Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 139 of 144
Found at i:36344636 original size:37 final size:37
Alignment explanation
Indices: 36344566--36344637 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
36344556 TATCACACTT
* *
36344566 GTTTAAAAATAATATATAATAAATAATATAATATACG
1 GTTTAAAAATAATAAATAATAAACAATATAATATACG
* *
36344603 GTTTAAAATTAATAAATAATAACACATTA-AATATA
1 GTTTAAAAATAATAAATAATAA-ACAATATAATATA
36344638 AATCATATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
37 26 0.87
38 4 0.13
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (37 bp):
GTTTAAAAATAATAAATAATAAACAATATAATATACG
Found at i:36346072 original size:35 final size:35
Alignment explanation
Indices: 36346018--36346093 Score: 107
Period size: 35 Copynumber: 2.2 Consensus size: 35
36346008 ATTTGACCCC
* * *
36346018 ATATATCTAAATTTATTCGGTCTCAAATTTTATTT
1 ATATATCAAAATCTATTCGGTATCAAATTTTATTT
* *
36346053 ATATATCAAAATCTGTTCGGTATCGAATTTTATTT
1 ATATATCAAAATCTATTCGGTATCAAATTTTATTT
36346088 ATATAT
1 ATATAT
36346094 TAATCTTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.33, C:0.11, G:0.08, T:0.49
Consensus pattern (35 bp):
ATATATCAAAATCTATTCGGTATCAAATTTTATTT
Found at i:36348067 original size:8 final size:8
Alignment explanation
Indices: 36348054--36348089 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
36348044 AGTAAAGGAC
*
36348054 AGAGAGAG
1 AGAGAGGG
36348062 AGAGAGGG
1 AGAGAGGG
36348070 AGAGAGGG
1 AGAGAGGG
*
36348078 AGAGAGGA
1 AGAGAGGG
36348086 AGAG
1 AGAG
36348090 GACGAGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.44, C:0.00, G:0.56, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Found at i:36348075 original size:16 final size:16
Alignment explanation
Indices: 36348049--36348089 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
36348039 TAGGAAGTAA
36348049 AGGACAGAGAGAGAGAG
1 AGGA-AGAGAGAGAGAG
* *
36348066 AGGGAGAGAGGGAGAG
1 AGGAAGAGAGAGAGAG
36348082 AGGAAGAG
1 AGGAAGAG
36348090 GACGAGCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.44, C:0.02, G:0.54, T:0.00
Consensus pattern (16 bp):
AGGAAGAGAGAGAGAG
Found at i:36349610 original size:6 final size:6
Alignment explanation
Indices: 36349599--36349634 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
36349589 ATCCCCAGAA
36349599 GCAAGG GCAAGG GCAAGG GCAAGG GCAAGG GCAAGG
1 GCAAGG GCAAGG GCAAGG GCAAGG GCAAGG GCAAGG
36349635 TAGGCATTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.17, G:0.50, T:0.00
Consensus pattern (6 bp):
GCAAGG
Found at i:36355514 original size:22 final size:23
Alignment explanation
Indices: 36355464--36355507 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
36355454 ATAAAGTTAT
36355464 TAAATA-TTAAAATAAAATAAAA
1 TAAATATTTAAAATAAAATAAAA
*
36355486 TAAATATTTAAAA-AAATTAAAA
1 TAAATATTTAAAATAAAATAAAA
36355508 ATAATATGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAATATTTAAAATAAAATAAAA
Found at i:36357861 original size:12 final size:12
Alignment explanation
Indices: 36357844--36357868 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36357834 CTAACAGCCC
36357844 CAGTATTAGGAG
1 CAGTATTAGGAG
36357856 CAGTATTAGGAG
1 CAGTATTAGGAG
36357868 C
1 C
36357869 CCTGATGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.12, G:0.32, T:0.24
Consensus pattern (12 bp):
CAGTATTAGGAG
Found at i:36364701 original size:26 final size:26
Alignment explanation
Indices: 36364665--36364716 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
36364655 GAAATGAATA
36364665 ATTTAATTAGTGGACTGTAAGAGGAG
1 ATTTAATTAGTGGACTGTAAGAGGAG
36364691 ATTTAATTAGTGGACTGTAAGAGGAG
1 ATTTAATTAGTGGACTGTAAGAGGAG
36364717 CTAAATTGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.04, G:0.31, T:0.31
Consensus pattern (26 bp):
ATTTAATTAGTGGACTGTAAGAGGAG
Found at i:36369447 original size:3 final size:3
Alignment explanation
Indices: 36369439--36369464 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
36369429 ACAAAGAACA
36369439 AGC AGC AGC AGC AGC AGC AGC AGC AG
1 AGC AGC AGC AGC AGC AGC AGC AGC AG
36369465 AAGGTGAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.35, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:36371110 original size:26 final size:26
Alignment explanation
Indices: 36371076--36371145 Score: 79
Period size: 26 Copynumber: 2.7 Consensus size: 26
36371066 GATAAAAATT
* *
36371076 AAATAAAATAAATTTTTT-TGTTATAA
1 AAATTAAATAAATTTTTTGTGATA-AA
*
36371102 AAATTAAATAAAATTTTTGTGATAAA
1 AAATTAAATAAATTTTTTGTGATAAA
*
36371128 AAATTAATATAAAATTTT
1 AAATTAA-ATAAATTTTT
36371146 AAATATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 25 0.64
27 14 0.36
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (26 bp):
AAATTAAATAAATTTTTTGTGATAAA
Found at i:36371126 original size:25 final size:26
Alignment explanation
Indices: 36371076--36371145 Score: 88
Period size: 27 Copynumber: 2.7 Consensus size: 26
36371066 GATAAAAATT
* * *
36371076 AAATAAAAT-AAATTTTTTTGTTATAA
1 AAATTAAATAAAATTTTTGTGATA-AA
36371102 AAATTAAATAAAATTTTTGTGATAAA
1 AAATTAAATAAAATTTTTGTGATAAA
36371128 AAATTAATATAAAATTTT
1 AAATTAA-ATAAAATTTT
36371146 AAATATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 17 0.44
27 22 0.56
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.43
Consensus pattern (26 bp):
AAATTAAATAAAATTTTTGTGATAAA
Found at i:36371367 original size:16 final size:16
Alignment explanation
Indices: 36371322--36371371 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
36371312 TAAACCAAGC
36371322 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
*
36371338 T-A-TAA-TATAAAAAA
1 TAATTAATTAT-CAAAA
36371352 TAATTAATTATCAAAA
1 TAATTAATTATCAAAA
36371368 TAAT
1 TAAT
36371372 ATCCCTATCA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
13 3 0.11
14 8 0.29
15 2 0.07
16 12 0.43
17 3 0.11
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATTAATTATCAAAA
Found at i:36372798 original size:23 final size:23
Alignment explanation
Indices: 36372753--36372896 Score: 150
Period size: 23 Copynumber: 6.3 Consensus size: 23
36372743 ACAGAACAAG
* *
36372753 CAGAGAGTAC-CAAAGTACT-AA
1 CAGAGAGCACACAAAGTGCTAAA
*
36372774 CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGCACACAAAGTGCTAAA
* * *
36372797 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
36372820 CGGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
36372843 CAGAGAGCACACATAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAA
* *
36372866 CAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGCAC-ACAAAGTGCTAAA
36372889 CAGAGAGC
1 CAGAGAGC
36372897 GCGCTAGTGT
Statistics
Matches: 104, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
21 9 0.09
22 7 0.07
23 87 0.84
24 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.12
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAA
Found at i:36372838 original size:46 final size:46
Alignment explanation
Indices: 36372753--36372895 Score: 184
Period size: 46 Copynumber: 3.2 Consensus size: 46
36372743 ACAGAACAAG
*
36372753 CAGAGAGTAC-CAAAGTACTAA-CAGAGAGCACACACAGTGCTAAA
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAAA
* *
36372797 CAGAGAGTACACAAAGTACTAATCGGAGAGCACACAAAGTGCTAAT
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAAA
* * * * *
36372843 CAGAGAGCACACATAGTGCTAATCAGAGAGCACGA-GACGTGCTAAA
1 CAGAGAGTACACAAAGTACTAATCAGAGAGCAC-ACAAAGTGCTAAA
36372889 CAGAGAG
1 CAGAGAG
36372896 CGCGCTAGTG
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
44 10 0.12
45 11 0.13
46 64 0.74
47 1 0.01
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.13
Consensus pattern (46 bp):
CAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCTAAA
Found at i:36374996 original size:27 final size:30
Alignment explanation
Indices: 36374932--36374997 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
36374922 ATATAAAAAA
*
36374932 TATATATGAACTTTGATTTGATATGCAATTG
1 TATACATGAACTTTGATTT-ATATGCAATTG
36374963 TATACATGAACTTT-ATTT-TAGTGCAA-T-
1 TATACATGAACTTTGATTTATA-TGCAATTG
36374990 TATACATG
1 TATACATG
36374998 TGAAACTCTA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 8 0.24
28 3 0.09
29 5 0.15
30 4 0.12
31 13 0.39
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (30 bp):
TATACATGAACTTTGATTTATATGCAATTG
Found at i:36376359 original size:40 final size:40
Alignment explanation
Indices: 36376304--36376383 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
