Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 8 of 335
Found at i:2757453 original size:18 final size:17
Alignment explanation
Indices: 2757432--2757465 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2757422 TATAATATTT
2757432 AAAATAAATAAAAGAAAC
1 AAAATAAA-AAAAGAAAC
*
2757450 AAAATAGAAAAAGAAA
1 AAAATAAAAAAAGAAA
2757466 GAACAGAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.03, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAATAAAAAAAGAAAC
Found at i:2757514 original size:33 final size:33
Alignment explanation
Indices: 2757442--2757519 Score: 79
Period size: 33 Copynumber: 2.4 Consensus size: 33
2757432 AAAATAAATA
* *
2757442 AAAG-AAACAAAATAGAAAAAGAAAGAACAGAG
1 AAAGAAAACGAAATAGAAAAAGAAAGAAAAGAG
* * *
2757474 AATGAAAACGAAATAG-AAAGGAAAGAAAAAGGG
1 AAAGAAAACGAAATAGAAAAAGAAAG-AAAAGAG
*
2757507 AAAGAAAAAGAAA
1 AAAGAAAACGAAA
2757520 GGAAAAACAG
Statistics
Matches: 37, Mismatches: 7, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
32 11 0.30
33 26 0.70
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.04
Consensus pattern (33 bp):
AAAGAAAACGAAATAGAAAAAGAAAGAAAAGAG
Found at i:2757525 original size:10 final size:10
Alignment explanation
Indices: 2757442--2757526 Score: 55
Period size: 11 Copynumber: 7.9 Consensus size: 10
2757432 AAAATAAATA
2757442 AAAGAAACAA-
1 AAAGAAA-AAG
2757452 AATAGAAAAAG
1 AA-AGAAAAAG
*
2757463 AAAGAACAGAG
1 AAAGAA-AAAG
* *
2757474 AATGAAAACG
1 AAAGAAAAAG
* *
2757484 AAATAGAAAGG
1 AAAGA-AAAAG
2757495 AAAGAAAAAGGG
1 AAAGAAAAA--G
2757507 AAAGAAAAAG
1 AAAGAAAAAG
2757517 AAAGGAAAAA
1 AAA-GAAAAA
2757527 CAGGGTTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
10 20 0.34
11 29 0.49
12 10 0.17
ACGTcount: A:0.71, C:0.04, G:0.22, T:0.04
Consensus pattern (10 bp):
AAAGAAAAAG
Found at i:2758668 original size:54 final size:56
Alignment explanation
Indices: 2758605--2758731 Score: 170
Period size: 61 Copynumber: 2.2 Consensus size: 56
2758595 CAACTCATTC
2758605 AATTTTTATCATC-T-CAATTAGCTTTTCAAATAAATTCACAACCATTTAAATAAT
1 AATTTTTATCATCTTACAATTAGCTTTTCAAATAAATTCACAACCATTTAAATAAT
*
2758659 AATTTTTATCATCTATTAACCCAATTAGCTTTTCAAATAAATTCACAATCATTTAAATAAT
1 AATTTTTATCATC--TT-A--CAATTAGCTTTTCAAATAAATTCACAACCATTTAAATAAT
2758720 AATATTTT-TCAT
1 AAT-TTTTATCAT
2758732 TCATATGTCT
Statistics
Matches: 64, Mismatches: 1, Indels: 9
0.86 0.01 0.12
Matches are distributed among these distances:
54 13 0.20
57 1 0.02
61 46 0.72
62 4 0.06
ACGTcount: A:0.40, C:0.16, G:0.02, T:0.43
Consensus pattern (56 bp):
AATTTTTATCATCTTACAATTAGCTTTTCAAATAAATTCACAACCATTTAAATAAT
Found at i:2758891 original size:18 final size:18
Alignment explanation
Indices: 2758870--2758994 Score: 92
Period size: 18 Copynumber: 6.9 Consensus size: 18
2758860 AGTCACTCTT
*
2758870 TAACAGTCAGTTATTCAG
1 TAACAGTCAATTATTCAG
*
2758888 TAAC-GATAAATTATTCAG
1 TAACAG-TCAATTATTCAG
* *
2758906 TAACAATCAATTATTAAG
1 TAACAGTCAATTATTCAG
* ** **
2758924 TAACAATCTTTTACACAG
1 TAACAGTCAATTATTCAG
* *
2758942 TAGCAGTCAGTTA-TCTAG
1 TAACAGTCAATTATTC-AG
* *
2758960 TTACAGTCAGTTATTCAG
1 TAACAGTCAATTATTCAG
*
2758978 TAGCAGTCAATTATTCA
1 TAACAGTCAATTATTCA
2758995 ATACATTTAT
Statistics
Matches: 83, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
17 2 0.02
18 79 0.95
19 2 0.02
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (18 bp):
TAACAGTCAATTATTCAG
Found at i:2759192 original size:45 final size:46
Alignment explanation
Indices: 2759110--2759218 Score: 157
Period size: 45 Copynumber: 2.3 Consensus size: 46
2759100 CCGTAACGGT
*
2759110 AACAGTAACAGTAGCGGTACACAGAGTACCTCATCGGAACAAATCCGG
1 AACAGTAACAGTA-AGGTA-ACAGAGTACCTCATCGGAACAAATCCGG
* *
2759158 AACAGTAACAGTAAGGT-ACAGAGTACCTCTTCGGAACGAATCCGG
1 AACAGTAACAGTAAGGTAACAGAGTACCTCATCGGAACAAATCCGG
*
2759203 AATAGTAACAGTAAGG
1 AACAGTAACAGTAAGG
2759219 CGACACTTAT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
45 41 0.72
47 3 0.05
48 13 0.23
ACGTcount: A:0.39, C:0.21, G:0.24, T:0.17
Consensus pattern (46 bp):
AACAGTAACAGTAAGGTAACAGAGTACCTCATCGGAACAAATCCGG
Found at i:2760227 original size:20 final size:18
Alignment explanation
Indices: 2760198--2760242 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 18
2760188 AACGAAAAGC
2760198 AGGG-AAAGAAAGAAAGAA
1 AGGGAAAAGAAAG-AAGAA
2760216 AGGAGAAAAGAAAGAAGAA
1 AGG-GAAAAGAAAGAAGAA
2760235 AGGGAAAA
1 AGGGAAAA
2760243 TTGAAGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.32
19 9 0.36
20 8 0.32
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (18 bp):
AGGGAAAAGAAAGAAGAA
Found at i:2762626 original size:14 final size:15
Alignment explanation
Indices: 2762601--2762631 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2762591 TTTTATTCTG
2762601 TTTCTTTCCTTTTTT
1 TTTCTTTCCTTTTTT
2762616 TTTCTTT-CTTTTTT
1 TTTCTTTCCTTTTTT
2762630 TT
1 TT
2762632 CATTAAGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTCTTTCCTTTTTT
Found at i:2762711 original size:19 final size:19
Alignment explanation
Indices: 2762679--2762717 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
2762669 AATACTTATT
* * *
2762679 TATTATTTATACATGTGTA
1 TATTATTAACACATATGTA
2762698 TATTATTAACACATATGTA
1 TATTATTAACACATATGTA
2762717 T
1 T
2762718 CCATTTATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.49
Consensus pattern (19 bp):
TATTATTAACACATATGTA
Found at i:2762811 original size:18 final size:19
Alignment explanation
Indices: 2762783--2762836 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
2762773 ATAATAGAAT
2762783 TATTTAATTAATAAATATC
1 TATTTAATTAATAAATATC
* *
2762802 T-TTTACTTAATAATTATC
1 TATTTAATTAATAAATATC
2762820 TATTTAA-TAATTAAATA
1 TATTTAATTAA-TAAATA
2762837 CAAGTATTAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 19 0.66
19 10 0.34
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (19 bp):
TATTTAATTAATAAATATC
Found at i:2763709 original size:6 final size:6
Alignment explanation
Indices: 2763691--2763726 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
2763681 TGTGTACCGA
* *
2763691 TACTGC TACTGT TATTGT TACTGT TACTGT TACTGT
1 TACTGT TACTGT TACTGT TACTGT TACTGT TACTGT
2763727 AACGGTGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.50
Consensus pattern (6 bp):
TACTGT
Found at i:2765888 original size:15 final size:13
Alignment explanation
Indices: 2765868--2765901 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
2765858 TAAAACATAT
2765868 AAAAATATAATAATA
1 AAAAATAT-ATAA-A
2765883 AAAAATATATAAA
1 AAAAATATATAAA
2765896 AAAAAT
1 AAAAAT
2765902 TACCTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.37
14 4 0.21
15 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
AAAAATATATAAA
Found at i:2766441 original size:3 final size:3
Alignment explanation
Indices: 2766433--2766471 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2766423 CTTTAATTTT
2766433 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2766472 CTTCTAATGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2770960 original size:20 final size:20
Alignment explanation
Indices: 2770935--2770974 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
2770925 TTTCCAAAAG
2770935 GTAAATGAAAGCTTCTATTT
1 GTAAATGAAAGCTTCTATTT
2770955 GTAAATGAAAGCTTCTATTT
1 GTAAATGAAAGCTTCTATTT
2770975 TCGCTCTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (20 bp):
GTAAATGAAAGCTTCTATTT
Found at i:2773423 original size:15 final size:15
Alignment explanation
Indices: 2773403--2773431 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2773393 TCGTCCTCAG
2773403 CCTCTCCTTCATCTC
1 CCTCTCCTTCATCTC
2773418 CCTCTCCTTCATCT
1 CCTCTCCTTCATCT
2773432 TCTTTGTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.52, G:0.00, T:0.41
Consensus pattern (15 bp):
CCTCTCCTTCATCTC
Found at i:2781264 original size:21 final size:21
Alignment explanation
Indices: 2781240--2781280 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2781230 ATCTGCTCAA
* *
2781240 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2781261 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2781281 TCGCTTGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2785042 original size:16 final size:17
Alignment explanation
Indices: 2785011--2785062 Score: 56
Period size: 16 Copynumber: 3.1 Consensus size: 17
2785001 TAGTAAAAAT
2785011 ATAATTTTAT-TATTTTA
