Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A03
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: 108673976
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.31
Warning! 5040000 characters in sequence are not A, C, G, or T
File 5 of 333
Found at i:1195787 original size:16 final size:17
Alignment explanation
Indices: 1195761--1195792 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1195751 AGTATGGGAT
1195761 ATGCAATGAATGAATGG
1 ATGCAATGAATGAATGG
1195778 ATGC-ATGAATGAATG
1 ATGCAATGAATGAATG
1195793 CATGAATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.41, C:0.06, G:0.28, T:0.25
Consensus pattern (17 bp):
ATGCAATGAATGAATGG
Found at i:1195809 original size:19 final size:19
Alignment explanation
Indices: 1195785--1195830 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
1195775 TGGATGCATG
1195785 AATGAATGCATGAATGTCA
1 AATGAATGCATGAATGTCA
1195804 AATGAATGCATGAATGTCA
1 AATGAATGCATGAATGTCA
1195823 AATGAATG
1 AATGAATG
1195831 TCAGTCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.43, C:0.09, G:0.22, T:0.26
Consensus pattern (19 bp):
AATGAATGCATGAATGTCA
Found at i:1195810 original size:11 final size:11
Alignment explanation
Indices: 1195794--1195833 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
1195784 GAATGAATGC
1195794 ATGAATGTCAA
1 ATGAATGTCAA
1195805 ATGAATG-C--
1 ATGAATGTCAA
1195813 ATGAATGTCAA
1 ATGAATGTCAA
1195824 ATGAATGTCA
1 ATGAATGTCA
1195834 GTCATGAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 7 0.27
9 1 0.04
10 1 0.04
11 17 0.65
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (11 bp):
ATGAATGTCAA
Found at i:1197433 original size:16 final size:15
Alignment explanation
Indices: 1197412--1197459 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
1197402 GATGTGAATA
1197412 ATAAAATATATAAAAT
1 ATAAAATAT-TAAAAT
1197428 ATAAAATATTAAAAT
1 ATAAAATATTAAAAT
*
1197443 ATCAAAATATTAGAAT
1 AT-AAAATATTAAAAT
1197459 A
1 A
1197460 ATAATAATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (15 bp):
ATAAAATATTAAAAT
Found at i:1197435 original size:24 final size:24
Alignment explanation
Indices: 1197408--1197463 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
1197398 TAATGATGTG
*
1197408 AATAATAAAATATATAAAATA-TAA
1 AATAATAAAATAT-CAAAATATTAA
* *
1197432 AATATTAAAATATCAAAATATTAG
1 AATAATAAAATATCAAAATATTAA
1197456 AATAATAA
1 AATAATAA
1197464 TAATTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 6 0.22
24 21 0.78
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (24 bp):
AATAATAAAATATCAAAATATTAA
Found at i:1197442 original size:8 final size:8
Alignment explanation
Indices: 1197408--1197459 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
1197398 TAATGATGTG
*
1197408 AATAATAA
1 AATATTAA
1197416 AATATATAA
1 AATAT-TAA
1197425 AATA-TAA
1 AATATTAA
1197432 AATATTAA
1 AATATTAA
*
1197440 AATATCAA
1 AATATTAA
*
1197448 AATATTAG
1 AATATTAA
1197456 AATA
1 AATA
1197460 ATAATAATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 24 0.63
9 7 0.18
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (8 bp):
AATATTAA
Found at i:1197724 original size:31 final size:31
Alignment explanation
Indices: 1197662--1197742 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
1197652 TATAGTTAAG
* * *
1197662 ATATATACATAAGATAACATGTAAAAAATAT
1 ATATATAAATAATATAATATGTAAAAAATAT
*
1197693 ATATATAAATAATATAATAT-T-AAAGATAT
1 ATATATAAATAATATAATATGTAAAAAATAT
* *
1197722 ATACATAAAATAGTATAATAT
1 ATATAT-AAATAATATAATAT
1197743 ATATATACGT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
29 12 0.28
30 14 0.33
31 17 0.40
ACGTcount: A:0.58, C:0.04, G:0.05, T:0.33
Consensus pattern (31 bp):
ATATATAAATAATATAATATGTAAAAAATAT
Found at i:1197729 original size:25 final size:25
Alignment explanation
Indices: 1197603--1197821 Score: 104
Period size: 25 Copynumber: 9.0 Consensus size: 25
1197593 TAAATACGTG
* *
1197603 ATAATATTAAAAATATGTACATAAT
1 ATAATATTAAAGATATATACATAAT
* * * *
1197628 ATAGTGTTAAAAATACATACATAAT
1 ATAATATTAAAGATATATACATAAT
* *
1197653 AT-A-GTT-AAGATATATACATAAG
1 ATAATATTAAAGATATATACATAAT
* * *
1197675 ATAACATGTAAAAAATATATATATAAATAAT
1 ATAATAT-T----AA-AGATATATACATAAT
*
1197706 ATAATATTAAAGATATATACATAAA
1 ATAATATTAAAGATATATACATAAT
* * *
1197731 ATAGTA-TAATATATATATACGTAAT
1 ATAATATTAA-AGATATATACATAAT
* *
1197756 ATAGA-ATTTAA-A-ATATACCT-A-
1 ATA-ATATTAAAGATATATACATAAT
*
1197777 AT-ATATTAAA-ATATATATATAAT
1 ATAATATTAAAGATATATACATAAT
*
1197800 ATAATATT-AAGAAATATA-ATAA
1 ATAATATTAAAGATATATACATAA
1197822 CAACAAAAAA
Statistics
Matches: 149, Mismatches: 27, Indels: 38
0.70 0.13 0.18
Matches are distributed among these distances:
19 1 0.01
20 6 0.04
21 8 0.05
22 17 0.11
23 19 0.13
24 16 0.11
25 58 0.39
26 4 0.03
30 2 0.01
31 18 0.12
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (25 bp):
ATAATATTAAAGATATATACATAAT
Found at i:1197745 original size:50 final size:48
Alignment explanation
Indices: 1197686--1197806 Score: 136
Period size: 48 Copynumber: 2.5 Consensus size: 48
1197676 TAACATGTAA
1197686 AAAATATATATATAAATAATATA-ATATTAAAGATATATACATAAAATAGT
1 AAAATATATATATAAATAATATAGA-ATTAAA-A-ATATACATAAAATAGT
* ** * * * *
1197736 ATAATATATATATACGTAATATAGAATTTAAAATATACCTAATATATT
1 AAAATATATATATAAATAATATAGAATTAAAAATATACATAAAATAGT
1197784 AAAATATATATATAATATAATAT
1 AAAATATATATATAA-ATAATAT
1197807 TAAGAAATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
48 26 0.44
49 7 0.12
50 25 0.42
51 1 0.02
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.37
Consensus pattern (48 bp):
AAAATATATATATAAATAATATAGAATTAAAAATATACATAAAATAGT
Found at i:1197756 original size:23 final size:22
Alignment explanation
Indices: 1197730--1197802 Score: 60
Period size: 23 Copynumber: 3.3 Consensus size: 22
1197720 ATATACATAA
*
1197730 AATAGTATAATATATATATACGT
1 AATA-TATAATATATATATACCT
* * *
1197753 AATATAGAATTTAAAATATACCT
1 AATATATAATAT-ATATATACCT
*
1197776 AATATATTAAAATATATATA--T
1 AATATA-TAATATATATATACCT
1197797 AATATA
1 AATATA
1197803 ATATTAAGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
21 7 0.17
22 6 0.15
23 24 0.60
24 3 0.08
ACGTcount: A:0.53, C:0.04, G:0.04, T:0.38
Consensus pattern (22 bp):
AATATATAATATATATATACCT
Found at i:1198119 original size:16 final size:16
Alignment explanation
Indices: 1198094--1198124 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1198084 TTTGATTAAT
1198094 CTTCTCCAAAAACTAG
1 CTTCTCCAAAAACTAG
*
1198110 CTTCTTCAAAAACTA
1 CTTCTCCAAAAACTA
1198125 ACCTTCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.29
Consensus pattern (16 bp):
CTTCTCCAAAAACTAG
Found at i:1198348 original size:30 final size:30
Alignment explanation
Indices: 1198327--1198395 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
1198317 TGGAGCAAGT
*
1198327 GTGGTTAGTGGAGTAGGTGGTGGAAAAGGA
1 GTGGCTAGTGGAGTAGGTGGTGGAAAAGGA
* *
1198357 GTGGCTAGTGGAGTTGGTGGTGGAAAAGGT
1 GTGGCTAGTGGAGTAGGTGGTGGAAAAGGA
1198387 GTGGCTAGT
1 GTGGCTAGT
1198396 TGAGAAAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.22, C:0.03, G:0.49, T:0.26
Consensus pattern (30 bp):
GTGGCTAGTGGAGTAGGTGGTGGAAAAGGA
Found at i:1199621 original size:24 final size:24
Alignment explanation
Indices: 1199570--1199621 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
1199560 TTTAGTATTT
* *
1199570 ATTAGTATAATATATTTATCATTT
1 ATTAGCATAATATATTTATCATTA
1199594 ATTAGCATAATATATTTGA-CATTA
1 ATTAGCATAATATATTT-ATCATTA
1199618 ATTA
1 ATTA
1199622 TAATTAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (24 bp):
ATTAGCATAATATATTTATCATTA
Found at i:1201527 original size:28 final size:28
Alignment explanation
Indices: 1201483--1201550 Score: 100
Period size: 28 Copynumber: 2.4 Consensus size: 28
1201473 ATAAAAATTT
* *
1201483 CACTAAGTGTGCGAGTTTGGTTAACGAG
1 CACTAAGTGTGCAAGTTTGATTAACGAG
*
1201511 CACTAAGTGTGCAAGTTTGATTATCGAG
1 CACTAAGTGTGCAAGTTTGATTAACGAG
*
1201539 CACTAGGTGTGC
1 CACTAAGTGTGC
1201551 GAAGGAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (28 bp):
CACTAAGTGTGCAAGTTTGATTAACGAG
Found at i:1203690 original size:18 final size:19
Alignment explanation
Indices: 1203661--1203696 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
1203651 CAGTATCATT
1203661 TTGTGCGTGATATTATTGC
1 TTGTGCGTGATATTATTGC
1203680 TTGTG-GTGATATTATTG
1 TTGTGCGTGATATTATTG
1203697 TAAGCAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.17, C:0.06, G:0.28, T:0.50
Consensus pattern (19 bp):
TTGTGCGTGATATTATTGC
Found at i:1204001 original size:24 final size:24
