Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009611.1 Hibiscus syriacus cultivar Beakdansim tig00116997_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: 6671611
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 27
Found at i:4334548 original size:64 final size:64
Alignment explanation
Indices: 4334479--4334606 Score: 256
Period size: 64 Copynumber: 2.0 Consensus size: 64
4334469 TTTCTTATAT
4334479 ATATATATATATATATATATATATGAAAGAAAAAGGAAAATACTGCAGGATGATACACTATCTG
1 ATATATATATATATATATATATATGAAAGAAAAAGGAAAATACTGCAGGATGATACACTATCTG
4334543 ATATATATATATATATATATATATGAAAGAAAAAGGAAAATACTGCAGGATGATACACTATCTG
1 ATATATATATATATATATATATATGAAAGAAAAAGGAAAATACTGCAGGATGATACACTATCTG
4334607 GGGCGGTGGC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
64 64 1.00
ACGTcount: A:0.48, C:0.08, G:0.14, T:0.30
Consensus pattern (64 bp):
ATATATATATATATATATATATATGAAAGAAAAAGGAAAATACTGCAGGATGATACACTATCTG
Found at i:4335158 original size:2 final size:2
Alignment explanation
Indices: 4335151--4335204 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
4335141 ATTGCATTTG
4335151 AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
4335192 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
4335205 AGTGTTATTA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4338767 original size:18 final size:17
Alignment explanation
Indices: 4338744--4338814 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 17
4338734 GCGTAGAATT
4338744 TGTCCCATAGGACCACTA
1 TGTCCCA-AGGACCACTA
*
4338762 TGTCCCAAAGGACCACTG
1 TGTCCC-AAGGACCACTA
*
4338780 TGTTCCGAAGGACCACTA
1 TG-TCCCAAGGACCACTA
*
4338798 TGTCCCGAAAGACCACT
1 TGTCCC-AAGGACCACT
4338815 GATAATCCCT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
17 3 0.07
18 38 0.84
19 4 0.09
ACGTcount: A:0.28, C:0.32, G:0.20, T:0.20
Consensus pattern (17 bp):
TGTCCCAAGGACCACTA
Found at i:4340752 original size:18 final size:18
Alignment explanation
Indices: 4340714--4340762 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
4340704 CCATATGGAG
* *
4340714 TATCGATATTGCAAGGCAA
1 TATCGATACT-CAAGGAAA
4340733 TATCGATACTCAAGGAAA
1 TATCGATACTCAAGGAAA
*
4340751 TATCAATACTCA
1 TATCGATACTCA
4340763 GGGTGATAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (18 bp):
TATCGATACTCAAGGAAA
Found at i:4343179 original size:19 final size:20
Alignment explanation
Indices: 4343136--4343183 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
4343126 TCTAAATCCT
*
4343136 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
4343156 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
4343175 TTTTCAAAA
1 TTTTCAAAA
4343184 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:4343206 original size:23 final size:24
Alignment explanation
Indices: 4343161--4343206 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
4343151 TTTGGCTTTC
*
4343161 AAAATCTATTTTTGTTTTCAAAAG
1 AAAATCTATTTTCGTTTTCAAAAG
4343185 AAAATC-ATTTTCGATTTT-AAAA
1 AAAATCTATTTTCG-TTTTCAAAA
4343207 TTTGAAATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (24 bp):
AAAATCTATTTTCGTTTTCAAAAG
Found at i:4344464 original size:21 final size:21
Alignment explanation
Indices: 4344439--4344478 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
4344429 TCGTTAGACA
4344439 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCGGTACCCCCTGG
*
4344460 GGGGGAATCTGTACCCCCT
1 GGGGGAATCGGTACCCCCT
4344479 AGACATTATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.15, C:0.30, G:0.38, T:0.17
Consensus pattern (21 bp):
GGGGGAATCGGTACCCCCTGG
Found at i:4348109 original size:26 final size:26
Alignment explanation
Indices: 4348073--4348127 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
4348063 AACATCGACA
4348073 AATCTTGTACATGTGCCTCTTCAGAT
1 AATCTTGTACATGTGCCTCTTCAGAT
4348099 AATCTTGTACATGTGCCTCTTCAGAT
1 AATCTTGTACATGTGCCTCTTCAGAT
4348125 AAT
1 AAT
4348128 TTCCTTCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.25, C:0.22, G:0.15, T:0.38
Consensus pattern (26 bp):
AATCTTGTACATGTGCCTCTTCAGAT
Found at i:4349850 original size:15 final size:15
Alignment explanation
Indices: 4349830--4349860 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4349820 AAACATTTTA
4349830 TGTGCACTGATGAAT
1 TGTGCACTGATGAAT
4349845 TGTGCACTGATGAAT
1 TGTGCACTGATGAAT
4349860 T
1 T
4349861 AGCAATGTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (15 bp):
TGTGCACTGATGAAT
Found at i:4362442 original size:29 final size:26
Alignment explanation
Indices: 4362389--4362440 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 26
4362379 TTTAACTCCA
4362389 AATTATTTTTTTTTAATTATGTTTAT
1 AATTATTTTTTTTTAATTATGTTTAT
4362415 AATTATATTTATTATTTAA-TATGTTT
1 AATTAT-TTT-TT-TTTAATTATGTTT
4362441 TACCTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 6 0.26
27 3 0.13
28 9 0.39
29 5 0.22
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (26 bp):
AATTATTTTTTTTTAATTATGTTTAT
Found at i:4364165 original size:13 final size:13
Alignment explanation
Indices: 4364147--4364172 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4364137 CTCATTGTAT
4364147 GTAATTACTTCTA
1 GTAATTACTTCTA
4364160 GTAATTACTTCTA
1 GTAATTACTTCTA
4364173 ATGTTACAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (13 bp):
GTAATTACTTCTA
Found at i:4364409 original size:90 final size:89
Alignment explanation
Indices: 4364295--4364469 Score: 253
Period size: 90 Copynumber: 2.0 Consensus size: 89
4364285 TCCTGAATAT
* * * * * **
4364295 TTAATTTCAATTAATTAAATATAGATTTATTTAATTTGAAATAATAAAATCCCTGATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTCGAAATAATAAAAACCCTAATATGACCAG
4364360 GGTAACTTGGA-TATAAAAGGATTA
66 GGTAACTT-GACTATAAAAGGATTA
*
4364384 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTCGAAATAATAAAAACTCTAATATGACCA
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTCGAAATAATAAAAACCCTAATATGACCA
4364449 GGGTAACTTGACTATAAAAGG
65 GGGTAACTTGACTATAAAAGG
4364470 GTGTGTTAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
89 9 0.12
90 67 0.88
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (89 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTCGAAATAATAAAAACCCTAATATGACCAG
GGTAACTTGACTATAAAAGGATTA
Found at i:4370192 original size:4 final size:4
Alignment explanation
Indices: 4370183--4370207 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4370173 AGGATAGATG
4370183 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
4370208 GAAGGTGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:4372329 original size:25 final size:25
Alignment explanation
Indices: 4372282--4372330 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
4372272 TAAGGTTCTA
*
4372282 AAAAATAATTAAACCATAAAAATTC
1 AAAAATAATTAAACCACAAAAATTC
*
4372307 AAAAATAATTAAACCACATAAATT
1 AAAAATAATTAAACCACAAAAATT
4372331 TGGGATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.24
Consensus pattern (25 bp):
AAAAATAATTAAACCACAAAAATTC
Found at i:4373667 original size:21 final size:21
Alignment explanation
Indices: 4373641--4373682 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
4373631 TATATTTTTA
4373641 ATTAAATAAAAAAATT-ATAAT
1 ATTAAA-AAAAAAATTCATAAT
*
4373662 ATTAAAAAAATAATTCATAAT
1 ATTAAAAAAAAAATTCATAAT
4373683 TCATTATCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATTAAAAAAAAAATTCATAAT
Found at i:4377778 original size:22 final size:20
Alignment explanation
Indices: 4377737--4377775 Score: 64
Period size: 18 Copynumber: 2.0 Consensus size: 20
4377727 AGTAACTGCG
4377737 TTTTATTATTATTTTTTAAA
1 TTTTATTATTATTTTTTAAA
4377757 TTTTATT-TTA-TTTTTAAA
1 TTTTATTATTATTTTTTAAA
4377775 T
1 T
4377776 AAAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.47
19 3 0.16
20 7 0.37
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTATTATTATTTTTTAAA
Found at i:4378185 original size:12 final size:10
Alignment explanation
Indices: 4378143--4378183 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
4378133 TTTATCACAC
4378143 CAAATTCTCT
1 CAAATTCTCT
4378153 CAAATTCTCT
1 CAAATTCTCT
4378163 -AAATTTCTCT
1 CAAA-TTCTCT
*
4378173 CAAATACTCT
1 CAAATTCTCT
4378183 C
1 C
4378184 TCTTTTTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:4378503 original size:111 final size:110
Alignment explanation
Indices: 4378309--4378640 Score: 567
Period size: 111 Copynumber: 3.0 Consensus size: 110
4378299 TGGAAATCAT
* *
4378309 ATATCTCTACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
4378374 TATTTAGTTGATTTATTTAATGCATGGTTATTAGATTAAGAATTAA
66 TA-TTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
4378420 ATATCTCGACATTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
4378485 TGATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 T-ATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
4378531 ATATCTCGACACTTTGTTGATACGTTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
4378596 TAATTAGTTGATTTATTTAATGCATGATTATTATA-TAAGAATTAA
66 T-ATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
4378641 TTTTTGTAAT
Statistics
Matches: 211, Mismatches: 9, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
110 10 0.05
111 200 0.95
112 1 0.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.46
