Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015020.1 Kokia drynarioides strain JFW-HI SEQ_130064, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1341705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 344 characters in sequence are not A, C, G, or T
File 4 of 5
Found at i:887686 original size:30 final size:31
Alignment explanation
Indices: 887623--887690 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 31
887613 AAATTAGTCA
*
887623 TTGAACTTGACAATTGTTCCTATATTAAGAT
1 TTGAACTTGACAATTATTCCTATATTAAGAT
887654 TTGAACTTGACAATTATT-CTCATATT-AGAT
1 TTGAACTTGACAATTATTCCT-ATATTAAGAT
887684 TTGAACT
1 TTGAACT
887691 CTAAGATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 13 0.37
31 22 0.63
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (31 bp):
TTGAACTTGACAATTATTCCTATATTAAGAT
Found at i:897104 original size:26 final size:26
Alignment explanation
Indices: 897074--897155 Score: 101
Period size: 26 Copynumber: 3.2 Consensus size: 26
897064 GTATACTAGT
* *
897074 TAAACTCTATTTGGGCTCGTAAGGGC
1 TAAACTCTATCTGGGCTCGTAAGAGC
* *
897100 TAAACTCTATCTGAGCTCGTAAGATC
1 TAAACTCTATCTGGGCTCGTAAGAGC
* * *
897126 TAAACTTTAACTGGGCTCGTATGAGC
1 TAAACTCTATCTGGGCTCGTAAGAGC
897152 TAAA
1 TAAA
897156 GTTTTGGAAG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 47 1.00
ACGTcount: A:0.29, C:0.20, G:0.21, T:0.30
Consensus pattern (26 bp):
TAAACTCTATCTGGGCTCGTAAGAGC
Found at i:910073 original size:12 final size:11
Alignment explanation
Indices: 910056--910090 Score: 54
Period size: 10 Copynumber: 3.2 Consensus size: 11
910046 TCCTAATTAA
910056 CTTAATTAATC
1 CTTAATTAATC
910067 TCTTAATTAA-C
1 -CTTAATTAATC
910078 CTTAATTAATC
1 CTTAATTAATC
910089 CT
1 CT
910091 ACTTATAGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 9 0.41
11 4 0.18
12 9 0.41
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (11 bp):
CTTAATTAATC
Found at i:912716 original size:545 final size:543
Alignment explanation
Indices: 911678--912769 Score: 1668
Period size: 545 Copynumber: 2.0 Consensus size: 543
911668 ACAAAAAAAC
* *
911678 TATAGACTAGCAAGTTGAAATGCTAAGTATGGATTGAGGAAGCAACTGTTCATGTCAGCTTGGTT
1 TATAGACTAGCAAGTTGAAATGCTAAGTATCGATTGAGGAAGCAACTGTTCATGTCAGCTCGGTT
* *** * *
911743 GAGTTATAACTGTTTTATGCGTATGATTGATAATTCTTTAACTCTTTGAACTTAATAAGCGATGA
66 GAGTTAGAACAACTTTATGCATATGATTGATAATTCTTTAACTCTTCGAACTTAATAAGCGATGA
* * *
911808 AGCTTACCAAAGATGTTATTATTGTCTTGTAGATTTACCTTGCCGTTGAAGATCGGGTCATCTTC
131 AGCTTACCAAAGATGTTATAATTGTCTTGTAGATTTACCTTGCCGTTGAAGATCGGATCATCTCC
* *
911873 ATGAAGTCACACTATCGAAGAGCTCGTTTGACAATTTCTACATACTTGGTCTTATGGCATGTACT
196 ACGAAGTCACACTATCGAAGAGCTCATTTGACAATTTCTACATACTTGGTCTTATGGCATGTACT
* *
911938 AGGATGATGTTATCTTTTGCTTTATCTATTGAGATTGTGATGATATTGTTATGTTTGATGACTAT
261 AGGATGATGCTATCTTTTGCTTTATCTATTGAGATTGTGATGATATTGTTATGTTTAATGACTAT
912003 TGAATGTAGTAAAGTATGTTGTTAAGTTAGAATATATACTTAAAAGCACAATGTAATGGCTTGGA
326 TGAATGTAGTAAAGTATGTTGTTAAGTTAGAATATATACTTAAAAGCACAATGTAATGGCTTGGA
* * * *
912068 AAATATTTATTTTGAAATGGCTTAATGTATGTTGATGCTATGAATGATATGTGTTGATAAACTTG
391 AAATATGTATTTTGAAATGACCTAATGTATGCTGATGCTATGAATGATATGTGTTGATAAACTTG
* * *
912133 TATTTTGGGTATGATTCTTAAGATTCTGCATGCTTGTTTCAGTAGATCTTTTGCATGTATCAG-T
456 TATTTTGGGTATGATTCTTAAGATTCTACATACTTGTTTCAGTAGATCTTATGCATGTAT-AGAT
912197 AGAAGTACAAGGTAGGAGAAAAGT
520 AGAAGTACAAGGTAGGAGAAAAGT
*
912221 TATAGA-TAGACAAGTTGAAATGTTAAGTATCGATTGAGGAAGCAACTGTTCATG-CTAGCTCGG
1 TATAGACTAG-CAAGTTGAAATGCTAAGTATCGATTGAGGAAGCAACTGTTCATGTC-AGCTCGG
* * * *
912284 TTGAGTTAGAACAACTTTATGCATATGATTGGTAATTCTTTAACTCTTCGAGCTTACTAAGCTAT
64 TTGAGTTAGAACAACTTTATGCATATGATTGATAATTCTTTAACTCTTCGAACTTAATAAGCGAT
* * **
912349 GAAGGTTACCGAAGATGTTATAATTGTCTTGTAGATTTACCTTGTTGTTGAAGATCGGATCATCT
129 GAAGCTTACCAAAGATGTTATAATTGTCTTGTAGATTTACCTTGCCGTTGAAGATCGGATCATCT
* ** * * *
912414 CCACGAAGTTACACTATCGTGGAGCTCATTTGGCAGTTTTTACATCACTTTGGTCTTATGGCATG
194 CCACGAAGTCACACTATCGAAGAGCTCATTTGACAATTTCTACAT-AC-TTGGTCTTATGGCATG
* *
912479 TACTAGGATGATGCTATCTTTTGCTTTATGTATTGTGATTGTGATGATATTGTTATGTTTAATGA
257 TACTAGGATGATGCTATCTTTTGCTTTATCTATTGAGATTGTGATGATATTGTTATGTTTAATGA
*
912544 CTATTGAATGTAGTAAAGTATGTTGTTAAGTTAGAATATATACTTAGAAGCACAATGTAATGGCT
322 CTATTGAATGTAGTAAAGTATGTTGTTAAGTTAGAATATATACTTAAAAGCACAATGTAATGGCT
*
912609 TGGAAAATATGTATTTTGAAATGACCTAATGTATGCTGATGTTATGAATGATATGTGTTGATAAA
387 TGGAAAATATGTATTTTGAAATGACCTAATGTATGCTGATGCTATGAATGATATGTGTTGATAAA
* * * * *
912674 TTTGTGTTTTGGGTATGATTCTTGAGATTCTATATACTTGTTTCAGTAGATCTTATGCATGTATT
452 CTTGTATTTTGGGTATGATTCTTAAGATTCTACATACTTGTTTCAGTAGATCTTATGCATGTATA
* * * *
912739 GATAGAAGTATATGGTAGGAGAGAGGT
517 GATAGAAGTACAAGGTAGGAGAAAAGT
912766 TATA
1 TATA
912770 TTCTGACTTG
Statistics
Matches: 494, Mismatches: 50, Indels: 8
0.89 0.09 0.01
Matches are distributed among these distances:
542 4 0.01
543 204 0.41
544 3 0.01
545 283 0.57
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.39
Consensus pattern (543 bp):
TATAGACTAGCAAGTTGAAATGCTAAGTATCGATTGAGGAAGCAACTGTTCATGTCAGCTCGGTT
GAGTTAGAACAACTTTATGCATATGATTGATAATTCTTTAACTCTTCGAACTTAATAAGCGATGA
AGCTTACCAAAGATGTTATAATTGTCTTGTAGATTTACCTTGCCGTTGAAGATCGGATCATCTCC
ACGAAGTCACACTATCGAAGAGCTCATTTGACAATTTCTACATACTTGGTCTTATGGCATGTACT
AGGATGATGCTATCTTTTGCTTTATCTATTGAGATTGTGATGATATTGTTATGTTTAATGACTAT
TGAATGTAGTAAAGTATGTTGTTAAGTTAGAATATATACTTAAAAGCACAATGTAATGGCTTGGA
AAATATGTATTTTGAAATGACCTAATGTATGCTGATGCTATGAATGATATGTGTTGATAAACTTG
TATTTTGGGTATGATTCTTAAGATTCTACATACTTGTTTCAGTAGATCTTATGCATGTATAGATA
GAAGTACAAGGTAGGAGAAAAGT
Found at i:926607 original size:24 final size:24
Alignment explanation
Indices: 926580--926638 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
926570 TTTAGTCCAC
*
926580 ACGAGACCAGAATGATTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
*
926604 ACGAGCCCAGAATGGTTAGCTCTT
1 ACGAGCCCAGAATGATTAGCTCTT
926628 ACGAGCCCAGA
1 ACGAGCCCAGA
926639 CAGAGTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.20
Consensus pattern (24 bp):
ACGAGCCCAGAATGATTAGCTCTT
Found at i:928673 original size:41 final size:41
Alignment explanation
Indices: 928588--928974 Score: 447
Period size: 41 Copynumber: 9.4 Consensus size: 41
928578 GGATGGTAGT
** * * * **
928588 TTCAATCTGCCTATCTTAATTAGTGGTAAAAGA-CGGGTTGC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAAT-C
* * *
928629 TTCAATCTGCCCCTCATGACTAAGGGTAAAAGATT-GAATTC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAA-TC
* * *
928670 TTCAATCTGTCCTTCTTGATTAGGGGTAAAAAAGATTGAAATC
1 TTCAATCTGCCCCTCTTGATTAGGGGT--AAAAGATTGGAATC
* * *
928713 TTCAATCTGCCCCTCTTGATTAGGGGCAAAATATTGGAAGC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATC
* * * *
928754 TTCAATCAGCCCCTCTTGATTA-GAGAAAAATATTGGAATC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATC
*
928794 TTCAATCAGCCCCTCTTGATTAGGGGTAAAAGATTGGAATC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATC
* * *
928835 TTCAATCTACCCCTCTTGACTAGGGGTAAAAGATTAGAATC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATC
* *
928876 TTCAATCTTCCCCTCTTGATTAGGGGTAAAAGATTGAAATC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATC
* *
928917 TTCAATCTGCCCCTCTTGATTAGGTGTAAAAGATTTGAATGGC
1 TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAAT--C
928960 TTCAATCTGCCCCTC
1 TTCAATCTGCCCCTC
928975 CTAACCAGAG
Statistics
Matches: 297, Mismatches: 41, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
40 37 0.12
41 207 0.70
42 1 0.00
43 50 0.17
44 2 0.01
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.32
Consensus pattern (41 bp):
TTCAATCTGCCCCTCTTGATTAGGGGTAAAAGATTGGAATC
Found at i:929262 original size:49 final size:49
Alignment explanation
Indices: 929205--929309 Score: 129
Period size: 49 Copynumber: 2.1 Consensus size: 49
929195 TTTGTCATTG
* ** * **
929205 CGGCCTCAATCTTTCCTGTCATATTTCTAGGGTACCAGGTTCGTCGTTA
1 CGGCCTCAACCTTTCCCATCATATTTCTAAGGTACCAGGTTCACCGTTA
* * *
929254 CGGCCTCAACCTTTCCCATCATGTTTCTAAGGTACCGGGTTCACCGTTG
1 CGGCCTCAACCTTTCCCATCATATTTCTAAGGTACCAGGTTCACCGTTA
929303 CGGCCTC
1 CGGCCTC
929310 TTGTGTAGAC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 47 1.00
ACGTcount: A:0.15, C:0.31, G:0.21, T:0.32
Consensus pattern (49 bp):
CGGCCTCAACCTTTCCCATCATATTTCTAAGGTACCAGGTTCACCGTTA
Found at i:930097 original size:14 final size:13
Alignment explanation
Indices: 930078--930116 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
930068 CTTTTGTTTC
930078 TTTTTTCTTTTTAT
1 TTTTTTCTTTTT-T
930092 TTTTTTCTTCTTTT
1 TTTTTTCTT-TTTT
*
930106 TGTTTTCTTTT
1 TTTTTTCTTTT
930117 CCTTCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 2 0.09
14 18 0.78
15 3 0.13
ACGTcount: A:0.03, C:0.10, G:0.03, T:0.85
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:930102 original size:17 final size:19
Alignment explanation
Indices: 930069--930125 Score: 68
Period size: 17 Copynumber: 3.2 Consensus size: 19
930059 AACCTCTCCC
930069 TTTTG-TTTCTTTT-TTCT
1 TTTTGATTTCTTTTCTTCT
930086 TTTT-ATTT-TTTTCTTCT
1 TTTTGATTTCTTTTCTTCT
*
930103 TTTTGTTTTCTTTTCCTTCT
1 TTTTGATTTCTTTT-CTTCT
930123 TTT
1 TTT
930126 CGGGTGAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
16 4 0.12
17 15 0.44
18 3 0.09
19 4 0.12
20 8 0.24
ACGTcount: A:0.02, C:0.14, G:0.04, T:0.81
Consensus pattern (19 bp):
TTTTGATTTCTTTTCTTCT
Found at i:942485 original size:18 final size:18
Alignment explanation
Indices: 942446--942486 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
942436 AGGGAACCAG
942446 GCATT-TCAGAACTCTCA
1 GCATTATCAGAACTCTCA
*
942463 ACATTATCAGACACT-TCA
1 GCATTATCAGA-ACTCTCA
942481 GCATTA
1 GCATTA
942487 GCAGCTTCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 4 0.20
18 13 0.65
19 3 0.15
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.29
Consensus pattern (18 bp):
GCATTATCAGAACTCTCA
Found at i:942997 original size:34 final size:34
Alignment explanation
Indices: 942948--943017 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
942938 TATCATTTGA
942948 AAACCAGCTTATTCTCTCACACTACAAAGTCAGT
1 AAACCAGCTTATTCTCTCACACTACAAAGTCAGT
* * * * *
942982 AAACCATCTTGTTCTCTCACATTACAGAGTCTGT
1 AAACCAGCTTATTCTCTCACACTACAAAGTCAGT
943016 AA
1 AA
943018 CATAATTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.33, C:0.27, G:0.10, T:0.30
Consensus pattern (34 bp):
AAACCAGCTTATTCTCTCACACTACAAAGTCAGT
Found at i:943662 original size:42 final size:42
Alignment explanation
Indices: 943615--943698 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
943605 AGTTAATTAA
943615 AATTTTATAATGATAATAAAAAAAAACCTAAAACTTATTCTC