36376294 CCATAACAAA
36376304 TTATATATGGATTAATTAAACCCTACTTCTCTAGACTATG
1 TTATATATGGATTAATTAAACCCTACTTCTCTAGACTATG
36376344 TTATATATGGATTAATTAAACCCTACTTCTCTAGACTATG
1 TTATATATGGATTAATTAAACCCTACTTCTCTAGACTATG
36376384 GACCAAACTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (40 bp):
TTATATATGGATTAATTAAACCCTACTTCTCTAGACTATG
Found at i:36388405 original size:17 final size:17
Alignment explanation
Indices: 36388383--36388415 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36388373 TTTTAAAAAT
36388383 ATTTTTTTATAATTTTC
1 ATTTTTTTATAATTTTC
*
36388400 ATTTTTTTATTATTTT
1 ATTTTTTTATAATTTT
36388416 AACGATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTTTATAATTTTC
Found at i:36394231 original size:21 final size:22
Alignment explanation
Indices: 36394206--36394248 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
36394196 TGTTATTATG
*
36394206 AAATAAAATATTTGTT-TGAAA
1 AAATAAAAGATTTGTTATGAAA
36394227 AAATAAAAGATTTGTTATGAAA
1 AAATAAAAGATTTGTTATGAAA
36394249 TCTCACATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (22 bp):
AAATAAAAGATTTGTTATGAAA
Found at i:36397753 original size:30 final size:30
Alignment explanation
Indices: 36397717--36397775 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
36397707 ACAAGACAGA
36397717 TTGGTTAAGTTCAAAGAACCCTAATCCAGG
1 TTGGTTAAGTTCAAAGAACCCTAATCCAGG
36397747 TTGGTTAAGTTCAAAGAACCCTAATCCAG
1 TTGGTTAAGTTCAAAGAACCCTAATCCAG
36397776 TCCCTGCCAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.27
Consensus pattern (30 bp):
TTGGTTAAGTTCAAAGAACCCTAATCCAGG
Found at i:36397900 original size:36 final size:36
Alignment explanation
Indices: 36397853--36397922 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
36397843 GAAGGAAAAG
36397853 TCAGTTTGATCAATGCTGTAAATCAAAAAAGCTAAT
1 TCAGTTTGATCAATGCTGTAAATCAAAAAAGCTAAT
*
36397889 TCAGTTTGATCAATGTTGTAAATCAAAAAAGCTA
1 TCAGTTTGATCAATGCTGTAAATCAAAAAAGCTA
36397923 CTTTAGAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (36 bp):
TCAGTTTGATCAATGCTGTAAATCAAAAAAGCTAAT
Found at i:36401046 original size:14 final size:14
Alignment explanation
Indices: 36401027--36401065 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
36401017 CTAGAAAAGT
36401027 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
36401041 AAATCATTTTCTAG
1 AAATCATTTTCCAG
*
36401055 AAACCATTTTC
1 AAATCATTTTC
36401066 AGGCAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:36404957 original size:61 final size:59
Alignment explanation
Indices: 36404802--36404958 Score: 147
Period size: 61 Copynumber: 2.6 Consensus size: 59
36404792 CTTGAACTTG
** * *
36404802 ATTTTTTTTTCTTAATTTGATATTTAAGCTTTTTTATTCAATTTGATACATAAACTTGAT
1 ATTTTTTTTTC-TAATTTGATACCTAAGCTTTTTTATCCAATTTGATACATAAACTTGAA
* * * ** *
36404862 A-CTTTCTTT-TAATTTGGTACCTAAATTTTATTTTTTATCCAATTTGATACTTAAACTTGACA
1 ATTTTTTTTTCTAATTTGATACCT-AA---GCTTTTTTATCCAATTTGATACATAAACTTGA-A
36404924 ATTTTGTTTTTCTAATTTGATACCTAAGCTTTTTT
1 ATTTT-TTTTTCTAATTTGATACCTAAGCTTTTTT
36404959 TTCACCCATT
Statistics
Matches: 74, Mismatches: 15, Indels: 15
0.71 0.14 0.14
Matches are distributed among these distances:
57 10 0.14
58 2 0.03
59 6 0.08
60 1 0.01
61 34 0.46
62 1 0.01
63 2 0.03
64 6 0.08
65 12 0.16
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.55
Consensus pattern (59 bp):
ATTTTTTTTTCTAATTTGATACCTAAGCTTTTTTATCCAATTTGATACATAAACTTGAA
Found at i:36411026 original size:16 final size:16
Alignment explanation
Indices: 36410980--36411034 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
36410970 TGTTTAGTTC
*
36410980 GCTGTAATGCAATAAA
1 GCTGTAATGCAATAGA
*
36410996 GCTGTAATGTAATAGA
1 GCTGTAATGCAATAGA
* * *
36411012 GTTGTAATGGAATAGG
1 GCTGTAATGCAATAGA
36411028 GCTGTAA
1 GCTGTAA
36411035 CCAGTATTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.36, C:0.07, G:0.27, T:0.29
Consensus pattern (16 bp):
GCTGTAATGCAATAGA
Found at i:36411068 original size:45 final size:44
Alignment explanation
Indices: 36411017--36411109 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 44
36411007 ATAGAGTTGT
*
36411017 AATGGAATAGGGCTGTAACCAGTA-TTTTAGTTATTTGGTTGAAT-G
1 AATGGAATAGAGCTGTAA-CAGTATTTTTA--TATTTGGTTGAATGG
* *
36411062 AATGGAATAGAGCTGTAATAGTATTTTTATGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAACAGTATTTTTATATTTGGTTGAATGG
36411106 AATG
1 AATG
36411110 ATGTTGTAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
43 12 0.28
44 9 0.21
45 22 0.51
ACGTcount: A:0.30, C:0.04, G:0.27, T:0.39
Consensus pattern (44 bp):
AATGGAATAGAGCTGTAACAGTATTTTTATATTTGGTTGAATGG
Found at i:36416311 original size:11 final size:12
Alignment explanation
Indices: 36416290--36416315 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
36416280 TGCTTCTTTA
36416290 TACGTTTTTTTC
1 TACGTTTTTTTC
36416302 TACGTTTTTTTC
1 TACGTTTTTTTC
36416314 TA
1 TA
36416316 TTTATGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.12, C:0.15, G:0.08, T:0.65
Consensus pattern (12 bp):
TACGTTTTTTTC
Found at i:36423148 original size:7 final size:7
Alignment explanation
Indices: 36423136--36423169 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
36423126 AAGAACTAGA
36423136 TCGGAAT
1 TCGGAAT
36423143 TCGGAAT
1 TCGGAAT
36423150 TCGGAAT
1 TCGGAAT
36423157 TCGGAAT
1 TCGGAAT
36423164 TCGGAA
1 TCGGAA
36423170 CTTGAAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.26
Consensus pattern (7 bp):
TCGGAAT
Found at i:36423965 original size:8 final size:8
Alignment explanation
Indices: 36423949--36424032 Score: 53
Period size: 8 Copynumber: 9.9 Consensus size: 8
36423939 TTTTGTGTTA
*
36423949 TTAATTTT
1 TTAAATTT
36423957 TTAAATTT
1 TTAAATTT
*
36423965 TTATATTT
1 TTAAATTT
36423973 TTAAA-TT
1 TTAAATTT
**
36423980 TTATTTTATT
1 TTA-AAT-TT
36423990 TTAAATTTTT
1 TTAAA--TTT
*
36424000 TTAAGTTT
1 TTAAATTT
36424008 TTAAATATT
1 TTAAAT-TT
*
36424017 TTATCATTT
1 TTA-AATTT
36424026 TTAAATT
1 TTAAATT
36424033 ATTAGTTGAC
Statistics
Matches: 58, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
7 5 0.09
8 29 0.50
9 10 0.17
10 13 0.22
11 1 0.02
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (8 bp):
TTAAATTT
Found at i:36423989 original size:18 final size:17
Alignment explanation
Indices: 36423954--36424032 Score: 81
Period size: 18 Copynumber: 4.6 Consensus size: 17
36423944 TGTTATTAAT
*
36423954 TTTTTAAA-TTTTTATA
1 TTTTTAAATTTTTTTTA
36423970 TTTTTAAATTTTATTTTA
1 TTTTTAAATTTT-TTTTA
*
36423988 -TTTTAAATTTTTTTAA
1 TTTTTAAATTTTTTTTA
* *
36424004 GTTTTTAAATATTTTATCA
1 -TTTTTAAAT-TTTTTTTA
36424023 TTTTTAAATT
1 TTTTTAAATT
36424033 ATTAGTTGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
16 12 0.22
17 15 0.28
18 21 0.39
19 6 0.11
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.67
Consensus pattern (17 bp):
TTTTTAAATTTTTTTTA
Found at i:36424018 original size:10 final size:9
Alignment explanation
Indices: 36423951--36424032 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 9
36423941 TTGTGTTATT
36423951 AATTTTTTA
1 AATTTTTTA
36423960 AA-TTTTTA
1 AATTTTTTA
*
36423968 TA-TTTTTA
1 AATTTTTTA
36423976 AATTTTATT-
1 AATTTT-TTA
36423985 --TTATTTTA
1 AATT-TTTTA
*
36423993 AATTTTTTT
1 AATTTTTTA
*
36424002 AAGTTTTTA
1 AATTTTTTA
*
36424011 AATATTTTA
1 AATTTTTTA
*
36424020 TCA-TTTTTA
1 -AATTTTTTA
36424029 AATT
1 AATT
36424033 ATTAGTTGAC
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
7 4 0.07
8 17 0.31
9 29 0.53
10 5 0.09
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.66
Consensus pattern (9 bp):
AATTTTTTA
Found at i:36424913 original size:154 final size:157
Alignment explanation
Indices: 36424623--36424949 Score: 473
Period size: 169 Copynumber: 2.0 Consensus size: 157
36424613 CAAACGAATA
* *
36424623 AAATCATTGAAAAATGTTTATTGTAATAGTAAGTCACACTTTATTTTCAAACGAATAAAATCATA
1 AAATCATTGAAAAATCTTTATTGTAATAGTAAGTCACACTTTATTTTCAAAAGAATAAAATCATA
*
36424688 CTCGATTTATTATGTTTTCTTTTCAAATATCAAACTATTAAATAAATATTTTAAATAAAAAAAAT
66 CTCGATCTATTATGTTTTCTTTTCAAATATCAAAC----------ATA-TTTAAATAAAAAAAAT
36424753 CATTGAATACCATTTTAAATTTAGAAAAATGTTTGCAT
120 CATTGAATACCATTTTAAATTTAGAAAAATGTTTGCAT
*
36424791 AAATCATTGAACAAATCTTTATTGTAATAGTAAGTTACACTTTATTTTCAAAAGAATAAAATCAT
1 AAATCATTGAA-AAATCTTTATTGTAATAGTAAGTCACACTTTATTTTCAAAAGAATAAAATCAT
*
36424856 ACTTGATCTATTATGTTTT-TTTTCAAATATCAAAC-TA-TTAAAT-AAAAAAATCATTGAATAC
65 ACTCGATCTATTATGTTTTCTTTTCAAATATCAAACATATTTAAATAAAAAAAATCATTGAATAC
36424917 CATTTTAAATTTAGAAAAATGTTTGCAT