Consensus pattern (110 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:4381220 original size:31 final size:31
Alignment explanation
Indices: 4381153--4381212 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
4381143 CAATTTAAGG
*
4381153 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
4381184 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
4381213 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:4381301 original size:19 final size:19
Alignment explanation
Indices: 4381277--4381342 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 19
4381267 AATGTTTTTA
**
4381277 TGAATAGTATTTTACTATT
1 TGAATAGTAAATTACTATT
4381296 TGAATAGTAAATTACTATT
1 TGAATAGTAAATTACTATT
* * *
4381315 TGAACAGTAAATCACTGTT
1 TGAATAGTAAATTACTATT
*
4381334 TGAACAGTA
1 TGAATAGTA
4381343 CCCCGAGACT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 42 1.00
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (19 bp):
TGAATAGTAAATTACTATT
Found at i:4381454 original size:20 final size:20
Alignment explanation
Indices: 4381429--4381468 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
4381419 ATTTGAATAT
*
4381429 TATGAAGGGGTATCGATTCC
1 TATGAAGGGGTACCGATTCC
4381449 TATGAAGGGGTACCGATTCC
1 TATGAAGGGGTACCGATTCC
4381469 CCCCATTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (20 bp):
TATGAAGGGGTACCGATTCC
Found at i:4383563 original size:25 final size:25
Alignment explanation
Indices: 4383512--4383564 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
4383502 ATTAAAGTTT
**
4383512 AATATGATAATTAACATGTTAAAAA
1 AATATGATAATTAACATAATAAAAA
*
4383537 AATATGATAGTTAACA-AATAAACAA
1 AATATGATAATTAACATAATAAA-AA
4383562 AAT
1 AAT
4383565 TTAATAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.28
Consensus pattern (25 bp):
AATATGATAATTAACATAATAAAAA
Found at i:4383738 original size:21 final size:21
Alignment explanation
Indices: 4383712--4383809 Score: 87
Period size: 21 Copynumber: 4.7 Consensus size: 21
4383702 ATCAGTTTCC
4383712 AAAATCGCAACGCGATTATTG
1 AAAATCGCAACGCGATTATTG
* *
4383733 AAAATCGCAATGCGA-TAGT-
1 AAAATCGCAACGCGATTATTG
** *
4383752 ACAAATTCGCATTGCGATT-TTCC
1 A-AAA-TCGCAACGCGATTATT-G
*
4383775 AAAATCGCAACGCGAATA-TG
1 AAAATCGCAACGCGATTATTG
4383795 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
4383810 ACACATAAAT
Statistics
Matches: 63, Mismatches: 8, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
19 1 0.02
20 21 0.33
21 36 0.57
22 4 0.06
23 1 0.02
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (21 bp):
AAAATCGCAACGCGATTATTG
Found at i:4383800 original size:20 final size:20
Alignment explanation
Indices: 4383776--4383969 Score: 210
Period size: 20 Copynumber: 9.7 Consensus size: 20
4383766 CGATTTTCCA
** *
4383776 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
4383796 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
4383816 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
4383836 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
4383856 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
4383876 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
4383896 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
4383916 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
4383936 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
4383956 AAATCGCAACGCGA
1 AAATCGCAACGCGA
4383970 TATTTAAAGC
Statistics
Matches: 149, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 148 0.99
21 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:4384387 original size:33 final size:33
Alignment explanation
Indices: 4384348--4384418 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
4384338 TTCACTTAGA
* *
4384348 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
4384381 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
4384414 TTTCA
1 TTTCA
4384419 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:4384555 original size:41 final size:38
Alignment explanation
Indices: 4384491--4384607 Score: 136
Period size: 41 Copynumber: 3.1 Consensus size: 38
4384481 TTCAATTTGC
* *
4384491 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
4384529 AGAATGACTGTCGCAACGAGAGAAATGACAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
4384570 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
4384603 AGAAT
1 AGAAT
4384608 CGCAACGCGA
Statistics
Matches: 69, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 32 0.46
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.11
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:4384571 original size:21 final size:21
Alignment explanation
Indices: 4384498--4384573 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
4384488 TGCAGAAGAG
* *
4384498 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGACAA
**
4384519 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGACAA
4384539 TCGCAACGAGAGAAATGACAA
1 TCGCAACGAGAGAAATGACAA
4384560 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
4384574 TCGCAACGCG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.45, C:0.18, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGACAA
Found at i:4384577 original size:14 final size:14
Alignment explanation
Indices: 4384558--4384614 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
4384548 GAGAAATGAC
4384558 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
4384572 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
4384591 AATCGCAACGAGAG
1 AATCGCAACGAGAG
4384605 AATCGCAACG
1 AATCGCAACG
4384615 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:4384595 original size:33 final size:33
Alignment explanation
Indices: 4384550--4384630 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
4384540 CGCAACGAGA
*
4384550 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
4384583 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
4384616 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
4384631 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:4384648 original size:19 final size:19
Alignment explanation
Indices: 4384626--4384723 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
4384616 GAAACCAAAA
*
4384626 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
4384645 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
4384659 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
4384678 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
4384692 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
4384711 TCGCGTTGCGATT
1 TCGCGTTGCGATT
4384724 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.33
16 4 0.07
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:4384667 original size:14 final size:14
Alignment explanation
Indices: 4384648--4384737 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
4384638 TTTCATTTCG
4384648 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
4384662 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
4384681 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
4384695 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
4384712 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
4384728 CGTTGCGATT
1 CGTTGCGATT
4384738 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 2 0.03
16 7 0.11
17 7 0.11
18 2 0.03
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:4384677 original size:33 final size:33
Alignment explanation
Indices: 4384631--4384745 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
4384621 CAAAATCGCA
*
4384631 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
4384664 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
4384697 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
4384730 TTGCGATTTTCATTTC
1 TTGCGATTGTCATTTC
4384746 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:4386706 original size:93 final size:93
Alignment explanation
Indices: 4386442--4386914 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
4386432 TAGATTGCTT
*
4386442 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4386507 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4386535 AGTAAATTTGTT-GGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4386599 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4386627 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4386692 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
4386720 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4386785 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4386813 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
4386878 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
4386906 AGTAAATTT
1 AGTAAATTT
4386915 ATCCATTCAA
Statistics
Matches: 376, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 92 0.24
93 284 0.76
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:4386998 original size:19 final size:19
Alignment explanation
Indices: 4386958--4387086 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
4386948 TAGTTTACTT
* *
4386958 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
4386978 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
