
Alignment explanation
Indices: 35305148--35305407 Score: 313
Period size: 40 Copynumber: 6.6 Consensus size: 39
35305138 AAATAAAGAA
* *
35305148 GTGCCCTTGTTTGTACTTCGGTACCGCTGAATGCACATTT
1 GTGCCCCTGTTTGTACTTCGGTACC-CTAAATGCACATTT
* * *
35305188 GTGCCACTGTTTGTACTTCGGTACCCCTGAATGTACATTT
1 GTGCCCCTGTTTGTACTTCGGTA-CCCTAAATGCACATTT
* * *
35305228 GTGCCCCTATTTGTACTTCGATACCCTTGAATGCACATTT
1 GTGCCCCTGTTTGTACTTCGGTACCC-TAAATGCACATTT
* * *
35305268 GTGCCCATGTTTGTGCTTCGGTACCCTAAATGCACATCT
1 GTGCCCCTGTTTGTACTTCGGTACCCTAAATGCACATTT
*
35305307 GTGCCCCTGTTTTTACTTCGGTACCCTAAATGCACATTT
1 GTGCCCCTGTTTGTACTTCGGTACCCTAAATGCACATTT
* * * *
35305346 TTGCCCCTGTTTGTACTTTGATGCCCTTAAATGCACATTT
1 GTGCCCCTGTTTGTACTTCGGTACCC-TAAATGCACATTT
** *
35305386 GTGCCCCTAATTGCACTTCGGT
1 GTGCCCCTGTTTGTACTTCGGT
35305408 GCCCCTGATC
Statistics
Matches: 189, Mismatches: 28, Indels: 6
0.85 0.13 0.03
Matches are distributed among these distances:
39 70 0.37
40 117 0.62
41 2 0.01
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.37
Consensus pattern (39 bp):
GTGCCCCTGTTTGTACTTCGGTACCCTAAATGCACATTT
Found at i:35305984 original size:20 final size:20
Alignment explanation
Indices: 35305959--35306030 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
35305949 AGAAACATTT
35305959 GTGCCCTTGATTACACTTCG
1 GTGCCCTTGATTACACTTCG
* *
35305979 GTGCCCCTGATCACACGTTC-
1 GTGCCCTTGATTACAC-TTCG
* * *
35305999 GTGCTCTTGATTGCACTTTG
1 GTGCCCTTGATTACACTTCG
35306019 GTGCCCTT-ATTA
1 GTGCCCTTGATTA
35306031 TGCATCTATG
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 5 0.12
20 33 0.80
21 3 0.07
ACGTcount: A:0.14, C:0.29, G:0.21, T:0.36
Consensus pattern (20 bp):
GTGCCCTTGATTACACTTCG
Found at i:35309666 original size:40 final size:40
Alignment explanation
Indices: 35309588--35309851 Score: 365
Period size: 40 Copynumber: 6.6 Consensus size: 40
35309578 AACCCAAGTA
* *
35309588 CCTTTGGGATTTAG-CCGGATATAG-CAACTCA-CACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAA-T-AGCACAAATG
* *
35309627 CCTTCGGGTCTTAGCCCGGATATAGTCAATAGCAAAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
35309667 CCTTCGGGATTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
*
35309707 CCTTCGGGACTTAGCCCAGATATAGTCAATAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
* *
35309747 CCTTCGAGACTTAGCCCGGATATAGTCAATA-CATCCAGGATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCA--CA-AATG
*
35309789 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
35309829 CCTTCGGGACTTAGCCCGGATAT
1 CCTTCGGGACTTAGCCCGGATAT
35309852 CATTCGAATA
Statistics
Matches: 201, Mismatches: 17, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
39 14 0.07
40 146 0.73
41 7 0.03
42 32 0.16
43 2 0.01
ACGTcount: A:0.28, C:0.25, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCAATAGCACAAATG
Found at i:35311761 original size:29 final size:29
Alignment explanation
Indices: 35311729--35311786 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
35311719 GAAATACGAA
35311729 AAAAATTATTTTAAAAATTTTTATATACT
1 AAAAATTATTTTAAAAATTTTTATATACT
*
35311758 AAAAATTATTTTAAAATTTTTTATATACT
1 AAAAATTATTTTAAAAATTTTTATATACT