Alignment explanation
Indices: 1203944--1203995 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
1203934 TTTCTAAAAG
* * *
1203944 ATTTAGTATTTATCAGTATAATAT
1 ATTTAGCATTTATTAGCATAATAT
1203968 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAATAT
1203992 ATTT
1 ATTT
1203996 GACATTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.08, T:0.50
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAATAT
Found at i:1204006 original size:24 final size:24
Alignment explanation
Indices: 1203961--1204007 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1203951 ATTTATCAGT
*
1203961 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATTGATTAGC
1203985 ATAATATATTT-GACATTGATTAG
1 ATAATATATTTAG-CATTGATTAG
1204008 AATTAGGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (24 bp):
ATAATATATTTAGCATTGATTAGC
Found at i:1204737 original size:110 final size:109
Alignment explanation
Indices: 1204553--1204755 Score: 379
Period size: 110 Copynumber: 1.9 Consensus size: 109
1204543 TTTTTAATAA
*
1204553 AAATGTTGAGCACCAAACGCACGATACGTATTAACAAGCTCAATGGTCTAAAGACTTAGACCGTA
1 AAATGTTGAGCACCAAACGCACGATACATATTAACAAGCTCAATGGTCTAAAGACTTAGACCGTA
1204618 AGCAAGACTCCAAAATGAAAAGTAATTGAAACGCATTTTCTAAT
66 AGCAAGACTCCAAAATGAAAAGTAATTGAAACGCATTTTCTAAT
1204662 AAATGTTGAGACACCAAACGCACGATACATATTAACAAGCTCAATGGTCTAAAGACTTAGACCGT
1 AAATGTTGAG-CACCAAACGCACGATACATATTAACAAGCTCAATGGTCTAAAGACTTAGACCGT
*
1204727 AAGCATGACTCCAAAATGAAAAGTAATTG
65 AAGCAAGACTCCAAAATGAAAAGTAATTG
1204756 TGACCATTTC
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
109 10 0.11
110 81 0.89
ACGTcount: A:0.42, C:0.19, G:0.17, T:0.22
Consensus pattern (109 bp):
AAATGTTGAGCACCAAACGCACGATACATATTAACAAGCTCAATGGTCTAAAGACTTAGACCGTA
AGCAAGACTCCAAAATGAAAAGTAATTGAAACGCATTTTCTAAT
Found at i:1206743 original size:20 final size:19
Alignment explanation
Indices: 1206707--1206744 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
1206697 ATGTATAGAT
*
1206707 GCATTTTTTAGTTAATTTA
1 GCATTTTTTAGTAAATTTA
1206726 GCATTTTTTAGTCAAATTT
1 GCATTTTTTAGT-AAATTT
1206745 CACTGAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (19 bp):
GCATTTTTTAGTAAATTTA
Found at i:1219104 original size:7 final size:7
Alignment explanation
Indices: 1219092--1219121 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1219082 TTTCTATACT
1219092 TTTCAAA
1 TTTCAAA
1219099 TTTCAAA
1 TTTCAAA
*
1219106 TTTTAAA
1 TTTCAAA
1219113 TTTCAAA
1 TTTCAAA
1219120 TT
1 TT
1219122 CAGTTGTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (7 bp):
TTTCAAA
Found at i:1225349 original size:21 final size:22
Alignment explanation
Indices: 1225309--1225355 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
1225299 CTCTGCTCAA
*
1225309 ACTCCACCTGCTGCGGAGTAC-
1 ACTCCACCTGCTGCGAAGTACT
*
1225330 ACTCCACCTGCTGTGAAGTACT
1 ACTCCACCTGCTGCGAAGTACT
1225352 ACTC
1 ACTC
1225356 ACTCCTTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.23
Consensus pattern (22 bp):
ACTCCACCTGCTGCGAAGTACT
Found at i:1235887 original size:22 final size:24
Alignment explanation
Indices: 1235847--1235890 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1235837 AATAAAGTTT
*
1235847 AATTTTATTTATATATAATATGGA
1 AATTTTATATATATATAATATGGA
1235871 AATTTTATATA-AT-TAATATG
1 AATTTTATATATATATAATATG
1235891 TTTATTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 2 0.11
24 10 0.53
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (24 bp):
AATTTTATATATATATAATATGGA
Found at i:1236470 original size:20 final size:18
Alignment explanation
Indices: 1236444--1236492 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
1236434 GTTATTATTA
1236444 ATTATTTTTAAATTATAT
1 ATTATTTTTAAATTATAT
1236462 ATTTTATTTTT--ATTATAT
1 A--TTATTTTTAAATTATAT
1236480 ATTATTTTTAAAT
1 ATTATTTTTAAAT
1236493 ACATACACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
16 8 0.30
18 11 0.41
20 8 0.30
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTATTTTTAAATTATAT
Found at i:1236476 original size:18 final size:19
Alignment explanation
Indices: 1236445--1236490 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 19
1236435 TTATTATTAA
1236445 TTATTTTTAAATTATATATT
1 TTATTTTT-AATTATATATT
1236465 TTATTTTT-ATTATATA--
1 TTATTTTTAATTATATATT
1236481 TTATTTTTAA
1 TTATTTTTAA
1236491 ATACATACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 8 0.32
17 1 0.04
18 8 0.32
20 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
TTATTTTTAATTATATATT
Found at i:1242231 original size:16 final size:17
Alignment explanation
Indices: 1242210--1242241 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1242200 GTGAATCTTC
1242210 TATTTTTTTT-ATTTTT
1 TATTTTTTTTCATTTTT
1242226 TATTTTTTTTCATTTT
1 TATTTTTTTTCATTTT
1242242 ATTTTCGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (17 bp):
TATTTTTTTTCATTTTT
Found at i:1242920 original size:22 final size:23
Alignment explanation
Indices: 1242881--1242929 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 23
1242871 AGTATTTTCG
*
1242881 TTATTTTATTTCACTTT-AAATA
1 TTATTTGATTTCACTTTAAAATA
1242903 TTATTTGATTATCA-TTTACAAATA
1 TTATTTGATT-TCACTTTA-AAATA
1242927 TTA
1 TTA
1242930 GTGTATATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 12 0.52
23 3 0.13
24 8 0.35
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (23 bp):
TTATTTGATTTCACTTTAAAATA
Found at i:1243086 original size:3 final size:3
Alignment explanation
Indices: 1243073--1243141 Score: 59
Period size: 3 Copynumber: 22.7 Consensus size: 3
1243063 TTTTCTTTTG
* ** * *
1243073 TAT TTT TAT TAT TAT TGC TAT TAT TGT TGT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
1243121 TA- TATT TAT ATAA TAT TAT TA
1 TAT TA-T TAT -TAT TAT TAT TA
1243142 ATAGGTACTT
Statistics
Matches: 53, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
2 2 0.04
3 47 0.89
4 4 0.08
ACGTcount: A:0.30, C:0.01, G:0.04, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:1243088 original size:12 final size:12
Alignment explanation
Indices: 1243073--1243123 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
1243063 TTTTCTTTTG
*
1243073 TATTTTTATTAT
1 TATTGTTATTAT
*
1243085 TATTGCTATTAT
1 TATTGTTATTAT
*
1243097 TGTTGTTATTAT
1 TATTGTTATTAT
*
1243109 TATTATTATTAT
1 TATTGTTATTAT
1243121 TAT
1 TAT
1243124 ATTTATATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 33 1.00
ACGTcount: A:0.25, C:0.02, G:0.06, T:0.67
Consensus pattern (12 bp):
TATTGTTATTAT
Found at i:1243407 original size:24 final size:22
Alignment explanation
Indices: 1243380--1243437 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
1243370 TAGTGTGTTT
1243380 TATTATATGTATATATACTCTCAA
1 TATTATAT-TAT-TATACTCTCAA
* *
1243404 TATTATATTCTTATACTCTTAA
1 TATTATATTATTATACTCTCAA
**
1243426 TACCATATTATT
1 TATTATATTATT
1243438 CTTATTATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
22 19 0.66
23 2 0.07
24 8 0.28
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (22 bp):
TATTATATTATTATACTCTCAA
Found at i:1243921 original size:34 final size:35
Alignment explanation
Indices: 1243827--1243923 Score: 101
Period size: 34 Copynumber: 2.7 Consensus size: 35
1243817 ATATTTATTT
* *
1243827 TATATATATGTAAATATTATGTATATATTTTTAAATAC
1 TATAT-TATGTATATATTA--TATATATTCTTAAATAC
* *
1243865 TATA-T-TGTATATGTATATATATATTCTT-AGTAC
1 TATATTATGTATATAT-TATATATATTCTTAAATAC
1243898 TATATTATGTATATATTATATATATT
1 TATATTATGTATATATTATATATATT
1243924 TATTTTTACC
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
33 8 0.16
34 21 0.41
35 15 0.29
36 3 0.06
38 4 0.08
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (35 bp):
TATATTATGTATATATTATATATATTCTTAAATAC
Found at i:1247301 original size:5 final size:5
Alignment explanation
Indices: 1247293--1247320 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
1247283 ATTTTATTTA
1247293 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTT
1247321 GAATTTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTCT
Found at i:1249367 original size:31 final size:33
Alignment explanation
Indices: 1249332--1249402 Score: 85
Period size: 31 Copynumber: 2.2 Consensus size: 33
1249322 GCTGTTTTTG
1249332 AAATTAATAACTAGAATTTAT-CATCA-TAAAT
1 AAATTAATAACTAGAATTTATACATCATTAAAT
* * * *
1249363 AAATTAATCATTTGAATTTATATATCATTAAAT
1 AAATTAATAACTAGAATTTATACATCATTAAAT
1249396 -AATTAAT
1 AAATTAAT
1249403 TAAATTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 18 0.53
32 11 0.32
33 5 0.15
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (33 bp):
AAATTAATAACTAGAATTTATACATCATTAAAT