4386997 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
4387016 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
4387030 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
4387049 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
4387063 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
4387082 TCGCA
1 TCGCA
4387087 TTGCGATTTC
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:4387037 original size:33 final size:32
Alignment explanation
Indices: 4386994--4387086 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
4386984 CGCGAAACCA
**
4386994 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
4387026 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
4387059 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
4387087 TTGCGATTTC
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:4387084 original size:52 final size:52
Alignment explanation
Indices: 4386958--4387086 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
4386948 TAGTTTACTT
**
4386958 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
4387010 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
4387063 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
4387087 TTGCGATTTC
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:4387140 original size:19 final size:19
Alignment explanation
Indices: 4387114--4387212 Score: 100
Period size: 19 Copynumber: 5.4 Consensus size: 19
4387104 GTTGATTCTT
4387114 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* *
4387133 CATTGCGA--TTC-TGT--
1 CGTTGCGATTTTCATTTCG
4387147 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
**
4387166 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTCATTTCG
*
4387185 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
4387205 TGTTGCGA
1 CGTTGCGA
4387213 AAGTAAACTA
Statistics
Matches: 65, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
14 7 0.11
16 5 0.08
17 5 0.08
19 36 0.55
20 12 0.18
ACGTcount: A:0.11, C:0.18, G:0.25, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:4387155 original size:33 final size:32
Alignment explanation
Indices: 4387087--4387175 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 32
4387077 CAAAATCGCA
4387087 TTGCGA-TTTCATTTCGCGTT--GATTCTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTTCG
*
4387116 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCT-TCG
4387149 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
4387176 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
29 6 0.11
30 13 0.24
32 6 0.11
33 29 0.54
ACGTcount: A:0.11, C:0.20, G:0.21, T:0.47
Consensus pattern (32 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTTCG
Found at i:4389154 original size:14 final size:14
Alignment explanation
Indices: 4389135--4389170 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
4389125 ATTGTTTAAT
4389135 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
4389149 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
4389163 TGATTTGT
1 TGATTTGT
4389171 GTAATTGATG
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:4389301 original size:19 final size:19
Alignment explanation
Indices: 4389277--4389376 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
4389267 AAAATTGACT
4389277 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4389296 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4389315 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4389329 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4389348 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
4389368 ATCGCAATG
1 ATCGCAATG
4389377 GGAGAATCGC
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 18 0.25
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4389406 original size:53 final size:53
Alignment explanation
Indices: 4389277--4389393 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
4389267 AAAATTGACT
4389277 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
* *
4389329 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAATGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
4389382 ATCGCAATGCGA
1 ATCGCAATGCGA
4389394 TTTTAATTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 29 0.47
53 33 0.53
ACGTcount: A:0.44, C:0.17, G:0.25, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:4389411 original size:19 final size:19
Alignment explanation
Indices: 4389383--4389531 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
4389373 AATGGGAGAA
* *
4389383 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
4389402 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
4389418 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
4389435 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
4389454 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
4389470 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
4389487 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
4389503 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
4389520 TCCGCATTGCGA
1 T-CGCATTGCGA
4389532 AATGTAATGG
Statistics
Matches: 107, Mismatches: 7, Indels: 31
0.74 0.05 0.21
Matches are distributed among these distances:
14 18 0.17
16 21 0.20
17 19 0.18
18 2 0.02
19 41 0.38
20 6 0.06
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:4389446 original size:52 final size:52
Alignment explanation
Indices: 4389383--4389499 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
4389373 AATGGGAGAA
*
4389383 TCGCAATGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* *
4389435 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
4389487 TCGCATTGCGATT
1 TCGCATTGCGATT
4389500 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:4389477 original size:33 final size:33
Alignment explanation
Indices: 4389440--4389531 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
4389430 TCATTTCGCA
4389440 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
4389473 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
4389506 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
4389532 AATGTAATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:4389478 original size:14 final size:14
Alignment explanation
Indices: 4389459--4389513 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
4389449 TCATTTCGCA
4389459 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
4389473 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
4389490 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
4389506 TTGCGATT
1 TTGCGATT
4389514 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:4389614 original size:19 final size:19
Alignment explanation
Indices: 4389590--4389687 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
4389580 AAAATTGACT
4389590 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4389609 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4389628 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4389642 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
4389661 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
4389681 ATCGCAA
1 ATCGCAA
4389688 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4389719 original size:53 final size:53
Alignment explanation
Indices: 4389590--4389703 Score: 221
Period size: 53 Copynumber: 2.2 Consensus size: 53
4389580 AAAATTGACT
4389590 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
4389642 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
4389695 ATCGCAATG
1 ATCGCAATG
4389704 TGATTTTCAT
Statistics
Matches: 61, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.48
53 32 0.52
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:4390843 original size:20 final size:20
Alignment explanation
Indices: 4390593--4390842 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
4390583 AAATTTCAGT
* * *
4390593 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
4390613 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
4390633 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
4390653 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
4390673 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
4390693 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
4390713 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
4390733 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
*
4390753 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
4390773 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
4390793 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
4390813 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
4390833 GTTGCGATTT
1 GTTGCGATTT
4390843 TGGAAAATCG
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:4398750 original size:209 final size:211
Alignment explanation
Indices: 4398390--4398810 Score: 819
Period size: 209 Copynumber: 2.0 Consensus size: 211
4398380 ATTCGATGAC
4398390 CCTGTCGATACGAAGAACCTGTTGGGACCGAAAAGGTACGAGGGACGATCCATAAACCTCGGAGA
1 CCTGTCGATACGAAGAACCTGTTGGGACCGAAAAGGTACGAGGGACGATCCATAAACCTCGGAGA
4398455 ATGAAGCAAAAACCCACCAGAGCTTCTTACAAGATGATGATCACCTTCATGGTCTTCTTCTGATC
