Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008425.1 Hibiscus syriacus cultivar Beakdansim tig00111208_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2340112
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 12
Found at i:896844 original size:6 final size:6
Alignment explanation
Indices: 896833--896908 Score: 138
Period size: 6 Copynumber: 13.0 Consensus size: 6
896823 GCTCACCCTT
896833 GAAGAG GAAGAG GAAGA- GAAGAG G-AGAG GAAGAG GAAGAG GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
896879 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
1 GAAGAG GAAGAG GAAGAG GAAGAG GAAGAG
896909 AGAAAAGAGA
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
5 10 0.15
6 58 0.85
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:898115 original size:30 final size:31
Alignment explanation
Indices: 898056--898115 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
898046 GATTTAGTTA
* * * *
898056 GTGACCAAATTATAAGATTTTGTAAAGTTTG
1 GTGACCAAAGTATAAAACTTTGAAAAGTTTG
898087 GTGACCAAAGTA-AAAACTTTGAAAAGTTT
1 GTGACCAAAGTATAAAACTTTGAAAAGTTT
898116 AGGGACTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.33
Consensus pattern (31 bp):
GTGACCAAAGTATAAAACTTTGAAAAGTTTG
Found at i:900301 original size:18 final size:18
Alignment explanation
Indices: 900278--900369 Score: 159
Period size: 18 Copynumber: 5.2 Consensus size: 18
900268 AGGTTTCTAT
900278 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
* *
900296 GTGGTCCTTTGGGACAAA
1 GTGGTCCTTCGGGACATA
900314 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
900332 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
900350 GTGGTCCTTCGGGACA-A
1 GTGGTCCTTCGGGACATA
900367 GTG
1 GTG
900370 TTCAATGCCC
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
17 4 0.06
18 66 0.94
ACGTcount: A:0.17, C:0.21, G:0.35, T:0.27
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:904347 original size:20 final size:20
Alignment explanation
Indices: 904302--904351 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
904292 AAATAATTTG
**
904302 ATTTTG-AAAACAAAACTTA
1 ATTTTGAAAAACAAAACAAA
**
904321 ACGTTGAAAAACAAAACAAA
1 ATTTTGAAAAACAAAACAAA
904341 ATTTTGAAAAA
1 ATTTTGAAAAA
904352 TGATTTTAGG
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.58, C:0.10, G:0.08, T:0.24
Consensus pattern (20 bp):
ATTTTGAAAAACAAAACAAA
Found at i:907737 original size:21 final size:21
Alignment explanation
Indices: 907707--907759 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
907697 GTGAGTTTGA
* *
907707 GATCGATCCCTTTACAAAATG
1 GATCGATCCCTTCACAAAAAG
*
907728 GATTGATCCCTTCACAAAAAG
1 GATCGATCCCTTCACAAAAAG
907749 GATCGATCCCT
1 GATCGATCCCT
907760 CGATGAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.26, G:0.15, T:0.26
Consensus pattern (21 bp):
GATCGATCCCTTCACAAAAAG
Found at i:908410 original size:29 final size:29
Alignment explanation
Indices: 908377--908516 Score: 122
Period size: 29 Copynumber: 4.8 Consensus size: 29
908367 TGGAGCTAAC
*
908377 AAAATATATTTTTAAATTAAGATAAGCAT
1 AAAATATATTTTTAAATTAAGATAAGAAT
* * *
908406 AAAATTTATATTTAAAATTAAAATAAGAAT
1 AAAATATAT-TTTTAAATTAAGATAAGAAT
** * * * *
908436 AGTATATATATTTAAATTAACATATGAAC
1 AAAATATATTTTTAAATTAAGATAAGAAT
* *
908465 AAAATATATTTAATAAGTTGAA-ATAA-AAT
1 AAAATATATTT-TTAAATT-AAGATAAGAAT
908494 AAAATATATTTTTAAAGTTAAGA
1 AAAATATATTTTTAAA-TTAAGA
908517 AATATAAAAT
Statistics
Matches: 85, Mismatches: 21, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
28 5 0.06
29 47 0.55
30 31 0.36
31 2 0.02
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.37
Consensus pattern (29 bp):
AAAATATATTTTTAAATTAAGATAAGAAT
Found at i:908450 original size:59 final size:58
Alignment explanation
Indices: 908377--908516 Score: 158
Period size: 59 Copynumber: 2.4 Consensus size: 58
908367 TGGAGCTAAC
* *
908377 AAAATATATTTTTAAATTAAGATAAGCATAAAATTTATATTTAA-AA-TTAAAATAAGAAT
1 AAAATATATTTTTAAATTAAGATAAGAACAAAA--TATATTTAATAAGTTAAAATAA-AAT
** * * * *
908436 AGTATATATATTTAAATTAACATATGAACAAAATATATTTAATAAGTTGAAATAAAAT
1 AAAATATATTTTTAAATTAAGATAAGAACAAAATATATTTAATAAGTTAAAATAAAAT
908494 AAAATATATTTTTAAAGTTAAGA
1 AAAATATATTTTTAAA-TTAAGA
908517 AATATAAAAT
Statistics
Matches: 66, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
57 9 0.14
58 18 0.27
59 39 0.59
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.37
Consensus pattern (58 bp):
AAAATATATTTTTAAATTAAGATAAGAACAAAATATATTTAATAAGTTAAAATAAAAT
Found at i:915197 original size:2 final size:2
Alignment explanation
Indices: 915180--915232 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
915170 TTTACATAGA
* *
915180 AT AT AA AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
915222 AT AT AT AT AT A
1 AT AT AT AT AT A
915233 ATTTAATGAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:915802 original size:19 final size:19
Alignment explanation
Indices: 915762--915803 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
915752 GTTAGAATAT
* *
915762 TTTAAAATTAAAAAATGCA
1 TTTAAAATGAAAAAATGAA
915781 TTTAAAATGAAAAACA-GAA
1 TTTAAAATGAAAAA-ATGAA
915800 TTTA
1 TTTA
915804 TAAACCATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 19 0.95
20 1 0.05
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (19 bp):
TTTAAAATGAAAAAATGAA
Found at i:929704 original size:32 final size:32
Alignment explanation
Indices: 929661--929732 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
929651 AATTTTAGTT
* * *
929661 AATATAAACTCTAATTTATATTTAGT-AGTAAA
1 AATAAAAACTCTAACTTA-ATGTAGTAAGTAAA
*
929693 AATAAAAACTCTAACTTAATGTATTAAGTAAA
1 AATAAAAACTCTAACTTAATGTAGTAAGTAAA
929725 AATAAAAA
1 AATAAAAA
929733 AAAATAAAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 5 0.14
32 30 0.86
ACGTcount: A:0.54, C:0.07, G:0.06, T:0.33
Consensus pattern (32 bp):
AATAAAAACTCTAACTTAATGTAGTAAGTAAA
Found at i:933028 original size:18 final size:19
Alignment explanation
Indices: 933005--933041 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
932995 TCAGTAATCC
933005 TATTCCC-TGGTAATCTTT
1 TATTCCCATGGTAATCTTT
933023 TATTCCCAATGGTAATCTT
1 TATTCCC-ATGGTAATCTT
933042 ACATTCCGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.46
Consensus pattern (19 bp):
TATTCCCATGGTAATCTTT
Found at i:934341 original size:12 final size:12
Alignment explanation
Indices: 934324--934355 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
934314 AACTCTTGCA
934324 GATTGAATAATT
1 GATTGAATAATT
934336 GATTGAATAATT
1 GATTGAATAATT
934348 GATTGAAT
1 GATTGAAT
934356 CCAGTGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (12 bp):
GATTGAATAATT
Found at i:937344 original size:2 final size:2
Alignment explanation
Indices: 937337--937384 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
937327 CTTGCATTTG
937337 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
937379 AT AT AT
1 AT AT AT
937385 TTTTTGAGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:938662 original size:21 final size:24
Alignment explanation
Indices: 938620--938666 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
938610 TCTCGCGCGC
938620 CGCCGCCGCCGTTCGTCTCGTGGT
1 CGCCGCCGCCGTTCGTCTCGTGGT
*
938644 CGCCGTCGCCG-TCG-C-CGTGGT
1 CGCCGCCGCCGTTCGTCTCGTGGT
938665 CG
1 CG
938667 TACTTAGGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 1 0.05
23 3 0.14
24 10 0.45
ACGTcount: A:0.00, C:0.43, G:0.36, T:0.21
Consensus pattern (24 bp):
CGCCGCCGCCGTTCGTCTCGTGGT
Found at i:939507 original size:28 final size:27
Alignment explanation
Indices: 939471--939528 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
939461 AAAGTTATCT
*
939471 TTTTAGTCAAAATAGATACCTAAAGTA
1 TTTTAGTCAAAATAGATACCTAAACTA
*
939498 TTTTATGTCAAAATAGGTACCTAAACTA
1 TTTTA-GTCAAAATAGATACCTAAACTA
939526 TTT
1 TTT
939529 AAGCTTTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 5 0.18
28 23 0.82
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (27 bp):
TTTTAGTCAAAATAGATACCTAAACTA
Found at i:948367 original size:5 final size:5
Alignment explanation
Indices: 948357--948394 Score: 51
Period size: 5 Copynumber: 7.8 Consensus size: 5
948347 TGACCGGTCT
* *
948357 GACCC GACCC GACCC GACCC GA-CT GACCT GACCC GACC
1 GACCC GACCC GACCC GACCC GACCC GACCC GACCC GACC
948395 GTTGACCGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 3 0.10
5 27 0.90
ACGTcount: A:0.21, C:0.53, G:0.21, T:0.05
Consensus pattern (5 bp):
GACCC
Found at i:955461 original size:9 final size:9
Alignment explanation
Indices: 955447--955515 Score: 84
Period size: 9 Copynumber: 7.3 Consensus size: 9
955437 AGGGCTGGAA
955447 ACCGGTTTG
1 ACCGGTTTG
955456 ACCGGTTTCG
1 ACCGGTTT-G
*
955466 ACCGGTTCG
1 ACCGGTTTG
955475 AACCGGTTTG
1 -ACCGGTTTG
*
955485 ACCGGTCTG
1 ACCGGTTTG
955494 AACCGGTTTG
1 -ACCGGTTTG
*
955504 ACCGGTCTG
1 ACCGGTTTG
955513 ACC
1 ACC
955516 CGACCCGACC
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
9 28 0.54
10 24 0.46
ACGTcount: A:0.14, C:0.29, G:0.30, T:0.26
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:955471 original size:19 final size:19
Alignment explanation
Indices: 955447--955513 Score: 93
Period size: 19 Copynumber: 3.5 Consensus size: 19
955437 AGGGCTGGAA
*
955447 ACCGGTTTG-ACCGGTTTCG
1 ACCGGTCTGAACCGGTTT-G
955466 ACCGGT-TCGAACCGGTTTG
1 ACCGGTCT-GAACCGGTTTG
955485 ACCGGTCTGAACCGGTTTG
1 ACCGGTCTGAACCGGTTTG
955504 ACCGGTCTGA
1 ACCGGTCTGA
955514 CCCGACCCGA
Statistics
Matches: 45, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
18 1 0.02
19 35 0.78
20 9 0.20
ACGTcount: A:0.15, C:0.27, G:0.31, T:0.27
Consensus pattern (19 bp):
ACCGGTCTGAACCGGTTTG
Found at i:955488 original size:29 final size:29
Alignment explanation
Indices: 955446--955515 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
955436 GAGGGCTGGA
*
955446 AACCGGTTTGACCGGTTTCG-ACCGGTTCG
1 AACCGGTTTGACCGGTCT-GAACCGGTTCG
*
955475 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 AACCGGTTTGACCGGTCTGAACCGGTTCG
*
955504 -ACCGGTCTGACC
1 AACCGGTTTGACC