1 ATAATTTTATAT-TTTTA
2785028 AT-ATTTTATATTTTT-
1 ATAATTTTATATTTTTA
2785043 ATAATTTTTATAATTTTTA
1 ATAA-TTTTAT-ATTTTTA
2785062 A
1 A
2785063 AAGATTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 12 0.40
17 9 0.30
18 6 0.20
19 1 0.03
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATAATTTTATATTTTTA
Found at i:2785042 original size:24 final size:25
Alignment explanation
Indices: 2785010--2785059 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
2785000 ATAGTAAAAA
*
2785010 TATAATTTTATTATTTTAAT-ATTT
1 TATAATTTTATAATTTTAATAATTT
* *
2785034 TATATTTTTATAATTTTTATAATTT
1 TATAATTTTATAATTTTAATAATTT
2785059 T
1 T
2785060 TAAAAGATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (25 bp):
TATAATTTTATAATTTTAATAATTT
Found at i:2785051 original size:9 final size:9
Alignment explanation
Indices: 2785010--2785061 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
2785000 ATAGTAAAAA
2785010 TATAA-TTT
1 TATAATTTT
*
2785018 TATTATTTT
1 TATAATTTT
*
2785027 AAT-A-TTT
1 TATAATTTT
2785034 TAT-ATTTT
1 TATAATTTT
2785042 TATAATTTT
1 TATAATTTT
2785051 TATAATTTT
1 TATAATTTT
2785060 TA
1 TA
2785062 AAAGATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
7 6 0.16
8 11 0.29
9 21 0.55
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (9 bp):
TATAATTTT
Found at i:2786526 original size:2 final size:2
Alignment explanation
Indices: 2786515--2786555 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2786505 ATTAAGTTAT
2786515 TA TA -A 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
2786556 AAGTAAAGGA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2786658 original size:16 final size:16
Alignment explanation
Indices: 2786630--2786669 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2786620 CAGAGAGCAG
*
2786630 GGGAAAGAAAGAAGGAA
1 GGGAAA-AAAGAAAGAA
2786647 GGGAAAAAAGAAAGAA
1 GGGAAAAAAGAAAGAA
2786663 -GGAAAAA
1 GGGAAAAA
2786670 GGGGAAAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 9 0.41
17 6 0.27
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (16 bp):
GGGAAAAAAGAAAGAA
Found at i:2789646 original size:44 final size:45
Alignment explanation
Indices: 2789563--2789685 Score: 140
Period size: 44 Copynumber: 2.7 Consensus size: 45
2789553 CAGAAATGAA
* * *
2789563 CCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGATTGAG
1 CCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGGAATAAG
* *
2789609 CCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGGAATAAT
1 CCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAATAAG
* * * *
2789653 TCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 CCATGTAAGTCCATATTAAA-ATATGGCATTGG
2789686 CAGGATATTG
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.55
45 1 0.02
46 28 0.43
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (45 bp):
CCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAATAAG
Found at i:2790991 original size:45 final size:45
Alignment explanation
Indices: 2790925--2791018 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
2790915 CGTTACACTA
* *
2790925 TTACTGTTACCGATTCGGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACCGTTACCGATTCAGCACTTTGTGTGTCGAATACTGTTACTG
* *
2790970 TTACCGTTATCGATTCAGCACTTTGTGTGTTGAATACTGTTACTG
1 TTACCGTTACCGATTCAGCACTTTGTGTGTCGAATACTGTTACTG
2791015 TTAC
1 TTAC
2791019 TGTTCTGAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.41
Consensus pattern (45 bp):
TTACCGTTACCGATTCAGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:2791219 original size:18 final size:18
Alignment explanation
Indices: 2791198--2791315 Score: 55
Period size: 18 Copynumber: 6.6 Consensus size: 18
2791188 TAACTGATTA
2791198 TTACTGAATAATTGACTG
1 TTACTGAATAATTGACTG
*
2791216 TTACCGAAT-A-T-ACTAG
1 TTACTGAATAATTGACT-G
* * *
2791232 ATAACCG-ATCAATTGATTG
1 -TTACTGAAT-AATTGACTG
* * ** *
2791251 ATACTGAATAACTGGTTA
1 TTACTGAATAATTGACTG
* *
2791269 TTATTGAATAATTGATTG
1 TTACTGAATAATTGACTG
* * *
2791287 TTACCGAATAAGTGGCTG
1 TTACTGAATAATTGACTG
2791305 TTACTGAATAA
1 TTACTGAATAA
2791316 ATAATTGTTC
Statistics
Matches: 73, Mismatches: 20, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
15 3 0.04
16 4 0.05
17 6 0.08
18 54 0.74
19 4 0.05
20 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (18 bp):
TTACTGAATAATTGACTG
Found at i:2791282 original size:36 final size:36
Alignment explanation
Indices: 2791186--2791315 Score: 104
Period size: 36 Copynumber: 3.6 Consensus size: 36
2791176 AAAGGTATAA
** * *
2791186 AATAACTGATTATTACTGAATAATTGACTGTTACCG
1 AATAACTGGCTATTACTGAATAATTGATTGATACCG
* * * *
2791222 AATATACTAG--ATAACCG-ATCAATTGATTGATACTG
1 AATA-ACTGGCTATTACTGAAT-AATTGATTGATACCG
* * *
2791257 AATAACTGGTTATTATTGAATAATTGATTGTTACCG
1 AATAACTGGCTATTACTGAATAATTGATTGATACCG
* *
2791293 AATAAGTGGCTGTTACTGAATAA
1 AATAACTGGCTATTACTGAATAA
2791316 ATAATTGTTC
Statistics
Matches: 72, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
34 6 0.08
35 21 0.29
36 40 0.56
37 5 0.07
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (36 bp):
AATAACTGGCTATTACTGAATAATTGATTGATACCG
Found at i:2802521 original size:45 final size:45
Alignment explanation
Indices: 2802456--2802546 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
2802446 GAAAAAGAAG
2802456 AAGAAGAGAAAAAATAGAGATGCTTGGAGATAAAACAGATGAAAA
1 AAGAAGAGAAAAAATAGAGATGCTTGGAGATAAAACAGATGAAAA
*
2802501 AAGAAGAGAAAAAATGGAGATGCTTGGAGATAAAACAGATGAAAA
1 AAGAAGAGAAAAAATAGAGATGCTTGGAGATAAAACAGATGAAAA
2802546 A
1 A
2802547 CATGTTCCCT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.57, C:0.04, G:0.25, T:0.13
Consensus pattern (45 bp):
AAGAAGAGAAAAAATAGAGATGCTTGGAGATAAAACAGATGAAAA
Found at i:2803673 original size:21 final size:20
Alignment explanation
Indices: 2803647--2803691 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
2803637 CAACGTGGCA
2803647 AGTTAACTGGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
*
2803667 TAGTTAACTTGCCACATCAGC
1 -AGTTAACTGGCCACATCAGC
2803688 AGTT
1 AGTT
2803692 CTGTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (20 bp):
AGTTAACTGGCCACATCAGC
Found at i:2805509 original size:3 final size:3
Alignment explanation
Indices: 2805501--2805540 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2805491 TGTTCTCTGC
2805501 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
2805541 TAAAAGAGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2811794 original size:39 final size:39
Alignment explanation
Indices: 2811677--2811797 Score: 188
Period size: 39 Copynumber: 3.1 Consensus size: 39
2811667 AATTATATTA
*
2811677 CCAGCACAAAGCCTGCGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* * *
2811716 ACTGCACGAAGCCTACGGGACTTTAGCCCGGATACATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
* *
2811755 CCAGCACGAAGCCTGCGGGACTTTAGCCGGGATGCATTT
1 CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
2811794 CCAG
1 CCAG
2811798 TATCTTGCAT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 73 1.00
ACGTcount: A:0.24, C:0.30, G:0.26, T:0.21
Consensus pattern (39 bp):
CCAGCACGAAGCCTGCGGGACTTTAGCCCGGATACATTT
Found at i:2812941 original size:5 final size:5
Alignment explanation
Indices: 2812931--2812966 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
2812921 AATAATTAAG
2812931 TATAT TATAT TATAT TATAT TATAT TATTAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TA-TAT TATAT
2812967 ATAAAAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (5 bp):
TATAT
Found at i:2815556 original size:2 final size:2
Alignment explanation
Indices: 2815549--2815579 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2815539 CAAATAAATG
2815549 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 T
2815580 TCACCTTCGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2818307 original size:93 final size:93
Alignment explanation
Indices: 2818195--2818366 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
2818185 GCCCATAAGT
* *
2818195 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
2818260 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
2818288 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
2818353 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
2818367 CAAATATCCC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:2818362 original size:46 final size:46
Alignment explanation