66 ATGAAGCAAAAACCCACCAGAGCTTCTTACAAGATGATGATCACCTTCATGGTCTTCTTCTGATC
4398520 TAACCTGTAAACATCTCTTTTCGTTAA-C-CGTCATCCTCTTCGATATACAGCGACCTGAAATTC
131 TAACCTGTAAACATCTCTTTTCGTTAACCTCGTCATCCTCTTCGATATACAGCGACCTGAAATTC
4398583 TCAAAGAGAAAACGAT
196 TCAAAGAGAAAACGAT
4398599 CCTGTCGATACGAAGAACCTGTTGGGACCGAAAAGGTACGAGGGACGATCCATAAACCTCGGAGA
1 CCTGTCGATACGAAGAACCTGTTGGGACCGAAAAGGTACGAGGGACGATCCATAAACCTCGGAGA
*
4398664 CTGAAGCAAAAACCCACCAGAGCTTCTTACAAGATGATGATCACCTTCATGGTCTTCTTCTGATC
66 ATGAAGCAAAAACCCACCAGAGCTTCTTACAAGATGATGATCACCTTCATGGTCTTCTTCTGATC
4398729 TAACCTGTAAACATCTCTTTTCGTTAACCTCGTCATCCTCTTCGATATACAGCGACCTGAAATTC
131 TAACCTGTAAACATCTCTTTTCGTTAACCTCGTCATCCTCTTCGATATACAGCGACCTGAAATTC
4398794 TCAAAGAGAAAACGAT
196 TCAAAGAGAAAACGAT
4398810 C
1 C
4398811 AACATCCGCA
Statistics
Matches: 209, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
209 156 0.75
210 1 0.00
211 52 0.25
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (211 bp):
CCTGTCGATACGAAGAACCTGTTGGGACCGAAAAGGTACGAGGGACGATCCATAAACCTCGGAGA
ATGAAGCAAAAACCCACCAGAGCTTCTTACAAGATGATGATCACCTTCATGGTCTTCTTCTGATC
TAACCTGTAAACATCTCTTTTCGTTAACCTCGTCATCCTCTTCGATATACAGCGACCTGAAATTC
TCAAAGAGAAAACGAT
Found at i:4407489 original size:24 final size:23
Alignment explanation
Indices: 4407448--4407497 Score: 66
Period size: 22 Copynumber: 2.1 Consensus size: 23
4407438 TTTTAAGTAG
*
4407448 TAATTCTAAAAAATAATT-TTTT
1 TAATTATAAAAAATAATTATTTT
4407470 TAATTATATAAAAATAAATTATTTT
1 TAATTATA-AAAAAT-AATTATTTT
4407495 TAA
1 TAA
4407498 AATTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 7 0.29
23 6 0.25
24 4 0.17
25 7 0.29
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
TAATTATAAAAAATAATTATTTT
Found at i:4407504 original size:23 final size:23
Alignment explanation
Indices: 4407456--4407506 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 23
4407446 AGTAATTCTA
*
4407456 AAAAATAATTTTTTTAATTATAT
1 AAAAATAATTTTTTTAATAATAT
4407479 AAAAATAAATTATTTTTAA-AAT-T
1 AAAAAT-AATT-TTTTTAATAATAT
4407502 AAAAA
1 AAAAA
4407507 ATATTTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 12 0.48
24 6 0.24
25 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAAATAATTTTTTTAATAATAT
Found at i:4407506 original size:24 final size:23
Alignment explanation
Indices: 4407454--4407509 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
4407444 GTAGTAATTC
*
4407454 TAAAAAAT-AATTTTTTTAATTA
1 TAAAAAATAAATTTTTTTAAATA
4407476 TATAAAAATAAATTATTTTTAAA-A
1 TA-AAAAATAAATT-TTTTTAAATA
4407500 TTAAAAAATA
1 -TAAAAAATA
4407510 TTTTCAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 2 0.07
23 6 0.21
24 12 0.41
25 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
TAAAAAATAAATTTTTTTAAATA
Found at i:4408524 original size:24 final size:23
Alignment explanation
Indices: 4408497--4408543 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
4408487 AAATTTTATT
4408497 TATATAAATTATAAAA-ATAAAATG
1 TATAT-AA-TATAAAAGATAAAATG
4408521 TATATAATATAAAAGGATAAAAT
1 TATATAATATAAAA-GATAAAAT
4408544 AATATTATTG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
22 7 0.33
23 2 0.10
24 12 0.57
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (23 bp):
TATATAATATAAAAGATAAAATG
Found at i:4417440 original size:44 final size:44
Alignment explanation
Indices: 4417390--4417476 Score: 147
Period size: 44 Copynumber: 2.0 Consensus size: 44
4417380 CTAGCAAAGA
* *
4417390 AAAGTATGAATTGTGTATGATGCTTAGTCTGCTACAATGTCTTC
1 AAAGTATGAATTGTCTATGATGCTTAATCTGCTACAATGTCTTC
*
4417434 AAAGTATGAATTGTCTATGATGCTTAATCTGCTATAATGTCTT
1 AAAGTATGAATTGTCTATGATGCTTAATCTGCTACAATGTCTT
4417477 AGTGTCTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 40 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (44 bp):
AAAGTATGAATTGTCTATGATGCTTAATCTGCTACAATGTCTTC
Found at i:4417714 original size:15 final size:15
Alignment explanation
Indices: 4417691--4417721 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4417681 TAAAAAATGA
4417691 TTAAAATAATATATT
1 TTAAAATAATATATT
*
4417706 TTAACATAATATATT
1 TTAAAATAATATATT
4417721 T
1 T
4417722 ATAATTGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TTAAAATAATATATT
Found at i:4417754 original size:19 final size:19
Alignment explanation
Indices: 4417715--4417750 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
4417705 TTTAACATAA
*
4417715 TATATTTATAATTGTTTAT
1 TATATTTATAATTGTTAAT
4417734 TATATTTA-AATTGTTAA
1 TATATTTATAATTGTTAA
4417751 ATTAATATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TATATTTATAATTGTTAAT
Found at i:4417792 original size:41 final size:42
Alignment explanation
Indices: 4417706--4417811 Score: 112
Period size: 41 Copynumber: 2.5 Consensus size: 42
4417696 ATAATATATT
**
4417706 TTAACATAATATA-TTTATAAT-TGTTTATTATATTTAAATTG
1 TTAA-ATAATATATTTTATAATATGTTTATTATATTTAAATAA
* *
4417747 TTAAATTAATATATTTTATAATATTTTTA-TAT-TTTTAATAA
1 TTAAA-TAATATATTTTATAATATGTTTATTATATTTAAATAA
*
4417788 TTAAATAATGTATTTTAATAATAT
1 TTAAATAATATATTTT-ATAATAT
4417812 AAAAATAATT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
40 11 0.20
41 29 0.52
42 11 0.20
43 5 0.09
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.55
Consensus pattern (42 bp):
TTAAATAATATATTTTATAATATGTTTATTATATTTAAATAA
Found at i:4417824 original size:21 final size:20
Alignment explanation
Indices: 4417775--4417824 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
4417765 TAATATTTTT
4417775 ATATTTTTAATAATTAAATA
1 ATATTTTTAATAATTAAATA
*
4417795 ATGTATTTTAATAATATAAA-A
1 ATAT-TTTTAATAAT-TAAATA
4417816 ATAATTTTT
1 AT-ATTTTT
4417825 TTAAATATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 3 0.12
21 17 0.68
22 5 0.20
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATATTTTTAATAATTAAATA
Found at i:4419362 original size:2 final size:2
Alignment explanation
Indices: 4419355--4419385 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4419345 CCTCCCTTAA
4419355 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
4419386 ACACAGGCGG
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:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:4421231 original size:16 final size:16
Alignment explanation
Indices: 4421210--4421244 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4421200 TGACAGAGGG
4421210 TTTGTTGTTGTTGTT-C
1 TTTGTTG-TGTTGTTGC
4421226 TTTGTTGTGTTGTTGC
1 TTTGTTGTGTTGTTGC
4421242 TTT
1 TTT
4421245 AACAATAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.00, C:0.06, G:0.26, T:0.69
Consensus pattern (16 bp):
TTTGTTGTGTTGTTGC
Found at i:4425854 original size:69 final size:69
Alignment explanation
Indices: 4425773--4425912 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 69
4425763 TTACCATAGA
*
4425773 ACTTATAATTATATTTATACATGATCTGTAAAACGATTCAAGTAAACATACCCCAAATTTCTCAA
1 ACTTATAATTATATGTATACATGATCTGTAAAACGATTCAAGTAAACATACCCCAAATTTCTCAA
4425838 AATG
66 AATG
4425842 ACTTATAATTATATGTATACATGATCTGTAAAACGATTCAAGTAAACATACCCCAAATTTCTCAA
1 ACTTATAATTATATGTATACATGATCTGTAAAACGATTCAAGTAAACATACCCCAAATTTCTCAA
4425907 AATG
66 AATG
4425911 AC
1 AC
4425913 CAATCACAAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 70 1.00
ACGTcount: A:0.42, C:0.18, G:0.08, T:0.32
Consensus pattern (69 bp):
ACTTATAATTATATGTATACATGATCTGTAAAACGATTCAAGTAAACATACCCCAAATTTCTCAA
AATG
Found at i:4430840 original size:18 final size:18
Alignment explanation
Indices: 4430819--4430880 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 18
4430809 TTCTATTTTA
4430819 ATTTTAATTATTGTTAAT
1 ATTTTAATTATTGTTAAT
*
4430837 ATTTTATTTA-T-TTAAGT
1 ATTTTAATTATTGTTAA-T
* *
4430854 TTTTTAA-TATTAGTTTAT
1 ATTTTAATTATT-GTTAAT
4430872 ATTTTAATT
1 ATTTTAATT
4430881 TCTATAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
16 6 0.18
17 8 0.24
18 16 0.47
19 4 0.12
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.65
Consensus pattern (18 bp):
ATTTTAATTATTGTTAAT
Found at i:4435321 original size:60 final size:60
Alignment explanation
Indices: 4435225--4435340 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 60
4435215 TACGCTGTCA
* * * * * *
4435225 ACATTTAGGTCGAACAAGTTAGTAGTTGCATACCTTCCCCTTGAACTTGAAGGCATCTCG
1 ACATTGAGGTCGAAAAAGCTAGCAGTTGAATACCTTCCCCTAGAACTTGAAGGCATCTCG
* * *
4435285 ACATTGAGGTCGAAAAAGCTCGCAGTTGAATGCCTTCCCCTAGAGCTTGAAGGCAT
1 ACATTGAGGTCGAAAAAGCTAGCAGTTGAATACCTTCCCCTAGAACTTGAAGGCAT
4435341 TGTATTAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 47 1.00
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (60 bp):
ACATTGAGGTCGAAAAAGCTAGCAGTTGAATACCTTCCCCTAGAACTTGAAGGCATCTCG
Found at i:4438653 original size:40 final size:40
Alignment explanation
Indices: 4438598--4438673 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
4438588 CATATGTAAT
4438598 GGGGTGAGGGGAGGTAAGGTAGTAGGCTGCCTCCAACGCC
1 GGGGTGAGGGGAGGTAAGGTAGTAGGCTGCCTCCAACGCC
4438638 GGGGTGAGGGGAGGTAAGGTAGTAGGCTGCCTCCAA
1 GGGGTGAGGGGAGGTAAGGTAGTAGGCTGCCTCCAA
4438674 TGCCATGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.21, C:0.17, G:0.46, T:0.16
Consensus pattern (40 bp):
GGGGTGAGGGGAGGTAAGGTAGTAGGCTGCCTCCAACGCC
Found at i:4450925 original size:22 final size:22
Alignment explanation