955516 CGACCCGACC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 12 0.32
29 25 0.68
ACGTcount: A:0.16, C:0.29, G:0.30, T:0.26
Consensus pattern (29 bp):
AACCGGTTTGACCGGTCTGAACCGGTTCG
Found at i:957069 original size:25 final size:26
Alignment explanation
Indices: 957036--957091 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 26
957026 ACCTATGGTG
*
957036 AAATACTACGAGGCACTATCGAGTGC
1 AAATACTACGAAGCACTATCGAGTGC
* *
957062 AAAT-CTACGAAGCACTTTCGAGTGT
1 AAATACTACGAAGCACTATCGAGTGC
957087 AAATA
1 AAATA
957092 TATCTACGAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 22 0.85
26 4 0.15
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.23
Consensus pattern (26 bp):
AAATACTACGAAGCACTATCGAGTGC
Found at i:957106 original size:29 final size:25
Alignment explanation
Indices: 957036--957108 Score: 74
Period size: 25 Copynumber: 2.7 Consensus size: 25
957026 ACCTATGGTG
* *
957036 AAATACTACGAGGCACTATCGAGTGC
1 AAAT-CTACGAGGCACTTTCGAGTGA
*
957062 AAATCTACGAAGCACTTTCGAGTGTAA
1 AAATCTACGAGGCACTTTCGAGTG--A
957089 ATATATCTACGAGGCACTTT
1 A-A-ATCTACGAGGCACTTT
957109 TAAGTGCATA
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
25 18 0.46
26 4 0.10
27 1 0.03
28 1 0.03
29 15 0.38
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (25 bp):
AAATCTACGAGGCACTTTCGAGTGA
Found at i:959068 original size:31 final size:30
Alignment explanation
Indices: 959020--959092 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
959010 TTGGTGTGCG
* * *
959020 GGTCGGGTTAATTTCGGATCGATTGGTTTT
1 GGTCGGGTCAATATCGGATCGATTGGTTTC
* *
959050 GAGTCGGGTCAATATCGGATTGGTTGGTTTC
1 G-GTCGGGTCAATATCGGATCGATTGGTTTC
959081 GGTTCGGGTCAA
1 GG-TCGGGTCAA
959093 GCTTTAGATT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
30 2 0.06
31 34 0.94
ACGTcount: A:0.15, C:0.12, G:0.36, T:0.37
Consensus pattern (30 bp):
GGTCGGGTCAATATCGGATCGATTGGTTTC
Found at i:959111 original size:51 final size:46
Alignment explanation
Indices: 959071--959197 Score: 175
Period size: 46 Copynumber: 2.8 Consensus size: 46
959061 ATATCGGATT
* *
959071 GGTTGGTTTCGGTTCGGGTCAAGCTTTAGATTTTCAGGTCAATTCA
1 GGTTGGTTTCGGTTCGGATCAACCTTTAGATTTTCAGGTCAATTCA
* *
959117 GGTTGGTTTCGGTTTGGATCAACCTTTAGATTTTCGGGTCAATTC-
1 GGTTGGTTTCGGTTCGGATCAACCTTTAGATTTTCAGGTCAATTCA
* * *
959162 GAGTTGGTTTTGGTTCAGATCAACTTTTAGATTTTC
1 G-GTTGGTTTCGGTTCGGATCAACCTTTAGATTTTC
959198 GAGTTAATTT
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.01
46 71 0.99
ACGTcount: A:0.17, C:0.14, G:0.26, T:0.43
Consensus pattern (46 bp):
GGTTGGTTTCGGTTCGGATCAACCTTTAGATTTTCAGGTCAATTCA
Found at i:959513 original size:3 final size:3
Alignment explanation
Indices: 959502--959555 Score: 67
Period size: 3 Copynumber: 18.3 Consensus size: 3
959492 AAAAATAATA
*
959502 TAT TA- TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT T-T TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
*
959546 TAT AAT TAT T
1 TAT TAT TAT T
959556 TTTGTGGGCC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 37 0.84
4 3 0.07
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:961793 original size:16 final size:16
Alignment explanation
Indices: 961774--961812 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
961764 CGAGTTATTT
*
961774 TCGGTTCGGGTTGCTA
1 TCGGTTCGGGTTCCTA
* *
961790 TCGGGTCGGGTTCCTT
1 TCGGTTCGGGTTCCTA
961806 TCGGTTC
1 TCGGTTC
961813 AGATTGATTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.03, C:0.23, G:0.36, T:0.38
Consensus pattern (16 bp):
TCGGTTCGGGTTCCTA
Found at i:965696 original size:187 final size:185
Alignment explanation
Indices: 965388--965766 Score: 607
Period size: 187 Copynumber: 2.0 Consensus size: 185
965378 TATAAAAATT
*
965388 AAATGTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAACTATAAAATAAAAA
1 AAAT-TTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAACTATAAAATAAAAA
* * *
965453 TTTCAGATAATTTTTTTAATTAATTAATATTGATTTATGTTTAAAAGTTATTGGATCTTAAATTA
65 TTTCAGATAACTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTGGATCTTAAATTA
* * *
965518 TTAATTGATTTTTAAATGGTTTGGGGTGAGCTCATATGTTATATATAATATATTTA
130 TTAATTGAGTTTTAAATGGTTTGGGGTGAGCCCAAATGTTATATATAATATATTTA
* *
965574 ATATTTTTTAATT-AAAAAAATAGTTTACAATTAATTTAAATAATATATAATTATAAAATAAAAA
1 AAATTTTTTAATTCAAAAAAA-AGTTTACAATTAATTTAAATAATATATAACTATAAAAT-AAAA
* *
965638 ATTTTATATAAACTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTGGATCTTAAAT
64 ATTTCAGAT-AACTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTGGATCTTAAAT
*
965703 TATTAATTGAGTTTTAAATGGTTTGGGTTGAGCCCAAATGTTATATATAATATATTTA
128 TATTAATTGAGTTTTAAATGGTTTGGGGTGAGCCCAAATGTTATATATAATATATTTA
965761 AAATTT
1 AAATTT
965767 AAAATTTAAT
Statistics
Matches: 177, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
184 7 0.04
185 45 0.25
186 14 0.08
187 111 0.63
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.46
Consensus pattern (185 bp):
AAATTTTTTAATTCAAAAAAAAGTTTACAATTAATTTAAATAATATATAACTATAAAATAAAAAT
TTCAGATAACTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAATTATTGGATCTTAAATTAT
TAATTGAGTTTTAAATGGTTTGGGGTGAGCCCAAATGTTATATATAATATATTTA
Found at i:968470 original size:30 final size:30
Alignment explanation
Indices: 968434--968514 Score: 87
Period size: 30 Copynumber: 2.7 Consensus size: 30
968424 AAATATATAT
* *
968434 AACTTTTCAAAATTATATTTTTGGTCC-CTA
1 AACTTTTCAAAATTATATTTTT-ATCCACCA
*
968464 AACTTTTACAAATTTATA-TTTTATCCACCA
1 AACTTTT-CAAAATTATATTTTTATCCACCA
968494 AAC-TTTCAAAACTTATATTTT
1 AACTTTTCAAAA-TTATATTTT
968515 AGTCACTAGC
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
28 4 0.09
29 11 0.26
30 19 0.44
31 9 0.21
ACGTcount: A:0.35, C:0.17, G:0.02, T:0.46
Consensus pattern (30 bp):
AACTTTTCAAAATTATATTTTTATCCACCA
Found at i:968514 original size:29 final size:27
Alignment explanation
Indices: 968438--968515 Score: 75
Period size: 29 Copynumber: 2.7 Consensus size: 27
968428 ATATATAACT
* *
968438 TTTCAAAATTATATTTTTGGTCCCTAAAC
1 TTTCAAAATTATA-TTTT-ATCCCCAAAC
*
968467 TTTTACAAATTTATATTTTATCCACCAAAC
1 -TTT-CAAAATTATATTTTATCC-CCAAAC
968497 TTTCAAAACTTATATTTTA
1 TTTCAAAA-TTATATTTTA
968516 GTCACTAGCC
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
28 4 0.10
29 16 0.39
30 12 0.29
31 9 0.22
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.46
Consensus pattern (27 bp):
TTTCAAAATTATATTTTATCCCCAAAC
Found at i:977377 original size:138 final size:136
Alignment explanation
Indices: 977110--977391 Score: 386
Period size: 138 Copynumber: 2.1 Consensus size: 136
977100 GTCATAGGTG
* *
977110 CATTTCGACATAAATTGTATATAAAAGTTATCGATCGATTTTGTGTAATGCATAAGGGTGCATTT
1 CATTTCGACATAAATTATATATAAAAGTTATCGATCAATTTTGTGTAATGCATAAGGGTGCATTT
* * * *
977175 TTATATCAATATTATGTGTACTTTCGGCACTAAATGTGCAATCATGGTATTCATAATGATTTTGT
66 TCATATCAATACTATGTGTACTTTCGGCACTAAATGTGCAATCATGGAATTCATAATGAGTTTGT
977240 GAATTAT
131 GAATT-T
* * * * *
977247 CATTTCGATATACAATTATGTATAAAAGTTATTGATCAATTTTGTGTAATGCATAATGGTGTATT
1 CATTTCGACATA-AATTATATATAAAAGTTATCGATCAATTTTGTGTAATGCATAAGGGTGCATT
* * **
977312 TTCATATCAGTACTATGTGTACTTTCGGCATTATGTGTGC-ATCCATGGAATTCATAATGAGTTT
65 TTCATATCAATACTATGTGTACTTTCGGCACTAAATGTGCAAT-CATGGAATTCATAATGAGTTT
977376 GTGAATTT
129 GTGAATTT
977384 CTATTTCG
1 C-ATTTCG
977392 GCACTTCGGT
Statistics
Matches: 127, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
137 15 0.12
138 112 0.88
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.42
Consensus pattern (136 bp):
CATTTCGACATAAATTATATATAAAAGTTATCGATCAATTTTGTGTAATGCATAAGGGTGCATTT
TCATATCAATACTATGTGTACTTTCGGCACTAAATGTGCAATCATGGAATTCATAATGAGTTTGT
GAATTT
Found at i:977705 original size:21 final size:21
Alignment explanation
Indices: 977679--977719 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
977669 ATTTCTCAGC
977679 CAATCAACAATCTCACATCAA
1 CAATCAACAATCTCACATCAA
*
977700 CAATCAACAATCTCTCATCA
1 CAATCAACAATCTCACATCA
977720 CGTATAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (21 bp):
CAATCAACAATCTCACATCAA
Found at i:977806 original size:21 final size:22
Alignment explanation
Indices: 977776--977821 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
977766 TGTCGATTTC
977776 TCAACCAATCAACAATCTCACA
1 TCAACCAATCAACAATCTCACA
*
977798 TCAA-CAATCAACAATCTCTCA
1 TCAACCAATCAACAATCTCACA
977819 TCA
1 TCA
977822 CGTGTAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.43, C:0.35, G:0.00, T:0.22
Consensus pattern (22 bp):
TCAACCAATCAACAATCTCACA
Found at i:980623 original size:16 final size:18
Alignment explanation
Indices: 980602--980643 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 18
980592 TAAAATATAT
980602 AAAAAAATTA-AT-TTTA
1 AAAAAAATTATATCTTTA
980618 AAAAAAA-TATATCTTTA
1 AAAAAAATTATATCTTTA
980635 ATAAAAAAT
1 A-AAAAAAT
980644 AAATATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 2 0.09
16 9 0.41
17 5 0.23
18 6 0.27
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAAATTATATCTTTA
Found at i:982289 original size:15 final size:16
Alignment explanation
Indices: 982269--982309 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
982259 GTTTACTTCA
*
982269 GAATGATT-AAGCGCT
1 GAATGATTCAAACGCT
*
982284 GAATGATTCAAATGCT
1 GAATGATTCAAACGCT
982300 GAATGATTCA
1 GAATGATTCA
982310 GAGGCTCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.35
16 15 0.65
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (16 bp):
GAATGATTCAAACGCT
Found at i:983591 original size:22 final size:21
Alignment explanation
Indices: 983566--983609 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
983556 GATCAAAAAG
*
983566 GGGAACCGATTCCCCTGCTACA
1 GGGAACCGA-TACCCTGCTACA
*
983588 GGGAATCGATACCCTGCTACA
1 GGGAACCGATACCCTGCTACA
983609 G
1 G
983610 TACTGCTACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.25, C:0.32, G:0.25, T:0.18
Consensus pattern (21 bp):
GGGAACCGATACCCTGCTACA
Found at i:983617 original size:11 final size:11
Alignment explanation
Indices: 983601--983635 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
983591 AATCGATACC
983601 CTGCTACAGTA
