Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011967.1 Kokia drynarioides strain JFW-HI SEQ_126965, whole genome shotgun sequence
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: 269595
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Warning! 80 characters in sequence are not A, C, G, or T
Found at i:129 original size:21 final size:21
Alignment explanation
Indices: 90--129 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
80 AATATCTAAA
* *
90 ATAAAAATATTTATTATAATT
1 ATAAAAATATTAATAATAATT
*
111 ATAAATATATTAATAATAA
1 ATAAAAATATTAATAATAA
130 ATGTTTTGTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAAAATATTAATAATAATT
Found at i:4664 original size:29 final size:30
Alignment explanation
Indices: 4599--4710 Score: 140
Period size: 30 Copynumber: 3.8 Consensus size: 30
4589 TAAAAAACAA
* *
4599 TCCTACAGA-CACTTGAAAATGTGGGGGGCA
1 TCCTACA-ACCACTTGAAAATGTAGGGGGCG
4629 TCCTACAACCACTTGAAAATGT-GGGGGCG
1 TCCTACAACCACTTGAAAATGTAGGGGGCG
* * *
4658 TCCTACAACCACTTAAAAAT-TCAGGAGGTG
1 TCCTACAACCACTTGAAAATGT-AGGGGGCG
4688 TCCTACAACCACTTGAAAATGTA
1 TCCTACAACCACTTGAAAATGTA
4711 AGGGTGTCTT
Statistics
Matches: 73, Mismatches: 5, Indels: 8
0.85 0.06 0.09
Matches are distributed among these distances:
28 1 0.01
29 26 0.36
30 45 0.62
31 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.22
Consensus pattern (30 bp):
TCCTACAACCACTTGAAAATGTAGGGGGCG
Found at i:9247 original size:11 final size:11
Alignment explanation
Indices: 9226--9263 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
9216 ATTTCTAATC
9226 TAATT-AAATA
1 TAATTAAAATA
9236 TAATTAAAATA
1 TAATTAAAATA
9247 TAATTATAAAGTA
1 TAATTA-AAA-TA
9260 TAAT
1 TAAT
9264 AATGCTCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 5 0.20
11 11 0.44
12 3 0.12
13 6 0.24
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (11 bp):
TAATTAAAATA
Found at i:9261 original size:13 final size:12
Alignment explanation
Indices: 9230--9263 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
9220 CTAATCTAAT
9230 TAAATATAATTA
1 TAAATATAATTA
9242 -AAATATAATTA
1 TAAATATAATTA
9253 TAAAGTATAAT
1 TAAA-TATAAT
9264 AATGCTCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 11 0.55
12 3 0.15
13 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (12 bp):
TAAATATAATTA
Found at i:10092 original size:34 final size:37
Alignment explanation
Indices: 10054--10125 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 37
10044 TTTCAAACTT
10054 GAGTAC-TCATGCTCT-TTTTCTT-T-TTTTTCTTTTG
1 GAGTACAT-ATGCTCTATTTTCTTCTCTTTTTCTTTTG
*
10088 GAGTACATATGCTCTATTTTTTTCTCTTTTTCTTTTG
1 GAGTACATATGCTCTATTTTCTTCTCTTTTTCTTTTG
10125 G
1 G
10126 CTTAATATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
34 13 0.39
35 7 0.21
36 1 0.03
37 12 0.36
ACGTcount: A:0.11, C:0.17, G:0.12, T:0.60
Consensus pattern (37 bp):
GAGTACATATGCTCTATTTTCTTCTCTTTTTCTTTTG
Found at i:10228 original size:30 final size:30
Alignment explanation
Indices: 10137--10292 Score: 112
Period size: 28 Copynumber: 5.3 Consensus size: 30
10127 TTAATATAAT
*
10137 ATTTGGTACTTGAACTTGACATTTTTTCTTA
1 ATTTGGTACTTGAACTTGACA-TTTTTCCTA
* * *
10168 ATTTGATACTTAAACTT---TTTTTTACCTA
1 ATTTGGTACTTGAACTTGACATTTTT-CCTA
*
10196 ATTTGGTACTTGAACTTGACACTTTTCCTA
1 ATTTGGTACTTGAACTTGACATTTTTCCTA
* * * *
10226 ATTTGGTACCTAAACTT---TTTTTTGACC-C
1 ATTTGGTACTTGAACTTGACATTTTT--CCTA
* *
10254 ATTTGGTACCTAAACTTGACATGTTTTCCTA
1 ATTTGGTACTTGAACTTGACAT-TTTTCCTA
10285 A-TTGGTAC
1 ATTTGGTAC
10293 CCAAGCTTTT
Statistics
Matches: 99, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
27 9 0.09
28 35 0.35
29 2 0.02
30 28 0.28
31 21 0.21
32 4 0.04
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.47
Consensus pattern (30 bp):
ATTTGGTACTTGAACTTGACATTTTTCCTA
Found at i:10244 original size:58 final size:59
Alignment explanation
Indices: 10137--10304 Score: 216
Period size: 58 Copynumber: 2.9 Consensus size: 59
10127 TTAATATAAT
* * * *
10137 ATTTGGTACTTGAACTTGACATTTTTTCTTAATTTGATACTTAAACTTTTTTTT-ACCTA
1 ATTTGGTACTTGAACTTGACATCTTTTCCTAATTTGGTACCTAAACTTTTTTTTGACC-A
*
10196 ATTTGGTACTTGAACTTGACA-CTTTTCCTAATTTGGTACCTAAACTTTTTTTTGACCC
1 ATTTGGTACTTGAACTTGACATCTTTTCCTAATTTGGTACCTAAACTTTTTTTTGACCA
* * * * *
10254 ATTTGGTACCTAAACTTGACATGTTTTCCTAA-TTGGTACCCAAGCTTTTTT
1 ATTTGGTACTTGAACTTGACATCTTTTCCTAATTTGGTACCTAAACTTTTTT
10305 CTGAGATTCA
Statistics
Matches: 97, Mismatches: 10, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
58 64 0.66
59 33 0.34
ACGTcount: A:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (59 bp):
ATTTGGTACTTGAACTTGACATCTTTTCCTAATTTGGTACCTAAACTTTTTTTTGACCA
Found at i:10560 original size:30 final size:31
Alignment explanation
Indices: 10526--10603 Score: 95
Period size: 33 Copynumber: 2.5 Consensus size: 31
10516 GGACCCCAAA
*
10526 AAGTTTAAGTACCAACTT-AAAAAAAGTGAC
1 AAGTTTAAGTACCAACTTGAAAAAAAATGAC
* *
10556 AAGTTTAAGTACCAAATTTGGAAAAAAAATGTC
1 AAGTTTAAGTACC-AACTT-GAAAAAAAATGAC
*
10589 AAGTTTGAGTACCAA
1 AAGTTTAAGTACCAA
10604 ATTGGACCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
30 13 0.32
31 4 0.10
32 2 0.05
33 22 0.54
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.26
Consensus pattern (31 bp):
AAGTTTAAGTACCAACTTGAAAAAAAATGAC
Found at i:12565 original size:40 final size:40
Alignment explanation
Indices: 12510--12589 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
12500 ACTCATTGAC
12510 GGTGCTCGACTTTAACGGTACCTTGATTCCTCGAACGACA
1 GGTGCTCGACTTTAACGGTACCTTGATTCCTCGAACGACA
12550 GGTGCTCGACTTTAACGGTACCTTGATTCCTCGAACGACA
1 GGTGCTCGACTTTAACGGTACCTTGATTCCTCGAACGACA
12590 ACTTCTGTAA
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:0.23, C:0.28, G:0.23, T:0.28
Consensus pattern (40 bp):
GGTGCTCGACTTTAACGGTACCTTGATTCCTCGAACGACA
Found at i:12993 original size:25 final size:26
Alignment explanation
Indices: 12946--12994 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
12936 GTATAAAATA
* *
12946 TTAATAATTTAAAATAAATTAAAAAG
1 TTAACAATTTAAAATAAACTAAAAAG
12972 TTAACAATTT-AAATAAACTAAAA
1 TTAACAATTTAAAATAAACTAAAA
12995 TTTAGGAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (26 bp):
TTAACAATTTAAAATAAACTAAAAAG
Found at i:19962 original size:21 final size:22
Alignment explanation
Indices: 19937--19977 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
19927 ATCATGTGAC
19937 CCTAAACCC-AAACCAATCTAG
1 CCTAAACCCTAAACCAATCTAG
19958 CCTAAACCCTAAACCAATCT
1 CCTAAACCCTAAACCAATCT
19978 TGAAGACCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.41, C:0.39, G:0.02, T:0.17
Consensus pattern (22 bp):
