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 7 of 25
Found at i:929173 original size:20 final size:20
Alignment explanation
Indices: 929137--929175 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
929127 TAATTTTTTT
*
929137 ATTAAATATAATGTCATATC
1 ATTAAATATAATATCATATC
*
929157 ATTAAATATATTATCATAT
1 ATTAAATATAATATCATAT
929176 AAATATCACG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.44
Consensus pattern (20 bp):
ATTAAATATAATATCATATC
Found at i:930326 original size:10 final size:11
Alignment explanation
Indices: 930304--930343 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 11
930294 TAATGTCATA
930304 AAAATATAA--
1 AAAATATAATT
930313 AAAAT-TAATT
1 AAAATATAATT
930323 AAAATATAATT
1 AAAATATAATT
930334 AAAAATATAA
1 -AAAATATAA
930344 AATATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 3 0.11
9 5 0.19
10 5 0.19
11 5 0.19
12 9 0.33
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (11 bp):
AAAATATAATT
Found at i:930362 original size:8 final size:8
Alignment explanation
Indices: 930336--930364 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
930326 ATATAATTAA
930336 AAATATA-
1 AAATATAT
930343 AAATATAT
1 AAATATAT
930351 AAATATAT
1 AAATATAT
930359 AAATAT
1 AAATAT
930365 TTTAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
AAATATAT
Found at i:930479 original size:17 final size:17
Alignment explanation
Indices: 930378--930487 Score: 63
Period size: 17 Copynumber: 6.6 Consensus size: 17
930368 AAAATTTATA
*
930378 TAAATATAAAATAAT-T
1 TAAATATAATATAATAT
*
930394 TAAGTATAAT-TAATAT
1 TAAATATAATATAATAT
930410 AATAAA-ATAGATAT-ATAT
1 --TAAATATA-ATATAATAT
* *
930428 TATATGATTATATAA-AT
1 TAAAT-ATAATATAATAT
* * *
930445 T-ATTA-AATTTAATTT
1 TAAATATAATATAATAT
930460 TAAATATAATATAATAT
1 TAAATATAATATAATAT
*
930477 TAAATTTAATA
1 TAAATATAATA
930488 ATTTAATAAT
Statistics
Matches: 69, Mismatches: 14, Indels: 21
0.66 0.13 0.20
Matches are distributed among these distances:
14 5 0.07
15 7 0.10
16 16 0.23
17 28 0.41
18 12 0.17
19 1 0.01
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
TAAATATAATATAATAT
Found at i:930511 original size:27 final size:27
Alignment explanation
Indices: 930481--930568 Score: 72
Period size: 27 Copynumber: 3.1 Consensus size: 27
930471 TAATATTAAA
930481 TTTAATAATTTAATAATTTATATTATT
1 TTTAATAATTTAATAATTTATATTATT
* * *
930508 TTTAAT-ATATTATTAATTTATTTTTTT
1 TTTAATAAT-TTAATAATTTATATTATT
* *
930535 AAATTTAATATTTTAA-ATATTTATATTATA
1 ---TTTAATAATTTAATA-ATTTATATTATT
930565 TTTA
1 TTTA
930569 TATATTATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
26 2 0.04
27 25 0.53
29 1 0.02
30 18 0.38
31 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTAATAATTTAATAATTTATATTATT
Found at i:930561 original size:15 final size:14
Alignment explanation
Indices: 930447--930552 Score: 53
Period size: 14 Copynumber: 7.4 Consensus size: 14
930437 ATATAAATTA
930447 TTAAATTT-A-ATT
1 TTAAATTTAATATT
*
930459 TTAAATATAATATAAT
1 TTAAATTTAATAT--T
930475 ATTAAATTTAATAATT
1 -TTAAATTTAAT-ATT
*
930491 TAATAATTT-ATATT
1 TTA-AATTTAATATT
930505 ATT---TTTAATATAT
1 -TTAAATTTAATAT-T
* * *
930518 TATTAATTTATTTTT
1 T-TAAATTTAATATT
930533 TTAAATTTAATATT
1 TTAAATTTAATATT
930547 TTAAAT
1 TTAAAT
930553 ATTTATATTA
Statistics
Matches: 71, Mismatches: 9, Indels: 26
0.67 0.08 0.25
Matches are distributed among these distances:
11 3 0.04
12 12 0.17
13 3 0.04
14 21 0.30
15 7 0.10
16 13 0.18
17 10 0.14
18 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTAAATTTAATATT
Found at i:930856 original size:29 final size:30
Alignment explanation
Indices: 930824--930885 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
930814 ATTATTTGAT
** *
930824 TTTAATTAAATTAATTTATTAA-AATAAAA
1 TTTAATTAAATTAATCAATTAATAAAAAAA
*
930853 TTTAATTTAATTAATCAATTAATAAAAAAA
1 TTTAATTAAATTAATCAATTAATAAAAAAA
930883 TTT
1 TTT
930886 CAGTTCAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTAATTAAATTAATCAATTAATAAAAAAA
Found at i:931505 original size:2 final size:2
Alignment explanation
Indices: 931492--931576 Score: 59
Period size: 2 Copynumber: 44.0 Consensus size: 2
931482 CGCGCATGTG
* * *
931492 TA TA TG TA TA TA TA TA TA AA T- TA TA TC 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
* * * * * * *
931533 TA TG TA TG TC TA TA TA TG TG CA T- TA TA TA TA TA AA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
931573 TA TA
1 TA TA
931577 ATTAAGCTGA
Statistics
Matches: 63, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
1 3 0.05
2 60 0.95
ACGTcount: A:0.42, C:0.04, G:0.06, T:0.48
Consensus pattern (2 bp):
TA
Found at i:944561 original size:20 final size:20
Alignment explanation
Indices: 944516--944567 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
944506 GTAGCCAAAC
* **
944516 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACAAAAAA
944536 -TGTATCGATACACAAAAAA
1 TTGTATCGATACACAAAAAA
944555 TTGTATCGATACA
1 TTGTATCGATACA
944568 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACAAAAAA
Found at i:947686 original size:19 final size:19
Alignment explanation
Indices: 947659--947695 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
947649 TTTAGCTTTT
*
947659 AAATCAAAACAGTTTTGGA
1 AAATAAAAACAGTTTTGGA
*
947678 AAATAAAAACATTTTTGG
1 AAATAAAAACAGTTTTGG
947696 TTTTAATAAA
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:0.49, C:0.08, G:0.14, T:0.30
Consensus pattern (19 bp):
AAATAAAAACAGTTTTGGA
Found at i:947800 original size:21 final size:21
Alignment explanation
Indices: 947761--947801 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
947751 AGCTCGAAAA
**
947761 TGAAAATAGTTTTGGTTTTAT
1 TGAAAATAGTTTCAGTTTTAT
*
947782 TGAAAATAGTTTCATTTTTA
1 TGAAAATAGTTTCAGTTTTA
947802 AGATCAAAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.02, G:0.15, T:0.51
Consensus pattern (21 bp):
TGAAAATAGTTTCAGTTTTAT
Found at i:947861 original size:29 final size:30
Alignment explanation
Indices: 947829--947885 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 30
947819 TTGAGCTCGT
* *
947829 AAATGAAAATAGGTTCAATTTT-AGCTTTA
1 AAATCAAAACAGGTTCAATTTTGAGCTTTA
* *
947858 AAATCAAAACAGTTTTAATTTTGAGCTT
1 AAATCAAAACAGGTTCAATTTTGAGCTT
947886 GGAAAAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
29 18 0.78
30 5 0.22
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (30 bp):
AAATCAAAACAGGTTCAATTTTGAGCTTTA
Found at i:948109 original size:23 final size:23
Alignment explanation
Indices: 948068--948113 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
948058 TGTTAGATCA
** *
948068 GTTTCGATTTTCATCAATTAAGT
1 GTTTCGATTTGAATAAATTAAGT
948091 GTTTCGATTTGAATAAATTAAGT
1 GTTTCGATTTGAATAAATTAAGT
948114 TAGTCCATTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (23 bp):
GTTTCGATTTGAATAAATTAAGT
Found at i:949091 original size:63 final size:62
Alignment explanation
Indices: 949012--949145 Score: 178
Period size: 63 Copynumber: 2.1 Consensus size: 62
949002 ATACACAATT
* * *
949012 AAACCCAAAACCTAATTTTTTTCCTTTGGTAGTCACAACTTTTATTTTCCTTAGCACCAGTAA
1 AAACCCAAAACCTAATTTTTTTCCTTTGGTAGCCACAACTCTTATTTTCCTTAGAACCAGT-A
* * ** * *
949075 AAACCCAAAACTTAATTTTTTTTCTTTGGTAGCCGTAACTCTTATTTTCTTTAGAATCAGTA
1 AAACCCAAAACCTAATTTTTTTCCTTTGGTAGCCACAACTCTTATTTTCCTTAGAACCAGTA
949137 AAACCCAAA
1 AAACCCAAA
949146 TTTGTTTTGA
Statistics
Matches: 62, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
62 10 0.16
63 52 0.84
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (62 bp):
AAACCCAAAACCTAATTTTTTTCCTTTGGTAGCCACAACTCTTATTTTCCTTAGAACCAGTA
Found at i:951435 original size:103 final size:96
Alignment explanation
Indices: 951313--951522 Score: 260
Period size: 97 Copynumber: 2.1 Consensus size: 96
951303 ATTAAATAGT
** * * *
951313 GTGAACAGTGATGTATCGATACTATTTACACTGTATCGATATATGA-ATGATGAACAGTGATTTT
1 GTGAACAGTGATGTATCGATAC-ATAAACACTG-AT-G-TAT-CGATA-GATGAACAATGA-TGT
*
951377 ATCGATATATAAATAGTGATACGTGAACAGTTATGAACA
59 ATCGATACATAAATAGTGATACGTGAACAG-TATGAACA
*
951416 GTGAACAGTGATGTATCGATACATAAACAGTGATGTATCGATAGATGAACAATGATGTATCGATA
1 GTGAACAGTGATGTATCGATACATAAACACTGATGTATCGATAGATGAACAATGATGTATCGATA
*
951481 CATGAATAGTGATACGTGAACAGTATGAACA
66 CATAAATAGTGATACGTGAACAGTATGAACA
*
951512 CTGAACAGTGA
1 GTGAACAGTGA
951523 ACAGTGATGT
Statistics
Matches: 97, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
96 18 0.19
97 30 0.31
98 13 0.13
99 4 0.04
100 1 0.01
101 2 0.02
102 7 0.07
103 22 0.23
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.29
Consensus pattern (96 bp):
GTGAACAGTGATGTATCGATACATAAACACTGATGTATCGATAGATGAACAATGATGTATCGATA
CATAAATAGTGATACGTGAACAGTATGAACA
Found at i:951444 original size:22 final size:22
Alignment explanation
Indices: 951417--951493 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
951407 TTATGAACAG
951417 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
* *
951439 TAAACAGTGATGTATCGATAGA
1 TGAACAGTGATGTATCGATACA
*
951461 TGAACAATGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
*
951483 TGAATAGTGAT
1 TGAACAGTGAT
951494 ACGTGAACAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:951508 original size:23 final size:24
Alignment explanation