1 CTGCTACAGTA
*
983612 CTGCTACAGGA
1 CTGCTACAGTA
*
983623 TTGCTACAGTA
1 CTGCTACAGTA
983634 CT
1 CT
983636 TCCGTAAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.29
Consensus pattern (11 bp):
CTGCTACAGTA
Found at i:984398 original size:21 final size:21
Alignment explanation
Indices: 984372--984449 Score: 129
Period size: 21 Copynumber: 3.7 Consensus size: 21
984362 CATATGAAAT
984372 TTGTCCCGAAGGACCATTGTA
1 TTGTCCCGAAGGACCATTGTA
* * *
984393 TTGTCCCGAAGGATCACTATA
1 TTGTCCCGAAGGACCATTGTA
984414 TTGTCCCGAAGGACCATTGTA
1 TTGTCCCGAAGGACCATTGTA
984435 TTGTCCCGAAGGACC
1 TTGTCCCGAAGGACC
984450 TATGAAACCC
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (21 bp):
TTGTCCCGAAGGACCATTGTA
Found at i:998586 original size:18 final size:18
Alignment explanation
Indices: 998560--998603 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
998550 ATATGATAGT
*
998560 ACTCCTGTAGATACTACA
1 ACTCATGTAGATACTACA
998578 ACTCATGTAGATACTACA
1 ACTCATGTAGATACTACA
998596 ACTCATGT
1 ACTCATGT
998604 GAAGCCAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.34, C:0.25, G:0.11, T:0.30
Consensus pattern (18 bp):
ACTCATGTAGATACTACA
Found at i:1001968 original size:98 final size:98
Alignment explanation
Indices: 1001742--1001968 Score: 276
Period size: 98 Copynumber: 2.3 Consensus size: 98
1001732 AAAGGGACAT
* * * ** *
1001742 AACCGAAAATATGAT-AAAAATATAATATTTTAGGTCGGACGTAATCACGTAACTTAAAGTGTTA
1 AACCGAAAATATTATGAAAAATATAATATTTTAAGTCGGACATAATCACACAACTTAAAATGTTA
*
1001806 AATGTTACGAAGAATGCAACATTTTATGTTGCA
66 AATGTTACAAAGAATGCAACATTTTATGTTGCA
* * * * **
1001839 AACCAAAAATGTTATGAAAAATAGAATATTTTAAGTTGGACATAATCACACAGTTTAAAATGTTA
1 AACCGAAAATATTATGAAAAATATAATATTTTAAGTCGGACATAATCACACAACTTAAAATGTTA
* * *
1001904 AATGTTATAAAGAATGTAACATTTTTTGTTGCA
66 AATGTTACAAAGAATGCAACATTTTATGTTGCA
* * *
1001937 AACCGAAAATATTATGAAGATTATAACATTTT
1 AACCGAAAATATTATGAAAAATATAATATTTT
1001969 CGGTTTCACC
Statistics
Matches: 107, Mismatches: 22, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
97 12 0.11
98 95 0.89
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (98 bp):
AACCGAAAATATTATGAAAAATATAATATTTTAAGTCGGACATAATCACACAACTTAAAATGTTA
AATGTTACAAAGAATGCAACATTTTATGTTGCA
Found at i:1002978 original size:101 final size:100
Alignment explanation
Indices: 1002869--1003066 Score: 351
Period size: 101 Copynumber: 2.0 Consensus size: 100
1002859 CTCCTTTTAT
*
1002869 TTTTTTATAGTTTAAATATTGGTGAAAATATGGATTAATTTAAGTATAAGGTGAACTTTGAAGTT
1 TTTTTTATAGTTTAAATATTAGTGAAAATATGGATTAATTTAAGTATAAGGTGAACTTTGAAGTT
**
1002934 CAGGGTGTAAAGGTTAAGGAAATTAAGGACTAGTTA
66 CAGACTGTAAAGGTTAA-GAAATTAAGGACTAGTTA
1002970 TTTTTTATAGTTTAAATATTAGTGAAAATATGGATTAATTTAAGTATAAGGTGAACTTTGAAGTT
1 TTTTTTATAGTTTAAATATTAGTGAAAATATGGATTAATTTAAGTATAAGGTGAACTTTGAAGTT
*
1003035 CAGACTGTAAAGGTTAAGAACTTAAGGACTAG
66 CAGACTGTAAAGGTTAAGAAATTAAGGACTAG
1003067 CGATGTAATT
Statistics
Matches: 93, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
100 14 0.15
101 79 0.85
ACGTcount: A:0.37, C:0.04, G:0.21, T:0.37
Consensus pattern (100 bp):
TTTTTTATAGTTTAAATATTAGTGAAAATATGGATTAATTTAAGTATAAGGTGAACTTTGAAGTT
CAGACTGTAAAGGTTAAGAAATTAAGGACTAGTTA
Found at i:1003162 original size:23 final size:23
Alignment explanation
Indices: 1003131--1003209 Score: 95
Period size: 23 Copynumber: 3.4 Consensus size: 23
1003121 CCGTCAAACA
* *
1003131 TTAATCGAATATGTTCACGAACG
1 TTAAACGAATATGTTCGCGAACG
*
1003154 TTAAACGAATATGTTCGGGAACG
1 TTAAACGAATATGTTCGCGAACG
* * * *
1003177 TTAAACGAACATATTCGTGAACA
1 TTAAACGAATATGTTCGCGAACG
1003200 TTAAACGAAT
1 TTAAACGAAT
1003210 GAACCCAAAA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 48 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (23 bp):
TTAAACGAATATGTTCGCGAACG
Found at i:1015810 original size:92 final size:93
Alignment explanation
Indices: 1015648--1015837 Score: 355
Period size: 92 Copynumber: 2.1 Consensus size: 93
1015638 CCAAACCACA
*
1015648 GAAAACATCCGAGTTGGATGTGAACAAGGAAGTCGATTCAATCAACCTCAAGTTCGTGGAGGCAA
1 GAAAGCATCCGAGTTGGATGTGAACAAGGAAGTCGATTCAATCAACCTCAAGTTCGTGGAGGCAA
1015713 GAGAGGAGATAGAGATGGCACT-GAGTC
66 GAGAGGAGATAGAGATGGCACTGGAGTC
1015740 GAAAGCATCCGAGTTGGATGTGAACAAGGAAGTCGATTCAATCAACCTCAAGTTCGTGGAGGCAA
1 GAAAGCATCCGAGTTGGATGTGAACAAGGAAGTCGATTCAATCAACCTCAAGTTCGTGGAGGCAA
1015805 GAGAGGAGATAGAGATGGCACTGGAGTC
66 GAGAGGAGATAGAGATGGCACTGGAGTC
*
1015833 TAAAG
1 GAAAG
1015838 AGACTGTTTA
Statistics
Matches: 95, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
92 86 0.91
93 9 0.09
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (93 bp):
GAAAGCATCCGAGTTGGATGTGAACAAGGAAGTCGATTCAATCAACCTCAAGTTCGTGGAGGCAA
GAGAGGAGATAGAGATGGCACTGGAGTC
Found at i:1022757 original size:24 final size:24
Alignment explanation
Indices: 1022711--1022758 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
1022701 AAAGAGCGAG
* *
1022711 TTTTAAATTATTTTGAAATTTATT
1 TTTTAAAATATTTTAAAATTTATT
1022735 TTTTAAAATA-TTTAAAATATTATT
1 TTTTAAAATATTTTAAAAT-TTATT
1022759 ATATTTATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (24 bp):
TTTTAAAATATTTTAAAATTTATT
Found at i:1023270 original size:2 final size:2
Alignment explanation
Indices: 1023263--1023290 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1023253 CACAATAATT
1023263 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1023291 AAGCTCATAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1023479 original size:22 final size:22
Alignment explanation
Indices: 1023445--1023486 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1023435 CCTAAGTATT
1023445 TAGGATTTATGGTTTAGAGGTAA
1 TAGGATTTATGGTTTA-AGGTAA
1023468 TAGGA-TTATGGTTTAAGGT
1 TAGGATTTATGGTTTAAGGT
1023487 TTATAAGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 10 0.53
23 5 0.26
ACGTcount: A:0.29, C:0.00, G:0.31, T:0.40
Consensus pattern (22 bp):
TAGGATTTATGGTTTAAGGTAA
Found at i:1025978 original size:12 final size:14
Alignment explanation
Indices: 1025959--1025995 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
1025949 ATATGAAATT
1025959 ATTTTAATTATAT-
1 ATTTTAATTATATG
1025972 A-TTTAATT-TATG
1 ATTTTAATTATATG
1025984 ATTTTAATTATA
1 ATTTTAATTATA
1025996 AATGTTAACT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 3 0.14
12 8 0.38
13 8 0.38
14 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (14 bp):
ATTTTAATTATATG
Found at i:1026215 original size:21 final size:21
Alignment explanation
Indices: 1026190--1026234 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1026180 GTAAAAAAAA
*
1026190 TTACCTAAAACATTATTATTT
1 TTACCTAAAACATTAATATTT
* *
1026211 TTACCTAAAATATTAATGTTT
1 TTACCTAAAACATTAATATTT
1026232 TTA
1 TTA
1026235 ACATTTTTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (21 bp):
TTACCTAAAACATTAATATTT
Found at i:1028500 original size:21 final size:20
Alignment explanation
Indices: 1028476--1028522 Score: 51
Period size: 20 Copynumber: 2.3 Consensus size: 20
1028466 TATTATAAAT
*
1028476 ATTTTGTAGAGTAAACTATGC-
1 ATTTTGTACA-TAAACTAT-CA
*
1028497 ATTTAGTACATAAACTATCA
1 ATTTTGTACATAAACTATCA
1028517 ATTTTG
1 ATTTTG
1028523 ATCCGTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 13 0.59
21 8 0.36
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (20 bp):
ATTTTGTACATAAACTATCA
Found at i:1031467 original size:44 final size:44
Alignment explanation
Indices: 1031385--1031470 Score: 120
Period size: 44 Copynumber: 1.9 Consensus size: 44
1031375 AAATATTTCT
1031385 GATATTAATATTTCCGTAGAAAAAACAACATATTAGGTATCATCC
1 GATATTAATATTTCCGTA-AAAAAACAACATATTAGGTATCATCC
* * *
1031430 GATATTAATATTTCCTGT-AAAAAATAATATTTTAGGTATCA
1 GATATTAATATTTCC-GTAAAAAAACAACATATTAGGTATCA
1031471 CCCTACTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
44 20 0.54
45 15 0.41
46 2 0.05
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.36
Consensus pattern (44 bp):
GATATTAATATTTCCGTAAAAAAACAACATATTAGGTATCATCC
Found at i:1032393 original size:11 final size:12
Alignment explanation
Indices: 1032351--1032395 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1032341 TTGTAGTTTT
1032351 TATTTAAAAATA
1 TATTTAAAAATA
* *
1032363 TATTCAAAAATG
1 TATTTAAAAATA
1032375 TATTTAAAAAT-
1 TATTTAAAAATA
*
1032386 TATGTAAAAA
1 TATTTAAAAA
1032396 GATAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
11 9 0.31
12 20 0.69
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (12 bp):
TATTTAAAAATA
Found at i:1035484 original size:21 final size:21
Alignment explanation
Indices: 1035458--1035509 Score: 104
Period size: 21 Copynumber: 2.5 Consensus size: 21
1035448 GTCCTTCGGG
1035458 ACATATATGTAATTATATGGA
1 ACATATATGTAATTATATGGA
1035479 ACATATATGTAATTATATGGA
1 ACATATATGTAATTATATGGA
1035500 ACATATATGT
1 ACATATATGT
1035510 GGTACTTCGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.38
Consensus pattern (21 bp):
ACATATATGTAATTATATGGA
Found at i:1035639 original size:42 final size:41
Alignment explanation
Indices: 1035563--1035699 Score: 168
Period size: 42 Copynumber: 3.5 Consensus size: 41
1035553 GTTGTTAAGG
*
1035563 AGTGGTCCTTCGGG---TATAGTGGTCCTTCCA-GACAAATC
1 AGTGGTCCTTCGGGACAAATAGTGGTCCTT-CAGGACAAATC
1035601 AGTGGTCCTTCGGGACAAATCAGTGGTCCTTCAGGACAAATC
1 AGTGGTCCTTCGGGACAAAT-AGTGGTCCTTCAGGACAAATC
1035643 AGTGGTCCTTCGGGAC--ATAGTGGTCCTTC-GTGAC--AT-
1 AGTGGTCCTTCGGGACAAATAGTGGTCCTTCAG-GACAAATC
1035679 AGTGGTCCTTCGGGACAAATA
1 AGTGGTCCTTCGGGACAAATA
1035700 TACAGTGCCC
Statistics
Matches: 90, Mismatches: 1, Indels: 16
0.84 0.01 0.15
Matches are distributed among these distances:
36 16 0.18
37 2 0.02
38 18 0.20
39 14 0.16
40 2 0.02
41 4 0.04
42 34 0.38
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (41 bp):
AGTGGTCCTTCGGGACAAATAGTGGTCCTTCAGGACAAATC
Found at i:1035658 original size:21 final size:21
Alignment explanation
Indices: 1035580--1035698 Score: 160
Period size: 21 Copynumber: 6.0 Consensus size: 21
1035570 CTTCGGGTAT
**
1035580 AGTGGTCCTTCCAGACAAATC
1 AGTGGTCCTTCGGGACAAATC
1035601 AGTGGTCCTTCGGGACAAATC