CCTAAACCCTAAACCAATCTAG
Found at i:21902 original size:20 final size:21
Alignment explanation
Indices: 21865--21916 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
21855 TGATTAGAAA
***
21865 AAATTAAATAAGTTAAAAT-T
1 AAATTAAATAAACCAAAATGT
21885 AAATTAAATAAACCAAAATGT
1 AAATTAAATAAACCAAAATGT
*
21906 AAAATAAATAA
1 AAATTAAATAA
21917 TTTCACAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
AAATTAAATAAACCAAAATGT
Found at i:23519 original size:13 final size:13
Alignment explanation
Indices: 23497--23532 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
23487 CTAATCCAAT
23497 TAAA-TATAATTA
1 TAAAGTATAATTA
23509 TAAAGTATAATTA
1 TAAAGTATAATTA
*
23522 TAATGTATAAT
1 TAAAGTATAAT
23533 AATGCTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.42
Consensus pattern (13 bp):
TAAAGTATAATTA
Found at i:25799 original size:18 final size:18
Alignment explanation
Indices: 25773--25807 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25763 AATAAATTGA
*
25773 TTTAATAATAAATTTTAT
1 TTTAATAATAAACTTTAT
*
25791 TTTACTAATAAACTTTA
1 TTTAATAATAAACTTTA
25808 ATAGTCTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAATAATAAACTTTAT
Found at i:27452 original size:18 final size:17
Alignment explanation
Indices: 27425--27461 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
27415 TCATTACATA
27425 AATAATAAACATAAATT
1 AATAATAAACATAAATT
*
27442 AATAGATAAACCTAAATT
1 AATA-ATAAACATAAATT
27460 AA
1 AA
27462 AACATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.62, C:0.08, G:0.03, T:0.27
Consensus pattern (17 bp):
AATAATAAACATAAATT
Found at i:28220 original size:17 final size:17
Alignment explanation
Indices: 28198--28230 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
28188 ATTCAAAAAT
28198 AATAAAAATAATATAAA
1 AATAAAAATAATATAAA
*
28215 AATAAAATTAATATAA
1 AATAAAAATAATATAA
28231 TTAGTCATAA
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:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (17 bp):
AATAAAAATAATATAAA
Found at i:29025 original size:18 final size:17
Alignment explanation
Indices: 28973--29022 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
28963 TGTTTTATAA
*
28973 TATTAATTAATAAAATAT
1 TATT-ATTAATAAAATAC
* *
28991 TATTACTTATTATAATAC
1 TATTA-TTAATAAAATAC
29009 TATTATTAATAAAA
1 TATTATTAATAAAA
29023 ATATCATTTG
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
17 8 0.31
18 18 0.69
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTATTAATAAAATAC
Found at i:32831 original size:59 final size:59
Alignment explanation
Indices: 32711--32911 Score: 280
Period size: 58 Copynumber: 3.4 Consensus size: 59
32701 GGAAATTCAA
* * * *
32711 GGTAAAAATGTGATTTTTGGAAGTTTG-GGGTAATAATGTAATTTCTGAGAAGTTTAGG
1 GGTAAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATGTAATTTTTGAGAAGTTTAGG
* * *
32769 GGTAAAAATGTGATTTTTGAAAGTTCGAGGGCAAAAATGTAATTTTTAAGAAGTTTAAG
1 GGTAAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATGTAATTTTTGAGAAGTTTAGG
* *
32828 GGT-AAAATGTGATTTTTGGAAGATCAAGGGCAAAAATGTAATTTTTGAGAAGTTTAGG
1 GGTAAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATGTAATTTTTGAGAAGTTTAGG
* *
32886 GGTCAAAATATGATTTTTGGAGAGTT
1 GGTAAAAATGTGATTTTTGGA-AGTT
32912 TAGGGACTTT
Statistics
Matches: 126, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
58 78 0.62
59 45 0.36
60 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.35
Consensus pattern (59 bp):
GGTAAAAATGTGATTTTTGGAAGTTCGAGGGCAAAAATGTAATTTTTGAGAAGTTTAGG
Found at i:32902 original size:30 final size:30
Alignment explanation
Indices: 32647--32916 Score: 185
Period size: 29 Copynumber: 9.3 Consensus size: 30
32637 AGTTTCAGAG
* * *
32647 AGTTT-GGGGTTAAAATGTAATTTTGGA-A
1 AGTTTAGGGGTCAAAATGTGATTTTTGAGA
*
32675 AGTTTTAGGGGT-AAAATGTCG--TTTTGGGA
1 AG-TTTAGGGGTCAAAATGT-GATTTTTGAGA
* * * *
32704 AATTCA-AGGTAAAAATGTGATTTTTG-GA
1 AGTTTAGGGGTCAAAATGTGATTTTTGAGA
* *
32732 AGTTT-GGGGT-AATAATGTAATTTCTGAGA
1 AGTTTAGGGGTCAA-AATGTGATTTTTGAGA
*
32761 AGTTTAGGGGTAAAAATGTGATTTTTGA-A
1 AGTTTAGGGGTCAAAATGTGATTTTTGAGA
* * *
32790 AG-TTCGAGGG-CAAAAATGTAATTTTTAAGA
1 AGTTTAG-GGGTC-AAAATGTGATTTTTGAGA
*
32820 AGTTTAAGGGT-AAAATGTGATTTTTG-GA
1 AGTTTAGGGGTCAAAATGTGATTTTTGAGA
* * * *
32848 AGATCAAGGG-CAAAAATGTAATTTTTGAGA
1 AGTTTAGGGGTC-AAAATGTGATTTTTGAGA
*
32878 AGTTTAGGGGTCAAAATATGATTTTTG-GA
1 AGTTTAGGGGTCAAAATGTGATTTTTGAGA
32907 GAGTTTAGGG
1 -AGTTTAGGG
32917 ACTTTTTGGG
Statistics
Matches: 191, Mismatches: 29, Indels: 42
0.73 0.11 0.16
Matches are distributed among these distances:
27 6 0.03
28 48 0.25
29 73 0.38
30 59 0.31
31 5 0.03
ACGTcount: A:0.34, C:0.03, G:0.28, T:0.36
Consensus pattern (30 bp):
AGTTTAGGGGTCAAAATGTGATTTTTGAGA
Found at i:34035 original size:13 final size:13
Alignment explanation
Indices: 34011--34044 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
34001 TCTTTTATTT
34011 TTATTA-TTAATA
1 TTATTATTTAATA
34023 TTATTATTTAATA
1 TTATTATTTAATA
34036 TTACTTATT
1 TTA-TTATT
34045 ATGCATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 9 0.45
14 5 0.25
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTATTTAATA
Found at i:34649 original size:22 final size:21
Alignment explanation
Indices: 34617--34662 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
34607 GGTTGTAAAA
34617 TTTGGATTTTGGATTTGAACT
1 TTTGGATTTTGGATTTGAACT
* *
34638 TTTGGAATTTTGTATTTGGACT
1 TTTGG-ATTTTGGATTTGAACT
34660 TTT
1 TTT
34663 AAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.17, C:0.04, G:0.22, T:0.57
Consensus pattern (21 bp):
TTTGGATTTTGGATTTGAACT
Found at i:34668 original size:22 final size:22
Alignment explanation
Indices: 34622--34669 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
34612 TAAAATTTGG
**
34622 ATTTTGGATTTGAACTTTTGGA
1 ATTTTGGATTTGAACTTTTAAA
* *
34644 ATTTTGTATTTGGACTTTTAAA
1 ATTTTGGATTTGAACTTTTAAA
34666 ATTT
1 ATTT
34670 AAATTTAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.25, C:0.04, G:0.17, T:0.54
Consensus pattern (22 bp):
ATTTTGGATTTGAACTTTTAAA
Found at i:34690 original size:17 final size:17
Alignment explanation
Indices: 34664--34719 Score: 78
Period size: 17 Copynumber: 3.3 Consensus size: 17
34654 TGGACTTTTA
*
34664 AAATTTAAATTTAAAAT
1 AAATTCAAATTTAAAAT
34681 AAATTCAAATTTAAAAT
1 AAATTCAAATTTAAAAT
*
34698 AAGTTTC-AATTTAAAAT
1 AA-ATTCAAATTTAAAAT
34715 AAATT
1 AAATT
34720 TGAACTTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
16 2 0.06
17 30 0.86
18 3 0.09
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATTCAAATTTAAAAT
Found at i:35044 original size:11 final size:11