Indices: 4450897--4450945 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
4450887 GACTGCCAGT
*
4450897 ATGTTTTCATATGCTTTATGGC
1 ATGTTTTCATATACTTTATGGC
* *
4450919 ATGTTTTCTTATACTTTTTGGC
1 ATGTTTTCATATACTTTATGGC
4450941 ATGTT
1 ATGTT
4450946 ATTCGGTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.16, C:0.12, G:0.16, T:0.55
Consensus pattern (22 bp):
ATGTTTTCATATACTTTATGGC
Found at i:4455224 original size:14 final size:14
Alignment explanation
Indices: 4455187--4455233 Score: 51
Period size: 15 Copynumber: 3.4 Consensus size: 14
4455177 TTTTTGTTTC
*
4455187 AATATAATTTTAA-
1 AATATTATTTTAAT
* *
4455200 AATTTTAATTTAATT
1 AATATTATTTTAA-T
4455215 AATATTATTTTAAT
1 AATATTATTTTAAT
4455229 AATAT
1 AATAT
4455234 ATTAATAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
13 10 0.37
14 6 0.22
15 11 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATATTATTTTAAT
Found at i:4458836 original size:19 final size:19
Alignment explanation
Indices: 4458814--4458860 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
4458804 ATTGGTCGTT
*
4458814 AAGTGCTCCATAGGTCACC
1 AAGTGCTCCATAAGTCACC
*
4458833 AAGTGCTCCATAAGTCACT
1 AAGTGCTCCATAAGTCACC
4458852 AAGTGCTCC
1 AAGTGCTCC
4458861 TTGCGACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (19 bp):
AAGTGCTCCATAAGTCACC
Found at i:4460395 original size:35 final size:34
Alignment explanation
Indices: 4460329--4460415 Score: 86
Period size: 35 Copynumber: 2.4 Consensus size: 34
4460319 TAGTATTTTT
* *
4460329 TAAATAGTTATTATATTTTATATTAATATATTTACG
1 TAAATA-TTATTAT-TTTTATATAAATATATTTACA
*
4460365 TAAATATTATTATTTTTAT-TAAAATAATATTTATA
1 TAAATATTATTATTTTTATAT-AAAT-ATATTTACA
*
4460400 TAATTATTATTTATTT
1 TAAATATTA-TTATTT
4460416 AGAATTATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
33 1 0.02
34 9 0.20
35 22 0.50
36 12 0.27
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.56
Consensus pattern (34 bp):
TAAATATTATTATTTTTATATAAATATATTTACA
Found at i:4460577 original size:17 final size:17
Alignment explanation
Indices: 4460555--4460608 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
4460545 AATGTTAATA
4460555 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
4460572 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
4460589 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
4460606 TTT
1 TTT
4460609 TTATAATATA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:4462165 original size:21 final size:21
Alignment explanation
Indices: 4462135--4462182 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
4462125 GCAGGGGTAC
* *
4462135 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
4462156 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
4462177 ATGCCA
1 ATGCCA
4462183 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:4462212 original size:21 final size:21
Alignment explanation
Indices: 4462186--4462258 Score: 112
Period size: 21 Copynumber: 3.5 Consensus size: 21
4462176 TATGCCATCT
*
4462186 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
4462207 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
4462228 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
4462249 CCGCAGGGTT
1 CCGCAGGGTT
4462259 TTATACCATA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
22 2 0.04
ACGTcount: A:0.18, C:0.34, G:0.27, T:0.21
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:4462809 original size:28 final size:28
Alignment explanation
Indices: 4462777--4462871 Score: 91
Period size: 28 Copynumber: 3.2 Consensus size: 28
4462767 GATAAATGTT
*
4462777 TTTAAAATACAAATTATATTATTCAAAA
1 TTTAAAATAAAAATTATATTATTCAAAA
*
4462805 TTTAAAATAAAAATAATATTATTCGAACATTAAA
1 TTTAAAATAAAAATTATATTATT----CA--AAA
* * *
4462839 TTTAAAATATAAATTATAGTATTCGAAA
1 TTTAAAATAAAAATTATATTATTCAAAA
4462867 TTTAA
1 TTTAA
4462872 CATTAAATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
28 29 0.53
30 1 0.02
32 2 0.04
34 23 0.42
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (28 bp):
TTTAAAATAAAAATTATATTATTCAAAA
Found at i:4462878 original size:34 final size:32
Alignment explanation
Indices: 4462778--4462878 Score: 95
Period size: 34 Copynumber: 3.2 Consensus size: 32
4462768 ATAAATGTTT
* *
4462778 TTAAAATACAAATTATATTATTCAAAATTTAAA
1 TTAAAATATAAATTATA-TATTCGAAATTTAAA
*
4462811 ATAAAA-AT-AA-TAT-TATTCGAACA-TTAAA
1 TTAAAATATAAATTATATATTCGAA-ATTTAAA
4462839 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATATAAATTATA-TATTCGAAATTTAA-A
4462874 TTAAA
1 TTAAA
4462879 TTTCAACTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 17
0.72 0.05 0.22
Matches are distributed among these distances:
28 12 0.22
29 6 0.11
30 5 0.09
31 4 0.07
32 4 0.07
33 6 0.11
34 17 0.31
35 1 0.02
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (32 bp):
TTAAAATATAAATTATATATTCGAAATTTAAA
Found at i:4463013 original size:15 final size:15
Alignment explanation
Indices: 4462995--4463024 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4462985 TTAACATATA
4462995 TGTTGAAAACATTTT
1 TGTTGAAAACATTTT
4463010 TGTTGAAAACATTTT
1 TGTTGAAAACATTTT
4463025 GATATTTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.13, T:0.47
Consensus pattern (15 bp):
TGTTGAAAACATTTT
Found at i:4463846 original size:128 final size:128
Alignment explanation
Indices: 4463686--4464179 Score: 767
Period size: 128 Copynumber: 3.8 Consensus size: 128
4463676 TTACCTGATT
*
4463686 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
4463751 TGACAAAATAATGGAAGGCGCGCCCCCAGGAATGCGCCTTCAAGTCCCCTGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
* * *
4463814 TACTAATATATATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGAAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
4463879 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
*
4463942 TACTGATATATCTAGTGTCCCCGAGGGACATGAGAGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * * *** * *
4464007 TGACAAAATAATGGAAGGCGAGCCCCCGGGAACGCGCATTCATGT-GAAT-AGTACTCCGATTAT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAG-A----AATAAT
4464070 AGG
126 AGG
*
4464073 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* *
4464138 TGACAAAATAATGGAAGGCGTGCCCCCGGGAATGCGCCTTCA
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCA
4464180 TGTGAATAGT
Statistics
Matches: 338, Mismatches: 23, Indels: 7
0.92 0.06 0.02
Matches are distributed among these distances:
126 2 0.01
127 2 0.01
128 225 0.67
131 109 0.32
ACGTcount: A:0.33, C:0.21, G:0.24, T:0.22
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGG
Found at i:4469379 original size:21 final size:21
Alignment explanation
Indices: 4469349--4469534 Score: 145
Period size: 21 Copynumber: 9.0 Consensus size: 21
4469339 GATTTACATA
* *
4469349 TTCGCATTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
4469370 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
*
4469391 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
4469410 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
4469433 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
4469452 TTCACGTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
*
4469475 TT--CGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
4469494 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
4469517 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
4469535 AATCGCAACT
Statistics
Matches: 132, Mismatches: 21, Indels: 26
0.74 0.12 0.15
Matches are distributed among these distances:
19 40 0.30
21 66 0.50
23 26 0.20
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:4469431 original size:42 final size:42
Alignment explanation
Indices: 4469355--4469531 Score: 313
Period size: 42 Copynumber: 4.3 Consensus size: 42
4469345 CATATTCGCA
4469355 TTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
4469395 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
* * *
4469437 TTGCGATAGTCCAAGTTCACGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
4469479 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
4469521 TTGCGATAGTC
1 TTGCGATAGTC
4469532 CAAAATCGCA
Statistics
Matches: 129, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
40 27 0.21
41 2 0.02
42 100 0.78
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:4470254 original size:19 final size:20
Alignment explanation
Indices: 4470230--4470284 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 20
4470220 TCATTGCGAT
4470230 TTTGGACTATCGCAA-CGAA
1 TTTGGACTATCGCAACCGAA
**
4470249 TTTGGAAAATCGCAACGCGAA
1 TTTGGACTATCGCAAC-CGAA
* *
4470270 CTTCGACTATCGCAA
1 TTTGGACTATCGCAA
4470285 TGCGAATATG
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 13 0.46
21 15 0.54
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (20 bp):
TTTGGACTATCGCAACCGAA
Found at i:4470330 original size:41 final size:40
Alignment explanation
Indices: 4470285--4470390 Score: 107
Period size: 41 Copynumber: 2.6 Consensus size: 40
4470275 ACTATCGCAA
*
4470285 TGCGAATATGTAAATCGCATTGCGATAGTCGAAGT-TCGCGT
1 TGCGAATATGTAAATCGCATTGCGATA-CCGAA-TATCGCGT
4470326 TGCGAATATAG-AAA-CTG-ATTTGCGATACCGAATATCGCGT
1 TGCGAATAT-GTAAATC-GCA-TTGCGATACCGAATATCGCGT
4470366 TGCGAATTAT-T-AATCGCATTGCGAT