35311787 TTCAAAGGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (29 bp):
AAAAATTATTTTAAAAATTTTTATATACT
Found at i:35322644 original size:21 final size:21
Alignment explanation
Indices: 35322620--35322686 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
35322610 TAGCTATCAT
35322620 ATTTTGGTAAGTTCGTATTAC
1 ATTTTGGTAAGTTCGTATTAC
* ** * *
35322641 A-TTTGTTACA-TTATTTATCAT
1 ATTTTGGTA-AGTT-CGTATTAC
35322662 ATTTTGGTAAGTTCGTATTAC
1 ATTTTGGTAAGTTCGTATTAC
35322683 ATTT
1 ATTT
35322687 GTTACATTAT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 8 0.25
21 16 0.50
22 8 0.25
ACGTcount: A:0.25, C:0.09, G:0.13, T:0.52
Consensus pattern (21 bp):
ATTTTGGTAAGTTCGTATTAC
Found at i:35322661 original size:42 final size:42
Alignment explanation
Indices: 35322614--35322700 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
35322604 TGTTGTTAGC
35322614 TATCATATTTTGGTAAGTTCGTATTACATTTGTTACATTATT
1 TATCATATTTTGGTAAGTTCGTATTACATTTGTTACATTATT
35322656 TATCATATTTTGGTAAGTTCGTATTACATTTGTTACATTATT
1 TATCATATTTTGGTAAGTTCGTATTACATTTGTTACATTATT
35322698 TAT
1 TAT
35322701 GTTTAACTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.53
Consensus pattern (42 bp):
TATCATATTTTGGTAAGTTCGTATTACATTTGTTACATTATT
Found at i:35324120 original size:30 final size:30
Alignment explanation
Indices: 35324086--35324142 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
35324076 GCCATATGGT
*
35324086 CGTGTGCCCCACACGGTCATGTGACACAGC
1 CGTGTGCCCCACACAGTCATGTGACACAGC
35324116 CGTGTGCCCCACACAGTCATGTGACAC
1 CGTGTGCCCCACACAGTCATGTGACAC
35324143 GACCGTATGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.37, G:0.25, T:0.18
Consensus pattern (30 bp):
CGTGTGCCCCACACAGTCATGTGACACAGC
Found at i:35326638 original size:20 final size:20
Alignment explanation
Indices: 35326608--35326660 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
35326598 GGTAGTTTAC
35326608 TTCTATCTTGATTTTCATGAG
1 TTCT-TCTTGATTTTCATGAG
35326629 TTCTTCTTGATTTTCATGAG
1 TTCTTCTTGATTTTCATGAG
35326649 TTCTTCTTGATT
1 TTCTTCTTGATT
35326661 CTACCTTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.15, C:0.15, G:0.13, T:0.57
Consensus pattern (20 bp):
TTCTTCTTGATTTTCATGAG
Found at i:35329172 original size:45 final size:43
Alignment explanation
Indices: 35329065--35329182 Score: 148
Period size: 45 Copynumber: 2.7 Consensus size: 43
35329055 CAGGCTTCGG
*
35329065 GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGGCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGCCTTTGA
* * * * *
35329108 GCTTAGTAAGCTTTGATGCCGGTGAAAT-ATTATTCGAGCCTTTGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGA-TA-TCG-GCCTTTGA
35329153 GCCTAGCAGGCTATAATGCCGGTGAAATGA
1 GCCTAGCAGGCTATAATGCCGGTGAAATGA
35329183 AATGTTATGT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
42 1 0.02
43 25 0.42
44 3 0.05
45 30 0.50
46 1 0.02
ACGTcount: A:0.26, C:0.18, G:0.28, T:0.28
Consensus pattern (43 bp):
GCCTAGCAGGCTATAATGCCGGTGAAATGATATCGGCCTTTGA
Found at i:35329583 original size:76 final size:76
Alignment explanation
Indices: 35329452--35329649 Score: 254
Period size: 76 Copynumber: 2.6 Consensus size: 76