Alignment explanation
Indices: 35028--35057 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
35018 TGTAACTTCA
35028 CTCAATTTGCT
1 CTCAATTTGCT
35039 CTCAATTTGCT
1 CTCAATTTGCT
35050 CTCAATTT
1 CTCAATTT
35058 CAAGGGTTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.27, G:0.07, T:0.47
Consensus pattern (11 bp):
CTCAATTTGCT
Found at i:35259 original size:43 final size:42
Alignment explanation
Indices: 35211--35498 Score: 190
Period size: 43 Copynumber: 7.0 Consensus size: 42
35201 GGTAAGAGAT
* * *
35211 TGGTTGATGGTGATCTGCCCCAAGCTCACGCTAAAAGATCAAA
1 TGGTTGATGGTGATCTGCCCCAAGCTCA-GGTAAGAGATCGAA
* *
35254 TGGTTGCA-----ATCTGCCCCAGGCTCGGGTTAAGAGAT----
1 TGGTTG-ATGGTGATCTGCCCCAAGCTCAGG-TAAGAGATCGAA
* *
35289 TGGTTGATGGTGATCTGCCCTAGGCTCAAGGTAAGAGATCGAA
1 TGGTTGATGGTGATCTGCCCCAAGCTC-AGGTAAGAGATCGAA
* * *
35332 TAGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAGAGATTGAA
1 TGGTTGATGGTGATCTGCCCCAAGCTC-AGGTAAGAGATCGAA
* * * * *
35375 TGGTTGATGGTGATCTGCCCTAGGCTCGGGGTAAAATATC---
1 TGGTTGATGGTGATCTGCCCCAAGCTC-AGGTAAGAGATCGAA
* * * *
35415 T-GATGACT-ATGATCTGCCCCAAACTCGGGGTAAGAGATCGAA
1 TGGTTGA-TGGTGATCTGCCCCAAGCTC-AGGTAAGAGATCGAA
* * * *
35457 TGGTTGATGGTGATCAGCCCCAGGCTCGGGGTAAGAAATCGA
1 TGGTTGATGGTGATCTGCCCCAAGCTC-AGGTAAGAGATCGA
35499 GTGGCTGCAA
Statistics
Matches: 194, Mismatches: 33, Indels: 36
0.74 0.13 0.14
Matches are distributed among these distances:
34 1 0.01
35 6 0.03
38 1 0.01
39 72 0.37
40 4 0.02
42 2 0.01
43 107 0.55
44 1 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (42 bp):
TGGTTGATGGTGATCTGCCCCAAGCTCAGGTAAGAGATCGAA
Found at i:35316 original size:78 final size:78
Alignment explanation
Indices: 35174--35612 Score: 346
Period size: 78 Copynumber: 5.5 Consensus size: 78
35164 TATTGCTTCG
* * * * * *
35174 AATGACTGCAATCTACCCCATGATCGAGGTAAGAGATTGGTTGATGGTGATCTGCCCCAAGCTCA
1 AATGATTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGCTCA
* *
35239 CGCTAAAAGATCA
66 GGGTAAAAGATCA
* * *
35252 AATGGTTGCAATCTGCCCCAGGCTCGGGTTAAGAGATTGGTTGATGGTGATCTGCCCTAGGCTCA
1 AATGATTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGCTCA
* *
35317 AGGTAAGAGATCGA
66 GGGTAAAAGATC-A
* ** * * *
35331 ATAGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAGAGATTGAATGGTTGATGGTGATCTGCCCT
1 A-A--TGATTGCAATCTGCCCCAGGCTCGGGGTAAGAGA-T---TGGTTGATGGTGATCTGCCCC
* * *
35396 AGGCTCGGGGTAAAATATCT
59 AGGCTCAGGGTAAAAGATCA
* ** *
35416 GATGACTATG--ATCTGCCCCAAACTCGGGGTAAGAGATCGAATGGTTGATGGTGATCAGCCCCA
1 AATGA-T-TGCAATCTGCCCCAGGCTCGGGGTAAGAGAT----TGGTTGATGGTGATCTGCCCCA
* *
35479 GGCTCGGGGTAAGAA-ATCG
60 GGCTCAGGGTAA-AAGATCA
* ** * * * *
35498 AGTGGCTGCAATCTGCCCCAGGCTCGGGGTAAAAGATTGGCTGATGGTGATCTTCCCCAAGCTC-
1 AATGATTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGCTCA
*
35562 GAGGTAAAAGATCT
66 G-GGTAAAAGATCA
* ** *
35576 GATGATTGTGATCTGCCCCAGACTCGGGGTAAGAGAT
1 AATGATTGCAATCTGCCCCAGGCTCGGGGTAAGAGAT
35613 CGAAATCTTC
Statistics
Matches: 294, Mismatches: 51, Indels: 32
0.78 0.14 0.08
Matches are distributed among these distances:
77 3 0.01
78 125 0.43
79 2 0.01
80 3 0.01
81 1 0.00
82 118 0.40
83 4 0.01
84 2 0.01
86 36 0.12
ACGTcount: A:0.26, C:0.21, G:0.30, T:0.24
Consensus pattern (78 bp):
AATGATTGCAATCTGCCCCAGGCTCGGGGTAAGAGATTGGTTGATGGTGATCTGCCCCAGGCTCA
GGGTAAAAGATCA
Found at i:35428 original size:82 final size:80
Alignment explanation
Indices: 35211--35612 Score: 327
Period size: 82 Copynumber: 5.0 Consensus size: 80
35201 GGTAAGAGAT
* ** * ** ** ** *
35211 TGGTTGATGGTGATCTGCCCCAAGCTCACGCTAAAAGATCAAATGGTTGCAATCTGCCCCAGGCT
1 TGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAA-ATCTGATGACTGTGATCTGCCCCAAGCT
*
35276 CGGGTTAAGAGAT---
65 CGGGGTAAGAGATGAA
* ** * *
35289 TGGTTGATGGTGATCTGCCCTAGGCTCAAGGTAAGAGATCGAATAGCTGA-TGGTGATCTGCCCC
1 TGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAA-AAATC---T-GATGACT-GTGATCTGCCCC
*
35353 AAGCTCGAGGTAAGAGATTGAA
60 AAGCTCGGGGTAAGAGA-TGAA
* * *
35375 TGGTTGATGGTGATCTGCCCTAGGCTCGGGGTAAAATATCTGATGACTATGATCTGCCCCAAACT
1 TGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAA-ATCTGATGACTGTGATCTGCCCCAAGCT
35440 CGGGGTAAGAGATCGAA
65 CGGGGTAAGAGAT-GAA
* * ** *
35457 TGGTTGATGGTGATCAGCCCCAGGCTCGGGGTAAGAAATC-GAGTGGCTGCAATCTGCCCCAGGC
1 TGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAA-AAATCTGA-TGACTGTGATCTGCCCCAAGC
*
35521 TCGGGGTAA-A-A-GAT
64 TCGGGGTAAGAGATGAA
* * * * *
35535 TGGCTGATGGTGATCTTCCCCAAGCTCGAGGTAAAAGATCTGATGATTGTGATCTGCCCC-AGAC
1 TGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAA-ATCTGATGACTGTGATCTGCCCCAAG-C
35599 TCGGGGTAAGAGAT
64 TCGGGGTAAGAGAT
35613 CGAAATCTTC
Statistics
Matches: 263, Mismatches: 40, Indels: 39
0.77 0.12 0.11
Matches are distributed among these distances:
77 3 0.01
78 90 0.34
79 4 0.02
80 2 0.01
81 5 0.02
82 118 0.45
83 5 0.02
85 1 0.00
86 35 0.13
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.24
Consensus pattern (80 bp):
TGGTTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAATCTGATGACTGTGATCTGCCCCAAGCTC
GGGGTAAGAGATGAA
Found at i:35613 original size:39 final size:40
Alignment explanation
Indices: 35201--35613 Score: 272
Period size: 39 Copynumber: 10.3 Consensus size: 40
35191 CCATGATCGA
* * **
35201 GGTAAGAGAT-TGGTTGATGGTGATCTGCCCCAAGCTCAC
1 GGTAAGAGATCTGGATGATGGTGATCTGCCCCAGGCTCGG
* * ** * * **
35240 GCTAAAAGATC-AAATGGTTGCAATCTGCCCCAGGCTCGG
1 GGTAAGAGATCTGGATGATGGTGATCTGCCCCAGGCTCGG
* * * **
35279 GTTAAGAGAT-TGGTTGATGGTGATCTGCCCTAGGCTCAA
1 GGTAAGAGATCTGGATGATGGTGATCTGCCCCAGGCTCGG
* * * *
35318 GGTAAGAGATCGAATAGCTGATGGTGATCTGCCCCAAGCTCGA
1 GGTAAGAGATC---TGGATGATGGTGATCTGCCCCAGGCTCGG
* * *
35361 GGTAAGAGATTGAATGGTTGATGGTGATCTGCCCTAGGCTCGG
1 GGTAAGAGA-T--CTGGATGATGGTGATCTGCCCCAGGCTCGG
* * * **
35404 GGTAAAATATCT-GATGACT-ATGATCTGCCCCAAACTCGG
1 GGTAAGAGATCTGGATGA-TGGTGATCTGCCCCAGGCTCGG
* *
35443 GGTAAGAGATCGAATGGTTGATGGTGATCAGCCCCAGGCTCGG
1 GGTAAGAGATC---TGGATGATGGTGATCTGCCCCAGGCTCGG
*
35486 GGTAAGAAATC--GA-G-TGGCTGCAATCTGCCCCAGGCTCGG
1 GGTAAGAGATCTGGATGATGG-TG--ATCTGCCCCAGGCTCGG
* * * * *
35525 GGTAAAAGAT-TGGCTGATGGTGATCTTCCCCAAGCTCGA
1 GGTAAGAGATCTGGATGATGGTGATCTGCCCCAGGCTCGG
* * *
35564 GGTAAAAGATCT-GATGATTGTGATCTGCCCCAGACTCGG
1 GGTAAGAGATCTGGATGATGGTGATCTGCCCCAGGCTCGG
35603 GGTAAGAGATC
1 GGTAAGAGATC
35614 GAAATCTTCA
Statistics
Matches: 284, Mismatches: 67, Indels: 46
0.72 0.17 0.12
Matches are distributed among these distances:
36 3 0.01
37 3 0.01
38 1 0.00
39 169 0.60
40 4 0.01
41 3 0.01
42 6 0.02
43 94 0.33
44 1 0.00
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (40 bp):