130 CATTTTAAATTTAGAAAAATGTTTGCAT
36424945 AAATC
1 AAATC
36424950 GAATCATGCA
Statistics
Matches: 153, Mismatches: 5, Indels: 16
0.88 0.03 0.09
Matches are distributed among these distances:
154 51 0.33
155 6 0.04
157 2 0.01
168 27 0.18
169 67 0.44
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (157 bp):
AAATCATTGAAAAATCTTTATTGTAATAGTAAGTCACACTTTATTTTCAAAAGAATAAAATCATA
CTCGATCTATTATGTTTTCTTTTCAAATATCAAACATATTTAAATAAAAAAAATCATTGAATACC
ATTTTAAATTTAGAAAAATGTTTGCAT
Found at i:36435210 original size:16 final size:17
Alignment explanation
Indices: 36435189--36435225 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
36435179 AATGGAATGA
36435189 AAATAAATTT-TTAATT
1 AAATAAATTTATTAATT
36435205 AAATAAATTTAATTAATT
1 AAATAAATTT-ATTAATT
36435223 AAA
1 AAA
36435226 AATTTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
18 9 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATAAATTTATTAATT
Found at i:36437230 original size:74 final size:73
Alignment explanation
Indices: 36437097--36437233 Score: 188
Period size: 74 Copynumber: 1.9 Consensus size: 73
36437087 AAAATTTAAC
* *
36437097 CATATTTCTAAAATATTTAAAAAAGAAAAGAAAAATAGCATAATAGTGTAGCATATGTCAACAAA
1 CATATTTCTAAAATATTTAAAAAAGAAAAGAAAAAGAGCAAAATAGTGTAGCATATGTCAACAAA
36437162 AGGAAGGT
66 AGGAAGGT
* * *
36437170 CATATTTCTAAAATA-TTAAAAAGAGAAGAAGAAAGAGGGCAAAATAGTGT-GCCATGTGTCAAC
1 CATATTTCTAAAATATTTAAAAA-AGAA-AAGAAAAAGAGCAAAATAGTGTAG-CATATGTCAAC
36437233 A
63 A
36437234 GTTATGTGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
72 7 0.12
73 20 0.36
74 29 0.52
ACGTcount: A:0.50, C:0.09, G:0.18, T:0.23
Consensus pattern (73 bp):
CATATTTCTAAAATATTTAAAAAAGAAAAGAAAAAGAGCAAAATAGTGTAGCATATGTCAACAAA
AGGAAGGT
Found at i:36443149 original size:31 final size:29
Alignment explanation
Indices: 36443075--36443155 Score: 98
Period size: 31 Copynumber: 2.8 Consensus size: 29
36443065 TTATTCGTAC
36443075 ATTT-AAAATTTAGTTC--TTA-TTTTTA
1 ATTTAAAAATTTAGTTCAATTATTTTTTA
*
36443100 TTTTAAATAATTTAGTTCAATTATTTTTTGA
1 ATTTAAA-AATTTAGTTCAATTATTTTTT-A
36443131 ATTTAAAAATTTATGTTCAATTATT
1 ATTTAAAAATTTA-GTTCAATTATT
36443156 AACACAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
25 3 0.06
26 2 0.04
27 10 0.21
29 3 0.06
30 11 0.23
31 18 0.38
ACGTcount: A:0.35, C:0.04, G:0.05, T:0.57
Consensus pattern (29 bp):
ATTTAAAAATTTAGTTCAATTATTTTTTA
Found at i:36459984 original size:2 final size:2
Alignment explanation
Indices: 36459966--36459999 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
36459956 CTACACATAC
* *
36459966 AT AT AC AT AT AT CT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
36460000 GTAGATAAGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36470190 original size:10 final size:9
Alignment explanation
Indices: 36470176--36470262 Score: 52
Period size: 10 Copynumber: 9.2 Consensus size: 9
36470166 TTTAAAATTT
36470176 TATAAAAAA
1 TATAAAAAA
36470185 TCATAAAAAA
1 T-ATAAAAAA
36470195 T-TAAAAATA
1 TATAAAAA-A
36470204 TATATAAAAA
1 TATA-AAAAA
*
36470214 TTAAAAAAAAA
1 -T-ATAAAAAA
* *
36470225 CATAATAAAT
1 TATAA-AAAA
*
36470235 TATATAAAA
1 TATAAAAAA
*
36470244 -ATAAAAAT
1 TATAAAAAA
*
36470252 TAAAAAAAA
1 TATAAAAAA
36470261 TA
1 TA
36470263 ATTTAAACCT
Statistics
Matches: 59, Mismatches: 11, Indels: 16
0.69 0.13 0.19
Matches are distributed among these distances:
8 12 0.20
9 17 0.29
10 18 0.31
11 10 0.17
12 2 0.03
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.25
Consensus pattern (9 bp):
TATAAAAAA
Found at i:36470198 original size:28 final size:29
Alignment explanation
Indices: 36470167--36470250 Score: 75
Period size: 31 Copynumber: 2.9 Consensus size: 29
36470157 TAAAACATAT
* * *
36470167 TTAAAATTTTATA-AAAAATCATAAAAAA
1 TTAAAAATATATATAAAAATCAAAAAAAA
*
36470195 TTAAAAATATATATAAAAATTAAAAAAAAA
1 TTAAAAATATATATAAAAA-TCAAAAAAAA
*
36470225 CATAATAAAT-TATATAAAAAT-AAAAA
1 -TTAA-AAATATATATAAAAATCAAAAA
36470251 TTAAAAAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 11 0.23
29 10 0.21
30 9 0.19
31 13 0.28
32 4 0.09
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (29 bp):
TTAAAAATATATATAAAAATCAAAAAAAA
Found at i:36470212 original size:19 final size:18
Alignment explanation
Indices: 36470178--36470221 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 18
36470168 TAAAATTTTA
36470178 TAAAAAATCATAAAAAAT
1 TAAAAAATCATAAAAAAT
36470196 TAAAAATAT-ATATAAAAAT
1 TAAAAA-ATCATA-AAAAAT
36470215 TAAAAAA
1 TAAAAAA
36470222 AAACATAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 10 0.42
19 14 0.58
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (18 bp):
TAAAAAATCATAAAAAAT
Found at i:36470222 original size:39 final size:37
Alignment explanation
Indices: 36470179--36470261 Score: 105
Period size: 39 Copynumber: 2.2 Consensus size: 37
36470169 AAAATTTTAT
36470179 AAAAAATCATAAAAAATTA-AAAATATATATAAAAATTAA
1 AAAAAATCATAAAAAATTATAAAA-A-A-ATAAAAATTAA
* * *
36470218 AAAAAAACATAATAAATTATATAAAAATAAAAATTAA
1 AAAAAATCATAAAAAATTATAAAAAAATAAAAATTAA
36470255 AAAAAAT
1 AAAAAAT
36470262 AATTTAAACC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 17 0.44
38 1 0.03
39 18 0.46
40 3 0.08
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (37 bp):
AAAAAATCATAAAAAATTATAAAAAAATAAAAATTAA
Found at i:36470249 original size:30 final size:28
Alignment explanation
Indices: 36470169--36470250 Score: 83
Period size: 30 Copynumber: 2.8 Consensus size: 28
36470159 AAACATATTT
* * * *
36470169 AAAATTTTATAAAAAATCATAAAAAATTA
1 AAAATTATAT-AAAAATAAAAAAAAAATA
36470198 AAAATATATATAAAAATTAAAAAAAAACATA
1 AAAAT-TATATAAAAA-TAAAAAAAAA-ATA
36470229 ATAAATTATATAAAAATAAAAA
1 A-AAATTATATAAAAATAAAAA
36470251 TTAAAAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
29 10 0.22
30 18 0.40
31 13 0.29
32 4 0.09
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (28 bp):
AAAATTATATAAAAATAAAAAAAAAATA
Found at i:36470263 original size:31 final size:32
Alignment explanation
Indices: 36470199--36470263 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 32
36470189 AAAAAATTAA
*
36470199 AAATATATATAAAAATTAAAAAAAAACATAAT
1 AAATATATATAAAAATTAAAAAAAAACAAAAT
36470231 AAAT-TATATAAAAA-TAAAAATTAAAA-AAAAT
1 AAATATATATAAAAATTAAAAA--AAAACAAAAT
36470262 AA
1 AA
36470264 TTTAAACCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 6 0.20
31 16 0.53
32 8 0.27
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.25
Consensus pattern (32 bp):
AAATATATATAAAAATTAAAAAAAAACAAAAT
Found at i:36470437 original size:20 final size:20
Alignment explanation
Indices: 36470412--36470450 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
36470402 AATGCTCTCC
36470412 TTTTTATTGATAAATTTTTA
1 TTTTTATTGATAAATTTTTA
**
36470432 TTTTTATTTTTAAATTTTT
1 TTTTTATTGATAAATTTTT
36470451 CATCTCCAGT
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:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (20 bp):
TTTTTATTGATAAATTTTTA
Found at i:36475422 original size:35 final size:34
Alignment explanation
Indices: 36475374--36475481 Score: 100
Period size: 33 Copynumber: 3.3 Consensus size: 34
36475364 TTTATTTATT
*
36475374 TAAA-AATTATA-ATTTAATCAAATTAAAATTTA
1 TAAATAATTATATAATTAATCAAATTAAAATTTA
*
36475406 TAAATAATTATATAATTATATCAAAATCAAAATTTA
1 TAAATAATTATATAATTA-ATC-AAATTAAAATTTA
* * ** *
36475442 T--AT-ATTAAATTACAAATTAAATTAAAATTTA
1 TAAATAATTATATAATTAATCAAATTAAAATTTA
36475473 TAAATAATT
1 TAAATAATT
36475482 TTGAAATTTA
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
31 13 0.21
32 6 0.10
33 17 0.28
34 9 0.15
35 3 0.05
36 13 0.21
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.41
Consensus pattern (34 bp):
TAAATAATTATATAATTAATCAAATTAAAATTTA
Found at i:36475786 original size:20 final size:19
Alignment explanation
Indices: 36475732--36475785 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
36475722 TGGTATTCTT
* *
36475732 TCATAATTTTTAGTATTTCC
1 TCATGATTTTTA-TATTCCC
*
36475752 TCATGTTTTCTTATATTCCC
1 TCATGATTT-TTATATTCCC
36475772 TCATGA-TTTTATAT
1 TCATGATTTTTATAT
36475786 ACATATAAGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 6 0.21
19 2 0.07
20 18 0.62
21 3 0.10
ACGTcount: A:0.22, C:0.17, G:0.06, T:0.56
Consensus pattern (19 bp):
TCATGATTTTTATATTCCC
Found at i:36484510 original size:20 final size:21
Alignment explanation
Indices: 36484477--36484515 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
36484467 TCTTACTTTT
*
36484477 ATTAAAAAGTGCATAACATCC
