Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold10
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: 3842500
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.31
Warning! 348197 characters in sequence are not A, C, G, or T
File 16 of 25
Found at i:2571379 original size:14 final size:14
Alignment explanation
Indices: 2571334--2571380 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
2571324 GTAATTGATC
*
2571334 AAATT-AATTAAAT
1 AAATTAAATTAATT
* *
2571347 AAATTAAATTGATA
1 AAATTAAATTAATT
2571361 AAATTAAATTAATT
1 AAATTAAATTAATT
*
2571375 TAATTA
1 AAATTA
2571381 TTTTAATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
13 5 0.19
14 22 0.81
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
AAATTAAATTAATT
Found at i:2573317 original size:13 final size:13
Alignment explanation
Indices: 2573299--2573323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2573289 TTGATTTGAT
2573299 TTAAAATATAAAA
1 TTAAAATATAAAA
2573312 TTAAAATATAAA
1 TTAAAATATAAA
2573324 TGACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TTAAAATATAAAA
Found at i:2575622 original size:21 final size:21
Alignment explanation
Indices: 2575598--2575649 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
2575588 TGTAATAGTG
2575598 TTGATAATCTAAGAAATAATT
1 TTGATAATCTAAGAAATAATT
** *
2575619 TTGATAAT-TTTGATATAATT
1 TTGATAATCTAAGAAATAATT
2575639 TTCGATAATCT
1 TT-GATAATCT
2575650 TTAATATAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 11 0.42
21 14 0.54
22 1 0.04
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (21 bp):
TTGATAATCTAAGAAATAATT
Found at i:2575738 original size:21 final size:21
Alignment explanation
Indices: 2575713--2575823 Score: 74
Period size: 21 Copynumber: 5.5 Consensus size: 21
2575703 ATTTGATACT
2575713 TAATAATTTTGATAACATTTA
1 TAATAATTTTGATAACATTTA
**
2575734 TAATAATTTTG-TAATTTTTA
1 TAATAATTTTGATAACATTTA
* *
2575754 -ATATAATTTTAAT-A-TTTTA
1 TA-ATAATTTTGATAACATTTA
*
2575773 T-ATAATTTTGATAATATTTA
1 TAATAATTTTGATAACATTTA
** *
2575793 -ATATTGTTTTGATAACCATTAA
1 TA-ATAATTTTGATAA-CATTTA
2575815 T-ATAATTTT
1 TAATAATTTT
2575824 ATATCAAAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
18 10 0.14
19 7 0.10
20 20 0.29
21 29 0.41
22 4 0.06
ACGTcount: A:0.39, C:0.03, G:0.05, T:0.54
Consensus pattern (21 bp):
TAATAATTTTGATAACATTTA
Found at i:2575750 original size:18 final size:19
Alignment explanation
Indices: 2575612--2575795 Score: 85
Period size: 21 Copynumber: 9.2 Consensus size: 19
2575602 TAATCTAAGA
*
2575612 AATAATTTTGATAATTTTG
1 AATAATTTTGATAATTTTT
*
2575631 ATATAATTTTCGATAATCTTTA
1 A-ATAATTTT-GATAAT-TTTT
2575653 ATATAATCTTT-ATAACTTTTT
1 A-ATAAT-TTTGATAA-TTTTT
* *
2575674 ATGTAATATTGATAATTTTTTT
1 A-ATAATTTTGATAA--TTTTT
* * *
2575696 AAAAAAAATTTGAT-A--CTT
1 --AATAATTTTGATAATTTTT
*
2575714 AATAATTTTGATAACATTTAT
1 AATAATTTTGAT-A-ATTTTT
2575735 AATAATTTTG-TAATTTTT
1 AATAATTTTGATAATTTTT
*
2575753 AATATAATTT--TAATATTTT
1 AATA-ATTTTGATAAT-TTTT
*
2575772 ATATAATTTTGATAATATTT
1 A-ATAATTTTGATAATTTTT
2575792 AATA
1 AATA
2575796 TTGTTTTGAT
Statistics
Matches: 128, Mismatches: 18, Indels: 38
0.70 0.10 0.21
Matches are distributed among these distances:
16 10 0.08
18 15 0.12
19 19 0.15
20 18 0.14
21 38 0.30
22 17 0.13
23 10 0.08
24 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (19 bp):
AATAATTTTGATAATTTTT
Found at i:2575755 original size:39 final size:41
Alignment explanation
Indices: 2575712--2575823 Score: 110
Period size: 39 Copynumber: 2.8 Consensus size: 41
2575702 AATTTGATAC
*
2575712 TTAATA-ATTTTGATAACATTTATAATAATTTTG-TAATTT
1 TTAATATATTTTGATAACATTTATAATAATTTTGATAATAT
* *
2575751 TTAATATAATTT--TAATATTT-TATATAATTTTGATAATAT
1 TTAATATATTTTGATAACATTTATA-ATAATTTTGATAATAT
* *
2575790 TTAATATTGTTTTGATAACCATTAAT-ATAATTTT
1 TTAATA-TATTTTGATAA-CATTTATAATAATTTT
2575824 ATATCAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
37 2 0.03
38 16 0.28
39 17 0.29
40 8 0.14
42 11 0.19
43 3 0.05
44 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.54
Consensus pattern (41 bp):
TTAATATATTTTGATAACATTTATAATAATTTTGATAATAT
Found at i:2580422 original size:27 final size:26
Alignment explanation
Indices: 2580375--2580426 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
2580365 TGATTTACGA
* *
2580375 TATTTATATATATATTTTTTTATTTTT
1 TATTTATATATAAATTATTTT-TTTTT
2580402 TATTTA-ATATTAAATTATTTTTTTT
1 TATTTATATA-TAAATTATTTTTTTT
2580427 AAATTGAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
26 7 0.32
27 15 0.68
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (26 bp):
TATTTATATATAAATTATTTTTTTTT
Found at i:2582371 original size:27 final size:23
Alignment explanation
Indices: 2582308--2582400 Score: 62
Period size: 27 Copynumber: 3.8 Consensus size: 23
2582298 ATATATTTAA
2582308 AATATTACATATTTATATAAATTTT
1 AATATT-CATA-TTATATAAATTTT
*
2582333 AATATTTTATATTATATAAATACGTTT
1 AATA-TTCATATTATATAAAT---TTT
** **
2582360 ATATATTCATATTACGT-TTTTTT
1 A-ATATTCATATTATATAAATTTT
*
2582383 AATATTTATATTATATAA
1 AATATTCATATTATATAA
2582401 TCATATTCGA
Statistics
Matches: 52, Mismatches: 10, Indels: 14
0.68 0.13 0.18
Matches are distributed among these distances:
22 12 0.23
23 4 0.08
24 10 0.19
25 7 0.13
26 3 0.06
27 13 0.25
28 3 0.06
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (23 bp):
AATATTCATATTATATAAATTTT
Found at i:2583135 original size:19 final size:19
Alignment explanation
Indices: 2583111--2583147 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2583101 ATCCATTTGT
2583111 TTGTCAAAAATGATGGTTA
1 TTGTCAAAAATGATGGTTA
*
2583130 TTGTCAAAAATGGTGGTT
1 TTGTCAAAAATGATGGTT
2583148 TCCTTTGAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.24, T:0.38
Consensus pattern (19 bp):
TTGTCAAAAATGATGGTTA
Found at i:2587705 original size:19 final size:19
Alignment explanation
Indices: 2587678--2587714 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2587668 ACCCATTTGT
2587678 TTGTAAAAAATGATGGTTA
1 TTGTAAAAAATGATGGTTA
* *
2587697 TTGTCAAAAATGGTGGTT
1 TTGTAAAAAATGATGGTT
2587715 TCCTTTGGAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (19 bp):
TTGTAAAAAATGATGGTTA
Found at i:2592967 original size:19 final size:19
Alignment explanation
Indices: 2592943--2592983 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
2592933 CGATTATACG
*
2592943 ATATAAATATAAACATAAT
1 ATATAAAAATAAACATAAT
**
2592962 ATATAAAAATAATTATAAT
1 ATATAAAAATAAACATAAT
2592981 ATA
1 ATA
2592984 GCAAGATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (19 bp):
ATATAAAAATAAACATAAT
Found at i:2594590 original size:39 final size:38
Alignment explanation
Indices: 2594546--2594633 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 38
2594536 TTATTTAATA
2594546 AAAAAATAATTA-AAATATAAT-ATAAATTATAAATATATT
1 AAAAAAT-ATTATAAATATAATGA-AAATT-TAAATATATT
* *
2594585 AAAAAATATTATTAATATAATGAATATTTAAATATATT
1 AAAAAATATTATAAATATAATGAAAATTTAAATATATT
2594623 AAAAAAATATT
1 -AAAAAATATT
2594634 TTTATAAAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
38 14 0.32
39 29 0.66
40 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (38 bp):
AAAAAATATTATAAATATAATGAAAATTTAAATATATT
Found at i:2594666 original size:27 final size:27
Alignment explanation
Indices: 2594634--2594704 Score: 83
Period size: 30 Copynumber: 2.6 Consensus size: 27
2594624 AAAAAATATT
*
2594634 TTTATA-AAATTTTAA-TATATTAAAA
1 TTTATATAAATATTAATTATATTAAAA
2594659 TTTATATAAATATTAATTATATTATCAAAA
1 TTTATATAAATATTAATTATA-T-T-AAAA
*
2594689 TATATATAAATATTAA
1 TTTATATAAATATTAA
2594705 AAAATTATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.15
26 8 0.21
27 4 0.10
28 1 0.03
29 1 0.03
30 19 0.49
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (27 bp):
TTTATATAAATATTAATTATATTAAAA
Found at i:2595561 original size:23 final size:25
Alignment explanation
Indices: 2595499--2595561 Score: 73
Period size: 23 Copynumber: 2.7 Consensus size: 25
2595489 TATAAATCAC
2595499 TAAATT-TAA-TATTAATTTTTATT
1 TAAATTATAATTATTAATTTTTATT
*
2595522 TAAATTATAATTTTTAA-TTTTA-T
1 TAAATTATAATTATTAATTTTTATT
2595545 TAAATTAT-ATTAATTAA
1 TAAATTATAATT-ATTAA
2595562 AATAAAATAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
22 3 0.09
23 19 0.54
24 8 0.23
25 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TAAATTATAATTATTAATTTTTATT
Found at i:2600916 original size:2 final size:2
Alignment explanation