1 AATTTTATAATGATAATAAAAAAAAACCTAAAACTTATTCTC
943657 AATTTTATAATGATAATAAAAAAAAACCTAAAACTTATTCTC
1 AATTTTATAATGATAATAAAAAAAAACCTAAAACTTATTCTC
943699 CAAATTGTTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.52, C:0.12, G:0.02, T:0.33
Consensus pattern (42 bp):
AATTTTATAATGATAATAAAAAAAAACCTAAAACTTATTCTC
Found at i:943769 original size:34 final size:34
Alignment explanation
Indices: 943725--943799 Score: 114
Period size: 34 Copynumber: 2.2 Consensus size: 34
943715 TATCTTTTTG
* * *
943725 TTTTTGTTAGTTTTCTGGCTAACTGTCACTCTTT
1 TTTTTCTTAGTTTTCGGGCTAACTGTCACTCTTC
*
943759 TTTTTCTTAGTTTTCGGGCTAATTGTCACTCTTC
1 TTTTTCTTAGTTTTCGGGCTAACTGTCACTCTTC
943793 TTTTTCT
1 TTTTTCT
943800 CTTGCCCATC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.11, C:0.19, G:0.13, T:0.57
Consensus pattern (34 bp):
TTTTTCTTAGTTTTCGGGCTAACTGTCACTCTTC
Found at i:946752 original size:20 final size:20
Alignment explanation
Indices: 946729--946777 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
946719 ATCCCTGCCT
946729 GCCTCGCATCATCTCCGCTC
1 GCCTCGCATCATCTCCGCTC
946749 GCCTCGCATCATCTCCGCTC
1 GCCTCGCATCATCTCCGCTC
946769 GCCTCGCAT
1 GCCTCGCAT
946778 AATATAATAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.10, C:0.49, G:0.16, T:0.24
Consensus pattern (20 bp):
GCCTCGCATCATCTCCGCTC
Found at i:953033 original size:2 final size:2
Alignment explanation
Indices: 953026--953056 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
953016 ACATTTCTTA
953026 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
953057 ATTCTAAATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:957581 original size:2 final size:2
Alignment explanation
Indices: 957574--957611 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
957564 CTAATACTTA
957574 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
957612 TAAATTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:958844 original size:72 final size:72
Alignment explanation
Indices: 958768--958903 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 72
958758 GTGTACATAC
* * * *
958768 TGACTTGAGATACACGGGCTAG-ACACACGGACGTGCGTCAGACTGTGTGTGCATACTGTTTTGT
1 TGACTTGAGACACACGGGC-AGCACACACAGACGTGCGTCAGACCGTGTGTGCATACTATTTTGT
958832 GTGTATAT
65 GTGTATAT
* * * *
958840 TGACTTGAGACACACGTGCGGCACCCACAGACGTGTGTCAGACCGTGTGTGCATACTATTTTGT
1 TGACTTGAGACACACGGGCAGCACACACAGACGTGCGTCAGACCGTGTGTGCATACTATTTTGT
958904 AAGATAACAT
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 1 0.02
72 54 0.98
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.29
Consensus pattern (72 bp):
TGACTTGAGACACACGGGCAGCACACACAGACGTGCGTCAGACCGTGTGTGCATACTATTTTGTG
TGTATAT
Found at i:959410 original size:40 final size:38
Alignment explanation
Indices: 959285--959459 Score: 156
Period size: 39 Copynumber: 4.5 Consensus size: 38
959275 ACTTAACTAA
* * * *
959285 TAGTGATACTGTAAACACTACAATGATATATCAAACTAG
1 TAGTGACACTGTAAACACTGCAATGATATACCGAACT-G
* *
959324 TAGTGACACTATAAACACTGCAATGATA-ACTGAACTG
1 TAGTGACACTGTAAACACTGCAATGATATACCGAACTG
* *
959361 ACAGTGACACTGTAAACACTGCAATTGTTATACCGAACTGG
1 -TAGTGACACTGTAAACACTGCAA-TGATATACCGAACT-G
* * * *
959402 T-GATGACACTGTAAACATTGCAATGCTATACTGAAGTTG
1 TAG-TGACACTGTAAACACTGCAATGATATACCGAA-CTG
* *
959441 TAGTAAGACTGTAAACACT
1 TAGTGACACTGTAAACACT
959460 ACAGGCTGTT
Statistics
Matches: 111, Mismatches: 18, Indels: 14
0.78 0.13 0.10
Matches are distributed among these distances:
37 1 0.01
38 26 0.23
39 55 0.50
40 28 0.25
41 1 0.01
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.27
Consensus pattern (38 bp):
TAGTGACACTGTAAACACTGCAATGATATACCGAACTG
Found at i:959424 original size:78 final size:78
Alignment explanation
Indices: 959286--959462 Score: 189
Period size: 78 Copynumber: 2.3 Consensus size: 78
959276 CTTAACTAAT
* *
959286 AGTGATACTGTAAACACTACAATGATATATCAAACTAGTAGTGACACTATAAACACTGCAATGAT
1 AGTGACACTGTAAACACTACAATGATATACCAAACTAGTAGTGACACTATAAACACTGCAATGAT
959351 A-ACTGAACTGAC
66 ATACTGAACTGAC
* * * * * *
959363 AGTGACACTGTAAACACTGCAATTGTTATACCGAACTGGT-GATGACACTGTAAACATTGCAATG
1 AGTGACACTGTAAACACTACAA-TGATATACCAAACTAGTAG-TGACACTATAAACACTGCAATG
* * *
959427 CTATACTGAAGTTG-T
64 ATATACTGAA-CTGAC
* *
959442 AGTAAGACTGTAAACACTACA
1 AGTGACACTGTAAACACTACA
959463 GGCTGTTGTT
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
77 21 0.26
78 35 0.43
79 24 0.29
80 2 0.02
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (78 bp):
AGTGACACTGTAAACACTACAATGATATACCAAACTAGTAGTGACACTATAAACACTGCAATGAT
ATACTGAACTGAC
Found at i:967289 original size:19 final size:18
Alignment explanation
Indices: 967256--967323 Score: 57
Period size: 19 Copynumber: 3.7 Consensus size: 18
967246 AATTATAAAA
*
967256 ATAAAAATCAATAAAATTT
1 ATAAAAAT-ATTAAAATTT
* *
967275 ATAAAAATGATT-AAACTA
1 ATAAAAAT-ATTAAAATTT
967293 ATAAAAAATATTAAAATTT
1 AT-AAAAATATTAAAATTT
* *
967312 AGAAAAAAATTA
1 ATAAAAATATTA
967324 TAAAATTTGA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
18 18 0.46
19 21 0.54
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (18 bp):
ATAAAAATATTAAAATTT
Found at i:967317 original size:18 final size:17
Alignment explanation
Indices: 967267--967323 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 17
967257 TAAAAATCAA
967267 TAAAATTTATAAAAATGAT
1 TAAAATTTA-AAAAAT-AT
* *
967286 TAAACTAATAAAAAATAT
1 TAAAAT-TTAAAAAATAT
*
967304 TAAAATTTAGAAAAAAAT
1 TAAAATTTA-AAAAATAT
967322 TA
1 TA
967324 TAAAATTTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.06
18 16 0.52
19 11 0.35
20 2 0.06
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.32
Consensus pattern (17 bp):
TAAAATTTAAAAAATAT
Found at i:967578 original size:19 final size:19
Alignment explanation
Indices: 967534--967579 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
967524 TTAGTATGAT
*
967534 AATTTTTATATTTTTTTAC
1 AATTTTTATATTTATTTAC
*
967553 AAATTTTATATTTATTTAC
1 AATTTTTATATTTATTTAC
*
967572 ATTTTTTA
1 AATTTTTA
967580 AAACTTTTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTTTATATTTATTTAC
Found at i:967614 original size:9 final size:9
Alignment explanation
Indices: 967532--967746 Score: 93
Period size: 9 Copynumber: 23.2 Consensus size: 9
967522 TTTTAGTATG
967532 ATAATTTTT
1 ATAATTTTT
*
967541 ATATTTTTTT
1 ATA-ATTTTT
* *
967551 ACAAATTTT
1 ATAATTTTT
*
967560 ATATTTATTT
1 ATAATT-TTT
* *
967570 ACATTTTTT
1 ATAATTTTT
* *
967579 AAAACTTTT
1 ATAATTTTT
*
967588 ATGAATTTAT
1 AT-AATTTTT
*
967598 A-AAATTTT
1 ATAATTTTT
967606 ATAATTTTT
1 ATAATTTTT
* *
967615 CTATATTTCT
1 ATA-ATTTTT
967625 AT-ATATTTT
1 ATAAT-TTTT
967634 ATAATTTTTT
1 ATAA-TTTTT
*
967644 ATGATTTTT
1 ATAATTTTT
**
967653 ATAAAAATTT
1 AT-AATTTTT
* *
967663 ACAATTGATT
1 ATAATT-TTT
967673 ATAATTTTTTT
1 ATAA--TTTTT
*
967684 ATGATTTTT
1 ATAATTTTT
967693 ATAATTTTT
1 ATAATTTTT
967702 -T--TTTCTT
1 ATAATTT-TT
*
967709 CTAATTTTT
1 ATAATTTTT
967718 AGTAATTTTT
1 A-TAATTTTT
967728 A-AATATTTT
1 ATAAT-TTTT
967737 AT-ATTTTT
1 ATAATTTTT
967745 AT
1 AT
967747 TAAAATTTAA
Statistics
Matches: 153, Mismatches: 34, Indels: 39
0.68 0.15 0.17
Matches are distributed among these distances:
6 3 0.02
7 2 0.01
8 19 0.12
9 64 0.42
10 57 0.37
11 6 0.04
12 2 0.01
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (9 bp):
ATAATTTTT
Found at i:967622 original size:10 final size:10
Alignment explanation
Indices: 967602--967702 Score: 59
Period size: 10 Copynumber: 10.4 Consensus size: 10
967592 ATTTATAAAA
967602 TTTTATAATT
1 TTTTATAATT
967612 TTTCTAT-A-T
1 TTT-TATAATT
* *
967621 TTCTAT-ATA
1 TTTTATAATT
967630 TTTTATAATT
1 TTTTATAATT
*
967640 TTTTATGA-T
1 TTTTATAATT
**
967649 TTTTATAAAA
1 TTTTATAATT
* *
967659 ATTTACAATT
1 TTTTATAATT
**
967669 GATTATAATTT
1 TTTTATAA-TT
*
967680 TTTTATGA-T
1 TTTTATAATT
967689 TTTTATAATT
1 TTTTATAATT
967699 TTTT
1 TTTT
967703 TTTCTTCTAA
Statistics
Matches: 67, Mismatches: 18, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
8 4 0.06
9 24 0.36
10 29 0.43
11 10 0.15
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTTATAATT
Found at i:967636 original size:28 final size:28
Alignment explanation
Indices: 967584--967655 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
967574 TTTTTAAAAC
* *
967584 TTTTATGAATT-TATAAAATTTTATAATT
1 TTTTATGATTTCTAT-ATATTTTATAATT
967612 TTTCTAT-ATTTCTATATATTTTATAATT
1 TTT-TATGATTTCTATATATTTTATAATT
*
967640 TTTTATGATTTTTATA
1 TTTTATGATTTCTATA
967656 AAAATTTACA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 3 0.08
28 29 0.76
29 6 0.16
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.62
Consensus pattern (28 bp):
TTTTATGATTTCTATATATTTTATAATT
Found at i:967694 original size:20 final size:19
Alignment explanation
Indices: 967630--967746 Score: 75
Period size: 19 Copynumber: 6.3 Consensus size: 19
967620 TTTCTATATA
967630 TTTTATAATTTTTTATGAT
1 TTTTATAATTTTTTATGAT
*** **
967649 TTTTATAAAAATTTACAAT
1 TTTTATAATTTTTTATGAT
*
967668 TGATTATAATTTTTTTATGAT
1 T-TTTATAA-TTTTTTATGAT
967689 TTTTATAATTTTTT-T--T
1 TTTTATAATTTTTTATGAT
* * *
967705 TCTTCTAA-TTTTTAGTAAT
1 TTTTATAATTTTTTA-TGAT
*
967724 TTTTA-AATATTTTAT-AT
1 TTTTATAATTTTTTATGAT
967741 TTTTAT
1 TTTTAT
967747 TAAAATTTAA
Statistics
Matches: 73, Mismatches: 17, Indels: 17
0.68 0.16 0.16
Matches are distributed among these distances:
15 5 0.07
16 7 0.10
17 8 0.11
18 4 0.05
19 30 0.41
20 12 0.16
21 7 0.10
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTATAATTTTTTATGAT
Found at i:967749 original size:20 final size:20
Alignment explanation
Indices: 967726--967783 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
967716 TTAGTAATTT
967726 TTAAATATTTTATATTTTTA
1 TTAAATATTTTATATTTTTA
*
967746 TTAAA-ATTTAATAGTTTTTA
1 TTAAATATTTTATA-TTTTTA
*
967766 TT-GATA-TTTAT-TTTTTA
1 TTAAATATTTTATATTTTTA
967783 T
1 T
967784 CATTTTTTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 7 0.21
19 12 0.36
20 14 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
TTAAATATTTTATATTTTTA
Found at i:968012 original size:91 final size:90
Alignment explanation
Indices: 967873--968087 Score: 236
Period size: 91 Copynumber: 2.4 Consensus size: 90
967863 CAATTGAGTG
* * * * * ** *
967873 AAAAAACAGGGGCTTAATTGTTTTTTTTTAAAAAGGTTTTAGGGTCTTTTTTATGCATTTTGAAA
1 AAAAAACAGAGGCTTAATTGTTTTTTTTGAAAAAGGTTTGAAGATCTTTTCGATGCATTATGAAA
* *
967938 GTTTAAGTATCC-AATTAAGTGCAAA
66 GTTCAAGTA-CCTAAATAAGTGCAAA
** * * *
967963 AAAATAGTAGTGGCTTAATTGTTTTTTGTTGATAAA-GTTTGAAGATCTTTTCGATGTATTATGA
1 AAAA-AACAGAGGCTTAATTGTTTTTT-TTGAAAAAGGTTTGAAGATCTTTTCGATGCATTATGA
* *
968027 AAGTTCAAGTACCTAAATGAGTGTAAA