Indices: 951482--951562 Score: 80
Period size: 23 Copynumber: 3.5 Consensus size: 24
951472 GTATCGATAC
951482 ATGAATAGTGATACGTGAACAGT-
1 ATGAATAGTGATACGTGAACAGTG
* *
951505 ATGAACACTGA-ACAGTGAACAGTG
1 ATGAATAGTGATAC-GTGAACAGTG
* * *
951529 ATGTATCG-G-TACATGAACAGTG
1 ATGAATAGTGATACGTGAACAGTG
951551 ATGAATAGTGAT
1 ATGAATAGTGAT
951563 GAACAGTGAA
Statistics
Matches: 44, Mismatches: 9, Indels: 9
0.71 0.15 0.15
Matches are distributed among these distances:
22 17 0.39
23 22 0.50
24 5 0.11
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.25
Consensus pattern (24 bp):
ATGAATAGTGATACGTGAACAGTG
Found at i:951560 original size:10 final size:10
Alignment explanation
Indices: 951541--951571 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
951531 GTATCGGTAC
951541 ATGAACAGTG
1 ATGAACAGTG
*
951551 ATGAATAGTG
1 ATGAACAGTG
951561 ATGAACAGTG
1 ATGAACAGTG
951571 A
1 A
951572 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:951617 original size:13 final size:13
Alignment explanation
Indices: 951599--951623 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
951589 TGTCAATGCT
951599 ATGTATCGATACA
1 ATGTATCGATACA
951612 ATGTATCGATAC
1 ATGTATCGATAC
951624 TTAGCAAAAT
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):
ATGTATCGATACA
Found at i:951744 original size:21 final size:21
Alignment explanation
Indices: 951704--951744 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
951694 GTCAACCTTG
*
951704 TGTATTGATACCAATAGTATA
1 TGTATTGATACCAACAGTATA
951725 TGTATTGATA-CAACACGTAT
1 TGTATTGATACCAACA-GTAT
951745 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (21 bp):
TGTATTGATACCAACAGTATA
Found at i:952564 original size:85 final size:85
Alignment explanation
Indices: 952461--952630 Score: 322
Period size: 85 Copynumber: 2.0 Consensus size: 85
952451 TATGCAAACT
*
952461 TTCCCTCTTAATACGTTATCACCCTTAAACCAATAAACAATAATTTCTCCCCCTTTTTGGTTCAT
1 TTCCCTCTCAATACGTTATCACCCTTAAACCAATAAACAATAATTTCTCCCCCTTTTTGGTTCAT
952526 AAGCTAAGTTGATAAAACCA
66 AAGCTAAGTTGATAAAACCA
*
952546 TTCCCTCTCAATACGTTATCACCCTTAAACCAATAAACAATAATTTCTCTCCCTTTTTGGTTCAT
1 TTCCCTCTCAATACGTTATCACCCTTAAACCAATAAACAATAATTTCTCCCCCTTTTTGGTTCAT
952611 AAGCTAAGTTGATAAAACCA
66 AAGCTAAGTTGATAAAACCA
952631 AATTTATACC
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 83 1.00
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.34
Consensus pattern (85 bp):
TTCCCTCTCAATACGTTATCACCCTTAAACCAATAAACAATAATTTCTCCCCCTTTTTGGTTCAT
AAGCTAAGTTGATAAAACCA
Found at i:953366 original size:13 final size:13
Alignment explanation
Indices: 953348--953372 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
953338 ACTAAAGCAA
953348 TGTATCGATACAT
1 TGTATCGATACAT
953361 TGTATCGATACA
1 TGTATCGATACA
953373 ATCTGAAAAA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:957108 original size:22 final size:22
Alignment explanation
Indices: 957080--957203 Score: 144
Period size: 22 Copynumber: 5.5 Consensus size: 22
957070 TTATGAACAG
957080 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
* *
957102 TGAACAGTGATGTATTGATAGA
1 TGAACAGTGATGTATCGATACA
*
957124 TGAACAGTGATGAATCGATACA
1 TGAACAGTGATGTATCGATACA
* * *
957146 TGAATAGTGATACGTGAAC-AGT-TA
1 TGAACAGTGAT--GT-ATCGA-TACA
957170 TGAACAGTGATGTATCGATACA
1 TGAACAGTGATGTATCGATACA
957192 TGAACAGTGATG
1 TGAACAGTGATG
957204 AATAGTGATG
Statistics
Matches: 84, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
21 3 0.04
22 65 0.77
24 13 0.15
25 3 0.04
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.27
Consensus pattern (22 bp):
TGAACAGTGATGTATCGATACA
Found at i:957210 original size:10 final size:10
Alignment explanation
Indices: 957191--957221 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
957181 GTATCGATAC
957191 ATGAACAGTG
1 ATGAACAGTG
*
957201 ATGAATAGTG
1 ATGAACAGTG
957211 ATGAACAGTG
1 ATGAACAGTG
957221 A
1 A
957222 AAATGAGATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.42, C:0.06, G:0.29, T:0.23
Consensus pattern (10 bp):
ATGAACAGTG
Found at i:958849 original size:18 final size:18
Alignment explanation
Indices: 958828--958876 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
958818 TAATTAAAAA
958828 TTTAATATTTAGTTATT-T
1 TTTAATATTTA-TTATTAT
*
958846 TTTAATTTTTATT-TTAT
1 TTTAATATTTATTATTAT
958863 TTT-ATATTTATTAT
1 TTTAATATTTATTAT
958877 CACAATGCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 10 0.37
17 7 0.26
18 10 0.37
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (18 bp):
TTTAATATTTATTATTAT
Found at i:959865 original size:22 final size:22
Alignment explanation
Indices: 959813--959856 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
959803 AAAGCTCATG
*
959813 ATATAATTTATTTTTTGATAAA
1 ATATAATTTACTTTTTGATAAA
959835 ATATAATTTACTTTTTGATAAA
1 ATATAATTTACTTTTTGATAAA
959857 TTACTATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (22 bp):
ATATAATTTACTTTTTGATAAA
Found at i:962050 original size:22 final size:21
Alignment explanation
Indices: 962023--962077 Score: 65
Period size: 22 Copynumber: 2.6 Consensus size: 21
962013 TTTTATTAAA
*
962023 ATTTTATTTTAAAATAAAATT
1 ATTTTAATTTAAAATAAAATT
* *
962044 ATATTTAATTTAAATTTAAATT
1 AT-TTTAATTTAAAATAAAATT
*
962066 ATTTTAAGTTAA
1 ATTTTAATTTAA
962078 TTATTTAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 11 0.38
22 18 0.62
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
ATTTTAATTTAAAATAAAATT
Found at i:962058 original size:16 final size:16
Alignment explanation
Indices: 962039--962175 Score: 57
Period size: 16 Copynumber: 8.4 Consensus size: 16
962029 TTTTAAAATA
962039 AAATTATATTTAATTT
1 AAATTATATTTAATTT
* *
962055 AAATT-TAAATTATTTT
1 AAATTAT-ATTTAATTT
*
962071 AAGTTAATTATTTAGA-TT
1 AAATT-A-TATTTA-ATTT
* *
962089 AATTTAAATTTAAATTT
1 AAATTATATTT-AATTT
*
962106 AAATTA-ATTTGATTT
1 AAATTATATTTAATTT
* *
962121 CAAATCCAT-TTAAATTT
1 -AAAT-TATATTTAATTT
* *
962138 ATATTATTTTTAATTT
1 AAATTATATTTAATTT
* * * *
962154 AGATTTTTTTTATTTT
1 AAATTATATTTAATTT
962170 AAATTA
1 AAATTA
962176 AATTAGATTT
Statistics
Matches: 90, Mismatches: 20, Indels: 22
0.68 0.15 0.17
Matches are distributed among these distances:
15 7 0.08
16 56 0.62
17 16 0.18
18 10 0.11
19 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.55
Consensus pattern (16 bp):
AAATTATATTTAATTT
Found at i:962153 original size:22 final size:21
Alignment explanation
Indices: 962128--962179 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
962118 TTTCAAATCC
962128 ATTTAAATTTATATTATTTTTA
1 ATTTAAATTTATATTA-TTTTA
* * *
962150 ATTTAGATTTTTTTTATTTTA
1 ATTTAAATTTATATTATTTTA
*
962171 AATTAAATT
1 ATTTAAATT
962180 AGATTTAGAT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 12 0.48
22 13 0.52
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
ATTTAAATTTATATTATTTTA
Found at i:962186 original size:32 final size:31
Alignment explanation
Indices: 962150--962210 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 31
962140 ATTATTTTTA
*
962150 ATTTAGATT-TTTTTTATTTTAAATTAAATTAG
1 ATTTAGATTATTTATT-TTTT-AATTAAATTAG
962182 ATTTAGATTATTTATTTTTTAATTAAATT
1 ATTTAGATTATTTATTTTTTAATTAAATT
962211 GAATTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
31 9 0.33
32 13 0.48
33 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (31 bp):
ATTTAGATTATTTATTTTTTAATTAAATTAG
Found at i:962273 original size:19 final size:18
Alignment explanation
Indices: 962251--962293 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
962241 TAATTTTTTA
962251 AATTTAAATAAAAAATATT
1 AATTTAAATAAAAAAT-TT
* * *
962270 AATTTATATTATAAATTT
1 AATTTAAATAAAAAATTT
962288 AATTTA
1 AATTTA
962294 TAATTATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTTAAATAAAAAATTT
Found at i:962291 original size:18 final size:20
Alignment explanation
Indices: 962263--962344 Score: 77
Period size: 19 Copynumber: 4.3 Consensus size: 20
962253 TTTAAATAAA
962263 AAATATTAATTTAT-ATTAT
1 AAATATTAATTTATAATTAT
962282 AAAT-TTAATTTATAATTAT
1 AAATATTAATTTATAATTAT
962301 AAATA-T-ATTGT-TAATTAT
1 AAATATTAATT-TATAATTAT
** *
962319 ATTTTATTTA-TTATAATTAT
1 A-AATATTAATTTATAATTAT
962339 AAATAT
1 AAATAT
962345 AATAAATATT
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
18 20 0.38
19 21 0.40
20 10 0.19
21 1 0.02
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (20 bp):
AAATATTAATTTATAATTAT
Found at i:962305 original size:38 final size:39
Alignment explanation
Indices: 962263--962344 Score: 91
Period size: 38 Copynumber: 2.2 Consensus size: 39
962253 TTTAAATAAA
962263 AAATATTAAT-TTATATTATAAATTTA-AT-TTATAATTAT
1 AAATATTAATGTTA-ATTAT-AATTTATATATTATAATTAT
* * *
962301 AAATA-TATTGTTAATTATATTTTATTTATTATAATTAT
1 AAATATTAATGTTAATTATAATTTATATATTATAATTAT
962339 AAATAT
1 AAATAT
962345 AATAAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
36 5 0.14
37 9 0.24
38 23 0.62
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (39 bp):
AAATATTAATGTTAATTATAATTTATATATTATAATTAT
Found at i:966320 original size:28 final size:27
Alignment explanation
Indices: 966281--966350 Score: 70
Period size: 28 Copynumber: 2.6 Consensus size: 27
966271 GTAAATTTAA
* *
966281 AAAATAATATTTTAATAATAAATAGAT
1 AAAATAAAATTTTAATAATAAATAAAT