Indices: 2818187--2818362 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
2818177 TGTAACCCGC
* * *
2818187 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
2818233 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
2818283 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
2818326 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
2818363 TGCCCAAATA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 2 0.02
46 68 0.61
47 32 0.29
48 2 0.02
49 1 0.01
50 3 0.03
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:2819637 original size:55 final size:53
Alignment explanation
Indices: 2819509--2819700 Score: 210
Period size: 55 Copynumber: 3.6 Consensus size: 53
2819499 TTGAACTTTC
* *
2819509 CAATGTCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCAC-
1 CAATGCCATGTCTTGACATGGTCTTACATGGTA-CCTTGCCTTATAGAACTC-CT
* *
2819562 CAATGCCATG-CTTTGGCATGGTCTTACATGGGACCTTCGCCTTATAGTAACTCCT
1 CAATGCCATGTC-TTGACATGGTCTTACATGGTACCTT-GCCTTATAG-AACTCCT
* * * **
2819617 CAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTATAGAATTTAT
1 CAATGCCATGTCTTGACATGGTCTTACATG-GTACCTTGCCTTATAGAACTCCT
* *
2819671 CAATGCCATGCCTTGGCATGGTCTTACATG
1 CAATGCCATGTCTTGACATGGTCTTACATG
2819701 ATATCCTTAT
Statistics
Matches: 119, Mismatches: 13, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
52 5 0.04
53 34 0.29
54 34 0.29
55 41 0.34
56 5 0.04
ACGTcount: A:0.21, C:0.24, G:0.19, T:0.35
Consensus pattern (53 bp):
CAATGCCATGTCTTGACATGGTCTTACATGGTACCTTGCCTTATAGAACTCCT
Found at i:2819965 original size:44 final size:44
Alignment explanation
Indices: 2819898--2819984 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
2819888 GTATCTTTAA
* *
2819898 CCGTCAATTCCTCCTTAAATGCCATGTTATGAA-CATGGACTTTT
1 CCGTCAATTCCTCCTTAAATGCCATGGTA-CAACCATGGACTTTT
* *
2819942 CCGTCAATTCTTCCTTAATTGCCATGGTACAACCATGGACTTT
1 CCGTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTT
2819985 GAGATATCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 2 0.05
44 36 0.95
ACGTcount: A:0.24, C:0.26, G:0.14, T:0.36
Consensus pattern (44 bp):
CCGTCAATTCCTCCTTAAATGCCATGGTACAACCATGGACTTTT
Found at i:2820425 original size:7 final size:7
Alignment explanation
Indices: 2820413--2820440 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2820403 CCAACTTTCC
2820413 CGATTTT
1 CGATTTT
2820420 CGATTTT
1 CGATTTT
2820427 CGATTTT
1 CGATTTT
2820434 CGATTTT
1 CGATTTT
2820441 TCTCTCGTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (7 bp):
CGATTTT
Found at i:2823931 original size:2 final size:2
Alignment explanation
Indices: 2823912--2823949 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
2823902 TTTTTTCCTG
*
2823912 TA TA TCA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2823950 GCAAGTAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2824168 original size:3 final size:3
Alignment explanation
Indices: 2824160--2824193 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2824150 AGAAGGCGAC
* *
2824160 GAA GAA GAA GAT GAT GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
2824194 GTTGAGATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.59, C:0.00, G:0.35, T:0.06
Consensus pattern (3 bp):
GAA
Found at i:2825235 original size:2 final size:2
Alignment explanation
Indices: 2825230--2825259 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2825220 ACACACACAC
2825230 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
2825260 TTCTTTTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2830796 original size:2 final size:2
Alignment explanation
Indices: 2830789--2830825 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2830779 ACGAATCGTG
2830789 TA TA 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 TA TA T
2830826 TAATTTCGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2832828 original size:19 final size:21
Alignment explanation
Indices: 2832793--2832837 Score: 76
Period size: 19 Copynumber: 2.2 Consensus size: 21
2832783 ACATCAGTCA
2832793 TTTTATCTTAAATTTTAATTT
1 TTTTATCTTAAATTTTAATTT
2832814 TTTTAT-TTAAA-TTTAATTT
1 TTTTATCTTAAATTTTAATTT
2832833 TTTTA
1 TTTTA
2832838 AATAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.54
20 5 0.21
21 6 0.25
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTATCTTAAATTTTAATTT
Found at i:2832843 original size:19 final size:20
Alignment explanation
Indices: 2832801--2832843 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
2832791 CATTTTATCT
**
2832801 TAAATTTTAATTTTTTTATT
1 TAAATTTTAATTTTTTTAAA
2832821 TAAA-TTTAATTTTTTTAAA
1 TAAATTTTAATTTTTTTAAA
2832840 TAAA
1 TAAA
2832844 AAAATTGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TAAATTTTAATTTTTTTAAA
Found at i:2833915 original size:7 final size:7
Alignment explanation
Indices: 2833903--2833930 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2833893 CAAAGAGGGT
2833903 GTAGGCC
1 GTAGGCC
2833910 GTAGGCC
1 GTAGGCC
2833917 GTAGGCC
1 GTAGGCC
2833924 GTAGGCC
1 GTAGGCC
2833931 ACTGGTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.29, G:0.43, T:0.14
Consensus pattern (7 bp):
GTAGGCC
Found at i:2838114 original size:18 final size:18
Alignment explanation
Indices: 2838091--2838125 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2838081 TAATTACCAT
2838091 TTTAATTACATTATAAGG
1 TTTAATTACATTATAAGG
**
2838109 TTTAATTGTATTATAAG
1 TTTAATTACATTATAAG
2838126 CTAGCTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.03, G:0.11, T:0.49
Consensus pattern (18 bp):
TTTAATTACATTATAAGG
Found at i:2839406 original size:24 final size:20
Alignment explanation
Indices: 2839378--2839434 Score: 53
Period size: 24 Copynumber: 2.6 Consensus size: 20
2839368 TTTTGATAAT
2839378 TTTTAAAAAAATACATAATTATCA
1 TTTTAAAAAAATACAT-A-T-T-A
*
2839402 TTTTAACCAAAAT-CATATTA
1 TTTTAA-AAAAATACATATTA
2839422 TTTTAAAAAAATA
1 TTTTAAAAAAATA
2839435 AATTTGTTAC
Statistics
Matches: 29, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
19 5 0.17
20 7 0.24
21 1 0.03
22 1 0.03
23 1 0.03
24 9 0.31
25 5 0.17
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.39
Consensus pattern (20 bp):
TTTTAAAAAAATACATATTA
Found at i:2840594 original size:2 final size:2
Alignment explanation
Indices: 2840587--2840611 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2840577 TAAAATTTCA
2840587 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2840612 AATTTTAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2840939 original size:6 final size:6
Alignment explanation
Indices: 2840928--2840968 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
2840918 TCAATTTTCA
2840928 ACCATC ACCATC ACCATC ACCATC ACCATC ACCATC ACCAT
1 ACCATC ACCATC ACCATC ACCATC ACCATC ACCATC ACCAT
2840969 TTTTTTTCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.34, C:0.49, G:0.00, T:0.17
Consensus pattern (6 bp):
ACCATC
Found at i:2844284 original size:8 final size:7
Alignment explanation
Indices: 2844263--2844287 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
2844253 GCATCACTAT
2844263 ATTAAAA
1 ATTAAAA
2844270 ATTAAAA
1 ATTAAAA
2844277 ATTAAAA
1 ATTAAAA
2844284 ATTA
1 ATTA
2844288 CAAACAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATTAAAA
Found at i:2846822 original size:2 final size:2
Alignment explanation
Indices: 2846811--2846844 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2846801 AAAAAGATGC
*
2846811 AT AT AA 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
2846845 TCTGAGAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2852866 original size:16 final size:17
Alignment explanation
Indices: 2852845--2852876 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2852835 TTACAATCTC
2852845 CTTTTTT-TTTTTTTTT
1 CTTTTTTGTTTTTTTTT
2852861 CTTTTTTGTTTTTTTT
1 CTTTTTTGTTTTTTTT
2852877 AAGGTCCCTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.00, C:0.06, G:0.03, T:0.91
Consensus pattern (17 bp):
CTTTTTTGTTTTTTTTT
Found at i:2855753 original size:18 final size:18
Alignment explanation
Indices: 2855730--2855764 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2855720 TCATACCTTA
*
2855730 TAATTTTTTATTGAATAC
1 TAATTTCTTATTGAATAC
*
2855748 TAATTTCTTATTTAATA
1 TAATTTCTTATTGAATA
2855765 AATTGTTCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.03, T:0.57
Consensus pattern (18 bp):
TAATTTCTTATTGAATAC