GGTAAGAGATCTGGATGATGGTGATCTGCCCCAGGCTCGG
Found at i:47581 original size:27 final size:27
Alignment explanation
Indices: 47540--47609 Score: 70
Period size: 27 Copynumber: 2.6 Consensus size: 27
47530 AAGTTTTAGG
* *
47540 GGTAAAATGTCATTTTGGGAAATTCGA
1 GGTAAAAAGTGATTTTGGGAAATTCGA
* * * *
47567 GGTAAAAAGTGATTTTTGGAAGTTTGG
1 GGTAAAAAGTGATTTTGGGAAATTCGA
47594 GGTAAAAA-TGTATTTT
1 GGTAAAAAGTG-ATTTT
47610 TTGATAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
26 2 0.06
27 34 0.94
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.37
Consensus pattern (27 bp):
GGTAAAAAGTGATTTTGGGAAATTCGA
Found at i:47584 original size:57 final size:57
Alignment explanation
Indices: 47523--47707 Score: 216
Period size: 57 Copynumber: 3.2 Consensus size: 57
47513 TAAAACATAA
* *
47523 TTTTGGAAAGTTTTAGGGGT-AAAATGTCA-TTTTGGGAAATTCGA-GGTAAAAAGTGAT
1 TTTTGG-AAG-TTTAGGGGTAAAAATGT-ATTTTTGAGAAATTCGAGGGTAAAATGTGAT
* *
47580 TTTTGGAAGTTT-GGGGTAAAAATGTATTTTTTGATAAATTTGAGGGTAAAATGTGAT
1 TTTTGGAAGTTTAGGGGTAAAAATGTA-TTTTTGAGAAATTCGAGGGTAAAATGTGAT
* * *
47637 TTTTGGAAGTTTAAGGGTAAAAATGTAATTTTTGAGAAGTTCAAGGGTCAAAATGTGAT
1 TTTTGGAAGTTTAGGGGTAAAAATGT-ATTTTTGAGAAATTCGAGGGT-AAAATGTGAT
47696 TTTTGGACAGTT
1 TTTTGGA-AGTT
47708 AAGGACCTTT
Statistics
Matches: 111, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
54 6 0.05
55 10 0.09
56 15 0.14
57 30 0.27
58 28 0.25
59 18 0.16
60 4 0.04
ACGTcount: A:0.32, C:0.03, G:0.26, T:0.38
Consensus pattern (57 bp):
TTTTGGAAGTTTAGGGGTAAAAATGTATTTTTGAGAAATTCGAGGGTAAAATGTGAT
Found at i:47700 original size:30 final size:29
Alignment explanation
Indices: 47523--47711 Score: 158
Period size: 29 Copynumber: 6.6 Consensus size: 29
47513 TAAAACATAA
* *
47523 TTTTGGAAAGTTTTAGGGGT-AAAATGTCAT
1 TTTTGG-AAG-TTTAAGGGTAAAAATGTGAT
* * **
47553 TTTGGGAAATTCGA-GGTAAAAA-GTGAT
1 TTTTGGAAGTTTAAGGGTAAAAATGTGAT
*
47580 TTTTGGAAGTTT-GGGGTAAAAATGT-ATT
1 TTTTGGAAGTTTAAGGGTAAAAATGTGA-T
* * *
47608 TTTTGATAAATTTGAGGGT-AAAATGTGAT
1 TTTTG-GAAGTTTAAGGGTAAAAATGTGAT
*
47637 TTTTGGAAGTTTAAGGGTAAAAATGTAAT
1 TTTTGGAAGTTTAAGGGTAAAAATGTGAT
* *
47666 TTTTGAGAAGTTCAAGGGTCAAAATGTGAT
1 TTTTG-GAAGTTTAAGGGTAAAAATGTGAT
47696 TTTTGGACAG-TTAAGG
1 TTTTGGA-AGTTTAAGG
47712 ACCTTTTGGG
Statistics
Matches: 128, Mismatches: 21, Indels: 21
0.75 0.12 0.12
Matches are distributed among these distances:
27 25 0.20
28 24 0.19
29 41 0.32
30 38 0.30
ACGTcount: A:0.33, C:0.03, G:0.27, T:0.38
Consensus pattern (29 bp):
TTTTGGAAGTTTAAGGGTAAAAATGTGAT
Found at i:48677 original size:6 final size:6
Alignment explanation
Indices: 48666--48693 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
48656 TTGTTTCACT
48666 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
48694 GTTTCGAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:48895 original size:13 final size:13
Alignment explanation
Indices: 48871--48904 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
48861 TCTTTTATTT
48871 TTATTA-TTAATA
1 TTATTATTTAATA
48883 TTATTATTTAATA
1 TTATTATTTAATA
48896 TTACTTATT
1 TTA-TTATT
48905 ATGCATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 9 0.45
14 5 0.25
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (13 bp):
TTATTATTTAATA
Found at i:49559 original size:17 final size:17
Alignment explanation
Indices: 49537--49590 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
49527 TAAATTTAAT
49537 TTAAAATAAATTCAAAC
1 TTAAAATAAATTCAAAC
* * *
49554 TTAAAATAAGTTTAAAT
1 TTAAAATAAATTCAAAC
*
49571 TTAAAATAAATTCGAAC
1 TTAAAATAAATTCAAAC
49588 TTA
1 TTA
49591 TTTAAACTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (17 bp):
TTAAAATAAATTCAAAC
Found at i:49575 original size:34 final size:33
Alignment explanation
Indices: 49526--49590 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 33
49516 CTTTTAAAAT
49526 ATAAATTTAATTTAAAATAAATTCAAACTTAAA
1 ATAAATTTAATTTAAAATAAATTCAAACTTAAA
* *
49559 ATAAGTTTAAATTTAAAATAAATTCGAACTTA
1 ATAAATTT-AATTTAAAATAAATTCAAACTTA
49591 TTTAAACTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 7 0.24
34 22 0.76
ACGTcount: A:0.54, C:0.06, G:0.03, T:0.37
Consensus pattern (33 bp):
ATAAATTTAATTTAAAATAAATTCAAACTTAAA
Found at i:49609 original size:33 final size:34
Alignment explanation
Indices: 49534--49610 Score: 93
Period size: 34 Copynumber: 2.3 Consensus size: 34
49524 ATATAAATTT
** *
49534 AATTTAAAATAAATTCAAACTTAAAATAAGTTTA
1 AATTTAAAATAAATTCAAACTTAAAATAAACTAA
* **
49568 AATTTAAAATAAATTCGAACTT-ATTTAAACTAA
1 AATTTAAAATAAATTCAAACTTAAAATAAACTAA
49601 AATTTAAAAT
1 AATTTAAAAT
49611 TTAAAATTGG
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
33 16 0.43
34 21 0.57
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (34 bp):
AATTTAAAATAAATTCAAACTTAAAATAAACTAA
Found at i:51644 original size:15 final size:16
Alignment explanation
Indices: 51616--51657 Score: 61
Period size: 14 Copynumber: 2.8 Consensus size: 16
51606 TGTTGTATAT
51616 GAATTTTGATTTTTTA
1 GAATTTTGATTTTTTA
*
51632 TAATTTT-A-TTTTTA
1 GAATTTTGATTTTTTA
51646 GAATTTTGATTT
1 GAATTTTGATTT
51658 AATTCAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 12 0.55
15 2 0.09
16 8 0.36
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (16 bp):
GAATTTTGATTTTTTA
Found at i:54634 original size:18 final size:20
Alignment explanation
Indices: 54613--54653 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
54603 TAATATTATA
54613 AAATTAT-ATAATTATT-TT
1 AAATTATCATAATTATTCTT
*
54631 AAA-TATCATTATTATTCTT
1 AAATTATCATAATTATTCTT
54650 AAAT
1 AAAT
54654 ATAATTTCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
17 3 0.16
18 11 0.58
19 5 0.26
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
AAATTATCATAATTATTCTT
Found at i:55029 original size:23 final size:22
Alignment explanation
Indices: 55003--55046 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
54993 ATTAAAAATG
55003 AATTAAAAT-TAATATATATTATA
1 AATTAAAATCT-ATAT-TATTATA
55026 AATTAAAATCTATATTATTAT
1 AATTAAAATCTATATTATTAT
55047 TTAAGTTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 13 0.65
24 1 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
AATTAAAATCTATATTATTATA
Found at i:56234 original size:9 final size:8
Alignment explanation
Indices: 56211--56276 Score: 52
Period size: 7 Copynumber: 8.5 Consensus size: 8
56201 TAAGAAGATG
56211 AATTTT-T
1 AATTTTAT
56218 AA-TTTAT
1 AATTTTAT
56225 ATATTTTAT
1 A-ATTTTAT
56234 AA-TTTAT
1 AATTTTAT
56241 AAATTTTA-
1 -AATTTTAT
*
56249 AATTATAT
1 AATTTTAT
*
56257 AATTTATAA
1 AATTT-TAT
56266 AATTTTA-
1 AATTTTAT
56273 AATT
1 AATT
56277 AATAATGATA