* **
966308 AATAATAAAATTTAAATTTTAAATAAAT
1 AA-AATAAAATTTTAATAATAAATAAAT
*
966336 TAAAT-AAATTTTAAT
1 AAAATAAAATTTTAAT
966351 TCTAACAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
26 9 0.26
27 5 0.14
28 21 0.60
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (27 bp):
AAAATAAAATTTTAATAATAAATAAAT
Found at i:966932 original size:14 final size:14
Alignment explanation
Indices: 966913--966955 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
966903 CAAGATATAA
966913 TATTTAAATAAAAT
1 TATTTAAATAAAAT
*
966927 TATTTATAATTAAAT
1 TATTTA-AATAAAAT
*
966942 T-TTTAAAAAAAAT
1 TATTTAAATAAAAT
966955 T
1 T
966956 TAAACACATA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 7 0.28
14 10 0.40
15 8 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TATTTAAATAAAAT
Found at i:971329 original size:20 final size:21
Alignment explanation
Indices: 971306--971346 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
971296 TATTAAAAAT
971306 ATTAAAATT-TTATTTTATAA
1 ATTAAAATTATTATTTTATAA
* *
971326 ATTAATATTATTTTTTTATAA
1 ATTAAAATTATTATTTTATAA
971347 CTAAATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
ATTAAAATTATTATTTTATAA
Found at i:971356 original size:20 final size:21
Alignment explanation
Indices: 971318--971356 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
971308 TAAAATTTTA
*
971318 TTTTATAAATTAATATTATTT
1 TTTTATAAATAAATATTATTT
*
971339 TTTTATAACTAAAT-TTAT
1 TTTTATAAATAAATATTAT
971357 ATAAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTTATAAATAAATATTATTT
Found at i:974664 original size:18 final size:18
Alignment explanation
Indices: 974643--974680 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
974633 TCATATCTAA
974643 TATTATCAAATCTATATC
1 TATTATCAAATCTATATC
*
974661 TATTATCAAATTTATATC
1 TATTATCAAATCTATATC
974679 TA
1 TA
974681 ATCATTTGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.47
Consensus pattern (18 bp):
TATTATCAAATCTATATC
Found at i:977193 original size:2 final size:2
Alignment explanation
Indices: 977186--977215 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
977176 GTAATATAAC
977186 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
977216 TTTTCTTTAC
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:977397 original size:25 final size:25
Alignment explanation
Indices: 977369--977423 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
977359 AAATTTTAAA
977369 AATAAATATAAATAAATTT-ATTT-TT
1 AATAAAT-T-AATAAATTTAATTTATT
*
977394 AATAAATTAATATATTTAATTTATT
1 AATAAATTAATAAATTTAATTTATT
977419 AATAA
1 AATAA
977424 TGTATTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 8 0.30
24 5 0.19
25 14 0.52
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATAAATTAATAAATTTAATTTATT
Found at i:977447 original size:23 final size:23
Alignment explanation
Indices: 977417--977460 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
977407 ATTTAATTTA
**
977417 TTAATAATGTATTAATTTATATG
1 TTAATAATACATTAATTTATATG
977440 TTAATAATACATTAATTTATA
1 TTAATAATACATTAATTTATA
977461 CATTATCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (23 bp):
TTAATAATACATTAATTTATATG
Found at i:977471 original size:23 final size:23
Alignment explanation
Indices: 977416--977465 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
977406 TATTTAATTT
** *
977416 ATTAATAATGTATTAATTTATAT
1 ATTAATAATACATTAATTTATAC
*
977439 GTTAATAATACATTAATTTATAC
1 ATTAATAATACATTAATTTATAC
977462 ATTA
1 ATTA
977466 TCAATATCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
ATTAATAATACATTAATTTATAC
Found at i:978884 original size:2 final size:2
Alignment explanation
Indices: 978877--978916 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
978867 TCCACTTGTT
978877 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
978917 ATGATCCTCT
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):
TA
Found at i:980567 original size:19 final size:18
Alignment explanation
Indices: 980526--980578 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
980516 TGATTTTTTA
*
980526 TATT-ATAAAAATATTATT
1 TATTAATAAAAAT-TAATT
*
980544 TATTAATTAAAATTAATT
1 TATTAATAAAAATTAATT
980562 TAATTAATAAAAATTAA
1 T-ATTAATAAAAATTAA
980579 AAATTTAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
18 9 0.30
19 21 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TATTAATAAAAATTAATT
Found at i:986449 original size:21 final size:20
Alignment explanation
Indices: 986402--986457 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 20
986392 AAAAACCCAA
* *
986402 AATGTATCAATACAATTAAT
1 AATGTATCAATACATTTAAG
986422 AATGTATCAATACATTGTAAG
1 AATGTATCAATACATT-TAAG
* *
986443 CATGTATCGATACAT
1 AATGTATCAATACAT
986458 ATACTTATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.34
Consensus pattern (20 bp):
AATGTATCAATACATTTAAG
Found at i:1007320 original size:2 final size:2
Alignment explanation
Indices: 1007313--1007348 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1007303 CATGGGCAAA
1007313 AT AT AT AT AT AT AT AT AT AT -T 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
1007349 CAGGACGTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1007338 original size:17 final size:17
Alignment explanation
Indices: 1007316--1007348 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1007306 GGGCAAAATA
1007316 TATATATATATATATAT
1 TATATATATATATATAT
1007333 TATATATATATATATA
1 TATATATATATATATA
1007349 CAGGACGTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:1011661 original size:18 final size:18
Alignment explanation
Indices: 1011638--1011672 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1011628 TTGTTAGTAT
*
1011638 ATAATTAAAAATTTATAA
1 ATAATTAAAAATATATAA
1011656 ATAATTAAAAATATATA
1 ATAATTAAAAATATATA
1011673 TATGAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATTAAAAATATATAA
Found at i:1011709 original size:42 final size:42
Alignment explanation
Indices: 1011657--1011764 Score: 123
Period size: 42 Copynumber: 2.5 Consensus size: 42
1011647 AATTTATAAA
* * *
1011657 TAATTAAAAATATATATATGAATAATAA-ATAAATA-TATTTAT
1 TAATTAAAAATATAAAAAT-AATAA-AATATAAATATTATTAAT
*
1011699 TAATTTAAAATATAAAAATAATAAAATATAAATATTATTAAT
1 TAATTAAAAATATAAAAATAATAAAATATAAATATTATTAAT
1011741 TATATTAAAAATA-AATAAATAATA
1 TA-ATTAAAAATATAA-AAATAATA
1011765 CTAACAATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
40 2 0.04
41 12 0.21
42 26 0.46
43 17 0.30
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (42 bp):
TAATTAAAAATATAAAAATAATAAAATATAAATATTATTAAT
Found at i:1011761 original size:35 final size:33
Alignment explanation
Indices: 1011671--1011761 Score: 87
Period size: 35 Copynumber: 2.6 Consensus size: 33
1011661 TAAAAATATA
* *
1011671 TATATGAATAATAAATAAATATATTTATTAATT
1 TATATTAAAAATAAATAAATATATTTATTAATT
*
1011704 TAAAATATAAAAAT-AATAAAATATAAATATTATTAA-T
1 T-ATAT-TAAAAATAAAT-AAATAT--AT-TTATTAATT
1011741 TATATTAAAAATAAATAAATA
1 TATATTAAAAATAAATAAATA
1011762 ATACTAACAA
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
33 1 0.02
34 6 0.13
35 23 0.49
36 6 0.13
37 4 0.09
38 7 0.15
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (33 bp):
TATATTAAAAATAAATAAATATATTTATTAATT
Found at i:1011946 original size:8 final size:8
Alignment explanation
Indices: 1011928--1011977 Score: 57
Period size: 8 Copynumber: 6.1 Consensus size: 8
1011918 TGCTCAATAA
1011928 TTATA-AT
1 TTATATAT
1011935 TTATATAT
1 TTATATAT
1011943 TTATATTAT
1 TTATA-TAT
1011952 ATTATATAT
1 -TTATATAT
*
1011961 ATATATAT
1 TTATATAT
*
1011969 ATATATAT
1 TTATATAT
1011977 T
1 T
1011978 AGAATTTGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
7 5 0.13
8 22 0.58
9 6 0.16
10 5 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (8 bp):
TTATATAT
Found at i:1011959 original size:2 final size:2
Alignment explanation
Indices: 1011936--1011976 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
1011926 AATTATAATT
*
1011936 TA TA TA TT TA TA T- TA TA T- 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
1011976 T
1 T
1011977 TAGAATTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (2 bp):
TA
Found at i:1012206 original size:11 final size:11
Alignment explanation
Indices: 1012190--1012216 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
1012180 TTATTTTATT
1012190 TTAAAAAATTA
1 TTAAAAAATTA
1012201 TTAAAAAATTA
1 TTAAAAAATTA
1012212 TTAAA
1 TTAAA
1012217 TTAATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TTAAAAAATTA
Found at i:1012251 original size:17 final size:18
Alignment explanation
Indices: 1012217--1012256 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
1012207 AATTATTAAA
1012217 TTAATTTTTTAATATATT
1 TTAATTTTTTAATATATT
*
1012235 TTAATTTTTTTAT-TATT
1 TTAATTTTTTAATATATT
1012252 TTAAT
1 TTAAT
1012257 GATTGAGTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTAATTTTTTAATATATT
Found at i:1012353 original size:22 final size:21
Alignment explanation
Indices: 1012328--1012407 Score: 62
Period size: 22 Copynumber: 3.9 Consensus size: 21
1012318 AAATTTTTAA
1012328 ATATTATAATCATATTTAATAT
1 ATATTATAAT-ATATTTAATAT
*
1012350 ATATT-TATATAAATATTAATAT
1 ATATTATA-ATATAT-TTAATAT
*
1012372 ATTATTATTATATA-TT-ATAT