Found at i:1256334 original size:5 final size:5
Alignment explanation
Indices: 1256324--1256349 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
1256314 ACTGTCGAAC
1256324 TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT T
1256350 GCGTCGTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:1259001 original size:3 final size:3
Alignment explanation
Indices: 1258995--1259019 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1258985 CTCGTCGTCC
1258995 TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT T
1259020 TTAATGGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:1262559 original size:33 final size:32
Alignment explanation
Indices: 1262484--1262565 Score: 96
Period size: 32 Copynumber: 2.5 Consensus size: 32
1262474 TAAAATTTAC
* *
1262484 CGATCATTTT-GATTCTGTGTCAATTTCTAGTT
1 CGATCATTTTGGGTT-TGGGTCAATTTCTAGTT
1262516 CGATCATTTTGGGTTTGGGTCAATTT-TAGGTT
1 CGATCATTTTGGGTTTGGGTCAATTTCTA-GTT
*
1262548 CTAGTCATTTTGGGTTTG
1 CGA-TCATTTTGGGTTTG
1262566 AGTTTGAGGC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
31 2 0.05
32 25 0.57
33 17 0.39
ACGTcount: A:0.16, C:0.12, G:0.23, T:0.49
Consensus pattern (32 bp):
CGATCATTTTGGGTTTGGGTCAATTTCTAGTT
Found at i:1262563 original size:16 final size:16
Alignment explanation
Indices: 1262519--1262568 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
1262509 TCTAGTTCGA
*
1262519 TCATTTTGGGTTTGGG
1 TCATTTTGGGTTTGAG
*
1262535 TCAATTTTAGGTTCT-AG
1 TC-ATTTTGGGTT-TGAG
1262552 TCATTTTGGGTTTGAG
1 TCATTTTGGGTTTGAG
1262568 T
1 T
1262569 TTGAGGCTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 1 0.04
16 14 0.50
17 12 0.43
18 1 0.04
ACGTcount: A:0.14, C:0.08, G:0.28, T:0.50
Consensus pattern (16 bp):
TCATTTTGGGTTTGAG
Found at i:1264254 original size:22 final size:23
Alignment explanation
Indices: 1264215--1264257 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
1264205 GTAACCTAAT
1264215 TTAAAATTAATAAAAATTAAACC
1 TTAAAATTAATAAAAATTAAACC
*
1264238 TTAAAGTTAA-AAAAATTAAA
1 TTAAAATTAATAAAAATTAAA
1264258 AGAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (23 bp):
TTAAAATTAATAAAAATTAAACC
Found at i:1264605 original size:32 final size:34
Alignment explanation
Indices: 1264541--1264606 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
1264531 CTTCACCTCA
1264541 TAATCTCAATGAAAAGTGGAAACAACTATGTTAT
1 TAATCTCAATGAAAAGTGGAAACAACTATGTTAT
1264575 TAATCTCAATGAAAAGTGG-AA-AACTATGTTAT
1 TAATCTCAATGAAAAGTGGAAACAACTATGTTAT
1264607 CAATTTAGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 11 0.34
33 2 0.06
34 19 0.59
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (34 bp):
TAATCTCAATGAAAAGTGGAAACAACTATGTTAT
Found at i:1271421 original size:21 final size:21
Alignment explanation
Indices: 1271397--1271440 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1271387 CATCTATAGT
*
1271397 AATATAT-AATATTATAATGTA
1 AATATATAAATATTA-AATATA
*
1271418 AATATTTAAATATTAAATATA
1 AATATATAAATATTAAATATA
1271439 AA
1 AA
1271441 ATTAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATATATAAATATTAAATATA
Found at i:1274584 original size:29 final size:29
Alignment explanation
Indices: 1274547--1274603 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
1274537 CCTCTTGTAT
* *
1274547 TTTCTAGATCTCCATCTTTTATGGTGAAC
1 TTTCCAGATCTCCATCTCTTATGGTGAAC
1274576 TTTCCAGATCTCCATCTCTTATGGTGAA
1 TTTCCAGATCTCCATCTCTTATGGTGAA
1274604 TTGGCGTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.21, C:0.23, G:0.14, T:0.42
Consensus pattern (29 bp):
TTTCCAGATCTCCATCTCTTATGGTGAAC
Found at i:1285734 original size:13 final size:13
Alignment explanation
Indices: 1285718--1285746 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1285708 TTCACAACTT
1285718 AAACGTAAGATAC
1 AAACGTAAGATAC
1285731 AAACGTAAGATAC
1 AAACGTAAGATAC
1285744 AAA
1 AAA
1285747 AACTAATAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (13 bp):
AAACGTAAGATAC
Found at i:1292037 original size:17 final size:17
Alignment explanation
Indices: 1292015--1292049 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1292005 ATACAGCTAC
1292015 ATATATATATATAAAAT
1 ATATATATATATAAAAT
*
1292032 ATATATATATATAGAAT
1 ATATATATATATAAAAT
1292049 A
1 A
1292050 GACTGCTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (17 bp):
ATATATATATATAAAAT
Found at i:1294997 original size:20 final size:20
Alignment explanation
Indices: 1294968--1295011 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
1294958 GAAGAGCTTT
1294968 ACCT-TTGCTTAGATTTCTA
1 ACCTATTGCTTAGATTTCTA
1294987 ACCTATTGCTTAGATTTCTA
1 ACCTATTGCTTAGATTTCTA
1295007 ACCTA
1 ACCTA
1295012 ACTCTCTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (20 bp):
ACCTATTGCTTAGATTTCTA
Found at i:1296689 original size:3 final size:3
Alignment explanation
Indices: 1296678--1296757 Score: 53
Period size: 3 Copynumber: 26.3 Consensus size: 3
1296668 TTTATTTTTT
* *
1296678 TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA TTA TTA TT- TCTCA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA T-T-A
1296723 TGTA TATA TTA TTA TT- TATA TTA TTA TTA -TA TTA T
1 T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA TTA TTA T
1296758 ATATACCCTC
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
2 7 0.11
3 46 0.74
4 7 0.11
5 2 0.03
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:1296694 original size:9 final size:9
Alignment explanation
Indices: 1296669--1296757 Score: 56
Period size: 9 Copynumber: 9.4 Consensus size: 9
1296659 GAGCTTTGTT
*
1296669 TTATTTTTT
1 TTATTTTTA
1296678 TTA-TTTTA
1 TTATTTTTA
1296686 TTATTTTTA
1 TTATTTTTA
*
1296695 CTATTATTTA
1 TTATT-TTTA
*
1296705 -TATTATTA
1 TTATTTTTA
*
1296713 TTATTTCTCA
1 TTATTT-TTA
*
1296723 TGTATATATTA
1 T-TAT-TTTTA
*
1296734 TTATTTATA
1 TTATTTTTA
1296743 TTATTATTATA
1 TTATT-TT-TA
1296754 TTAT
1 TTAT
1296758 ATATACCCTC
Statistics
Matches: 62, Mismatches: 10, Indels: 14
0.72 0.12 0.16
Matches are distributed among these distances:
8 10 0.16
9 28 0.45
10 11 0.18
11 12 0.19
12 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.67
Consensus pattern (9 bp):
TTATTTTTA
Found at i:1296699 original size:17 final size:14
Alignment explanation
Indices: 1296667--1296718 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
1296657 GAGAGCTTTG
1296667 TTTTATTTTTTTTA
1 TTTTATTTTTTTTA
*
1296681 TTTTATTATTTTTA
1 TTTTATTTTTTTTA
* * *
1296695 CTATTATTTATATTA
1 -TTTTATTTTTTTTA
1296710 TTATTATTT
1 TT-TTATTT
1296719 CTCATGTATA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
14 14 0.47
15 16 0.53
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTTTTTTA
Found at i:1296717 original size:18 final size:18
Alignment explanation
Indices: 1296682--1296761 Score: 67
Period size: 18 Copynumber: 4.4 Consensus size: 18
1296672 TTTTTTTTAT
* *
1296682 TTTATTATTTTTACTATTA
1 TTTA-TATTATTATTATTA
1296701 TTTATATTATTATTATT-
1 TTTATATTATTATTATTA
* *
1296718 TCTCAT-GTATATATTATTA
1 T-TTATATTAT-TATTATTA
1296737 TTTATATTATTATTA-TA
1 TTTATATTATTATTATTA
1296754 TTATATAT
1 TT-TATAT
1296762 ACCCTCTCCA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
17 8 0.16
18 34 0.68
19 8 0.16
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (18 bp):
TTTATATTATTATTATTA
Found at i:1296744 original size:12 final size:12
Alignment explanation
Indices: 1296677--1296757 Score: 78
Period size: 12 Copynumber: 6.8 Consensus size: 12
1296667 TTTTATTTTT
*
1296677 TTTATTTTATTA
1 TTTATATTATTA
* *
1296689 TTTTTACTATTA
1 TTTATATTATTA
1296701 TTTATATTATTA
1 TTTATATTATTA
* *
1296713 -TTAT-TTCTCA
1 TTTATATTATTA
1296723 TGTATATATTATTA
1 T-T-TATATTATTA
1296737 TTTATATTATTA
1 TTTATATTATTA
1296749 -TTATATTAT
1 TTTATATTAT
1296758 ATATACCCTC
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
10 4 0.07
11 13 0.23
12 30 0.54
13 4 0.07
14 5 0.09
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (12 bp):
TTTATATTATTA
Found at i:1296838 original size:3 final size:3
Alignment explanation
Indices: 1296832--1296882 Score: 50
Period size: 3 Copynumber: 16.0 Consensus size: 3
1296822 TTCTGACTAC
*
1296832 TAT TAT TAT ATAT ATAT GTAT TAT TGT T-T GTAT TAT TAT TAT TAT TAT
1 TAT TAT TAT -TAT -TAT -TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
1296880 TAT
1 TAT
1296883 CACCCCTATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 1 0.02
3 31 0.72
4 11 0.26
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1314753 original size:2 final size:2
Alignment explanation