64 AAGTTCAAGTACCTAAATAAGTGCAAA
968054 AAAAAACAGAGGCTTAATTGTTTTTTTTGAAAAA
1 AAAAAACAGAGGCTTAATTGTTTTTTTTGAAAAA
968088 ATTTTAAGGA
Statistics
Matches: 102, Mismatches: 20, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
89 7 0.07
90 25 0.25
91 64 0.63
92 6 0.06
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.40
Consensus pattern (90 bp):
AAAAAACAGAGGCTTAATTGTTTTTTTTGAAAAAGGTTTGAAGATCTTTTCGATGCATTATGAAA
GTTCAAGTACCTAAATAAGTGCAAA
Found at i:968373 original size:28 final size:28
Alignment explanation
Indices: 968342--968399 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
968332 AAAAAAAAAA
968342 GAAAGACAAACAAAATATAATTATCACT
1 GAAAGACAAACAAAATATAATTATCACT
968370 GAAAGACAAACAAAATATAATTATCACT
1 GAAAGACAAACAAAATATAATTATCACT
968398 GA
1 GA
968400 TAACCATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.21
Consensus pattern (28 bp):
GAAAGACAAACAAAATATAATTATCACT
Found at i:968542 original size:4 final size:4
Alignment explanation
Indices: 968533--968561 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
968523 AATCGATCAA
968533 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
968562 TATTATCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:969329 original size:20 final size:21
Alignment explanation
Indices: 969260--969331 Score: 112
Period size: 20 Copynumber: 3.5 Consensus size: 21
969250 TATATTGTTA
*
969260 TTTTGG-TGTTTTTTTTACTG
1 TTTTGGTTGTATTTTTTACTG
969280 TTTTGGTTGCTATTTTTTACTG
1 TTTTGGTTG-TATTTTTTACTG
969302 TTTTGGTTGTA-TTTTTACTG
1 TTTTGGTTGTATTTTTTACTG
969322 TTTTGGTTGT
1 TTTTGGTTGT
969332 TGTTTTGGTG
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
20 25 0.51
21 4 0.08
22 20 0.41
ACGTcount: A:0.07, C:0.06, G:0.21, T:0.67
Consensus pattern (21 bp):
TTTTGGTTGTATTTTTTACTG
Found at i:969339 original size:32 final size:32
Alignment explanation
Indices: 969300--969370 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 32
969290 TATTTTTTAC
*
969300 TGTTTTGGTTG-TA-TTTTTACTGTTTTGGTTGT
1 TGTTTTGG-TGCTATTTTTTACTATTTTGG-TGT
969332 TGTTTTGGTGCTATTTTTTTACTATTTTGGTGT
1 TGTTTTGGTGCTA-TTTTTTACTATTTTGGTGT
969365 TGTTTT
1 TGTTTT
969371 TATTGTTATT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
31 2 0.06
32 10 0.29
33 9 0.26
34 14 0.40
ACGTcount: A:0.07, C:0.04, G:0.23, T:0.66
Consensus pattern (32 bp):
TGTTTTGGTGCTATTTTTTACTATTTTGGTGT
Found at i:969359 original size:22 final size:22
Alignment explanation
Indices: 969334--969431 Score: 88
Period size: 22 Copynumber: 4.3 Consensus size: 22
969324 TTGGTTGTTG
*
969334 TTTTGGTGCTATTTTTTTACTA
1 TTTTGGTGCTATTTTTTTGCTA
* * *
969356 TTTTGGTGTTGTTTTTATTGTTA
1 TTTTGGTGCTATTTTT-TTGCTA
* *
969379 TTTTTGTTGCTATTTTTCTGCTA
1 -TTTTGGTGCTATTTTTTTGCTA
* * *
969402 TTTTGCTGCTATTTTGGTTGTTA
1 TTTTGGTGCTATTTT-TTTGCTA
969425 TTTTGGT
1 TTTTGGT
969432 TGTTTGGATG
Statistics
Matches: 59, Mismatches: 14, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
22 28 0.47
23 18 0.31
24 13 0.22
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.65
Consensus pattern (22 bp):
TTTTGGTGCTATTTTTTTGCTA
Found at i:969383 original size:33 final size:34
Alignment explanation
Indices: 969313--969394 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 34
969303 TTTGGTTGTA
* *
969313 TTTTTACTGTTTTGGTTGTTGTTTTGGTGCTATT
1 TTTTTACTATTTTGGTTGTTGTTTTAGTGCTATT
* *
969347 TTTTTACTATTTTGG-TGTTGTTTTTATTGTTATT
1 TTTTTACTATTTTGGTTGTTG-TTTTAGTGCTATT
*
969381 TTTGTTGCTATTTT
1 TTT-TTACTATTTT
969395 TCTGCTATTT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 5 0.12
34 27 0.66
35 9 0.22
ACGTcount: A:0.09, C:0.05, G:0.18, T:0.68
Consensus pattern (34 bp):
TTTTTACTATTTTGGTTGTTGTTTTAGTGCTATT
Found at i:969391 original size:46 final size:46
Alignment explanation
Indices: 969334--969433 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 46
969324 TTGGTTGTTG
* * * * * *
969334 TTTTGGTGCTATTTTTTTACTATTTTGGTGTTGTTTTTATTGTTAT
1 TTTTGTTGCTATTTTTCTACTATTTTGCTGCTATTTTGATTGTTAT
* *
969380 TTTTGTTGCTATTTTTCTGCTATTTTGCTGCTATTTTGGTTGTTAT
1 TTTTGTTGCTATTTTTCTACTATTTTGCTGCTATTTTGATTGTTAT
*
969426 TTTGGTTG
1 TTTTGTTG
969434 TTTGGATGTT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.09, C:0.07, G:0.19, T:0.65
Consensus pattern (46 bp):
TTTTGTTGCTATTTTTCTACTATTTTGCTGCTATTTTGATTGTTAT
Found at i:969394 original size:11 final size:11
Alignment explanation
Indices: 969334--969429 Score: 59
Period size: 11 Copynumber: 8.5 Consensus size: 11
969324 TTGGTTGTTG
*
969334 TTTTGGTGCTA
1 TTTTGTTGCTA
* *
969345 TTTTTTTACTA
1 TTTTGTTGCTA
* * *
969356 TTTTGGTGTTGT
1 TTTTGTTGCT-A
* *
969368 TTTTATTGTTA
1 TTTTGTTGCTA
969379 TTTTTGTTGCTA
1 -TTTTGTTGCTA
969391 TTTT-TCTGCTA
1 TTTTGT-TGCTA
*
969402 TTTTGCTGCTA
1 TTTTGTTGCTA
*
969413 TTTTGGTTGTTA
1 TTTT-GTTGCTA
969425 TTTTG
1 TTTTG
969430 GTTGTTTGGA
Statistics
Matches: 64, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
10 1 0.02
11 37 0.58
12 26 0.41
ACGTcount: A:0.09, C:0.07, G:0.18, T:0.66
Consensus pattern (11 bp):
TTTTGTTGCTA
Found at i:969435 original size:12 final size:12
Alignment explanation
Indices: 969280--969433 Score: 71
Period size: 12 Copynumber: 13.8 Consensus size: 12
969270 TTTTTTACTG
969280 TTTTGGTTGCTA
1 TTTTGGTTGCTA
* *
969292 TTTT--TTACTG
1 TTTTGGTTGCTA
969302 TTTTGGTTG-TA
1 TTTTGGTTGCTA
* *
969313 -TTT--TTACTG
1 TTTTGGTTGCTA
* *
969322 TTTTGGTTGTTG
1 TTTTGGTTGCTA
969334 TTTTGG-TGCTA
1 TTTTGGTTGCTA
* *
969345 TTTT-TTTACTA
1 TTTTGGTTGCTA
* *
969356 TTTTGG-TGTTG
1 TTTTGGTTGCTA
** *
969367 TTTTTATTGTTA
1 TTTTGGTTGCTA
*
969379 TTTTTGTTGCTA
1 TTTTGGTTGCTA
969391 TTTT--TCTGCTA
1 TTTTGGT-TGCTA
*
969402 TTTT-GCTGCTA
1 TTTTGGTTGCTA
*
969413 TTTTGGTTGTTA
1 TTTTGGTTGCTA
969425 TTTTGGTTG
1 TTTTGGTTG
969434 TTTGGATGTT
Statistics
Matches: 106, Mismatches: 24, Indels: 24
0.69 0.16 0.16
Matches are distributed among these distances:
8 2 0.02
9 1 0.01
10 15 0.14
11 40 0.38
12 48 0.45
ACGTcount: A:0.08, C:0.06, G:0.20, T:0.65
Consensus pattern (12 bp):
TTTTGGTTGCTA
Found at i:981428 original size:244 final size:244
Alignment explanation
Indices: 980999--981482 Score: 941
Period size: 244 Copynumber: 2.0 Consensus size: 244
980989 TGCCATTTTT
980999 TTTTTTTTTAGGAGTGATCTCACATGATCTATATGTATATATATAAGCTTGTATCTATTTCCGAT
1 TTTTTTTTTAGGAGTGATCTCACATGATCTATATGTATATATATAAGCTTGTATCTATTTCCGAT
*
981064 TAAAAAATACCCATGACTGCATATAATTCAAGTCGGGTATGAAAATTTTATTCCAACAAAACTTT
66 TAAAAAATACCCATGACTGCATATAATTCAAGTCGGGTATGAAAATTTTATTCCAACAAAACTTA
981129 GATTATGACTGCACATAATCCCTATATGATCATGTTTCCAAATGGATTCAAACAAAATATATAGG
131 GATTATGACTGCACATAATCCCTATATGATCATGTTTCCAAATGGATTCAAACAAAATATATAGG
981194 TATGTGAATACTGTTCAAAATGGCTATCTTCTAAAAATGACAAATGCCA
196 TATGTGAATACTGTTCAAAATGGCTATCTTCTAAAAATGACAAATGCCA
* *
981243 TTTTTTTTTATGAGTGATCTCACATTATCTATATGTATATATATAAGCTTGTATCTATTTCCGAT
1 TTTTTTTTTAGGAGTGATCTCACATGATCTATATGTATATATATAAGCTTGTATCTATTTCCGAT
981308 TAAAAAATACCCATGACTGCATATAATTCAAGTCGGGTATGAAAATTTTATTCCAACAAAACTTA
66 TAAAAAATACCCATGACTGCATATAATTCAAGTCGGGTATGAAAATTTTATTCCAACAAAACTTA
981373 GATTATGACTGCACATAATCCCTATATGATCATGTTTCCAAATGGATTCAAACAAAATATATAGG
131 GATTATGACTGCACATAATCCCTATATGATCATGTTTCCAAATGGATTCAAACAAAATATATAGG
981438 TATGTGAATACTGTTCAAAATGGCTATCTTCTAAAAATGACAAAT
196 TATGTGAATACTGTTCAAAATGGCTATCTTCTAAAAATGACAAAT
981483 AATGCTAAAC
Statistics
Matches: 237, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
244 237 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (244 bp):
TTTTTTTTTAGGAGTGATCTCACATGATCTATATGTATATATATAAGCTTGTATCTATTTCCGAT
TAAAAAATACCCATGACTGCATATAATTCAAGTCGGGTATGAAAATTTTATTCCAACAAAACTTA
GATTATGACTGCACATAATCCCTATATGATCATGTTTCCAAATGGATTCAAACAAAATATATAGG
TATGTGAATACTGTTCAAAATGGCTATCTTCTAAAAATGACAAATGCCA
Found at i:985128 original size:11 final size:14
Alignment explanation
Indices: 985092--985123 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
985082 GGAAGAACTT
985092 AAGATGAACAAATG
1 AAGATGAACAAATG
985106 AAGATGAACAAATG
1 AAGATGAACAAATG
985120 AAGA
1 AAGA
985124 ACAAAGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.59, C:0.06, G:0.22, T:0.12
Consensus pattern (14 bp):
AAGATGAACAAATG
Found at i:985145 original size:2 final size:2
Alignment explanation
Indices: 985138--985169 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
985128 AGAACACAAA
985138 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
985170 TTTTGAGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:989624 original size:20 final size:20
Alignment explanation
Indices: 989587--989624 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
989577 TCTTGAACAA
* *
989587 AAATCTCTAATATTACAATC
1 AAATCTCTAAGATCACAATC
989607 AAATCTCTAAGATCACAA
1 AAATCTCTAAGATCACAA
989625 GGATCATATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.21, G:0.03, T:0.29
Consensus pattern (20 bp):
AAATCTCTAAGATCACAATC
Found at i:993756 original size:23 final size:23
Alignment explanation
Indices: 993730--993791 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
993720 AGATATGCTA
993730 ATCTCGA-TCGTTGGTTTAATTTG
1 ATCTCGACT-GTTGGTTTAATTTG
*
993753 ATCTTGACTGTTGGTTTAATTTG
1 ATCTCGACTGTTGGTTTAATTTG
* *
993776 ATTTTGACTGTTGGTT
1 ATCTCGACTGTTGGTT
993792 ATGGAGGAGC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 35 0.97
24 1 0.03
ACGTcount: A:0.16, C:0.10, G:0.23, T:0.52
Consensus pattern (23 bp):
ATCTCGACTGTTGGTTTAATTTG
Found at i:999444 original size:30 final size:30
Alignment explanation
Indices: 999408--999464 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
999398 AGAGCATGGT
999408 ATGAAAGAATTGACAATCATCTAACAGAGA
1 ATGAAAGAATTGACAATCATCTAACAGAGA
999438 ATGAAAGAATTGACAATCATCTAACAG
1 ATGAAAGAATTGACAATCATCTAACAG
999465 GGAAGAGTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.49, C:0.14, G:0.16, T:0.21
Consensus pattern (30 bp):
ATGAAAGAATTGACAATCATCTAACAGAGA
Found at i:1000621 original size:28 final size:28
Alignment explanation
Indices: 1000577--1000631 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
1000567 TGACACAAAG
1000577 TGCGAGCTCTATCAGGCGAACCCATACA
1 TGCGAGCTCTATCAGGCGAACCCATACA
*
1000605 TGCGAGCTCTATTAGGCGAACCCATAC
1 TGCGAGCTCTATCAGGCGAACCCATAC
1000632 CTACAAGCTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.20
Consensus pattern (28 bp):
TGCGAGCTCTATCAGGCGAACCCATACA
Found at i:1000640 original size:28 final size:28
Alignment explanation
Indices: 1000581--1000641 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
1000571 ACAAAGTGCG
* *
1000581 AGCTCTATCAGGCGAACCCATACATGCG