1 ATTAAAAAGCGCATAACATCC
*
36484498 ATTAAAAA-CGCATCACAT
1 ATTAAAAAGCGCATAACAT
36484516 ATCACATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.23
Consensus pattern (21 bp):
ATTAAAAAGCGCATAACATCC
Found at i:36486962 original size:18 final size:20
Alignment explanation
Indices: 36486918--36486962 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
36486908 CACTAGTATT
36486918 TTTTAAAAAAAATCATTCTA
1 TTTTAAAAAAAATCATTCTA
* *
36486938 TTATAAAAAAAATTA-TC-A
1 TTTTAAAAAAAATCATTCTA
36486956 TTTTAAA
1 TTTTAAA
36486963 CATTCAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 2 0.09
20 13 0.59
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (20 bp):
TTTTAAAAAAAATCATTCTA
Found at i:36495491 original size:21 final size:22
Alignment explanation
Indices: 36495467--36495525 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
36495457 GTTATTAAAT
* *
36495467 AAAATAATCATTTTATTT-TTA
1 AAAAAAATAATTTTATTTATTA
*
36495488 AAAAAAATAATTTTCTTTATTA
1 AAAAAAATAATTTTATTTATTA
**
36495510 AATAAATCTAATTTTA
1 AA-AAAAATAATTTTA
36495526 CCATTTCAAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
21 15 0.50
22 5 0.17
23 10 0.33
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (22 bp):
AAAAAAATAATTTTATTTATTA
Found at i:36501446 original size:123 final size:123
Alignment explanation
Indices: 36501227--36501612 Score: 553
Period size: 123 Copynumber: 3.1 Consensus size: 123
36501217 AACCCTTCGA
* * *
36501227 TTCAGGATGCTGCC-AAAAGGTGTCCCTATTTCTCCGTCGGGACCTAGTATGCGTACATCAAATC
1 TTCAGGATGCTACCTAAAA-GTGTGCCTATTCCTCCGTCGGGACCTAGTATGCGTACATCAAATC
36501291 CGCCTCCATCC-CCACCATCATTGACATCGACATCTTTGTCAATTTCAAAAAGTTTGAAC
65 CGCCTCCA-CCTCCACCATCATTGACATCGACATCTTTGTCAATTTCAAAAAGTTTGAAC
* * *
36501350 TTCAGGATGCTACCTAAAAGTGTGCCTATTCCTCCGTCGGGACCTAGTACGCATACATCATATCC
1 TTCAGGATGCTACCTAAAAGTGTGCCTATTCCTCCGTCGGGACCTAGTATGCGTACATCAAATCC
* * *
36501415 GCCTCCACCTCCATCATCATTGACACCGACATTTTTGTCAATTTCAAAAAGTTTGAAC
66 GCCTCCACCTCCACCATCATTGACATCGACATCTTTGTCAATTTCAAAAAGTTTGAAC
* * * * *
36501473 TTCGGGATGCTACCTAAAGGTGTGCCTATCCCTCCGTCAGGACCTAGTATGCGTACATCAGATCC
1 TTCAGGATGCTACCTAAAAGTGTGCCTATTCCTCCGTCGGGACCTAGTATGCGTACATCAAATCC
* * * * *
36501538 GCCTCCACCTCCACCATCATTGATATCAACTTCTTTGTCAATTT-TAAAGGTTTGAAC
66 GCCTCCACCTCCACCATCATTGACATCGACATCTTTGTCAATTTCAAAAAGTTTGAAC
*
36501595 TTCGGGATGCTACCTAAA
1 TTCAGGATGCTACCTAAA
36501613 GGTCCTCCAT
Statistics
Matches: 237, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
122 31 0.13
123 202 0.85
124 4 0.02
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (123 bp):
TTCAGGATGCTACCTAAAAGTGTGCCTATTCCTCCGTCGGGACCTAGTATGCGTACATCAAATCC
GCCTCCACCTCCACCATCATTGACATCGACATCTTTGTCAATTTCAAAAAGTTTGAAC
Found at i:36503899 original size:3 final size:3
Alignment explanation
Indices: 36503891--36503953 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
36503881 TACATAAAAA
36503891 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36503939 TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT
36503954 ATTCTGCCAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:36506641 original size:23 final size:22
Alignment explanation
Indices: 36506615--36506869 Score: 204
Period size: 23 Copynumber: 11.2 Consensus size: 22
36506605 ACACTAGCGC
36506615 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGATTAGCACT-TGTGT
36506638 GCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACT-TGTGT
*
36506663 GCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTT-GTGT
36506686 GCTCTCTGATTAGCACTT-TGT
1 GCTCTCTGATTAGCACTTGTGT
* *
36506707 G-TGCTC--AGTA-C-TTTGTGT
1 GCT-CTCTGATTAGCACTTGTGT
* *
36506725 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGATTAGCAC-TTGTGT
*
36506748 GCTCTCTG-TTGCCCAGCACTTATGT
1 GCTCTCTGATT----AGCACTTGTGT
*
36506773 GCTCTCTG-TTCAGTACTTCG-GT
1 GCTCTCTGATT-AGCACTT-GTGT
*
36506795 ACTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCTG--ATTAGCACT-TGTGT
*
36506820 GCTCTCCGATTAGCACTTCGTGT
1 GCTCTCTGATTAGCACTT-GTGT
36506843 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGATTAGCAC-TTGTGT
36506866 GCTC
1 GCTC
36506870 AGTACTTTGT
Statistics
Matches: 192, Mismatches: 17, Indels: 46
0.75 0.07 0.18
Matches are distributed among these distances:
17 2 0.01
18 7 0.04
19 4 0.02
20 3 0.02
21 8 0.04
22 20 0.10
23 87 0.45
24 8 0.04
25 48 0.25
26 5 0.03
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.41
Consensus pattern (22 bp):
GCTCTCTGATTAGCACTTGTGT
Found at i:36506686 original size:48 final size:46
Alignment explanation
Indices: 36506615--36506869 Score: 169
Period size: 48 Copynumber: 5.6 Consensus size: 46
36506605 ACACTAGCGC
*
36506615 GCTCTCTGATTAGCACTGTGTGTGCTCTCTGTTATTAGCACTGTGTGT
1 GCTCTCCGATTAGCACTGTGTGTGCTCTCTG--ATTAGCACTGTGTGT
*
36506663 GCTCTCCGATTAGCACT-TCGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCCGATTAGCACTGT-GTGTGCTCTCTGATTAGCACTGTGTGT
* * * * *
36506709 G--CT-C----AGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCCGATTAGCACTGTGTGTGCTCTCTGATTAGCACTGTGTGT
* * *
36506748 GCTCTCTG-TTGCCCAGCACT-TATGTGCTCTCTG-TTCAGTACT-TCG-GT
1 GCTCTCCGATT----AGCACTGTGTGTGCTCTCTGATT-AGCACTGT-GTGT
* * *
36506795 ACTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACT-TCGTGT
1 GCTCTCCG--ATTAGCACTGTGTGTGCTCTCTGATTAGCACTGT-GTGT
* *
36506843 GCTCTCTGATTAGCACTTTGTGTGCTC
1 GCTCTCCGATTAGCACTGTGTGTGCTC
36506870 AGTACTTTGT
Statistics
Matches: 171, Mismatches: 16, Indels: 42
0.75 0.07 0.18
Matches are distributed among these distances:
39 31 0.18
40 1 0.01
41 2 0.01
43 1 0.01
44 2 0.01
46 39 0.23
47 32 0.19
48 56 0.33
49 5 0.03
50 2 0.01
ACGTcount: A:0.13, C:0.25, G:0.22, T:0.41
Consensus pattern (46 bp):
GCTCTCCGATTAGCACTGTGTGTGCTCTCTGATTAGCACTGTGTGT
Found at i:36506741 original size:39 final size:39
Alignment explanation
Indices: 36506677--36506751 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
36506667 TCCGATTAGC
*
36506677 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
36506716 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
36506752 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:36506755 original size:62 final size:62
Alignment explanation
Indices: 36506658--36506846 Score: 175
Period size: 62 Copynumber: 2.9 Consensus size: 62
36506648 ATTAGCACTG
* * * *
36506658 TGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
1 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
*
36506720 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTG-TTGCCCAGCACTTATGTGCTCTCTGTTC
1 TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGATT----AGCACTT-TGTG-----TGCTC
36506784 AGTACTT
56 AGTACTT
* * * *
36506791 CG-GTACTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTC
1 TGTGTACTCTCTG-T-TTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTC
36506847 TCTGATTAGC
Statistics
Matches: 104, Mismatches: 10, Indels: 25
0.75 0.07 0.18
Matches are distributed among these distances:
61 2 0.02
62 32 0.31
63 4 0.04
65 7 0.07
66 4 0.04
68 3 0.03
69 7 0.07
70 10 0.10
71 13 0.12
72 20 0.19
73 2 0.02
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (62 bp):
TGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGTACTT
Found at i:36506844 original size:70 final size:68
Alignment explanation
Indices: 36506711--36506850 Score: 167
Period size: 70 Copynumber: 2.0 Consensus size: 68
36506701 CTTTGTGTGC
* * *
36506711 TCAGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCT
1 TCAGTACTTCGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCCGTT---CAGCACTTATGTGCT
36506776 CTCTGT
63 CTCTGT
*
36506782 TCAGTACTTCG-GTACTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATT-AGCACTTCGTGTGC
1 TCAGTACTTCGTGTACTCTCTG-T-TTAGCACTGTGTGTGCTCTCCG-TTCAGCACTT-ATGTGC
36506845 TCTCTG
62 TCTCTG
36506851 ATTAGCACTT
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
69 7 0.11
70 21 0.34
71 11 0.18
72 20 0.33
73 2 0.03
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.41
Consensus pattern (68 bp):
TCAGTACTTCGTGTACTCTCTGTTTAGCACTGTGTGTGCTCTCCGTTCAGCACTTATGTGCTCTC
TGT
Found at i:36506898 original size:39 final size:39
Alignment explanation
Indices: 36506834--36506908 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
36506824 TCCGATTAGC
*
36506834 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
36506873 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