Indices: 2600909--2600957 Score: 80
Period size: 2 Copynumber: 24.5 Consensus size: 2
2600899 CCTTCCATGC
* *
2600909 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2600951 TA TA TA T
1 TA TA TA T
2600958 CTTGCAGATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2602628 original size:21 final size:21
Alignment explanation
Indices: 2602581--2602644 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 21
2602571 TGGAATTTTT
*
2602581 TTTTTTATATT-ATTAAAATA
1 TTTTTTATATTAATTTAAATA
**
2602601 TTATTTTATATTAATTTTTATA
1 TT-TTTTATATTAATTTAAATA
2602623 TTTTTTATAATTAATTTAAATA
1 TTTTTTAT-ATTAATTTAAATA
2602645 AAATATTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 2 0.06
21 15 0.42
22 19 0.53
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (21 bp):
TTTTTTATATTAATTTAAATA
Found at i:2603499 original size:23 final size:21
Alignment explanation
Indices: 2603459--2603506 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
2603449 ATATGATATA
2603459 ATATAATATATAAATATTTATTT
1 ATATAATATATAAATA-TTA-TT
2603482 ATATAA-ATATAAATTATTATT
1 ATATAATATATAAA-TATTATT
2603503 ATAT
1 ATAT
2603507 TAAAATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.25
22 10 0.42
23 8 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATAATATATAAATATTATT
Found at i:2603530 original size:27 final size:25
Alignment explanation
Indices: 2603500--2603606 Score: 76
Period size: 27 Copynumber: 4.0 Consensus size: 25
2603490 ATAAATTATT
2603500 ATTATATTAAAATTTATATAAATATAA
1 ATTATATT-AAATTTATA-AAATATAA
* *
2603527 ATTATTTTAAATATAATTATAATATAATAA
1 ATTATATT-AA-AT--TTATAAAAT-ATAA
2603557 ATTATA-TAAATTTAATACAAATAAATAA
1 ATTATATTAAATTT-ATA-AAAT--ATAA
2603585 A-TA-ATTAAATTTATAAAATATA
1 ATTATATTAAATTTATAAAATATA
2603607 TATCATCTCA
Statistics
Matches: 68, Mismatches: 4, Indels: 20
0.74 0.04 0.22
Matches are distributed among these distances:
23 3 0.04
25 6 0.09
26 7 0.10
27 24 0.35
28 10 0.15
29 4 0.06
30 14 0.21
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTATATTAAATTTATAAAATATAA
Found at i:2603552 original size:33 final size:33
Alignment explanation
Indices: 2603478--2603561 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 33
2603468 ATAAATATTT
*
2603478 ATTTATATAAATATAAATTATTATTATATTAAA
1 ATTTATATAAATATAAATTATTATTATAATAAA
*
2603511 ATTTATATAAATATAAATTATT-TTA-AATATA
1 ATTTATATAAATATAAATTATTATTATAATAAA
*
2603542 A-TTATA-ATATAATAAATTAT
1 ATTTATATAAAT-ATAAATTAT
2603562 ATAAATTTAA
Statistics
Matches: 47, Mismatches: 3, Indels: 5
0.85 0.05 0.09
Matches are distributed among these distances:
29 3 0.06
30 14 0.30
31 5 0.11
32 3 0.06
33 22 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
ATTTATATAAATATAAATTATTATTATAATAAA
Found at i:2603564 original size:23 final size:22
Alignment explanation
Indices: 2603537--2603608 Score: 60
Period size: 23 Copynumber: 3.2 Consensus size: 22
2603527 ATTATTTTAA
2603537 ATATAATTATAATATAATAAATT
1 ATATAATTATAATATAATAAA-T
*
2603560 ATATAAATT-TAATACAAATAAAT
1 ATAT-AATTATAATA-TAATAAAT
* *
2603583 AAATAATTA-AAT-TTATAAAAT
1 ATATAATTATAATATAAT-AAAT
2603604 ATATA
1 ATATA
2603609 TCATCTCACT
Statistics
Matches: 40, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
20 2 0.05
21 8 0.20
22 7 0.17
23 13 0.32
24 10 0.25
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATAATTATAATATAATAAAT
Found at i:2604348 original size:22 final size:22
Alignment explanation
Indices: 2604322--2604363 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
2604312 ATTTTTTAAA
2604322 ATTTAAAT-TTAATTATAAAAAT
1 ATTTAAATATTAA-TATAAAAAT
2604344 ATTTAAATATTAATATAAAA
1 ATTTAAATATTAATATAAAA
2604364 TACTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTTAAATATTAATATAAAAAT
Found at i:2609764 original size:2 final size:2
Alignment explanation
Indices: 2609752--2609784 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
2609742 AATAAGGATG
2609752 AT AT A- 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
2609785 GATACAATGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2611846 original size:28 final size:26
Alignment explanation
Indices: 2611814--2611870 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 26
2611804 TATAAATATA
*
2611814 ATACAAGAAATAT-GAATATGATATTAAT
1 ATACAA-AAATATCAAATAT-ATA-TAAT
2611842 ATACAAAAATATCAAATATATATAAT
1 ATACAAAAATATCAAATATATATAAT
2611868 ATA
1 ATA
2611871 AATTTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 7 0.26
27 9 0.33
28 11 0.41
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (26 bp):
ATACAAAAATATCAAATATATATAAT
Found at i:2613146 original size:13 final size:13
Alignment explanation
Indices: 2613128--2613158 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
2613118 TTAAACAGTT
2613128 AATTTAGTTTTTC
1 AATTTAGTTTTTC
2613141 AATTTAGTTTTTC
1 AATTTAGTTTTTC
2613154 AATTT
1 AATTT
2613159 CATTTAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.26, C:0.06, G:0.06, T:0.61
Consensus pattern (13 bp):
AATTTAGTTTTTC
Found at i:2614702 original size:13 final size:12
Alignment explanation
Indices: 2614672--2614744 Score: 52
Period size: 11 Copynumber: 6.5 Consensus size: 12
2614662 AATAAATGTT
2614672 ATTTTAAAAAT-
1 ATTTTAAAAATA
*
2614683 TTTTTAAAATATA
1 ATTTTAAAA-ATA
2614696 ATTTTAAAAAATA
1 ATTTT-AAAAATA
* *
2614709 A--CT-AAAGTA
1 ATTTTAAAAATA
2614718 ATTTT-AAAAT-
1 ATTTTAAAAATA
2614728 -TTTTAAAAATA
1 ATTTTAAAAATA
2614739 ATTTTA
1 ATTTTA
2614745 GAGATACTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 15
0.70 0.09 0.22
Matches are distributed among these distances:
9 10 0.21
10 5 0.10
11 14 0.29
12 7 0.15
13 8 0.17
14 4 0.08
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (12 bp):
ATTTTAAAAATA
Found at i:2618844 original size:13 final size:13
Alignment explanation
Indices: 2618826--2618850 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2618816 ATTGGTCTGC
2618826 AAAATATTTTATA
1 AAAATATTTTATA
2618839 AAAATATTTTAT
1 AAAATATTTTAT
2618851 TTTTATATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATATTTTATA
Found at i:2620174 original size:2 final size:2
Alignment explanation
Indices: 2620167--2620203 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2620157 GGCTTGTTTG
2620167 AT AT AT AT AT AT 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 AT AT AT AT AT AT A
2620204 CATACCTACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2620208 original size:4 final size:4
Alignment explanation
Indices: 2620201--2620236 Score: 54
Period size: 4 Copynumber: 9.0 Consensus size: 4
2620191 ATATATATAT
* *
2620201 ATAC ATAC CTAC ATAC ATAC AAAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
2620237 TAATCATAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.28, G:0.00, T:0.22
Consensus pattern (4 bp):
ATAC
Found at i:2621652 original size:2 final size:2
Alignment explanation
Indices: 2621645--2621671 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2621635 AGCATTCTTT
2621645 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 T
2621672 TGCAATGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2622564 original size:20 final size:21
Alignment explanation
Indices: 2622523--2622568 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
2622513 TTTTTTATTT
* *
2622523 ATTAAATAATTATTATTTTAA
1 ATTAAAAAATTAATATTTTAA
2622544 ATTAAAAAATTAATA-TTTAA
1 ATTAAAAAATTAATATTTTAA
2622564 ATTAA
1 ATTAA
2622569 TTTATTTCGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTAAAAAATTAATATTTTAA
Found at i:2622833 original size:12 final size:12
Alignment explanation
Indices: 2622801--2622834 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2622791 ATTATACCTT
* *
2622801 ATATATATATAT
1 ATATATATCTAA
2622813 ATATATATCTAA
1 ATATATATCTAA
2622825 ATATATATCT
1 ATATATATCT
2622835 TCATAAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATATCTAA
Found at i:2623399 original size:6 final size:6
Alignment explanation
Indices: 2623368--2623436 Score: 52
Period size: 6 Copynumber: 11.3 Consensus size: 6
2623358 TTAATAATTT
* * * * *
2623368 TAAATA -AAATA TAATTA CATATA TAAATA TAATACA AAAATA TAAATA
1 TAAATA TAAATA TAAATA TAAATA TAAATA TAA-ATA TAAATA TAAATA
2623416 T-AATA TTAATATA TAAATA TA
1 TAAATA -TAA-ATA TAAATA TA
2623437 TTAAATTTAT
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
5 9 0.19
6 28 0.58
7 8 0.17
8 3 0.06
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAATA
Found at i:2623410 original size:19 final size:19
Alignment explanation
Indices: 2623388--2623436 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
2623378 ATAATTACAT
2623388 ATATAAATATAATACAAAA
1 ATATAAATATAATACAAAA
** *
2623407 ATATAAATATAATATTAAT
1 ATATAAATATAATACAAAA
2623426 ATATAAATATA
1 ATATAAATATA
2623437 TTAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (19 bp):
ATATAAATATAATACAAAA
Found at i:2623416 original size:25 final size:25
Alignment explanation
Indices: 2623388--2623436 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2623378 ATAATTACAT
2623388 ATATAA-ATATAATACAAAAATATAA
1 ATATAATAT-TAATACAAAAATATAA
* *
2623413 ATATAATATTAATATATAAATATA
1 ATATAATATTAATACAAAAATATA
2623437 TTAAATTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (25 bp):
ATATAATATTAATACAAAAATATAA
Found at i:2623439 original size:16 final size:18
Alignment explanation
Indices: 2623405--2623454 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
2623395 TATAATACAA
*
2623405 AAATATAAAT-ATAATATT
1 AAATATATATAAT-ATATT
2623423 -AATATATA-AATATATT
1 AAATATATATAATATATT
*
2623439 AAATTTATATAATATA
1 AAATATATATAATATA
2623455 ATTTTTTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 5 0.19
17 16 0.59
18 6 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AAATATATATAATATATT
Found at i:2626201 original size:14 final size:14
Alignment explanation
Indices: 2626182--2626216 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
2626172 AGATGAAAAT
*
2626182 AATTAATAATTTAA
1 AATTAACAATTTAA
2626196 AATTAAACAATTTAA
1 AATT-AACAATTTAA
2626211 AATTAA
1 AATTAA
2626217 AAATAACTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (14 bp):
AATTAACAATTTAA
Found at i:2626209 original size:15 final size:15
Alignment explanation
Indices: 2626189--2626217 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2626179 AATAATTAAT
2626189 AATTTAAAATTAAAC
1 AATTTAAAATTAAAC
2626204 AATTTAAAATTAAA
1 AATTTAAAATTAAA
2626218 AATAACTTGA
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:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (15 bp):
AATTTAAAATTAAAC
Found at i:2626213 original size:32 final size:33
Alignment explanation
Indices: 2626177--2626252 Score: 77
Period size: 32 Copynumber: 2.4 Consensus size: 33
2626167 AGTTTAGATG
* *
2626177 AAAATAATTAATAATTTAAAATTAAACA-ATTT
1 AAAATAATTAATAACTTAAAATTAAAAAGATTT
* * *
2626209 AAAATTAA-AAATAACTTGAACTTAAAAAGATTT
1 AAAA-TAATTAATAACTTAAAATTAAAAAGATTT
2626242 AAAA-AATTAAT
1 AAAATAATTAAT
2626253 TCAAAATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
31 2 0.06
32 22 0.63
33 11 0.31
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.33
Consensus pattern (33 bp):
AAAATAATTAATAACTTAAAATTAAAAAGATTT
Found at i:2627264 original size:16 final size:16
Alignment explanation
Indices: 2627233--2627275 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2627223 GTACTAAATG
2627233 AATTAGTTTATTTAAAAA
1 AATTA-TTT-TTTAAAAA
*
2627251 AATTATTTTTTAAAAT
1 AATTATTTTTTAAAAA
*
2627267 AGTTATTTT
1 AATTATTTT
2627276 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.65
17 3 0.13
18 5 0.22
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
AATTATTTTTTAAAAA
Found at i:2627414 original size:29 final size:32
Alignment explanation
Indices: 2627369--2627438 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
2627359 TTAAATATGT
*
2627369 TATATT-AATCATTTTTA-TA-ATTTTT-AAA
1 TATATTAAATCATATTTATTATATTTTTCAAA
*
2627397 TATATTAAATCATATTTATTATATTTTTCATA
1 TATATTAAATCATATTTATTATATTTTTCAAA
*
2627429 TCTATTAAAT
1 TATATTAAAT
2627439 GTTTCTTGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.17
29 10 0.29
30 2 0.06
31 6 0.17
32 11 0.31
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (32 bp):
TATATTAAATCATATTTATTATATTTTTCAAA
Found at i:2633509 original size:77 final size:78
Alignment explanation
Indices: 2633361--2633513 Score: 202
Period size: 78 Copynumber: 2.0 Consensus size: 78
2633351 GTTTCATTAT
* * * * * *
2633361 TAATAATTATTTATTGTAATAATAGTAGATAAAAATATTTTTAATTTATTGGTGTTAATTTTGTA
1 TAATAATTATTTACTATAATAATAATAAATAAAAATATTTTTAATTTAGTGGTGTTAATTTTATA
2633426 ATTCTTTCAAATC
66 ATTCTTTCAAATC
* **
2633439 TAATAATTATTTACTATAATGATAATAAATAATAAATATTTTTTGTTTAGT-G-GTTAATTTTAT
1 TAATAATTATTTACTATAATAATAATAAATAA-AAATATTTTTAATTTAGTGGTGTTAATTTTAT
2633502 AATTCTTTCAAA
65 AATTCTTTCAAA
2633514 AATTTCTAAC
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
77 22 0.34
78 28 0.43
79 15 0.23
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.50
Consensus pattern (78 bp):
TAATAATTATTTACTATAATAATAATAAATAAAAATATTTTTAATTTAGTGGTGTTAATTTTATA
ATTCTTTCAAATC
Found at i:2633531 original size:2 final size:2
Alignment explanation
Indices: 2633524--2633554 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2633514 AATTTCTAAC
2633524 AT AT AT 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 AT AT AT A
2633555 GAGAGAGAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2633559 original size:2 final size:2
Alignment explanation
Indices: 2633554--2633582 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2633544 ATATATATAT
2633554 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2633583 TTGAATATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2638655 original size:186 final size:186
Alignment explanation
Indices: 2638312--2638697 Score: 567
Period size: 186 Copynumber: 2.1 Consensus size: 186
2638302 TTATAATATC
* * * *
2638312 AATTAA-AAGATAGTACATATTAATTTCATTTTATCTTCATTTTGAGAAAATGATTTTAATTTTA
1 AATTAAGAAG-TAATACATATTAATTTCATGTTATCTTCATTTTGAAAAAATAATTTTAATTTTA
*
2638376 ATACTTAAAATAATTCACTTAATGCATTTTACTAAAAACATTATTATATTTCTCGTAATGTCTTT
65 ATACTTAAAATAATTCACTTAATACATTTTACTAAAAACATTATTATATTTCTCGTAATGTCTTT
* * * * * *
2638441 TTATTTAAAAATTTTTGACATTGAAGACTTCATCTAAATTTCTAAACATTTAAGTGG
130 TTATTTAAAAATTTTTAACATCGAAGACTTCATCTAAATTCCCAAACATTCAAGTGA
*
2638498 AATTAAGAAGTAATACATATTAATTTCATGTTATCTTTATTTTGAAAAAATAATTTTAATTTTAA
1 AATTAAGAAGTAATACATATTAATTTCATGTTATCTTCATTTTGAAAAAATAATTTTAATTTTAA
* * * *
2638563 TACTTAAAATAATTTACTTAATACATTTTATTAGAAATATTATTATATTTCTCGTAATGTCTTTT
66 TACTTAAAATAATTCACTTAATACATTTTACTAAAAACATTATTATATTTCTCGTAATGTCTTTT
* * * *
2638628 TATTTAAAAGTTTTTAACGTCGAAGACTTCATCTATATTCCCAACCATTCAAGTGA
131 TATTTAAAAATTTTTAACATCGAAGACTTCATCTAAATTCCCAAACATTCAAGTGA
*
2638684 AATTCAGAAGTAAT
1 AATTAAGAAGTAAT
2638698 TCTCCCTTGC
Statistics
Matches: 178, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
186 175 0.98
187 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (186 bp):
AATTAAGAAGTAATACATATTAATTTCATGTTATCTTCATTTTGAAAAAATAATTTTAATTTTAA
TACTTAAAATAATTCACTTAATACATTTTACTAAAAACATTATTATATTTCTCGTAATGTCTTTT
TATTTAAAAATTTTTAACATCGAAGACTTCATCTAAATTCCCAAACATTCAAGTGA
Found at i:2638829 original size:97 final size:97
Alignment explanation
Indices: 2638673--2638850 Score: 239
Period size: 97 Copynumber: 1.8 Consensus size: 97
2638663 TATTCCCAAC
*
2638673 CATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCGTAACAATCCCTTGAATTT
1 CATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCATAACAATCCCTTGAATTT
*
2638738 GAGATGGAGCACCCTTAATCTAAATCCCCCAG
66 GAGATAGAGCACCCTTAATCTAAATCCCCCAG
* * * * * * ** * *
2638770 CATTCAAGTGGAATTCAGATGTAATTTTCCTTTGTAAGGAAATTTTATAATAATTCCTTGAATTT
1 CATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCATAACAATCCCTTGAATTT
*
2638835 GAGATAGAGCATCCTT
66 GAGATAGAGCACCCTT
2638851 CGTAGAAAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
97 68 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (97 bp):
CATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCATAACAATCCCTTGAATTT
GAGATAGAGCACCCTTAATCTAAATCCCCCAG
Found at i:2639373 original size:24 final size:27
Alignment explanation
Indices: 2639300--2639370 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
2639290 AAACAAGCCT
* *
2639300 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
2639328 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
2639355 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
2639371 AATGGATGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:2641292 original size:21 final size:22
Alignment explanation
Indices: 2641254--2641299 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2641244 ATCTGTTGAA
* **
2641254 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