Found at i:2856105 original size:22 final size:23
Alignment explanation
Indices: 2856066--2856115 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 23
2856056 ATTATAATGA
*
2856066 AATAAAACTGAAAATAAATATT-T
1 AATAAAAATGAAAATAAA-ATTAT
2856089 AATAAAAATG-AAATAAAATTAT
1 AATAAAAATGAAAATAAAATTAT
2856111 AATAA
1 AATAA
2856116 TATAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
21 3 0.12
22 13 0.52
23 9 0.36
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (23 bp):
AATAAAAATGAAAATAAAATTAT
Found at i:2860390 original size:10 final size:10
Alignment explanation
Indices: 2860369--2860438 Score: 53
Period size: 10 Copynumber: 7.3 Consensus size: 10
2860359 CAACCCAATC
2860369 TTTATTTTTA
1 TTTATTTTTA
2860379 TTT-TTATTTA
1 TTTATT-TTTA
**
2860389 -TTATTTTCC
1 TTTATTTTTA
2860398 TTTATTTTCT-
1 TTTATTTT-TA
2860408 TTTATTATTTA
1 TTTATT-TTTA
2860419 -TTATTTTT-
1 TTTATTTTTA
2860427 TTTA-TTTTA
1 TTTATTTTTA
2860436 TTT
1 TTT
2860439 TAGTTAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 17
0.71 0.04 0.25
Matches are distributed among these distances:
8 4 0.08
9 15 0.31
10 28 0.57
11 2 0.04
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTTTA
Found at i:2860428 original size:23 final size:22
Alignment explanation
Indices: 2860369--2860437 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
2860359 CAACCCAATC
2860369 TTTATTTTTATTTTTATTTATTA
1 TTTATTTTTATTTTT-TTTATTA
*
2860392 TTT-TCCTTTATTTTCTTTTATTA
1 TTTAT-TTTTATTTT-TTTTATTA
*
2860415 TTTATTATTTTTTTTATTTTATT
1 TTTATT-TTTATTTT-TTTTATT
2860438 TTAGTTAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
22 1 0.03
23 21 0.55
24 16 0.42
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (22 bp):
TTTATTTTTATTTTTTTTATTA
Found at i:2860430 original size:29 final size:29
Alignment explanation
Indices: 2860368--2860440 Score: 96
Period size: 29 Copynumber: 2.5 Consensus size: 29
2860358 GCAACCCAAT
2860368 CTTTATTTTTATTT-TTATTTATTATTTTC
1 CTTTATTTTT-TTTATTATTTATTATTTTC
2860397 CTTTATTTTCTTTTATTATTTATTATTTT-
1 CTTTATTTT-TTTTATTATTTATTATTTTC
*
2860426 TTTTATTTTATTTTA
1 CTTTATTTT-TTTTA
2860441 GTTAAATATT
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
29 25 0.62
30 15 0.38
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (29 bp):
CTTTATTTTTTTTATTATTTATTATTTTC
Found at i:2860451 original size:30 final size:30
Alignment explanation
Indices: 2860387--2860451 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
2860377 TATTTTTATT
* **
2860387 TATTATTTTCCTTTATTTTCTTTTATTATT
1 TATTATTTTCCTTTATTTTATTTTATTAAA
*
2860417 TATTATTTT-TTTTATTTTATTTTAGTTAAA
1 TATTATTTTCCTTTATTTTATTTTA-TTAAA
2860447 TATTA
1 TATTA
2860452 ATAAATTTCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.71
Consensus pattern (30 bp):
TATTATTTTCCTTTATTTTATTTTATTAAA
Found at i:2861578 original size:118 final size:117
Alignment explanation
Indices: 2861371--2861600 Score: 379
Period size: 118 Copynumber: 2.0 Consensus size: 117
2861361 TGTTTTCCAT
* *
2861371 GGTTATGAGTACAGCTTAGATCGTGACTGACTGAGTAACCGGGTAGGGTGCTTGGGTTGTCATTC
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGTAGGGTGCTTGGGTTGTCATTC
2861436 TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
66 TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
**
2861488 GGTTATGAGTATGGCTCAAATCGTGACTGACTGAGTAACCGGGGTAGGGTGCTTGGGTTGTCATT
1 GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACC-GGGTAGGGTGCTTGGGTTGTCATT
****
2861553 CTACTTCGCGTCAAAAGGTTGTGTGACGTGTTGGGTAAAACTCCGCTA
65 CTACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTA
2861601 ACCGGAAATA
Statistics
Matches: 104, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
117 36 0.35
118 68 0.65
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.29
Consensus pattern (117 bp):
GGTTATGAGTACAGCTCAAATCGTGACTGACTGAGTAACCGGGTAGGGTGCTTGGGTTGTCATTC
TACTTCGCGTCAAAAGGTTGTGTGACGTGACAAGTAAAACTCCGCTAGCCGA
Found at i:2861748 original size:10 final size:11
Alignment explanation
Indices: 2861735--2861769 Score: 56
Period size: 10 Copynumber: 3.4 Consensus size: 11
2861725 AAAAAAAATC
2861735 AAAA-AAGAAA
1 AAAAGAAGAAA
2861745 AAAAGAA-AAA
1 AAAAGAAGAAA
2861755 AAAAGAAGAAA
1 AAAAGAAGAAA
2861766 AAAA
1 AAAA
2861770 TAAGTACTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 14 0.61
11 9 0.39
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:2861753 original size:13 final size:13
Alignment explanation
Indices: 2861736--2861769 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2861726 AAAAAAATCA
*
2861736 AAAAAGAAAAAAAG
1 AAAAA-AAAAGAAG
2861750 AAAAAAAAAGAAG
1 AAAAAAAAAGAAG
2861763 AAAAAAA
1 AAAAAAA
2861770 TAAGTACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAG
Found at i:2865690 original size:16 final size:16
Alignment explanation
Indices: 2865669--2865699 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2865659 GATATTTTAA
2865669 TATATTATATTAATAT
1 TATATTATATTAATAT
*
2865685 TATATTATGTTAATA
1 TATATTATATTAATA
2865700 AAATAATAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATATTATATTAATAT
Found at i:2865717 original size:15 final size:17
Alignment explanation
Indices: 2865697--2865733 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
2865687 TATTATGTTA
*
2865697 ATAAAATAA-TAAAG-T
1 ATAAAAGAATTAAAGAT
2865712 ATAAAAGAATTAAAGAT
1 ATAAAAGAATTAAAGAT
2865729 ATAAA
1 ATAAA
2865734 GAAACAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 5 0.26
17 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (17 bp):
ATAAAAGAATTAAAGAT
Found at i:2866922 original size:30 final size:27
Alignment explanation
Indices: 2866858--2866909 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
2866848 ATGCCTTATT
*
2866858 GGTGTGTTCGGGAGGATATATAATACC
1 GGTGTGTTAGGGAGGATATATAATACC
* *
2866885 GGTGTGTTATGGAGGATTTATAATA
1 GGTGTGTTAGGGAGGATATATAATA
2866910 TTCCGGGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.27, C:0.06, G:0.33, T:0.35
Consensus pattern (27 bp):
GGTGTGTTAGGGAGGATATATAATACC
Found at i:2869786 original size:8 final size:8
Alignment explanation
Indices: 2869744--2869768 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
2869734 ATATAGACTA
2869744 AATAAAAT
1 AATAAAAT
2869752 AATAAAAT
1 AATAAAAT
2869760 AATAAAAT
1 AATAAAAT
2869768 A
1 A
2869769 TCTTATTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:2870658 original size:3 final size:3
Alignment explanation
Indices: 2870652--2870729 Score: 92
Period size: 3 Copynumber: 27.0 Consensus size: 3
2870642 ATCTAAGATT
* **
2870652 TTA TTA TTA TTA TTAA TTA TTA GTA TGG TT- TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2870696 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2870730 AGTTAAAGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
2 8 0.12
3 54 0.83
4 3 0.05
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:2870848 original size:25 final size:23
Alignment explanation
Indices: 2870803--2870861 Score: 84
Period size: 25 Copynumber: 2.5 Consensus size: 23
2870793 ATAATGACAA
2870803 TTGTAATAAAAATATTGGTACAT
1 TTGTAATAAAAATATTGGTACAT
2870826 TTGTAATAAATAGATATAT-GTACAT
1 TTGTAATAAA-A-ATAT-TGGTACAT
2870851 TTGTAATAAAA
1 TTGTAATAAAA
2870862 TAATTAAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.30
24 2 0.06
25 20 0.61
26 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.39
Consensus pattern (23 bp):
TTGTAATAAAAATATTGGTACAT
Found at i:2873866 original size:14 final size:15
Alignment explanation
Indices: 2873849--2873877 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2873839 GAGTATGGTA
2873849 AAATA-TTAAAAAAT
1 AAATATTTAAAAAAT
2873863 AAATATTTAAAAAAT
1 AAATATTTAAAAAAT
2873878 TACTAATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAATATTTAAAAAAT
Found at i:2883201 original size:27 final size:28
Alignment explanation
Indices: 2883143--2883201 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 28
2883133 ATTAAGAATA
*
2883143 AAAATTATAAAAATATTAATAATTATTT
1 AAAATTATAAAAATATTAATAATTATTC
2883171 AAAATT-TAAAAA-ATTAAATAATT-TTAC
1 AAAATTATAAAAATATT-AATAATTATT-C
2883198 AAAA
1 AAAA
2883202 ATAATTTTCT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 5 0.18
27 17 0.61
28 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (28 bp):
AAAATTATAAAAATATTAATAATTATTC
Found at i:2885032 original size:15 final size:15