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
6 3 0.06
7 19 0.39
8 10 0.20
9 17 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (8 bp):
AATTTTAT
Found at i:56236 original size:16 final size:16
Alignment explanation
Indices: 56212--56265 Score: 69
Period size: 16 Copynumber: 3.6 Consensus size: 16
56202 AAGAAGATGA
56212 ATTTT-TAATTTATAT
1 ATTTTATAATTTATAT
*
56227 ATTTTATAATTTATAA
1 ATTTTATAATTTATAT
56243 ATTTTA-AA-TTATAT
1 ATTTTATAATTTATAT
*
56257 AATTTATAA
1 ATTTTATAA
56266 AATTTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
14 10 0.29
15 9 0.26
16 15 0.44
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTTATAATTTATAT
Found at i:56237 original size:23 final size:23
Alignment explanation
Indices: 56231--56291 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
56221 TTATATATTT
56231 TATAATTTATAAATTTTAAATTA
1 TATAATTTATAAATTTTAAATTA
56254 TATAATTTATAAAATTTTAAATTA
1 TATAATTTAT-AAATTTTAAATTA
*
56278 -ATAA-TGATAAATTT
1 TATAATTTATAAATTT
56292 ATATTTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 6 0.17
22 3 0.08
23 14 0.39
24 13 0.36
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATAATTTATAAATTTTAAATTA
Found at i:56276 original size:16 final size:15
Alignment explanation
Indices: 56211--56276 Score: 64
Period size: 16 Copynumber: 4.3 Consensus size: 15
56201 TAAGAAGATG
*
56211 AATTTTTAATTTATA
1 AATTTTAAATTTATA
*
56226 TATTTTATAATTTATA
1 AATTTTA-AATTTATA
56242 AATTTTAAA-TTATA
1 AATTTTAAATTTATA
56256 TAATTTATAAAATTT-TA
1 -AATTT-T-AAATTTATA
56273 AATT
1 AATT
56277 AATAATGATA
Statistics
Matches: 43, Mismatches: 3, Indels: 9
0.78 0.05 0.16
Matches are distributed among these distances:
14 5 0.12
15 12 0.28
16 19 0.44
17 5 0.12
18 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AATTTTAAATTTATA
Found at i:56314 original size:30 final size:28
Alignment explanation
Indices: 56275--56348 Score: 76
Period size: 30 Copynumber: 2.5 Consensus size: 28
56265 AAATTTTAAA
* * *
56275 TTAATAATGATAAATTTATATTTTAATCTT
1 TTAAAAATGATAAATTT-GA-TTTAATCAT
56305 TTAAAAATGATAAAAATTTGATTTAATCAT
1 TTAAAAATGAT--AAATTTGATTTAATCAT
*
56335 TTAAAAATTATAAA
1 TTAAAAATGATAAA
56349 AATATATAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
28 3 0.08
30 28 0.74
31 1 0.03
32 6 0.16
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (28 bp):
TTAAAAATGATAAATTTGATTTAATCAT
Found at i:57418 original size:3 final size:3
Alignment explanation
Indices: 57410--57454 Score: 81
Period size: 3 Copynumber: 14.7 Consensus size: 3
57400 TTTTCCCTTT
57410 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TCTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T-TC TT
57455 TTTTGAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:85302 original size:24 final size:24
Alignment explanation
Indices: 85274--85355 Score: 137
Period size: 24 Copynumber: 3.4 Consensus size: 24
85264 AATAATCTTT
* * *
85274 CAATTAAACTTTGTTTATTTGTTT
1 CAATTAAACTCTATTTATTTGTTC
85298 CAATTAAACTCTATTTATTTGTTC
1 CAATTAAACTCTATTTATTTGTTC
85322 CAATTAAACTCTATTTATTTGTTC
1 CAATTAAACTCTATTTATTTGTTC
85346 CAATTAAACT
1 CAATTAAACT
85356 GTTTATTTAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.30, C:0.15, G:0.05, T:0.50
Consensus pattern (24 bp):
CAATTAAACTCTATTTATTTGTTC
Found at i:87319 original size:24 final size:24
Alignment explanation
Indices: 87290--87336 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
87280 AGAAATAATC
87290 TTTCAATTAAACTCTATTTATTTA
1 TTTCAATTAAACTCTATTTATTTA
* *
87314 TTTCAATTAAACTTTGTTTATTT
1 TTTCAATTAAACTCTATTTATTT
87337 GTTTGAGTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.11, G:0.02, T:0.57
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTA
Found at i:88213 original size:6 final size:6
Alignment explanation
Indices: 88202--88232 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
88192 ACCCGAAATC
88202 TAATTA TAATTA TAATTA TAATTA TAATTA T
1 TAATTA TAATTA TAATTA TAATTA TAATTA T
88233 TTTATATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TAATTA
Found at i:88787 original size:29 final size:30
Alignment explanation
Indices: 88750--88806 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
88740 AAAAAACTTG
* *
88750 GATTATTAT-TATTTTTAATTTATATTAAAT
1 GATTATTATAGATTTATAATTT-TATTAAAT
88780 GATT-TTATAGATTTATAATTTTATTAA
1 GATTATTATAGATTTATAATTTTATTAA
88807 TTAATAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (30 bp):
GATTATTATAGATTTATAATTTTATTAAAT
Found at i:89071 original size:14 final size:13
Alignment explanation
Indices: 89036--89073 Score: 51
Period size: 12 Copynumber: 2.9 Consensus size: 13
89026 TCTATTTGTT
*
89036 TAATTTTTTT-AT
1 TAATTTTTTTAAA
89048 TAATTTTTTTAAA
1 TAATTTTTTTAAA
89061 TAATTTATTTTAA
1 TAATTT-TTTTAA
89074 TTATTGTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.43
13 7 0.30
14 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TAATTTTTTTAAA
Found at i:99048 original size:30 final size:29
Alignment explanation
Indices: 98989--99048 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
98979 GATGAGAGGA
**
98989 GAGTAAAAGTTTTTGGGGAAAGTGGGAAT
1 GAGTAAAAGTTTTTGGGGAAAGTAAGAAT
99018 GAGTAAAAG-TTTTGAGGGAAAAGTAAGAAT
1 GAGTAAAAGTTTTTG-GGG-AAAGTAAGAAT
99048 G
1 G
99049 TTTTAGGGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 5 0.19
29 12 0.44
30 10 0.37
ACGTcount: A:0.40, C:0.00, G:0.35, T:0.25
Consensus pattern (29 bp):
GAGTAAAAGTTTTTGGGGAAAGTAAGAAT
Found at i:103287 original size:49 final size:49
Alignment explanation
Indices: 103218--103323 Score: 133
Period size: 49 Copynumber: 2.2 Consensus size: 49
103208 TCACTCTTTG
* * * *
103218 ATTTCAAGGTGTTAGATCCGCCGTCTTGGCTTCAATCTA-TCCTTCTTCA
1 ATTTTAAGGTATTAGATCCGCCGTCGTGGCTTCAACCTATTCC-TCTTCA
* *
103267 ATTTTAAGGTATTAGGTCCGCCGTCGTGGCTTCAACCTATTCCTCTTCG
1 ATTTTAAGGTATTAGATCCGCCGTCGTGGCTTCAACCTATTCCTCTTCA
*
103316 GTTTTAAG
1 ATTTTAAG
103324 ATGTAAGATT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
49 46 0.94
50 3 0.06
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.39
Consensus pattern (49 bp):
ATTTTAAGGTATTAGATCCGCCGTCGTGGCTTCAACCTATTCCTCTTCA
Found at i:103419 original size:34 final size:34
Alignment explanation
Indices: 103365--103434 Score: 97
Period size: 34 Copynumber: 2.1 Consensus size: 34
103355 CCCCTCATCG
*
103365 ATTTTAACGTGTTAAGTCCACCGTTGCGGCTTCA
1 ATTTTAACGTGTTAAGTCCACCGTTGCGACTTCA
* *
103399 ATTTTAAGGTG-TAAGATCCACTGTTGCGACTTCA
1 ATTTTAACGTGTTAAG-TCCACCGTTGCGACTTCA
103433 AT
1 AT
103435 CTTTCCCTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