1 A-TATTATAATATATTTAATAT
*
1012392 AT-TT-TAAAATATTTAA
1 ATATTATAATATATTTAA
1012408 ATTTTGATTA
Statistics
Matches: 47, Mismatches: 5, Indels: 15
0.70 0.07 0.22
Matches are distributed among these distances:
17 5 0.11
18 4 0.09
19 2 0.04
20 5 0.11
21 7 0.15
22 15 0.32
23 8 0.17
24 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (21 bp):
ATATTATAATATATTTAATAT
Found at i:1012375 original size:42 final size:37
Alignment explanation
Indices: 1012324--1012409 Score: 91
Period size: 40 Copynumber: 2.2 Consensus size: 37
1012314 ATAAAAATTT
*
1012324 TTAAATATTATAATCATATTTAATATATATTTATATAAATA
1 TTAAATATTATAAT--TATATAATATATATTT-TA-AAATA
* *
1012365 TTAATATATTATTATTATATATTATATATTTTAAAATA
1 TTAA-ATATTATAATTATATAATATATATTTTAAAATA
1012403 TTTAAAT
1 -TTAAAT
1012410 TTTGATTATT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
38 7 0.17
39 6 0.15
40 14 0.35
41 4 0.10
42 9 0.22
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (37 bp):
TTAAATATTATAATTATATAATATATATTTTAAAATA
Found at i:1013571 original size:18 final size:18
Alignment explanation
Indices: 1013529--1013571 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
1013519 AGAGAGATAT
* **
1013529 AAAAAAAAAATTACATTA
1 AAAAAAAAAATTAAAAAA
*
1013547 AATAAAAAAATTAAAAAA
1 AAAAAAAAAATTAAAAAA
1013565 AAAAAAA
1 AAAAAAA
1013572 GCTAATCAAG
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.16
Consensus pattern (18 bp):
AAAAAAAAAATTAAAAAA
Found at i:1013791 original size:18 final size:18
Alignment explanation
Indices: 1013764--1013798 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1013754 AATTTTAAAT
1013764 TAAAATTTA-TTAAATTA
1 TAAAATTTATTTAAATTA
1013781 TAAATATTTATTTAAATT
1 TAAA-ATTTATTTAAATT
1013799 TTTTATTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 5 0.31
19 7 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAAAATTTATTTAAATTA
Found at i:1013938 original size:2 final size:2
Alignment explanation
Indices: 1013931--1013955 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1013921 TTAATTCCTT
1013931 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 T
1013956 CATTTAAAAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1016583 original size:17 final size:17
Alignment explanation
Indices: 1016561--1016599 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
1016551 TTTTATCGTA
*
1016561 TTTTTTTAAC-CTAAAC
1 TTTTTTTAACTCCAAAC
1016577 TTTTTTTAACTCCAAAC
1 TTTTTTTAACTCCAAAC
1016594 TTTTTT
1 TTTTTT
1016600 AACAGTAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTTTTAACTCCAAAC
Found at i:1016914 original size:24 final size:24
Alignment explanation
Indices: 1016886--1016931 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1016876 TATATTCTTT
1016886 AATTAAAATATATAAAAT-TAAATG
1 AATTAAAAT-TATAAAATATAAATG
*
1016910 AATTAAAATTTTAAAATATAAA
1 AATTAAAATTATAAAATATAAA
1016932 AAAATAAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AATTAAAATTATAAAATATAAATG
Found at i:1021183 original size:89 final size:88
Alignment explanation
Indices: 1021054--1021227 Score: 206
Period size: 89 Copynumber: 2.0 Consensus size: 88
1021044 TTTATCATAT
* * * * * * *
1021054 CATTAGTTAAATTTTTTCTGTTGTGTTAGAAAGAACCTGATATCCATATGCATCTATCACATTTT
1 CATTAGTCAAATTTTTTCTATCGTGTCAGAAAGAACCTGATACCCACATGCATCTATCACATCTT
*
1021119 TTGGGTTTCAAAAAATTTATTAGA
66 TTGAG-TTCAAAAAATTTATTAGA
* * *
1021143 CATTAGTCAAATATTTTTC-ATCGTGTCAGAAGGAATCTGATACCCACATGCATCTGTCACATCT
1 CATTAGTCAAAT-TTTTTCTATCGTGTCAGAAAGAACCTGATACCCACATGCATCTATCACATCT
* *
1021207 TTTGAGTTCCAAGAATTTATT
65 TTTGAGTTCAAAAAATTTATT
1021228 TTATTAGAAC
Statistics
Matches: 71, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
88 13 0.18
89 52 0.73
90 6 0.08
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (88 bp):
CATTAGTCAAATTTTTTCTATCGTGTCAGAAAGAACCTGATACCCACATGCATCTATCACATCTT
TTGAGTTCAAAAAATTTATTAGA
Found at i:1021386 original size:15 final size:15
Alignment explanation
Indices: 1021313--1021386 Score: 51
Period size: 15 Copynumber: 4.7 Consensus size: 15
1021303 AAAAATTTTT
1021313 TAATGATAAAAATACA
1 TAAT-ATAAAAATACA
* **
1021329 TATTATGGAAATGACA
1 TAATATAAAAAT-ACA
1021345 CTAATGATAAAAATACA
1 -TAAT-ATAAAAATACA
* *
1021362 TATTAAAAAAATTA-A
1 TAATATAAAAA-TACA
1021377 TAATATAAAA
1 TAATATAAAA
1021387 CTTTATTGAT
Statistics
Matches: 44, Mismatches: 10, Indels: 9
0.70 0.16 0.14
Matches are distributed among these distances:
15 21 0.48
16 11 0.25
17 6 0.14
18 6 0.14
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.28
Consensus pattern (15 bp):
TAATATAAAAATACA
Found at i:1022674 original size:114 final size:114
Alignment explanation
Indices: 1022469--1022674 Score: 288
Period size: 114 Copynumber: 1.8 Consensus size: 114
1022459 TTTTAAAATG
* * * * *
1022469 TTTACCTAATTAGAAGTTATGCATTCAACTTTTGTTCTGATATTTTTGAGCTCAGTTGGGGTTCA
1 TTTACCTAATCAGAAGTTATGCATTCAACTTTTGTTCTAATATTTTCGAGCTCAATTGGGATTCA
1022534 TGTAAAATCTTTTCTACTGCACTATCTATTAGGTTAAATACATACATAC
66 TGTAAAATCTTTTCTACTGCACTATCTATTAGGTTAAATACATACATAC
* ** * *
1022583 TTTACCTGATCAGAAGTTATGTGTTCAAGTTTTGCTT-TAATATTTTCGAGCTCAATTGGGATTT
1 TTTACCTAATCAGAAGTTATGCATTCAACTTTTG-TTCTAATATTTTCGAGCTCAATTGGGATTC
* *
1022647 TTGTAAAATCTTTTCTACTGCATTATCT
65 ATGTAAAATCTTTTCTACTGCACTATCT
1022675 GTTCAAATAT
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
114 77 0.97
115 2 0.03
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (114 bp):
TTTACCTAATCAGAAGTTATGCATTCAACTTTTGTTCTAATATTTTCGAGCTCAATTGGGATTCA
TGTAAAATCTTTTCTACTGCACTATCTATTAGGTTAAATACATACATAC
Found at i:1031462 original size:13 final size:13
Alignment explanation
Indices: 1031444--1031468 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1031434 CAAAGATTAG
1031444 TGTATCGATACAA
1 TGTATCGATACAA
1031457 TGTATCGATACA
1 TGTATCGATACA
1031469 TTTGAAATGT
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:1031533 original size:19 final size:19
Alignment explanation
Indices: 1031509--1031675 Score: 181
Period size: 19 Copynumber: 9.7 Consensus size: 19
1031499 TAGCTTATAT
*
1031509 TGTATCGATACAAAACTTA
1 TGTATCGATACAACACTTA
1031528 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1031547 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1031566 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1031579 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1031598 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
1031611 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
*
1031630 TGTATC-A-A-TACA-TT-
1 TGTATCGATACAACACTTA
1031644 T-TATCGATACAACACTTTA
1 TGTATCGATACAACAC-TTA
1031663 TGTATCGATACAA
1 TGTATCGATACAA
1031676 ATCGTTGAAA
Statistics
Matches: 126, Mismatches: 3, Indels: 37
0.76 0.02 0.22
Matches are distributed among these distances:
13 22 0.17
14 4 0.03
15 3 0.02
16 18 0.14
17 1 0.01
18 5 0.04
19 62 0.49
20 11 0.09
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1031584 original size:13 final size:13
Alignment explanation
Indices: 1031566--1031622 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1031556 ACAACACTTA
1031566 TGTATCGATACAT
1 TGTATCGATACAT
1031579 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
1031597 ATGTATCGATACAT
1 -TGTATCGATACAT
1031611 TGTATCGATACA
1 TGTATCGATACA
1031623 ACACTTATGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1031588 original size:32 final size:32
Alignment explanation
Indices: 1031507--1031674 Score: 246
Period size: 32 Copynumber: 5.0 Consensus size: 32
1031497 AGTAGCTTAT
*
1031507 ATTGTATCGATACAAAACTTATGTATCGATACAAC
1 ATTGTATCGATACAACACTTATGTATCGAT---AC
1031542 ACTTATGTATCGATACAACACTTATGTATCGATAC
1 A--T-TGTATCGATACAACACTTATGTATCGATAC
1031577 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
1031609 ATTGTATCGATACAACACTTATGTATCAATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
1031641 ATTTTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
1031674 A
1 A
1031675 AATCGTTGAA
Statistics
Matches: 125, Mismatches: 4, Indels: 10
0.90 0.03 0.07
Matches are distributed among these distances:
32 78 0.62
33 15 0.12
35 4 0.03
37 1 0.01
38 27 0.22
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:1031634 original size:51 final size:52
Alignment explanation
Indices: 1031507--1031641 Score: 158
Period size: 51 Copynumber: 2.6 Consensus size: 52
1031497 AGTAGCTTAT
*
1031507 ATTGTATCGATACAAAACTTATGTATCGATACAACACTTATGTATCGATACAAC
1 ATTGTATCGATACAACACTTATGTATCGATACAACACTTATGTATCGAT--AAC
1031561 ACTTATGTATCGAT---ACA--T-TGTATCGATACAACACTTATGTATCGAT-AC
1 A--T-TGTATCGATACAACACTTATGTATCGATACAACACTTATGTATCGATAAC
*
1031609 ATTGTATCGATACAACACTTATGTATCAATACA
1 ATTGTATCGATACAACACTTATGTATCGATACA
1031642 TTTTATCGAT
Statistics
Matches: 70, Mismatches: 2, Indels: 21
0.75 0.02 0.23
Matches are distributed among these distances:
45 9 0.13
46 1 0.01
48 6 0.09
50 1 0.01
51 39 0.56
52 1 0.01
54 3 0.04
56 1 0.01
57 9 0.13
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.33
Consensus pattern (52 bp):
ATTGTATCGATACAACACTTATGTATCGATACAACACTTATGTATCGATAAC
Found at i:1041833 original size:27 final size:27
Alignment explanation
Indices: 1041809--1041866 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