Alignment explanation
Indices: 2885008--2885057 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2884998 CTCCTCATCT
*
2885008 TCATCGTCATCCTCA
1 TCATCTTCATCCTCA
* *
2885023 TCATCTTCATCAAT-T
1 TCATCTTCATC-CTCA
2885038 TCATCTTCATCCTCA
1 TCATCTTCATCCTCA
2885053 TCATC
1 TCATC
2885058 CAACTCAAGC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 1 0.04
15 26 0.93
16 1 0.04
ACGTcount: A:0.22, C:0.36, G:0.02, T:0.40
Consensus pattern (15 bp):
TCATCTTCATCCTCA
Found at i:2885072 original size:30 final size:29
Alignment explanation
Indices: 2885008--2885073 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
2884998 CTCCTCATCT
* **
2885008 TCATCGTCATCCTCATCATCTTCATCAATT
1 TCATCTTCATCCTCATCATC-TCATCAAGC
2885038 TCATCTTCATCCTCATCATC-CAACTCAAGC
1 TCATCTTCATCCTCATCATCTC-A-TCAAGC
2885068 TCATCT
1 TCATCT
2885074 CCCTGAATAG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 1 0.03
30 29 0.94
ACGTcount: A:0.24, C:0.36, G:0.03, T:0.36
Consensus pattern (29 bp):
TCATCTTCATCCTCATCATCTCATCAAGC
Found at i:2890602 original size:2 final size:2
Alignment explanation
Indices: 2890595--2890634 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2890585 CCAAATGGGA
2890595 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
2890635 GATGAGAAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2892640 original size:30 final size:30
Alignment explanation
Indices: 2892604--2892664 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
2892594 GATATACTCT
2892604 TAGATGATGCAGTAGTATCAGAAAAAAAGG
1 TAGATGATGCAGTAGTATCAGAAAAAAAGG
* * *
2892634 TAGATGATGCTGTGGTATCAGGAAAAAAGG
1 TAGATGATGCAGTAGTATCAGAAAAAAAGG
2892664 T
1 T
2892665 GGAAGAGACG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.41, C:0.07, G:0.30, T:0.23
Consensus pattern (30 bp):
TAGATGATGCAGTAGTATCAGAAAAAAAGG
Found at i:2900948 original size:2 final size:2
Alignment explanation
Indices: 2900941--2900987 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
2900931 TTATTTTATA
*
2900941 TG TG TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
2900983 TG TG T
1 TG TG T
2900988 TTTCATGGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.02, C:0.00, G:0.47, T:0.51
Consensus pattern (2 bp):
TG
Found at i:2903200 original size:78 final size:78
Alignment explanation
Indices: 2903071--2903218 Score: 251
Period size: 78 Copynumber: 1.9 Consensus size: 78
2903061 CACATCTCAG
* *
2903071 GTAACTGTAGTGAATCAGGATTACATTTTCAAGTCAAATCCTATCCACCTTAGGTTACCATAATG
1 GTAACTGTAGCGAATCAGGATTACATTTTCAAGTCAAATCCTATCCACCTTAAGTTACCATAATG
2903136 AATCATATATCAT
66 AATCATATATCAT
* * *
2903149 GTAACTGTAGCGAATCAGGATTACCTTTTCAGGTCAAATCCTATCCACCTTAAGTTACCATAGTG
1 GTAACTGTAGCGAATCAGGATTACATTTTCAAGTCAAATCCTATCCACCTTAAGTTACCATAATG
2903214 AATCA
66 AATCA
2903219 GGAATAAATC
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 65 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.32
Consensus pattern (78 bp):
GTAACTGTAGCGAATCAGGATTACATTTTCAAGTCAAATCCTATCCACCTTAAGTTACCATAATG
AATCATATATCAT
Found at i:2903231 original size:40 final size:40
Alignment explanation
Indices: 2903183--2903320 Score: 204
Period size: 40 Copynumber: 3.5 Consensus size: 40
2903173 CTTTTCAGGT
*
2903183 CAAATCCTATCCACCTTAAGTTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
* * *
2903223 TAAATCCTATTCACTTTAAATTACCATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
* * **
2903263 CAAATCCTATCCACTTTGAGGTATTATAGTGAATCAGGAA
1 CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
2903303 CAAATCCTATCCACTTTA
1 CAAATCCTATCCACTTTA
2903321 TATTCTCGAG
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 86 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.30
Consensus pattern (40 bp):
CAAATCCTATCCACTTTAAGTTACCATAGTGAATCAGGAA
Found at i:2922266 original size:13 final size:14
Alignment explanation
Indices: 2922248--2922276 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2922238 CTTCTAATCA
2922248 AACTAAATT-AATT
1 AACTAAATTAAATT
2922261 AACTAAATTAAATT
1 AACTAAATTAAATT
2922275 AA
1 AA
2922277 TTCCATCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (14 bp):
AACTAAATTAAATT
Found at i:2925739 original size:22 final size:22
Alignment explanation
Indices: 2925714--2925756 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
2925704 TATCTAAACA
2925714 ATAACAACAAAATAGTAACAAT
1 ATAACAACAAAATAGTAACAAT
* * *
2925736 ATAATAGCAAAATGGTAACAA
1 ATAACAACAAAATAGTAACAA
2925757 AACAACATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.09, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAACAAT
Found at i:2933009 original size:13 final size:13
Alignment explanation
Indices: 2932991--2933028 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2932981 CAGTAATTCT
2932991 ATATTTTTTAAAA
1 ATATTTTTTAAAA
*
2933004 ATATTTTGTTCAAA
1 ATATTTT-TTAAAA
2933018 AT-TTTTTTAAA
1 ATATTTTTTAAA
2933029 TATTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 4 0.18
13 11 0.50
14 7 0.32
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (13 bp):
ATATTTTTTAAAA
Found at i:2933056 original size:20 final size:22
Alignment explanation
Indices: 2933031--2933083 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
2933021 TTTTTAAATA
*
2933031 TTAAAAATAAAT-ATAA-ATTG
1 TTAAAAATAAATGAAAATATTG
* *
2933051 TTAAAAATATATGAAAATATTT
1 TTAAAAATAAATGAAAATATTG
2933073 TTAAAAATAAA
1 TTAAAAATAAA
2933084 AAATCTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 11 0.41
21 3 0.11
22 13 0.48
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (22 bp):
TTAAAAATAAATGAAAATATTG
Found at i:2934700 original size:27 final size:28
Alignment explanation
Indices: 2934652--2934716 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 28
2934642 ACACATTTAA
* *
2934652 AAATATATATCATTTTTTTATAT-TATAT
1 AAATATA-ATCATTTATGTATATATATAT
*
2934680 AAATATAATTATTTATGTATATAATATAT
1 AAATATAATCATTTATGTATAT-ATATAT
2934709 AAATATAA
1 AAATATAA
2934717 AATACTATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 12 0.38
28 7 0.22
29 13 0.41
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.49
Consensus pattern (28 bp):
AAATATAATCATTTATGTATATATATAT
Found at i:2934733 original size:29 final size:29
Alignment explanation
Indices: 2934670--2934734 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
2934660 ATCATTTTTT
* * *
2934670 TATATTATATAAATATAATTATTTATGTA
1 TATAATATATAAATATAAATATCTATGTA
2934699 TATAATATATAAATATAAA-ATACTAT-TA
1 TATAATATATAAATATAAATAT-CTATGTA
2934727 TATTAATA
1 TA-TAATA
2934735 ATTATGTTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 6 0.19
29 25 0.81
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (29 bp):
TATAATATATAAATATAAATATCTATGTA
Found at i:2946873 original size:30 final size:30
Alignment explanation
Indices: 2946814--2946874 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
2946804 AATAAGCCTC
**
2946814 AATTACTTGCAGAACACCAAATGGCGATTA
1 AATTACTTGCAGAACACCAAATGAAGATTA
2946844 AATTACTTGCAGAACACCAAATGAAGATTA
1 AATTACTTGCAGAACACCAAATGAAGATTA
2946874 A
1 A
2946875 TGTTAAGACG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.44, C:0.18, G:0.15, T:0.23
Consensus pattern (30 bp):
AATTACTTGCAGAACACCAAATGAAGATTA
Found at i:2949915 original size:15 final size:16
Alignment explanation
Indices: 2949887--2949917 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2949877 TATACCTGAT
2949887 ATTTGTACTTTGATGC
1 ATTTGTACTTTGATGC
2949903 ATTTGTA-TTTGATGC
1 ATTTGTACTTTGATGC
2949918 CTATTTGGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (16 bp):
ATTTGTACTTTGATGC
Found at i:2956267 original size:43 final size:43
Alignment explanation
Indices: 2956206--2956295 Score: 180
Period size: 43 Copynumber: 2.1 Consensus size: 43
2956196 GCATGCTTGC
2956206 ATTCCATGATTGAAAGAAATTAGTAGAATATACATTGGAAGAT
1 ATTCCATGATTGAAAGAAATTAGTAGAATATACATTGGAAGAT
2956249 ATTCCATGATTGAAAGAAATTAGTAGAATATACATTGGAAGAT
1 ATTCCATGATTGAAAGAAATTAGTAGAATATACATTGGAAGAT
2956292 ATTC
1 ATTC
2956296 AGGATTTTTG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 47 1.00
ACGTcount: A:0.43, C:0.08, G:0.18, T:0.31
Consensus pattern (43 bp):
ATTCCATGATTGAAAGAAATTAGTAGAATATACATTGGAAGAT
Found at i:2960205 original size:20 final size:18
Alignment explanation
Indices: 2960162--2960206 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