2641275 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
2641297 ACT
1 ACT
2641300 TGTCTGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:2643785 original size:20 final size:20
Alignment explanation
Indices: 2643751--2643796 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
2643741 AAGAATTGAA
* *
2643751 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGAGAG
**
2643771 GAGGGATACTTGAGAGAGAG
1 GAGGGATACAAGAGAGAGAG
2643791 GAGGGA
1 GAGGGA
2643797 GCCTCTATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.04, G:0.48, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGAGAG
Found at i:2643931 original size:27 final size:28
Alignment explanation
Indices: 2643872--2643942 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 28
2643862 AAACAAGCCT
* *
2643872 CCATATTTGACAAATACAAAGAAAACCA
1 CCATTTTTGACAAACACAAAGAAAACCA
* *
2643900 CCATTTTTAACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGAAAACCA
2643927 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
2643943 AATAGGTGGC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.23
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAGAAAACCA
Found at i:2645245 original size:7 final size:8
Alignment explanation
Indices: 2645217--2645244 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
2645207 AATAACAATC
2645217 TTTTTATT
1 TTTTTATT
2645225 TTTTTATT
1 TTTTTATT
2645233 TTTTTATT
1 TTTTTATT
2645241 TTTT
1 TTTT
2645245 ACTATCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTATT
Found at i:2645790 original size:17 final size:17
Alignment explanation
Indices: 2645768--2645808 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2645758 GATTTCAAGG
* *
2645768 ATAAAATCACTTTAGTC
1 ATAAAATCAATTTAATC
2645785 ATAAAATCAATTTAATC
1 ATAAAATCAATTTAATC
*
2645802 ATTAAAT
1 ATAAAAT
2645809 TACTATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (17 bp):
ATAAAATCAATTTAATC
Found at i:2684507 original size:17 final size:17
Alignment explanation
Indices: 2684485--2684538 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
2684475 GTTAATTATG
2684485 TAAATATAAATATAATA
1 TAAATATAAATATAATA
*
2684502 TAAATATTAAATATATTA
1 TAAATA-TAAATATAATA
*
2684520 -AAATTTTAAATATAA-A
1 TAAA-TATAAATATAATA
2684536 TAA
1 TAA
2684539 TATGTATTAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 1 0.03
17 19 0.61
18 11 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TAAATATAAATATAATA
Found at i:2684600 original size:29 final size:32
Alignment explanation
Indices: 2684555--2684624 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
2684545 TTAAATATGT
*
2684555 TATATT-AATCATTTTTA-TA-ATTTTT-AAA
1 TATATTAAATCATATTTATTATATTTTTCAAA
*
2684583 TATATTAAATCATATTTATTATATTTTTCATA
1 TATATTAAATCATATTTATTATATTTTTCAAA
*
2684615 TCTATTAAAT
1 TATATTAAAT
2684625 GTTTCTTGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 6 0.17
29 10 0.29
30 2 0.06
31 6 0.17
32 11 0.31
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (32 bp):
TATATTAAATCATATTTATTATATTTTTCAAA
Found at i:2690692 original size:77 final size:78
Alignment explanation
Indices: 2690544--2690696 Score: 202
Period size: 78 Copynumber: 2.0 Consensus size: 78
2690534 GTTTCATTAT
* * * * * *
2690544 TAATAATTATTTATTGTAATAATAGTAGATAAAAATATTTTTAATTTATTGGTGTTAATTTTGTA
1 TAATAATTATTTACTATAATAATAATAAATAAAAATATTTTTAATTTAGTGGTGTTAATTTTATA
2690609 ATTCTTTCAAATC
66 ATTCTTTCAAATC
* **
2690622 TAATAATTATTTACTATAATGATAATAAATAATAAATATTTTTTGTTTAGT-G-GTTAATTTTAT
1 TAATAATTATTTACTATAATAATAATAAATAA-AAATATTTTTAATTTAGTGGTGTTAATTTTAT
2690685 AATTCTTTCAAA
65 AATTCTTTCAAA
2690697 AAATTTCTAA
Statistics
Matches: 65, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
77 22 0.34
78 28 0.43
79 15 0.23
ACGTcount: A:0.39, C:0.04, G:0.08, T:0.50
Consensus pattern (78 bp):
TAATAATTATTTACTATAATAATAATAAATAAAAATATTTTTAATTTAGTGGTGTTAATTTTATA
ATTCTTTCAAATC
Found at i:2690713 original size:2 final size:2
Alignment explanation
Indices: 2690708--2690740 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2690698 AATTTCTAAC
2690708 AT AT AT AT 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 AT AT AT AT A
2690741 GAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2690745 original size:2 final size:2
Alignment explanation
Indices: 2690740--2690768 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2690730 ATATATATAT
2690740 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2690769 TTGAATATCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2695844 original size:186 final size:186
Alignment explanation
Indices: 2695501--2695886 Score: 567
Period size: 186 Copynumber: 2.1 Consensus size: 186
2695491 TTATAATATC
* * * *
2695501 AATTAA-AAGATAGTACATATTAATTTCATTTTATCTTCATTTTGAGAAAATGATTTTAATTTTA
1 AATTAAGAAG-TAATACATATTAATTTCATGTTATCTTCATTTTGAAAAAATAATTTTAATTTTA
*
2695565 ATACTTAAAATAATTCACTTAATGCATTTTACTAAAAACATTATTATATTTCTCGTAATGTCTTT
65 ATACTTAAAATAATTCACTTAATACATTTTACTAAAAACATTATTATATTTCTCGTAATGTCTTT
* * * * * *
2695630 TTATTTAAAAATTTTTGACATTGAAGACTTCATCTAAATTTCTAAACATTTAAGTGG
130 TTATTTAAAAATTTTTAACATCGAAGACTTCATCTAAATTCCCAAACATTCAAGTGA
*
2695687 AATTAAGAAGTAATACATATTAATTTCATGTTATCTTTATTTTGAAAAAATAATTTTAATTTTAA
1 AATTAAGAAGTAATACATATTAATTTCATGTTATCTTCATTTTGAAAAAATAATTTTAATTTTAA
* * * *
2695752 TACTTAAAATAATTTACTTAATACATTTTATTAGAAATATTATTATATTTCTCGTAATGTCTTTT
66 TACTTAAAATAATTCACTTAATACATTTTACTAAAAACATTATTATATTTCTCGTAATGTCTTTT
* * * *
2695817 TATTTAAAAGTTTTTAACGTCGAAGACTTCATCTATATTCCCAACCATTCAAGTGA
131 TATTTAAAAATTTTTAACATCGAAGACTTCATCTAAATTCCCAAACATTCAAGTGA
*
2695873 AATTCAGAAGTAAT
1 AATTAAGAAGTAAT
2695887 TCTCCCTTGC
Statistics
Matches: 178, Mismatches: 21, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
186 175 0.98
187 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.08, T:0.44
Consensus pattern (186 bp):
AATTAAGAAGTAATACATATTAATTTCATGTTATCTTCATTTTGAAAAAATAATTTTAATTTTAA
TACTTAAAATAATTCACTTAATACATTTTACTAAAAACATTATTATATTTCTCGTAATGTCTTTT
TATTTAAAAATTTTTAACATCGAAGACTTCATCTAAATTCCCAAACATTCAAGTGA
Found at i:2696018 original size:97 final size:97
Alignment explanation
Indices: 2695862--2696039 Score: 239
Period size: 97 Copynumber: 1.8 Consensus size: 97
2695852 TATTCCCAAC
*
2695862 CATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCGTAACAATCCCTTGAATTT
1 CATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCATAACAATCCCTTGAATTT
*
2695927 GAGATGGAGCACCCTTAATCTAAATCCCCCAG
66 GAGATAGAGCACCCTTAATCTAAATCCCCCAG
* * * * * * ** * *
2695959 CATTCAAGTGGAATTCAGATGTAATTTTCCTTTGTAAGGAAATTTTATAATAATTCCTTGAATTT
1 CATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCATAACAATCCCTTGAATTT
*
2696024 GAGATAGAGCATCCTT
66 GAGATAGAGCACCCTT
2696040 CGTAGAAAAT
Statistics
Matches: 68, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
97 68 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (97 bp):
CATTCAAGTGAAATTCAGAAGTAATTCTCCCTTGCAAAGAAATTCCATAACAATCCCTTGAATTT
GAGATAGAGCACCCTTAATCTAAATCCCCCAG
Found at i:2696562 original size:24 final size:27
Alignment explanation
Indices: 2696489--2696559 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
2696479 AAACAAGCCT
* *
2696489 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
2696517 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
2696544 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
2696560 AATGGATGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:2698481 original size:21 final size:22
Alignment explanation
Indices: 2698443--2698488 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
2698433 ATCTGTTGAA
* **
2698443 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
2698464 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
2698486 ACT
1 ACT
2698489 TGTCTGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:2700965 original size:20 final size:20
Alignment explanation
Indices: 2700940--2700985 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
2700930 AAGAATTGAA
*
2700940 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
**
2700960 GAGGGATACTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
2700980 GAGGGA
1 GAGGGA
2700986 GCCTCTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.04, G:0.50, T:0.11
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:2701120 original size:27 final size:28
Alignment explanation