Indices: 1314746--1314777 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1314736 TGAACTCGTA
1314746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1314778 CTCAATTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1318713 original size:21 final size:20
Alignment explanation
Indices: 1318655--1318715 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 20
1318645 CGTATTTTCT
*
1318655 TTTGAGATTTAAAATTTA-G
1 TTTGAAATTTAAAATTTAGG
* **
1318674 TTTATAAGATTTATTATTTAGG
1 TTT-GAA-ATTTAAAATTTAGG
1318696 ATTTGAAATTTAAAATTTAG
1 -TTTGAAATTTAAAATTTAG
1318716 AGCTTAGAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
19 3 0.10
20 1 0.03
21 21 0.68
22 3 0.10
23 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (20 bp):
TTTGAAATTTAAAATTTAGG
Found at i:1320459 original size:892 final size:892
Alignment explanation
Indices: 1318736--1320481 Score: 3483
Period size: 892 Copynumber: 2.0 Consensus size: 892
1318726 TTTAAATTCC
1318736 AACATTTAGGATATAAGATAAATTTATTTTTGTACTTAAATATTTAAATTATAAATATAATAATA
1 AACATTTAGGATATAAGATAAATTTATTTTTGTACTTAAATATTTAAATTATAAATATAATAATA
1318801 ATTTTTTGCCGCTGTTAAAGTAATTACGTGGGTTTGATGAAATTGATAACACTATTAACAATTAT
66 ATTTTTTGCCGCTGTTAAAGTAATTACGTGGGTTTGATGAAATTGATAACACTATTAACAATTAT
1318866 CAATTAACAATTAATATTGTTAGAGGATTTAATAGTAGCAATTAACAATATTATCAATTTGGATA
131 CAATTAACAATTAATATTGTTAGAGGATTTAATAGTAGCAATTAACAATATTATCAATTTGGATA
1318931 GGGTGAAGACAGGATCAAAATTGAATTATAAATTATTGAGGGGTATGCAAAAGAAAATTTTATCA
196 GGGTGAAGACAGGATCAAAATTGAATTATAAATTATTGAGGGGTATGCAAAAGAAAATTTTATCA
1318996 TTATACTAATTTATATTTTTATAAGTTTTCAAGGGACCTTAAAAGCAATTTTACCATTTGGAGGG
261 TTATACTAATTTATATTTTTATAAGTTTTCAAGGGACCTTAAAAGCAATTTTACCATTTGGAGGG
1319061 GTCACCTACCCCTTGCATTCACCCCTCAATTTGGACCTACTAATTACGTTATAAAAATGTACATA
326 GTCACCTACCCCTTGCATTCACCCCTCAATTTGGACCTACTAATTACGTTATAAAAATGTACATA
1319126 TTAATTTCAAAAATGAAAAAAAAAGGAAAAGTAGAGAAATTAAATGTAAAATATCAACATAACAA
391 TTAATTTCAAAAATGAAAAAAAAAGGAAAAGTAGAGAAATTAAATGTAAAATATCAACATAACAA
1319191 AGGAACTAAAAGTAAAATTAGACCAAATAAAAAACAACCCAAAGTAGTCTTGTCTTTATACTTAT
456 AGGAACTAAAAGTAAAATTAGACCAAATAAAAAACAACCCAAAGTAGTCTTGTCTTTATACTTAT
1319256 AATGGTGAAGTGTTGTTTTTAAGTGCTTTGTGGTCAACAACAACTTCATCTGTCCTCGTCTAAAG
521 AATGGTGAAGTGTTGTTTTTAAGTGCTTTGTGGTCAACAACAACTTCATCTGTCCTCGTCTAAAG
1319321 GACAGGTTCTGCCATATTTTGAACACCCAATGTCGATAATGACGAATAATGTCTTTGAAATTGTA
586 GACAGGTTCTGCCATATTTTGAACACCCAATGTCGATAATGACGAATAATGTCTTTGAAATTGTA
1319386 TATCATCATCCCCCAACCGATCTGTGTACATTGTCATGTTTTTGAAATTATAATCGTATATGACG
651 TATCATCATCCCCCAACCGATCTGTGTACATTGTCATGTTTTTGAAATTATAATCGTATATGACG
1319451 TGAAATATATATATACTCGAATCATGGAATTTTACAAAGGCTTTTCTTGGTTGTTCTAAGTACAA
716 TGAAATATATATATACTCGAATCATGGAATTTTACAAAGGCTTTTCTTGGTTGTTCTAAGTACAA
1319516 CCTAATTCAACTTATCCAAAATGTCTTTTTATTGTCTCCAACAAGATAATCGAATCGTATGTAAT
781 CCTAATTCAACTTATCCAAAATGTCTTTTTATTGTCTCCAACAAGATAATCGAATCGTATGTAAT
1319581 CTTTGTAATAGTGTTATAATCGTATATGACGTGAAATGACCTAAAAA
846 CTTTGTAATAGTGTTATAATCGTATATGACGTGAAATGACCTAAAAA
1319628 AACATTTAGGATATAAGATAAATTTATTTTTGTACTTAAATATTTAAATTATAAATATAATAATA
1 AACATTTAGGATATAAGATAAATTTATTTTTGTACTTAAATATTTAAATTATAAATATAATAATA
1319693 ATTTTTTGCCGCTGTTAAAGTAATTACGTGGGTTTGATGAAATTGATAACACTATTAACAATTAT
66 ATTTTTTGCCGCTGTTAAAGTAATTACGTGGGTTTGATGAAATTGATAACACTATTAACAATTAT
1319758 CAATTAACAATTAATATTGTTAGAGGATTTAATAGTAGCAATTAACAATATTATCAATTTGGATA
131 CAATTAACAATTAATATTGTTAGAGGATTTAATAGTAGCAATTAACAATATTATCAATTTGGATA
1319823 GGGTGAAGACAGGATCAAAATTGAATTATAAATTATTGAGGGGTATGCAAAAGAAAATTTTATCA
196 GGGTGAAGACAGGATCAAAATTGAATTATAAATTATTGAGGGGTATGCAAAAGAAAATTTTATCA
1319888 TTATACTAATTTATATTTTTATAAGTTTTCAAGGGACCTTAAAAGCAATTTTACCATTTGGAGGG
261 TTATACTAATTTATATTTTTATAAGTTTTCAAGGGACCTTAAAAGCAATTTTACCATTTGGAGGG
1319953 GTCACCTACCCCTTGCATTCACCCCTCAATTTGGACCTACTAATTACGTTATAAAAATGTACATA
326 GTCACCTACCCCTTGCATTCACCCCTCAATTTGGACCTACTAATTACGTTATAAAAATGTACATA
1320018 TTAATTTCAAAAATGAAAAAAAAAGGAAAAGTAGAGAAATTAAATGTAAAATATCAACATAACAA
391 TTAATTTCAAAAATGAAAAAAAAAGGAAAAGTAGAGAAATTAAATGTAAAATATCAACATAACAA
1320083 AGGAACTAAAAGTAAAATTAGACCAAATAAAAAACAACCCAAAGTAGTCTTGTCTTTATACTTAT
456 AGGAACTAAAAGTAAAATTAGACCAAATAAAAAACAACCCAAAGTAGTCTTGTCTTTATACTTAT
1320148 AATGGTGAAGTGTTGTTTTTAAGTGCTTTGTGGTCAACAACAACTTCATCTGTCCTCGTCTAAAG
521 AATGGTGAAGTGTTGTTTTTAAGTGCTTTGTGGTCAACAACAACTTCATCTGTCCTCGTCTAAAG
1320213 GACAGGTTCTGCCATATTTTGAACACCCAATGTCGATAATGACGAATAATGTCTTTGAAATTGTA
586 GACAGGTTCTGCCATATTTTGAACACCCAATGTCGATAATGACGAATAATGTCTTTGAAATTGTA
1320278 TATCATCATCCCCCAACCGATCTGTGTACATTGTCATGTTTTTGAAATTATAATCGTATATGACG
651 TATCATCATCCCCCAACCGATCTGTGTACATTGTCATGTTTTTGAAATTATAATCGTATATGACG
1320343 TGAAATATATATATACTCGAATCATGGAATTTTACAAAGGCTTTTCTTGGTTGTTCTAAGTACAA
716 TGAAATATATATATACTCGAATCATGGAATTTTACAAAGGCTTTTCTTGGTTGTTCTAAGTACAA
*
1320408 CCTAATTCAACTTATCCAAAATGTCTTTTTATTGTCTCCAACAAGATAATCGAATCGTATGTATT
781 CCTAATTCAACTTATCCAAAATGTCTTTTTATTGTCTCCAACAAGATAATCGAATCGTATGTAAT
1320473 CTTTGTAAT
846 CTTTGTAAT
1320482 TGCTTGGTTA
Statistics
Matches: 853, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
892 853 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (892 bp):
AACATTTAGGATATAAGATAAATTTATTTTTGTACTTAAATATTTAAATTATAAATATAATAATA
ATTTTTTGCCGCTGTTAAAGTAATTACGTGGGTTTGATGAAATTGATAACACTATTAACAATTAT
CAATTAACAATTAATATTGTTAGAGGATTTAATAGTAGCAATTAACAATATTATCAATTTGGATA
GGGTGAAGACAGGATCAAAATTGAATTATAAATTATTGAGGGGTATGCAAAAGAAAATTTTATCA
TTATACTAATTTATATTTTTATAAGTTTTCAAGGGACCTTAAAAGCAATTTTACCATTTGGAGGG
GTCACCTACCCCTTGCATTCACCCCTCAATTTGGACCTACTAATTACGTTATAAAAATGTACATA
TTAATTTCAAAAATGAAAAAAAAAGGAAAAGTAGAGAAATTAAATGTAAAATATCAACATAACAA
AGGAACTAAAAGTAAAATTAGACCAAATAAAAAACAACCCAAAGTAGTCTTGTCTTTATACTTAT
AATGGTGAAGTGTTGTTTTTAAGTGCTTTGTGGTCAACAACAACTTCATCTGTCCTCGTCTAAAG
GACAGGTTCTGCCATATTTTGAACACCCAATGTCGATAATGACGAATAATGTCTTTGAAATTGTA
TATCATCATCCCCCAACCGATCTGTGTACATTGTCATGTTTTTGAAATTATAATCGTATATGACG
TGAAATATATATATACTCGAATCATGGAATTTTACAAAGGCTTTTCTTGGTTGTTCTAAGTACAA
CCTAATTCAACTTATCCAAAATGTCTTTTTATTGTCTCCAACAAGATAATCGAATCGTATGTAAT
CTTTGTAATAGTGTTATAATCGTATATGACGTGAAATGACCTAAAAA
Found at i:1323377 original size:20 final size:22
Alignment explanation
Indices: 1323323--1323365 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1323313 CATCCACCAA
1323323 ACACTAC-AATTAGAGAGTTTG
1 ACACTACAAATTAGAGAGTTTG
1323344 ACACTACAAATTAGAGAGTTTG
1 ACACTACAAATTAGAGAGTTTG
1323366 TATCCAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.28
Consensus pattern (22 bp):
ACACTACAAATTAGAGAGTTTG
Found at i:1324880 original size:13 final size:13
Alignment explanation
Indices: 1324862--1324888 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1324852 ATTAGCCCTT
1324862 ATACATTAAATTA
1 ATACATTAAATTA
1324875 ATACATTAAATTA
1 ATACATTAAATTA
1324888 A
1 A
1324889 AGAACATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATACATTAAATTA
Found at i:1335761 original size:19 final size:19
Alignment explanation
Indices: 1335731--1335775 Score: 65
Period size: 19 Copynumber: 2.3 Consensus size: 19
1335721 AGTATTGTGA
1335731 AATTTATAATTTAATCTATTT
1 AATTT-TAATTTAATCT-TTT
1335752 -ATTTTAATTTAATCTTTT
1 AATTTTAATTTAATCTTTT
1335770 AATTTT
1 AATTTT
1335776 TTAAAATATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 3 0.13
19 16 0.70
20 4 0.17
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (19 bp):
AATTTTAATTTAATCTTTT
Found at i:1336045 original size:31 final size:30
Alignment explanation
Indices: 1336010--1336079 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
1336000 CTAAAAGTAC
1336010 TGAAAATTTTAATTAAAT-CTTTCAAAATTTT
1 TGAAAATTTTAATT-AATCCTTT-AAAATTTT
* * *
1336041 TGAAAATTTTTATTATTCCTTTTAAATTTT
1 TGAAAATTTTAATTAATCCTTTAAAATTTT
1336071 T-AAAATTTT
1 TGAAAATTTT
1336080 TTGAAAATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 8 0.23
30 10 0.29
31 17 0.49
ACGTcount: A:0.37, C:0.06, G:0.03, T:0.54
Consensus pattern (30 bp):
TGAAAATTTTAATTAATCCTTTAAAATTTT
Found at i:1341706 original size:23 final size:24
Alignment explanation
Indices: 1341666--1341711 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1341656 AAGCCTTATA
1341666 TTTTTTATATATTTAG-AATTTAG
1 TTTTTTATATATTTAGAAATTTAG
*
1341689 TTTTTTTTAT-TTTAAGAAATTTA
1 TTTTTTATATATTT-AGAAATTTA
1341712 AATTGTCTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 11 0.55
24 6 0.30
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (24 bp):
TTTTTTATATATTTAGAAATTTAG
Found at i:1346609 original size:33 final size:32
Alignment explanation
Indices: 1346544--1346609 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