2960152 TTTAATTGTG
* *
2960162 AATATTTTTAAATTTTTT
1 AATATTTTTAAAATTTTA
2960180 AATATTTTTATAAATTTTA
1 AATATTTTTA-AAATTTTA
2960199 AATTATTT
1 AA-TATTT
2960207 GTTGATATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 10 0.43
19 8 0.35
20 5 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
AATATTTTTAAAATTTTA
Found at i:2970290 original size:31 final size:31
Alignment explanation
Indices: 2970253--2970318 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
2970243 ATAGTAAAAA
*
2970253 TATAATTTCAT-AATTTAATAGTTTATATTTT
1 TATAATTT-ATCAATTTAATAATTTATATTTT
* *
2970284 TATAATTTATCATTTTATTAATTTATATTTT
1 TATAATTTATCAATTTAATAATTTATATTTT
2970315 TATA
1 TATA
2970319 TTTTTTAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 2 0.06
31 29 0.94
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (31 bp):
TATAATTTATCAATTTAATAATTTATATTTT
Found at i:2970298 original size:16 final size:15
Alignment explanation
Indices: 2970253--2970318 Score: 71
Period size: 15 Copynumber: 4.3 Consensus size: 15
2970243 ATAGTAAAAA
*
2970253 TATAATTTCATAATTT
1 TATAATTT-ATATTTT
* *
2970269 AATAGTTTATATTTT
1 TATAATTTATATTTT
2970284 TATAATTTATCA-TTT
1 TATAATTTAT-ATTTT
2970299 TATTAATTTATATTTT
1 TA-TAATTTATATTTT
2970315 TATA
1 TATA
2970319 TTTTTTAAGT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
15 22 0.52
16 20 0.48
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.61
Consensus pattern (15 bp):
TATAATTTATATTTT
Found at i:2970308 original size:23 final size:22
Alignment explanation
Indices: 2970282--2970326 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2970272 AGTTTATATT
2970282 TTTATA-ATTTATCATTTTATTAA
1 TTTATATATTTAT-ATTTT-TTAA
*
2970305 TTTATATTTTTATATTTTTTAA
1 TTTATATATTTATATTTTTTAA
2970327 GTGATTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 4 0.20
23 11 0.55
24 5 0.25
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTATATATTTATATTTTTTAA
Found at i:2970364 original size:30 final size:30
Alignment explanation
Indices: 2970300--2970375 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
2970290 TTATCATTTT
* * **
2970300 ATTAATTTATATTTTTATATTTTTTAAGTG
1 ATTAAATTAAATTTTTATATTTTTTAAAAG
2970330 ATTAAATTAAATTTTTAT-TTTTTTAAAAG
1 ATTAAATTAAATTTTTATATTTTTTAAAAG
*
2970359 AATTAAAATATAATTTT
1 -ATTAAATTA-AATTTT
2970376 ATTATTAATA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 9 0.23
30 24 0.62
31 6 0.15
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (30 bp):
ATTAAATTAAATTTTTATATTTTTTAAAAG
Found at i:2971385 original size:30 final size:30
Alignment explanation
Indices: 2971351--2971413 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
2971341 ACTTATTTTA
2971351 TTGTTAATTTTGTTATTATTTTA-AAGACAT
1 TTGTTAATTTTGTTATTATTTTAGAAG-CAT
2971381 TTGTTAATTTTGTTATTATTTTAGAAGCAT
1 TTGTTAATTTTGTTATTATTTTAGAAGCAT
2971411 TTG
1 TTG
2971414 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 29 0.91
31 3 0.09
ACGTcount: A:0.27, C:0.03, G:0.13, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAAGCAT
Found at i:2971570 original size:12 final size:12
Alignment explanation
Indices: 2971540--2971572 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
2971530 TATATATTTT
2971540 AAAATT-ATATA
1 AAAATTAATATA
2971551 AAAA-TAATATA
1 AAAATTAATATA
2971562 AAAATTAATAT
1 AAAATTAATAT
2971573 GATCGGGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 13 0.65
12 6 0.30
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:2974710 original size:26 final size:26
Alignment explanation
Indices: 2974673--2974777 Score: 176
Period size: 26 Copynumber: 4.1 Consensus size: 26
2974663 TGATACAAAT
2974673 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
2974699 TGATAATGGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
2974724 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
2974750 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
2974776 TG
1 TG
2974778 TCTTTTGTAT
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
25 24 0.33
26 49 0.67
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:2974733 original size:51 final size:52
Alignment explanation
Indices: 2974673--2974777 Score: 194
Period size: 51 Copynumber: 2.0 Consensus size: 52
2974663 TGATACAAAT
*
2974673 TGATAATAGGTTAGGTAAATGTTTCATGATAATGGGTTAGGTAAATG-TTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
2974724 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
2974776 TG
1 TG
2974778 TCTTTTGTAT
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 46 0.88
52 6 0.12
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (52 bp):
TGATAATAGGTTAGGTAAATGTTCCATGATAATGGGTTAGGTAAATGTTTCA
Found at i:2977526 original size:19 final size:20
Alignment explanation
Indices: 2977489--2977526 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
2977479 TTAAGTTAAA
*
2977489 TTTTATAATTTATCCTTTAT
1 TTTTATAATTTATACTTTAT
*
2977509 TTTTAT-ATTTATATTTTA
1 TTTTATAATTTATACTTTA
2977527 AGTAATTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTTATAATTTATACTTTAT
Found at i:2977795 original size:22 final size:21
Alignment explanation
Indices: 2977771--2977813 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2977761 AATAAAAAAT
2977771 AAAGAAAAATAAAAAGAAAGTTA
1 AAAG-AAAATAAAAA-AAAGTTA
*
2977794 AAAGAACATAAAAAAAAGTT
1 AAAGAAAATAAAAAAAAGTT
2977814 TAAATTACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 9 0.47
23 4 0.21
ACGTcount: A:0.72, C:0.02, G:0.12, T:0.14
Consensus pattern (21 bp):
AAAGAAAATAAAAAAAAGTTA
Found at i:2977999 original size:29 final size:29
Alignment explanation
Indices: 2977959--2978026 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 29
2977949 TGCAAAAACG
*
2977959 TAAGTGACTAAAATATAACATTTTAAATA
1 TAAGTGACTAAAACATAACATTTTAAATA
2977988 TAAGTGACTAAAACATAACATTTTAAATA
1 TAAGTGACTAAAACATAACATTTTAAATA
*
2978017 AAAGTGACTA
1 TAAGTGACTA
2978027 TTTTAATTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.31
Consensus pattern (29 bp):
TAAGTGACTAAAACATAACATTTTAAATA
Found at i:2979049 original size:48 final size:48
Alignment explanation
Indices: 2978966--2979065 Score: 148
Period size: 48 Copynumber: 2.1 Consensus size: 48
2978956 ATCGATACAT
* * * *
2978966 CACCAACTCAACATATTTTTATTTCCCTACTAATTTTGTGAAAAGAGA
1 CACCAACTCAACATATCTTTATTTCCCTACCAATTTCGTGAAAAAAGA
2979014 CACCTAACT-AACATATCTTTATTTCCCTACCAATTTCGTGAAAAAAGA
1 CACC-AACTCAACATATCTTTATTTCCCTACCAATTTCGTGAAAAAAGA
2979062 CACC
1 CACC
2979066 CAATTAACGA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
48 43 0.91
49 4 0.09
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (48 bp):
CACCAACTCAACATATCTTTATTTCCCTACCAATTTCGTGAAAAAAGA
Found at i:2979365 original size:21 final size:21
Alignment explanation
Indices: 2979341--2979387 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
2979331 TTTTAAAATA
2979341 ATTTTTAA-AAATATTTATATT
1 ATTTTTAATAAATATTTA-ATT
*
2979362 ATTTTTAATTTAATATTTAATT
1 ATTTTTAA-TAAATATTTAATT
2979384 ATTT
1 ATTT
2979388 ATATATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
22 7 0.30
23 8 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTTTAATAAATATTTAATT
Found at i:2979395 original size:23 final size:23
Alignment explanation
Indices: 2979350--2979395 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2979340 AATTTTTAAA
*
2979350 AATATTTATATTATTTTTAATTT
1 AATATTTATATTATTTATAATTT
2979373 AATATTTA-ATTATTTATATATTT
1 AATATTTATATTATTTATA-ATTT
2979396 TCTTTTTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
AATATTTATATTATTTATAATTT
Found at i:2979924 original size:21 final size:21
Alignment explanation
Indices: 2979895--2979934 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
2979885 ATAAAATTAG
*
2979895 AAAATAAATAATAA-CTCTTGT
1 AAAAAAAATAA-AAGCTCTTGT
2979916 AAAAAAAATAAAAGCTCTT
1 AAAAAAAATAAAAGCTCTT
2979935 AAAAAAGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (21 bp):
AAAAAAAATAAAAGCTCTTGT
Found at i:2981104 original size:21 final size:20
Alignment explanation
Indices: 2981063--2981104 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
2981053 AAAAAAAATT
*
2981063 AAATTTAAATAAAAATCCTA
1 AAATTTAAATAAAAATACTA
*
2981083 AAATTTAAAATAAAATTACTA
1 AAATTT-AAATAAAAATACTA
2981104 A
1 A
2981105 TGTGAGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (20 bp):
AAATTTAAATAAAAATACTA