Indices: 2701061--2701131 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 28
2701051 AAACAAGCCT
* *
2701061 CCATATTTGACAAATACAAAGAAAACCA
1 CCATTTTTGACAAACACAAAGAAAACCA
* *
2701089 CCATTTTTAACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGAAAACCA
2701116 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
2701132 AATAGGTGGC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
27 21 0.55
28 17 0.45
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.23
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAGAAAACCA
Found at i:2702416 original size:5 final size:5
Alignment explanation
Indices: 2702401--2702429 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
2702391 AAAAATAACA
2702401 ATTTT -TTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
2702430 TTACTATCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
ATTTT
Found at i:2702976 original size:17 final size:17
Alignment explanation
Indices: 2702954--2702994 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
2702944 GATTTCAAGG
* *
2702954 ATAAAATCACTTTAGTC
1 ATAAAATCAATTTAATC
2702971 ATAAAATCAATTTAATC
1 ATAAAATCAATTTAATC
*
2702988 ATTAAAT
1 ATAAAAT
2702995 TACTATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (17 bp):
ATAAAATCAATTTAATC
Found at i:2706588 original size:20 final size:22
Alignment explanation
Indices: 2706560--2706616 Score: 66
Period size: 22 Copynumber: 2.7 Consensus size: 22
2706550 TTTTCTTGTC
*
2706560 ATGTCATTTTA-ATTAT-TTTT
1 ATGTAATTTTATATTATATTTT
2706580 ATGTAATTTTATATTATATTTT
1 ATGTAATTTTATATTATATTTT
*
2706602 AAT-TTATTTTATATT
1 -ATGTAATTTTATATT
2706617 TTATAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 10 0.31
21 5 0.16
22 15 0.47
23 2 0.06
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.65
Consensus pattern (22 bp):
ATGTAATTTTATATTATATTTT
Found at i:2706619 original size:12 final size:12
Alignment explanation
Indices: 2706572--2706620 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
2706562 GTCATTTTAA
*
2706572 TTATTTT-TATG
1 TTATTTTATATT
*
2706583 TAATTTTATATT
1 TTATTTTATATT
*
2706595 ATATTTTA-A-T
1 TTATTTTATATT
2706605 TTATTTTATATT
1 TTATTTTATATT
2706617 TTAT
1 TTAT
2706621 AAAATATCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 5
0.75 0.12 0.12
Matches are distributed among these distances:
10 8 0.27
11 8 0.27
12 14 0.47
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (12 bp):
TTATTTTATATT
Found at i:2706972 original size:13 final size:12
Alignment explanation
Indices: 2706942--2706984 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
2706932 TAGTTAAATT
*
2706942 TTTTTATTATTT
1 TTTTTATTATTA
2706954 TGTTTTATTAATTA
1 T-TTTTATT-ATTA
2706968 TTTTTATT-TTA
1 TTTTTATTATTA
2706979 TTTTTA
1 TTTTTA
2706985 AAGAAAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 9 0.32
12 1 0.04
13 14 0.50
14 4 0.14
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (12 bp):
TTTTTATTATTA
Found at i:2706977 original size:18 final size:17
Alignment explanation
Indices: 2706947--2706980 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2706937 AAATTTTTTT
*
2706947 ATTATTTTGTTTTATTA
1 ATTATTTTATTTTATTA
2706964 ATTATTTTTATTTTATT
1 ATTA-TTTTATTTTATT
2706981 TTTAAAGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTATTTTATTTTATTA
Found at i:2707093 original size:16 final size:18
Alignment explanation
Indices: 2707069--2707110 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2707059 AATATTATTT
2707069 AATATAA-TTTAATTAAA
1 AATATAATTTTAATTAAA
*
2707086 AATA-AATTTTTATTAAA
1 AATATAATTTTAATTAAA
2707103 AATTATAA
1 AA-TATAA
2707111 AAAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 2 0.10
17 15 0.71
18 2 0.10
19 2 0.10
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATATAATTTTAATTAAA
Found at i:2709337 original size:18 final size:18
Alignment explanation
Indices: 2709314--2709349 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2709304 ACCTAGTAGG
2709314 CTAGCAATTATTTAAAAA
1 CTAGCAATTATTTAAAAA
2709332 CTAGCAATTATTTAAAAA
1 CTAGCAATTATTTAAAAA
2709350 AAATCAAAGA
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:0.50, C:0.11, G:0.06, T:0.33
Consensus pattern (18 bp):
CTAGCAATTATTTAAAAA
Found at i:2709533 original size:28 final size:31
Alignment explanation
Indices: 2709481--2709537 Score: 84
Period size: 28 Copynumber: 1.9 Consensus size: 31
2709471 GCATCAAAAA
2709481 GTTATGTTGAAAGAACACAACATTTAAATTT
1 GTTATGTTGAAAGAACACAACATTTAAATTT
*
2709512 GTTATG-T-AAAG-ACATAACATTTAAAT
1 GTTATGTTGAAAGAACACAACATTTAAAT
2709538 AAAAAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 14 0.56
29 4 0.16
30 1 0.04
31 6 0.24
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (31 bp):
GTTATGTTGAAAGAACACAACATTTAAATTT
Found at i:2715571 original size:20 final size:19
Alignment explanation
Indices: 2715535--2715571 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2715525 ATTTTTTATT
2715535 TAAATTTAATTATAAAAAA
1 TAAATTTAATTATAAAAAA
2715554 TAAATATTAA-TATAAAAA
1 TAAAT-TTAATTATAAAAA
2715572 TAATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATTTAATTATAAAAAA
Found at i:2715646 original size:18 final size:19
Alignment explanation
Indices: 2715591--2715646 Score: 51
Period size: 24 Copynumber: 2.7 Consensus size: 19
2715581 ATTTTTTATT
*
2715591 TTTTAAATAATAATTTAAA
1 TTTTAAATAAAAATTTAAA
2715610 TTTATAAATCAAATTAAATTTAAA
1 TTT-TAAAT--AA--AAATTTAAA
2715634 -TTTAAATAAAAAT
1 TTTTAAATAAAAAT
2715647 ATTTAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
18 4 0.13
19 3 0.10
20 7 0.23
22 7 0.23
23 2 0.06
24 8 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTAAATAAAAATTTAAA
Found at i:2719768 original size:63 final size:63
Alignment explanation
Indices: 2719688--2719819 Score: 228
Period size: 63 Copynumber: 2.1 Consensus size: 63
2719678 AGCATAACAC
*
2719688 TTAGATCAGCACAAGTCGTTTTTCAATGTCATTAATCACGCTAGTACAACTTGCAATCACTAA
1 TTAGATCAGCACAAGTCGCTTTTCAATGTCATTAATCACGCTAGTACAACTTGCAATCACTAA
* * *
2719751 TTAGATCAGCACAAGTCGCTTTTCAATGTCCTTAATCATGCTAGTACAAGTTGCAATCACTAA
1 TTAGATCAGCACAAGTCGCTTTTCAATGTCATTAATCACGCTAGTACAACTTGCAATCACTAA
2719814 TTAGAT
1 TTAGAT
2719820 ATGCTGATGG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.33
Consensus pattern (63 bp):
TTAGATCAGCACAAGTCGCTTTTCAATGTCATTAATCACGCTAGTACAACTTGCAATCACTAA
Found at i:2720633 original size:34 final size:34
Alignment explanation
Indices: 2720595--2720659 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
2720585 ATTTCTTAGA
2720595 AGTTTATAAAGTGTTGATTAAAT-GGTGATTTCGT
1 AGTTTA-AAAGTGTTGATTAAATAGGTGATTTCGT
** *
2720629 AGTTTACCATTGTTGATTAAATAGGTGATTT
1 AGTTTAAAAGTGTTGATTAAATAGGTGATTT
2720660 GGTGGTTTGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 13 0.48
34 14 0.52
ACGTcount: A:0.29, C:0.05, G:0.22, T:0.45
Consensus pattern (34 bp):
AGTTTAAAAGTGTTGATTAAATAGGTGATTTCGT
Found at i:2720673 original size:34 final size:33
Alignment explanation
Indices: 2720606--2720794 Score: 227
Period size: 34 Copynumber: 5.6 Consensus size: 33
2720596 GTTTATAAAG
* * *
2720606 TGTTGATTAAATGGTGATTTCGTAGTTTACCAT
1 TGTTGATTAAATGGTGATTTGGTGGCTTACCAT
* *
2720639 TGTTGATTAAATAGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAAT-GGTGATTTGGTGGCTTACCAT
** *
2720673 TGTTGATTAAATGAGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATG-GTGATTTGGTGGCTTACCAT
*
2720707 TATTGATTAAATAGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAAT-GGTGATTTGGTGGCTTACCAT
* *
2720741 TGTTGACTAAATGGTAGATTTGGTAGG-TTGCCAT
1 TGTTGATTAAATGGT-GATTTGGT-GGCTTACCAT
2720775 TGTTGATTAAATGGTGATTT
1 TGTTGATTAAATGGTGATTT
2720795 TTACCAAACC
Statistics
Matches: 135, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
33 21 0.16
34 111 0.82
35 3 0.02
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (33 bp):
TGTTGATTAAATGGTGATTTGGTGGCTTACCAT
Found at i:2720714 original size:68 final size:67
Alignment explanation
Indices: 2720606--2720794 Score: 263
Period size: 68 Copynumber: 2.8 Consensus size: 67
2720596 GTTTATAAAG
* * * * *
2720606 TGTTGATTAAATGGTGATTTCGTAGTTTACCATTGTTGATTAAATAGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATAGGTGATTTGGTGGCTTACC
2720671 AT
66 AT
* *
2720673 TGTTGATTAAATGAGAAATTTGGTAGCTTACCATTATTGATTAAATAGGTGATTTGGTGGCTTAC
1 TGTTGATTAAATG-GAGATTTGGTAGCTTACCATTGTTGATTAAATAGGTGATTTGGTGGCTTAC
2720738 CAT
65 CAT
* * *