1 AGCTCTATCAGGCGAACCCATACATACA
* *
1000609 AGCTCTATTAGGCGAACCCATACCTACA
1 AGCTCTATCAGGCGAACCCATACATACA
1000637 AGCTC
1 AGCTC
1000642 CTTACTTTGC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.30, C:0.33, G:0.18, T:0.20
Consensus pattern (28 bp):
AGCTCTATCAGGCGAACCCATACATACA
Found at i:1003378 original size:43 final size:42
Alignment explanation
Indices: 1003314--1003412 Score: 119
Period size: 43 Copynumber: 2.3 Consensus size: 42
1003304 CTGTAAATTA
*
1003314 GATAA-ATTTGCTATTAATTTTAATTTTTAAATAATGAATTTT
1 GATAAGATTT-CTTTTAATTTTAATTTTTAAATAATGAATTTT
** * * *
1003356 GATAATTTTTCTTTTAATTTTTAATTTTTAAATACTTAGTTTT
1 GATAAGATTTCTTTTAA-TTTTAATTTTTAAATAATGAATTTT
1003399 GATAAGATTTCTTT
1 GATAAGATTTCTTT
1003413 AAGTTTTCCT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
42 11 0.23
43 37 0.77
ACGTcount: A:0.32, C:0.04, G:0.07, T:0.57
Consensus pattern (42 bp):
GATAAGATTTCTTTTAATTTTAATTTTTAAATAATGAATTTT
Found at i:1014476 original size:8 final size:8
Alignment explanation
Indices: 1014463--1014488 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1014453 CAAAACGCTT
1014463 GTTTTAGG
1 GTTTTAGG
1014471 GTTTTAGG
1 GTTTTAGG
1014479 GTTTTAGG
1 GTTTTAGG
1014487 GT
1 GT
1014489 AAAAGAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.38, T:0.50
Consensus pattern (8 bp):
GTTTTAGG
Found at i:1015109 original size:27 final size:27
Alignment explanation
Indices: 1015071--1015125 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1015061 GAATAATATG
1015071 AAAACATAAAATAAAATTTTAAAATTT
1 AAAACATAAAATAAAATTTTAAAATTT
1015098 AAAACATAAAATAAAATTTTAAAATTT
1 AAAACATAAAATAAAATTTTAAAATTT
1015125 A
1 A
1015126 GAAGGAGATT
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:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (27 bp):
AAAACATAAAATAAAATTTTAAAATTT
Found at i:1015857 original size:30 final size:28
Alignment explanation
Indices: 1015823--1015888 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 28
1015813 ATTAGATTTG
* *
1015823 AATTTTACAAACTAAAAAGTATAGGGACTA
1 AATTTTACAAA-T-AAAAGTATAAGAACTA
*
1015853 AATTTCTAGAAATAAAAGTATAAGAACTA
1 AATTT-TACAAATAAAAGTATAAGAACTA
1015882 AATTTTA
1 AATTTTA
1015889 AATTTTCAGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.06
29 19 0.59
30 6 0.19
31 5 0.16
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.30
Consensus pattern (28 bp):
AATTTTACAAATAAAAGTATAAGAACTA
Found at i:1016741 original size:34 final size:34
Alignment explanation
Indices: 1016680--1016757 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
1016670 AATTAGGCCG
* * * *
1016680 ACAACGATTGCTTAGTGATATGTGAATCGGGTCA
1 ACAACGATTGCTTAGTAAAATGCGAATCGGATCA
* *
1016714 ACAACGATTGCTTCGTAAAATGCGAATCGGATCG
1 ACAACGATTGCTTAGTAAAATGCGAATCGGATCA
*
1016748 ACAATGATTG
1 ACAACGATTG
1016758 TCTGTTACTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (34 bp):
ACAACGATTGCTTAGTAAAATGCGAATCGGATCA
Found at i:1017812 original size:37 final size:34
Alignment explanation
Indices: 1017756--1017850 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 34
1017746 TTTAATATAA
* *
1017756 TTTAATATAAAACTAA-A-AAATTAATATAAAATAT
1 TTTAATAT-AATCTAATATAAAATAATA-AAAATAT
1017790 TTTAATATAATCTAATAT-AAA-AATAAAAATAT
1 TTTAATATAATCTAATATAAAATAATAAAAATAT
* *
1017822 TTTAATTTAATTTAATATCAAAATAATAA
1 TTTAATATAATCTAATAT-AAAATAATAA
1017851 TATTAAGAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
32 23 0.44
33 10 0.19
34 14 0.27
35 5 0.10
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (34 bp):
TTTAATATAATCTAATATAAAATAATAAAAATAT
Found at i:1017824 original size:32 final size:32
Alignment explanation
Indices: 1017778--1017854 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
1017768 CTAAAAAATT
1017778 AATATAAAATATTTTAATATAATCTAATATAAA
1 AATA-AAAATATTTTAATATAATCTAATATAAA
* * *
1017811 AATAAAAATATTTTAATTTAATTTAATATCAA
1 AATAAAAATATTTTAATATAATCTAATATAAA
*
1017843 AATAATAATATT
1 AATAAAAATATT
1017855 AAGAATGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 36 0.90
33 4 0.10
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (32 bp):
AATAAAAATATTTTAATATAATCTAATATAAA
Found at i:1017913 original size:16 final size:16
Alignment explanation
Indices: 1017892--1017956 Score: 57
Period size: 15 Copynumber: 4.2 Consensus size: 16
1017882 ATTTTTATTA
1017892 AATTATAATTAATAAT
1 AATTATAATTAATAAT
1017908 AATTAT-ATTAA-AAT
1 AATTATAATTAATAAT
* * *
1017922 -ATGATTAATTTATTA-
1 AATTA-TAATTAATAAT
*
1017937 AATTATATTTAATAAT
1 AATTATAATTAATAAT
1017953 AATT
1 AATT
1017957 CAATTCTATT
Statistics
Matches: 37, Mismatches: 7, Indels: 10
0.69 0.13 0.19
Matches are distributed among these distances:
13 3 0.08
14 4 0.11
15 16 0.43
16 14 0.38
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (16 bp):
AATTATAATTAATAAT
Found at i:1017916 original size:26 final size:25
Alignment explanation
Indices: 1017863--1017956 Score: 85
Period size: 26 Copynumber: 4.0 Consensus size: 25
1017853 TTAAGAATGT
* * *
1017863 TATTAAATTATA-TAATATTATTTT
1 TATTAAATTATATTAATAATAATTA
1017887 TATTAAATTATAATTAATAATAATTA
1 TATTAAATTAT-ATTAATAATAATTA
*
1017913 TATTAAA--ATA-TGAT--TAATT-
1 TATTAAATTATATTAATAATAATTA
1017932 TATTAAATTATATTTAATAATAATT
1 TATTAAATTATA-TTAATAATAATT
1017957 CAATTCTATT
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
19 7 0.12
20 5 0.09
21 3 0.05
22 3 0.05
23 4 0.07
24 13 0.23
25 6 0.11
26 16 0.28
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
TATTAAATTATATTAATAATAATTA
Found at i:1022447 original size:24 final size:24
Alignment explanation
Indices: 1022398--1022448 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1022388 AGTTTGTCTC
* *
1022398 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAATAGAGTTCAACTG
1022422 AAACAAATAAATAGAGTTCAACTG
1 AAACAAATAAATAGAGTTCAACTG
1022446 AAA
1 AAA
1022449 GATTATTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAATAGAGTTCAACTG
Found at i:1029116 original size:39 final size:39
Alignment explanation
Indices: 1029073--1029151 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
1029063 AGTGAATGAC
1029073 ACACCCAGCAGGCCCAAAGGCAAGTGGGAGAGAGAGACT
1 ACACCCAGCAGGCCCAAAGGCAAGTGGGAGAGAGAGACT
1029112 ACACCCAGCAGGCCCAAAGGCAAGTGGGAGAGAGAGACT
1 ACACCCAGCAGGCCCAAAGGCAAGTGGGAGAGAGAGACT
1029151 A
1 A
1029152 TGTCATAGGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.37, C:0.25, G:0.33, T:0.05
Consensus pattern (39 bp):
ACACCCAGCAGGCCCAAAGGCAAGTGGGAGAGAGAGACT
Found at i:1037364 original size:49 final size:49
Alignment explanation
Indices: 1037240--1037864 Score: 401
Period size: 49 Copynumber: 12.7 Consensus size: 49
1037230 ACCATGAAGA
* * ** *
1037240 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACGATGAT
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAA-CCTAGTACCTC-AAAAG
* * *
1037290 AAT-AGAGGGAAA-AGTTTAAGTCGCAACGACGAACCTCGTACCTCAAAAG
1 CATGA-AGGGAAAGA-TTTAAGCCGCAACGACGAACCTAGTACCTCAAAAG
* * *
1037339 CATGAAGGGAAAGATTTAAGCCGCAACGATGAATCTAGTACCAC-AAAG
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAAAAG
* * * * * * * * *
1037387 -ATACGAAGAGAATGGTTTAAGCCGTAACGACAAACCTTGTACTTTAGAAG
1 CAT--GAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAAAAG
* *
1037437 CATGAAGGGAAAGATTTAAGCCGTAACGACGAATCC-AGTACCAC-AAAG
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAA-CCTAGTACCTCAAAAG
* * * * * *
1037485 ACAATGGAGGGAAAGGTTTAAGTCGCAATGATGAACCTTGTACCTCAAAAG
1 -C-ATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAAAAG
* * * **
1037536 CATGAAGGGAAAGGTTTAAGTCGCAACGGCGAACCTTCTACCTCAAAAG
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAAAAG
* * *
1037585 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAG
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAA-CCTAGTACCTCAAAAG
* * * * * * *
1037633 ACAAT-AGAGGGAAAGGTTTAAGTCACAATGATGAACCTTGCACCTCAAAAG
1 -C-ATGA-AGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAAAAG
* ** * * **
1037684 CATGAAGGGAAAGGTTTAAGTTGCAACGGCAAACCTTCTACCTCAAAAG
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAAAAG
* * ** * * *
1037733 CATGAAGGGAAAGATTTAAGCTGCAATGGTGAATCC-AGTACCACGAAGAT
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAA-CCTAGTACCTC-AAAAG
* * * * ** * *
1037783 AATCG-AGGGAAAGGTTTAAGTCGTAACGACGAATTTTGTACCTTAAAAG
1 CAT-GAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAAAAG
* * * *
1037832 CACGGAGGAAAAGATTTAAGCCGCAACGGCGAA
1 CATGAAGGGAAAGATTTAAGCCGCAACGACGAA
1037865 TCTATTATCG
Statistics
Matches: 445, Mismatches: 104, Indels: 53
0.74 0.17 0.09
Matches are distributed among these distances:
47 2 0.00
48 11 0.02
49 284 0.64
50 138 0.31
51 10 0.02
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.18
Consensus pattern (49 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGACGAACCTAGTACCTCAAAAG
Found at i:1037518 original size:148 final size:148
Alignment explanation
Indices: 1037344--1037861 Score: 653
Period size: 148 Copynumber: 3.5 Consensus size: 148
1037334 AAAAGCATGA
* * * * * * * *
1037344 AGGGAAAGATTTAAGCCGCAACGATGAATCTAGTACCAC-AAAG-ATACGAAGAGAATGGTTTAA
1 AGGGAAAGGTTTAAGTCGCAATGATGAACCTTGTACCTCAAAAGCAT--GAAGGGAAAGGTTTAA
* * * * * * * * *
1037407 GCCGTAACGACAAACCTTGTACTTTAGAAGCATGAAGGGAAAGATTTAAGCCGTAACGACGAATC
64 GTCGCAACGGCAAACCTTCTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
* *
1037472 CAGTACCACAAAGACAATGG
129 CAGTACCACGAAGACAATAG
1037492 AGGGAAAGGTTTAAGTCGCAATGATGAACCTTGTACCTCAAAAGCATGAAGGGAAAGGTTTAAGT
1 AGGGAAAGGTTTAAGTCGCAATGATGAACCTTGTACCTCAAAAGCATGAAGGGAAAGGTTTAAGT
*
1037557 CGCAACGGCGAACCTTCTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
66 CGCAACGGCAAACCTTCTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
1037622 GTACCACGAAGACAATAG
131 GTACCACGAAGACAATAG
* *
1037640 AGGGAAAGGTTTAAGTCACAATGATGAACCTTGCACCTCAAAAGCATGAAGGGAAAGGTTTAAGT
1 AGGGAAAGGTTTAAGTCGCAATGATGAACCTTGTACCTCAAAAGCATGAAGGGAAAGGTTTAAGT
* * * *
1037705 TGCAACGGCAAACCTTCTACCTCAAAAGCATGAAGGGAAAGATTTAAGCTGCAATGGTGAATCCA
66 CGCAACGGCAAACCTTCTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
* *
1037770 GTACCACGAAGATAATCG
131 GTACCACGAAGACAATAG
* * * ** * * * * * *
1037788 AGGGAAAGGTTTAAGTCGTAACGACGAATTTTGTACCTTAAAAGCACGGAGGAAAAGATTTAAGC
1 AGGGAAAGGTTTAAGTCGCAATGATGAACCTTGTACCTCAAAAGCATGAAGGGAAAGGTTTAAGT
1037853 CGCAACGGC
66 CGCAACGGC
1037862 GAATCTATTA
Statistics
Matches: 325, Mismatches: 43, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
148 319 0.98
149 4 0.01
150 2 0.01
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (148 bp):