1346534 ATATTCAAAA
* *
1346544 CATGTTAGGAATAGCTCTTGTTAAGAACAACT
1 CATGTTAGGAATAGATCTTATTAAGAACAACT
* * *
1346576 CATGTTTGGAGTAGATCTTATTCAAGAATAACT
1 CATGTTAGGAATAGATCTTATT-AAGAACAACT
1346609 C
1 C
1346610 TTATTCAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 18 0.64
33 10 0.36
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.33
Consensus pattern (32 bp):
CATGTTAGGAATAGATCTTATTAAGAACAACT
Found at i:1351357 original size:27 final size:27
Alignment explanation
Indices: 1351309--1351466 Score: 191
Period size: 27 Copynumber: 5.9 Consensus size: 27
1351299 GCGAGGTTGC
* *
1351309 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
1351336 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
1351362 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
1351389 CAGATAATCGTGGCATAGCCACCAGA-A
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
1351416 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
1351443 CAGATAATTGTGGCATAGCCACCA
1 CAGAT-ATTGTGGCAGAGCCACCA
1351467 AGACGCTTCC
Statistics
Matches: 116, Mismatches: 7, Indels: 16
0.83 0.05 0.12
Matches are distributed among these distances:
26 10 0.09
27 101 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:1351402 original size:54 final size:54
Alignment explanation
Indices: 1351327--1351466 Score: 246
Period size: 54 Copynumber: 2.6 Consensus size: 54
1351317 GTGACGAAGT
*
1351327 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
*
1351381 CACCAGATCAGATAATCGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
1351435 CACCAGATCAGATAATTGTGGCATAGCCACCA
1 CACCAGATCAGATAATTGTGGCATAGCCACCA
1351467 AGACGCTTCC
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
53 5 0.06
54 77 0.94
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGAACAGATATATGTGGCAGAGC
Found at i:1351598 original size:26 final size:26
Alignment explanation
Indices: 1351569--1351645 Score: 73
Period size: 26 Copynumber: 2.9 Consensus size: 26
1351559 GTCAAAATTA
* **
1351569 ACCTTGGGGTATAATGGTAATTTTAC
1 ACCTAGGGGTATAACAGTAATTTTAC
*
1351595 ACCTAGGGGTATAACAGTAATTTTCCAT
1 ACCTAGGGGTATAACAGTAATTTT--AC
* * *
1351623 ACATAGGGGTATTATAGTAATTT
1 ACCTAGGGGTATAACAGTAATTT
1351646 AGCTGCTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 21 0.50
28 21 0.50
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (26 bp):
ACCTAGGGGTATAACAGTAATTTTAC
Found at i:1353118 original size:26 final size:26
Alignment explanation
Indices: 1353083--1353190 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
1353073 TGAAATGCCC
*
1353083 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
1353109 ATCATAGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* * *
1353135 ATAATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
1353161 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
1353187 ATCA
1 ATCA
1353191 ATTTGTACCA
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 73 1.00
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:1354009 original size:49 final size:50
Alignment explanation
Indices: 1353912--1354010 Score: 121
Period size: 49 Copynumber: 2.0 Consensus size: 50
1353902 ATCTCAAACA
* *
1353912 AATTTACACATAATAAAAAATCACAAGTCTAACAAAATAACTACTATGCAT
1 AATTTACACA-AATAAAAAATCACAACTATAACAAAATAACTACTATGCAT
* * *
1353963 AATTTACAC-AATAAAAAATTACAACTATAATAAAGTAAC-ACTTATGCA
1 AATTTACACAAATAAAAAATCACAACTATAACAAAATAACTAC-TATGCA
1354011 CACAAAACTC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
48 2 0.05
49 31 0.74
51 9 0.21
ACGTcount: A:0.54, C:0.16, G:0.04, T:0.26
Consensus pattern (50 bp):
AATTTACACAAATAAAAAATCACAACTATAACAAAATAACTACTATGCAT
Found at i:1355522 original size:15 final size:14
Alignment explanation
Indices: 1355497--1355530 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
1355487 ATCCAAAGTT
*
1355497 AGTGATGATGCATG
1 AGTGATGATGCACG
1355511 AGTGATTGATGCACG
1 AGTGA-TGATGCACG
1355526 AGTGA
1 AGTGA
1355531 AACATGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.29, C:0.09, G:0.35, T:0.26
Consensus pattern (14 bp):
AGTGATGATGCACG
Found at i:1357142 original size:27 final size:27
Alignment explanation
Indices: 1357112--1357169 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1357102 TCAGATTATT
1357112 TCAACCACGAATCATTTCAAATTCAAG
1 TCAACCACGAATCATTTCAAATTCAAG
*****
1357139 TCAATTTTTAATCATTTCAAATTCAAG
1 TCAACCACGAATCATTTCAAATTCAAG
1357166 TCAA
1 TCAA
1357170 TTCTTACTTA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (27 bp):
TCAACCACGAATCATTTCAAATTCAAG
Found at i:1359264 original size:110 final size:110
Alignment explanation
Indices: 1359071--1359310 Score: 324
Period size: 110 Copynumber: 2.2 Consensus size: 110
1359061 CATTTTTTAA
1359071 ATTAGTTGCCTTGGACATATGCCGCTATGCAATAGCTAATTTATATCCGTTTGTTGATTTTTCCA
1 ATTAGTTGCCTTGGACATATGCCGCTATGCAATAGCTAATTTATATCCGTTTGTTGATTTTTCCA
** **
1359136 TTGGGAATCATCGTTTCATTCTTGAAACCCCCA-TTCTGTATACTG
66 TAAGGAATCATCGTTTCATTCTTGAAA-CCCCATTTCCATATACTG
* * * * * * *
1359181 ATTAGATGCCTTGGGCTTATGCTG-TCATGCAATTGCTTATTTAT-TTCGATTTGTTGATTTTTC
1 ATTAGTTGCCTTGGACATATGCCGCT-ATGCAATAGCTAATTTATATCCG-TTTGTTGATTTTTC
*
1359244 CGTAAGGAATCATCGTTTCATTCTTGAAACCCCATTTCCATATACTG
64 CATAAGGAATCATCGTTTCATTCTTGAAACCCCATTTCCATATACTG
1359291 ATTAGTTGCCTTGGACATAT
1 ATTAGTTGCCTTGGACATAT
1359311 ATCAAAGCTA
Statistics
Matches: 112, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
109 9 0.08
110 103 0.92
ACGTcount: A:0.23, C:0.20, G:0.17, T:0.41
Consensus pattern (110 bp):
ATTAGTTGCCTTGGACATATGCCGCTATGCAATAGCTAATTTATATCCGTTTGTTGATTTTTCCA
TAAGGAATCATCGTTTCATTCTTGAAACCCCATTTCCATATACTG
Found at i:1372171 original size:13 final size:13
Alignment explanation
Indices: 1372153--1372177 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1372143 CACACAGACA
1372153 AAAAAGAAAAAGG
1 AAAAAGAAAAAGG
1372166 AAAAAGAAAAAG
1 AAAAAGAAAAAG
1372178 CTGAGTTAGA
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:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGG
Found at i:1373998 original size:10 final size:10
Alignment explanation
Indices: 1373983--1374009 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
1373973 ATTTTTTAAT
1373983 TAAATAAATA
1 TAAATAAATA
1373993 TAAATAAATA
1 TAAATAAATA
1374003 TAAATAA
1 TAAATAA
1374010 TATTTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (10 bp):
TAAATAAATA
Found at i:1374074 original size:42 final size:39
Alignment explanation
Indices: 1373972--1374079 Score: 98
Period size: 42 Copynumber: 2.7 Consensus size: 39
1373962 ATAAAAAACC
*
1373972 AATTTTTT-AATTAA-ATAAATATAAATAAATATAAATA
1 AATTTTTTAAATTAATAAAAATATAAATAAATATAAATA
* * *
1374009 ATATTTTATTTAAAAT-ATGAAAATAATTAATAAATATAAAATA
1 A-A-TTT-TTTAAATTAATAAAAAT-ATAAATAAATAT-AAATA
1374052 AATTTTTTACAATTAATAAAAAT-TAAAT
1 AATTTTTTA-AATTAATAAAAATATAAAT
1374080 GTGTGAGATT
Statistics
Matches: 55, Mismatches: 7, Indels: 15
0.71 0.09 0.19
Matches are distributed among these distances:
37 1 0.02
38 1 0.02
39 3 0.05
40 12 0.22
41 13 0.24
42 19 0.35
43 6 0.11
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (39 bp):
AATTTTTTAAATTAATAAAAATATAAATAAATATAAATA
Found at i:1395715 original size:32 final size:33
Alignment explanation
Indices: 1395651--1395717 Score: 109
Period size: 34 Copynumber: 2.0 Consensus size: 33
1395641 AGCTTAAAAT
*
1395651 TTTGTTGTAGAGTAATCTATGTTTTTTTTTTATA
1 TTTGTTGTAGAGTAATATATG-TTTTTTTTTATA
1395685 TTTGTTGTAGAGTAATATATG-TTTTTTTTATA
1 TTTGTTGTAGAGTAATATATGTTTTTTTTTATA
1395717 T
1 T
1395718 GACTTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 12 0.38
34 20 0.62
ACGTcount: A:0.22, C:0.01, G:0.15, T:0.61
Consensus pattern (33 bp):
TTTGTTGTAGAGTAATATATGTTTTTTTTTATA
Found at i:1401089 original size:13 final size:13
Alignment explanation
Indices: 1401068--1401095 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1401058 TAATTAAGTA
1401068 AACTAATTTAATT
1 AACTAATTTAATT
1401081 AACTAATTTAATT
1 AACTAATTTAATT
1401094 AA
1 AA
1401096 GTTTAGTTAA
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:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
AACTAATTTAATT
Found at i:1404167 original size:18 final size:18
Alignment explanation
Indices: 1404144--1404178 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1404134 AATAAAGAGG
*
1404144 AAAAATCTGATTTGTCAA
1 AAAAATCTAATTTGTCAA
1404162 AAAAATCTAATTTGTCA
1 AAAAATCTAATTTGTCA
1404179 TTCTCCTATT
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:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (18 bp):