2720741 TGTTGACTAAATGGTAGATTTGGTAGGTTGCCATTGTTGATTAAAT-GGTGATTT
1 TGTTGATTAAATGG-AGATTTGGTAGCTTACCATTGTTGATTAAATAGGTGATTT
2720795 TTACCAAACC
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
67 22 0.20
68 86 0.80
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.42
Consensus pattern (67 bp):
TGTTGATTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATAGGTGATTTGGTGGCTTACC
AT
Found at i:2725266 original size:34 final size:34
Alignment explanation
Indices: 2725197--2725415 Score: 257
Period size: 34 Copynumber: 6.5 Consensus size: 34
2725187 AAGTGGGAGA
*
2725197 ATTGTTGATTAAATGG-TGATTTGGTAGTTTACC
1 ATTGTTGATTAAATGGATGATTTGGTAGCTTACC
* * *
2725230 ATTGTTGATTAAATGGATGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGATGATTTGGTAGCTTACC
*
2725264 ATTGTTGACTAAATGGGA-GATTTGGTAGCTTACC
1 ATTGTTGATTAAAT-GGATGATTTGGTAGCTTACC
* *
2725298 ATTGTTGATTAAATGAGA-AATTTGATAGCTTACC
1 ATTGTTGATTAAATG-GATGATTTGGTAGCTTACC
* * *
2725332 ATTATTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGATGATTTGGTAGCTTACC
* * **
2725366 ATTGTTGACTAAATGG-TAGATTTGGTAGGTTGTC
1 ATTGTTGATTAAATGGAT-GATTTGGTAGCTTACC
2725400 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2725416 TGGTTTTTAT
Statistics
Matches: 160, Mismatches: 21, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
33 19 0.12
34 138 0.86
35 3 0.02
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (34 bp):
ATTGTTGATTAAATGGATGATTTGGTAGCTTACC
Found at i:2725342 original size:102 final size:101
Alignment explanation
Indices: 2725197--2725415 Score: 321
Period size: 102 Copynumber: 2.2 Consensus size: 101
2725187 AAGTGGGAGA
** * * * * *
2725197 ATTGTTGATTAAATGGTGATTTGGTAGTTTACCATTGTTGATTAAATGGATGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATGGATGATTTGGTGGCTTA
2725262 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
66 CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
*
2725298 ATTGTTGATTAAATGAGAAATTTGATAGCTTACCATTATTGATTAAATGGGTGATTTGGTGGCTT
1 ATTGTTGATTAAATG-GAAATTTGATAGCTTACCATTATTGATTAAATGGATGATTTGGTGGCTT
* * **
2725363 ACCATTGTTGACTAAATGGTAGATTTGGTAGGTTGTC
65 ACCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
2725400 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2725416 TGGTTTTTAT
Statistics
Matches: 105, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
101 16 0.15
102 89 0.85
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (101 bp):
ATTGTTGATTAAATGGAAATTTGATAGCTTACCATTATTGATTAAATGGATGATTTGGTGGCTTA
CCATTGTTGACTAAATGGGAGATTTGGTAGCTTACC
Found at i:2727678 original size:1 final size:1
Alignment explanation
Indices: 2727672--2727764 Score: 78
Period size: 1 Copynumber: 93.0 Consensus size: 1
2727662 AAATCTTCAC
* * * ** * * * *
2727672 TTTTTTTTTTTGTTTTTTGTTTTTTTCTTTTTTCCTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
2727737 TTTTTTTTTGTTTTGTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
2727765 CCAATTGCCA
Statistics
Matches: 70, Mismatches: 22, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 70 1.00
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (1 bp):
T
Found at i:2727696 original size:16 final size:15
Alignment explanation
Indices: 2727672--2727758 Score: 102
Period size: 16 Copynumber: 5.5 Consensus size: 15
2727662 AAATCTTCAC
2727672 TTTTTTTTTTTGTTT
1 TTTTTTTTTTTGTTT
* *
2727687 TTTGTTTTTTTCTTT
1 TTTTTTTTTTTGTTT
*
2727702 TTTCCTTTTTTTGTTT
1 TTT-TTTTTTTTGTTT
*
2727718 TGTTTTTTTTTTCTTT
1 T-TTTTTTTTTTGTTT
2727734 TTCTTTTTTTTTGTTT
1 TT-TTTTTTTTTGTTT
2727750 TGTTTTTTT
1 T-TTTTTTT
2727759 CTTTTTCCAA
Statistics
Matches: 61, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
15 17 0.28
16 41 0.67
17 3 0.05
ACGTcount: A:0.00, C:0.06, G:0.07, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTTTGTTT
Found at i:2727711 original size:24 final size:23
Alignment explanation
Indices: 2727672--2727764 Score: 86
Period size: 24 Copynumber: 4.1 Consensus size: 23
2727662 AAATCTTCAC
*
2727672 TTTTTTTTTTT--GTTTTTTGTT
1 TTTTTTTTTTTCCTTTTTTTGTT
2727693 TTTTTCTTTTTTCCTTTTTTTGTT
1 TTTTT-TTTTTTCCTTTTTTTGTT
* *
2727717 TTGTTTTTTTTTTCTTTTTCT-TT
1 TT-TTTTTTTTTCCTTTTTTTGTT
* * *
2727740 TTTTTTGTTTT-GTTTTTTTCTT
1 TTTTTTTTTTTCCTTTTTTTGTT
2727762 TTT
1 TTT
2727765 CCAATTGCCA
Statistics
Matches: 61, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
21 11 0.18
22 19 0.31
23 4 0.07
24 24 0.39
25 3 0.05
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (23 bp):
TTTTTTTTTTTCCTTTTTTTGTT
Found at i:2727714 original size:31 final size:30
Alignment explanation
Indices: 2727672--2727764 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 30
2727662 AAATCTTCAC
2727672 TTTT-TTTTTTTGTTTTTTGTTTTTTTCTT
1 TTTTCTTTTTTTGTTTTTTGTTTTTTTCTT
*
2727701 TTTTCCTTTTTTTGTTTTGTTTTTTTTTTC-T
1 TTTT-CTTTTTTTGTTTT-TTGTTTTTTTCTT
2727732 TTTTCTTTTTTT-TTGTTTTGTTTTTTTCTT
1 TTTTCTTTTTTTGTT-TTTTGTTTTTTTCTT
2727762 TTT
1 TTT
2727765 CCAATTGCCA
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
29 16 0.28
30 14 0.25
31 17 0.30
32 10 0.18
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.87
Consensus pattern (30 bp):
TTTTCTTTTTTTGTTTTTTGTTTTTTTCTT
Found at i:2727727 original size:32 final size:32
Alignment explanation
Indices: 2727676--2727758 Score: 125
Period size: 32 Copynumber: 2.6 Consensus size: 32
2727666 CTTCACTTTT
*
2727676 TTTTTTTGTTTT-TTGTTTTTTTCTTTTT-TCC
1 TTTTTTTGTTTTGTTTTTTTTTTCTTTTTCT-C
*
2727707 TTTTTTTGTTTTGTTTTTTTTTTCTTTTTCTT
1 TTTTTTTGTTTTGTTTTTTTTTTCTTTTTCTC
2727739 TTTTTTTGTTTTGTTTTTTT
1 TTTTTTTGTTTTGTTTTTTT
2727759 CTTTTTCCAA
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
31 12 0.25
32 35 0.73
33 1 0.02
ACGTcount: A:0.00, C:0.06, G:0.07, T:0.87
Consensus pattern (32 bp):
TTTTTTTGTTTTGTTTTTTTTTTCTTTTTCTC
Found at i:2736238 original size:35 final size:36
Alignment explanation
Indices: 2736195--2736265 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
2736185 GTTGAAATTG
*
2736195 GGAAGGAAATGAA-AGAAAAAAAAAAGGAAAAAGAA
1 GGAAGGAAAAGAAGAGAAAAAAAAAAGGAAAAAGAA
** * *
2736230 GGAAGGAAAAGAAGAGGGAGAAAAAAGTAAAAAGAA
1 GGAAGGAAAAGAAGAGAAAAAAAAAAGGAAAAAGAA
2736266 AAAAATTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
35 12 0.40
36 18 0.60
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.03
Consensus pattern (36 bp):
GGAAGGAAAAGAAGAGAAAAAAAAAAGGAAAAAGAA
Found at i:2736306 original size:21 final size:20
Alignment explanation
Indices: 2736271--2736311 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
2736261 AAGAAAAAAA
*
2736271 TTTTGTTATTGTTTTGTATT
1 TTTTGTTATTGTTTTATATT
*
2736291 TTTTGTGTATTTTTTTATATT
1 TTTTGT-TATTGTTTTATATT
2736312 AATTAAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (20 bp):
TTTTGTTATTGTTTTATATT
Found at i:2738918 original size:2 final size:2
Alignment explanation
Indices: 2738911--2738939 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2738901 CGTTTGATAC
2738911 AT AT 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 AT AT A
2738940 CACCAATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2740348 original size:2 final size:2
Alignment explanation
Indices: 2740341--2740366 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2740331 GCATTCTTTA
2740341 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
2740367 TGCAATGGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2741245 original size:21 final size:20
Alignment explanation
Indices: 2741189--2741266 Score: 58
Period size: 20 Copynumber: 3.9 Consensus size: 20
2741179 ATATATCTTT
*
2741189 ATAATTAATTTAAA-TAAAA
1 ATAATTATTTTAAATTAAAA
*
2741208 AT-ATT-TTTTATTTATTAAATA
1 ATAATTATTTTA--AATTAAA-A
2741229 ATAATTATTTTAAATT-AAA
1 ATAATTATTTTAAATTAAAA
2741248 A-AATTAATATTTAAATTAA
1 ATAATT-AT-TTTAAATTAA
2741267 TTTGTTTCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
17 4 0.09
18 7 0.15
19 7 0.15
20 14 0.30
21 7 0.15
22 3 0.06
23 5 0.11
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATAATTATTTTAAATTAAAA
Found at i:2742262 original size:16 final size:16
Alignment explanation
Indices: 2742219--2742264 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
2742209 AATATTAAAA
*
2742219 TAAAAAAATAATTTTT
1 TAAAATAATAATTTTT
* **
2742235 TAATATTTTAATTTTT
1 TAAAATAATAATTTTT
2742251 TAAAATAATAATTT
1 TAAAATAATAATTT
2742265 AAATTTATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAAAATAATAATTTTT
Found at i:2742265 original size:21 final size:21
Alignment explanation
Indices: 2742235--2742295 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2742225 AATAATTTTT
* * *
2742235 TAATATTTTAATTTTTTAAAA
1 TAATAATTTAAATTTATAAAA
*
2742256 TAATAATTTAAATTTATAAAT
1 TAATAATTTAAATTTATAAAA
2742277 TAAATTAAATTTAAATTTA
1 T-AA-T-AATTTAAATTTA
2742296 AACAAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 18 0.55
22 2 0.06
23 1 0.03
24 12 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TAATAATTTAAATTTATAAAA
Found at i:2742271 original size:6 final size:6
Alignment explanation
Indices: 2742260--2742297 Score: 51
Period size: 6 Copynumber: 6.3 Consensus size: 6
2742250 TTAAAATAAT
*
2742260 AATTTA AATTTA TAAATTA AA-TTA AATTTA AATTTA AA
1 AATTTA AATTTA -AATTTA AATTTA AATTTA AATTTA AA
2742298 CAAATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 5 0.17
6 19 0.66
7 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
AATTTA
Found at i:2742764 original size:35 final size:35
Alignment explanation
Indices: 2742682--2742804 Score: 133
Period size: 35 Copynumber: 3.5 Consensus size: 35
2742672 AAAAAGACAA
* *
2742682 GTCTACCTCTCAAT-CTCCCGTTCCACAAGTTAAT
1 GTCTACCTCTCAATCCCCCCATTCCACAAGTTAAT
* * *
2742716 ATCTACCAT-TCAATCCCCCCATTTCACAAGTTGAT
1 GTCTACC-TCTCAATCCCCCCATTCCACAAGTTAAT
* * *
2742751 GTCTGCCTCTCAATCACACCACATTCCACAAGGTAAT
1 GTCTACCTCTCAATC-C-CCCCATTCCACAAGTTAAT
2742788 GTCTACCTCTCAATCCC
1 GTCTACCTCTCAATCCC
2742805 ACCTCATGTA
Statistics
Matches: 72, Mismatches: 12, Indels: 9
0.77 0.13 0.10
Matches are distributed among these distances:
34 12 0.17
35 29 0.40
36 2 0.03
37 29 0.40
ACGTcount: A:0.26, C:0.37, G:0.08, T:0.29
Consensus pattern (35 bp):
GTCTACCTCTCAATCCCCCCATTCCACAAGTTAAT
Found at i:2742782 original size:37 final size:36
Alignment explanation
Indices: 2742682--2742803 Score: 126
Period size: 37 Copynumber: 3.4 Consensus size: 36
2742672 AAAAAGACAA
* *
2742682 GTCTACCTCTCAAT-CTCC-CGTTCCACAAGTTAAT
1 GTCTACCTCTCAATCCACCACATTCCACAAGTTAAT
* * * *
2742716 ATCTACCAT-TCAATCC-CCCCATTTCACAAGTTGAT
1 GTCTACC-TCTCAATCCACCACATTCCACAAGTTAAT
* *
2742751 GTCTGCCTCTCAATCACACCACATTCCACAAGGTAAT
1 GTCTACCTCTCAATC-CACCACATTCCACAAGTTAAT
2742788 GTCTACCTCTCAATCC
1 GTCTACCTCTCAATCC
2742804 CACCTCATGT
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
34 14 0.20
35 26 0.37
36 2 0.03
37 29 0.41
ACGTcount: A:0.26, C:0.36, G:0.08, T:0.30
Consensus pattern (36 bp):
GTCTACCTCTCAATCCACCACATTCCACAAGTTAAT
Found at i:2743000 original size:246 final size:245
Alignment explanation
Indices: 2742567--2743053 Score: 784
Period size: 246 Copynumber: 2.0 Consensus size: 245
2742557 ATGGTGATTG
* *
2742567 GTATAGTTGACTTCTCAACTTTCGAGTAATCTATGCTTTCTTTGATTGAGTCGTTTTTTTATATA
1 GTATAGTTGACTTCTCAACTTTAGAGTAATCTATGCTTTCTTTGATTGAGTCATTTTTTTATATA
* *
2742632 GAGGTTACCAAGACGGTTCTCAGTATCATGATTGACTTGCAAAAAGACAAGTCTACCTCTCAATC
66 GAGGTTACCAAGACGGTCCTCAATATCATGATTGACTTGCAAAAAGACAAGTCTACCTCTCAATC
* * *
2742697 TCCCGTTCCACAAGTTAATATCTACCATTCAATCCCCCCATTTCACAAGTTGATGTCTGCCTCTC
131 CCCCGTTCCACAAGTTAATATCTACCACTCAATCCCCCCATTTCACAAGTTGATGTCTACCTCTC
2742762 AATCACAC-CACATTCCACAAGGTAATGTCTACCTCTCAATCCCACCTCAT
196 AATCACACTC-CATTCCACAAGGTAATGTCTACCTCTCAATCCCACCTCAT
* *
2742812 GTATAGTTGACTTTTCAACTTTA-AGGTGATCTATG-TCTTCTTTGATTCGAGTCATTTTTTTAT
1 GTATAGTTGACTTCTCAACTTTAGA-GTAATCTATGCT-TTCTTTGATT-GAGTCATTTTTTTAT
* *
2742875 ATAGAGGTTACCAAGGCGGTCCTCAATATCATGATTGACTTGCAAAAAGCCAAGTCTACCTCTCA
63 ATAGAGGTTACCAAGACGGTCCTCAATATCATGATTGACTTGCAAAAAGACAAGTCTACCTCTCA
*
2742940 ATCCCCCGTTCCACAAGTTAATGTCTACCACTCAATCCCCCCA-TTCTACAAGTTGATGTCTACC
128 ATCCCCCGTTCCACAAGTTAATATCTACCACTCAATCCCCCCATTTC-ACAAGTTGATGTCTACC
*
2743004 TCTCAATCATACTCCATTCCACAAGGTAATGTCTACCTCTCAATCCCACC
192 TCTCAATCACACTCCATTCCACAAGGTAATGTCTACCTCTCAATCCCACC
2743054 CCATTCCACA
Statistics
Matches: 224, Mismatches: 13, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
244 2 0.01
245 43 0.19
246 178 0.79
247 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.13, T:0.33
Consensus pattern (245 bp):
GTATAGTTGACTTCTCAACTTTAGAGTAATCTATGCTTTCTTTGATTGAGTCATTTTTTTATATA
GAGGTTACCAAGACGGTCCTCAATATCATGATTGACTTGCAAAAAGACAAGTCTACCTCTCAATC
CCCCGTTCCACAAGTTAATATCTACCACTCAATCCCCCCATTTCACAAGTTGATGTCTACCTCTC
AATCACACTCCATTCCACAAGGTAATGTCTACCTCTCAATCCCACCTCAT
Found at i:2743035 original size:72 final size:71
Alignment explanation
Indices: 2742928--2743067 Score: 194
Period size: 72 Copynumber: 2.0 Consensus size: 71
2742918 AAAAAGCCAA
* * *
2742928 GTCTACCTCTCAATCCCCCGTTCCACAAGTTAATGTCTACCACTCAAT-CC-CCCCATTCTACAA
1 GTCTACCTCTCAATCCCCCATTCCACAAGGTAATGTCTACCACTCAATCCCACCCCATTCCACAA
2742991 GTTGAT
66 GTTGAT
* *
2742997 GTCTACCTCTCAATCATACTCCATTCCACAAGGTAATGTCTACCTCTCAATCCCACCCCATTCCA
1 GTCTACCTCTCAATC---CCCCATTCCACAAGGTAATGTCTACCACTCAATCCCACCCCATTCCA
2743062 CAAGTT
63 CAAGTT
2743068 AATATACGAC
Statistics
Matches: 61, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
69 15 0.25
72 29 0.48
73 2 0.03
74 15 0.25
ACGTcount: A:0.26, C:0.38, G:0.08, T:0.29
Consensus pattern (71 bp):
GTCTACCTCTCAATCCCCCATTCCACAAGGTAATGTCTACCACTCAATCCCACCCCATTCCACAA
GTTGAT
Found at i:2743036 original size:37 final size:35
Alignment explanation
Indices: 2742928--2743070 Score: 180
Period size: 37 Copynumber: 4.0 Consensus size: 35
2742918 AAAAAGCCAA
*
2742928 GTCTACCTCTCAATC-CCCCGTTCCACAAGTTAAT
1 GTCTACCTCTCAATCACCCCATTCCACAAGTTAAT
* * * *
2742962 GTCTACCACTCAATCCCCCCATTCTACAAGTTGAT
1 GTCTACCTCTCAATCACCCCATTCCACAAGTTAAT
* *
2742997 GTCTACCTCTCAATCATACTCCATTCCACAAGGTAAT
1 GTCTACCTCTCAATC--ACCCCATTCCACAAGTTAAT
2743034 GTCTACCTCTCAATCCCACCCCATTCCACAAGTTAAT
1 GTCTACCTCTCAAT--CACCCCATTCCACAAGTTAAT
2743071 ATACGACACT
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
34 14 0.15
35 30 0.33
37 47 0.51
39 1 0.01
ACGTcount: A:0.27, C:0.37, G:0.08, T:0.29
Consensus pattern (35 bp):
GTCTACCTCTCAATCACCCCATTCCACAAGTTAAT
Found at i:2743586 original size:2 final size:2
Alignment explanation
Indices: 2743579--2743607 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2743569 ACCATTCTTT
2743579 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 T
2743608 TTTGCAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2744199 original size:32 final size:31
Alignment explanation
Indices: 2744146--2744206 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
2744136 TATTAATAAA
2744146 TTTAAAAATAAATAATAATAATTTTTTATTT
1 TTTAAAAATAAATAATAATAATTTTTTATTT
*
2744177 TTTAATAAAT-AATATTATATAATTTTTTAT
1 TTTAA-AAATAAATAATA-ATAATTTTTTAT
2744207 CAATGTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 11 0.41
32 16 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
TTTAAAAATAAATAATAATAATTTTTTATTT
Found at i:2745048 original size:20 final size:19
Alignment explanation
Indices: 2745012--2745048 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
2745002 ATTTTTTATT
2745012 TAAATTTAATTATAAAAAA
1 TAAATTTAATTATAAAAAA
2745031 TAAATATTAA-TATAAAAA
1 TAAAT-TTAATTATAAAAA
2745049 TAATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAATTTAATTATAAAAAA
Found at i:2745123 original size:18 final size:19
Alignment explanation
Indices: 2745068--2745123 Score: 51
Period size: 24 Copynumber: 2.7 Consensus size: 19
2745058 ATTTTTTATT
*
2745068 TTTTAAATAATAATTTAAA
1 TTTTAAATAAAAATTTAAA
2745087 TTTATAAATCAAATTAAATTTAAA
1 TTT-TAAAT--AA--AAATTTAAA
2745111 -TTTAAATAAAAAT
1 TTTTAAATAAAAAT
2745124 ATTTAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 11
0.72 0.02 0.26
Matches are distributed among these distances:
18 4 0.13
19 3 0.10
20 7 0.23
22 7 0.23
23 2 0.06
24 8 0.26
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTTAAATAAAAATTTAAA
Found at i:2746518 original size:16 final size:16
Alignment explanation
Indices: 2746497--2746528 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2746487 TGCTTTCTAA
2746497 AACACATACTAAGTTC
1 AACACATACTAAGTTC
2746513 AACACATACTAAGTTC
1 AACACATACTAAGTTC
2746529 TGTAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
AACACATACTAAGTTC
Found at i:2748850 original size:20 final size:22
Alignment explanation
Indices: 2748825--2748879 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
2748815 CATTTTACTA
2748825 TTATATAATATA-TAT-TAATT
1 TTATATAATATATTATGTAATT
*
2748845 TTATATGTTATATATTATGTAATT
1 TTATA--TAATATATTATGTAATT
2748869 TT-TATAATATA