AGGGAAAGGTTTAAGTCGCAATGATGAACCTTGTACCTCAAAAGCATGAAGGGAAAGGTTTAAGT
CGCAACGGCAAACCTTCTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCA
GTACCACGAAGACAATAG
Found at i:1037605 original size:197 final size:197
Alignment explanation
Indices: 1037235--1037758 Score: 521
Period size: 197 Copynumber: 2.7 Consensus size: 197
1037225 TCATTACCAT
* * * *
1037235 GAAGACATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGATGATAATAGAGGGA
1 GAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACAAAGACAATAGAGGGA
1037300 AAAGTTTAAGTCGCAACGACGAACCTCGTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAA
66 AAAGTTTAAGTCGCAACGACGAACCTCGTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAA
* * * * * *
1037365 CGATGAATCTAGTACCACAAAGATACGAAGAGAATGGTTTAAGCCGTAACGACAAACCTTGTACT
131 CGACGAACCTACTACCACAAAGATA-GAAGAGAAAGATTTAAGCCGCAACGACAAACCTTGTACT
1037430 TTA
195 TTA
* *
1037433 GAAG-CATGAAGGGAAAGATTTAAGCCGTAACGACGAATCCAGTACCACAAAGACAATGGAGGGA
1 GAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACAAAGACAATAGAGGGA
* * * * * *
1037497 AAGGTTTAAGTCGCAATGATGAACCTTGTACCTCAAAAGCATGAAGGGAAAGGTTTAAGTCGCAA
66 AAAGTTTAAGTCGCAACGACGAACCTCGTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAA
* * * * * * *
1037562 CGGCGAACCTTCTACCTCAAAAGCAT-GAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTA
131 CGACGAACCTACTACCAC-AAAG-ATAGAAGAGAAAGATTTAAGCCGCAACGAC-AAACCTTGTA
*
1037625 C--CA
193 CTTTA
* * * * * * * *
1037628 CGAAGACAAT-AGAGGGAAAGGTTTAAGTCACAATGATGAA-CCTTGCACCTCAAA-AGC-AT-G
1 -GAAGAC-ATGA-AGGGAAAGATTTAAGCCGCAACGACGAATCC-AGTACCACAAAGA-CAATAG
* * * *
1037688 AAGGGAAAGGTTTAAGTTGCAACGGCAAACCTTC-TACCTCAAAAGCATGAAGGGAAAGATTTAA
61 -AGGGAAAAGTTTAAGTCGCAACGACGAACC-TCGTACCTCAAAAGCATGAAGGGAAAGATTTAA
*
1037752 GCTGCAA
124 GCCGCAA
1037759 TGGTGAATCC
Statistics
Matches: 271, Mismatches: 44, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
195 1 0.00
196 5 0.02
197 217 0.80
198 46 0.17
199 2 0.01
ACGTcount: A:0.39, C:0.19, G:0.24, T:0.18
Consensus pattern (197 bp):
GAAGACATGAAGGGAAAGATTTAAGCCGCAACGACGAATCCAGTACCACAAAGACAATAGAGGGA
AAAGTTTAAGTCGCAACGACGAACCTCGTACCTCAAAAGCATGAAGGGAAAGATTTAAGCCGCAA
CGACGAACCTACTACCACAAAGATAGAAGAGAAAGATTTAAGCCGCAACGACAAACCTTGTACTT
TA
Found at i:1037792 original size:99 final size:98
Alignment explanation
Indices: 1037240--1037866 Score: 523
Period size: 99 Copynumber: 6.4 Consensus size: 98
1037230 ACCATGAAGA
* *
1037240 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACGATGATAAT-AGAGGGAAAAG
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGATAATGA-AGGGAAAGG
* *
1037304 TTTAAGTCGCAACGACGAACCTCGTACCTCAAAAG
64 TTTAAGTCGCAACGACAAACCTTGTACCTCAAAAG
** * * * *
1037339 CATGAAGGGAAAGATTTAAGCCGCAACGATGAATCTAGTACCACAAAGAT-ACGAAGAGAATGGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGATAATGAAGGGAAAGGT
* * * * *
1037403 TTAAGCCGTAACGACAAACCTTGTACTTTAGAAG
65 TTAAGTCGCAACGACAAACCTTGTACCTCAAAAG
* * * *
1037437 CATGAAGGGAAAGATTTAAGCCGTAACGACGAATCCAGTACCACAAAGACAATGGAGGGAAAGGT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGATAATGAAGGGAAAGGT
* **
1037502 TTAAGTCGCAATGATGAACCTTGTACCTCAAAAG
65 TTAAGTCGCAACGACAAACCTTGTACCTCAAAAG
* * ** * * ** *
1037536 CATGAAGGGAAAGGTTTAAGTCGCAACGGCGAA-CCTTCTACCTCAAAAGCATGAAGGGAAAGAT
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACAAGATAATGAAGGGAAAGGT
* * * * * *
1037600 TTAAGCCGCAACGGCGAATCC-AGTACCAC-GAAG
65 TTAAGTCGCAACGAC-AAACCTTGTACCTCAAAAG
* * * * ** * * * * **
1037633 ACAAT-AGAGGGAAAGGTTTAAGTCACAATGATGAA-CCTTGCACCTCAAAAGCATGAAGGGAAA
1 -C-ATGA-AGGGAAAGATTTAAGCCGCAACGGCGAATCC-AGTACCACAAGATAATGAAGGGAAA
* * *
1037696 GGTTTAAGTTGCAACGGCAAACCTTCTACCTCAAAAG
62 GGTTTAAGTCGCAACGACAAACCTTGTACCTCAAAAG
* * *
1037733 CATGAAGGGAAAGATTTAAGCTGCAATGGTGAATCCAGTACCACGAAGATAATCG-AGGGAAAGG
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCAC-AAGATAAT-GAAGGGAAAGG
* * ** *
1037797 TTTAAGTCGTAACGACGAATTTTGTACCTTAAAAG
64 TTTAAGTCGCAACGACAAACCTTGTACCTCAAAAG
* * *
1037832 CACGGAGGAAAAGATTTAAGCCGCAACGGCGAATC
1 CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATC
1037867 TATTATCGCA
Statistics
Matches: 423, Mismatches: 92, Indels: 26
0.78 0.17 0.05
Matches are distributed among these distances:
97 3 0.01
98 151 0.36
99 265 0.63
100 4 0.01
ACGTcount: A:0.38, C:0.19, G:0.24, T:0.19
Consensus pattern (98 bp):
CATGAAGGGAAAGATTTAAGCCGCAACGGCGAATCCAGTACCACAAGATAATGAAGGGAAAGGTT
TAAGTCGCAACGACAAACCTTGTACCTCAAAAG
Found at i:1044688 original size:147 final size:147
Alignment explanation
Indices: 1044421--1044722 Score: 516
Period size: 147 Copynumber: 2.1 Consensus size: 147
1044411 GGAGGCACTA
* *
1044421 ATTTATGTTGAGAGAGTGGTGGCTACAGACTGGGAAGCATGAGTTCGTCGGAGGACGGATAACAT
1 ATTTATGTTGAGAGAGTGGTGGCTACAGACTGGGAAGCATGAGTTCGTCAGAGGACGGATAACAA
* *
1044486 GTTTTTTTAACTTTGAAATTGGAAAAGGTTTGATGGAATCTCTAATGAGGACTTAAAAGTTGTTC
66 GTTTTTTTAACTTTAAAATTGGAAAAGGTTTGATGGAATCTCTAAGGAGGACTTAAAAGTTGTTC
1044551 CTTCCTATAGAGTGCTG
131 CTTCCTATAGAGTGCTG
* * *
1044568 ATTTATGTTGAGAGAGTGGTGGCTGCAGACTGGGAAGCTTGAGTTCGTCAGAGGACGGGTAACAA
1 ATTTATGTTGAGAGAGTGGTGGCTACAGACTGGGAAGCATGAGTTCGTCAGAGGACGGATAACAA
*
1044633 GTTTTTTTAACTTTAAAATTGGAAAAGGTTTGATGGAATTTCTAAGGAGGACTTAAAAGTTGTTC
66 GTTTTTTTAACTTTAAAATTGGAAAAGGTTTGATGGAATCTCTAAGGAGGACTTAAAAGTTGTTC
*
1044698 CTTCCTATAGAGTGTTG
131 CTTCCTATAGAGTGCTG
1044715 ATTT-TGTT
1 ATTTATGTT
1044723 TTCATGGAGA
Statistics
Matches: 146, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
146 4 0.03
147 142 0.97
ACGTcount: A:0.27, C:0.11, G:0.28, T:0.34
Consensus pattern (147 bp):
ATTTATGTTGAGAGAGTGGTGGCTACAGACTGGGAAGCATGAGTTCGTCAGAGGACGGATAACAA
GTTTTTTTAACTTTAAAATTGGAAAAGGTTTGATGGAATCTCTAAGGAGGACTTAAAAGTTGTTC
CTTCCTATAGAGTGCTG
Found at i:1045940 original size:26 final size:28
Alignment explanation
Indices: 1045888--1045943 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
1045878 AAAAATTAAA
*
1045888 AAAAATATTTTTTATATTTTTAATTTTT
1 AAAAATATCTTTTATATTTTTAATTTTT
*
1045916 AAAAATA-CTTTTAT-TTTTTTATTTTT
1 AAAAATATCTTTTATATTTTTAATTTTT
1045942 AA
1 AA
1045944 TTTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 13 0.50
27 6 0.23
28 7 0.27
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (28 bp):
AAAAATATCTTTTATATTTTTAATTTTT
Found at i:1059178 original size:50 final size:52
Alignment explanation
Indices: 1059071--1059198 Score: 138
Period size: 50 Copynumber: 2.5 Consensus size: 52
1059061 TGAAAAAATG
* * * *
1059071 TGTAAATGTTATGGGCTAAATTTGTTAAATTAGGACCAAGTTGACAAAATTCA
1 TGTAAATGTTGT-GGCTAAATTTATTAAATCAAGACCAAGTTGACAAAATTCA
*
1059124 --TAAATGTTGTGGCTAAATTTATTAAATCAAGACCAAGTTGAC-ATATT-A
1 TGTAAATGTTGTGGCTAAATTTATTAAATCAAGACCAAGTTGACAAAATTCA
* * *
1059172 TGTAAATTTTGAGAGCTAAACTTATTA
1 TGTAAATGTTGTG-GCTAAATTTATTA
1059199 TATTAATGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
48 1 0.02
49 4 0.06
50 38 0.59
51 21 0.33
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (52 bp):
TGTAAATGTTGTGGCTAAATTTATTAAATCAAGACCAAGTTGACAAAATTCA
Found at i:1066257 original size:23 final size:24
Alignment explanation
Indices: 1066231--1066280 Score: 84
Period size: 23 Copynumber: 2.1 Consensus size: 24
1066221 TAACAGTTTA
*
1066231 GTTCAGTCAAATTCAATGGGTC-G
1 GTTCAGTCAAAGTCAATGGGTCAG
1066254 GTTCAGTCAAAGTCAATGGGTCAG
1 GTTCAGTCAAAGTCAATGGGTCAG
1066278 GTT
1 GTT
1066281 GGATCGATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 21 0.84
24 4 0.16
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (24 bp):
GTTCAGTCAAAGTCAATGGGTCAG
Found at i:1066296 original size:22 final size:23
Alignment explanation
Indices: 1066264--1066326 Score: 65
Period size: 22 Copynumber: 2.7 Consensus size: 23
1066254 GTTCAGTCAA
*
1066264 AGTCAATGGGTCAGGTTGGATCG
1 AGTCAACGGGTCAGGTTGGATCG
* * *
1066287 A-TCAACGGGTCGGGTCGGGTCG
1 AGTCAACGGGTCAGGTTGGATCG
*
1066309 AGTCACACGGTTCAGGTT
1 AGTCA-ACGGGTCAGGTT
1066327 AGGGCTTGGT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 18 0.58
23 4 0.13
24 9 0.29
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.24
Consensus pattern (23 bp):
AGTCAACGGGTCAGGTTGGATCG
Found at i:1081201 original size:27 final size:27
Alignment explanation
Indices: 1081170--1081226 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1081160 TCATTTTATA
1081170 CCTCTTTTGTTCATCCTTTAATTTTTT
1 CCTCTTTTGTTCATCCTTTAATTTTTT
**
1081197 CCTCTTTTGTTCATCCTTTTGTTTTTT
1 CCTCTTTTGTTCATCCTTTAATTTTTT
1081224 CCT
1 CCT
1081227 TTCACCATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.07, C:0.25, G:0.05, T:0.63
Consensus pattern (27 bp):
CCTCTTTTGTTCATCCTTTAATTTTTT
Found at i:1085508 original size:31 final size:31
Alignment explanation
Indices: 1085467--1085599 Score: 155
Period size: 31 Copynumber: 4.3 Consensus size: 31
1085457 GGGTCTAACA
*
1085467 CATACCATACATAACATACA-AGCTAATATAT
1 CATAACATACATAACATACACA-CTAATATAT
* *
1085498 CATAACATACATAATATACACACTAAAATAT
1 CATAACATACATAACATACACACTAATATAT
*
1085529 CATAACATACATAATACACACACACTAATATAT
1 CATAACATACAT-A-ACATACACACTAATATAT
* * *
1085562 CATAACATACATAATATTCATACTAATATA-
1 CATAACATACATAACATACACACTAATATAT
1085592 CAT-ACATA
1 CATAACATA
1085600 ATATACGTAC
Statistics
Matches: 89, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
29 5 0.06
30 3 0.03
31 51 0.57
32 3 0.03
33 27 0.30
ACGTcount: A:0.51, C:0.21, G:0.01, T:0.27
Consensus pattern (31 bp):
CATAACATACATAACATACACACTAATATAT
Found at i:1085552 original size:33 final size:32
Alignment explanation
Indices: 1085466--1085577 Score: 145
Period size: 33 Copynumber: 3.4 Consensus size: 32
1085456 AGGGTCTAAC
*
1085466 ACATACCATACATAACATACAAGCTAATATATCATA
1 ACATA-CATA-ATAACACAC-A-CTAATATATCATA
* *
1085502 ACATACATAAT-ATACACACTAAAATATCATA
1 ACATACATAATAACACACACTAATATATCATA
1085533 ACATACATAATACACACACACTAATATATCATA
1 ACATACATAATA-ACACACACTAATATATCATA
1085566 ACATACATAATA
1 ACATACATAATA
1085578 TTCATACTAA
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
31 23 0.33
32 1 0.01
33 34 0.49
34 2 0.03
35 4 0.06
36 5 0.07
ACGTcount: A:0.53, C:0.21, G:0.01, T:0.25
Consensus pattern (32 bp):
ACATACATAATAACACACACTAATATATCATA
Found at i:1085590 original size:12 final size:13
Alignment explanation
Indices: 1085566--1085616 Score: 70
Period size: 12 Copynumber: 4.1 Consensus size: 13
1085556 ATATATCATA
1085566 ACATACATAATAT
1 ACATACATAATAT
*
1085579 TCATAC-TAATAT
1 ACATACATAATAT
1085591 ACATACATAATAT
1 ACATACATAATAT
*
1085604 ACGTAC-TAATAT
1 ACATACATAATAT
1085616 A
1 A
1085617 TCAATTGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
12 18 0.53
13 16 0.47