AAAAATCTAATTTGTCAA
Found at i:1404706 original size:56 final size:56
Alignment explanation
Indices: 1404606--1404718 Score: 183
Period size: 58 Copynumber: 2.0 Consensus size: 56
1404596 TGAATTTTTG
*
1404606 TTCGCATATTCATGCCATTCAAAGTTGTTAATTTCATTTAAAAAAATAAACTACAA
1 TTCGCAAATTCATGCCATTCAAAGTTGTTAATTTCATTTAAAAAAATAAACTACAA
*
1404662 TTCGCAAATTCATGCCATATTCAAAGTTGTTAATTTCA-TTAAAAAAATGAACTACAA
1 TTCGCAAATTCATGCC--ATTCAAAGTTGTTAATTTCATTTAAAAAAATAAACTACAA
1404719 AAGGTGAGAA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
56 15 0.28
57 18 0.34
58 20 0.38
ACGTcount: A:0.42, C:0.16, G:0.08, T:0.35
Consensus pattern (56 bp):
TTCGCAAATTCATGCCATTCAAAGTTGTTAATTTCATTTAAAAAAATAAACTACAA
Found at i:1408064 original size:32 final size:32
Alignment explanation
Indices: 1407998--1408065 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 32
1407988 AACAATAGTC
* *
1407998 TTCTAAACATAGTTGTTCTTGCAACATAATTA
1 TTCTAAACAGAGTTGTTCTTGCAACATAACTA
*
1408030 TTCTAAACAAGAGTTGTTC-T-CAACATGAGCTA
1 TTCTAAAC-AGAGTTGTTCTTGCAACAT-AACTA
1408062 TTCT
1 TTCT
1408066 CAAATGACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
31 6 0.19
32 16 0.52
33 9 0.29
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (32 bp):
TTCTAAACAGAGTTGTTCTTGCAACATAACTA
Found at i:1408138 original size:15 final size:16
Alignment explanation
Indices: 1408118--1408152 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1408108 CCTTGATTTG
*
1408118 AACATAGCTATTC-CA
1 AACATAACTATTCTCA
1408133 AACATAACTATTCTCA
1 AACATAACTATTCTCA
1408149 AACA
1 AACA
1408153 AAAGTTGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.46, C:0.26, G:0.03, T:0.26
Consensus pattern (16 bp):
AACATAACTATTCTCA
Found at i:1411898 original size:18 final size:18
Alignment explanation
Indices: 1411867--1411907 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
1411857 AATCTCAATT
* *
1411867 TTTTAGATTATTTTGGAA
1 TTTTAAATTATTTTAGAA
*
1411885 TTTTAAATTTTTTTAGAA
1 TTTTAAATTATTTTAGAA
1411903 TTTTA
1 TTTTA
1411908 TGAATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.00, G:0.10, T:0.61
Consensus pattern (18 bp):
TTTTAAATTATTTTAGAA
Found at i:1411912 original size:27 final size:26
Alignment explanation
Indices: 1411865--1411923 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 26
1411855 GAAATCTCAA
1411865 TTTTTTAGATTATTTTGGAATTTTAAAT
1 TTTTTTAGA-TATTTTGGAATTTT-AAT
* *
1411893 TTTTTTAGA-ATTTTATGAATTTTTAT
1 TTTTTTAGATATTTT-GGAATTTTAAT
1411919 TTTTT
1 TTTTT
1411924 CTCATAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 12 0.43
27 7 0.25
28 9 0.32
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.66
Consensus pattern (26 bp):
TTTTTTAGATATTTTGGAATTTTAAT
Found at i:1412686 original size:30 final size:29
Alignment explanation
Indices: 1412648--1412713 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
1412638 GTTAATGATT
1412648 TGTA-AAAATTGAATCAAAGAAAAATTTCA
1 TGTATAAAATTGAATCAAAGAAAAA-TTCA
* * **
1412677 TGTATAAAATTGCATGAAATCAAAATTCA
1 TGTATAAAATTGAATCAAAGAAAAATTCA
1412706 TGTATAAA
1 TGTATAAA
1412714 TTTACACACT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 16 0.50
30 16 0.50
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.30
Consensus pattern (29 bp):
TGTATAAAATTGAATCAAAGAAAAATTCA
Found at i:1412967 original size:26 final size:27
Alignment explanation
Indices: 1412938--1412988 Score: 86
Period size: 26 Copynumber: 1.9 Consensus size: 27
1412928 TATTTAAGGG
1412938 TTTAAAAAGAAATA-TAATTATATTAT
1 TTTAAAAAGAAATATTAATTATATTAT
*
1412964 TTTAAAAATAAATATTAATTATATT
1 TTTAAAAAGAAATATTAATTATATT
1412989 TATTAAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (27 bp):
TTTAAAAAGAAATATTAATTATATTAT
Found at i:1412994 original size:26 final size:26
Alignment explanation
Indices: 1412939--1413001 Score: 83
Period size: 26 Copynumber: 2.4 Consensus size: 26
1412929 ATTTAAGGGT
* *
1412939 TTAAAAAGAAATATAATTATATTATT
1 TTAAAAATAAATATAATTATATTATA
1412965 TTAAAAATAAATATTAATTATATT-TA
1 TTAAAAATAAATA-TAATTATATTATA
*
1412991 TTAAACATAAA
1 TTAAAAATAAA
1413002 AAATCAAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 23 0.70
27 10 0.30
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.41
Consensus pattern (26 bp):
TTAAAAATAAATATAATTATATTATA
Found at i:1413128 original size:25 final size:26
Alignment explanation
Indices: 1413075--1413132 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 26
1413065 TAAATTTTAA
*
1413075 TTATATTTAAATAATTTTAATAGTAT
1 TTATTTTTAAATAATTTTAATAGTAT
* * *
1413101 TTATTTTTAAAT-CTTTTAATATTTT
1 TTATTTTTAAATAATTTTAATAGTAT
1413126 TTATTTT
1 TTATTTT
1413133 ACACCAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
25 17 0.61
26 11 0.39
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
TTATTTTTAAATAATTTTAATAGTAT
Found at i:1415097 original size:27 final size:26
Alignment explanation
Indices: 1415044--1415096 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 26
1415034 GATTTTATTA
*
1415044 ATATTTATAATGCAAAACTTCAAAAAT
1 ATATTTATAATGAAAAACTT-AAAAAT
1415071 ATATTTATAATGTAAAATACTTAAAA
1 ATATTTATAATG-AAAA-ACTTAAAA
1415097 TTAAATAACC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
27 12 0.52
28 7 0.30
29 4 0.17
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.36
Consensus pattern (26 bp):
ATATTTATAATGAAAAACTTAAAAAT
Found at i:1426302 original size:38 final size:38
Alignment explanation
Indices: 1426200--1426302 Score: 109
Period size: 38 Copynumber: 2.7 Consensus size: 38
1426190 GTGGAATGGA
* * *
1426200 TATCTACTGGTTTTTTGGGGTGACACCATGTTAACGAT
1 TATCTACTGGTTCTTCGGGGTGACACCATATTAACGAT
* * *** *
1426238 TATCTACTGGTCCTTCAGGACAACACCGTATTAAC-AGT
1 TATCTACTGGTTCTTCGGGGTGACACCATATTAACGA-T
1426276 TATCTACTGGTTCTTCGGGGTGACACC
1 TATCTACTGGTTCTTCGGGGTGACACC
1426303 TCAAAAAGGG
Statistics
Matches: 50, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
37 1 0.02
38 49 0.98
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.34
Consensus pattern (38 bp):
TATCTACTGGTTCTTCGGGGTGACACCATATTAACGAT
Found at i:1434431 original size:12 final size:13
Alignment explanation
Indices: 1434401--1434431 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1434391 AAATATGTTA
1434401 GAAAAAGTAATTT
1 GAAAAAGTAATTT
1434414 GAAAAAGTAATTT
1 GAAAAAGTAATTT
*
1434427 CAAAA
1 GAAAA
1434432 CATATAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.13, T:0.26
Consensus pattern (13 bp):
GAAAAAGTAATTT
Found at i:1442275 original size:5 final size:6
Alignment explanation
Indices: 1442246--1442285 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
1442236 AATAATTTAG
* *
1442246 TTCTTT TT-TTT ATGTTT TTCTTT TTCTTT TTCTTT TTCTT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTT
1442286 GAGTAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.03, C:0.12, G:0.03, T:0.82
Consensus pattern (6 bp):
TTCTTT
Found at i:1453414 original size:29 final size:30
Alignment explanation
Indices: 1453354--1453415 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 30
1453344 ATTTATTTTA
*
1453354 TTGTTAATTTTCTTATTATTTTAAAGGTAT
1 TTGTTAATTTTCTTATTATTTTAAAGGCAT
1453384 TTGTTAATTTT-TTATTATTTTAGAA-GCAT
1 TTGTTAATTTTCTTATTATTTTA-AAGGCAT
1453413 TTG
1 TTG
1453416 CTTGTTAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 17 0.57
30 13 0.43
ACGTcount: A:0.26, C:0.03, G:0.11, T:0.60
Consensus pattern (30 bp):
TTGTTAATTTTCTTATTATTTTAAAGGCAT
Found at i:1454002 original size:30 final size:30
Alignment explanation
Indices: 1453966--1454033 Score: 118
Period size: 30 Copynumber: 2.2 Consensus size: 30
1453956 TTTAAAATAT
1453966 TATAATTGAGTAGTTAAAGTATCGATATTA
1 TATAATTGAGTAGTTAAAGTATCGATATTA
*
1453996 TATAATTGAGTAGTTAAAGTATTGATATTA
1 TATAATTGAGTAGTTAAAGTATCGATATTA
1454026 TATTAATT
1 TA-TAATT
1454034 ATGCTCTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
30 31 0.86
31 5 0.14
ACGTcount: A:0.40, C:0.01, G:0.15, T:0.44
Consensus pattern (30 bp):
TATAATTGAGTAGTTAAAGTATCGATATTA
Found at i:1456397 original size:6 final size:7
Alignment explanation
Indices: 1456382--1456407 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1456372 CGCTTTGAAA
1456382 TTTTATT
1 TTTTATT
1456389 TTTTATT
1 TTTTATT
1456396 TTTTATT
1 TTTTATT
1456403 TTTTA
1 TTTTA
1456408 AAAGGGAGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTTATT
Found at i:1456507 original size:19 final size:19
Alignment explanation
Indices: 1456483--1456520 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1456473 GAAATGAATA
1456483 ATTTCAGGCAAATAGGTTG