33 4 0.12
34 28 0.88
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (34 bp):
ATTTTAACGTGTTAAGTCCACCGTTGCGACTTCA
Found at i:103632 original size:49 final size:49
Alignment explanation
Indices: 103394--103644 Score: 145
Period size: 49 Copynumber: 5.1 Consensus size: 49
103384 ACCGTTGCGG
* * * * ** *
103394 CTTCAATTTTAAGGTGTAAGATCCACTGTTGCGACTTCAATCTTTCCCT
1 CTTCAGTTTTAGGGTGTTAGATCTACCATTGTGACTTCAATCTTTCCCT
* ** * ** *
103443 TTTTGGTTATAGGGTGTTAGAT-T-CGTCATTACGACTTCAAT-TTATTCCT
1 CTTCAGTTTTAGGGTGTTAGATCTAC--CATTGTGACTTCAATCTT-TCCCT
* * * * * * *
103492 CTTC-GATTTTCGGGTATTAGGTCCACCATTGT-AGCTTTAACCTATCCCT
1 CTTCAG-TTTTAGGGTGTTAGATCTACCATTGTGA-CTTCAATCTTTCCCT
* * * * *
103541 CTTCAGTTTTAAGGTGTAAAATCTACCGTT-TCGACTTTAATCTTTCCCT
1 CTTCAGTTTTAGGGTGTTAGATCTACCATTGT-GACTTCAATCTTTCCCT
* *
103590 CTTCAGTTTTAGGGTGTTAGATCTACCATTGTGGCTTCAATCTATCCCT
1 CTTCAGTTTTAGGGTGTTAGATCTACCATTGTGACTTCAATCTTTCCCT
*
103639 TTTCAG
1 CTTCAG
103645 ACTCTATGAT
Statistics
Matches: 147, Mismatches: 43, Indels: 24
0.69 0.20 0.11
Matches are distributed among these distances:
47 1 0.01
48 5 0.03
49 136 0.93
50 4 0.03
51 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (49 bp):
CTTCAGTTTTAGGGTGTTAGATCTACCATTGTGACTTCAATCTTTCCCT
Found at i:108833 original size:34 final size:36
Alignment explanation
Indices: 108794--108860 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
108784 AAAAAGGACA
108794 AAAGAGGAAGCGCAAG-G-TC-AAGAAAAAGAAGGGC
1 AAAGAGGAAG-GCAAGCGCTCAAAGAAAAAGAAGGGC
*
108828 AAAGAGGAAGGCGAGCGCTCAAAGAAAAAGAAG
1 AAAGAGGAAGGCAAGCGCTCAAAGAAAAAGAAG
108861 AAGAAAGCCA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
33 4 0.14
34 11 0.38
35 2 0.07
36 12 0.41
ACGTcount: A:0.51, C:0.12, G:0.34, T:0.03
Consensus pattern (36 bp):
AAAGAGGAAGGCAAGCGCTCAAAGAAAAAGAAGGGC
Found at i:108979 original size:17 final size:18
Alignment explanation
Indices: 108957--108994 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
108947 TTACATTGTT
108957 ATTTGTCACTGCATTT-C
1 ATTTGTCACTGCATTTGC
* *
108974 ATTTGTTAGTGCATTTGC
1 ATTTGTCACTGCATTTGC
108992 ATT
1 ATT
108995 GTAGTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.18, C:0.16, G:0.16, T:0.50
Consensus pattern (18 bp):
ATTTGTCACTGCATTTGC
Found at i:109011 original size:17 final size:16
Alignment explanation
Indices: 108966--109007 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
108956 TATTTGTCAC
108966 TGCATTTCATTTGTTAG
1 TGCATTTCA-TTGTTAG
108983 TGCATTTGCATTG-TAG
1 TGCATTT-CATTGTTAG
108999 TTGCATTTC
1 -TGCATTTC
109008 CATTCTTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 17 0.74
18 2 0.09
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (16 bp):
TGCATTTCATTGTTAG
Found at i:115414 original size:34 final size:34
Alignment explanation
Indices: 115371--115438 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
115361 CCCCCTCTAC
**
115371 TTGGCTATAGCACTTGTCACTACGGGTGATTAAA
1 TTGGCTATAGCACTTCCCACTACGGGTGATTAAA
115405 TTGGCTATAGCACTTCCCACTACGGGTGATTAAA
1 TTGGCTATAGCACTTCCCACTACGGGTGATTAAA
115439 CCTACATTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (34 bp):
TTGGCTATAGCACTTCCCACTACGGGTGATTAAA
Found at i:120238 original size:26 final size:26
Alignment explanation
Indices: 120182--120243 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
120172 ATACATAACA
* *
120182 AAAATAAAATGCAAAGCAACATATAT
1 AAAATAAAATGCAAAGCAACACAAAT
120208 AAAATAAAATGCAAAG-AATCACAAAT
1 AAAATAAAATGCAAAGCAA-CACAAAT
* *
120234 TAAATTAAAT
1 AAAATAAAAT
120244 CGAATTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 2 0.06
26 29 0.94
ACGTcount: A:0.63, C:0.10, G:0.06, T:0.21
Consensus pattern (26 bp):
AAAATAAAATGCAAAGCAACACAAAT
Found at i:121280 original size:22 final size:22
Alignment explanation
Indices: 121237--121282 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
121227 CAAAATTGAG
* *
121237 AATAAATAAAATACCTATAAAA
1 AATAAATAAAATACATAAAAAA
* *
121259 AATAAATAAAGTTCATAAAAAA
1 AATAAATAAAATACATAAAAAA
121281 AA
1 AA
121283 ATCATAAATA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.70, C:0.07, G:0.02, T:0.22
Consensus pattern (22 bp):
AATAAATAAAATACATAAAAAA
Found at i:144773 original size:132 final size:132
Alignment explanation
Indices: 144461--144830 Score: 620
Period size: 132 Copynumber: 2.8 Consensus size: 132
144451 GGTTCCTACG
*
144461 AATAAATAAATGCTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAGTTGAA
1 AATAAATAAATGCTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAATTGAA
144526 TACAAAGGATTAATG-AAATATTTGAATTGTTATATATATATTGATATGCATATTTGGTGGTTGG
66 TACAAAGGATTAATGAAAAT-TTTGAATTG-T-TATATATATTGATATGCATATTTGGTGGTTGG
144590 AAATA
128 AAATA
* *
144595 AGTAAATAAATGCTTTTTGACATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAATTGAA
1 AATAAATAAATGCTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAATTGAA
144660 TACAAAGGATTAATGAAAATTTTGAATTGTTATATATATTGATATGCATATTTGGTGGTTGGAAA
66 TACAAAGGATTAATGAAAATTTTGAATTGTTATATATATTGATATGCATATTTGGTGGTTGGAAA
144725 TA
131 TA
*
144727 AATAAATAAATGTTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAAT-AAGTTGA
1 AATAAATAAATGCTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAA-TTGA
* *
144791 ATACAAAGGATTAATGAAAGA-TTTGAAGTGTTCTATATAT
65 ATACAAAGGATTAATGAAA-ATTTTGAATTGTTATATATAT
144831 AGAGCAAGAA
Statistics
Matches: 225, Mismatches: 8, Indels: 8
0.93 0.03 0.03
Matches are distributed among these distances:
131 2 0.01
132 131 0.58
133 2 0.01
134 86 0.38
135 4 0.02
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.40
Consensus pattern (132 bp):
AATAAATAAATGCTTTTTGCCATGTGAATTATATTGAACATTTTGGATTGTTGAAATGAATTGAA
TACAAAGGATTAATGAAAATTTTGAATTGTTATATATATTGATATGCATATTTGGTGGTTGGAAA
TA
Found at i:145396 original size:102 final size:101
Alignment explanation
Indices: 145220--145489 Score: 344
Period size: 102 Copynumber: 2.6 Consensus size: 101
145210 ATGGATTATT
* * *
145220 CGTTGGTTAATCTAACTAGAGCTGGACTCACATATCACGGTTTATCCGCTAGGCACTGGGTGTCA
1 CGTTGGTTAATCCAACTAGAGCTGG-CTCACATATCGCGGTTTATCCGCTAGGCACTGGGTGCCA
* * * *
145285 TAACTGTCGGTTTATCCGACTAGTGTTGGGTGCAAAC
65 TAACCGTCGGTTTATCCGACTAGAGCTGGGCGCAAAC
* * *
145322 CGTTGGTTAATCCAACCAGAGCTAGGCTCACATATCGCGGTTTATCCACTAGGCATTGGGTGCCA
1 CGTTGGTTAATCCAACTAGAGCT-GGCTCACATATCGCGGTTTATCCGCTAGGCACTGGGTGCCA
*
145387 TAACCGTCGGTTTATTCGACTAGAGCTGGGCGCAAAC
65 TAACCGTCGGTTTATCCGACTAGAGCTGGGCGCAAAC
* * * * * *
145424 AGTTGGATAATCCAACTAGAGCTGAGCTCACATA-CGACGGTATATCCGCTAGACACCGAGTGCC
1 CGTTGGTTAATCCAACTAGAGCTG-GCTCACATATCG-CGGTTTATCCGCTAGGCACTGGGTGCC
145488 AT