35329442 ATGATATTTG
* ** * * * *
35329452 TATCCGGCTTAAAGACCGTAGGCTATATGCTGG-AACTATATTCGAGTTAAATCCCGCAGGCTTC
1 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAA-TATATTCGGGTTAAATCCCGCAGGCTTC
35329516 GTGCTAGTAATA
65 GTGCTAGTAATA
* *
35329528 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATATATCCGGGTTAATTCCCGCAGGCTTCG
1 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATATATTCGGGTTAAATCCCGCAGGCTTCG
* *
35329593 TGCTGGTATTA
66 TGCTAGTAATA
* * *
35329604 TATCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTATATTCGGG
1 TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATATATTCGGG
35329650 CCTTTGAGCC
Statistics
Matches: 106, Mismatches: 15, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
76 104 0.98
77 2 0.02
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (76 bp):
TATCCGGGTTAAATCCCGCAGGCTTTGTGCTGGTAATATATTCGGGTTAAATCCCGCAGGCTTCG
TGCTAGTAATA
Found at i:35329637 original size:38 final size:38
Alignment explanation
Indices: 35329479--35329649 Score: 236
Period size: 38 Copynumber: 4.5 Consensus size: 38
35329469 GTAGGCTATA
* *
35329479 TGCTGG-AACTATATTCGAGTTAAATCCCGCAGGCTTCG
1 TGCTGGTAA-TATATCCGGGTTAAATCCCGCAGGCTTCG
* *
35329517 TGCTAGTAATATATCCGGGTTAAATCCCGCAGGCTTTG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
*
35329555 TGCTGGTAATATATCCGGGTTAATTCCCGCAGGCTTCG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
* * *
35329593 TGCTGGTATTATATCCGGGTTAAATCCCGCAGGCCTAG
1 TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
* *
35329631 TGCTGGTATTATATTCGGG
1 TGCTGGTAATATATCCGGG
35329650 CCTTTGAGCC
Statistics
Matches: 120, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
38 118 0.98
39 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.32
Consensus pattern (38 bp):
TGCTGGTAATATATCCGGGTTAAATCCCGCAGGCTTCG
Found at i:35329784 original size:45 final size:44
Alignment explanation
Indices: 35329642--35329810 Score: 189
Period size: 45 Copynumber: 3.8 Consensus size: 44
35329632 GCTGGTATTA
* *
35329642 TATTCGGGCCTTTGAGCCTAGCAGGCTATTATGCCGATGAGACAC
1 TATTCGGG-CTTTGAGCCTAGCAGGCTATAATGCCGATGAGATAC
* * *
35329687 TATTCAGGCCTTTGGGCCTAGCAGGCTATAATGCCGGTGAGATAC
1 TATTC-GGGCTTTGAGCCTAGCAGGCTATAATGCCGATGAGATAC
*
35329732 TATTCGGGCTTTCGAGCCTAGCAGGCTATAATGCCGATGAAATGA-
1 TATTCGGGCTTT-GAGCCTAGCAGGCTATAATGCCGATGAGAT-AC
* * * * *
35329777 TAATCGGGCCTCGATCCTAGCAGGCGA-AATGCCG
1 TATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCG
35329811 GTGATTTGAG
Statistics
Matches: 107, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
43 7 0.07
44 19 0.18
45 78 0.73
46 3 0.03
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.25
Consensus pattern (44 bp):
TATTCGGGCTTTGAGCCTAGCAGGCTATAATGCCGATGAGATAC
Found at i:35341588 original size:56 final size:57
Alignment explanation
Indices: 35341521--35341636 Score: 207
Period size: 56 Copynumber: 2.1 Consensus size: 57
35341511 AAATTGTAAT
* *
35341521 TTACCATAATAATAGTGAATATAATTTCTACTTATGATGTTTACAACTTATTTTA-A
1 TTACCATAATAATAGTGAATATAATTTCTAATTATGATGTTTACAACTCATTTTATA
35341577 TTACCATAATAATAGTGAATATAATTTCTAATTATGATGTTTACAACTCATTTTATA