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (13 bp):
ACATACATAATAT
Found at i:1085595 original size:25 final size:25
Alignment explanation
Indices: 1085566--1085616 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1085556 ATATATCATA
*
1085566 ACATACATAATATTCATACTAATAT
1 ACATACATAATATACATACTAATAT
*
1085591 ACATACATAATATACGTACTAATAT
1 ACATACATAATATACATACTAATAT
1085616 A
1 A
1085617 TCAATTGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (25 bp):
ACATACATAATATACATACTAATAT
Found at i:1086642 original size:23 final size:24
Alignment explanation
Indices: 1086615--1086664 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
1086605 AATTTGACTC
* *
1086615 AAACAACTAAACA-AGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
1086638 AAACAAATAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
1086662 AAA
1 AAA
1086665 GGTTATTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:1089023 original size:29 final size:29
Alignment explanation
Indices: 1088933--1089115 Score: 181
Period size: 29 Copynumber: 6.3 Consensus size: 29
1088923 AGATATCCAT
*
1088933 AAAGGCTCACATATAACCGAATT-AGCCAC
1 AAAGGCTCACATATAA-CAAATTCAGCCAC
** * * * *
1088962 AAAAACCCACATATAACAGATTCAACCAT
1 AAAGGCTCACATATAACAAATTCAGCCAC
* **
1088991 AAAGGTTCACATATAACAAATTCAGTAAC
1 AAAGGCTCACATATAACAAATTCAGCCAC
* ** *
1089020 AAAGGCTCGCATATAACAAATTTGGCTAC
1 AAAGGCTCACATATAACAAATTCAGCCAC
*
1089049 AAAAGCTCACATATAACAGAATT-AGCCAC
1 AAAGGCTCACATATAACA-AATTCAGCCAC
* *
1089078 AAAGGCTCGCATATAACAAAATCAGCCAC
1 AAAGGCTCACATATAACAAATTCAGCCAC
1089107 AAAGGCTCA
1 AAAGGCTCA
1089116 TTTTTTGGTA
Statistics
Matches: 121, Mismatches: 30, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
28 7 0.06
29 110 0.91
30 4 0.03
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (29 bp):
AAAGGCTCACATATAACAAATTCAGCCAC
Found at i:1089082 original size:87 final size:87
Alignment explanation
Indices: 1088933--1089115 Score: 217
Period size: 87 Copynumber: 2.1 Consensus size: 87
1088923 AGATATCCAT
* * *
1088933 AAAGGCTCACATATAACCGAATTAGCCACAAAAACCCACATATAACAGATTCAACCATAAAGGTT
1 AAAGGCTCACATATAACCAAATTAGCCACAAAAACCCACATATAACAGATTCAACCACAAAGGCT
* *
1088998 CACATATAACAAATTCAGTAAC
66 CACATATAACAAAATCAGCAAC
* * * * * *
1089020 AAAGGCTCGCATATAA-CAAATTTGGCTACAAAAGCTCACATATAACAGAATT-AGCCACAAAGG
1 AAAGGCTCACATATAACCAAA-TTAGCCACAAAAACCCACATATAACAG-ATTCAACCACAAAGG
* *
1089083 CTCGCATATAACAAAATCAGCCAC
64 CTCACATATAACAAAATCAGCAAC
1089107 AAAGGCTCA
1 AAAGGCTCA
1089116 TTTTTTGGTA
Statistics
Matches: 80, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
86 3 0.04
87 74 0.93
88 3 0.04
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (87 bp):
AAAGGCTCACATATAACCAAATTAGCCACAAAAACCCACATATAACAGATTCAACCACAAAGGCT
CACATATAACAAAATCAGCAAC
Found at i:1097801 original size:11 final size:11
Alignment explanation
Indices: 1097785--1097816 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1097775 AAATAATGGA
1097785 AATGCAACTAT
1 AATGCAACTAT
1097796 AATGCAACTAT
1 AATGCAACTAT
1097807 AATGCAACTA
1 AATGCAACTA
1097817 AGTTAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.09, T:0.25
Consensus pattern (11 bp):
AATGCAACTAT
Found at i:1117852 original size:12 final size:12
Alignment explanation
Indices: 1117829--1117882 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
1117819 GCAAACATTT
1117829 TTTTCTTCTTTTC
1 TTTTC-TCTTTTC
*
1117842 TTTTCTCTTTTT
1 TTTTCTCTTTTC
*
1117854 TTTTTTC-TTTC
1 TTTTCTCTTTTC
1117865 TTTTTCTCATTTTC
1 -TTTTCTC-TTTTC
1117879 TTTT
1 TTTT
1117883 TTCAAGTGAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.53
13 9 0.26
14 4 0.12
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTCTCTTTTC
Found at i:1117864 original size:23 final size:26
Alignment explanation
Indices: 1117826--1117885 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 26
1117816 ATAGCAAACA
*
1117826 TTTTTTTCTTCTTTTC-TTTTCTC-T
1 TTTTTTTTTTCTTTTCTTTTTCTCAT
1117850 TTTTTTTTTTC-TTTCTTTTTCTCAT
1 TTTTTTTTTTCTTTTCTTTTTCTCAT
*
1117875 TTTCTTTTTTC
1 TTTTTTTTTTC
1117886 AAGTGATTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
23 4 0.12
24 17 0.53
25 11 0.34
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTTTTTTTCTTTTCTTTTTCTCAT
Found at i:1124432 original size:17 final size:17
Alignment explanation
Indices: 1124408--1124448 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1124398 TCTTAAAGTG
1124408 TATTTCCATTTCAATTT
1 TATTTCCATTTCAATTT
*
1124425 TGTTTCCATTTCAATTT
1 TATTTCCATTTCAATTT
1124442 TATTTCC
1 TATTTCC
1124449 TTTATGTTCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.20, C:0.20, G:0.02, T:0.59
Consensus pattern (17 bp):
TATTTCCATTTCAATTT
Found at i:1136599 original size:23 final size:23
Alignment explanation
Indices: 1136523--1136761 Score: 199
Period size: 23 Copynumber: 10.5 Consensus size: 23
1136513 TAAACGGAAC
* * *
1136523 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
1136545 AAACAGAGAGCACA-TAAGTGTT
1 AAACAGAGAGCACACAAAGTGCT
*
1136567 GGGTAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* * *
1136593 AATCAGAGAGTAAACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
1136613 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
1136632 AATCAGAGAGCAGACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
1136655 AATAACAGAGAGCACACACAGTGCT
1 -A-AACAGAGAGCACACAAAGTGCT
*
1136680 AAACAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
1136703 AACAACAGAGAGCACACATAGTGCT
1 -A-AACAGAGAGCACACAAAGTGCT
*
1136728 AAACAGAGAGCACACATAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
1136751 AAACAGAGAGC
1 AAACAGAGAGC
1136762 GCGCTAGTGT
Statistics
Matches: 174, Mismatches: 27, Indels: 31
0.75 0.12 0.13
Matches are distributed among these distances:
16 9 0.05
18 2 0.01
19 1 0.01
20 1 0.01
21 2 0.01
22 17 0.10
23 81 0.47
24 4 0.02
25 51 0.29
26 6 0.03
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:1136687 original size:48 final size:47
Alignment explanation
Indices: 1136616--1136761 Score: 215
Period size: 48 Copynumber: 3.1 Consensus size: 47
1136606 ACAAAGTACT
* *
1136616 GAGCACACAAAGTGCTAATCAGAGAGCAGACGAAGTGCTAATAACAGA
1 GAGCACACAAAGTGCTAAACAGAGAGCACACGAAGTGCTAA-AACAGA
*
1136664 GAGCACACACAGTGCTAAACAGAGAGCACACGAAGTGCTAACAACAGA
1 GAGCACACAAAGTGCTAAACAGAGAGCACACGAAGTGCTAA-AACAGA
*
1136712 GAGCACACATAGTGCTAAACAGAGAGCACAC-ATAGTGCT-AAACAGA
1 GAGCACACAAAGTGCTAAACAGAGAGCACACGA-AGTGCTAAAACAGA
1136758 GAGC
1 GAGC
1136762 GCGCTAGTGT
Statistics
Matches: 92, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
46 10 0.11
47 2 0.02
48 80 0.87
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (47 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACGAAGTGCTAAAACAGA
Found at i:1136733 original size:71 final size:71
Alignment explanation
Indices: 1136616--1136761 Score: 208
Period size: 71 Copynumber: 2.1 Consensus size: 71
1136606 ACAAAGTACT
* *
1136616 GAGCACACAAAGTGCTAATCAGAGAGCAGACGAAGTGCTAATAACAGAGAGCACACACAGTGCTA
1 GAGCACACAAAGTGCTAAACAGAGAGCACACGAAGTGCTAATAACAGAGAGCACACACAGTGCTA
1136681 AACAGA
66 AACAGA
* *
1136687 GAGCACACGAAGTGCTAACAACAGAGAGCACAC-ATAGTGCT-A-AACAGAGAGCACACATAGTG
1 GAGCACACAAAGTGCT-A-AACAGAGAGCACACGA-AGTGCTAATAACAGAGAGCACACACAGTG
1136749 CTAAACAGA
63 CTAAACAGA
1136758 GAGC
1 GAGC
1136762 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
71 47 0.69
72 3 0.04
73 18 0.26
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (71 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACGAAGTGCTAATAACAGAGAGCACACACAGTGCTA
AACAGA
Found at i:1138610 original size:41 final size:41
Alignment explanation
Indices: 1138565--1138648 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
1138555 GATGTTACAT
*
1138565 CATTAACAATCGATACCTCATACAGTTTTATCCCTGACTCC
1 CATTAACAATCGATACCTCATACAGTTCTATCCCTGACTCC
* *
1138606 CATTAACAATCGATACCTCATTCAGTTCTGTCCCTGACTCC
1 CATTAACAATCGATACCTCATACAGTTCTATCCCTGACTCC
1138647 CA
1 CA
1138649 AGTATCAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.27, C:0.33, G:0.08, T:0.31
Consensus pattern (41 bp):
CATTAACAATCGATACCTCATACAGTTCTATCCCTGACTCC
Found at i:1145443 original size:23 final size:23
Alignment explanation
Indices: 1145367--1145605 Score: 199
Period size: 23 Copynumber: 10.5 Consensus size: 23
1145357 TAAACGGAAC
* * *
1145367 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
1145389 AAACAGAGAGCACA-TAAGTGTT
1 AAACAGAGAGCACACAAAGTGCT
*
1145411 GGGTAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* * *
1145437 AATCAGAGAGTAAACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
1145457 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
1145476 AATCAGAGAGCAGACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
1145499 AATAACAGAGAGCACACACAGTGCT
1 -A-AACAGAGAGCACACAAAGTGCT
*
1145524 AAACAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
1145547 AACAACAGAGAGCACACATAGTGCT
1 -A-AACAGAGAGCACACAAAGTGCT
*
1145572 AAACAGAGAGCACACATAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
1145595 AAACAGAGAGC
1 AAACAGAGAGC
1145606 GCGCTAGTGT
Statistics
Matches: 174, Mismatches: 27, Indels: 31
0.75 0.12 0.13
Matches are distributed among these distances:
16 9 0.05
18 2 0.01
19 1 0.01
20 1 0.01
21 2 0.01
22 17 0.10
23 81 0.47
24 4 0.02
25 51 0.29
26 6 0.03
ACGTcount: A:0.44, C:0.20, G:0.24, T:0.13
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:1145531 original size:48 final size:47
Alignment explanation
Indices: 1145460--1145605 Score: 215
Period size: 48 Copynumber: 3.1 Consensus size: 47
1145450 ACAAAGTACT
* *
1145460 GAGCACACAAAGTGCTAATCAGAGAGCAGACGAAGTGCTAATAACAGA
1 GAGCACACAAAGTGCTAAACAGAGAGCACACGAAGTGCTAA-AACAGA
*
1145508 GAGCACACACAGTGCTAAACAGAGAGCACACGAAGTGCTAACAACAGA
1 GAGCACACAAAGTGCTAAACAGAGAGCACACGAAGTGCTAA-AACAGA
*
1145556 GAGCACACATAGTGCTAAACAGAGAGCACAC-ATAGTGCT-AAACAGA
1 GAGCACACAAAGTGCTAAACAGAGAGCACACGA-AGTGCTAAAACAGA
1145602 GAGC
1 GAGC
1145606 GCGCTAGTGT
Statistics
Matches: 92, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
46 10 0.11
47 2 0.02
48 80 0.87
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (47 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACGAAGTGCTAAAACAGA
Found at i:1145577 original size:71 final size:71
Alignment explanation
Indices: 1145460--1145605 Score: 208
Period size: 71 Copynumber: 2.1 Consensus size: 71
1145450 ACAAAGTACT
* *
1145460 GAGCACACAAAGTGCTAATCAGAGAGCAGACGAAGTGCTAATAACAGAGAGCACACACAGTGCTA
1 GAGCACACAAAGTGCTAAACAGAGAGCACACGAAGTGCTAATAACAGAGAGCACACACAGTGCTA
1145525 AACAGA