64 AT
145490 GAATTGACGG
Statistics
Matches: 145, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
101 3 0.02
102 140 0.97
103 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (101 bp):
CGTTGGTTAATCCAACTAGAGCTGGCTCACATATCGCGGTTTATCCGCTAGGCACTGGGTGCCAT
AACCGTCGGTTTATCCGACTAGAGCTGGGCGCAAAC
Found at i:145398 original size:35 final size:36
Alignment explanation
Indices: 145276--145446 Score: 94
Period size: 33 Copynumber: 5.0 Consensus size: 36
145266 CGCTAGGCAC
* * * *
145276 TGGGTGTCATAACTGTCGGTTTATCCGACTAGTG-T
1 TGGGTGCCATAACCGTCGGTTTATCCAACTAGAGCT
* * *
145311 TGGGTG-CA-AACCGTTGGTTAATCCAACCAGAGCT
1 TGGGTGCCATAACCGTCGGTTTATCCAACTAGAGCT
* * *
145345 AGGCT-CACAT-ATCG-CGGTTTATCC-ACTAG-GCAT
1 TGGGTGC-CATAACCGTCGGTTTATCCAACTAGAGC-T
* *
145378 TGGGTGCCATAACCGTCGGTTTATTCGACTAGAGC-
1 TGGGTGCCATAACCGTCGGTTTATCCAACTAGAGCT
* * * * *
145413 TGGGCG-CA-AACAGTTGGATAATCCAACTAGAGCT
1 TGGGTGCCATAACCGTCGGTTTATCCAACTAGAGCT
145447 GAGCTCACAT
Statistics
Matches: 102, Mismatches: 23, Indels: 23
0.69 0.16 0.16
Matches are distributed among these distances:
32 2 0.02
33 48 0.47
34 20 0.20
35 25 0.25
36 5 0.05
37 2 0.02
ACGTcount: A:0.24, C:0.22, G:0.26, T:0.27
Consensus pattern (36 bp):
TGGGTGCCATAACCGTCGGTTTATCCAACTAGAGCT
Found at i:149926 original size:21 final size:20
Alignment explanation
Indices: 149885--149940 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 20
149875 AATAGCTAAA
*
149885 AAAAATTAAAAAATTTGTTT
1 AAAAATTAAAAAATTTCTTT
**
149905 AAAAATTAAAATTTTTTCTTT
1 AAAAATTAAAA-AATTTCTTT
149926 AAAATCATTAAAAAA
1 AAAA--ATTAAAAAA
149941 CAGATTTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 11 0.39
21 10 0.36
23 7 0.25
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (20 bp):
AAAAATTAAAAAATTTCTTT
Found at i:150250 original size:150 final size:149
Alignment explanation
Indices: 149981--150338 Score: 585
Period size: 150 Copynumber: 2.4 Consensus size: 149
149971 CTCTCTCTTT
* * * * *
149981 TTTTTTTTTTTTAAAGAAAATCACTATTTTACCTAAAAATTTAAAC-TTTATTTCGAACTAGTTA
1 TTTTTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTAA
* *
150045 AAAACAATCAAAACTTTGTTTAAGAATTTAAACTTTTTCCTTAAAATAACTAAAAAACAGATTTT
66 AAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCCTTAAAATAACTAAAAAACAGATTTT
150110 TATTTTTAAAAATATAAAC
131 TATTTTTAAAAATATAAAC
150129 TTTTTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTAA
1 TTTTTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGT-A
*
150194 AAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTT
65 AAAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCCTTAAAATAACTAAAAAACAGATTT
150259 TTATTTTTAAAAATATAAAC
130 TTATTTTTAAAAATATAAAC
* * *
150279 TTTCTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAA-TCAAAATTTTTAATTCGAAAT
1 TTTTTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATTC-AAACTTTTATTTCGAAAT
150339 TATTAATTTT
Statistics
Matches: 196, Mismatches: 11, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
148 43 0.22
149 17 0.09
150 136 0.69
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.42
Consensus pattern (149 bp):
TTTTTCTTTTTTAAAGAAAATCACTATTTTACTTAAAAATTCAAACTTTTATTTCGAAATAGTAA
AAAAAAATCAAAACTTTGTTTAAAAATTTAAACTTTTTCCTTAAAATAACTAAAAAACAGATTTT
TATTTTTAAAAATATAAAC
Found at i:150272 original size:51 final size:50
Alignment explanation
Indices: 150063--150287 Score: 151
Period size: 51 Copynumber: 4.5 Consensus size: 50
150053 CAAAACTTTG
* *
150063 TTTAAGAATTTAAACTTTTTCCTTAAAATAACTAAAAAACAGATTTTTATT
1 TTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACA-ATTTTTATT
* ** * *
150114 TTTAAAAATATAAACTTTTTCTTT--TTTAA--AGAAAATCACTATTTTA--
1 TTTAAAAATTTAAACTTTTTCTTTAAAATAACTA-AAAAACAAT-TTTTATT
* * * ** *** *
150160 CTTAAAAATTCAAACTTTTAT-TTCGAAATAGTAAAAAAAAAATCAAAACTT-TG
1 TTTAAAAATTTAAACTTTT-TCTT-TAAA-A-TAACTAAAAAA-CAATTTTTATT
150213 TTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAGATTTTTATT
1 TTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACA-ATTTTTATT
* *
150264 TTTAAAAATATAAACTTTCTCTTT
1 TTTAAAAATTTAAACTTTTTCTTT
150288 TTTAAAGAAA
Statistics
Matches: 129, Mismatches: 29, Indels: 32
0.68 0.15 0.17
Matches are distributed among these distances:
46 18 0.14
47 3 0.02
48 11 0.09
49 5 0.04
50 12 0.09
51 48 0.37
52 10 0.08
53 22 0.17
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.43
Consensus pattern (50 bp):
TTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAACAATTTTTATT
Found at i:154759 original size:18 final size:19
Alignment explanation
Indices: 154736--154779 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
154726 AGGGTGATTA
154736 TTAAACATATTAAAA-ATT
1 TTAAACATATTAAAATATT
*
154754 TTAAAC-TTTTAAAATATT
1 TTAAACATATTAAAATATT
154772 TGTAAACA
1 T-TAAACA
154780 CATTTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 10 0.45
19 5 0.23
ACGTcount: A:0.50, C:0.07, G:0.02, T:0.41
Consensus pattern (19 bp):
TTAAACATATTAAAATATT
Found at i:160716 original size:20 final size:20
Alignment explanation
Indices: 160680--160718 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
160670 AAAACAATAA
*
160680 ATTCAAGAACAAGAATAAAG
1 ATTCAAGAACAAAAATAAAG
160700 ATTCAA-AACAATAAATAAA
1 ATTCAAGAACAA-AAATAAA
160719 TAAATAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.64, C:0.10, G:0.08, T:0.18
Consensus pattern (20 bp):
ATTCAAGAACAAAAATAAAG
Found at i:178412 original size:20 final size:22
Alignment explanation
Indices: 178375--178416 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
178365 GATTTATATT
*
178375 GATTATAAATAGGTTTAATTAA
1 GATTAAAAATAGGTTTAATTAA
178397 GATTAAAAAT-GG-TTAATTAA
1 GATTAAAAATAGGTTTAATTAA
178417 AGCTTAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (22 bp):
GATTAAAAATAGGTTTAATTAA
Found at i:182263 original size:20 final size:20
Alignment explanation
Indices: 182240--182281 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
182230 GTTCCCTTGA
182240 TTGCAC-TTTAGTGCCCCTAT
1 TTGCACGTTT-GTGCCCCTAT
182260 TTGCACGTTTGTGCCCCTAT
1 TTGCACGTTTGTGCCCCTAT
182280 TT
1 TT
182282 TGCGTATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.12, C:0.29, G:0.17, T:0.43
Consensus pattern (20 bp):
TTGCACGTTTGTGCCCCTAT
Found at i:185425 original size:21 final size:20
Alignment explanation
Indices: 185392--185436 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
185382 AGGGGAAAAA
* *
185392 TATCGATACTTTAATAGAAGG
1 TATCAATACTTT-ATAAAAGG
*
185413 TATCAATATTTTATAAAAGG
1 TATCAATACTTTATAAAAGG
185433 TATC
1 TATC
185437 TATAACATTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (20 bp):