1 AGTGGTCCTTCGGGACAAATC
*
1035622 AGTGGTCCTTCAGGACAAATC
1 AGTGGTCCTTCGGGACAAATC
1035643 AGTGGTCCTTCGGGAC--AT-
1 AGTGGTCCTTCGGGACAAATC
*
1035661 AGTGGTCCTTCGTGAC--AT-
1 AGTGGTCCTTCGGGACAAATC
1035679 AGTGGTCCTTCGGGACAAAT
1 AGTGGTCCTTCGGGACAAAT
1035699 ATACAGTGCC
Statistics
Matches: 90, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
18 32 0.36
19 2 0.02
20 2 0.02
21 54 0.60
ACGTcount: A:0.24, C:0.24, G:0.27, T:0.26
Consensus pattern (21 bp):
AGTGGTCCTTCGGGACAAATC
Found at i:1035666 original size:18 final size:19
Alignment explanation
Indices: 1035563--1035695 Score: 139
Period size: 21 Copynumber: 6.9 Consensus size: 19
1035553 GTTGTTAAGG
*
1035563 AGTGGTCCTTCGGG-TAT-
1 AGTGGTCCTTCGGGACATC
**
1035580 AGTGGTCCTTCCAGACAAATC
1 AGTGGTCCTTCGGGAC--ATC
1035601 AGTGGTCCTTCGGGACAAATC
1 AGTGGTCCTTCGGGAC--ATC
*
1035622 AGTGGTCCTTCAGGACAAATC
1 AGTGGTCCTTCGGGAC--ATC
1035643 AGTGGTCCTTCGGGACAT-
1 AGTGGTCCTTCGGGACATC
*
1035661 AGTGGTCCTTCGTGACAT-
1 AGTGGTCCTTCGGGACATC
1035679 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
1035696 AATATACAGT
Statistics
Matches: 103, Mismatches: 9, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
17 12 0.12
18 33 0.32
19 2 0.02
20 2 0.02
21 54 0.52
ACGTcount: A:0.21, C:0.23, G:0.29, T:0.27
Consensus pattern (19 bp):
AGTGGTCCTTCGGGACATC
Found at i:1036128 original size:21 final size:22
Alignment explanation
Indices: 1036088--1036128 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1036078 TTAATTGAGA
*
1036088 AAAAGGGTATATAAATAAGTAT
1 AAAAGGATATATAAATAAGTAT
*
1036110 AAAAGGATAT-TAGATAAGT
1 AAAAGGATATATAAATAAGT
1036129 TGTGTAGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.27
Consensus pattern (22 bp):
AAAAGGATATATAAATAAGTAT
Found at i:1040223 original size:20 final size:20
Alignment explanation
Indices: 1040174--1040226 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
1040164 CGTCAAGGGA
*
1040174 TGCATCGATACATGGTGTAG
1 TGCATCGATGCATGGTGTAG
1040194 TGCATCGATGCATGGTGTAG
1 TGCATCGATGCATGGTGTAG
1040214 TGCATCGATGCAT
1 TGCATCGATGCAT
1040227 ACCTTCATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (20 bp):
TGCATCGATGCATGGTGTAG
Found at i:1040963 original size:18 final size:18
Alignment explanation
Indices: 1040940--1041013 Score: 78
Period size: 18 Copynumber: 3.9 Consensus size: 18
1040930 ATTCTTAAGG
1040940 AGTGGTCTTTCGGGACAT
1 AGTGGTCTTTCGGGACAT
*
1040958 AGTGGTCATTCGGGACAAAT
1 AGTGGTCTTTCGGGAC--AT
1040978 CAGTGGT-TCTTCGGGACAT
1 -AGTGGTCT-TTCGGGACAT
* *
1040997 AATGGTCCTTCGGGACA
1 AGTGGTCTTTCGGGACA
1041014 AATATACAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
18 29 0.62
19 2 0.04
20 2 0.04
21 14 0.30
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (18 bp):
AGTGGTCTTTCGGGACAT
Found at i:1040994 original size:39 final size:39
Alignment explanation
Indices: 1040940--1041016 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
1040930 ATTCTTAAGG
*
1040940 AGTGGTCTTTCGGGACATAGTGGTCATTCGGGACAAATC
1 AGTGGTCTTTCGGGACATAATGGTCATTCGGGACAAATC
*
1040979 AGTGGT-TCTTCGGGACATAATGGTCCTTCGGGACAAAT
1 AGTGGTCT-TTCGGGACATAATGGTCATTCGGGACAAAT
1041017 ATACAGTGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (39 bp):
AGTGGTCTTTCGGGACATAATGGTCATTCGGGACAAATC
Found at i:1045794 original size:13 final size:13
Alignment explanation
Indices: 1045755--1045883 Score: 56
Period size: 13 Copynumber: 9.8 Consensus size: 13
1045745 TTCAAATTGA
*
1045755 AATTAATAAAAAAT
1 AATTAAT-AATAAT
*
1045769 AAATATAACAATAAT
1 -AAT-TAATAATAAT
*
1045784 AATTAATAATATT
1 AATTAATAATAAT
*
1045797 AATTATTAA-AGAT
1 AATTAATAATA-AT
*
1045810 AATAAATAATTAA-
1 AATTAATAA-TAAT
1045823 AA-T-ATAATAAT
1 AATTAATAATAAT
* *
1045834 AAATAGAT-ATAGT
1 AATTA-ATAATAAT
1045847 AATTAA-AATAGAT
1 AATTAATAATA-AT
* *
1045860 ATTTTATAAATAAT
1 AATTAAT-AATAAT
1045874 AATT-ATAATA
1 AATTAATAATA
1045884 TATTTTGTAA
Statistics
Matches: 87, Mismatches: 15, Indels: 27
0.67 0.12 0.21
Matches are distributed among these distances:
10 3 0.03
11 6 0.07
12 10 0.11
13 41 0.47
14 11 0.13
15 13 0.15
16 3 0.03
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (13 bp):
AATTAATAATAAT
Found at i:1045799 original size:16 final size:14
Alignment explanation
Indices: 1045779--1045856 Score: 66
Period size: 16 Copynumber: 5.1 Consensus size: 14
1045769 AAATATAACA
1045779 ATAATAATTAATAAT
1 ATAATAATTAA-AAT
*
1045794 ATTAATTATTAAAGAT
1 A-TAATAATTAAA-AT
1045810 AATAAATAATTAAAAT
1 -AT-AATAATTAAAAT
*
1045826 ATAATAATAAATAGAT
1 ATAATAATTAA-A-AT
*
1045842 ATAGTAATTAAAAT
1 ATAATAATTAAAAT
1045856 A
1 A
1045857 GATATTTTAT
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
14 11 0.21
15 6 0.12
16 25 0.48
17 10 0.19
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
ATAATAATTAAAAT
Found at i:1048229 original size:3 final size:3
Alignment explanation
Indices: 1048221--1048249 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1048211 TTTGGGTTTG
1048221 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1048250 TAACACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1049047 original size:14 final size:12
Alignment explanation
Indices: 1049015--1049039 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1049005 ATAGTTTATG
1049015 ACAATATGTCAT
1 ACAATATGTCAT
1049027 ACAATATGTCAT
1 ACAATATGTCAT
1049039 A
1 A
1049040 AACAATATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (12 bp):
ACAATATGTCAT
Found at i:1051873 original size:14 final size:14
Alignment explanation
Indices: 1051854--1051882 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1051844 ATGAGGAGGA
1051854 TGCCTCCCCCATAT
1 TGCCTCCCCCATAT
1051868 TGCCTCCCCCATAT
1 TGCCTCCCCCATAT
1051882 T
1 T
1051883 ACATCCCCAT
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:0.14, C:0.48, G:0.07, T:0.31
Consensus pattern (14 bp):
TGCCTCCCCCATAT
Found at i:1053872 original size:4 final size:4
Alignment explanation
Indices: 1053863--1053953 Score: 53
Period size: 4 Copynumber: 22.0 Consensus size: 4
1053853 TTAATTACTA
* * * * *
1053863 TATT TATT TA-T TATT ATATTT TAAT TATT TATT ATATC TAAT AATT AATAT
1 TATT TATT TATT TATT -TA-TT TATT TATT TATT -TATT TATT TATT TAT-T
*
1053914 TA-T TAAT TA-T TATTT TATT TATT TATT ATATT TATT TATT
1 TATT TATT TATT TA-TT TATT TATT TATT -TATT TATT TATT
1053954 ATTAATTTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
3 9 0.13
4 43 0.61
5 16 0.23
6 2 0.03
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (4 bp):
TATT
Found at i:1053880 original size:16 final size:16
Alignment explanation
Indices: 1053856--1053961 Score: 96
Period size: 16 Copynumber: 6.8 Consensus size: 16
1053846 ATCTAGTTTA
*
1053856 ATTACTATATTTATTT
1 ATTATTATATTTATTT
*
1053872 ATTATTATATTTTAATT
1 ATTATTATA-TTTATTT
* * *
1053889 ATTTATTATATCTAATA
1 A-TTATTATATTTATTT
*
1053906 ATTA--ATA-TTATTA
1 ATTATTATATTTATTT
1053919 ATTATTAT-TTTATTT
1 ATTATTATATTTATTT
1053934 ATTTATTATATTTATTT
1 A-TTATTATATTTATTT
1053951 ATTATTA-ATTT
1 ATTATTATATTT
1053962 TAATTTAAAA
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
13 8 0.11
14 3 0.04
15 12 0.16
16 24 0.32
17 21 0.28
18 8 0.11
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTATTATATTTATTT
Found at i:1053950 original size:13 final size:13
Alignment explanation
Indices: 1053861--1053955 Score: 65
Period size: 13 Copynumber: 7.2 Consensus size: 13
1053851 GTTTAATTAC
1053861 TATATTTATTTAT
1 TATATTTATTTAT
*
1053874 TAT-TATATTT-T
1 TATATTTATTTAT
*
1053885 AATTATTTATTATAT
1 TA-TATTTATT-TAT
*
1053900 CTAATAATTAATATTAT
1 -T-AT-ATTTAT-TTAT
1053917 TA-A-TTA-TTAT
1 TATATTTATTTAT
*
1053927 TTTATTTATTTAT
1 TATATTTATTTAT
1053940 TATATTTATTTAT
1 TATATTTATTTAT
1053953 TAT
1 TAT
1053956 TAATTTTAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 22
0.68 0.09 0.24
Matches are distributed among these distances:
10 5 0.08
11 3 0.05
12 12 0.19
13 28 0.44
14 1 0.02
15 2 0.03
16 2 0.03
17 9 0.14
18 1 0.02
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATTTATTTAT
Found at i:1064069 original size:21 final size:21
Alignment explanation
Indices: 1064040--1064145 Score: 169
Period size: 21 Copynumber: 5.0 Consensus size: 21
1064030 CCCTACCAAG
1064040 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
*
1064061 GATGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
1064082 GACGAGAAGACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
*
1064103 GACGAGAAAACCATTCATAAA
1 GACGAGAAGACCATTCATAAA
*
1064124 GAC-ATGAAGACCCTTCATAAA
1 GACGA-GAAGACCATTCATAAA
1064145 G
1 G
1064146 GCATGAAGAC
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
20 1 0.01
21 78 0.99
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.16
Consensus pattern (21 bp):
GACGAGAAGACCATTCATAAA
Found at i:1064150 original size:21 final size:21
Alignment explanation
Indices: 1064045--1064157 Score: 142
Period size: 21 Copynumber: 5.4 Consensus size: 21
1064035 CCAAGGACGA
*
1064045 GAAGACCATTCATAAAGATGA-
1 GAAGACCATTCATAAAGA-CAT
1064066 GAAGACCATTCATAAAGACGA-
1 GAAGACCATTCATAAAGAC-AT
1064087 GAAGACCATTCATAAAGACGA-
1 GAAGACCATTCATAAAGAC-AT
*
1064108 GAAAACCATTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
* *
1064129 GAAGACCCTTCATAAAGGCAT
1 GAAGACCATTCATAAAGACAT
1064150 GAAGACCA
1 GAAGACCA
1064158 CTTCGCATTG
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
20 1 0.01
21 83 0.99
ACGTcount: A:0.47, C:0.19, G:0.18, T:0.16
Consensus pattern (21 bp):
GAAGACCATTCATAAAGACAT
Found at i:1064415 original size:6 final size:6
Alignment explanation
Indices: 1064404--1064445 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
1064394 TAACACCTCG
* * *
1064404 TGCATT TGCATT TGCATT TACATT TTCTTT TGCATT TGCATT
1 TGCATT TGCATT TGCATT TGCATT TGCATT TGCATT TGCATT
1064446 ATTATTTTTG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.12, T:0.55
Consensus pattern (6 bp):
TGCATT
Found at i:1064435 original size:18 final size:20
Alignment explanation
Indices: 1064414--1064459 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