36506909 TCTGTTGCCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:36506903 original size:23 final size:23
Alignment explanation
Indices: 36506868--36506961 Score: 86
Period size: 23 Copynumber: 4.0 Consensus size: 23
36506858 CTTTGTGTGC
*
36506868 TCAGTACTTTGTGTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
* *
36506891 TTAGCACTTTGTGTGCTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
36506914 TGCCCAGCACTTATGTG--CTCTCTGT
1 T---CAGCACTT-TGTGTACTCTCTGT
* *
36506939 TCAGTACTTCG-GTACTCTCTGT
1 TCAGCACTTTGTGTACTCTCTGT
36506961 T
1 T
36506962 TGTTCCGTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 13
0.76 0.08 0.17
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 16 0.27
23 21 0.36
25 9 0.15
26 7 0.12
27 4 0.07
ACGTcount: A:0.12, C:0.26, G:0.19, T:0.44
Consensus pattern (23 bp):
TCAGCACTTTGTGTACTCTCTGT
Found at i:36506925 original size:157 final size:157
Alignment explanation
Indices: 36506639--36506961 Score: 646
Period size: 157 Copynumber: 2.1 Consensus size: 157
36506629 ACTGTGTGTG
36506639 CTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTT
36506704 TGTGTGCTCAGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTT
66 TGTGTGCTCAGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTT
36506769 ATGTGCTCTCTGTTCAGTACTTCGGTA
131 ATGTGCTCTCTGTTCAGTACTTCGGTA
36506796 CTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTT
1 CTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTT
36506861 TGTGTGCTCAGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTT
66 TGTGTGCTCAGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTT
36506926 ATGTGCTCTCTGTTCAGTACTTCGGTA
131 ATGTGCTCTCTGTTCAGTACTTCGGTA
36506953 CTCTCTGTT
1 CTCTCTGTT
36506962 TGTTCCGTTT
Statistics
Matches: 166, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
157 166 1.00
ACGTcount: A:0.12, C:0.25, G:0.21, T:0.42
Consensus pattern (157 bp):
CTCTCTGTTATTAGCACTGTGTGTGCTCTCCGATTAGCACTTCGTGTGCTCTCTGATTAGCACTT
TGTGTGCTCAGTACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTCTCTGTTGCCCAGCACTT
ATGTGCTCTCTGTTCAGTACTTCGGTA
Found at i:36507914 original size:123 final size:123
Alignment explanation
Indices: 36507764--36508205 Score: 751
Period size: 123 Copynumber: 3.6 Consensus size: 123
36507754 AGGGGTGTTA
* ** *
36507764 CACCTCCACCATCATTGATATTGACATCTGTGTCAATTTCAAAAAGTTTGAACTTCGGGATGCTA
1 CACCTCCACCATCATTGACATCAACATCTTTGTCAATTTCAAAAAGTTTGAACTTCGGGATGCTA
* * *
36507829 CCTAAAGGTGTGCCTATTCCTCCGTCGGGACCTAGTGCGCGTACATCAGATTCGCCTC
66 CCTAAAGGTGTGCCTATTCCTCCGTCAGGACCTAGTACGCGTACATCAGATCCGCCTC
*
36507887 CACCTCCACCATCATTGACATCAACATCTTTGTCAATTTCGAAAAGTTTGAACTTCGGGATGCTA
1 CACCTCCACCATCATTGACATCAACATCTTTGTCAATTTCAAAAAGTTTGAACTTCGGGATGCTA
* *
36507952 CCTAAAGGTATACCTATTCCTCCGTCAGGACCTAGTACGCGTACATCAGATCCGCCTC
66 CCTAAAGGTGTGCCTATTCCTCCGTCAGGACCTAGTACGCGTACATCAGATCCGCCTC
* *
36508010 CACCTCCACCATCATTGACATCAACATCTTTGTTAATTTCAAAAAGCTTGAACTTCGGGATGCTA
1 CACCTCCACCATCATTGACATCAACATCTTTGTCAATTTCAAAAAGTTTGAACTTCGGGATGCTA
*
36508075 CCTAAAGGTGTGCCTATCCCTCCGTCAGGACCTAGTACGCGTACATCAGATCCGCCTC
66 CCTAAAGGTGTGCCTATTCCTCCGTCAGGACCTAGTACGCGTACATCAGATCCGCCTC
*
36508133 CACCTCCACCATCATTGACATCAACATCTTTGTCAATTTC-AAAGGTTTGAACTTCGGGATGCTA
1 CACCTCCACCATCATTGACATCAACATCTTTGTCAATTTCAAAAAGTTTGAACTTCGGGATGCTA
36508197 CCTAAAGGT
66 CCTAAAGGT
36508206 CCTCCATCGA
Statistics
Matches: 300, Mismatches: 19, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
122 31 0.10
123 269 0.90
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.28
Consensus pattern (123 bp):
CACCTCCACCATCATTGACATCAACATCTTTGTCAATTTCAAAAAGTTTGAACTTCGGGATGCTA
CCTAAAGGTGTGCCTATTCCTCCGTCAGGACCTAGTACGCGTACATCAGATCCGCCTC
Found at i:36515829 original size:20 final size:19
Alignment explanation
Indices: 36515786--36515829 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
36515776 ATTTATTTTA
36515786 ATAATATTATTTTTAAAAT
1 ATAATATTATTTTTAAAAT
*
36515805 TTAATATGTA-TTTTAATAAT
1 ATAATAT-TATTTTTAA-AAT
36515825 ATAAT
1 ATAAT
36515830 GTGTTTTACT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
ATAATATTATTTTTAAAAT
Found at i:36516306 original size:19 final size:17
Alignment explanation
Indices: 36516273--36516311 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
36516263 TTTTAAAAAC
36516273 TTTAAAAATTAAAAATA
1 TTTAAAAATTAAAAATA
36516290 TTTAAAAAGTATAAAAATA
1 TTTAAAAA-T-TAAAAATA
36516309 TTT
1 TTT
36516312 TCTAAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
19 11 0.55
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TTTAAAAATTAAAAATA
Found at i:36517374 original size:22 final size:20
Alignment explanation
Indices: 36517349--36517389 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
36517339 ACTATTTTTA
36517349 ATTTAATTTATGTATTATAATG
1 ATTTAATTT-TG-ATTATAATG
*
36517371 ATTTGATTTTGATTATAAT
1 ATTTAATTTTGATTATAAT
36517390 ATTAGAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 2 0.11
22 8 0.44
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
ATTTAATTTTGATTATAATG
Found at i:36520685 original size:17 final size:17
Alignment explanation
Indices: 36520639--36520692 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
36520629 TATTTCTTCA
36520639 ATTTA-ATGTATTATTT
1 ATTTATATGTATTATTT
* *
36520655 ATTTATTTTTATTATTT
1 ATTTATATGTATTATTT
36520672 -TTTATATGTAATTATCTT
1 ATTTATATGT-ATTAT-TT
36520690 ATT
1 ATT
36520693 GGGTAATCTA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
16 12 0.40
17 14 0.47
18 2 0.07
19 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.67
Consensus pattern (17 bp):
ATTTATATGTATTATTT
Found at i:36521234 original size:22 final size:22
Alignment explanation
Indices: 36521207--36521249 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
36521197 ACTTAAACAA
*
36521207 TTCACATCAATTATA-CACATAT
1 TTCACAT-AATTAAATCACATAT
36521229 TTCACATAATTAAATCACATA
1 TTCACATAATTAAATCACATA
36521250 AATTACTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (22 bp):
TTCACATAATTAAATCACATAT
Found at i:36528786 original size:9 final size:9
Alignment explanation
Indices: 36528772--36528797 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
36528762 TAATTTTCGA
36528772 ATTCGAATT
1 ATTCGAATT
36528781 ATTCGAATT
1 ATTCGAATT
36528790 ATTCGAAT
1 ATTCGAAT
36528798 AAACCGAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (9 bp):
ATTCGAATT
Found at i:36531887 original size:12 final size:12
Alignment explanation
Indices: 36531870--36531894 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
36531860 AGAAAATATT
36531870 AAAATAAAATGG
1 AAAATAAAATGG
36531882 AAAATAAAATGG
1 AAAATAAAATGG
36531894 A
1 A
36531895 GAGAAATGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (12 bp):
AAAATAAAATGG
Found at i:36532004 original size:21 final size:22
Alignment explanation
Indices: 36531970--36532024 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
36531960 AGTAGGAAGG
* *
36531970 AGTAAAATTTTTTGG-GAAAAA
1 AGTAAAAATATTTGGAGAAAAA
*
36531991 AGTAAAAATATTTGGAGTAAAA
1 AGTAAAAATATTTGGAGAAAAA
36532013 A-TATAAAATATT
1 AGTA-AAAATATT
36532025 ATAGTTTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 15 0.52
22 14 0.48
ACGTcount: A:0.53, C:0.00, G:0.15, T:0.33
Consensus pattern (22 bp):
AGTAAAAATATTTGGAGAAAAA
Found at i:36532682 original size:18 final size:18
Alignment explanation
Indices: 36532659--36532694 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
36532649 TGAAGCATCG
* *
36532659 TTTTAATTTTATTTATAT
1 TTTTAATATTATTCATAT
36532677 TTTTAATATTATTCATAT
1 TTTTAATATTATTCATAT
36532695 ATCTTTATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTTAATATTATTCATAT
Found at i:36540258 original size:20 final size:20
Alignment explanation
Indices: 36540230--36540267 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
36540220 AAAGTTCAAA
36540230 GGTTCAAAATTTTAGATTAC
1 GGTTCAAAATTTTAGATTAC
*
36540250 GGTTTAAAATTTTAGATT
1 GGTTCAAAATTTTAGATT
36540268 TTGGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.45
Consensus pattern (20 bp):
GGTTCAAAATTTTAGATTAC
Found at i:36544268 original size:28 final size:28
Alignment explanation
Indices: 36544237--36544291 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
36544227 GCTGCAGGGT
*
36544237 TTAATTA-ATTTTTAAAAAAATTTAAAGA
1 TTAATTAGAATTTTAAAAAAA-TTAAAGA
*
36544265 TTAATTAGAATTTTCAAAAAATTAAAG
1 TTAATTAGAATTTTAAAAAAATTAAAG
36544292 GGTCCAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.53, C:0.02, G:0.05, T:0.40