1041799 AAAATACTTT
*
1041809 AACCCCATTTTTTCGAAGGGATACTCC
1 AACCCCATTCTTTCGAAGGGATACTCC
* * *
1041836 AACCGCATTCTTTCGAGGGGAAACTCC
1 AACCCCATTCTTTCGAAGGGATACTCC
1041863 AACC
1 AACC
1041867 TTATTTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.28, C:0.31, G:0.17, T:0.24
Consensus pattern (27 bp):
AACCCCATTCTTTCGAAGGGATACTCC
Found at i:1044787 original size:31 final size:31
Alignment explanation
Indices: 1044752--1044850 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
1044742 TCAAGCGTCG
* *
1044752 CCAACTCGTGCTGACTTTGACTTGGGTGCCA
1 CCAACTCGTGCTGGCTTTGACTAGGGTGCCA
* * * *
1044783 CCAACTTGT-CTAGGCTTTGACTCGGGCGTCA
1 CCAACTCGTGCT-GGCTTTGACTAGGGTGCCA
* *
1044814 CCAACTCATGCAGGCTTTGACTAGGGTGCCA
1 CCAACTCGTGCTGGCTTTGACTAGGGTGCCA
1044845 CCAACT
1 CCAACT
1044851 TGTAGGCGTT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
30 2 0.04
31 52 0.95
32 1 0.02
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.26
Consensus pattern (31 bp):
CCAACTCGTGCTGGCTTTGACTAGGGTGCCA
Found at i:1044798 original size:62 final size:62
Alignment explanation
Indices: 1044718--1044853 Score: 209
Period size: 62 Copynumber: 2.2 Consensus size: 62
1044708 GACATAGGCA
* * * *
1044718 CCACCAACTTGTCTAGGCTTTGACTCAAGCGTCGCCAACTCGTGCTGACTTTGACTTGGGTG
1 CCACCAACTTGTCTAGGCTTTGACTCAAGCGTCACCAACTCATGCAGACTTTGACTAGGGTG
** *
1044780 CCACCAACTTGTCTAGGCTTTGACTCGGGCGTCACCAACTCATGCAGGCTTTGACTAGGGTG
1 CCACCAACTTGTCTAGGCTTTGACTCAAGCGTCACCAACTCATGCAGACTTTGACTAGGGTG
1044842 CCACCAACTTGT
1 CCACCAACTTGT
1044854 AGGCGTTGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.19, C:0.30, G:0.24, T:0.27
Consensus pattern (62 bp):
CCACCAACTTGTCTAGGCTTTGACTCAAGCGTCACCAACTCATGCAGACTTTGACTAGGGTG
Found at i:1044908 original size:28 final size:28
Alignment explanation
Indices: 1044836--1045758 Score: 481
Period size: 28 Copynumber: 33.0 Consensus size: 28
1044826 GGCTTTGACT
** * *
1044836 AGGGTGCCACCAACTTGTAGGCGTTGAAA
1 AGGGTGCCACTGACTTGTGGGC-TTTAAA
* *
1044865 AGGGTGCCACTAACTTGTGAGCTTTAAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* *
1044893 AGGGTGCCATTGACTTGTGGGCTTTGAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * * * *
1044921 AGGGTACCATTAACTTGTGGGCTCTGAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * *
1044949 AGGGTGCCACTAACTTTTGGGGTTTAAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * *
1044977 AGGATCCCACTGACTTGTGGGCTTTGAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* *
1045005 AGAGT-CACATTGACTTGTGGG-TTTGAAA
1 AGGGTGC-CACTGACTTGTGGGCTTT-AAA
* * * * *
1045033 A-AGT-CTGATTAACTTGTGGGCTGTAAA
1 AGGGTGC-CACTGACTTGTGGGCTTTAAA
** *
1045060 AGAATGCCACCGACTTGTGGGCTTTGAAA
1 AGGGTGCCACTGACTTGTGGGCTTT-AAA
** * * * * * *
1045089 A-AATGCCGCTAACTGGTGCGCTCTACA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * * *
1045116 AGGATG-C-C-GACTTATGGGTTTTGAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * *
1045141 AGAGTGCCACTAACTTATGGGCTTTAAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
** * ** * *
1045169 AAAGTGCCACTAACTTGTTAGTTTTGAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * *
1045197 AGGATGCCACTGACTTGTGGGTTTTTAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* *
1045225 AGAGTGCCACTAACTTGTGGGCTTTAAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
** * * * * *
1045253 AAAGTGCCACTAACTTATGTGCTCTGAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * * *
1045281 AGGATG-CATTGACTTGTGGGTTTTGAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
** * * **
1045308 AGGGTGCCA-TCGACTAATTGTCTTTGGA
1 AGGGTGCCACT-GACTTGTGGGCTTTAAA
* * * * *
1045336 AGGATGCCACTAACTTATAGGCTTTGAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * *
1045364 AGGGTGCCACTGGCTTAT-AGCTTTTAAA
1 AGGGTGCCACTGACTTGTGGGC-TTTAAA
* * *
1045392 AGGGTGCCACTGGCTTATGGGCTTTGTAA
1 AGGGTGCCACTGACTTGTGGGCTTT-AAA
* *
1045421 A-TGTGCCACTGACTTGTGGGCTTTGAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * *
1045448 AGGGTGCCACTAACTTGTGCGCTTAAAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* *
1045476 AGAGTGCCACTGACTTGTGGGCTCTAAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * * *
1045504 AGGATGCAATTGACTTGTGGGCTCTAAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* ** *
1045532 AGGATGCCTTTGACTTGTGGGCTCTAAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * *
1045560 AAGGTGCCATTGACTTTGTAGGCTTTGAAA
1 AGGGTGCCACTGAC-TTGTGGGCTTT-AAA
* * * *
1045590 A-AGTGCTACTGACTTGTAGGCTTTTAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
** * *
1045617 AGAATGCCACTGACTTATGTGCTTTAAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * * * *
1045645 AGAGTGCTATTGACTTATGGGCCTTGAAA
1 AGGGTGCCACTGACTTGTGGG-CTTTAAA
* * * *
1045674 A-GATGCCATTGACTTGT-GCCTTTTGAA
1 AGGGTGCCACTGACTTGTGGGC-TTTAAA
* * * *
1045701 AGGGTGCCATTAACTTATGGGCTTTGAA
1 AGGGTGCCACTGACTTGTGGGCTTTAAA
* * * *
1045729 AGGATGCCACTTACTCGTGCGCTTTGAAA
1 AGGGTGCCACTGACTTGTGGGCTTT-AAA
1045758 A
1 A
1045759 AGATCGTATT
Statistics
Matches: 701, Mismatches: 168, Indels: 50
0.76 0.18 0.05
Matches are distributed among these distances:
25 13 0.02
26 3 0.00
27 64 0.09
28 557 0.79
29 60 0.09
30 4 0.01
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (28 bp):
AGGGTGCCACTGACTTGTGGGCTTTAAA
Found at i:1044963 original size:84 final size:84
Alignment explanation
Indices: 1044839--1045760 Score: 603
Period size: 84 Copynumber: 11.0 Consensus size: 84
1044829 TTTGACTAGG
* * * * *
1044839 GTGCCACCAACTTGTAGGCGTTGAAAAGGGTGCCACTAACTTGTGAGCTTTAAAAGGGTGCCATT
1 GTGCCACTAACTTGTGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACT
**
1044904 GACTTGTGGGCTTTGAAAGG
65 GACTTGTGGGCTTTGAAAAA
* * * * * * *
1044924 GTACCATTAACTTGTGGGCTCTGAAAGGGTGCCACTAACTTTTGGGGTTTAAAAGGATCCCACTG
1 GTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTG
*
1044989 ACTTGTGGGCTTTGAAAGA
66 ACTTGTGGGCTTTGAAAAA
* * ** * * * **
1045008 GT-CACATTGACTTGTGGG-TTTGAAAAAGT-CTGATTAACTTGTGGGCTGTAAAAGAATGCCAC
1 GTGC-CACTAACTTGTGGGCTTTGAAAGGGTGC-CACTAACTTGTGGGCTTTAAAAGGGTGCCAC
*
1045070 CGACTTGTGGGCTTTGAAAAA
64 TGACTTGTGGGCTTTGAAAAA
* * * * * * * * * * *
1045091 ATGCCGCTAACTGGTGCGCTCT-ACAAGGATG-C-C-GACTTATGGGTTTTGAAAGAGTGCCACT
1 GTGCCACTAACTTGTGGGCTTTGA-AAGGGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACT
* * *
1045152 AACTTATGGGCTTTAAAAAA
65 GACTTGTGGGCTTTGAAAAA
** * * * * * * *
1045172 GTGCCACTAACTTGTTAGTTTTGAAAGGATGCCACTGACTTGTGGGTTTTTAAAGAGTGCCACTA
1 GTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTG
*
1045237 ACTTGTGGGCTTTAAAAAA
66 ACTTGTGGGCTTTGAAAAA
* * * * * * * *
1045256 GTGCCACTAACTTATGTGCTCTGAAAGGATG-CATTGACTTGTGGGTTTTGAAAGGGTGCCA-TC
1 GTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACT-
** * * * *
1045319 GACTAATTGTCTTTG-GAAG
65 GACTTGTGGGCTTTGAAAAA
* * ** * *
1045338 GATGCCACTAACTTATAGGCTTTGAAAGGGTGCCACTGGCTTAT-AGCTTTTAAAAGGGTGCCAC
1 G-TGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGC-TTTAAAAGGGTGCCAC
* * * *
1045402 TGGCTTATGGGCTTTGTAAAT
64 TGACTTGTGGGCTTTGAAAAA
* * * *
1045423 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGCGCTTAAAAAGAGTGCCACTG
1 GTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTG
* *
1045488 ACTTGTGGGCTCT-AAAAG
66 ACTTGTGGGCTTTGAAAAA
* * * * * * ** * * * *
1045506 GATGCAATTGACTTGTGGGCTCTAAAAGGATGCCTTTGACTTGTGGGCTCTAAAAAGGTGCCATT
1 G-TGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACT
*
1045571 GACTTTGTAGGCTTTGAAAAA
65 GAC-TTGTGGGCTTTGAAAAA
* * * * ** * * * * * *
1045592 GTGCTACTGACTTGTAGGCTTTTAAAGAATGCCACTGACTTATGTGCTTTAAAAGAGTGCTATTG
1 GTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTG
* *
1045657 ACTTATGGGCCTTG-AAAA
66 ACTTGTGGGCTTTGAAAAA
* * * * * * *
1045675 GATGCCATTGACTTGT-GCCTTTTGAAAGGGTGCCATTAACTTATGGGCTTTGAAAGGATGCCAC
1 G-TGCCACTAACTTGTGGGC-TTTGAAAGGGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCAC
* * *
1045739 TTACTCGTGCGCTTTGAAAAA
64 TGACTTGTGGGCTTTGAAAAA
1045760 G
1 G
1045761 ATCGTATTGA
Statistics
Matches: 657, Mismatches: 157, Indels: 46
0.76 0.18 0.05
Matches are distributed among these distances:
81 60 0.09
82 7 0.01
83 138 0.21
84 358 0.54
85 89 0.14
86 5 0.01
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (84 bp):
GTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTAAAAGGGTGCCACTG
ACTTGTGGGCTTTGAAAAA
Found at i:1045629 original size:141 final size:140
Alignment explanation
Indices: 1045423--1045691 Score: 330
Period size: 141 Copynumber: 1.9 Consensus size: 140
1045413 CTTTGTAAAT
* ** *
1045423 GTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGCGCTTAAAAAGAGTGCCACTG
1 GTGCCACTGACTTGTAGGCTTTGAAAAAGTGCCACTAACTTGTGCGCTTAAAAAGAATGCCACTG
* * *
1045488 ACTTGTGGGCTCTAAAAG-GATGCAATTGACTTGTGGG-CTCT-AAAAGGATGCCTTTGACTTGT
66 ACTTATGGGCTCTAAAAGAG-TGCAATTGACTTATGGGCCT-TGAAAA-GATGCCATTGACTTGT
1045550 GGGCTCTAAAAAG
128 GGGCTCTAAAAAG
* * * **
1045563 GTGCCATTGACTTTGTAGGCTTTGAAAAAGTGCTACTGACTTGTAG-GCTTTTAAAGAATGCCAC
1 GTGCCACTGAC-TTGTAGGCTTTGAAAAAGTGCCACTAACTTGT-GCGCTTAAAAAGAATGCCAC
* * *
1045627 TGACTTATGTGCTTTAAAAGAGTGCTATTGACTTATGGGCCTTGAAAAGATGCCATTGACTTGTG
64 TGACTTATGGGCTCTAAAAGAGTGCAATTGACTTATGGGCCTTGAAAAGATGCCATTGACTTGTG
1045692 CCTTTTGAAA