66 AACAGA
* *
1145531 GAGCACACGAAGTGCTAACAACAGAGAGCACAC-ATAGTGCT-A-AACAGAGAGCACACATAGTG
1 GAGCACACAAAGTGCT-A-AACAGAGAGCACACGA-AGTGCTAATAACAGAGAGCACACACAGTG
1145593 CTAAACAGA
63 CTAAACAGA
1145602 GAGC
1 GAGC
1145606 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
71 47 0.69
72 3 0.04
73 18 0.26
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (71 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACGAAGTGCTAATAACAGAGAGCACACACAGTGCTA
AACAGA
Found at i:1147454 original size:41 final size:41
Alignment explanation
Indices: 1147409--1147492 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
1147399 GATGTTACAT
*
1147409 CATTAACAATCGATACCTCATACAGTTTTATCCCTGACTCC
1 CATTAACAATCGATACCTCATACAGTTCTATCCCTGACTCC
* *
1147450 CATTAACAATCGATACCTCATTCAGTTCTGTCCCTGACTCC
1 CATTAACAATCGATACCTCATACAGTTCTATCCCTGACTCC
1147491 CA
1 CA
1147493 AGTATCAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.27, C:0.33, G:0.08, T:0.31
Consensus pattern (41 bp):
CATTAACAATCGATACCTCATACAGTTCTATCCCTGACTCC
Found at i:1150438 original size:26 final size:27
Alignment explanation
Indices: 1150394--1150495 Score: 152
Period size: 27 Copynumber: 3.8 Consensus size: 27
1150384 ATAGCTTATT
**
1150394 CGAGCCCAAAACACTGTTTAGCTCTTA
1 CGAGCCCAAAACAGAGTTTAGCTCTTA
1150421 CGAGCCC-AAACAGAGTTTAGCTCTTA
1 CGAGCCCAAAACAGAGTTTAGCTCTTA
*
1150447 CAAGCCCAAAACAGAGTTTAGCTCTTA
1 CGAGCCCAAAACAGAGTTTAGCTCTTA
*
1150474 CGAGCCCAAAATCAAAGTTTAG
1 CGAGCCCAAAA-CAGAGTTTAG
1150496 ACCGATCTAT
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
26 23 0.34
27 36 0.53
28 9 0.13
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (27 bp):
CGAGCCCAAAACAGAGTTTAGCTCTTA
Found at i:1150652 original size:81 final size:80
Alignment explanation
Indices: 1150500--1150656 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 80
1150490 GTTTAGACCG
* * * * *
1150500 ATCTATGATGCTACTCGCACAAGCTGATGAGAATTCGCAACATATGCGAGACCTCAGCCATCGTT
1 ATCTATGATGCTACTCACACAAGCTGATGAGAATCCGCAACATATGCGAAACCTCAACCATCGTA
1150565 ACGGTCCATATCATC
66 ACGGTCCATATCATC
* * * *
1150580 ATCTCATGATGCTACTCACACAAGCTGATGAGAATCCGTAACATATGCGAAATCTTAACCGTCGT
1 ATCT-ATGATGCTACTCACACAAGCTGATGAGAATCCGCAACATATGCGAAACCTCAACCATCGT
*
1150645 AAGGGTCCATAT
65 AACGGTCCATAT
1150657 AATTAGAATC
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
80 4 0.06
81 62 0.94
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.25
Consensus pattern (80 bp):
ATCTATGATGCTACTCACACAAGCTGATGAGAATCCGCAACATATGCGAAACCTCAACCATCGTA
ACGGTCCATATCATC
Found at i:1160249 original size:26 final size:24
Alignment explanation
Indices: 1160207--1160260 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 24
1160197 ATTTTATGGG
*
1160207 TTTTAATTTCTAGGTTAATGGAAGTT
1 TTTTAATTTCTACGTTAAT-GAA-TT
1160233 TTTTAAATTTCT-CGTTAATGAATT
1 TTTT-AATTTCTACGTTAATGAATT
1160257 TTTT
1 TTTT
1160261 GGGTAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 6 0.23
25 3 0.12
26 10 0.38
27 7 0.27
ACGTcount: A:0.26, C:0.06, G:0.13, T:0.56
Consensus pattern (24 bp):
TTTTAATTTCTACGTTAATGAATT
Found at i:1168463 original size:31 final size:30
Alignment explanation
Indices: 1168416--1168483 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
1168406 AAATTTTAAA
* * * *
1168416 TTAATAATAGTAAAATTATATTTTAACTTTT
1 TTAAAAATAATAAAATTATAATTTAA-TCTT
*
1168447 TTAAAAATAATAAAATTTTAATTTAATCTT
1 TTAAAAATAATAAAATTATAATTTAATCTT
1168477 TTAAAAA
1 TTAAAAA
1168484 ATTATAAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 10 0.31
31 22 0.69
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (30 bp):
TTAAAAATAATAAAATTATAATTTAATCTT
Found at i:1168484 original size:31 final size:31
Alignment explanation
Indices: 1168421--1168491 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
1168411 TTAAATTAAT
* * *
1168421 AATAGTAAAATTATATTTTAACTTTTTTAAA
1 AATAATAAAATTATAATTTAACTTTTTAAAA
*
1168452 AATAATAAAATTTTAATTTAA-TCTTTTAAAA
1 AATAATAAAATTATAATTTAACT-TTTTAAAA
*
1168483 AATTATAAA
1 AATAATAAA
1168492 TATATAAACT
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 33 0.97
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (31 bp):
AATAATAAAATTATAATTTAACTTTTTAAAA
Found at i:1174636 original size:98 final size:99
Alignment explanation
Indices: 1174503--1174708 Score: 378
Period size: 98 Copynumber: 2.1 Consensus size: 99
1174493 TAAGAGAATT
1174503 GAAAGTTGATTTTAAGGACCAGATAAAAATACATAGTGGCAGTCAATCCGTTATAAGCATTGCTA
1 GAAA-TTGATTTTAAGGACCAGATAAAAATACATAGTGGCAGTCAATCCGTTATAAGCATTGCTA
*
1174568 AAAATCCAGTACACCTTGACAGGACCAAGCATGTG
65 AAAATCCAGTACACCATGACAGGACCAAGCATGTG
*
1174603 GAAATTGA-TTTAAGGACCAGATAAAAATACATAGTGGCAGTCAATGCGTTATAAGCATTGCTAA
1 GAAATTGATTTTAAGGACCAGATAAAAATACATAGTGGCAGTCAATCCGTTATAAGCATTGCTAA
1174667 AAATCCAGTACACCATGACAGGACCAAGCATGTG
66 AAATCCAGTACACCATGACAGGACCAAGCATGTG
1174701 GAAATTGA
1 GAAATTGA
1174709 CAGACATTTC
Statistics
Matches: 104, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
98 96 0.92
99 4 0.04
100 4 0.04
ACGTcount: A:0.39, C:0.17, G:0.20, T:0.23
Consensus pattern (99 bp):
GAAATTGATTTTAAGGACCAGATAAAAATACATAGTGGCAGTCAATCCGTTATAAGCATTGCTAA
AAATCCAGTACACCATGACAGGACCAAGCATGTG
Found at i:1179227 original size:17 final size:16
Alignment explanation
Indices: 1179205--1179237 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
1179195 AAAAAATCAG
1179205 AAAAAAATGCAAAAGAA
1 AAAAAAATG-AAAAGAA
1179222 AAAAAAATGAAAAGAA
1 AAAAAAATGAAAAGAA
1179238 TGTGTTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.79, C:0.03, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAAAAATGAAAAGAA
Found at i:1181376 original size:25 final size:25
Alignment explanation
Indices: 1181348--1181425 Score: 156
Period size: 25 Copynumber: 3.1 Consensus size: 25
1181338 TTTCTATGAA
1181348 ATTCGTTTTAATACAGGGTTTATTT
1 ATTCGTTTTAATACAGGGTTTATTT
1181373 ATTCGTTTTAATACAGGGTTTATTT
1 ATTCGTTTTAATACAGGGTTTATTT
1181398 ATTCGTTTTAATACAGGGTTTATTT
1 ATTCGTTTTAATACAGGGTTTATTT
1181423 ATT
1 ATT
1181426 TATTTATTTG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 53 1.00
ACGTcount: A:0.24, C:0.08, G:0.15, T:0.53
Consensus pattern (25 bp):
ATTCGTTTTAATACAGGGTTTATTT
Found at i:1186244 original size:3 final size:3
Alignment explanation
Indices: 1186236--1186273 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1186226 TTTAAAGCAA
1186236 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1186274 GATACTTTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1186988 original size:4 final size:4
Alignment explanation
Indices: 1186979--1187006 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1186969 GACATATGTC
1186979 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CTTT
1187007 TTTTTTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (4 bp):
CTTT
Found at i:1187920 original size:263 final size:263
Alignment explanation
Indices: 1187439--1187925 Score: 583
Period size: 263 Copynumber: 1.9 Consensus size: 263
1187429 GCATTTTATC
** * * *
1187439 AAAATGATTAAATTTCAGTTTTGGTCCTCTAATATGTCTAAATTTGATATTTAATCTCTATACTT
1 AAAATGATTAAATTTCAACTTTGGTCCTCTAATATGCCTAAATTTGAGATTTAATCTCTACACTT
* * * *
1187504 TAATTTTTAATATCGATTGGTTCCTATATTTTTATAATATTATTAATTAGTCCAAATAGTTGACT
66 TAATTTCTAATATCAATTGGTTCCTATATTTTTATAATATTATTAATTAATCCAAATAGTTGAAT
** * * * *
1187569 TTGTTAACTTTTCGATTAAAACATTACATGGTTGTATATAAATTGAATACCCTAAGAGTCCTAGA
131 TCATTAACTTTTCAATTAAAACATTACATGATTATATATAAATTGAATACCCTAAGAGACCTAGA
* *
1187634 GACCGACACGTGGTTTCCTATTTCTTTTAGGTTTGCATCGGTCTTACCCTTTTTCTTATAGTTTT
196 GACAGACACGTGCTTTCCTATTTCTTTTAGGTTTGCATCGGTCTTACCCTTTTTCTTATAGTTTT
1187699 AGA
261 AGA
* *
1187702 AAAATGATTATATTTCAACTTTGGTCCCTCTATTATGCCTAAATTTGAGATTTAA-CTACTACAC
1 AAAATGATTAAATTTCAACTTTGGT-CCTCTAATATGCCTAAATTTGAGATTTAATCT-CTACAC
* *
1187766 TTTAATTTCTAATGT-AATTTGG-TCC-ATGTATTTTATAATATTATTAATTAATCCAAATAGTT
64 TTTAATTTCTAATATCAA-TTGGTTCCTATAT-TTTTATAATATTATTAATTAATCCAAATAGTT
* * * * * *
1187828 -AATATCATT-ATTTTATCAATTAAAATATTACGTGATTATATATAATTTGAATGCCCTAAGGGA
127 GAAT-TCATTAACTTT-TCAATTAAAACATTACATGATTATATATAAATTGAATACCCTAAGAGA
* * **
1187891 CTTAGAGACATATGCGTAGCTTT-CTATTTCTTTTA
190 CCTAGAGACAGACACGT-GCTTTCCTATTTCTTTTA
1187926 CAATGAGCAA
Statistics
Matches: 186, Mismatches: 31, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
262 9 0.05
263 125 0.67
264 52 0.28
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (263 bp):
AAAATGATTAAATTTCAACTTTGGTCCTCTAATATGCCTAAATTTGAGATTTAATCTCTACACTT
TAATTTCTAATATCAATTGGTTCCTATATTTTTATAATATTATTAATTAATCCAAATAGTTGAAT
TCATTAACTTTTCAATTAAAACATTACATGATTATATATAAATTGAATACCCTAAGAGACCTAGA
GACAGACACGTGCTTTCCTATTTCTTTTAGGTTTGCATCGGTCTTACCCTTTTTCTTATAGTTTT
AGA
Found at i:1188030 original size:26 final size:26
Alignment explanation
Indices: 1187975--1188030 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
1187965 AACTTGGGAT
* *
1187975 TATTTTAAATATTTAATATCATTAAT
1 TATTCTAAATATTTAATATCATTAAC
**
1188001 TATTCTAAATATTTAATATTGTTAAC
1 TATTCTAAATATTTAATATCATTAAC
1188027 TATT
1 TATT
1188031 TTAATCAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (26 bp):
TATTCTAAATATTTAATATCATTAAC
Found at i:1189192 original size:20 final size:20
Alignment explanation
Indices: 1189153--1189208 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
1189143 GGTGTTTAAT
* *
1189153 TAATTTCTAATAATTATTATA
1 TAATTT-TAATAATTTTTTTA
1189174 -AATTTTAAT-ATTTTTTTA
1 TAATTTTAATAATTTTTTTA
*
1189192 TAATTTTCATAATTTTT
1 TAATTTTAATAATTTTT
1189209 ATGTATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
18 7 0.23
19 12 0.40
20 11 0.37
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.61
Consensus pattern (20 bp):
TAATTTTAATAATTTTTTTA
Found at i:1189196 original size:19 final size:21
Alignment explanation
Indices: 1189169--1189208 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
1189159 CTAATAATTA
1189169 TTATAAATTTTAAT-ATTTTT
1 TTATAAATTTTAATAATTTTT
*
1189189 TTAT-AATTTTCATAATTTTT
1 TTATAAATTTTAATAATTTTT
1189209 ATGTATTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATAAATTTTAATAATTTTT
Found at i:1190490 original size:12 final size:12
Alignment explanation
Indices: 1190473--1190515 Score: 61
Period size: 12 Copynumber: 3.6 Consensus size: 12
1190463 CACGAACTAG
1190473 CTCGTTTATTGA
1 CTCGTTTATTGA
*
1190485 CTCGTTTA-TAA
1 CTCGTTTATTGA
1190496 GCTCGTTTATTGA
1 -CTCGTTTATTGA
1190509 CTCGTTT
1 CTCGTTT
1190516 GTAGCTTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 2 0.07
12 23 0.85
13 2 0.07
ACGTcount: A:0.16, C:0.19, G:0.16, T:0.49