Consensus pattern (28 bp):
TTAATTAGAATTTTAAAAAAATTAAAGA
Found at i:36548611 original size:21 final size:21
Alignment explanation
Indices: 36548587--36548627 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
36548577 AGATTAATTA
*
36548587 TATAGATATATCCAACTTTTC
1 TATAGATATATACAACTTTTC
*
36548608 TATAGATATATAGAACTTTT
1 TATAGATATATACAACTTTT
36548628 ATCAGCAATT
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:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (21 bp):
TATAGATATATACAACTTTTC
Found at i:36549960 original size:9 final size:9
Alignment explanation
Indices: 36549925--36549976 Score: 52
Period size: 11 Copynumber: 5.4 Consensus size: 9
36549915 CGTTCCTGCC
36549925 TTATCTTTAT
1 TTAT-TTTAT
36549935 CTTATTTATAT
1 -TTATTT-TAT
36549946 TCTATTTTAT
1 T-TATTTTAT
36549956 TTA-TTTAT
1 TTATTTTAT
*
36549964 TTTTTTTAT
1 TTATTTTAT
36549973 TTAT
1 TTAT
36549977 CCATCTTCCA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
8 7 0.19
9 10 0.28
10 7 0.19
11 12 0.33
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (9 bp):
TTATTTTAT
Found at i:36549966 original size:13 final size:13
Alignment explanation
Indices: 36549943--36549976 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
36549933 ATCTTATTTA
36549943 TATTCTATTTTATT
1 TATT-TATTTTATT
*
36549957 TATTTATTTTTTT
1 TATTTATTTTATT
36549970 TATTTAT
1 TATTTAT
36549977 CCATCTTCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTATTTTATT
Found at i:36550645 original size:6 final size:6
Alignment explanation
Indices: 36550634--36550663 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
36550624 CTTTAAAACA
36550634 AATCCT AATCCT AATCCT AATCCT AATCCT
1 AATCCT AATCCT AATCCT AATCCT AATCCT
36550664 GCTTCCTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (6 bp):
AATCCT
Found at i:36557907 original size:17 final size:17
Alignment explanation
Indices: 36557863--36557958 Score: 51
Period size: 17 Copynumber: 5.6 Consensus size: 17
36557853 ATATAATTTT
36557863 TAAAAAATATA-AT-AA
1 TAAAAAATATATATAAA
36557878 TAAATTTAAATATATATAAA
1 TAAA---AAATATATATAAA
*
36557898 TAAAAAATAT-TGTTGACAA
1 TAAAAAATATAT-AT-A-AA
*
36557917 TAAATAATATATA-AAA
1 TAAAAAATATATATAAA
*
36557933 TTTAAAAATATATA-AAA
1 -TAAAAAATATATATAAA
*
36557950 -AATAAATAT
1 TAAAAAATAT
36557959 TTTCAAAAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
15 11 0.17
16 3 0.05
17 22 0.34
18 8 0.12
19 13 0.20
20 7 0.11
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (17 bp):
TAAAAAATATATATAAA
Found at i:36557922 original size:51 final size:48
Alignment explanation
Indices: 36557832--36557985 Score: 172
Period size: 51 Copynumber: 3.1 Consensus size: 48
36557822 CCTATTTTAA
*
36557832 AAATTCAAAAATATATAAAAAATATAAT-TTTT-AAAAAATATAATAAT
1 AAATTTAAAAATATATAAAAAATA-AATATTTTCAAAAAATATAATAAT
* * *
36557879 AAATTTAAATATATATAAATAAA-AAATATTGTTGACAATAA-ATAATATAT
1 AAATTTAAAAATATATAAA-AAATAAATATT-TTCA-AAAAATATAATA-AT
36557929 AAAATTTAAAAATATATAAAAAATAAATATTTTCAAAAAATATATGATAAT
1 -AAATTTAAAAATATATAAAAAATAAATATTTTCAAAAAATATA--ATAAT
36557980 AAATTT
1 AAATTT
36557986 TATATTAATA
Statistics
Matches: 90, Mismatches: 6, Indels: 19
0.78 0.05 0.17
Matches are distributed among these distances:
46 3 0.03
47 20 0.22
48 5 0.06
49 11 0.12
50 21 0.23
51 27 0.30
52 3 0.03
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (48 bp):
AAATTTAAAAATATATAAAAAATAAATATTTTCAAAAAATATAATAAT
Found at i:36559313 original size:22 final size:22
Alignment explanation
Indices: 36559281--36559322 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
36559271 AACCATGAAA
*
36559281 AAAAACCCTCAAGTATCAAACT
1 AAAAACACTCAAGTATCAAACT
*
36559303 AAAAACACTCAAGTTTCAAA
1 AAAAACACTCAAGTATCAAA
36559323 TTGAACATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.52, C:0.24, G:0.05, T:0.19
Consensus pattern (22 bp):
AAAAACACTCAAGTATCAAACT
Found at i:36561389 original size:22 final size:22
Alignment explanation
Indices: 36561364--36561405 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
36561354 AAGCAGTGAG
*
36561364 AAAACAACAATAAAATAATAGC
1 AAAACAACAAGAAAATAATAGC
**
36561386 AAAACAGTAAGAAAATAATA
1 AAAACAACAAGAAAATAATA
36561406 TTTTTTTGTC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.69, C:0.10, G:0.07, T:0.14
Consensus pattern (22 bp):
AAAACAACAAGAAAATAATAGC
Found at i:36562098 original size:16 final size:16
Alignment explanation
Indices: 36562079--36562124 Score: 65
Period size: 16 Copynumber: 2.9 Consensus size: 16
36562069 AATATAATGA
*
36562079 AATATAGTTGTAATAG
1 AATAAAGTTGTAATAG
*
36562095 AATAAAGTTGTAATGG
1 AATAAAGTTGTAATAG
*
36562111 AATAGAGTTGTAAT
1 AATAAAGTTGTAAT
36562125 TAGTAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (16 bp):
AATAAAGTTGTAATAG
Found at i:36562188 original size:44 final size:45
Alignment explanation
Indices: 36562103--36562192 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 45
36562093 AGAATAAAGT
* *
36562103 TGTAATGGAATAGAGTTGTAATTAGTAATTCATTGTTTGGTTGAA
1 TGTAATGAAATAGAATTGTAATTAGTAATTCATTGTTTGGTTGAA
36562148 TGTAATGAAATAGAATTGTAA-TAGT-ATT-ATTGTGTTTGGTTGAA
1 TGTAATGAAATAGAATTGTAATTAGTAATTCA-T-TGTTTGGTTGAA
36562192 T
1 T
36562193 AGAATAGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
42 1 0.02
43 4 0.10
44 17 0.41
45 19 0.46
ACGTcount: A:0.32, C:0.01, G:0.23, T:0.43
Consensus pattern (45 bp):
TGTAATGAAATAGAATTGTAATTAGTAATTCATTGTTTGGTTGAA
Found at i:36562318 original size:26 final size:24
Alignment explanation
Indices: 36562275--36562326 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 24
36562265 AATTATTGTT
36562275 ATTATTATTAAATTTTTAA-AAAA
1 ATTATTATTAAATTTTTAATAAAA
36562298 ATTATTATTAAATATAATTTAATAAAA
1 ATTATTATTAAAT-T--TTTAATAAAA
36562325 AT
1 AT
36562327 AAAATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
23 13 0.52
24 1 0.04
26 5 0.20
27 6 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATTATTATTAAATTTTTAATAAAA
Found at i:36562644 original size:81 final size:82
Alignment explanation
Indices: 36562513--36562666 Score: 231
Period size: 83 Copynumber: 1.9 Consensus size: 82
36562503 TGCTCTCTCT
* * * *
36562513 CACTTTGAAAGATGAACCGTTCATTTTTTTTTTCTAGAAAATTATCTTCTCTAATTTCTTTTTTT
1 CACTTTGAAAGATGAACCGTTCATTCTTTTTTTCTAAAAAATCATCTTCTCTAATTTC-CTTTTT
*
36562578 AATTCAAACTCTCCCTCA
65 AAATCAAACTCTCCCTCA
*
36562596 CACTTTGAAATATGAACCGTTCA-TCTTTTTTTC-AAAAAATCATCTTCTCTAATTTCCTTTTTA
1 CACTTTGAAAGATGAACCGTTCATTCTTTTTTTCTAAAAAATCATCTTCTCTAATTTCCTTTTTA
36562659 AATCAAAC
66 AATCAAAC
36562667 GGAATGTTCA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
80 13 0.20
81 21 0.32
82 9 0.14
83 22 0.34
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (82 bp):
CACTTTGAAAGATGAACCGTTCATTCTTTTTTTCTAAAAAATCATCTTCTCTAATTTCCTTTTTA
AATCAAACTCTCCCTCA
Found at i:36563594 original size:18 final size:18
Alignment explanation
Indices: 36563571--36563606 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
36563561 TCATAAGATT
36563571 ACCATGTTCGAACAATGA
1 ACCATGTTCGAACAATGA
36563589 ACCATGTTCGAACAATGA
1 ACCATGTTCGAACAATGA
36563607 GCTCATTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (18 bp):
ACCATGTTCGAACAATGA
Found at i:36564265 original size:2 final size:2
Alignment explanation
Indices: 36564258--36564288 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
36564248 AATACTTAAA
36564258 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
36564289 GTATATATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:36570544 original size:25 final size:26
Alignment explanation
Indices: 36570494--36570544 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
36570484 AAAACTCGAA
*
36570494 TTTAAATATTCGAAAAAATAATTTTT
1 TTTAAATATTCGAAAAAATAAATTTT
*
36570520 TTTAAATATT-GAAAAATTAAATTTT
1 TTTAAATATTCGAAAAAATAAATTTT
36570545 AAACATAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (26 bp):
TTTAAATATTCGAAAAAATAAATTTT
Found at i:36578570 original size:16 final size:16
Alignment explanation
Indices: 36578538--36578572 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
36578528 TAGTAATTCC
**
36578538 ATTTACTTCAAGTTTA
1 ATTTACTTCAAAATTA
36578554 ATTTACTTCAAAATTA
1 ATTTACTTCAAAATTA
36578570 ATT
1 ATT
36578573 ATTTAGTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.49
Consensus pattern (16 bp):
ATTTACTTCAAAATTA
Found at i:36587750 original size:20 final size:20
Alignment explanation