1 TGCGAA-TATGTAAATCGCATTGCGAT
4470391 TTAGTTGGTC
Statistics
Matches: 56, Mismatches: 1, Indels: 18
0.75 0.01 0.24
Matches are distributed among these distances:
39 11 0.20
40 20 0.36
41 24 0.43
42 1 0.02
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (40 bp):
TGCGAATATGTAAATCGCATTGCGATACCGAATATCGCGT
Found at i:4471121 original size:325 final size:322
Alignment explanation
Indices: 4470743--4471395 Score: 1070
Period size: 325 Copynumber: 2.0 Consensus size: 322
4470733 GACTTTTAAA
4470743 ATTAATTGTTTAAAAATATATAAAAAATATTAAAATAAACTTTTAAATTTTTTAACAACAGTTAA
1 ATTAATTGTTTAAAAATATATAAAAAATATTAAAATAAACTTTTAAATTTTTTAACAACAGTTAA
4470808 TAATGTTTATTTATTTTTAATAAAATTAGAATTTAATATTTATTTTATATTTTTTAAAATTAATA
66 TAATGTTTATTTATTTTTAATAAAATTAGAATTTAATATTTATTTTATATTTTTTAAAATTAATA
4470873 TTATAAAGAATA-TTTTAAATAAAGA-TGTAATA-TTTTTAGCTTT-ATATTCTCTTTTTATTGA
131 TTATAAAGAATATTTTTAAATAAAGAGT-TAATATTTTTTAG-TTTCATATTCT-TTTTTATTGA
* *
4470934 ATTTT-ATTGATTTATTACATTTTTATTATTTTTTTAGAAAATTGAATAATAATTCATTTTATCT
193 ATTTTAATT--TTTATTACA-TTTT-TTA----TTTAAAAAAATGAATAATAATTCATTTTATCT
*
4470998 ATCAATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTT-ACAATTAATATTAAAATTCAA
250 ATCAATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAACAATTAATATTAAAAGTCAA
4471062 TAAACATT
315 TAAACATT
* *
4471070 ATTAATTGTTT-AAAA-ATATAAAAAATATTAAAATAAACTTTTAATTTTTTTAACAATAGTTAA
1 ATTAATTGTTTAAAAATATATAAAAAATATTAAAATAAACTTTTAAATTTTTTAACAACAGTTAA
*
4471133 TAATGTTTATTTATTTTTAATAAAATTATAATTTAATATTTATTTTATATTTTTTAAAATTAATA
66 TAATGTTTATTTATTTTTAATAAAATTAGAATTTAATATTTATTTTATATTTTTTAAAATTAATA
*
4471198 TTATAAAGAATATTTTTAAATAAAGAGTTGATATTTTTTAGTTTCATATTCTTTTTTATTGAATT
131 TTATAAAGAATATTTTTAAATAAAGAGTTAATATTTTTTAGTTTCATATTCTTTTTTATTGAATT
*
4471263 TTAATTTTTATTGCATTTTTTATTTAAAAAAATGAATAATAATTCATTTTATCTATCAATTGTAA
196 TTAATTTTTATTACATTTTTTATTTAAAAAAATGAATAATAATTCATTTTATCTATCAATTGTAA
4471328 TTAAAAGTTTATTTTAATATTTTTATATTTTTAAACAATTAATATTAAAAGTCAATAAACATT
261 TTAAAAGTTTATTTTAATATTTTTATATTTTT-AACAATTAATATTAAAAGTCAATAAACATT
4471391 ATTAA
1 ATTAA
4471396 CTATTATTAA
Statistics
Matches: 311, Mismatches: 8, Indels: 20
0.92 0.02 0.06
Matches are distributed among these distances:
319 73 0.23
321 33 0.11
323 3 0.01
324 4 0.01
325 130 0.42
326 39 0.13
327 29 0.09
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.51
Consensus pattern (322 bp):
ATTAATTGTTTAAAAATATATAAAAAATATTAAAATAAACTTTTAAATTTTTTAACAACAGTTAA
TAATGTTTATTTATTTTTAATAAAATTAGAATTTAATATTTATTTTATATTTTTTAAAATTAATA
TTATAAAGAATATTTTTAAATAAAGAGTTAATATTTTTTAGTTTCATATTCTTTTTTATTGAATT
TTAATTTTTATTACATTTTTTATTTAAAAAAATGAATAATAATTCATTTTATCTATCAATTGTAA
TTAAAAGTTTATTTTAATATTTTTATATTTTTAACAATTAATATTAAAAGTCAATAAACATT
Found at i:4478231 original size:3 final size:3
Alignment explanation
Indices: 4478223--4478252 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
4478213 CTGATGTTCA
4478223 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
4478253 TCTATACTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:4481206 original size:24 final size:24
Alignment explanation
Indices: 4481168--4481216 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
4481158 AATTTTAATA
4481168 AAAATAGTAATTATTAAAATATTTT
1 AAAATAGTAATTATTAAAA-ATTTT
* *
4481193 AAAAT-GTATTTATTAATAATTTT
1 AAAATAGTAATTATTAAAAATTTT
4481216 A
1 A
4481217 GACTTGGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 6 0.27
24 11 0.50
25 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (24 bp):
AAAATAGTAATTATTAAAAATTTT
Found at i:4485480 original size:104 final size:104
Alignment explanation
Indices: 4485300--4485501 Score: 404
Period size: 104 Copynumber: 1.9 Consensus size: 104
4485290 TACGTTTTAA
4485300 AAATAAATTATATTATTTTTGGTCTTATTGTTTGAAAGAAAAAGAATTGATTCAATGACACTATG
1 AAATAAATTATATTATTTTTGGTCTTATTGTTTGAAAGAAAAAGAATTGATTCAATGACACTATG
4485365 TTACAGAAGAAGAAGAAGGAGGAGGAGGAGGAGAAGAAG
66 TTACAGAAGAAGAAGAAGGAGGAGGAGGAGGAGAAGAAG
4485404 AAATAAATTATATTATTTTTGGTCTTATTGTTTGAAAGAAAAAGAATTGATTCAATGACACTATG
1 AAATAAATTATATTATTTTTGGTCTTATTGTTTGAAAGAAAAAGAATTGATTCAATGACACTATG
4485469 TTACAGAAGAAGAAGAAGGAGGAGGAGGAGGAG
66 TTACAGAAGAAGAAGAAGGAGGAGGAGGAGGAG
4485502 GAGGAGGAGG
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 98 1.00
ACGTcount: A:0.43, C:0.05, G:0.25, T:0.28
Consensus pattern (104 bp):
AAATAAATTATATTATTTTTGGTCTTATTGTTTGAAAGAAAAAGAATTGATTCAATGACACTATG
TTACAGAAGAAGAAGAAGGAGGAGGAGGAGGAGAAGAAG
Found at i:4485494 original size:6 final size:6
Alignment explanation
Indices: 4485485--4485727 Score: 180
Period size: 6 Copynumber: 40.3 Consensus size: 6
4485475 AAGAAGAAGA
* *
4485485 AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGA AGGAGA
1 AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG
* * * * * * * * * * *
4485533 AGAAGA AGGAGA AGAAGG AGCAGA AGAAGG AGAAGA AGGAGA AGAAGG
1 AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG
* * * * * * * * * *
4485581 AGGAGA AGGAGA AGAAGC AGAAGA AGGAGA AGGAGA AGGAGA AGGAGA
1 AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG
* * * * * * *
4485629 AGAAGG AGAAGG AGAAGG AGAAGG AGGAGA AGAAGG AGGAGA AGGAGG
1 AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG AGGAGG
* * *
4485677 AGAAGG AGAAGT AGGAGG AGGAGG AGGAGGG AGGAGG AGGAGG AGGAGG
1 AGGAGG AGGAGG AGGAGG AGGAGG AGGA-GG AGGAGG AGGAGG AGGAGG
4485726 AG
1 AG
4485728 TCATTGGTTC
Statistics
Matches: 204, Mismatches: 32, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
6 198 0.97
7 6 0.03
ACGTcount: A:0.46, C:0.01, G:0.53, T:0.00
Consensus pattern (6 bp):
AGGAGG
Found at i:4485497 original size:9 final size:9
Alignment explanation
Indices: 4485485--4485727 Score: 180
Period size: 9 Copynumber: 26.9 Consensus size: 9
4485475 AAGAAGAAGA
4485485 AGGAGGAGG
1 AGGAGGAGG
4485494 AGGAGGAGG
1 AGGAGGAGG
4485503 AGGAGGAGG
1 AGGAGGAGG
4485512 AGGAGGAGG
1 AGGAGGAGG
*
4485521 AGGAGAAGG
1 AGGAGGAGG
* * *
4485530 AGAAGAAGA
1 AGGAGGAGG
* *
4485539 AGGAGAAGA
1 AGGAGGAGG
* *
4485548 AGGAGCAGA
1 AGGAGGAGG
* *
4485557 AGAAGGAGA
1 AGGAGGAGG
* *
4485566 AGAAGGAGA
1 AGGAGGAGG
*
4485575 AGAAGGAGG
1 AGGAGGAGG
* *
4485584 AGAAGGAGA
1 AGGAGGAGG
* * *
4485593 AGAAGCAGA
1 AGGAGGAGG
* *
4485602 AGAAGGAGA
1 AGGAGGAGG
*
4485611 AGGAGAAGG
1 AGGAGGAGG
* *
4485620 AGAAGGAGA
1 AGGAGGAGG
* *
4485629 AGAAGGAGA
1 AGGAGGAGG
*
4485638 AGGAGAAGG
1 AGGAGGAGG
*
4485647 AGAAGGAGG
1 AGGAGGAGG
* *
4485656 AGAAGAAGG
1 AGGAGGAGG
*
4485665 AGGAGAAGG
1 AGGAGGAGG
*
4485674 AGGAGAAGG
1 AGGAGGAGG
* *
4485683 AGAAGTAGG
1 AGGAGGAGG
4485692 AGGAGGAGG
1 AGGAGGAGG
4485701 AGGAGGGAGG
1 AGGA-GGAGG
4485711 AGGAGGAGG
1 AGGAGGAGG
4485720 AGGAGGAG
1 AGGAGGAG
4485728 TCATTGGTTC
Statistics
Matches: 205, Mismatches: 28, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
9 196 0.96
10 9 0.04
ACGTcount: A:0.46, C:0.01, G:0.53, T:0.00
Consensus pattern (9 bp):
AGGAGGAGG
Found at i:4494400 original size:59 final size:59
Alignment explanation
Indices: 4494326--4494454 Score: 240
Period size: 59 Copynumber: 2.2 Consensus size: 59
4494316 GGCTTTAAAA
* *
4494326 CATCTCATAACTCTAAAACGTGCATCTTACCATGAAAATCTACTCAACATGTTCGATAT
1 CATCTCATAAGTCTAAAACGTGCATCTTACCATGAAAAGCTACTCAACATGTTCGATAT
4494385 CATCTCATAAGTCTAAAACGTGCATCTTACCATGAAAAGCTACTCAACATGTTCGATAT
1 CATCTCATAAGTCTAAAACGTGCATCTTACCATGAAAAGCTACTCAACATGTTCGATAT
4494444 CATCTCATAAG
1 CATCTCATAAG
4494455 ATCTCTTGTA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 68 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (59 bp):
CATCTCATAAGTCTAAAACGTGCATCTTACCATGAAAAGCTACTCAACATGTTCGATAT
Found at i:4495174 original size:32 final size:32
Alignment explanation
Indices: 4495136--4495202 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
4495126 GTCGGAGCCA
* * * *
4495136 GGTGGAGGGTATATATTTTTCGGGTCAGGTCG
1 GGTGGAGGATATAAAATTTTCAGGTCAGGTCG
*
4495168 GGTGGAGGATATAAAATTTTCAGGTCGGGTCG
1 GGTGGAGGATATAAAATTTTCAGGTCAGGTCG
4495200 GGT
1 GGT
4495203 TGACCAAAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.09, G:0.40, T:0.31
Consensus pattern (32 bp):
GGTGGAGGATATAAAATTTTCAGGTCAGGTCG
Found at i:4498120 original size:15 final size:15
Alignment explanation
Indices: 4498097--4498129 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4498087 TAGGAATGGG
*
4498097 TAAATTCAATTTATA
1 TAAAATCAATTTATA
4498112 TAAAATCAATTTATA
1 TAAAATCAATTTATA
4498127 TAA
1 TAA
4498130 TGAATTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATCAATTTATA
Found at i:4498523 original size:16 final size:16
Alignment explanation
Indices: 4498502--4498535 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
4498492 TTACTATTCA
*
4498502 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
4498518 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
4498534 CG
1 CG
4498536 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:4507418 original size:24 final size:24
Alignment explanation
Indices: 4507391--4507442 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
4507381 GTTCGTGAAC
4507391 GTTCAATTATATTCGTTCAGTTAT
1 GTTCAATTATATTCGTTCAGTTAT
** * * *
4507415 GTTCGTTTATGTTTGTTCGGTTAT
1 GTTCAATTATATTCGTTCAGTTAT