Found at i:2989962 original size:18 final size:18
Alignment explanation
Indices: 2989914--2989968 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
2989904 TTTATATATG
*
2989914 ATATTA-ATAATTATAAA
1 ATATTATATGATTATAAA
* *
2989931 ATATTATCTTATTATAAA
1 ATATTATATGATTATAAA
2989949 ATAATT-TATGATTATGAAA
1 AT-ATTATATGATTAT-AAA
2989968 A
1 A
2989969 AGAAATGATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
17 6 0.19
18 18 0.58
19 7 0.23
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (18 bp):
ATATTATATGATTATAAA
Found at i:2989993 original size:18 final size:18
Alignment explanation
Indices: 2989970--2990005 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2989960 TTATGAAAAA
2989970 GAAATGATACTATAATTT
1 GAAATGATACTATAATTT
2989988 GAAATGATACTATAATTT
1 GAAATGATACTATAATTT
2990006 TTCTTGTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (18 bp):
GAAATGATACTATAATTT
Found at i:3003793 original size:36 final size:36
Alignment explanation
Indices: 3003698--3003794 Score: 124
Period size: 36 Copynumber: 2.7 Consensus size: 36
3003688 GAGATTTTGG
* * * * *
3003698 TCCTATATATGGGGAAAGGCTTACGTGAGGTCCTGC
1 TCCTATACATGGGGGAAGGCTTATGGGAGGTCCTAC
*
3003734 TCCCATACATGGGAGG-AGGCTTATGGGAGGTCCTAC
1 TCCTATACATGGG-GGAAGGCTTATGGGAGGTCCTAC
3003770 TCCTATACATGGGGGAAGGCTTATG
1 TCCTATACATGGGGGAAGGCTTATG
3003795 AGAAGTGATA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
35 2 0.04
36 49 0.94
37 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.26
Consensus pattern (36 bp):
TCCTATACATGGGGGAAGGCTTATGGGAGGTCCTAC
Found at i:3006935 original size:5 final size:5
Alignment explanation
Indices: 3006917--3006952 Score: 63
Period size: 5 Copynumber: 7.0 Consensus size: 5
3006907 TCTCTTTTAT
3006917 ATATA ATAATA ATATA ATATA ATATA ATATA ATATA
1 ATATA AT-ATA ATATA ATATA ATATA ATATA ATATA
3006953 CTTAATTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 25 0.83
6 5 0.17
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:3008903 original size:46 final size:47
Alignment explanation
Indices: 3008811--3008912 Score: 118
Period size: 46 Copynumber: 2.1 Consensus size: 47
3008801 TAGTAAAACT
* *
3008811 ATGGTCTTGCACATAGTCATATATCACACACTGAAGCCATAGCCCAGCC
1 ATGGTCTT-CACATAGTCACATAT-ACACACTGAAGCCATAGCCCAGAC
* * *
3008860 ATGGTCTT-ACATAGATCACATAT-CACACTGATGCCATATCCCAGAT
1 ATGGTCTTCACATAG-TCACATATACACACTGAAGCCATAGCCCAGAC
3008906 ATGGTCT
1 ATGGTCT
3008913 ATATTGAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
46 26 0.55
47 6 0.13
48 7 0.15
49 8 0.17
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.26
Consensus pattern (47 bp):
ATGGTCTTCACATAGTCACATATACACACTGAAGCCATAGCCCAGAC
Found at i:3010053 original size:25 final size:25
Alignment explanation
Indices: 3009943--3010055 Score: 147
Period size: 25 Copynumber: 4.5 Consensus size: 25
3009933 ATAAATGTGC
* * *
3009943 TAATCAGAGAGCACTGACGTACTAA
1 TAATCAGAGAACACTGGCGTGCTAA
*
3009968 -ATATCAGAGAGCACTGGCGTGCTAA
1 TA-ATCAGAGAACACTGGCGTGCTAA
*
3009993 TAATCAGAGATCACTGGCGTGCTAA
1 TAATCAGAGAACACTGGCGTGCTAA
* *
3010018 TATTCAGAGAACACTAGCGTGCTAA
1 TAATCAGAGAACACTGGCGTGCTAA
3010043 TAATCAGAGAACA
1 TAATCAGAGAACA
3010056 TGCTGAGGTC
Statistics
Matches: 79, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
24 1 0.01
25 77 0.97
26 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.21
Consensus pattern (25 bp):
TAATCAGAGAACACTGGCGTGCTAA
Found at i:3016230 original size:32 final size:32
Alignment explanation
Indices: 3016194--3016257 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
3016184 CCCTCGCGAG
3016194 TTCCCTTTCTAACAATATTGTTATATGAACAT
1 TTCCCTTTCTAACAATATTGTTATATGAACAT
3016226 TTCCCTTTCTAACAATATTGTTATATGAACAT
1 TTCCCTTTCTAACAATATTGTTATATGAACAT
3016258 ACATATATGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (32 bp):
TTCCCTTTCTAACAATATTGTTATATGAACAT
Found at i:3033843 original size:13 final size:13
Alignment explanation
Indices: 3033827--3033859 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
3033817 TTTAATTAAA
*
3033827 TTAGTTAATTAGT
1 TTAGATAATTAGT
3033840 TTAGATAATTAGT
1 TTAGATAATTAGT
3033853 TTA-ATAA
1 TTAGATAA
3033860 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:3035207 original size:46 final size:44
Alignment explanation
Indices: 3035148--3035262 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
3035138 ACAGGACAGA
* *
3035148 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
3035194 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
3035238 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
3035263 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:3035243 original size:44 final size:45
Alignment explanation
Indices: 3035148--3035281 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
3035138 ACAGGACAGA
* *
3035148 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
3035194 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
3035238 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
3035282 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:3039613 original size:16 final size:16
Alignment explanation
Indices: 3039579--3039616 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
3039569 AAAAGTTAAC
**
3039579 AAAATATATGATAGTA
1 AAAATATATGATACAA
3039595 AAAATATATGATACAA
1 AAAATATATGATACAA
3039611 AAAATA
1 AAAATA
3039617 CCTGACAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (16 bp):
AAAATATATGATACAA
Found at i:3041363 original size:15 final size:14
Alignment explanation
Indices: 3041335--3041369 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
3041325 TTTATATATT
3041335 TTTTGTATTTTTTG
1 TTTTGTATTTTTTG
*
3041349 TTTTGTTTTTGTTTG
1 TTTTGTATTT-TTTG
3041364 TTTTGT
1 TTTTGT
3041370 GTTTACACGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.03, C:0.00, G:0.17, T:0.80
Consensus pattern (14 bp):
TTTTGTATTTTTTG
Found at i:3041651 original size:44 final size:44
Alignment explanation
Indices: 3041588--3042605 Score: 1315
Period size: 44 Copynumber: 23.1 Consensus size: 44
3041578 CAGGAACACC
* * * * *
3041588 AATCTGTTATTTTCGATCTGTTCTCTGCCAATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * * *
3041632 AATCTG-TCATCTTCAATCTGCTCTCTGTCAACACAGAGACGCCA
1 AATCTGCT-ATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * * *
3041676 AATTTGCCATCTTCGATCTGC-CGGCTGCCAATACAGAGACG-CA
1 AATCTGCTATCTTCGATCTGCTC-TCCGCCAATACAGAGACGCCA
* *
3041719 ATATCTG-TCATCTTCGATCTGCTCTCCGACAATACAGAGACACCA
1 A-ATCTGCT-ATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
** * * *
3041764 AATCTATTATCTTCGATCTGCTCTCTGACGATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
*
3041808 AATCTACTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * ** *
3041852 AATCTGCTATCTTCGATCTGCCCTCTGATAATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * * * *
3041896 AATCTGCTATCTTCGATCTGCCCTCTGACGATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * * *
3041940 AATCTACTATCTTCTATCTGCTCTCCGCCAATATAGAGAGGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
*
3041984 AATCTGCTATCTTCGATCTGCTCTCCGCCAACACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
*
3042028 AATCTGCTATCTTCGATCTGCTCTCCGCCAACACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* *
3042072 AATCTGCTATCTTCGATCTGCTCTCCGCCAACACAGCGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
*
3042116 AATCTGCTATCTTCGATCTACTCTCCGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* ***
3042160 AATCTGCTATCTTCGATCTGCCCTCCGATGATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
** * * *
3042204 AATCTATTATATTCGATCTGCTCTCTGCCACTACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
*
3042248 AATCTACTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
*
3042292 AATCTGCTATCTTTGATCTGCTCTCCGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
** * * * *
3042336 AATCTATTATATTCGATCTGCTCTCCGCCACTACAGATATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * * *
3042380 AATCTGTTATCTTCGATCTGCCCTCTGACAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * * *
3042424 AATCTGCTATCTTCGATCTGCCCTCCGACGATACAGAGATGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
*
3042468 AATCTGCTATCTTCGATCTACTCTCCGCCAATACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * *
3042512 AATCTGCTATCTTCGATTTGCTCTCCGCCACTACAGATACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