Indices: 36587728--36587791 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
36587718 TTTAGAATTT
*
36587728 TTTTTATAAA-TATTTTGAA
1 TTTTTAAAAATTATTTTGAA
*
36587747 -TTTTAAAAATTATTTTCAA
1 TTTTTAAAAATTATTTTGAA
36587766 TTTTTAAAAATTATTTTGTAA
1 TTTTTAAAAATTATTTTG-AA
36587787 TTTTT
1 TTTTT
36587792 GTTAAGAGAA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
18 8 0.21
19 8 0.21
20 16 0.41
21 7 0.18
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTAAAAATTATTTTGAA
Found at i:36591571 original size:18 final size:18
Alignment explanation
Indices: 36591548--36591583 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
36591538 CTCATATTTA
*
36591548 CTCATACTGATGGTTTGT
1 CTCATACTGATGATTTGT
36591566 CTCATACTGATGATTTGT
1 CTCATACTGATGATTTGT
36591584 TTTACCCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.17, G:0.19, T:0.44
Consensus pattern (18 bp):
CTCATACTGATGATTTGT
Found at i:36593804 original size:15 final size:16
Alignment explanation
Indices: 36593772--36593806 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
36593762 TGCATGGATT
*
36593772 AATTTTTAATAGATAA
1 AATTTTTAATAGAAAA
36593788 AATTTTTAATA-AAAA
1 AATTTTTAATAGAAAA
36593803 AATT
1 AATT
36593807 AAATTACTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AATTTTTAATAGAAAA
Found at i:36593862 original size:31 final size:30
Alignment explanation
Indices: 36593790--36593891 Score: 82
Period size: 31 Copynumber: 3.3 Consensus size: 30
36593780 ATAGATAAAA
36593790 TTTTT-AATAAAAAAATTAAATTACTCTTT
1 TTTTTAAATAAAAAAATTAAATTACTCTTT
** * * *
36593819 GATCTAATATAAAAGAATTAATTTACTCATTT
1 TTTTTAA-ATAAAAAAATTAAATTACTC-TTT
*
36593851 TTTTTAAATAAAAAAGA-TAAAATACAATCATTT
1 TTTTTAAATAAAAAA-ATTAAATTAC--TC-TTT
36593884 TTTTTAAA
1 TTTTTAAA
36593892 ATAACGGAGA
Statistics
Matches: 56, Mismatches: 11, Indels: 8
0.75 0.15 0.11
Matches are distributed among these distances:
29 2 0.04
30 1 0.02
31 31 0.55
32 8 0.14
33 14 0.25
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (30 bp):
TTTTTAAATAAAAAAATTAAATTACTCTTT
Found at i:36600018 original size:20 final size:19
Alignment explanation
Indices: 36599993--36600049 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 19
36599983 TATATTACAG
*
36599993 ATATTTATATTTTTAATAAT
1 ATATTTATATTTTT-ATAAA
36600013 ATATTTATAGGTTTTT-TAAA
1 ATATTTATA--TTTTTATAAA
*
36600033 ATACTTATATTTTTATA
1 ATATTTATATTTTTATA
36600050 CATTAATCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 5 0.16
19 2 0.06
20 20 0.62
22 5 0.16
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
ATATTTATATTTTTATAAA
Found at i:36601611 original size:2 final size:2
Alignment explanation
Indices: 36601604--36601632 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
36601594 ATATCATTTC
36601604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36601633 AGAGAGAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36601638 original size:2 final size:2
Alignment explanation
Indices: 36601633--36601658 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
36601623 TATATATATA
36601633 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
36601659 GTGTATAATT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:36601761 original size:6 final size:6
Alignment explanation
Indices: 36601750--36601783 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
36601740 ATGAGTTGGA
36601750 AGGAGT AGGAGT AGGAGT AGGAGT AGGAGT AGGA
1 AGGAGT AGGAGT AGGAGT AGGAGT AGGAGT AGGA
36601784 AGATAGATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.50, T:0.15
Consensus pattern (6 bp):
AGGAGT
Found at i:36604388 original size:2 final size:2
Alignment explanation
Indices: 36604381--36604407 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36604371 CTAATATACG
36604381 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
36604408 AAAGCATGAG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36606476 original size:23 final size:22
Alignment explanation
Indices: 36606450--36606500 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
36606440 TTTTTGAAAA
*
36606450 ATTAAAATATAATTTTATTATAT
1 ATTAAAATATAATTTCATTAT-T
**
36606473 ATTAATTTATAATTTCATTATT
1 ATTAAAATATAATTTCATTATT
36606495 -TTAAAA
1 ATTAAAA
36606501 AAATTAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 4 0.17
22 1 0.04
23 18 0.78
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTAAAATATAATTTCATTATT
Found at i:36608734 original size:49 final size:49
Alignment explanation
Indices: 36608676--36608769 Score: 179
Period size: 49 Copynumber: 1.9 Consensus size: 49
36608666 ATAAACAAGC
36608676 ATAAATAAATAAAAATTAAACTATTTGTAAATTGTTGATTGAAAGCTCT
1 ATAAATAAATAAAAATTAAACTATTTGTAAATTGTTGATTGAAAGCTCT
*
36608725 ATAAATAAATAAAAATTGAACTATTTGTAAATTGTTGATTGAAAG
1 ATAAATAAATAAAAATTAAACTATTTGTAAATTGTTGATTGAAAG
36608770 TTAGATTCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (49 bp):
ATAAATAAATAAAAATTAAACTATTTGTAAATTGTTGATTGAAAGCTCT
Found at i:36608896 original size:9 final size:9
Alignment explanation
Indices: 36608882--36608911 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
36608872 ATCTAAAAGC
36608882 AATTTTTAA
1 AATTTTTAA
36608891 AA-TTTTAA
1 AATTTTTAA
36608899 AATTTTTAA
1 AATTTTTAA
36608908 AATT
1 AATT
36608912 AAGTAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
AATTTTTAA
Found at i:36609749 original size:19 final size:19
Alignment explanation
Indices: 36609708--36609749 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
36609698 TATATATTTT
*
36609708 ATTTAAATTCGATTTCAAC
1 ATTTAAATTCGATTTCAAA
*
36609727 ATTTAAATT-GATATTTAAA
1 ATTTAAATTCGAT-TTCAAA
36609746 ATTT
1 ATTT
36609750 TAAAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.40, C:0.07, G:0.05, T:0.48
Consensus pattern (19 bp):
ATTTAAATTCGATTTCAAA
Found at i:36609749 original size:27 final size:27
Alignment explanation
Indices: 36609719--36609776 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
36609709 TTTAAATTCG
* * *
36609719 ATTTCAACATTTAAATTGATATTTAAA
1 ATTTCAAAATTTAAATTAATATCTAAA
* *
36609746 ATTTTAAAATTTAATTTAATATCTAAA
1 ATTTCAAAATTTAAATTAATATCTAAA
36609773 ATTT
1 ATTT
36609777 ATTCGAGTTC
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:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTTCAAAATTTAAATTAATATCTAAA
Found at i:36610554 original size:33 final size:31
Alignment explanation
Indices: 36610488--36610558 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 31
36610478 CCTTCACCTT
36610488 CTCATATGGATACTTCCCCTCATTCTGAGAACC
1 CTCATATGGATACTTCCCCTCA-T-TGAGAACC
*
36610521 CTCATATGGATACTACTCCCCCTCA-TGATAACC
1 CTCATATGGATACT--T-CCCCTCATTGAGAACC
36610554 CTCAT
1 CTCAT
36610559 GACATGGGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
33 26 0.76
35 1 0.03
36 7 0.21
ACGTcount: A:0.25, C:0.35, G:0.10, T:0.30
Consensus pattern (31 bp):
CTCATATGGATACTTCCCCTCATTGAGAACC
Found at i:36615499 original size:21 final size:21
Alignment explanation
Indices: 36615475--36615514 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36615465 CTTTCTTTTG
36615475 TTCT-CTTCAAAGATATAATTA
1 TTCTACTTCAAA-ATATAATTA
*
36615496 TTCTACTTTAAAATATAAT
1 TTCTACTTCAAAATATAAT
36615515 AAACTAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.40, C:0.12, G:0.03, T:0.45
Consensus pattern (21 bp):
TTCTACTTCAAAATATAATTA
Found at i:36616574 original size:36 final size:35
Alignment explanation
Indices: 36616473--36616582 Score: 130
Period size: 36 Copynumber: 3.1 Consensus size: 35
36616463 ATACCTTAAT
*
36616473 TGGAGTAACGGTTAAAGTTCTTATCTGACATCTAGA
1 TGGAGT-ACGGTTAAAGTTCTTATCTGACATATAGA
* * * * *
36616509 TGGAGTCACGATTATAGTTATCATTTGACATATAGA
1 TGGAGT-ACGGTTAAAGTTCTTATCTGACATATAGA
*
36616545 TGGAGTATCGGTTAAAGTTCTTATCTGACATTTAGA
1 TGGAGTA-CGGTTAAAGTTCTTATCTGACATATAGA
36616581 TG
1 TG
36616583 ACACAAGTTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
35 1 0.02
36 59 0.98
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.36
Consensus pattern (35 bp):
TGGAGTACGGTTAAAGTTCTTATCTGACATATAGA
Found at i:36616756 original size:6 final size:6
Alignment explanation
Indices: 36616745--36616773 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
36616735 TCTATCACCC
36616745 TGGTCA TGGTCA TGGTCA TGGTCA TGGTC
1 TGGTCA TGGTCA TGGTCA TGGTCA TGGTC
36616774 TTGGCATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.17, G:0.34, T:0.34
Consensus pattern (6 bp):
TGGTCA