Statistics
Matches: 109, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
140 10 0.09
141 91 0.83
142 8 0.07
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (140 bp):
GTGCCACTGACTTGTAGGCTTTGAAAAAGTGCCACTAACTTGTGCGCTTAAAAAGAATGCCACTG
ACTTATGGGCTCTAAAAGAGTGCAATTGACTTATGGGCCTTGAAAAGATGCCATTGACTTGTGGG
CTCTAAAAAG
Found at i:1045707 original size:141 final size:140
Alignment explanation
Indices: 1045423--1045761 Score: 325
Period size: 141 Copynumber: 2.4 Consensus size: 140
1045413 CTTTGTAAAT
* ** *
1045423 GTGCCACTGAC-TTGTGGGCTTTGAAAGGGTGCCACTAACTTGTGCGCTTAAAAAGAGTGCCACT
1 GTGCCATTGACTTTGT-GGCTTTGAAAAAGTGCCACTAACTTGTGCGCTTAAAAAGAATGCCACT
* * *
1045487 GACTTGTGGGCTCTAAAAGGATGCAATTGACTTGTGGGCTCTAAAAGGATGCCTTTGACTTGTGG
65 GACTTATGGGCTCTAAAAGGATGCAATTGACTTATGGGCTCTAAAAGGATGCCATTGACTTGTGG
*
1045552 GCTCTAAAAAG
130 CCTCTAAAAAG
* * **
1045563 GTGCCATTGACTTTGTAGGCTTTGAAAAAGTGCTACTGACTTGTAG-GCTTTTAAAGAATGCCAC
1 GTGCCATTGACTTTGT-GGCTTTGAAAAAGTGCCACTAACTTGT-GCGCTTAAAAAGAATGCCAC
* * *
1045627 TGACTTATGTGCTTTAAAA-GAGTGCTATTGACTTATGGGC-CTTGAAAA-GATGCCATTGACTT
64 TGACTTATGGGCTCTAAAAGGA-TGCAATTGACTTATGGGCTC-T-AAAAGGATGCCATTGACTT
* * *
1045689 GT-GCCTTTTGAAAGG
126 GTGGCC-TCTAAAAAG
* * * *
1045704 GTGCCATTAACTTATG-GGCTTTG-AAAGGATGCCACTTACTCGTGCGCTTTGAAAAAGA
1 GTGCCATTGACTT-TGTGGCTTTGAAAAAG-TGCCACTAACTTGTGCGC-TT-AAAAAGA
1045762 TCGTATTGAC
Statistics
Matches: 162, Mismatches: 26, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
139 5 0.03
140 35 0.22
141 110 0.68
142 12 0.07
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (140 bp):
GTGCCATTGACTTTGTGGCTTTGAAAAAGTGCCACTAACTTGTGCGCTTAAAAAGAATGCCACTG
ACTTATGGGCTCTAAAAGGATGCAATTGACTTATGGGCTCTAAAAGGATGCCATTGACTTGTGGC
CTCTAAAAAG
Found at i:1049438 original size:20 final size:20
Alignment explanation
Indices: 1049400--1049450 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1049390 ATGAGCTTAT
1049400 GATGAGATGATAGTGGATGAA
1 GATGA-ATGATAGTGGATGAA
*
1049421 GATGAATGACTAGT-GATGTA
1 GATGAATGA-TAGTGGATGAA
*
1049441 GATGCATGAT
1 GATGAATGAT
1049451 CAAGACAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
19 1 0.04
20 17 0.63
21 9 0.33
ACGTcount: A:0.35, C:0.04, G:0.33, T:0.27
Consensus pattern (20 bp):
GATGAATGATAGTGGATGAA
Found at i:1050290 original size:28 final size:28
Alignment explanation
Indices: 1050259--1050312 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1050249 CTTTGAAACA
* *
1050259 ATGCCA-TGAACTTGTGGGCTTTAAAAGG
1 ATGCCACT-AACTCGTGAGCTTTAAAAGG
1050287 ATGCCACTAACTCGTGAGCTTTAAAA
1 ATGCCACTAACTCGTGAGCTTTAAAA
1050313 AAGGGTCGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 22 0.96
29 1 0.04
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (28 bp):
ATGCCACTAACTCGTGAGCTTTAAAAGG
Found at i:1051148 original size:28 final size:28
Alignment explanation
Indices: 1051112--1051366 Score: 234
Period size: 28 Copynumber: 9.1 Consensus size: 28
1051102 GTTACTCACG
* *
1051112 AAAGATGCCACTGACTTGTGAGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
*
1051140 AAAGGTGCCACTGACTTGTGGGCTCTG-
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
*
1051167 GAAGGATGCCACTGACTTGTGGGCTTTG-
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
* *
1051195 GAAGGTTGCCACTAACTTGTGGGCTTT-A
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
* * *
1051223 AAAGGGTACCACTAACTTGTGGGCTTCGA
1 AAA-GGTGCCACTGACTTGTGGGCTTTGA
* * *
1051252 AAGGGTGTCACTGACTTGTGGGTTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
* * * *
1051280 AATGGTGCTACTAACTTGTAGGCTTTGA
1 AAAGGTGCCACTGACTTGTGGGCTTTGA
*
1051308 AACA-ATGCCA-TGAACTTGTGGGCTTT-A
1 AA-AGGTGCCACTG-ACTTGTGGGCTTTGA
* * *
1051335 AAAGGATGCCACTAACTCGTGGGCTTTAA
1 AAAGG-TGCCACTGACTTGTGGGCTTTGA
1051364 AAA
1 AAA
1051367 AGGGTCGTAT
Statistics
Matches: 187, Mismatches: 30, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
26 1 0.01
27 8 0.04
28 168 0.90
29 10 0.05
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (28 bp):
AAAGGTGCCACTGACTTGTGGGCTTTGA
Found at i:1052579 original size:16 final size:17
Alignment explanation
Indices: 1052559--1052607 Score: 75
Period size: 17 Copynumber: 2.9 Consensus size: 17
1052549 GTTAAAAATC
1052559 AAAAAAATTCAAATAAT
1 AAAAAAATTCAAATAAT
1052576 AAAAAAATTCAAATTAAT
1 AAAAAAATTCAAA-TAAT
1052594 -AAAAAA-TCAAATAA
1 AAAAAAATTCAAATAA
1052608 AAATCAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.10
16 5 0.16
17 19 0.61
18 4 0.13
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.22
Consensus pattern (17 bp):
AAAAAAATTCAAATAAT
Found at i:1052583 original size:41 final size:43
Alignment explanation
Indices: 1052519--1052623 Score: 119
Period size: 41 Copynumber: 2.5 Consensus size: 43
1052509 CTTTTTTAAT
* * * *
1052519 ATAAAATTAAAATAATAATAAAA-TGAAA-AAGTTAAAAATCAA
1 ATAAAATTCAAATAATAAAAAAATTCAAATAA-TAAAAAATCAA
1052561 A-AAAATTCAAATAATAAAAAAATTCAAATTAATAAAAAATCAA
1 ATAAAATTCAAATAATAAAAAAATTCAAA-TAATAAAAAATCAA
*
1052604 ATAAAAATCAAA-AATAAAAA
1 ATAAAATTCAAATAATAAAAA
1052624 TCAAAGAAAT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
41 19 0.35
42 5 0.09
43 19 0.35
44 11 0.20
ACGTcount: A:0.71, C:0.05, G:0.02, T:0.22
Consensus pattern (43 bp):
ATAAAATTCAAATAATAAAAAAATTCAAATAATAAAAAATCAA
Found at i:1052608 original size:12 final size:12
Alignment explanation
Indices: 1052591--1052628 Score: 51
Period size: 11 Copynumber: 3.2 Consensus size: 12
1052581 AATTCAAATT
1052591 AATAAAAAATCA
1 AATAAAAAATCA
1052603 AAT-AAAAATCA
1 AATAAAAAATCA
*
1052614 AAAATAAAAATCA
1 AATA-AAAAATCA
1052627 AA
1 AA
1052629 GAAATCATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
11 10 0.43
12 3 0.13
13 10 0.43
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (12 bp):
AATAAAAAATCA
Found at i:1054464 original size:21 final size:21
Alignment explanation
Indices: 1054439--1054486 Score: 55
Period size: 21 Copynumber: 2.2 Consensus size: 21
1054429 CGGAATGAAT
1054439 TTTTG-GAGTTTTCACTTTTTA-
1 TTTTGAGAGTTTT-A-TTTTTAG
1054460 TTTTGATGAGTTTTATTTTTAG
1 TTTTGA-GAGTTTTATTTTTAG
1054482 TTTTG
1 TTTTG
1054487 TGAATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 11 0.46
22 6 0.25
23 7 0.29
ACGTcount: A:0.15, C:0.04, G:0.17, T:0.65
Consensus pattern (21 bp):
TTTTGAGAGTTTTATTTTTAG
Found at i:1054471 original size:23 final size:22
Alignment explanation
Indices: 1054444--1054486 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
1054434 TGAATTTTTG
1054444 GAGTTTTCACTTTTTA-TTTTGAT
1 GAGTTTT-A-TTTTTAGTTTTGAT
1054467 GAGTTTTATTTTTAGTTTTG
1 GAGTTTTATTTTTAGTTTTG
1054487 TGAATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 6 0.32
23 7 0.37
ACGTcount: A:0.16, C:0.05, G:0.16, T:0.63
Consensus pattern (22 bp):
GAGTTTTATTTTTAGTTTTGAT
Found at i:1058325 original size:13 final size:13
Alignment explanation
Indices: 1058307--1058334 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1058297 ATGGAAACTA
1058307 AACTTCAACGTCC
1 AACTTCAACGTCC
1058320 AACTTCAACGTCC
1 AACTTCAACGTCC
1058333 AA
1 AA
1058335 GTGTTGATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.36, G:0.07, T:0.21
Consensus pattern (13 bp):
AACTTCAACGTCC
Found at i:1063096 original size:25 final size:24
Alignment explanation
Indices: 1063059--1063123 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 24
1063049 ATTTTTTATT
1063059 TTTTATTTGATTTTTCACTAATTTGAA
1 TTTT-TTT-ATTTTTCA-TAATTTGAA
* * *
1063086 TTTTTTTATTTTTTGATTATTTTAA
1 TTTTTTTA-TTTTTCATAATTTGAA
1063111 TTTTTTTATTTTT
1 TTTTTTTATTTTT
1063124 AATTTTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 5 0.15
25 16 0.47
26 9 0.26
27 4 0.12
ACGTcount: A:0.20, C:0.03, G:0.05, T:0.72
Consensus pattern (24 bp):
TTTTTTTATTTTTCATAATTTGAA
Found at i:1063098 original size:8 final size:8
Alignment explanation
Indices: 1063085--1063137 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
1063075 ACTAATTTGA
1063085 ATTTTTTT
1 ATTTTTTT
*
1063093 ATTTTTTG
1 ATTTTTTT
*
1063101 ATTATTTTA
1 ATT-TTTTT
1063110 ATTTTTTT
1 ATTTTTTT
*
1063118 A-TTTTTA
1 ATTTTTTT
1063125 ATTTTTTT
1 ATTTTTTT
*
1063133 GTTTT
1 ATTTT
1063138 AATAGACATA
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
7 6 0.16
8 24 0.65
9 7 0.19
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (8 bp):
ATTTTTTT
Found at i:1063121 original size:14 final size:14
Alignment explanation
Indices: 1063102--1063140 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
1063092 TATTTTTTGA
1063102 TTATTTTAATTTTT
1 TTATTTTAATTTTT
1063116 TTATTTTTAATTTTT
1 TTA-TTTTAATTTTT
*
1063131 TTGTTTTAAT
1 TTATTTTAAT
1063141 AGACATAGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTATTTTAATTTTT
Found at i:1067307 original size:14 final size:14
Alignment explanation
Indices: 1067285--1067369 Score: 65
Period size: 14 Copynumber: 6.5 Consensus size: 14
1067275 ATTTGCCATT
*
1067285 TTGTAAAGAAATTG
1 TTGTCAAGAAATTG
1067299 TTGTCAAGAAATTG
1 TTGTCAAGAAATTG
** *
1067313 TCATCAAGAACTT-
1 TTGTCAAGAAATTG
1067326 TTGTCAAG-AA-TG
1 TTGTCAAGAAATTG
* *
1067338 ATGT--AGAAACT-
1 TTGTCAAGAAATTG
*
1067349 TTGTCAAGAAATTT
1 TTGTCAAGAAATTG
1067363 TTGTCAA
1 TTGTCAA
1067370 TACAACCCTT