1064404 TGCATTTGCA
1064414 TTTGCATTTACATT-TT-CT
1 TTTGCATTTACATTATTACT
* *
1064432 TTTGCATTTGCATTATTATT
1 TTTGCATTTACATTATTACT
1064452 TTTGCATT
1 TTTGCATT
1064460 AGCTTATTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 13 0.54
19 2 0.08
20 9 0.38
ACGTcount: A:0.17, C:0.13, G:0.09, T:0.61
Consensus pattern (20 bp):
TTTGCATTTACATTATTACT
Found at i:1064472 original size:20 final size:20
Alignment explanation
Indices: 1064431--1064468 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1064421 TTACATTTTC
*
1064431 TTTTGCATTTGCATTATTAT
1 TTTTGCATTAGCATTATTAT
1064451 TTTTGCATTAGC-TTATTA
1 TTTTGCATTAGCATTATTA
1064469 ATTTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.58
Consensus pattern (20 bp):
TTTTGCATTAGCATTATTAT
Found at i:1070387 original size:35 final size:37
Alignment explanation
Indices: 1070318--1070402 Score: 122
Period size: 36 Copynumber: 2.3 Consensus size: 37
1070308 GGGCAAGTCA
*
1070318 ATCTTAAGCCTTCACCGAAGAGTAGTGAAGCAAAC-C
1 ATCTTAAGCCTTCACCGAAGAGTAGTGAAACAAACTC
1070354 ATCTTAAGCCTTCACC--AGAGGTAGTGAAACAAACTC
1 ATCTTAAGCCTTCACCGAAGA-GTAGTGAAACAAACTC
1070390 ATCTGTAAGCCTT
1 ATCT-TAAGCCTT
1070403 TAGGGCAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
34 3 0.07
35 13 0.29
36 21 0.47
37 8 0.18
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (37 bp):
ATCTTAAGCCTTCACCGAAGAGTAGTGAAACAAACTC
Found at i:1071062 original size:42 final size:41
Alignment explanation
Indices: 1070990--1071076 Score: 95
Period size: 42 Copynumber: 2.1 Consensus size: 41
1070980 CAGGCTATTA
* * * * * *
1070990 GTAAGTCTTTCGAGCATGATGCTTAATTCTTTCGGGTCATCT
1 GTAAGCCTTTAGAGCAAGATGCATAATTC-TTCGGGCCATCC
1071032 GTAAGCCTTTAGAGCAAGATG-ATAAGTTCTTCGGGCCATCC
1 GTAAGCCTTTAGAGCAAGATGCATAA-TTCTTCGGGCCATCC
1071073 GTAA
1 GTAA
1071077 AACCTTCTGG
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
41 17 0.45
42 21 0.55
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (41 bp):
GTAAGCCTTTAGAGCAAGATGCATAATTCTTCGGGCCATCC
Found at i:1071258 original size:214 final size:214
Alignment explanation
Indices: 1070388--1071738 Score: 2124
Period size: 214 Copynumber: 6.3 Consensus size: 214
1070378 TGAAACAAAC
* *
1070388 TCATCTGTAAGCCTTTAGGGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
* **
1070453 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAAATAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
1070518 GAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
131 GAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* *
1070583 GATGCTTAATTCCTTCGAG
196 GATGCTTAAATCCTTCGGG
* * * *
1070602 TCATCTGTAAGCCTTTATAGCAAGATGATAAGTCCTTCGGGCCATCCGTAAAACATTCAGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
*
1070667 ATATTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGA---AATTTTTGAAAACGAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
*
1070729 GAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGTGCAT
131 GAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* *
1070794 GATGTTTAATTCCTTCGGG
196 GATGCTTAAATCCTTCGGG
* * *
1070813 TCATCTATAAGCCTTTAGAGAAAGATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
1070878 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGG-ATTTTTGAAAACGAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
* * *
1070942 GAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCAGGCTATTAGTAAGTCTTTCGAGCAT
131 GAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* *
1071007 GATGCTTAATTCTTTCGGG
196 GATGCTTAAATCCTTCGGG
* * *
1071026 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTTCTTCGGGCCATCCGTAAAACCTTCTGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
*
1071091 ATGTTTTCACATGAATTTGAAAATGAAAATTGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
* * *
1071156 AAATGCAATTTTCAAAATTTCATAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
131 GAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
1071221 GATGCTTAAATCCTTCGGG
196 GATGCTTAAATCCTTCGGG
* *
1071240 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAAACCTTCAGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
*
1071305 ATATTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
66 ATGTTTTCACATGAATTTGAAAATG-AAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
* * *
1071370 AGAATGTGATTTCCAAAA--TCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCA
130 AGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
1071433 TGATGCTTAAATCCTTCGGG
195 TGATGCTTAAATCCTTCGGG
* * *
1071453 TCATCTGTAAGCCTTTTGAGCAAGATGACAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
* * *
1071518 ATGTTTTCACATGAATTTGAAAATAAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAACTAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
* *
1071583 GAATGCGATTTTCAAAATTTCATAATTTATAAGTCCTTCGAGCCATCAGTAAGTCTTTCGAGCAT
131 GAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
*
1071648 GATGCTTAAATCCTTCGGA
196 GATGCTTAAATCCTTCGGG
* ** * * * * * * *
1071667 TCATTTGCGAGTCTCTCGAGCAAGA-GAATAAATCATTCGGGTCATCCATAAGAA-CTTCGGGCA
1 TCATCTGTAAGCCTTTAGAGCAAGATG-ATAAGTCCTTCGGGCCATCCATAA-AACCTTCGGGTA
1071730 GGATGTTTT
64 GGATGTTTT
1071739 TCACCAAGAT
Statistics
Matches: 1052, Mismatches: 76, Indels: 18
0.92 0.07 0.02
Matches are distributed among these distances:
211 200 0.19
212 53 0.05
213 349 0.33
214 397 0.38
215 53 0.05
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (214 bp):
TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
GAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
GATGCTTAAATCCTTCGGG
Found at i:1071394 original size:427 final size:426
Alignment explanation
Indices: 1070388--1071738 Score: 2138
Period size: 427 Copynumber: 3.2 Consensus size: 426
1070378 TGAAACAAAC
* *
1070388 TCATCTGTAAGCCTTTAGGGCAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
* **
1070453 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGAAATTTTTGAAAAATAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
1070518 GAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
131 GAATGCGATTTTCAAAA-TTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* *
1070583 GATGCTTAATTCCTTCGAGTCATCTGTAAGCCTTTATAGCAAGATGATAAGTCCTTCGGGCCATC
195 GATGCTTAATTCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATC
* *
1070648 CGTAAAACATTCAGGTAGGATATTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGA
260 CGTAAAACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGA
*
1070713 --AATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATC
325 TGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCATAATTTATAAGTCCTTCGGGCCATC
* * *
1070776 AGTAAGTCTTTCGTGCATGATGTTTAATTCCTTCGGG
390 AGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
* * *
1070813 TCATCTATAAGCCTTTAGAGAAAGATGATAAGTCCTTCGGGCCATCCGTAAAACCTTCGGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
1070878 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGG-ATTTTTGAAAACGAA
66 ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
* * *
1070942 GAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCAGGCTATTAGTAAGTCTTTCGAGCAT
131 GAATGCGATTTTCAAAA-TTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* *
1071007 GATGCTTAATTCTTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTTCTTCGGGCCATC
195 GATGCTTAATTCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATC
* *
1071072 CGTAAAACCTTCTGGTAGGATGTTTTCACATGAATTTGAAAATGAAAATTGATGTTTTAAGAAGA
260 CGTAAAACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGA
* *
1071137 TGGAATTTTTGAAAACGAAAAATGCAATTTTCAAAATTTCATAATTTATAAGTCCTTCGGGCCAT
325 T-GAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCATAATTTATAAGTCCTTCGGGCCAT
1071202 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
389 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
* *
1071240 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGAGCCATCCATAAAACCTTCAGGTAGG
1 TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
*
1071305 ATATTTTCACATGAATTTGAAAATGAAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
66 ATGTTTTCACATGAATTTGAAAATG-AAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGA
* * *
1071370 AGAATGTGATTTCCAAAA-TCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAGCAT
130 AGAATGCGATTTTCAAAATTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * *
1071434 GATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTTGAGCAAGATGACAAGTCCTTCGGGCCATC
195 GATGCTTAATTCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATC
* * * *
1071499 CATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATAAAAAATGATGTTTTAAGAAGA
260 CGTAAAACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGA
* *
1071564 TGAAATTTTTGAAAACTAAGAATGCGATTTTCAAAATTTCATAATTTATAAGTCCTTCGAGCCAT
325 TG-AATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCATAATTTATAAGTCCTTCGGGCCAT
*
1071629 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGA
389 CAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
* ** * * * * * * *
1071667 TCATTTGCGAGTCTCTCGAGCAAGA-GAATAAATCATTCGGGTCATCCATAAGAA-CTTCGGGCA
1 TCATCTGTAAGCCTTTAGAGCAAGATG-ATAAGTCCTTCGGGCCATCCATAA-AACCTTCGGGTA
1071730 GGATGTTTT
64 GGATGTTTT
1071739 TCACCAAGAT
Statistics
Matches: 853, Mismatches: 65, Indels: 14
0.92 0.07 0.02
Matches are distributed among these distances:
424 197 0.23
425 108 0.13
426 2 0.00
427 490 0.57
428 26 0.03
429 30 0.04
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (426 bp):
TCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCCATAAAACCTTCGGGTAGG
ATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGATGGAATTTTTGAAAACGAA
GAATGCGATTTTCAAAATTCACAATTTATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATG
ATGCTTAATTCCTTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGTCCTTCGGGCCATCC
GTAAAACCTTCAGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAAGAAGAT
GAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCATAATTTATAAGTCCTTCGGGCCATCA
GTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGG
Found at i:1074888 original size:20 final size:20
Alignment explanation
Indices: 1074840--1074901 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
1074830 AACTTAAATC
*
1074840 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
1074860 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
1074878 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
1074897 AAAAT
1 AAAAT
1074902 TAAATATCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:1074934 original size:14 final size:14
Alignment explanation
Indices: 1074917--1074965 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 14
1074907 ATCTATAATA
1074917 TAATATTAAAAAAT
1 TAATATTAAAAAAT
*
1074931 TAATATT---TAAT
1 TAATATTAAAAAAT
*
1074942 TTAT-TTAAAAAAT
1 TAATATTAAAAAAT
1074955 TAATATTAAAA
1 TAATATTAAAA
1074966 TTAAAATCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
10 2 0.07
11 6 0.22
13 6 0.22
14 13 0.48
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTAAAAAAT
Found at i:1074935 original size:28 final size:24
Alignment explanation
Indices: 1074897--1074961 Score: 76
Period size: 24 Copynumber: 2.5 Consensus size: 24
1074887 TATATGATAT
1074897 AAAATTAAATATCTATAATATAATATTAA
1 AAAATT-AATAT-T-TAAT-TAAT-TTAA
*
1074926 AAAATTAATATTTAATTTATTTAA
1 AAAATTAATATTTAATTAATTTAA
1074950 AAAATTAATATT
1 AAAATTAATATT
1074962 AAAATTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
24 16 0.46
25 3 0.09
26 4 0.11
27 1 0.03
28 5 0.14
29 6 0.17
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATTAATATTTAATTAATTTAA
Found at i:1076456 original size:81 final size:81
Alignment explanation
Indices: 1076321--1076481 Score: 250
Period size: 81 Copynumber: 2.0 Consensus size: 81
1076311 CCCGTCGTTG
* * * * *
1076321 GAGAATACTTCCTAGGTCCACCCTTTGGCCCTCGCGATGATCTCGTGTCATCTTAGGTCAATATG
1 GAGAACACTTCCTAGGACAACCCTTTAGCCCTCGCAATGATCTCGTGTCATCTTAGGTCAATATG
1076386 CACCTATGAGGTTATC
66 CACCTATGAGGTTATC
* *
1076402 GAGAACACTTCCTAGGACAACCCTTTAGCCCTCGCAATGATCTCGTGTCGTCTTAGGTCACTATG
1 GAGAACACTTCCTAGGACAACCCTTTAGCCCTCGCAATGATCTCGTGTCATCTTAGGTCAATATG
*
1076467 TACCTATGAGGTTAT
66 CACCTATGAGGTTAT
1076482 TTATCTCTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 72 1.00
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.30
Consensus pattern (81 bp):
GAGAACACTTCCTAGGACAACCCTTTAGCCCTCGCAATGATCTCGTGTCATCTTAGGTCAATATG
CACCTATGAGGTTATC
Found at i:1078694 original size:13 final size:13
Alignment explanation
Indices: 1078676--1078700 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1078666 TACAGACGCG
1078676 CATATGAAGACTA
1 CATATGAAGACTA
1078689 CATATGAAGACT
1 CATATGAAGACT
1078701 GTTCAACTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.16, T:0.24
Consensus pattern (13 bp):
CATATGAAGACTA
Found at i:1080091 original size:2 final size:2
Alignment explanation
Indices: 1080084--1080163 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
1080074 CAAAATCAGT
1080084 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1080126 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1080164 GCACACAAGG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1080612 original size:15 final size:15
Alignment explanation
Indices: 1080589--1080618 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1080579 AAGTTGACTT
*
1080589 TTTGGTCAAAGTCAA
1 TTTGATCAAAGTCAA
1080604 TTTGATCAAAGTCAA
1 TTTGATCAAAGTCAA
1080619 CAGATCTGGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (15 bp):
TTTGATCAAAGTCAA
Found at i:1081822 original size:39 final size:40
Alignment explanation
Indices: 1081779--1081862 Score: 127
Period size: 39 Copynumber: 2.1 Consensus size: 40
1081769 TTTAATATTT
* *
1081779 TAAATTTC-TAATTTCTTAAATTTTGTCACCATAACATTC
1 TAAATTTCTTAAATTCTTAAATTTTGTCACAATAACATTC
*
1081818 TAAA-TTCTTAAATTCTTAAATTTTTTCACAATAACATTC
1 TAAATTTCTTAAATTCTTAAATTTTGTCACAATAACATTC
1081857 TAAATT
1 TAAATT
1081863 ATTTTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 3 0.08
39 36 0.90
40 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.01, T:0.46
Consensus pattern (40 bp):
TAAATTTCTTAAATTCTTAAATTTTGTCACAATAACATTC
Found at i:1083022 original size:60 final size:59
Alignment explanation
Indices: 1082941--1083105 Score: 154
Period size: 60 Copynumber: 2.8 Consensus size: 59
1082931 GATGACTTTG
* ** * * *** *
1082941 GGGATGAAATT-GAAAGATTCAAAAGTTTGGGGACTAATTTAGAGTGAGGGTCGTAGTTT
1 GGGATGAAATTGGAATG-TTCAAAAGTTTAAGGACTAATTTAAAATGAAACTCATAGTTT
* *
1083000 GTGGATGAAATTGGAATGTTCAAAAGCTTAATGACTAATTTAAAATGAAACTCATAGTTT
1 G-GGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAAACTCATAGTTT
* * **
1083060 AGGGATGAATTTGGAATATTCAAAAGTTTAAGGGTTAA-TTAAAATG
1 -GGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAAAATG
1083106 GAAATTATAA
Statistics
Matches: 86, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
59 9 0.10
60 72 0.84
61 5 0.06
ACGTcount: A:0.38, C:0.05, G:0.25, T:0.32
Consensus pattern (59 bp):
GGGATGAAATTGGAATGTTCAAAAGTTTAAGGACTAATTTAAAATGAAACTCATAGTTT
Found at i:1083688 original size:23 final size:22
Alignment explanation
Indices: 1083645--1083705 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
1083635 ATCAGCTTAA
*
1083645 ATAAATGAAAAAATAAAAATAAT
1 ATAAAT-AAAAATTAAAAATAAT
**
1083668 ATCGATAAAATATTAAAAATAAT
1 ATAAATAAAA-ATTAAAAATAAT
1083691 ATAAATAAAAATTAA
1 ATAAATAAAAATTAA
1083706 TTTAAATAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
22 9 0.28
23 23 0.72
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (22 bp):
ATAAATAAAAATTAAAAATAAT
Found at i:1083701 original size:15 final size:16
Alignment explanation
Indices: 1083681--1083714 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1083671 GATAAAATAT
1083681 TAAAAA-TAATATAAA
1 TAAAAATTAATATAAA
*
1083696 TAAAAATTAATTTAAA
1 TAAAAATTAATATAAA
1083712 TAA
1 TAA
1083715 TTAATGTTGA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAAATTAATATAAA
Found at i:1086519 original size:80 final size:80
Alignment explanation
Indices: 1086259--1086572 Score: 342
Period size: 80 Copynumber: 3.9 Consensus size: 80
1086249 TGTATTTATG
* * * * *
1086259 GAATTTTGGGTTGTTATTTGCT-TGCAATATTAGATTGATGGGTTTTC-ATATCTGGTTTTGCAT
1 GAATTCTGGGTTGTCATTTG-TATGCAA-ATTAGCTTGATGGGTTTTCTATAGCTGTTTTTGCAT
1086322 ATATATATATATGTTCATT
64 ATATATATATA--TTCATT
*
1086341 GAATTCTGGGTTGTCATTTGTATGCAATTTAGCTTGATGGG-TTTCTATAGCTGTTTTTTGC--A
1 GAATTCTGGGTTGTCATTTGTATGCAAATTAGCTTGATGGGTTTTCTATAGCTG-TTTTTGCATA
*
1086403 TATATGTATA-T-ATT
65 TATATATATATTCATT
* *
1086417 GAATTTTGGGTTGTCATATGTATG-AAATTAGCTTGATGGGTTTTTCTATAGCTGTTTTTGCATA
1 GAATTCTGGGTTGTCATTTGTATGCAAATTAGCTTGATGGG-TTTTCTATAGCTGTTTTTGCATA
1086481 TATATATATATTCATT
65 TATATATATATTCATT
* * * * * *
1086497 GAATTCTGGGTTGTTATTTGTATGCAATTTAGC-TCAT-GTTCTTTTTATATCTGTTTTTGCATG
1 GAATTCTGGGTTGTCATTTGTATGCAAATTAGCTTGATGGGT-TTTCTATAGCTGTTTTTGCAT-
1086560 CATATATATATAT
64 -ATATATATATAT
1086573 ATATATATAT
Statistics
Matches: 200, Mismatches: 19, Indels: 27
0.81 0.08 0.11
Matches are distributed among these distances:
75 15 0.08
76 32 0.16
77 13 0.06
78 11 0.05
79 21 0.10
80 41 0.20
81 38 0.19
82 29 0.14
ACGTcount: A:0.23, C:0.09, G:0.19, T:0.50
Consensus pattern (80 bp):
GAATTCTGGGTTGTCATTTGTATGCAAATTAGCTTGATGGGTTTTCTATAGCTGTTTTTGCATAT
ATATATATATTCATT
Found at i:1086551 original size:156 final size:158
Alignment explanation
Indices: 1086249--1086574 Score: 421
Period size: 156 Copynumber: 2.1 Consensus size: 158
1086239 TGTGTGTGTG
* * * *
1086249 TGTATTTATGGAATTTTGGGTTGTTATTTGCTTGCAATATTAGATTGATGGGTTTTCATATCTGG
1 TGTATATATGGAATTTTGGGTTGTCATATGCTTGCAATATTAGATTGATGGGTTTTCATAGCTGG
*
1086314 TTTTGCATATATATATATATGTTCATTGAATTCTGGGTTGTCATTTGTATGCAATTTAGCTTGAT
66 TTTTGCATATATATATATA-GTTCATTGAATTCTGGGTTGTCATTTGTATGCAATTTAGCTTCAT
*
1086379 GGGTTTCTATAGCTGTTTTT-TGCATATA
130 GGCTTTCTATAGCTGTTTTTATGCATATA
* *
1086407 TGTATATATTGAATTTTGGGTTGTCATATG-TATG-AA-ATTAGCTTGATGGGTTTTTCTATAGC
1 TGTATATATGGAATTTTGGGTTGTCATATGCT-TGCAATATTAGATTGATGGG-TTTTC-ATAGC
* *
1086469 TGTTTTTGCATATATATATATA-TTCATTGAATTCTGGGTTGTTATTTGTATGCAATTTAGC-TC
63 TGGTTTTGCATATATATATATAGTTCATTGAATTCTGGGTTGTCATTTGTATGCAATTTAGCTTC
* * *
1086532 ATGTTCTTTTTATATCTGTTTTTGCATGCATATA
128 ATG-GCTTTCTATAGCTGTTTTT--ATGCATATA
*
1086566 TATATATAT
1 TGTATATAT
1086575 ATATATATAG
Statistics
Matches: 147, Mismatches: 14, Indels: 13
0.84 0.08 0.07
Matches are distributed among these distances:
155 4 0.03
156 66 0.45
157 8 0.05
158 53 0.36
159 16 0.11
ACGTcount: A:0.23, C:0.08, G:0.19, T:0.50
Consensus pattern (158 bp):
TGTATATATGGAATTTTGGGTTGTCATATGCTTGCAATATTAGATTGATGGGTTTTCATAGCTGG
TTTTGCATATATATATATAGTTCATTGAATTCTGGGTTGTCATTTGTATGCAATTTAGCTTCATG
GCTTTCTATAGCTGTTTTTATGCATATA
Found at i:1094067 original size:23 final size:23
Alignment explanation
Indices: 1094037--1094094 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1094027 TATTAAAAAT
1094037 TTATTGAAAATGACAAAAAATTA
1 TTATTGAAAATGACAAAAAATTA
* *
1094060 TTATTGAAATTGACAAAAATTTA
1 TTATTGAAAATGACAAAAAATTA
1094083 TTATTGAAAATG
1 TTATTGAAAATG
1094095 TCATTTTGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.10, T:0.36
Consensus pattern (23 bp):
TTATTGAAAATGACAAAAAATTA
Found at i:1094532 original size:19 final size:19
Alignment explanation
Indices: 1094508--1094558 Score: 102
Period size: 19 Copynumber: 2.7 Consensus size: 19
1094498 AATGACCAAC
1094508 AAAATCGCAATGCGAAATA
1 AAAATCGCAATGCGAAATA
1094527 AAAATCGCAATGCGAAATA
1 AAAATCGCAATGCGAAATA
1094546 AAAATCGCAATGC
1 AAAATCGCAATGC
1094559 TATAGTACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.51, C:0.18, G:0.16, T:0.16
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATA
Found at i:1094615 original size:20 final size:20
Alignment explanation
Indices: 1094590--1094642 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1094580 GATTTTCCAG
*
1094590 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
1094610 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
*