Found at i:36623417 original size:16 final size:16
Alignment explanation
Indices: 36623373--36623422 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
36623363 GTTTTAATTT
*
36623373 TTTTGGATCATTTTAAG
1 TTTT-GATCATTTTAGG
*
36623390 -TTTGAATGATTTTAGG
1 TTTTG-ATCATTTTAGG
36623406 TTTTGATCA-TTTAGG
1 TTTTGATCATTTTAGG
36623421 TT
1 TT
36623423 GTTTTAAGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 9 0.32
16 15 0.54
17 4 0.14
ACGTcount: A:0.22, C:0.04, G:0.20, T:0.54
Consensus pattern (16 bp):
TTTTGATCATTTTAGG
Found at i:36636883 original size:20 final size:19
Alignment explanation
Indices: 36636858--36636897 Score: 71
Period size: 20 Copynumber: 2.1 Consensus size: 19
36636848 TATTAATAAA
36636858 ATATATTTTAATTAATATTT
1 ATATATTTTAATTAA-ATTT
36636878 ATATATTTTAATTAAATTT
1 ATATATTTTAATTAAATTT
36636897 A
1 A
36636898 AATTTAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
ATATATTTTAATTAAATTT
Found at i:36637150 original size:3 final size:3
Alignment explanation
Indices: 36637142--36637175 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
36637132 ATATAAAGTG
*
36637142 TGA TGA TGA TGA TGA TGA TGA TGA TAA TGA TGA T
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA T
36637176 ATGGGACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.29, T:0.35
Consensus pattern (3 bp):
TGA
Found at i:36637663 original size:22 final size:22
Alignment explanation
Indices: 36637616--36637666 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
36637606 TTATATAGAT
* *
36637616 AAAAAAATTTATTTTAATTTTT
1 AAAAAAATTTATTTTAATATTG
*
36637638 AAAAATAA-TTATTTTCATATTG
1 AAAAA-AATTTATTTTAATATTG
36637660 AAAAAAA
1 AAAAAAA
36637667 ATATAATTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 21 0.84
23 2 0.08
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
AAAAAAATTTATTTTAATATTG
Found at i:36637962 original size:3 final size:3
Alignment explanation
Indices: 36637954--36638015 Score: 117
Period size: 3 Copynumber: 21.0 Consensus size: 3
36637944 AGTTGAATGA
36637954 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
36638002 AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT
36638016 TTTAAAAACC
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 56 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:36644509 original size:15 final size:15
Alignment explanation
Indices: 36644489--36644533 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
36644479 AAAAAATATT
36644489 ATAAAAATAAAAATG
1 ATAAAAATAAAAATG
* *
36644504 ATAAAAATGAAATTG
1 ATAAAAATAAAAATG
*
36644519 ATATAAAAAAAAAAT
1 ATA-AAAATAAAAAT
36644534 TCATGTCAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (15 bp):
ATAAAAATAAAAATG
Found at i:36650067 original size:36 final size:36
Alignment explanation
Indices: 36649999--36650067 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
36649989 CGAAATAATA
* * *
36649999 TGAAAACTGTGAAGAAAGCATAGACGGAGGTAAGGC
1 TGAAAACTATGAAGAAAGCATAAACAGAGGTAAGGC
36650035 TGAAAACTATGAAGAAAGCATGAAACAG-GGTAA
1 TGAAAACTATGAAGAAAGCAT-AAACAGAGGTAA
36650068 TGAGCCATGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 25 0.86
37 4 0.14
ACGTcount: A:0.46, C:0.10, G:0.29, T:0.14
Consensus pattern (36 bp):
TGAAAACTATGAAGAAAGCATAAACAGAGGTAAGGC
Found at i:36666038 original size:64 final size:61
Alignment explanation
Indices: 36665937--36666074 Score: 161
Period size: 63 Copynumber: 2.2 Consensus size: 61
36665927 ATGTATTAGG
* * *
36665937 GTTAATTTTGTTGAATTTTTTAGAATTAGGACTAAATTGATAGAATCTATAAATATTGTAGAA
1 GTTAAATTTGTTAAATTTTTTAGAATTAAGACTAAATTGATA-AATCTATAAATATTGTAG-A
* * * *
36666000 GTTAAATTTGTTAAATTTTTTTAGAATTAAGA-TGAAATTGATAAATTTGTAATTATTTTAGA
1 GTTAAATTTGTTAAA-TTTTTTAGAATTAAGACT-AAATTGATAAATCTATAAATATTGTAGA
*
36666062 GCTAAATTTGTTA
1 GTTAAATTTGTTA
36666075 TTATGTAAAT
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
62 13 0.20
63 28 0.43
64 24 0.37
ACGTcount: A:0.38, C:0.02, G:0.14, T:0.46
Consensus pattern (61 bp):
GTTAAATTTGTTAAATTTTTTAGAATTAAGACTAAATTGATAAATCTATAAATATTGTAGA
Found at i:36674758 original size:3 final size:3
Alignment explanation
Indices: 36674750--36674787 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
36674740 ACAAGAAACA
36674750 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
36674788 ACTCACTGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:36677668 original size:28 final size:29
Alignment explanation
Indices: 36677623--36677708 Score: 79
Period size: 27 Copynumber: 2.9 Consensus size: 29
36677613 AAAATAATGT
*
36677623 TAAAATCATTATATAAAAATTTTT-AATAAA
1 TAAAAT-AATATATAAAAATTTTTAAAT-AA
* *
36677653 TAAAA-AATATAT-AAAATTATTAAATAT
1 TAAAATAATATATAAAAATTTTTAAATAA
36677680 TAAAATAATATAATATAAATATTTTTAAA
1 TAAAATAATAT-ATA-AAA-ATTTTTAAA
36677709 AAAATTAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
27 14 0.30
28 14 0.30
29 2 0.04
30 5 0.11
31 3 0.07
32 8 0.17
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAATAATATATAAAAATTTTTAAATAA
Found at i:36679239 original size:9 final size:9
Alignment explanation
Indices: 36679225--36679249 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
36679215 TCTCCTTTCA
36679225 TCTTCTTGT
1 TCTTCTTGT
36679234 TCTTCTTGT
1 TCTTCTTGT
36679243 TCTTCTT
1 TCTTCTT
36679250 CCTCTCTGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.24, G:0.08, T:0.68
Consensus pattern (9 bp):
TCTTCTTGT
Found at i:36680517 original size:3 final size:3
Alignment explanation
Indices: 36680511--36680540 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
36680501 TTCACTTTCC
*
36680511 TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
36680541 CTCCACCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:36688636 original size:2 final size:2
Alignment explanation
Indices: 36688629--36688658 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
36688619 TTTATAAGTT
36688629 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
36688659 AGGAATGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36690783 original size:14 final size:14
Alignment explanation
Indices: 36690764--36690824 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
36690754 CTTCCTTGGA
36690764 TTAAATTATTAAAT
1 TTAAATTATTAAAT
36690778 TTAAATTATTAAA-
1 TTAAATTATTAAAT
36690791 -TAAATTA--AAAT
1 TTAAATTATTAAAT
* **
36690802 TAAAAAAATTAAAT
1 TTAAATTATTAAAT
36690816 TATAAATTA
1 T-TAAATTA
36690825 AAGGGGTCAG
Statistics
Matches: 36, Mismatches: 6, Indels: 9
0.71 0.12 0.18
Matches are distributed among these distances:
10 3 0.08
12 11 0.31
14 18 0.50
15 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTAAATTATTAAAT
Found at i:36690804 original size:23 final size:22
Alignment explanation
Indices: 36690763--36690805 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
36690753 ACTTCCTTGG
* *
36690763 ATTAAATTATTAAATTTAAATT
1 ATTAAATAATTAAAATTAAATT
36690785 ATTAAATAAATTAAAATTAAA
1 ATTAAAT-AATTAAAATTAAA
36690806 AAAATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTAAATAATTAAAATTAAATT
Found at i:36690805 original size:15 final size:15
Alignment explanation
Indices: 36690785--36690826 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
36690775 AATTTAAATT
36690785 ATTAAATAAATTAAA
1 ATTAAATAAATTAAA
*
36690800 ATTAAAAAAATT-AA
1 ATTAAATAAATTAAA
36690814 ATT--ATAAATTAAA
1 ATTAAATAAATTAAA
36690827 GGGGTCAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 6 0.25
13 2 0.08
14 5 0.21
15 11 0.46
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
ATTAAATAAATTAAA
Found at i:36696529 original size:18 final size:18
Alignment explanation
Indices: 36696506--36696557 Score: 59
Period size: 18 Copynumber: 2.9 Consensus size: 18
36696496 ACCCCATCTG
* *
36696506 GAGTAATCACTAGGTCTA
1 GAGTAATCACTAGGCCGA
* *
36696524 GAGTAATCGCTAGGCCGG
1 GAGTAATCACTAGGCCGA
*
36696542 GAGTAATCACTGGGCC
1 GAGTAATCACTAGGCC
36696558 TATTACCCCA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.27, C:0.21, G:0.31, T:0.21
Consensus pattern (18 bp):
GAGTAATCACTAGGCCGA
Found at i:36702061 original size:17 final size:17
Alignment explanation
Indices: 36702039--36702077 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
36702029 AGGTGGAGAA
* *
36702039 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
36702056 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
36702073 CTTGT
1 CTTGT
36702078 CAAGGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Done.