1 ATTTCAGGCAAATAGGTTG
1456502 ATTTCAGGCAAATAGGTTG
1 ATTTCAGGCAAATAGGTTG
1456521 GCAATCTCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (19 bp):
ATTTCAGGCAAATAGGTTG
Found at i:1457445 original size:19 final size:20
Alignment explanation
Indices: 1457412--1457451 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
1457402 ATATATGTAT
1457412 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
1457431 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
1457451 A
1 A
1457452 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:1465943 original size:17 final size:17
Alignment explanation
Indices: 1465921--1465954 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1465911 TTGAAATCAC
*
1465921 AATTTCATATAATTCTT
1 AATTTCATACAATTCTT
1465938 AATTTCATACAATTCTT
1 AATTTCATACAATTCTT
1465955 TCTCTGGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTTCATACAATTCTT
Found at i:1466156 original size:32 final size:29
Alignment explanation
Indices: 1466116--1466185 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 29
1466106 GTCCCCTCAT
*
1466116 ATTTTAAAACTTT-TAATTAAGCTCTCTTAAAA
1 ATTTTAAAA-TTTCTAATTAA--TCTC-AAAAA
*
1466148 ATTTTAAAATTTCTCATTAATCTCAAAAA
1 ATTTTAAAATTTCTAATTAATCTCAAAAA
1466177 ATTTTAAAA
1 ATTTTAAAA
1466186 AATATAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 13 0.37
30 4 0.11
31 3 0.09
32 15 0.43
ACGTcount: A:0.44, C:0.11, G:0.01, T:0.43
Consensus pattern (29 bp):
ATTTTAAAATTTCTAATTAATCTCAAAAA
Found at i:1467885 original size:16 final size:16
Alignment explanation
Indices: 1467864--1467895 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
1467854 AATTGGTGGT
1467864 ATTAAATTCTGCATAA
1 ATTAAATTCTGCATAA
1467880 ATTAAATTCTGCATAA
1 ATTAAATTCTGCATAA
1467896 GTATTCGCCA
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:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTAAATTCTGCATAA
Found at i:1468567 original size:48 final size:49
Alignment explanation
Indices: 1468486--1468584 Score: 182
Period size: 48 Copynumber: 2.0 Consensus size: 49
1468476 ATAACAAGTT
1468486 TAAAGAAATAAGAAATTGTAACTGTTTTCGTTAATGGTTAAGCTTTGTG
1 TAAAGAAATAAGAAATTGTAACTGTTTTCGTTAATGGTTAAGCTTTGTG
*
1468535 TAAAGAAATGAGAAATT-TAACTGTTTTCGTTAATGGTTAAGCTTTGTG
1 TAAAGAAATAAGAAATTGTAACTGTTTTCGTTAATGGTTAAGCTTTGTG
1468583 TA
1 TA
1468585 GTAACACCCG
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 33 0.67
49 16 0.33
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.39
Consensus pattern (49 bp):
TAAAGAAATAAGAAATTGTAACTGTTTTCGTTAATGGTTAAGCTTTGTG
Found at i:1471129 original size:23 final size:24
Alignment explanation
Indices: 1471043--1471166 Score: 116
Period size: 23 Copynumber: 5.2 Consensus size: 24
1471033 AGACTCACCA
*
1471043 CAGCTCGTA-AGAGCTTACTGATATAT
1 CAGCTCGTATAGAGCTTACCG-T-T-T
*
1471069 CAGCTCGTA-AGAGCTTACTGTTTT
1 CAGCTCGTATAGAGCTTACCG-TTT
* *
1471093 CAGCTCAT-TGGAGCTTACCGTTT
1 CAGCTCGTATAGAGCTTACCGTTT
* *
1471116 CAGGTCGTAT-GAGCTTACTGTTT
1 CAGCTCGTATAGAGCTTACCGTTT
1471139 -AGCTCG-ATAGAGCTTACCGTTT
1 CAGCTCGTATAGAGCTTACCGTTT
1471161 CAGCTC
1 CAGCTC
1471167 ATTAGACCTT
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
21 2 0.02
22 17 0.20
23 26 0.31
24 18 0.21
25 1 0.01
26 21 0.25
ACGTcount: A:0.22, C:0.23, G:0.22, T:0.34
Consensus pattern (24 bp):
CAGCTCGTATAGAGCTTACCGTTT
Found at i:1471158 original size:45 final size:47
Alignment explanation
Indices: 1471068--1471166 Score: 141
Period size: 45 Copynumber: 2.1 Consensus size: 47
1471058 TACTGATATA
*
1471068 TCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCGTT
1 TCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTAGAGCTTACCGTT
* *
1471115 TCAGGTCGTATGAGCTTACTG-TTT-AGCTCGA-TAGAGCTTACCGTT
1 TCAGCTCGTAAGAGCTTACTGTTTTCAGCTC-ATTAGAGCTTACCGTT
1471160 TCAGCTC
1 TCAGCTC
1471167 ATTAGACCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
45 24 0.51
46 4 0.09
47 19 0.40
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.35
Consensus pattern (47 bp):
TCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTAGAGCTTACCGTT
Found at i:1471172 original size:23 final size:23
Alignment explanation
Indices: 1471068--1471178 Score: 102
Period size: 23 Copynumber: 4.8 Consensus size: 23
1471058 TACTGATATA
* * *
1471068 TCAGCTCGTAAGAGCTTACTGTTT
1 TCAGCTCATTAGAGCTTACCG-TT
*
1471092 TCAGCTCATTGGAGCTTACCGTT
1 TCAGCTCATTAGAGCTTACCGTT
* * *
1471115 TCAGGTC-GTATGAGCTTACTGTT
1 TCAGCTCATTA-GAGCTTACCGTT
1471138 T-AGCTCGA-TAGAGCTTACCGTT
1 TCAGCTC-ATTAGAGCTTACCGTT
*
1471160 TCAGCTCATTAGACCTTAC
1 TCAGCTCATTAGAGCTTAC
1471179 TATTCATTAG
Statistics
Matches: 71, Mismatches: 11, Indels: 11
0.76 0.12 0.12
Matches are distributed among these distances:
22 18 0.25
23 36 0.51
24 17 0.24
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (23 bp):
TCAGCTCATTAGAGCTTACCGTT
Found at i:1471178 original size:45 final size:46
Alignment explanation
Indices: 1471068--1471179 Score: 122
Period size: 45 Copynumber: 2.4 Consensus size: 46
1471058 TACTGATATA
* *
1471068 TCAGCTCGTAAGAGCTTACTGTTTTCAGCTCATTGGAGCTTACCGTT
1 TCAGCTC-TTAGAGCTTACTGTTTTCAGCTCATTAGAGCTTACCGTT
* *
1471115 TCAGGTCGTATGAGCTTACTG-TTT-AGCTCGA-TAGAGCTTACCGTT
1 TCAGCTCTTA-GAGCTTACTGTTTTCAGCTC-ATTAGAGCTTACCGTT
*
1471160 TCAGCTCATTAGACCTTACT
1 TCAGCTC-TTAGAGCTTACT
1471180 ATTCATTAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
45 32 0.58
46 7 0.13
47 16 0.29
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.36
Consensus pattern (46 bp):
TCAGCTCTTAGAGCTTACTGTTTTCAGCTCATTAGAGCTTACCGTT
Found at i:1488250 original size:29 final size:30
Alignment explanation
Indices: 1488210--1488266 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
1488200 TGGTCAAATG
1488210 TGCAATGTTATACAT-AAACTTTGATTTTA
1 TGCAATGTTATACATGAAACTTTGATTTTA
*
1488239 TGCAAT-TCTATACATGAAATTTTGATTT
1 TGCAATGT-TATACATGAAACTTTGATTT
1488267 AATTTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
28 1 0.04
29 13 0.52
30 11 0.44
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (30 bp):
TGCAATGTTATACATGAAACTTTGATTTTA
Found at i:1490591 original size:20 final size:21
Alignment explanation
Indices: 1490566--1490604 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1490556 GACAAATTTA
1490566 ACTCAAA-AAACAATAATGGT
1 ACTCAAATAAACAATAATGGT
*
1490586 ACTCAAATAAATAATAATG
1 ACTCAAATAAACAATAATG
1490605 TAAACATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.56, C:0.13, G:0.08, T:0.23
Consensus pattern (21 bp):
ACTCAAATAAACAATAATGGT
Found at i:1490876 original size:13 final size:14
Alignment explanation
Indices: 1490852--1490893 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
1490842 CATTTGTTTA
*
1490852 AGTTTTTATTTAAT
1 AGTTTTTTTTTAAT
*
1490866 A-TTTTTTTTTAAA
1 AGTTTTTTTTTAAT
1490879 AGTTTTTTATTTAAT
1 AGTTTTTT-TTTAAT
1490894 TATGTTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
13 11 0.48
14 7 0.30
15 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (14 bp):
AGTTTTTTTTTAAT
Found at i:1492539 original size:153 final size:153
Alignment explanation
Indices: 1492261--1492568 Score: 580
Period size: 153 Copynumber: 2.0 Consensus size: 153
1492251 GGGACATTGC
* *
1492261 GACATGGCGACGTGTTCTCACATAAATCGGGTTTCTTTTCCTAGTTAAACTTTGTTATCTTTTCT
1 GACATGGCGACGTGTTCTCACATAAATCGGGTTTCTTTTCCTAGTTAAACTTTGGTATCTTTTCC
1492326 CAGTTAATATTTAATTATTCTACGGATATTTTAATCATATATTCACACGAATTTCAACCTATAAA
66 CAGTTAATATTTAATTATTCTACGGATATTTTAATCATATATTCACACGAATTTCAACCTATAAA
*
1492391 AGGGCCTTTATAACCTTATAATT
131 AGGGCCTTTATAACCTTACAATT
1492414 GACATGGCGACGTGTTCTCACATAAATCGGGTTTCTTTTCCTAGTTAAACTTTGGTATCTTTTCC
1 GACATGGCGACGTGTTCTCACATAAATCGGGTTTCTTTTCCTAGTTAAACTTTGGTATCTTTTCC
*
1492479 CAGTTAATATTTAATTATTTTACGGATATTTTAATCATATATTCACACGAATTTCAACCTATAAA
66 CAGTTAATATTTAATTATTCTACGGATATTTTAATCATATATTCACACGAATTTCAACCTATAAA
1492544 AGGGCCTTTATAACCTTACAATT
131 AGGGCCTTTATAACCTTACAATT
1492567 GA
1 GA
1492569 TATCTTCATC
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
153 151 1.00
ACGTcount: A:0.30, C:0.18, G:0.12, T:0.40
Consensus pattern (153 bp):
GACATGGCGACGTGTTCTCACATAAATCGGGTTTCTTTTCCTAGTTAAACTTTGGTATCTTTTCC
CAGTTAATATTTAATTATTCTACGGATATTTTAATCATATATTCACACGAATTTCAACCTATAAA
AGGGCCTTTATAACCTTACAATT
Found at i:1493586 original size:15 final size:15
Alignment explanation
Indices: 1493566--1493595 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1493556 GATGCTTTAT
*
1493566 ATATATTTTTATATA
1 ATATATATTTATATA
1493581 ATATATATTTATATA
1 ATATATATTTATATA