Consensus pattern (12 bp):
CTCGTTTATTGA
Found at i:1190526 original size:23 final size:23
Alignment explanation
Indices: 1190470--1190529 Score: 93
Period size: 24 Copynumber: 2.6 Consensus size: 23
1190460 GTTCACGAAC
1190470 TAGCTCGTTTATTGACTCGTTTA
1 TAGCTCGTTTATTGACTCGTTTA
*
1190493 TAAGCTCGTTTATTGACTCGTTTG
1 T-AGCTCGTTTATTGACTCGTTTA
*
1190517 TAGCTTGTTTATT
1 TAGCTCGTTTATT
1190530 TATTAATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
23 12 0.35
24 22 0.65
ACGTcount: A:0.17, C:0.15, G:0.18, T:0.50
Consensus pattern (23 bp):
TAGCTCGTTTATTGACTCGTTTA
Found at i:1190646 original size:24 final size:23
Alignment explanation
Indices: 1190619--1190678 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 23
1190609 TCATTAACAT
1190619 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTA-A
* **
1190643 TGTTCATGAACATGTTCGTTTAA
1 TGTTCGTGAACATGTTCAATTAA
1190666 TGTTCGTGAACAT
1 TGTTCGTGAACAT
1190679 TAAACAAACG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.27, C:0.13, G:0.18, T:0.42
Consensus pattern (23 bp):
TGTTCGTGAACATGTTCAATTAA
Found at i:1190952 original size:4 final size:5
Alignment explanation
Indices: 1190917--1190957 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
1190907 AATTATCAAA
* *
1190917 AAAAT AAAAT AAAAG AAAAG AAAAG AAAAG -AAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
1190958 CAAAATTTGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
4 4 0.12
5 30 0.88
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (5 bp):
AAAAG
Found at i:1190952 original size:9 final size:9
Alignment explanation
Indices: 1190928--1190957 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
1190918 AAATAAAATA
1190928 AAAGAAAAG
1 AAAGAAAAG
1190937 AAAAGAAAAG
1 -AAAGAAAAG
1190947 AAAGAAAAG
1 AAAGAAAAG
1190956 AA
1 AA
1190958 CAAAATTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:1197046 original size:14 final size:14
Alignment explanation
Indices: 1197027--1197055 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1197017 TCCTCCCTTC
1197027 ATACTTAGTTCCAA
1 ATACTTAGTTCCAA
1197041 ATACTTAGTTCCAA
1 ATACTTAGTTCCAA
1197055 A
1 A
1197056 CAAAAGACTT
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:0.38, C:0.21, G:0.07, T:0.34
Consensus pattern (14 bp):
ATACTTAGTTCCAA
Found at i:1203015 original size:3 final size:3
Alignment explanation
Indices: 1203009--1203036 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1202999 TATTATAGTC
1203009 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1203037 ATGAAGCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1207053 original size:31 final size:30
Alignment explanation
Indices: 1206987--1207053 Score: 71
Period size: 31 Copynumber: 2.2 Consensus size: 30
1206977 ACTTAAATTT
* ** * *
1206987 TTTTATCCTATTTGGTACTTGGACTTTATAT
1 TTTT-TCCTATTTGGTACCTAAACTTGATAC
1207018 TTTTTCCTAATTTGGTACCTAAACTTGATAC
1 TTTTTCCT-ATTTGGTACCTAAACTTGATAC
1207049 TTTTT
1 TTTTT
1207054 TTTATGTTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.54
Consensus pattern (30 bp):
TTTTTCCTATTTGGTACCTAAACTTGATAC
Found at i:1207123 original size:59 final size:59
Alignment explanation
Indices: 1207025--1207136 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
1207015 TATTTTTTCC
* *
1207025 TAATTTGGTACCTAAACTTGATACTTTTTTTTATGTTGATACTTAAGTTTTTTGGGGTT
1 TAATTTGGTACCTAAACTTGATACTTTTTTTAATGTTGATACATAAGTTTTTTGGGGTT
* *
1207084 TAATTTGGTATCTAAACTT-A-ACTCTTTTTCCTAAT-TTGATACATAATTTTTTT
1 TAATTTGGTACCTAAACTTGATACT-TTTTT--TAATGTTGATACATAAGTTTTTT
1207137 TAATATTAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
57 3 0.07
58 6 0.13
59 34 0.74
60 3 0.07
ACGTcount: A:0.25, C:0.11, G:0.12, T:0.53
Consensus pattern (59 bp):
TAATTTGGTACCTAAACTTGATACTTTTTTTAATGTTGATACATAAGTTTTTTGGGGTT
Found at i:1214824 original size:17 final size:17
Alignment explanation
Indices: 1214791--1214851 Score: 79
Period size: 17 Copynumber: 3.5 Consensus size: 17
1214781 CATTAATTTA
*
1214791 CAATGACAAATGGAAATG
1 CAATGAC-AATGTAAATG
1214809 CAATGACAATGTAAATG
1 CAATGACAATGTAAATG
*
1214826 CAGTGACAAT-TAAAATG
1 CAATGACAATGT-AAATG
1214843 CAATGACAA
1 CAATGACAA
1214852 AGGGAATGTG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
16 1 0.03
17 31 0.79
18 7 0.18
ACGTcount: A:0.49, C:0.13, G:0.18, T:0.20
Consensus pattern (17 bp):
CAATGACAATGTAAATG
Found at i:1214859 original size:17 final size:17
Alignment explanation
Indices: 1214791--1214859 Score: 66
Period size: 17 Copynumber: 4.0 Consensus size: 17
1214781 CATTAATTTA
1214791 CAATGACAAATGGAAATG
1 CAATGACAAA-GGAAATG
* *
1214809 CAATGACAATGTAAATG
1 CAATGACAAAGGAAATG
* ***
1214826 CAGTGACAATTAAAATG
1 CAATGACAAAGGAAATG
*
1214843 CAATGACAAAGGGAATG
1 CAATGACAAAGGAAATG
1214860 TGGTGACAAT
Statistics
Matches: 41, Mismatches: 10, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
17 32 0.78
18 9 0.22
ACGTcount: A:0.48, C:0.12, G:0.22, T:0.19
Consensus pattern (17 bp):
CAATGACAAAGGAAATG
Found at i:1214866 original size:34 final size:34
Alignment explanation
Indices: 1214804--1214873 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 34
1214794 TGACAAATGG
* *
1214804 AAATGCAATGACAATGTAAATGCAGTGACAATTA
1 AAATGCAATGACAAAGGAAATGCAGTGACAATTA
* **
1214838 AAATGCAATGACAAAGGGAATGTGGTGACAATTA
1 AAATGCAATGACAAAGGAAATGCAGTGACAATTA
1214872 AA
1 AA
1214874 TTACAGCTAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.47, C:0.10, G:0.21, T:0.21
Consensus pattern (34 bp):
AAATGCAATGACAAAGGAAATGCAGTGACAATTA
Found at i:1215290 original size:18 final size:19
Alignment explanation
Indices: 1215267--1215304 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
1215257 TTGTCTCTAC
1215267 TTCTTTTCCTTCC-CTTCT
1 TTCTTTTCCTTCCACTTCT
*
1215285 TTCTTTTTCTTCCACTTCT
1 TTCTTTTCCTTCCACTTCT
1215304 T
1 T
1215305 CCACTTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (19 bp):
TTCTTTTCCTTCCACTTCT
Found at i:1218326 original size:30 final size:31
Alignment explanation
Indices: 1218274--1218334 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
1218264 TGCGTACTTT
1218274 GAATAAGTATGCCTCATTCTAGTAGTATTTC
1 GAATAAGTATGCCTCATTCTAGTAGTATTTC
*
1218305 GAATAAGTATG-CTCGTTCTAGTAGTATTTC
1 GAATAAGTATGCCTCATTCTAGTAGTATTTC
1218335 TCTATATCGT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 18 0.62
31 11 0.38
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (31 bp):
GAATAAGTATGCCTCATTCTAGTAGTATTTC
Found at i:1235076 original size:17 final size:17
Alignment explanation
Indices: 1235054--1235092 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1235044 AGGTGGAGAA
* * *
1235054 CTTGTTCGTTGAGAGTT
1 CTTGTTCATAGAGAATT
1235071 CTTGTTCATAGAGAATT
1 CTTGTTCATAGAGAATT
1235088 CTTGT
1 CTTGT
1235093 CAAAGTGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.13, G:0.23, T:0.46
Consensus pattern (17 bp):
CTTGTTCATAGAGAATT
Found at i:1235547 original size:16 final size:16
Alignment explanation
Indices: 1235526--1235557 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1235516 ACTCGAACTT
1235526 TGTAATTAATTATTTA
1 TGTAATTAATTATTTA
1235542 TGTAATTAATTATTTA
1 TGTAATTAATTATTTA
1235558 AATTTATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TGTAATTAATTATTTA
Found at i:1238422 original size:21 final size:21
Alignment explanation
Indices: 1238396--1238437 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1238386 TTTTTGGTTA
*
1238396 CGATAGATG-CATGACTTGTAT
1 CGATAGAAGTCAT-ACTTGTAT
1238417 CGATAGAAGTCATACTTGTAT
1 CGATAGAAGTCATACTTGTAT
1238438 TGGTAGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.33
Consensus pattern (21 bp):
CGATAGAAGTCATACTTGTAT
Found at i:1238874 original size:77 final size:76
Alignment explanation
Indices: 1238786--1238954 Score: 212
Period size: 77 Copynumber: 2.2 Consensus size: 76
1238776 TATTCGTCGG
* * *
1238786 TTATCCGACTAGCACTAGGCGCAAAACATTTGTTGGTATATCTAACTAGAGATGGGTTCACTATT
1 TTATCCGACTAGCACTAGGCGCAAAACATTTGTTGGCATATCTAACTAGAGATAGGCTCACTATT
* * *
1238851 TACATTGTTGAT
66 GACATTATCG-T
* * * * * *
1238863 TTATCCGACTAGCATTGGGTGCAAAACATTTTTTGGCATATCTAACTAGAGCTAGGCTCATTATT
1 TTATCCGACTAGCACTAGGCGCAAAACATTTGTTGGCATATCTAACTAGAGATAGGCTCACTATT
*
1238928 GATATTATCGT
66 GACATTATCGT
1238939 TTATCCGACTAGCACT
1 TTATCCGACTAGCACT
1238955 GAGCACAAAC
Statistics
Matches: 78, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
76 16 0.21
77 62 0.79
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (76 bp):
TTATCCGACTAGCACTAGGCGCAAAACATTTGTTGGCATATCTAACTAGAGATAGGCTCACTATT
GACATTATCGT
Found at i:1242882 original size:34 final size:33
Alignment explanation
Indices: 1242836--1242953 Score: 137
Period size: 34 Copynumber: 3.5 Consensus size: 33
1242826 TTACAGTGTT
*
1242836 TTTGTGTGTTGGATGGACTAGCTCTTACGAGCA
1 TTTGTGTGTTGGATGGACTAGCTCTTACAAGCA
*
1242869 TTTAGTGTGTTGGATGGACTAGCTCATACAAGCA
1 TTT-GTGTGTTGGATGGACTAGCTCTTACAAGCA
* * * * *
1242903 TTTGCTGTGTTGGTTGGTCTAACTCTTATATGCA
1 TTTG-TGTGTTGGATGGACTAGCTCTTACAAGCA
*
1242937 TTTGGTGTGTTAGATGG
1 TTT-GTGTGTTGGATGG
1242954 TTCACTGTGT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
33 4 0.06
34 67 0.93
35 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.29, T:0.40
Consensus pattern (33 bp):
TTTGTGTGTTGGATGGACTAGCTCTTACAAGCA
Found at i:1243886 original size:21 final size:21
Alignment explanation
Indices: 1243847--1243888 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1243837 GTGGATTGAC
**
1243847 GGGTAGCCACACGGGCATGTT
1 GGGTAGCCACACGACCATGTT
1243868 GGGTAGCCACACGACCATGTT
1 GGGTAGCCACACGACCATGTT
1243889 TAGAGGCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.33, T:0.19
Consensus pattern (21 bp):
GGGTAGCCACACGACCATGTT
Found at i:1248829 original size:34 final size:33
Alignment explanation
Indices: 1248791--1248943 Score: 207
Period size: 34 Copynumber: 4.5 Consensus size: 33
1248781 GTTATAGTGT
*
1248791 TTTGGTGTGTTGAATGGACTAGCTCTTACTAGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTA-TAGCA
* *
1248825 TTTGGTGTGTCGGATGGACTAGCTCTTACGAGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTA-TAGCA
*
1248859 TTTAGTGTGTTGGATGGACTAGCTCTTATGAGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTAT-AGCA
* * *
1248893 TTTGGTGTGTTGGTTGGACTGGATCTTATATGCA
1 TTTGGTGTGTTGGATGGACTAGCTCTTATA-GCA
1248927 TTTGGTGTGTTGGATGG
1 TTTGGTGTGTTGGATGG
1248944 TTAACTGTGT
Statistics
Matches: 106, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
33 1 0.01
34 105 0.99
ACGTcount: A:0.17, C:0.12, G:0.32, T:0.39
Consensus pattern (33 bp):
TTTGGTGTGTTGGATGGACTAGCTCTTATAGCA
Done.