1 TTATATAATATA
2748880 AAAAATATAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
20 5 0.17
21 6 0.21
22 6 0.21
23 5 0.17
24 7 0.24
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (22 bp):
TTATATAATATATTATGTAATT
Found at i:2748998 original size:14 final size:14
Alignment explanation
Indices: 2748979--2749018 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
2748969 AAGATTAAAC
*
2748979 TTAAAAAATATTTT
1 TTAAAAAATATATT
*
2748993 TTAAAAAATAAATT
1 TTAAAAAATATATT
*
2749007 ATAAAAAATATA
1 TTAAAAAATATA
2749019 ATATAGGTAG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAAAAATATATT
Found at i:2749538 original size:17 final size:17
Alignment explanation
Indices: 2749507--2749550 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
2749497 TATTTTCAAA
2749507 TTATTTTGG-TTTACAT
1 TTATTTTGGATTTACAT
2749523 TTATTTTGGATTTACAT
1 TTATTTTGGATTTACAT
*
2749540 TT-TTTTAGATT
1 TTATTTTGGATT
2749551 GGAGTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 17 0.65
17 9 0.35
ACGTcount: A:0.20, C:0.05, G:0.11, T:0.64
Consensus pattern (17 bp):
TTATTTTGGATTTACAT
Found at i:2750330 original size:18 final size:19
Alignment explanation
Indices: 2750293--2750333 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2750283 GAAAATTTGG
*
2750293 ATTTCAAAAATATATTTAA
1 ATTTCAAAAATATATGTAA
2750312 ATTTCAAAAATA-ATGTAA
1 ATTTCAAAAATATATGTAA
2750330 ATTT
1 ATTT
2750334 TGTAGTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 9 0.43
19 12 0.57
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (19 bp):
ATTTCAAAAATATATGTAA
Found at i:2752801 original size:13 final size:12
Alignment explanation
Indices: 2752752--2752802 Score: 57
Period size: 12 Copynumber: 3.9 Consensus size: 12
2752742 ACCTTCACTG
2752752 TTTCAAATTGAA
1 TTTCAAATTGAA
*
2752764 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
2752779 TTTCAAATTGAA
1 TTTCAAATTGAA
2752791 TTTCAAAATTGA
1 TTTC-AAATTGA
2752803 CGGCACAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
12 11 0.33
13 11 0.33
14 4 0.12
15 7 0.21
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:2755558 original size:13 final size:12
Alignment explanation
Indices: 2755509--2755554 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
2755499 ACCTTCACTG
2755509 TTTCAAATTGAA
1 TTTCAAATTGAA
*
2755521 TTTCAACATTTACTA
1 TTTCAA-ATTGA--A
2755536 TTTCAAATTGAA
1 TTTCAAATTGAA
2755548 TTTCAAA
1 TTTCAAA
2755555 ATTGGCGGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
12 14 0.48
13 4 0.14
14 4 0.14
15 7 0.24
ACGTcount: A:0.39, C:0.13, G:0.04, T:0.43
Consensus pattern (12 bp):
TTTCAAATTGAA
Found at i:2755569 original size:12 final size:12
Alignment explanation
Indices: 2755554--2755587 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2755544 TGAATTTCAA
*
2755554 AATTGGCGGCAC
1 AATTGGCAGCAC
2755566 AATTGGCAGCAC
1 AATTGGCAGCAC
*
2755578 AGTTGGCAGC
1 AATTGGCAGC
2755588 CTTTGTCTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.32, T:0.18
Consensus pattern (12 bp):
AATTGGCAGCAC
Found at i:2755822 original size:18 final size:18
Alignment explanation
Indices: 2755801--2755878 Score: 59
Period size: 18 Copynumber: 4.0 Consensus size: 18
2755791 AATATGATGT
2755801 AATTAAATAATATAAAAA
1 AATTAAATAATATAAAAA
2755819 AATTAAATATAATATAATACGAA
1 AATT-AA-ATAATATAA-A--AA
* *
2755842 AATAAAATAAATATATAAA
1 AATTAAAT-AATATAAAAA
*
2755861 TATATAAA-AATATAAAAA
1 AAT-TAAATAATATAAAAA
2755879 TATAAATATT
Statistics
Matches: 48, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
18 13 0.27
19 6 0.12
20 12 0.25
21 4 0.08
22 8 0.17
23 5 0.10
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (18 bp):
AATTAAATAATATAAAAA
Found at i:2755859 original size:8 final size:8
Alignment explanation
Indices: 2755848--2755898 Score: 66
Period size: 8 Copynumber: 6.4 Consensus size: 8
2755838 CGAAAATAAA
2755848 ATAAATAT
1 ATAAATAT
2755856 ATAAATAT
1 ATAAATAT
*
2755864 ATAAAAAT
1 ATAAATAT
*
2755872 ATAAAAAT
1 ATAAATAT
2755880 ATAAATAT
1 ATAAATAT
* *
2755888 TTGAATAT
1 ATAAATAT
2755896 ATA
1 ATA
2755899 TTAAAATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (8 bp):
ATAAATAT
Found at i:2755875 original size:24 final size:23
Alignment explanation
Indices: 2755809--2755887 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 23
2755799 GTAATTAAAT
2755809 AATATAAAAAA-ATTAAATATAATA
1 AATATAAAAAATA-TAAATAT-ATA
* *
2755833 TAATACGAAAATAAAATAAATATATA
1 -AATA-TAAAA-AATATAAATATATA
*
2755859 AATATATAAAAATATAAAAATATA
1 AATATA-AAAAATATAAATATATA
2755883 AATAT
1 AATAT
2755888 TTGAATATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
24 18 0.39
25 11 0.24
26 7 0.15
27 9 0.20
28 1 0.02
ACGTcount: A:0.68, C:0.01, G:0.01, T:0.29
Consensus pattern (23 bp):
AATATAAAAAATATAAATATATA
Found at i:2756342 original size:17 final size:19
Alignment explanation
Indices: 2756310--2756359 Score: 59
Period size: 17 Copynumber: 2.7 Consensus size: 19
2756300 ACATATCAAA
* *
2756310 ATATATATAAATAAAAATT
1 ATATAAATATATAAAAATT
*
2756329 AT-T-AATATATAAAATTT
1 ATATAAATATATAAAAATT
2756346 ATATAAATATATAA
1 ATATAAATATATAA
2756360 TATTTTAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
17 13 0.50
18 2 0.08
19 11 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
ATATAAATATATAAAAATT
Found at i:2756354 original size:19 final size:19
Alignment explanation
Indices: 2756310--2756364 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
2756300 ACATATCAAA
* * *
2756310 ATATATATAAATAAAAATT
1 ATATAAATATATAAAATTT
2756329 AT-T-AATATATAAAATTT
1 ATATAAATATATAAAATTT
*
2756346 ATATAAATATATAATATTT
1 ATATAAATATATAAAATTT
2756365 TAAATATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATAAATATATAAAATTT
Found at i:2759846 original size:52 final size:52
Alignment explanation
Indices: 2759701--2759826 Score: 234
Period size: 52 Copynumber: 2.4 Consensus size: 52
2759691 AATATGAAAT
2759701 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
* *
2759753 TTTGCCTGTATGTATCAATACATTTCATAGTGTATCGATACATCTGGGCAAA
1 TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
2759805 TTTGCCTGCATGTATCGATACA
1 TTTGCCTGCATGTATCGATACA
2759827 AAGATCAGTG
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (52 bp):
TTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGCAAA
Found at i:2759853 original size:13 final size:13
Alignment explanation
Indices: 2759835--2759859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2759825 CAAAGATCAG
2759835 TGTATCGATACAA
1 TGTATCGATACAA
2759848 TGTATCGATACA
1 TGTATCGATACA
2759860 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:2759936 original size:19 final size:19
Alignment explanation
Indices: 2759912--2759995 Score: 99
Period size: 19 Copynumber: 4.7 Consensus size: 19
2759902 AGCGATACAT
2759912 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
2759931 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
2759950 TGTATCGATAC---A-TTA
1 TGTATCGATACAAAACTTA
*
2759965 --TATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
2759982 TGTATCCATACAAA
1 TGTATCGATACAAA
2759996 TCGTTGAAAT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
13 9 0.16
15 3 0.05
16 2 0.04
17 3 0.05
19 39 0.70
ACGTcount: A:0.39, C:0.19, G:0.10, T:0.32
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:2759969 original size:32 final size:32
Alignment explanation
Indices: 2759933--2759993 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
2759923 AAAACTTATG
*
2759933 TATCGATACAACACTTATGTATCGATACATTA
1 TATCGATACAACACTTATGTATCCATACATTA
2759965 TATCGATACAACACTTATGTATCCATACA
1 TATCGATACAACACTTATGTATCCATACA
2759994 AATCGTTGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.33
Consensus pattern (32 bp):
TATCGATACAACACTTATGTATCCATACATTA
Found at i:2760588 original size:3 final size:3
Alignment explanation
Indices: 2760580--2760608 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2760570 TTGATGGGAT
2760580 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2760609 TTGTCATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2763732 original size:6 final size:6
Alignment explanation
Indices: 2763721--2763749 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
2763711 CAAGGCATAT
2763721 ATATTA ATATTA ATATTA ATATTA ATATT
1 ATATTA ATATTA ATATTA ATATTA ATATT
2763750 GAGCTGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATATTA
Done.