1493596 TAACTTACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
ATATATATTTATATA
Found at i:1493586 original size:17 final size:17
Alignment explanation
Indices: 1493564--1493598 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
1493554 TTGATGCTTT
*
1493564 ATATATATTTTTATATA
1 ATATATATTTATATATA
1493581 ATATATATTTATATATA
1 ATATATATTTATATATA
1493598 A
1 A
1493599 CTTACCTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATATATATTTATATATA
Found at i:1501916 original size:17 final size:17
Alignment explanation
Indices: 1501896--1501930 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1501886 TGAATTTAAA
1501896 TTTAA-AAAATTTATATT
1 TTTAAGAAAATTT-TATT
1501913 TTTAAGAAAATTTTATT
1 TTTAAGAAAATTTTATT
1501930 T
1 T
1501931 GAATATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTAAGAAAATTTTATT
Found at i:1502002 original size:4 final size:4
Alignment explanation
Indices: 1501995--1502021 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1501985 AGAAAAAAAA
1501995 AGTG AGTG AGTG AGTG AGTG AGTG AGT
1 AGTG AGTG AGTG AGTG AGTG AGTG AGT
1502022 AAGTAAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (4 bp):
AGTG
Found at i:1502527 original size:25 final size:24
Alignment explanation
Indices: 1502490--1502536 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1502480 TTCTCTTCTG
*
1502490 TCTATATTGTTATAAAACTTTTTTA
1 TCTATATTATTATAAAA-TTTTTTA
*
1502515 TCTATTTTATTATAAAATTTTT
1 TCTATATTATTATAAAATTTTT
1502537 ATTTAATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 5 0.25
25 15 0.75
ACGTcount: A:0.32, C:0.06, G:0.02, T:0.60
Consensus pattern (24 bp):
TCTATATTATTATAAAATTTTTTA
Found at i:1502826 original size:11 final size:11
Alignment explanation
Indices: 1502818--1502869 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
1502808 AATATTTTTT
*
1502818 TATTATTTTTC
1 TATTATTTTGC
1502829 TATTATTTTGC
1 TATTATTTTGC
* *
1502840 TATTATATTGA
1 TATTATTTTGC
* *
1502851 TACTATTTTGT
1 TATTATTTTGC
1502862 TATTATTT
1 TATTATTT
1502870 GAATATTGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 34 1.00
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (11 bp):
TATTATTTTGC
Found at i:1503922 original size:32 final size:32
Alignment explanation
Indices: 1503886--1503952 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
1503876 TCCTCAACAA
1503886 TTAAATATATTACGATTATCTATAATACTAAT
1 TTAAATATATTACGATTATCTATAATACTAAT
*
1503918 TTAAATATATTATGATTATCTATAATACTAAT
1 TTAAATATATTACGATTATCTATAATACTAAT
1503950 TTA
1 TTA
1503953 CTAACATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (32 bp):
TTAAATATATTACGATTATCTATAATACTAAT
Found at i:1511504 original size:11 final size:11
Alignment explanation
Indices: 1511490--1511514 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1511480 TAAGGACGAA
1511490 ATAATCAAATT
1 ATAATCAAATT
1511501 ATAATCAAATT
1 ATAATCAAATT
1511512 ATA
1 ATA
1511515 GGTGATCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (11 bp):
ATAATCAAATT
Found at i:1513496 original size:123 final size:123
Alignment explanation
Indices: 1513276--1513514 Score: 284
Period size: 123 Copynumber: 1.9 Consensus size: 123
1513266 AAAAATCAAT
* ** * *
1513276 ACCTTATTTAAAAGGCATTGAACTACTTACCATTTGACCCCAGAGATGAGCAGGTCTAAGCCCAT
1 ACCTTACTTAAAAGGCATCAAACTACTTACCATTTGACCCCAAAGATGAACAGGTCTAAGCCCAT
** * *
1513341 TTCTTCGTACCGTGCACTATCTTTTTGGGGTACATTTATAATTAATTCACATGCATAA
66 TTCTTAATACCATGCACTATCTTTTTGGGGTACATTTATAATTAACTCACATGCATAA
* ** * *
1513399 ACCTTACTTATAAGGCATCAAACTACTTGTCATTTGACCCCATAAGATGAATATGTCTAAGCCCA
1 ACCTTACTTAAAAGGCATCAAACTACTTACCATTTGACCCCA-AAGATGAACAGGTCTAAGCCCA
** * *
1513464 TTTCTTAATATTATGCACTAAT-TTTTT-TGGTACATTTATACTTAACTCACA
65 TTTCTTAATACCATGCACT-ATCTTTTTGGGGTACATTTATAATTAACTCACA
1513515 CACATTGATT
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
123 57 0.59
124 37 0.39
125 2 0.02
ACGTcount: A:0.31, C:0.21, G:0.13, T:0.36
Consensus pattern (123 bp):
ACCTTACTTAAAAGGCATCAAACTACTTACCATTTGACCCCAAAGATGAACAGGTCTAAGCCCAT
TTCTTAATACCATGCACTATCTTTTTGGGGTACATTTATAATTAACTCACATGCATAA
Found at i:1513665 original size:137 final size:137
Alignment explanation
Indices: 1513410--1513665 Score: 295
Period size: 137 Copynumber: 1.9 Consensus size: 137
1513400 CCTTACTTAT
* *
1513410 AAGGCATCAAACTACTTGTCATTTGACCCCATAAGATGAATATGTCTAAGCCCATTTCTTAATAT
1 AAGGCATCAAACTACTTGTCATTTGACCCCATAAGATGAATATGTCTAAACCCATTTCGTAATAT
* * ** *
1513475 TATGCACTAATTTTTTTGGTACATTTATACTTAACTCACACACATTGATTTGAATTTGAGACCAT
66 TATGCACTAATTTTTTTGCTACATTTATAATTAACTCACACACATCAAATTGAATTTGAGACCAT
1513540 ACTTAAA
131 ACTTAAA
* * * *
1513547 AAGGCATCGAACTACTTGGT-ATTTGACCTC-TAAAGATGAGTA-GATCTAAACCCATTTCGTCA
1 AAGGCATCAAACTACTT-GTCATTTGACCCCAT-AAGATGAATATG-TCTAAACCCATTTCGTAA
* * * * * *
1513609 TACTTA-GCACTATTTTTTTTTCTACATTTTTAATTGACTCACACGCCTCAAATTGAA
63 TA-TTATGCACTAATTTTTTTGCTACATTTATAATTAACTCACACACATCAAATTGAA
1513666 CTAAGCAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 8
0.80 0.14 0.07
Matches are distributed among these distances:
136 2 0.02
137 91 0.93
138 5 0.05
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (137 bp):
AAGGCATCAAACTACTTGTCATTTGACCCCATAAGATGAATATGTCTAAACCCATTTCGTAATAT
TATGCACTAATTTTTTTGCTACATTTATAATTAACTCACACACATCAAATTGAATTTGAGACCAT
ACTTAAA
Found at i:1515019 original size:5 final size:6
Alignment explanation
Indices: 1515003--1515027 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1514993 ACTGAAAATT
1515003 TAAAAA TAAAAA TAAAAA TAAAAA T
1 TAAAAA TAAAAA TAAAAA TAAAAA T
1515028 GTATAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (6 bp):
TAAAAA
Found at i:1539975 original size:24 final size:24
Alignment explanation
Indices: 1539943--1539993 Score: 70
Period size: 22 Copynumber: 2.2 Consensus size: 24
1539933 CTTTTATTAA
* *
1539943 ATATATATACATATT-A-AAAAAT
1 ATATATATATAAATTCACAAAAAT
1539965 ATATATATATAAATTCACAAAAAT
1 ATATATATATAAATTCACAAAAAT
1539989 ATATA
1 ATATA
1539994 ATTTAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 13 0.52
23 1 0.04
24 11 0.44
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (24 bp):
ATATATATATAAATTCACAAAAAT
Found at i:1540074 original size:21 final size:20
Alignment explanation
Indices: 1540048--1540095 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1540038 ATATATAAAA
*
1540048 TTTTAATATTATGTTTATAT
1 TTTTAATATTATGTTTATAC
* *
1540068 TGTTTAAGATTATTTTTATAC
1 T-TTTAATATTATGTTTATAC
1540089 TTTTAAT
1 TTTTAAT
1540096 TTTTAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.62
Consensus pattern (20 bp):
TTTTAATATTATGTTTATAC
Found at i:1540220 original size:20 final size:20
Alignment explanation
Indices: 1540178--1540220 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1540168 AGTTTTTCAC
* * *
1540178 TTTCTATATTTTATATTTTT
1 TTTCTAGATTTTATATATAT
1540198 TTTCTAGATTTTATATATAT
1 TTTCTAGATTTTATATATAT
1540218 TTT
1 TTT
1540221 TTAATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTCTAGATTTTATATATAT
Found at i:1547027 original size:15 final size:16
Alignment explanation
Indices: 1547007--1547036 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1546997 TAAAAAAGGT
1547007 GATTTGAAG-CTAATG
1 GATTTGAAGCCTAATG
1547022 GATTTGAAGCCTAAT
1 GATTTGAAGCCTAAT
1547037 CATTCATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (16 bp):
GATTTGAAGCCTAATG
Found at i:1558211 original size:21 final size:21
Alignment explanation
Indices: 1558185--1558225 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1558175 AGACGAGCAA
* *
1558185 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1558206 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1558226 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1560956 original size:23 final size:23
Alignment explanation
Indices: 1560929--1560974 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 23
1560919 TTAACTGGTG
1560929 AATTT-ATGATATAATTTATATCA
1 AATTTAAT-ATATAATTTATATCA
1560952 AATTTGACATATATAATTTATAT
1 AATTT-A-ATATATAATTTATAT
1560975 GAATAAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.25
25 13 0.65
26 2 0.10
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (23 bp):
AATTTAATATATAATTTATATCA
Found at i:1568920 original size:10 final size:10
Alignment explanation
Indices: 1568905--1568929 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
1568895 GTATTTCCAT
1568905 ATATATATAC
1 ATATATATAC
1568915 ATATATATAC
1 ATATATATAC
1568925 ATATA
1 ATATA
1568930 CTCAAAGGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATATAC
Done.