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
10 2 0.04
11 6 0.11
12 5 0.09
13 12 0.22
14 30 0.55
ACGTcount: A:0.38, C:0.09, G:0.18, T:0.35
Consensus pattern (14 bp):
TTGTCAAGAAATTG
Found at i:1067467 original size:28 final size:28
Alignment explanation
Indices: 1067381--1067649 Score: 150
Period size: 28 Copynumber: 9.6 Consensus size: 28
1067371 ACAACCCTTT
* * * * *
1067381 TTTCAAAGCCCACAAGTTAGTGGCACCA
1 TTTCAAAACCCACAAGTCAATAGCACCC
* * *
1067409 TTCCAAAGCCCACAAATCAATAGCACCC
1 TTTCAAAACCCACAAGTCAATAGCACCC
* * **
1067437 TTTTAAAACCCACAAGTCAGTAGCATTC
1 TTTCAAAACCCACAAGTCAATAGCACCC
* *
1067465 TTTCAGAACCCATAAGT---TAGCGACACTC
1 TTTCAAAACCCACAAGTCAATAGC-AC-C-C
* * * * *
1067493 TTTCAAAGCCAACAAGTCAATGGGATCC
1 TTTCAAAACCCACAAGTCAATAGCACCC
* * * * *
1067521 TTTCAAAACTCATAAGTCAGTGGCAGCC
1 TTTCAAAACCCACAAGTCAATAGCACCC
* * * *
1067549 TTTCAAAGCTCACAAGTCAA-CGACATCC
1 TTTCAAAACCCACAAGTCAATAG-CACCC
* * * *
1067577 TTTCAAAGCCCACAACTAAATAACACCC
1 TTTCAAAACCCACAAGTCAATAGCACCC
* * *
1067605 TTTCAAAACTCACAAGTCAATGGCACCT
1 TTTCAAAACCCACAAGTCAATAGCACCC
*
1067633 TTTCAAAGCCCACAAGT
1 TTTCAAAACCCACAAGT
1067650 TGATGGCACC
Statistics
Matches: 181, Mismatches: 52, Indels: 16
0.73 0.21 0.06
Matches are distributed among these distances:
25 4 0.02
26 1 0.01
27 1 0.01
28 171 0.94
29 1 0.01
30 1 0.01
31 2 0.01
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (28 bp):
TTTCAAAACCCACAAGTCAATAGCACCC
Found at i:1067552 original size:84 final size:83
Alignment explanation
Indices: 1067381--1067649 Score: 256
Period size: 84 Copynumber: 3.2 Consensus size: 83
1067371 ACAACCCTTT
* ** * * *
1067381 TTTCAAAGCCCACAAGTTAGTGGCA-CCATTCCAAAGCCCACAAATCAATAGCACCCTTTTAAAA
1 TTTCAAAGCCCACAAGTCAACGACATCC-TTTCAAAGCCCACAAATCAATAGCACCCTTTCAAAA
* * *
1067445 CCCACAAGTCAGTAGCATTC
65 CTCACAAGTCAGTGGCA-CC
* * * * * * * *
1067465 TTTCAGAA-CCCATAAGTTAGCGACA-CTCTTTCAAAGCCAACAAGTCAATGGGATCCTTTCAAA
1 TTTCA-AAGCCCACAAGTCAACGACATC-CTTTCAAAGCCCACAAATCAATAGCACCCTTTCAAA
*
1067528 ACTCATAAGTCAGTGGCAGCC
64 ACTCACAAGTCAGTGGCA-CC
* * * *
1067549 TTTCAAAGCTCACAAGTCAACGACATCCTTTCAAAGCCCACAACTAAATAACACCCTTTCAAAAC
1 TTTCAAAGCCCACAAGTCAACGACATCCTTTCAAAGCCCACAAATCAATAGCACCCTTTCAAAAC
*
1067614 TCACAAGTCAATGGCACC
66 TCACAAGTCAGTGGCACC
1067632 TTTTCAAAGCCCACAAGT
1 -TTTCAAAGCCCACAAGT
1067650 TGATGGCACC
Statistics
Matches: 151, Mismatches: 29, Indels: 10
0.79 0.15 0.05
Matches are distributed among these distances:
83 4 0.03
84 143 0.95
85 4 0.03
ACGTcount: A:0.36, C:0.30, G:0.12, T:0.22
Consensus pattern (83 bp):
TTTCAAAGCCCACAAGTCAACGACATCCTTTCAAAGCCCACAAATCAATAGCACCCTTTCAAAAC
TCACAAGTCAGTGGCACC
Found at i:1067660 original size:56 final size:55
Alignment explanation
Indices: 1067381--1067680 Score: 197
Period size: 56 Copynumber: 5.3 Consensus size: 55
1067371 ACAACCCTTT
* * * * * *
1067381 TTTCAAAGCCCACAAGTTAGTGGCACCATTCCAAAGCCCACAAATCAATAGCACCC
1 TTTCAAAGCCCACAAGTCAATGGCACC-TTTCAAAGCCCACAAGTTAATGGCACCC
* * * * * * ** * *
1067437 TTTTAAAACCCACAAGTCAGTAGCATTCTTTCAGAA-CCCATAAGTTAGCGACACTC
1 TTTCAAAGCCCACAAGTCAATGGCA-CCTTTCA-AAGCCCACAAGTTAATGGCACCC
* * * * * * * *
1067493 TTTCAAAGCCAACAAGTCAATGGGATCCTTTCAAAACTCATAAGTCAGTGGCAGCC
1 TTTCAAAGCCCACAAGTCAATGGCA-CCTTTCAAAGCCCACAAGTTAATGGCACCC
* * * * * **
1067549 TTTCAAAGCTCACAAGTCAACGACATCCTTTCAAAGCCCACAACTAAATAACACCC
1 TTTCAAAGCCCACAAGTCAATGGCA-CCTTTCAAAGCCCACAAGTTAATGGCACCC
* * *
1067605 TTTCAAAACTCACAAGTCAATGGCACCTTTTCAAAGCCCACAAGTTGATGGCACCC
1 TTTCAAAGCCCACAAGTCAATGGCACC-TTTCAAAGCCCACAAGTTAATGGCACCC
*
1067661 TAGTCAAAGCCTGCACAAGT
1 T-TTCAAAGCC--CACAAGT
1067681 TGACGATGCT
Statistics
Matches: 185, Mismatches: 52, Indels: 11
0.75 0.21 0.04
Matches are distributed among these distances:
55 4 0.02
56 165 0.89
57 9 0.05
59 7 0.04
ACGTcount: A:0.35, C:0.30, G:0.13, T:0.22
Consensus pattern (55 bp):
TTTCAAAGCCCACAAGTCAATGGCACCTTTCAAAGCCCACAAGTTAATGGCACCC
Found at i:1068452 original size:18 final size:18
Alignment explanation
Indices: 1068427--1068472 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
1068417 GAGACTTAAC
1068427 GAAAAAAATAATGCAAAACT
1 GAAAAAAA-AA-GCAAAACT
*
1068447 -AAAAAAAAAGTAAAACT
1 GAAAAAAAAAGCAAAACT
1068464 GAAAAAAAA
1 GAAAAAAAA
1068473 CATTACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 7 0.29
18 10 0.42
19 7 0.29
ACGTcount: A:0.74, C:0.07, G:0.09, T:0.11
Consensus pattern (18 bp):
GAAAAAAAAAGCAAAACT
Found at i:1068655 original size:8 final size:8
Alignment explanation
Indices: 1068606--1068662 Score: 51
Period size: 9 Copynumber: 6.5 Consensus size: 8
1068596 ACATACTTAA
1068606 AAAATAAAT
1 AAAA-AAAT
1068615 AAAAAAACT
1 AAAAAAA-T
*
1068624 AAAAATTAT
1 AAAAA-AAT
*
1068633 AAAATAATT
1 AAAA-AAAT
1068642 ATAAAAAAT
1 A-AAAAAAT
1068651 AAAAAAAT
1 AAAAAAAT
1068659 AAAA
1 AAAA
1068663 GAAAGGAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
8 14 0.35
9 21 0.52
10 5 0.12
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (8 bp):
AAAAAAAT
Found at i:1070668 original size:3 final size:3
Alignment explanation
Indices: 1070655--1070685 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1070645 AATTTAAATA
*
1070655 AAT ATT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1070686 TTTATAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:1077337 original size:17 final size:16
Alignment explanation
Indices: 1077314--1077358 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
1077304 GAGTTTTAAT
1077314 ATTAATAAAATTTTTA
1 ATTAATAAAATTTTTA
*
1077330 ATTAAATAAAA-TTATA
1 ATT-AATAAAATTTTTA
1077346 ATTAATAAAATTT
1 ATTAATAAAATTT
1077359 ATTTAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 7 0.27
16 12 0.46
17 7 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
ATTAATAAAATTTTTA
Found at i:1077385 original size:13 final size:14
Alignment explanation
Indices: 1077326--1077401 Score: 68
Period size: 13 Copynumber: 5.4 Consensus size: 14
1077316 TAATAAAATT
1077326 TTTAATTAAATAAAA
1 TTTAA-TAAATAAAA
*
1077341 TTATAATTAATAAAA
1 TT-TAATAAATAAAA
* *
1077356 TTTATTTAAA-AATA
1 TTTA-ATAAATAAAA
1077370 TTTAATAAAT-AAA
1 TTTAATAAATAAAA
*
1077383 TTTAA-AATTAAAA
1 TTTAATAAATAAAA
1077396 TTTAAT
1 TTTAAT
1077402 CATATAAAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
12 3 0.06
13 19 0.39
14 9 0.18
15 15 0.31
16 3 0.06
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAATAAATAAAA
Found at i:1078861 original size:32 final size:31
Alignment explanation
Indices: 1078824--1078895 Score: 74
Period size: 32 Copynumber: 2.3 Consensus size: 31
1078814 TATATTAAAT
* * *
1078824 AAAATAAAT-TATTAATATATAAAAATTATATA
1 AAAATAAATAT-TTAAAATA-AAAAATAATACA
1078856 AAAATATAATATTTAAAATAAAAAATAATACA
1 AAAATA-AATATTTAAAATAAAAAATAATACA
*
1078888 AATATAAA
1 AAAATAAA
1078896 CAAATAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
31 2 0.06
32 21 0.62
33 10 0.29
34 1 0.03
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (31 bp):
AAAATAAATATTTAAAATAAAAAATAATACA
Found at i:1078918 original size:9 final size:9
Alignment explanation
Indices: 1078904--1078987 Score: 57
Period size: 9 Copynumber: 9.3 Consensus size: 9
1078894 AACAAATAAA
1078904 TTTTTTCTC
1 TTTTTTCTC
1078913 TTTTTT-TC
1 TTTTTTCTC
*
1078921 TTTTTTTTC
1 TTTTTTCTC
* *
1078930 CTTCTTCT-
1 TTTTTTCTC
*
1078938 TCTTTTCTC
1 TTTTTTCTC
* *
1078947 CTTTCTCTC
1 TTTTTTCTC
1078956 TTTCTTTCT-
1 TTT-TTTCTC
1078965 TTTTTTCTTTC
1 TTTTTTC--TC
*
1078976 TTTTTTTTC
1 TTTTTTCTC
1078985 TTT
1 TTT
1078988 GTTTGTCAGG
Statistics
Matches: 57, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
8 17 0.30
9 29 0.51
10 5 0.09
11 6 0.11
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTTTTCTC
Found at i:1079209 original size:43 final size:44
Alignment explanation
Indices: 1079142--1079242 Score: 122
Period size: 44 Copynumber: 2.3 Consensus size: 44
1079132 TAGGTTTTAA
*
1079142 TATTTATAAAATTTTTAATTAAATAAAATTATAATTA-ATAAAATT
1 TATTTATAAAATATTTAATTAAAT-AAATT-TAATTATATAAAATT
1079187 TATTTA-AAAATATTTAA-TAAATAAATTTAATTATATAAAAAATT
1 TATTTATAAAATATTTAATTAAATAAATTTAATTATAT--AAAATT
1079231 TA--TATAAAATAT
1 TATTTATAAAATAT
1079243 AAGACAAATT
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
41 6 0.12
42 9 0.18
43 12 0.24
44 18 0.35
45 6 0.12
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (44 bp):
TATTTATAAAATATTTAATTAAATAAATTTAATTATATAAAATT
Found at i:1079222 original size:23 final size:24
Alignment explanation
Indices: 1079168--1079222 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
1079158 AATTAAATAA
* **
1079168 AATTATAATTAATAAAATTTATTT
1 AATTATATTTAATAAAATAAATTT
**
1079192 AAAAATATTTAAT-AAATAAATTT
1 AATTATATTTAATAAAATAAATTT
1079215 AATTATAT
1 AATTATAT
1079223 AAAAAATTTA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AATTATATTTAATAAAATAAATTT
Found at i:1079233 original size:44 final size:44
Alignment explanation
Indices: 1079142--1079226 Score: 122
Period size: 42 Copynumber: 2.0 Consensus size: 44
1079132 TAGGTTTTAA
*
1079142 TATTTATAAAATTTTTAATTAAATAAAATTATAATTAATAAAATT
1 TATTTA-AAAATATTTAATTAAATAAAATTATAATTAATAAAATT
1079187 TATTTAAAAATATTTAA-TAAAT-AAATT-TAATTATATAAAA
1 TATTTAAAAATATTTAATTAAATAAAATTATAATTA-ATAAAA