* * * *
3042556 AATCTGCTAACTTCGATTTGCTCTCCGCTACTACAGAGACGCCA
1 AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
3042600 AATCTG
1 AATCTG
3042606 TCTGGTCTTC
Statistics
Matches: 864, Mismatches: 102, Indels: 16
0.88 0.10 0.02
Matches are distributed among these distances:
43 5 0.01
44 854 0.99
45 5 0.01
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.27
Consensus pattern (44 bp):
AATCTGCTATCTTCGATCTGCTCTCCGCCAATACAGAGACGCCA
Found at i:3043383 original size:132 final size:132
Alignment explanation
Indices: 3042837--3043724 Score: 1145
Period size: 132 Copynumber: 6.8 Consensus size: 132
3042827 GCTAGGACTT
* * *** * * *
3042837 GCTTAAATATGCTTCACTGCATCTTCAGGAAGC-CAAGATTTATCGTCTTTGATTTGCCTCACTG
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTC-AGATTCGCCGTCTTCGATCTGCTTCACTG
* * * * * * *
3042901 CAACTTCAGGAAGACGAGGTCTACAATCCTCAGCCTACTCCACTACAACTTTA-GAGAGCTAGGA
65 CAACTTCAGGAAAACAAGATCTAAAAT-TTTAGCCTACTCCACTACAACCTTAGGA-AGCTAGGA
3042965 CT--T-
128 -TGGTG
* **
3042968 GCTTAAATCTGCTTCACTGCAACATCAGGAAGC-CTAGATTCGCCGTCTTCGATCTGCCCCACTG
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTC-AGATTCGCCGTCTTCGATCTGCTTCACTG
* * * * *
3043032 CAA-TCTCAGGGAAACAAGATCTATAATCTTCAGCCTACTCTACTACAACCTTAGGGAGCTAGGA
65 CAACT-TCAGGAAAACAAGATCTAAAAT-TTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGA
3043096 ---T-
128 TGGTG
* * * * **
3043097 GCTTAAATTTGCTTCGCTGCATCATCAGGAAGC-CTAGATTCGCCGTCTTCGATCTGCCCCACTG
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTC-AGATTCGCCGTCTTCGATCTGCTTCACTG
* *
3043161 CAA-TCTCAGGGAAACAAGATCTATAATTTTCAGCCTACTCCACTACAACCTTAGGAAGCTAGGA
65 CAACT-TCAGGAAAACAAGATCTAAAATTTT-AGCCTACTCCACTACAACCTTAGGAAGCTAGGA
3043225 TGGTG
128 TGGTG
* * *
3043230 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTTGCCGTCTTCGATTTGTTTCACTGC
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGC
*
3043295 AACTTCAGGAAAACAAGATCTAAAATTTTAGCTTACTCCACTACAACCTTAGGAAGCTAGGATGG
66 AACTTCAGGAAAACAAGATCTAAAATTTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGATGG
3043360 TG
131 TG
* **
3043362 GCTTAAATTTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTTTTTCACTGC
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGC
*
3043427 AACTTCAGGAAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGATGG
66 AACTTCAGGAAAACAAGATCTAAAATTTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGATGG
3043492 TG
131 TG
* *
3043494 GCTTAAATTTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGTTTCACTGC
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGC
* * * *
3043559 AACTTCAGGAAAACAAGATCTGAAATTTTAGCCTACTCCACTACAACTTTAGGGAGCTAGGTTGG
66 AACTTCAGGAAAACAAGATCTAAAATTTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGATGG
3043624 TG
131 TG
* * *
3043626 GCTTAAATCTGTTTCACTGCAACTTTAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTTC
1 GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGC
* *
3043691 AATTTCAGGGAAACAAGATCTAAAATTTTAGCCT
66 AACTTCAGGAAAACAAGATCTAAAATTTTAGCCT
3043725 CATAGGCCCA
Statistics
Matches: 693, Mismatches: 55, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
128 2 0.00
129 120 0.17
130 1 0.00
131 105 0.15
132 384 0.55
133 79 0.11
134 2 0.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (132 bp):
GCTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGTCTTCGATCTGCTTCACTGC
AACTTCAGGAAAACAAGATCTAAAATTTTAGCCTACTCCACTACAACCTTAGGAAGCTAGGATGG
TG
Found at i:3043687 original size:45 final size:45
Alignment explanation
Indices: 3043231--3043699 Score: 148
Period size: 45 Copynumber: 10.6 Consensus size: 45
3043221 AGGATGGTGG
* *
3043231 CTTAAATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTTGCCGT
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
* * * * * ****
3043276 CTTCGATTTGTTTCACTGCAACTTCAGGAAAAC-AAGA-TCTAAAAT
1 CTTAGATCTGCTTCACTGCAACTTCAGG-AAGCTCAGATTC-GCCGT
* * * * * ** *
3043321 TTTAGCT-TACTCCACTACAACCTT-AGGAAGCT-AGGA-T-GGTGG
1 CTTAGATCTGCTTCACTGCAA-CTTCAGGAAGCTCA-GATTCGCCGT
* *
3043363 CTTAAATTTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
* ** * * ***
3043408 CTTCGATCTTTTTCACTGCAACTTCAGGAAAAC-AAGA-TCTGAAAT
1 CTTAGATCTGCTTCACTGCAACTTCAGG-AAGCTCAGATTC-GCCGT
* * * * * ** *
3043453 TTTAG-CCTACTCCACTACAACCTT-AGGAAGCT-AGGA-T-GGTGG
1 CTTAGATCTGCTTCACTGCAA-CTTCAGGAAGCTCA-GATTCGCCGT
* *
3043495 CTTAAATTTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
* * * * ***
3043540 CTTCGATCTGTTTCACTGCAACTTCAGGAAAAC-AAGA-TCTGAAAT
1 CTTAGATCTGCTTCACTGCAACTTCAGG-AAGCTCAGATTC-GCCGT
* * * * * * * * ** *
3043585 TTTAG-CCTACTCCACTACAACTTTAGGGAGCT-AGGTT-GGTGG
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
* * *
3043627 CTTAAATCTGTTTCACTGCAACTTTAGGAAGCTCAGATTCGCCGT
1 CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
* * *
3043672 CTTCGATCTGCTTCACTTCAATTTCAGG
1 CTTAGATCTGCTTCACTGCAACTTCAGG
3043700 GAAACAAGAT
Statistics
Matches: 290, Mismatches: 107, Indels: 54
0.64 0.24 0.12
Matches are distributed among these distances:
42 18 0.06
43 73 0.25
44 61 0.21
45 129 0.44
46 9 0.03
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (45 bp):
CTTAGATCTGCTTCACTGCAACTTCAGGAAGCTCAGATTCGCCGT
Found at i:3045110 original size:97 final size:98
Alignment explanation
Indices: 3044902--3045127 Score: 400
Period size: 97 Copynumber: 2.3 Consensus size: 98
3044892 CAAGGCGCCC
* * * *
3044902 TTTGCGGGTTTTCACTTTGGCCTCTCCTTTTCTTTCTTTCTTTCTTTCTCTTTTTTTTATTTTTT
1 TTTGAGGGTTTTCGCTGTGGCCTTTCCTTTTCTTTCTTTCTTTCTTTCTCTTTTTTTTATTTTTT
3044967 ATTTTATTATTTTTTGAAGATCTCAGAGTATCA
66 ATTTTATTATTTTTTGAAGATCTCAGAGTATCA
3045000 TTTGAGGGTTTTCGCTGTGGCCTTTCCTTTTCTTTCTTTCTTTCTTTCTCTTTTTTTTA-TTTTT
1 TTTGAGGGTTTTCGCTGTGGCCTTTCCTTTTCTTTCTTTCTTTCTTTCTCTTTTTTTTATTTTTT
3045064 ATTTTATTATTTTTTGAAGATCTCAGAGTATCA
66 ATTTTATTATTTTTTGAAGATCTCAGAGTATCA
3045097 TTTGAGGGTTTTCGCTGTGGCCTTTCACTTT
1 TTTGAGGGTTTTCGCTGTGGCCTTTC-CTTT
3045128 CCTTGGAGGA
Statistics
Matches: 123, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
97 64 0.52
98 59 0.48
ACGTcount: A:0.12, C:0.17, G:0.13, T:0.58
Consensus pattern (98 bp):
TTTGAGGGTTTTCGCTGTGGCCTTTCCTTTTCTTTCTTTCTTTCTTTCTCTTTTTTTTATTTTTT
ATTTTATTATTTTTTGAAGATCTCAGAGTATCA
Found at i:3045695 original size:15 final size:15
Alignment explanation
Indices: 3045656--3045700 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
3045646 CAGCAACCGC
3045656 TTCTC-TTTTTCTTT
1 TTCTCTTTTTTCTTT
3045670 CTTCTCTTTTTTCTTT
1 -TTCTCTTTTTTCTTT
3045686 TTCT-TTTTTT-TTT
1 TTCTCTTTTTTCTTT
3045699 TT
1 TT
3045701 GAAATTTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 5 0.17
14 6 0.21
15 9 0.31
16 9 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTCTCTTTTTTCTTT
Found at i:3045697 original size:16 final size:16
Alignment explanation
Indices: 3045655--3045695 Score: 61
Period size: 15 Copynumber: 2.8 Consensus size: 16
3045645 TCAGCAACCG
3045655 CTTCTC-TTTTTCTTT
1 CTTCTCTTTTTTCTTT
3045670 CTTCTCTTTTTTCTTT
1 CTTCTCTTTTTTCTTT
3045686 -TTCT-TTTTTT
1 CTTCTCTTTTTT
3045696 TTTTTGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.24
15 10 0.40
16 9 0.36
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
CTTCTCTTTTTTCTTT
Found at i:3047671 original size:24 final size:24
Alignment explanation
Indices: 3047639--3047684 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
3047629 TGGGAAATTT
3047639 AATGCAAATGATGCAATACAATGC
1 AATGCAAATGATGCAATACAATGC
*
3047663 AATGCAAATGATGCAATGCAAT
1 AATGCAAATGATGCAATACAAT
3047685 ATAAATGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (24 bp):
AATGCAAATGATGCAATACAATGC
Found at i:3048675 original size:46 final size:46
Alignment explanation
Indices: 3048622--3048746 Score: 196
Period size: 46 Copynumber: 2.7 Consensus size: 46
3048612 TGGGCATCCG
* *
3048622 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCA
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCA
* *
3048668 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCA
* *
3048714 AGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 AACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
3048747 GCGGGTTACA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 73 1.00
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
AACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCA
Done.