4507439 GTTC
1 GTTC
4507443 GTTCATGTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.12, G:0.19, T:0.54
Consensus pattern (24 bp):
GTTCAATTATATTCGTTCAGTTAT
Found at i:4507443 original size:24 final size:24
Alignment explanation
Indices: 4507405--4507465 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
4507395 AATTATATTC
*
4507405 GTTCAGTTATGTTCGTTTATGTTT
1 GTTCAGTTATGTTCGTTCATGTTT
* *
4507429 GTTCGGTTATGTTCGTTCATGTTC
1 GTTCAGTTATGTTCGTTCATGTTT
* *
4507453 ATTCATTTATGTT
1 GTTCAGTTATGTT
4507466 TAAGCCAATC
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.13, C:0.11, G:0.20, T:0.56
Consensus pattern (24 bp):
GTTCAGTTATGTTCGTTCATGTTT
Found at i:4508148 original size:16 final size:16
Alignment explanation
Indices: 4508129--4508187 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
4508119 CCAATGTTTA
4508129 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
4508145 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
4508161 TGGTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
4508177 TGTTCGTTTAT
1 TGTTCGTTTAT
4508188 TTATTAAATG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.08, C:0.10, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:4511470 original size:21 final size:21
Alignment explanation
Indices: 4511381--4511473 Score: 57
Period size: 21 Copynumber: 4.4 Consensus size: 21
4511371 CAACCATTTT
* *
4511381 AGATGTCACTGCAGTTGGGTC
1 AGATGCCACTGCAGTCGGGTC
* * ***
4511402 AGACGCCACTGC-TTCCATATC
1 AGATGCCACTGCAGT-CGGGTC
4511423 AGATGCCACTGCAGTCGGGTC
1 AGATGCCACTGCAGTCGGGTC
* *
4511444 ATATGCCA-TCGCAG-CTGGTTC
1 AGATGCCACT-GCAGTC-GGGTC
4511465 AGATGCCAC
1 AGATGCCAC
4511474 CGTCGTAGGT
Statistics
Matches: 52, Mismatches: 15, Indels: 9
0.68 0.20 0.12
Matches are distributed among these distances:
20 3 0.06
21 48 0.92
22 1 0.02
ACGTcount: A:0.22, C:0.29, G:0.26, T:0.24
Consensus pattern (21 bp):
AGATGCCACTGCAGTCGGGTC
Found at i:4516004 original size:85 final size:83
Alignment explanation
Indices: 4515900--4516065 Score: 271
Period size: 85 Copynumber: 2.0 Consensus size: 83
4515890 GGTTTCTGCA
*
4515900 CCTTTTAAATTCTTGACTCTCTCTTATTA-TAACACCCAACTACATACATTGTAATTCGTGCAAT
1 CCTTTTAAATTCTTGACTCTCTCTTATTACAAACACCCAACTACATACATTGTAATTCGTGC-A-
4515964 TTTTTTTCTTCCGCTTATTTT
64 -TTTTTTCTTCCGCTTATTTT
*
4515985 CCTTTTAAATTCTTGACTCTCTCTTATTACAAACACCCAAGTACATACATTGTAATTCGTGCATT
1 CCTTTTAAATTCTTGACTCTCTCTTATTACAAACACCCAACTACATACATTGTAATTCGTGCATT
*
4516050 TTTTCTTCTGCTTATT
66 TTTTCTTCCGCTTATT
4516066 CACTATTCCT
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
83 17 0.22
85 30 0.39
86 30 0.39
ACGTcount: A:0.24, C:0.23, G:0.07, T:0.46
Consensus pattern (83 bp):
CCTTTTAAATTCTTGACTCTCTCTTATTACAAACACCCAACTACATACATTGTAATTCGTGCATT
TTTTCTTCCGCTTATTTT
Found at i:4520394 original size:2 final size:2
Alignment explanation
Indices: 4520387--4520445 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
4520377 ATAATAACAT
4520387 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
4520429 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
4520446 CCACAATTAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4520937 original size:35 final size:35
Alignment explanation
Indices: 4520891--4520978 Score: 167
Period size: 35 Copynumber: 2.5 Consensus size: 35
4520881 GGTATTTATT
4520891 AGTAATTATTATTATATATATATTTTTTGATACAC
1 AGTAATTATTATTATATATATATTTTTTGATACAC
*
4520926 AGTAATTATTATTATGTATATATTTTTTGATACAC
1 AGTAATTATTATTATATATATATTTTTTGATACAC
4520961 AGTAATTATTATTATATA
1 AGTAATTATTATTATATA
4520979 AAAGAAAACC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 51 1.00
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.51
Consensus pattern (35 bp):
AGTAATTATTATTATATATATATTTTTTGATACAC
Found at i:4530708 original size:59 final size:57
Alignment explanation
Indices: 4530645--4530786 Score: 137
Period size: 58 Copynumber: 2.4 Consensus size: 57
4530635 TAAATATTTG
** *
4530645 ATGCTTTGGGGTTTAACCTAAGAAAAATAACATCACGTGGAGAGCGTTGC-GAAGGCTTA
1 ATGC-TTGGGGTTTAA-CTAAGAAAAATAACATCAC-TGGAGAGCAATGCAAAAGGCTTA
* * * *
4530704 ATGCTCTGGGGTTTGAACT-AGAAAACTAACGTCACTGGGGCGCAATGCAAAAGGCTTA
1 ATGCT-TGGGGTTT-AACTAAGAAAAATAACATCACTGGAGAGCAATGCAAAAGGCTTA
*
4530762 ATGC-TGGGGATTAAGCTAAGAAAAA
1 ATGCTTGGGGTTTAA-CTAAGAAAAA
4530787 AACTAACGTT
Statistics
Matches: 69, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
55 2 0.03
56 9 0.13
57 15 0.22
58 27 0.39
59 14 0.20
60 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.23
Consensus pattern (57 bp):
ATGCTTGGGGTTTAACTAAGAAAAATAACATCACTGGAGAGCAATGCAAAAGGCTTA
Found at i:4535734 original size:3 final size:3
Alignment explanation
Indices: 4535726--4535751 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4535716 CAACACCCTC
4535726 TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TC
4535752 ATCGTCTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
TCT
Found at i:4538192 original size:29 final size:29
Alignment explanation
Indices: 4538149--4538258 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
4538139 TTTTATATGT
4538149 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
4538177 TCATGTAGTTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
4538206 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
*
4538235 TCATGTAGTTCATGTCATGTTCTC
1 TCATGTAGCTCATGTCAT-TTCTC
4538259 ATATCACATA
Statistics
Matches: 77, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
28 7 0.09
29 65 0.84
30 5 0.06
ACGTcount: A:0.17, C:0.20, G:0.16, T:0.46
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:4539950 original size:19 final size:19
Alignment explanation
Indices: 4539884--4539951 Score: 52
Period size: 22 Copynumber: 3.5 Consensus size: 19
4539874 TATATTATTT
*
4539884 TAATATCATTTTAATAA-A
1 TAATATAATTTTAATAATA
4539902 -AATATTAATTATTAA-AATA
1 TAATA-TAATT-TTAATAATA
*
4539921 TCTATTGATAATTTTAATAATA
1 --TAAT-ATAATTTTAATAATA
4539943 TAATATAAT
1 TAATATAAT
4539952 ATTTTATTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 15
0.68 0.05 0.26
Matches are distributed among these distances:
17 4 0.10
18 6 0.15
19 10 0.26
20 3 0.08
21 4 0.10
22 11 0.28
23 1 0.03
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (19 bp):
TAATATAATTTTAATAATA
Found at i:4539955 original size:21 final size:21
Alignment explanation
Indices: 4539931--4540030 Score: 60
Period size: 21 Copynumber: 4.5 Consensus size: 21
4539921 TCTATTGATA
4539931 ATTTTAATAATATAATATAAT
1 ATTTTAATAATATAATATAAT
* ** *
4539952 ATTTTATTGTTATAATTATATT
1 ATTTTAATAATATAA-TATAAT
* *
4539974 ATTATAATATATAATATTATAATCTT
1 ATTTTAATA-AT-ATAATATAA---T
4540000 ATTTTAATAATAT-ATA-ATAT
1 ATTTTAATAATATAATATA-AT
4540020 ATTATTAATAA
1 ATT-TTAATAA
4540031 AATTATTATT
Statistics
Matches: 59, Mismatches: 12, Indels: 16
0.68 0.14 0.18
Matches are distributed among these distances:
20 4 0.07
21 19 0.32
22 12 0.20
23 8 0.14
24 5 0.08
25 2 0.03
26 9 0.15
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (21 bp):
ATTTTAATAATATAATATAAT
Found at i:4539993 original size:29 final size:29
Alignment explanation
Indices: 4539961--4540019 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 29
4539951 TATTTTATTG
4539961 TTATAAT-TATATTATT-ATAATATATAATA
1 TTATAATCT-TATT-TTAATAATATATAATA
4539990 TTATAATCTTATTTTAATAATATATAATA
1 TTATAATCTTATTTTAATAATATATAATA
4540019 T
1 T
4540020 ATTATTAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
28 2 0.07
29 25 0.89
30 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATAATCTTATTTTAATAATATATAATA
Found at i:4540097 original size:21 final size:20
Alignment explanation
Indices: 4540073--4540169 Score: 62
Period size: 21 Copynumber: 4.8 Consensus size: 20
4540063 ATATTATCGA
4540073 ATTGTTGAATATTTAATATAT
1 ATTGTT-AATATTTAATATAT
* *
4540094 ATTGTTTAAAATATAATATAGT
1 ATTG-TTAATATTTAATATA-T
*
4540116 ATTCTT-AT-TTTAATATTAT
1 ATTGTTAATATTTAATA-TAT
4540135 AATT-TTAATATTTTAATA-AT
1 -ATTGTTAATA-TTTAATATAT
*
4540155 ATTCTT-AT-TTTAATA
1 ATTGTTAATATTTAATA
4540170 AATAATTAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 20
0.72 0.06 0.23
Matches are distributed among these distances:
17 7 0.11
19 14 0.22
20 12 0.19
21 17 0.27
22 13 0.21
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (20 bp):
ATTGTTAATATTTAATATAT
Found at i:4540125 original size:39 final size:39
Alignment explanation
Indices: 4540084--4540202 Score: 110
Period size: 39 Copynumber: 3.2 Consensus size: 39
4540074 TTGTTGAATA
*
4540084 TTTAATA-TATATTGTTTAA-AATATAATATAGTATTCTTAT
1 TTTAATATTATAAT-TTTAATAATATAATA-A-TATTCTTAT
* *
4540124 TTTAATATTATAATTTTAATATTTTAATAATATTCTTAT
1 TTTAATATTATAATTTTAATAATATAATAATATTCTTAT
* *
4540163 TTTAATA-AATAA--TTAATAATAT-AT--TATTCTCAT
1 TTTAATATTATAATTTTAATAATATAATAATATTCTTAT
4540196 TTTAATA
1 TTTAATA
4540203 AAAATTAATA
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
33 15 0.21
35 2 0.03
36 8 0.11
38 4 0.06
39 16 0.23
40 13 0.19
41 12 0.17
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (39 bp):
TTTAATATTATAATTTTAATAATATAATAATATTCTTAT
Found at i:4540163 original size:17 final size:17
Alignment explanation