1 TTACCATAATAATAGTGAATATAATTTCTAATTATGATGTTTACAACTCATTTTATA
35341634 TTA
1 TTA
35341637 AACCTTATTT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
56 53 0.93
57 4 0.07
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (57 bp):
TTACCATAATAATAGTGAATATAATTTCTAATTATGATGTTTACAACTCATTTTATA
Found at i:35342048 original size:20 final size:21
Alignment explanation
Indices: 35341996--35342049 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
35341986 TAACCTTATT
* * *
35341996 TTTCTATTTAATTTTTTTCTA
1 TTTCTATTTTATATCTTTCTA
*
35342017 TTT-TACTTTATATCTTT-TA
1 TTTCTATTTTATATCTTTCTA
35342036 TTTCTATTTTATAT
1 TTTCTATTTTATAT
35342050 AATTTATTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.19
20 19 0.70
21 3 0.11
ACGTcount: A:0.20, C:0.09, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTATTTTATATCTTTCTA
Found at i:35342059 original size:25 final size:24
Alignment explanation
Indices: 35342001--35342060 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
35341991 TTATTTTTCT
*
35342001 ATTTAATTTTTTTCTATTTTACTTT
1 ATTT-ATTTTTTTCTATTTTACTTA
* *
35342026 ATATCTTTTATTTCTATTTTA-TATA
1 ATTTATTTT-TTTCTATTTTACT-TA
35342051 ATTTATTTTT
1 ATTTATTTTT
35342061 ACATAATTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (24 bp):
ATTTATTTTTTTCTATTTTACTTA
Found at i:35342066 original size:15 final size:15
Alignment explanation
Indices: 35342042--35342072 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35342032 TTTATTTCTA
*
35342042 TTTTATATAATTTAT
1 TTTTACATAATTTAT
35342057 TTTTACATAATTTAT
1 TTTTACATAATTTAT
35342072 T
1 T
35342073 CTCAATTTTT
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:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (15 bp):
TTTTACATAATTTAT
Found at i:35343081 original size:27 final size:27
Alignment explanation
Indices: 35343051--35343105 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
35343041 TGGGTGAGAT
35343051 TGAATTCAGAAAGATTCAAGGAAGGCA
1 TGAATTCAGAAAGATTCAAGGAAGGCA
35343078 TGAATTCAGAAAGATTCAAGGAAGGCA
1 TGAATTCAGAAAGATTCAAGGAAGGCA
35343105 T
1 T
35343106 TTCCTGATCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.44, C:0.11, G:0.25, T:0.20
Consensus pattern (27 bp):
TGAATTCAGAAAGATTCAAGGAAGGCA
Found at i:35366130 original size:31 final size:31
Alignment explanation
Indices: 35366092--35366157 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
35366082 TTACACTCCA
35366092 GTGTAAATGGGCCGTGTGTACTCACACGCCC
1 GTGTAAATGGGCCGTGTGTACTCACACGCCC
35366123 GTGTAAATGGGCCGTGTGTACTCACACGCCC
1 GTGTAAATGGGCCGTGTGTACTCACACGCCC
35366154 GTGT
1 GTGT
35366158 GACTTGGGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.18, C:0.27, G:0.30, T:0.24
Consensus pattern (31 bp):
GTGTAAATGGGCCGTGTGTACTCACACGCCC
Found at i:35378376 original size:56 final size:56
Alignment explanation
Indices: 35378290--35378409 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
35378280 ACAAGGGATG
35378290 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
35378346 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
35378402 ATGGGCAA
1 ATGGGCAA
35378410 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Done.