1079227 AATTTATATA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
41 6 0.16
42 11 0.29
43 5 0.13
44 10 0.26
45 6 0.16
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (44 bp):
TATTTAAAAATATTTAATTAAATAAAATTATAATTAATAAAATT
Found at i:1080240 original size:19 final size:19
Alignment explanation
Indices: 1080216--1080276 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
1080206 ATAAATAATT
1080216 TTTTTCTTTTTTTCTTTCC
1 TTTTTCTTTTTTTCTTTCC
1080235 TTTTTCTTTTTTTC--TCC
1 TTTTTCTTTTTTTCTTTCC
* *
1080252 -TTTT-TTTCTTTCTTT-T
1 TTTTTCTTTTTTTCTTTCC
1080268 TTTTTCTTT
1 TTTTTCTTT
1080277 ATTGACAGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
15 7 0.19
16 4 0.11
17 8 0.22
18 3 0.08
19 14 0.39
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTCTTTTTTTCTTTCC
Found at i:1081268 original size:17 final size:17
Alignment explanation
Indices: 1081246--1081299 Score: 67
Period size: 17 Copynumber: 3.1 Consensus size: 17
1081236 ACAGTACAAA
1081246 TTTTTTTCTCTTTTTCT
1 TTTTTTTCTCTTTTTCT
1081263 TTTTTTT-TCTCTTTTCT
1 TTTTTTTCTCT-TTTTCT
1081280 TTTATTTTCT-TTCTTTCT
1 TTT-TTTTCTCTT-TTTCT
1081298 TT
1 TT
1081300 CTCTCCTGTC
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
16 3 0.09
17 17 0.52
18 12 0.36
19 1 0.03
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTTTTCTCTTTTTCT
Found at i:1081269 original size:18 final size:18
Alignment explanation
Indices: 1081246--1081299 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
1081236 ACAGTACAAA
1081246 TTTTTTTCTCTTTTTCTT
1 TTTTTTTCTCTTTTTCTT
1081264 TTTTTTTCTC-TTTTCTT
1 TTTTTTTCTCTTTTTCTT
*
1081281 TTATTTTCT-TTCTTTCTT
1 TTTTTTTCTCTT-TTTCTT
1081299 T
1 T
1081300 CTCTCCTGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
17 16 0.48
18 17 0.52
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTTCTCTTTTTCTT
Found at i:1081745 original size:2 final size:2
Alignment explanation
Indices: 1081738--1081763 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1081728 CTTCAGCAAA
1081738 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
1081764 GCAGTCAGTA
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:1082637 original size:17 final size:17
Alignment explanation
Indices: 1082597--1082638 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
1082587 TAAATATAAT
*
1082597 TATA-TTAATTTTAAAT
1 TATATTTAATTTTAAAA
1082613 TA-ATTTTAATTTTAAAA
1 TATA-TTTAATTTTAAAA
1082630 TATATTTAA
1 TATATTTAA
1082639 AAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
15 1 0.05
16 2 0.09
17 18 0.82
18 1 0.05
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATATTTAATTTTAAAA
Found at i:1083141 original size:2 final size:2
Alignment explanation
Indices: 1083136--1083165 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1083126 TGAGTGGGGG
1083136 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1083166 AAGGCGGCTT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1086387 original size:24 final size:23
Alignment explanation
Indices: 1086344--1086390 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
1086334 CATTAGAAAA
*
1086344 ATAATTTAAATATTATTAAATAT
1 ATAATTTAAATATTAATAAATAT
*
1086367 ATAATTTTAATATTAAATAAATAT
1 ATAATTTAAATATT-AATAAATAT
1086391 TAAATATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATAATTTAAATATTAATAAATAT
Found at i:1086400 original size:23 final size:23
Alignment explanation
Indices: 1086352--1086401 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
1086342 AAATAATTTA
* * *
1086352 AATATTATTAAATATATAATTTT
1 AATATTAATAAATATATAAATAT
1086375 AATATTAAATAAATAT-TAAATAT
1 AATATT-AATAAATATATAAATAT
1086398 AATA
1 AATA
1086402 AATACTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATATTAATAAATATATAAATAT
Found at i:1086541 original size:21 final size:21
Alignment explanation
Indices: 1086513--1086562 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
1086503 AAATTATTTT
1086513 TTAA-TTTTTTACTAATTTAA
1 TTAATTTTTTTACTAATTTAA
*
1086533 TTAATTTTTTTACTGATTTAA
1 TTAATTTTTTTACTAATTTAA
*
1086554 -AAATTTTTT
1 TTAATTTTTT
1086563 GGTTTTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.32, C:0.04, G:0.02, T:0.62
Consensus pattern (21 bp):
TTAATTTTTTTACTAATTTAA
Found at i:1086699 original size:2 final size:2
Alignment explanation
Indices: 1086692--1086718 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1086682 TTTACACGTG
1086692 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
1086719 CAAACTAGAG
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:1087321 original size:31 final size:32
Alignment explanation
Indices: 1087260--1087321 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
1087250 GCTAAAGTTC
** *
1087260 GATACGGACATCCAATTTTTATTTTTATAATT
1 GATACGGACATCCAATTTTTAAATTCATAATT
*
1087292 GATATGGACATCCAA-TTTTAAATTCATAAT
1 GATACGGACATCCAATTTTTAAATTCATAAT
1087322 GAAGATTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (32 bp):
GATACGGACATCCAATTTTTAAATTCATAATT
Found at i:1088403 original size:11 final size:11
Alignment explanation
Indices: 1088389--1088428 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
1088379 TTAATTAATA
1088389 AAAATTATTTT
1 AAAATTATTTT
*
1088400 AAAATTAATTT
1 AAAATTATTTT
1088411 AAAA-TATTTT
1 AAAATTATTTT
1088421 AATAATTA
1 AA-AATTA
1088429 AATAATATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 7 0.28
11 16 0.64
12 2 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
AAAATTATTTT
Found at i:1088405 original size:21 final size:22
Alignment explanation
Indices: 1088380--1088429 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
1088370 TATTATTATT
1088380 TAATTAA-TAAAAATTATTTTAA
1 TAATTAATTAAAAA-TATTTTAA
*
1088402 -AATTAATTTAAAATATTTTAA
1 TAATTAATTAAAAATATTTTAA
1088423 TAATTAA
1 TAATTAA
1088430 ATAATATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
TAATTAATTAAAAATATTTTAA
Found at i:1088693 original size:27 final size:27
Alignment explanation
Indices: 1088663--1088809 Score: 81
Period size: 26 Copynumber: 5.3 Consensus size: 27
1088653 TTTTATTTTG
1088663 TTTATATATTTTTATATTATAATTATA
1 TTTATATATTTTTATATTATAATTATA
*
1088690 TTTAAAAATATTTTATATATATATAAATTTTAATA
1 TTT--ATATATTTT-TATAT-TAT-AA--TT-ATA
* **
1088725 TATTA-ATA-ATTTATATTATAAAAAT-
1 T-TTATATATTTTTATATTATAATTATA
* *
1088750 TTTA-ATATTTTTTATTTTATATTTATA
1 TTTATATA-TTTTTATATTATAATTATA
**
1088777 TTTTATATATTTTTA-ATTATTTTTATA
1 -TTTATATATTTTTATATTATAATTATA
1088804 -TTATAT
1 TTTATAT
1088810 TTAAAATTAA
Statistics
Matches: 95, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
24 6 0.06
25 7 0.07
26 14 0.15
27 13 0.14
28 10 0.11
29 13 0.14
30 8 0.08
31 8 0.08
32 4 0.04
33 3 0.03
34 3 0.03
35 4 0.04
36 2 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (27 bp):
TTTATATATTTTTATATTATAATTATA
Found at i:1088727 original size:18 final size:16
Alignment explanation
Indices: 1088685--1088757 Score: 55
Period size: 17 Copynumber: 4.5 Consensus size: 16
1088675 TATATTATAA
* *
1088685 TTATATTTAAAAATATT
1 TTATATATATAAA-ATT
1088702 TTATATATATATAAATT
1 TTATATATATA-AAATT
1088719 TTA-ATATATTAATAA-T
1 TTATATATA-TAA-AATT
1088735 TTATAT-TATAAAAATT
1 TTATATATAT-AAAATT
1088751 TTA-ATAT
1 TTATATAT
1088758 TTTTTATTTT
Statistics
Matches: 47, Mismatches: 2, Indels: 15
0.73 0.03 0.23
Matches are distributed among these distances:
15 5 0.11
16 19 0.40
17 21 0.45
18 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TTATATATATAAAATT
Found at i:1088767 original size:7 final size:7
Alignment explanation
Indices: 1088748--1088805 Score: 50
Period size: 7 Copynumber: 8.4 Consensus size: 7
1088738 TATTATAAAA
1088748 ATTTTAAT
1 ATTTT-AT
*
1088756 ATTTTTT
1 ATTTTAT
1088763 ATTTTAT
1 ATTTTAT
1088770 A-TTTAT
1 ATTTTAT
1088776 ATTTTAT
1 ATTTTAT
*
1088783 ATATTTTT
1 AT-TTTAT
*
1088791 A-ATTAT
1 ATTTTAT
1088797 -TTTTAT
1 ATTTTAT
1088803 ATT
1 ATT
1088806 ATATTTAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
6 13 0.32
7 17 0.43
8 10 0.25
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTTTAT
Found at i:1088776 original size:32 final size:33
Alignment explanation
Indices: 1088696--1088776 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 33
1088686 TATATTTAAA
* *
1088696 AATATTTTATATATATATAAATTTTAATATATT
1 AATATTTTATATTTATAAAAATTTTAATATATT
*
1088729 AATAATTTATA-TTATAAAAATTTTAATAT-TT
1 AATATTTTATATTTATAAAAATTTTAATATATT
**
1088760 TTTATTTTATATTTATA
1 AATATTTTATATTTATA
1088777 TTTTATATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
31 10 0.24
32 21 0.51
33 10 0.24
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (33 bp):
AATATTTTATATTTATAAAAATTTTAATATATT
Found at i:1088802 original size:20 final size:19
Alignment explanation
Indices: 1088749--1088805 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 19
1088739 ATTATAAAAA
1088749 TTTTAA-TATTTTT-TATT
1 TTTTAATTATTTTTATATT
* *
1088766 TTATATTTATATTTTATATAT
1 TTTTAATTAT-TTTTATAT-T
1088787 TTTTAATTATTTTTATATT
1 TTTTAATTATTTTTATATT
1088806 ATATTTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
17 4 0.12
18 3 0.09
19 5 0.16
20 11 0.34
21 9 0.28
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTAATTATTTTTATATT
Done.