Indices: 4540115--4540170 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 17
4540105 TATAATATAG
4540115 TATTCTTATTTTAATATTA
1 TATTCTTATTTTAATA--A
*
4540134 TAATTTTAATATTTTAATAA
1 T-ATTCT--TATTTTAATAA
4540154 TATTCTTATTTTAATAA
1 TATTCTTATTTTAATAA
4540171 ATAATTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
17 11 0.34
19 5 0.16
20 6 0.19
22 10 0.31
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTCTTATTTTAATAA
Found at i:4540168 original size:14 final size:14
Alignment explanation
Indices: 4540115--4540169 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
4540105 TATAATATAG
4540115 TATTCTTATTTTAA
1 TATTCTTATTTTAA
* *
4540129 TATTATAATTTTAA
1 TATTCTTATTTTAA
*
4540143 TATT-TTA--ATAA
1 TATTCTTATTTTAA
4540154 TATTCTTATTTTAA
1 TATTCTTATTTTAA
4540168 TA
1 TA
4540170 AATAATTAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
11 7 0.21
12 3 0.09
13 2 0.06
14 21 0.64
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (14 bp):
TATTCTTATTTTAA
Found at i:4540179 original size:25 final size:26
Alignment explanation
Indices: 4540125--4540185 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 26
4540115 TATTCTTATT
**
4540125 TTAATATTATAATTTTAATATTTTAA
1 TTAATATTATAATTTTAATATAATAA
* *
4540151 -TAATATTCTTATTTTAATA-AATAA
1 TTAATATTATAATTTTAATATAATAA
*
4540175 TTAATAATATA
1 TTAATATTATA
4540186 TTATTCTCAT
Statistics
Matches: 27, Mismatches: 7, Indels: 3
0.73 0.19 0.08
Matches are distributed among these distances:
24 3 0.11
25 24 0.89
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TTAATATTATAATTTTAATATAATAA
Found at i:4540182 original size:72 final size:69
Alignment explanation
Indices: 4540106--4540297 Score: 178
Period size: 69 Copynumber: 2.7 Consensus size: 69
4540096 TGTTTAAAAT
*
4540106 ATAATATAGTATTCTTATTTTAATATTATAATTTTAATATTTTAATAATATTCTTATTTTAATAA
1 ATAATATAATATTCTTATTTTAATATTATAA-TTTAATATTTTAATAATATT-TTATTTTAATAA
4540171 ATA-ATTA
64 A-ACA-TA
* * *
4540178 ATAATATATTATTCTCATTTTAATA--A-AAATTAATATAATTT-ATAATAATTTTATTTTAATA
1 ATAATATAATATTCTTATTTTAATATTATAATTTAATAT--TTTAATAAT-ATTTTATTTTAATA
4540239 AAACATA
63 AAACATA
* * * * *
4540246 ATAATCGTAATATTTTTATGTGTAAAATTATAGATATAATATTTTAATAATA
1 ATAAT-ATAATATTCTTAT-TTTAATATTATA-ATTTAATATTTTAATAATA
4540298 ATATGACATA
Statistics
Matches: 98, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
68 15 0.15
69 30 0.31
70 12 0.12
72 28 0.29
73 6 0.06
74 7 0.07
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (69 bp):
ATAATATAATATTCTTATTTTAATATTATAATTTAATATTTTAATAATATTTTATTTTAATAAAA
CATA
Found at i:4540192 original size:33 final size:33
Alignment explanation
Indices: 4540106--4540240 Score: 112
Period size: 36 Copynumber: 3.8 Consensus size: 33
4540096 TGTTTAAAAT
* *
4540106 ATAATATAGTATTCTTATTTTAATATTATAATTTTA
1 ATAATATAATATTCTTATTTTAATA-AATAA--TTA
*
4540142 ATATTTTAATAATATTCTTATTTTAATAAATAATTA
1 ATA--AT-ATAATATTCTTATTTTAATAAATAATTA
* *
4540178 ATAATATATTATTCTCATTTTAATAAA-AATTAA
1 ATAATATAATATTCTTATTTTAATAAATAATT-A
4540211 TATAATTTATAATAATT-TTATTTTAATAAA
1 -ATAA--TATAAT-ATTCTTATTTTAATAAA
4540241 ACATAATAAT
Statistics
Matches: 83, Mismatches: 8, Indels: 16
0.78 0.07 0.15
Matches are distributed among these distances:
32 4 0.05
33 21 0.25
34 5 0.06
36 26 0.31
37 3 0.04
38 5 0.06
39 19 0.23
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (33 bp):
ATAATATAATATTCTTATTTTAATAAATAATTA
Found at i:4540240 original size:69 final size:71
Alignment explanation
Indices: 4540106--4540240 Score: 172
Period size: 72 Copynumber: 1.9 Consensus size: 71
4540096 TGTTTAAAAT
* *
4540106 ATAATATAGTATTCTTATTTTAATATTATAATTTTAATATTTTAATAATATTCTTATTTTAATAA
1 ATAATATAGTATTCTCATTTTAATA-TATAATATTAATATTTTAATAATATTCTTATTTTAATAA
4540171 ATAATTA
65 ATAATTA
*
4540178 ATAATATATTATTCTCATTTTAATA-A-AA-ATTAATATAATTT-ATAATAATT-TTATTTTAAT
1 ATAATATAGTATTCTCATTTTAATATATAATATTAATAT--TTTAATAAT-ATTCTTATTTTAAT
4540238 AAA
63 AAA
4540241 ACATAATAAT
Statistics
Matches: 57, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
68 7 0.12
69 20 0.35
70 7 0.12
72 23 0.40
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.52
Consensus pattern (71 bp):
ATAATATAGTATTCTCATTTTAATATATAATATTAATATTTTAATAATATTCTTATTTTAATAAA
TAATTA
Found at i:4540263 original size:33 final size:32
Alignment explanation
Indices: 4540150--4540264 Score: 108
Period size: 33 Copynumber: 3.4 Consensus size: 32
4540140 TAATATTTTA
4540150 ATAATATTCTTATTTTAATAAATAATTAATAAT
1 ATAATATTCTTATTTTAATAAA-AATTAATAAT
* *
4540183 ATATTATTCTCATTTTAATAAAAATTAATATAATTT
1 ATAATATTCTTATTTTAATAAAAATT-A-ATAA--T
4540219 ATAATAATT-TTATTTTAATAAAACA-TAATAAT
1 ATAAT-ATTCTTATTTTAATAAAA-ATTAATAAT
* *
4540251 CGTAATATTTTTAT
1 -ATAATATTCTTAT
4540265 GTGTAAAATT
Statistics
Matches: 69, Mismatches: 5, Indels: 16
0.77 0.06 0.18
Matches are distributed among these distances:
32 8 0.12
33 29 0.42
34 8 0.12
35 1 0.01
36 19 0.28
37 4 0.06
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (32 bp):
ATAATATTCTTATTTTAATAAAAATTAATAAT
Found at i:4540474 original size:38 final size:38
Alignment explanation
Indices: 4540432--4540507 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
4540422 CATCCAATGA
4540432 AAAATGAATTACACAACGTCATCCAAACACCGTAAGAT
1 AAAATGAATTACACAACGTCATCCAAACACCGTAAGAT
* *
4540470 AAAATGAATTACACGACGTCATCCAAACACTGTAAGAT
1 AAAATGAATTACACAACGTCATCCAAACACCGTAAGAT
4540508 GATCTTCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.46, C:0.22, G:0.12, T:0.20
Consensus pattern (38 bp):
AAAATGAATTACACAACGTCATCCAAACACCGTAAGAT
Found at i:4541167 original size:2 final size:2
Alignment explanation
Indices: 4541160--4541234 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
4541150 TTGAGTCTCT
4541160 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
4541202 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4541235 CTCAGTCCAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:4544454 original size:3 final size:3
Alignment explanation
Indices: 4544446--4544480 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
4544436 TTATCAGAAT
4544446 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
4544481 AAAATTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:4547883 original size:15 final size:15
Alignment explanation
Indices: 4547863--4547893 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4547853 GTTTCATGTT
4547863 GAAATATTCTTGAGG
1 GAAATATTCTTGAGG
4547878 GAAATATTCTTGAGG
1 GAAATATTCTTGAGG
4547893 G
1 G
4547894 GTGGTAGGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.29, T:0.32
Consensus pattern (15 bp):
GAAATATTCTTGAGG
Found at i:4558353 original size:31 final size:29
Alignment explanation
Indices: 4558285--4558354 Score: 70
Period size: 31 Copynumber: 2.2 Consensus size: 29
4558275 ACTATTGTTT
*
4558285 TTATAATTTTATTAATAAAAATATTAATAT
1 TTAT-ATTTTATTAATAAAAATATTAATAA
4558315 TGGTATATTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTATT--AATAAAAATATTAAT-AA
4558348 TTATATT
1 TTATATT
4558355 AATTATTTAT
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
30 1 0.03
31 14 0.41
32 5 0.15
33 14 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (29 bp):
TTATATTTTATTAATAAAAATATTAATAA
Found at i:4558434 original size:23 final size:23
Alignment explanation
Indices: 4558385--4558435 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
4558375 GTGTTCTATT
**
4558385 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
4558408 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
4558431 ATATT
1 ATATT
4558436 ATTATATTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:4558571 original size:29 final size:29
Alignment explanation
Indices: 4558546--4558639 Score: 82
Period size: 29 Copynumber: 3.2 Consensus size: 29
4558536 ATTAATAATT
4558546 TATTATATATTATTAAAATAAAAATATAA
1 TATTATATATTATTAAAATAAAAATATAA
* * ** *
4558575 TATTTTATATTATTATAATATAATTTATTA
1 TATTATATATTATTAAAATA-AAAATATAA
* * *
4558605 TTTTATTATAATATTTAAAAT-ATAATATAA
1 TATTA-TATATTA-TTAAAATAAAAATATAA
4558635 TATTA
1 TATTA
4558640 ATAAATATAT
Statistics
Matches: 48, Mismatches: 14, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
29 18 0.38
30 18 0.38
31 6 0.12
32 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TATTATATATTATTAAAATAAAAATATAA
Found at i:4558598 original size:23 final size:23
Alignment explanation
Indices: 4558568--4558618 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
4558558 TTAAAATAAA
4558568 AATATAATATT-TTATATTATTAT
1 AATATAAT-TTATTATATTATTAT
*
4558591 AATATAATTTATTATTTTATTAT
1 AATATAATTTATTATATTATTAT
4558614 AATAT
1 AATAT
4558619 TTAAAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 2 0.08
23 24 0.92
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AATATAATTTATTATATTATTAT
Found at i:4558635 original size:19 final size:20
Alignment explanation
Indices: 4558611--4558648 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
4558601 ATTATTTTAT
*
4558611 TATAATATTTA-AAATATAA
1 TATAATATTAATAAATATAA
4558630 TATAATATTAATAAATATA
1 TATAATATTAATAAATATA
4558649 TTTTAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATAATATTAATAAATATAA
Done.