1094630 AATTGCAACGCGA
1 AATCGCAACGCGA
1094643 TTCTTACTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.43, C:0.23, G:0.19, T:0.15
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:1094700 original size:20 final size:21
Alignment explanation
Indices: 1094651--1094744 Score: 113
Period size: 20 Copynumber: 4.5 Consensus size: 21
1094641 GATTCTTACT
*
1094651 ATCGCAACGAGTATCCGTAAAA
1 ATCGCAACGCGTATCCGT-AAA
*
1094673 AGCGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
* *
1094693 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGTAAA
1094714 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGCGTATCCGTAAA
1094734 ATCGCAACGCG
1 ATCGCAACGCG
1094745 ATTTTTAAAG
Statistics
Matches: 62, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
20 29 0.47
21 17 0.27
22 16 0.26
ACGTcount: A:0.36, C:0.28, G:0.20, T:0.16
Consensus pattern (21 bp):
ATCGCAACGCGTATCCGTAAA
Found at i:1094732 original size:41 final size:42
Alignment explanation
Indices: 1094651--1094742 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 42
1094641 GATTCTTACT
** *
1094651 ATCGCAACGAGTATCCGTAAAAAGCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAAAGCGCAACGCGTATCCGTAA
*
1094693 ATCGCAACGACAATACGT-AAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGACAATACGTAAAAAGCGCAACGCGTATCCGTAA
1094734 ATCGCAACG
1 ATCGCAACG
1094743 CGATTTTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 31 0.67
42 15 0.33
ACGTcount: A:0.37, C:0.27, G:0.20, T:0.16
Consensus pattern (42 bp):
ATCGCAACGACAATACGTAAAAAGCGCAACGCGTATCCGTAA
Found at i:1095292 original size:20 final size:20
Alignment explanation
Indices: 1095253--1095308 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
1095243 TTTGCAGAAG
*
1095253 AATCGCAACGAGAGAAATGAA
1 AATCGCAACGCGA-AAATGAA
*
1095274 AATCGCAACGCGAAAATGAC
1 AATCGCAACGCGAAAATGAA
*
1095294 TATCGCAACGCGAAA
1 AATCGCAACGCGAAA
1095309 CCAAAATCGC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
20 20 0.62
21 12 0.38
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.11
Consensus pattern (20 bp):
AATCGCAACGCGAAAATGAA
Found at i:1097214 original size:63 final size:64
Alignment explanation
Indices: 1097136--1097262 Score: 211
Period size: 64 Copynumber: 2.0 Consensus size: 64
1097126 GCTAATTCTG
*
1097136 CTAAACTGTGTATTCTTTAACACTGTGAA-ATAGTATTTGTCTTTGTTTTATCTTTTGGTTGAA
1 CTAAACTGTGTATTCTTTAACACTCTGAAGATAGTATTTGTCTTTGTTTTATCTTTTGGTTGAA
* * *
1097199 CTAAACTGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1 CTAAACTGTGTATTCTTTAACACTCTGAAGATAGTATTTGTCTTTGTTTTATCTTTTGGTTGAA
1097263 GTAATGCAAT
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
63 27 0.46
64 32 0.54
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (64 bp):
CTAAACTGTGTATTCTTTAACACTCTGAAGATAGTATTTGTCTTTGTTTTATCTTTTGGTTGAA
Found at i:1097354 original size:19 final size:19
Alignment explanation
Indices: 1097314--1097450 Score: 123
Period size: 19 Copynumber: 7.7 Consensus size: 19
1097304 TAGTTTACTT
* *
1097314 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
1097334 TCACAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1097353 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
*
1097367 TCGCAACGAGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1097386 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1097405 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
**
1097419 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1097438 TCGCAACGCGAAA
1 TCGCAACGCGAAA
1097451 CTATAATCGC
Statistics
Matches: 98, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
14 20 0.20
15 2 0.02
16 3 0.03
17 4 0.04
18 2 0.02
19 56 0.57
20 11 0.11
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1097370 original size:14 final size:14
Alignment explanation
Indices: 1097351--1097377 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1097341 GCGAAATGAA
1097351 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1097365 AATCGCAACGAGA
1 AATCGCAACGAGA
1097378 AATGAAAATC
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:0.44, C:0.22, G:0.26, T:0.07
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1097419 original size:33 final size:33
Alignment explanation
Indices: 1097382--1097445 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
1097372 ACGAGAAATG
**
1097382 AAAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAAATCGCAACGCGAAACCAAAATCGCAACGAC
1097415 AAAATCGCAACGCGAAACCAAAATCGCAACG
1 AAAATCGCAACGCGAAACCAAAATCGCAACG
1097446 CGAAACTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.48, C:0.27, G:0.17, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1097460 original size:52 final size:52
Alignment explanation
Indices: 1097314--1097450 Score: 193
Period size: 52 Copynumber: 2.6 Consensus size: 52
1097304 TAGTTTACTT
* * * * *
1097314 TCGCAACACGAAACTTAAAATCACAACGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAACGCGAAAC-CAAAATCGCAACGCGAAATGAAAATCGCAACGACAAAA
* **
1097367 TCGCAACGAGAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGACAAAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGACAAAA
1097419 TCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACCAAAATCGCAACGCGAAA
1097451 CTATAATCGC
Statistics
Matches: 74, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
52 63 0.85
53 11 0.15
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAATCGCAACGACAAAA
Found at i:1097498 original size:19 final size:20
Alignment explanation
Indices: 1097474--1097541 Score: 57
Period size: 21 Copynumber: 3.4 Consensus size: 20
1097464 GCGATTCTCT
1097474 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTCATTTTCG
*** *
1097493 CGTTGCGAAAGTCATTTTTCA
1 CGTTGCGATTTTCA-TTTTCG
* *
1097514 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCATTTTCG
*
1097534 TGTTGCGA
1 CGTTGCGA
1097542 AAGTAAACTA
Statistics
Matches: 36, Mismatches: 11, Indels: 3
0.72 0.22 0.06
Matches are distributed among these distances:
19 11 0.31
20 11 0.31
21 14 0.39
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTTCG
Found at i:1099494 original size:14 final size:14
Alignment explanation
Indices: 1099475--1099510 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1099465 ATTGTTTAAT
1099475 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1099489 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1099503 TGATTTGT
1 TGATTTGT
1099511 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1099665 original size:14 final size:14
Alignment explanation
Indices: 1099646--1099732 Score: 66
Period size: 14 Copynumber: 5.5 Consensus size: 14
1099636 TCGCAACGAG
1099646 TGCGATTCTCTCGT
1 TGCGATTCTCTCGT
*
1099660 TGCGATTTTCATTTCGCAT
1 TGCGA--TTC-TCTCG--T
1099679 TGCGATTCTCTCGT
1 TGCGATTCTCTCGT
*
1099693 TGCGATTTTCATTTCGCAT
1 TGCGA--TTC-TCTCG--T
1099712 TGCGATTCTCTCGT
1 TGCGATTCTCTCGT
1099726 TGCGATT
1 TGCGATT
1099733 TTCATTTCGC
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 19 0.32
16 14 0.24
17 14 0.24
19 12 0.20
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TGCGATTCTCTCGT
Found at i:1099688 original size:33 final size:33
Alignment explanation
Indices: 1099646--1099751 Score: 212
Period size: 33 Copynumber: 3.2 Consensus size: 33
1099636 TCGCAACGAG
1099646 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1099679 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1099712 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1 TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
1099745 TGCGATT
1 TGCGATT
1099752 TTCATTTCGC
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
TGCGATTCTCTCGTTGCGATTTTCATTTCGCAT
Found at i:1099748 original size:52 final size:52
Alignment explanation
Indices: 1099692--1099822 Score: 244
Period size: 52 Copynumber: 2.5 Consensus size: 52
1099682 GATTCTCTCG
1099692 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1099744 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
*
1099796 TTGCGATTTTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTT-CGCATTGCGAT
1099823 AGTCAAATGA
Statistics
Matches: 77, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
52 67 0.87
53 10 0.13
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:1102329 original size:24 final size:24
Alignment explanation
Indices: 1102295--1102348 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1102285 CTGAAACATC
1102295 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1102319 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1102343 ATCAAA
1 ATCAAA
1102349 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1102362 original size:24 final size:24
Alignment explanation
Indices: 1102295--1102362 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
1102285 CTGAAACATC
* * *
1102295 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1102319 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1102343 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1102363 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1102495 original size:12 final size:12
Alignment explanation
Indices: 1102474--1102507 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
1102464 GGTTGTAGGT
*
1102474 TTTGAGATTGTG
1 TTTGATATTGTG
1102486 TTTGATATTGTG
1 TTTGATATTGTG
*
1102498 TTTGGTATTG
1 TTTGATATTG
1102508 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:1103200 original size:20 final size:20
Alignment explanation
Indices: 1103175--1103446 Score: 221
Period size: 20 Copynumber: 13.4 Consensus size: 20
1103165 AAATTTAAGT
1103175 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
* *
1103195 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCTC
* *
1103215 GTTGCGATTTTCAGATTATC
1 GTTGCGATTTACAGATTCTC
*
1103235 GTTTCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTCTC
* * *
1103255 GTTGCGA-TAATCAGAATCGC
1 GTTGCGATTTA-CAGATTCTC
1103275 GTTGCGATTTTAC-GTATTCTC
1 GTTGCGA-TTTACAG-ATTCTC
* * *
1103296 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACAGATTCTC
1103316 GTTGCGATTTTAC-GTATTCTC
1 GTTGCGA-TTTACAG-ATTCTC
* * *
1103337 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACAGATTCTC
* *
1103357 GTTGCGATTTTACGGATACTC
1 GTTGCGA-TTTACAGATTCTC
* * *
1103378 GTTGCGATAGT-CAGAATCGC
1 GTTGCGAT-TTACAGATTCTC
* *
1103398 GTTGCGATTTATATG-TTCGC
1 GTTGCGATTTACA-GATTCTC
* * *
1103418 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACAGATTCTC
1103438 GTTGCGATT
1 GTTGCGATT
1103447 CTGGAAAATT
Statistics
Matches: 207, Mismatches: 32, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
19 3 0.01
20 151 0.73
21 51 0.25
22 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCTC
Found at i:1103230 original size:40 final size:40
Alignment explanation
Indices: 1103175--1103446 Score: 267
Period size: 41 Copynumber: 6.7 Consensus size: 40
1103165 AAATTTAAGT
* * *
1103175 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTTCAGATTCGCGTTGCGATTTACGGATTCTC
** * *
1103215 GTTGCGATTTTCAGATTATCGTTTCGATTTACAGATTCTC
1 GTTGCGATTTTCAGATTCGCGTTGCGATTTACGGATTCTC
** * *
1103255 GTTGCGATAATCAGAATCGCGTTGCGATTTTACGTATTCTC
1 GTTGCGATTTTCAGATTCGCGTTGCGA-TTTACGGATTCTC
* * * *
1103296 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
1 GTTGCGATTTTCAGATTCGCGTTGCGA-TTTACGGATTCTC
* * * *
1103337 GTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTC
1 GTTGCGATTTTCAGATTCGCGTTGCGA-TTTACGGATTCTC
** * ** *
1103378 GTTGCGATAGTCAGAATCGCGTTGCGATTTATATG-TTCGC
1 GTTGCGATTTTCAGATTCGCGTTGCGATTTA-CGGATTCTC
*
1103418 GTTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTTCAGATTCGCGTTGCGATT
1103447 CTGGAAAATT
Statistics
Matches: 195, Mismatches: 35, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
40 88 0.45
41 107 0.55
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (40 bp):
GTTGCGATTTTCAGATTCGCGTTGCGATTTACGGATTCTC
Found at i:1103428 original size:61 final size:60
Alignment explanation
Indices: 1103234--1103427 Score: 187
Period size: 61 Copynumber: 3.2 Consensus size: 60
1103224 TTCAGATTAT
* * * * *
1103234 CGTTTCGATTTACAGATTCTCGTTGCGATAATCAGAATCGCGTTGCGATTT-TACGTATTCT
1 CGTTGCGATTTACGGATACTCGTTGCGATAATCAGAATCGCGTTGCGATTTATA--TGTTCG
* * * * * ** *
1103295 CGTTGCGATTTACGGATACGCGTTGCGAT-TTTACGTATTCTCGTTGCGATTTA-CGGATACG
1 CGTTGCGATTTACGGATACTCGTTGCGATAATCA-G-AATCGCGTTGCGATTTATATG-TTCG
*
1103356 CGTTGCGATTTTACGGATACTCGTTGCGATAGTCAGAATCGCGTTGCGATTTATATGTTCG
1 CGTTGCGA-TTTACGGATACTCGTTGCGATAATCAGAATCGCGTTGCGATTTATATGTTCG
1103417 CGTTGCGATTT
1 CGTTGCGATTT
1103428 TCATATTCGC
Statistics
Matches: 105, Mismatches: 21, Indels: 15
0.74 0.15 0.11
Matches are distributed among these distances:
60 5 0.05
61 62 0.59
62 36 0.34
63 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACTCGTTGCGATAATCAGAATCGCGTTGCGATTTATATGTTCG
Found at i:1104842 original size:32 final size:32
Alignment explanation
Indices: 1104801--1104867 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
1104791 CATGACTAAG
1104801 AAACATAGAAGAGCATTCCAACTTACTTCTAT
1 AAACATAGAAGAGCATTCCAACTTACTTCTAT
1104833 AAACATAGAAGAGCATTCCAACTTACTTCTAT
1 AAACATAGAAGAGCATTCCAACTTACTTCTAT
1104865 AAA
1 AAA
1104868 TAATAGAGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.27
Consensus pattern (32 bp):
AAACATAGAAGAGCATTCCAACTTACTTCTAT
Found at i:1105907 original size:188 final size:186
Alignment explanation
Indices: 1105667--1106060 Score: 607
Period size: 189 Copynumber: 2.1 Consensus size: 186
1105657 TTTTCTAATT
* * *
1105667 TATATAA-AAATTAAATATTTTATAATTCAAAAAAACAGTTATAATTAATTTAAAT-A-ATATAT
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTACAATTAATTTAAATAATATATAT
* *
1105729 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAAGTTTAAAAGTT
66 AAATATAAAATAAAAATTTTATATAAA-ATTTTAATTAATTAATATTGATTTAAGTTTAAAAGTT
* *
1105794 ATTGAATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAACCCATATGTTA
130 ATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAACCCATATGTTA
*
1105851 TATATAATAATATATATAATATTTTTTAATT-AAAAAAACAGTTTACAATTAATTTAAATAATAT
1 TATATAAT-ATAT-T-TAATATTTTATAATTCAAAAAAACAG-TTACAATTAATTTAAATAATAT
* *
1105915 ATATAAATATAAAATATAAATTTTATATAAAATTTTAATTAATTAATATTGATTTAGGTTTAAAA
62 ATATAAATATAAAATAAAAATTTTATATAAAATTTTAATTAATTAATATTGATTTAAGTTTAAAA
* *
1105980 GTTATTGGATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAGCCCATATGTTA
127 GTTATTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAACCCATATGTTA
1106040 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
1106061 AAAATTTTAT
Statistics
Matches: 191, Mismatches: 12, Indels: 12
0.89 0.06 0.06
Matches are distributed among these distances:
184 7 0.04
186 11 0.06
187 12 0.06
188 33 0.17
189 97 0.51
190 31 0.16
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.45
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAACAGTTACAATTAATTTAAATAATATATAT
AAATATAAAATAAAAATTTTATATAAAATTTTAATTAATTAATATTGATTTAAGTTTAAAAGTTA
TTGAATCTTAAATTATTAATTGGATTTTAAATGGTTTGGGCTGAACCCATATGTTA
Found at i:1109328 original size:48 final size:48
Alignment explanation
Indices: 1109272--1109363 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
1109262 CTTAATTGAT
* *
1109272 TTAATTTCTTAGT-TTGAAGGTTTAATTAGATAGGAAAATTTTAAAGAC
1 TTAATTTCTTA-TATTGAAGGTTTAATTAGATAAGAAAAATTTAAAGAC
1109320 TTAATTTCTTATATTGAAGGTTTAATTAGATAAGAAAAATTTAA
1 TTAATTTCTTATATTGAAGGTTTAATTAGATAAGAAAAATTTAA
1109364 TATAAAGATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 1 0.02
48 40 0.98
ACGTcount: A:0.40, C:0.03, G:0.14, T:0.42
Consensus pattern (48 bp):
TTAATTTCTTATATTGAAGGTTTAATTAGATAAGAAAAATTTAAAGAC
Found at i:1109961 original size:13 final size:13
Alignment explanation
Indices: 1109933--1109971 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1109923 TAACCAAAAT
*
1109933 TATTAAATAT-TA
1 TATTATATATATA
1109945 TATTATATATATA
1 TATTATATATATA
*
1109958 TATTATAAATATA
1 TATTATATATATA
1109971 T
1 T
1109972 TTTAAGCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATTATATATATA
Found at i:1109969 original size:15 final size:15
Alignment explanation
Indices: 1109931--1109971 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
1109921 ATTAACCAAA
1109931 ATTATTAAATAT-TAT
1 ATTA-TAAATATATAT
1109946 ATTAT--ATATATAT
1 ATTATAAATATATAT
1109959 ATTATAAATATAT
1 ATTATAAATATAT
1109972 TTTAAGCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 4 0.17
13 8 0.35
14 1 0.04
15 10 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATTATAAATATATAT
Found at i:1110117 original size:15 final size:16
Alignment explanation
Indices: 1110083--1110118 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1110073 ATATACATCT
1110083 ATTAT-ATTTAAAATA
1 ATTATAATTTAAAATA
1110098 A-TATAATTTAAAA-A
1 ATTATAATTTAAAATA
1110112 ATTATAA
1 ATTATAA
1110119 AAAAATAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATTATAATTTAAAATA
Found at i:1110624 original size:18 final size:19
Alignment explanation
Indices: 1110575--1110624 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
1110565 TATTATTTTT
*
1110575 AATTTATATATTTTCATTAA
1 AATTTATATA-ATTCATTAA
*
1110595 AATTTTTA-AATTCA-TAA
1 AATTTATATAATTCATTAA
1110612 AATTTATATAATT
1 AATTTATATAATT
1110625 TTTTTACAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 10 0.38
18 8 0.31
19 1 0.04
20 7 0.27
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (19 bp):
AATTTATATAATTCATTAA
Found at i:1113972 original size:24 final size:24
Alignment explanation
Indices: 1113945--1113992 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1113935 GATGAAATTG
* *
1113945 AAAAGATAGAATAAAATAAAATAA
1 AAAAGAGAAAATAAAATAAAATAA
* *
1113969 AAAAGGGAAAATAATATAAAATAA
1 AAAAGAGAAAATAAAATAAAATAA
1113993 TAAATAATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (24 bp):
AAAAGAGAAAATAAAATAAAATAA
Found at i:1114631 original size:76 final size:75
Alignment explanation
Indices: 1114462--1114673 Score: 272
Period size: 76 Copynumber: 2.9 Consensus size: 75
1114452 TAAAACATCT
* * * *
1114462 TAAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCT--AAAAA-ATAATAT-TTA
1 TAAAACCTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAAAAAGATAAAATATAA
* *
1114522 AAATAATATTA
65 AAATAAAATCA
* *
1114533 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAGAATACCTAAAATAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAA-AAAGATAAAATATAA
*
1114598 AAATAAAATCC
65 AAATAAAATCA
*
1114609 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAA-AAAGATAAAATATAA
1114674 TGTTTAAAAT
Statistics
Matches: 124, Mismatches: 11, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
70 5 0.04
71 37 0.30
73 2 0.02
74 3 0.02
75 6 0.05
76 71 0.57
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.28
Consensus pattern (75 bp):
TAAAACCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAAAAGATAAAATATAAA
AATAAAATCA
Found at i:1114641 original size:19 final size:19
Alignment explanation
Indices: 1114601--1114642 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1114591 AATATAAAAA
* *
1114601 TAAAATCCTAAAACTTAAT
1 TAAAATACTAAAACCTAAT
*
1114620 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
1114639 TAAA
1 TAAA
1114643 CTAAAATACC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:1120186 original size:24 final size:24
Alignment explanation
Indices: 1120159--1120275 Score: 83
Period size: 25 Copynumber: 4.7 Consensus size: 24
1120149 AAATCCTAAT
**
1120159 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATTTAAAC
** *
1120183 TAAAATACCTAAAACAAAGATAAAA
1 TAAAATA-CTAAAACAAATTTAAAC
* * * *
1120208 TATAAA-AATAATATCAAAATTTTAAT
1 TA-AAATACTAA-AAC-AAATTTAAAC
**
1120234 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACAAATTTAAAC
1120258 TAAAATACCTAAAACAAA
1 TAAAATA-CTAAAACAAA
1120276 GATAAAAGAT
Statistics
Matches: 68, Mismatches: 19, Indels: 11
0.69 0.19 0.11
Matches are distributed among these distances:
24 23 0.34
25 30 0.44
26 15 0.22
ACGTcount: A:0.60, C:0.13, G:0.01, T:0.26
Consensus pattern (24 bp):
TAAAATACTAAAACAAATTTAAAC
Done.