TATCAATACTTTATAAAAGG
Found at i:187536 original size:22 final size:22
Alignment explanation
Indices: 187509--187555 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
187499 CAATGAATAA
*
187509 AATT-AACCCAATTTAAATAATT
1 AATTAAACCCAAATT-AATAATT
*
187531 AATTAAACCCAAATTATTAATT
1 AATTAAACCCAAATTAATAATT
187553 AAT
1 AAT
187556 ATTTTATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (22 bp):
AATTAAACCCAAATTAATAATT
Found at i:187575 original size:25 final size:25
Alignment explanation
Indices: 187541--187588 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
187531 AATTAAACCC
*
187541 AAATTATTAATTA-ATATTTTATAAT
1 AAATTATTAAATATA-ATTTTATAAT
187566 AAATTATTAAATATAATTTTATA
1 AAATTATTAAATATAATTTTATA
187589 TTTTATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
AAATTATTAAATATAATTTTATAAT
Found at i:191200 original size:30 final size:31
Alignment explanation
Indices: 191150--191209 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
191140 CCCCTTTATT
* *
191150 AACATAAAAATTAAAATT-AAAATTTTAAAC
1 AACAAAAAAATGAAAATTAAAAATTTTAAAC
*
191180 AACAAAAAAATGAAACTTAAAAATTTTAAA
1 AACAAAAAAATGAAAATTAAAAATTTTAAA
191210 ACTCAATTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.27
Consensus pattern (31 bp):
AACAAAAAAATGAAAATTAAAAATTTTAAAC
Found at i:199124 original size:30 final size:29
Alignment explanation
Indices: 199055--199136 Score: 101
Period size: 29 Copynumber: 2.8 Consensus size: 29
199045 TGCAAATAAT
* * *
199055 GATAAGCACCAAAGAGCAAAAATAATAAC
1 GATAAGCACCAAAGTGCAAATATAACAAC
* *
199084 GATAAGCACCAAAGTGCAAATTTTACAAC
1 GATAAGCACCAAAGTGCAAATATAACAAC
199113 GATATAGCACCAAAGTGCTAAATA
1 GATA-AGCACCAAAGTGC-AAATA
199137 ATACAATAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 28 0.62
30 13 0.29
31 4 0.09
ACGTcount: A:0.50, C:0.18, G:0.15, T:0.17
Consensus pattern (29 bp):
GATAAGCACCAAAGTGCAAATATAACAAC
Found at i:199565 original size:17 final size:17
Alignment explanation
Indices: 199545--199582 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
199535 ATAATAATTA
199545 AATTACCTAATTAACAT
1 AATTACCTAATTAACAT
*
199562 AATTAGCTAATTAACAT
1 AATTACCTAATTAACAT
199579 AATT
1 AATT
199583 TAAACAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTACCTAATTAACAT
Found at i:205493 original size:21 final size:21
Alignment explanation
Indices: 205451--205502 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
205441 TAGAGGTAAA
* *
205451 ACTTGTATTGGTAGAAGAGTC
1 ACTTGTATCGGTAGAACAGTC
*
205472 ACTTGTATCGGTAGAACTGTC
1 ACTTGTATCGGTAGAACAGTC
*
205493 ATTTGTATCG
1 ACTTGTATCG
205503 ATACAAATCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.37
Consensus pattern (21 bp):
ACTTGTATCGGTAGAACAGTC
Found at i:208286 original size:39 final size:39
Alignment explanation
Indices: 208242--208320 Score: 106
Period size: 39 Copynumber: 2.0 Consensus size: 39
208232 GTTTATTTAA
* *
208242 TTTTGAT-TTAAATATTGATTTTCATTTTTGATTTAGGGT
1 TTTTGATATT-AATATTCATTTTCAATTTTGATTTAGGGT
* *
208281 TTTTGATATTGATGTTCATTTTCAATTTTGATTTAGGGT
1 TTTTGATATTAATATTCATTTTCAATTTTGATTTAGGGT
208320 T
1 T
208321 ATCTAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 33 0.94
40 2 0.06
ACGTcount: A:0.22, C:0.04, G:0.16, T:0.58
Consensus pattern (39 bp):
TTTTGATATTAATATTCATTTTCAATTTTGATTTAGGGT
Found at i:212370 original size:3 final size:3
Alignment explanation
Indices: 212362--212414 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
212352 AATCTCCATT
*
212362 TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC -TC TTC TT- TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
212408 TT- TTC TT
1 TTC TTC TT
212415 TTTAAACCCT
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
2 6 0.13
3 39 0.87
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (3 bp):
TTC
Found at i:220372 original size:17 final size:17
Alignment explanation
Indices: 220337--220382 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
220327 TTATCATTTG
*
220337 TTTAAAAAAAATT--AT
1 TTTAAAATAAATTAAAT
*
220352 TTTAAATTAAATTAAAT
1 TTTAAAATAAATTAAAT
220369 TTTAAAATAAATTA
1 TTTAAAATAAATTA
220383 CTAAAATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
15 11 0.42
17 15 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTTAAAATAAATTAAAT
Found at i:225827 original size:6 final size:6
Alignment explanation
Indices: 225816--225866 Score: 66
Period size: 6 Copynumber: 8.5 Consensus size: 6
225806 AAGCTGGAAT
* * * *
225816 TATATA TATATA TATGGA TATAGA TATAGA TATAGA TATAAA TATAGA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA TATAGA
225864 TAT
1 TAT
225867 GTATGTCAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (6 bp):
TATAGA
Found at i:226456 original size:10 final size:10
Alignment explanation
Indices: 226443--226485 Score: 61
Period size: 10 Copynumber: 4.4 Consensus size: 10
226433 TAAAATTCAA
226443 TAAAAATTAT
1 TAAAAATTAT
*
226453 TAAAAATTAA
1 TAAAAATTAT
*
226463 TAAAAGTTA-
1 TAAAAATTAT
226472 TAAAAATTAT
1 TAAAAATTAT
226482 TAAA
1 TAAA
226486 TTTTAATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
9 8 0.28
10 21 0.72
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (10 bp):
TAAAAATTAT
Found at i:227716 original size:6 final size:6
Alignment explanation
Indices: 227705--227729 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
227695 ATTGATAATA
227705 ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT A
227730 AACACTTTTA
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:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:227905 original size:19 final size:19
Alignment explanation
Indices: 227883--227921 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
227873 ATGTTTCAAT
*
227883 TTTATTTTAATAATAAATA
1 TTTATTATAATAATAAATA
*
227902 TTTATTATAATTATAAATA
1 TTTATTATAATAATAAATA
227921 T
1 T
227922 ATTAATGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATTATAATAATAAATA
Found at i:228514 original size:21 final size:21
Alignment explanation
Indices: 228479--228529 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
228469 GGATTATGTA
* *
228479 ATTTTGATTTATAAATTTTAT
1 ATTTGGATTTATAAACTTTAT
* *
228500 GTTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
228521 ATTTGGATT
1 ATTTGGATT
228530 ATACTATTAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.27, C:0.04, G:0.12, T:0.57
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:239707 original size:21 final size:21
Alignment explanation
Indices: 239662--239714 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
239652 ACTCTTCTAG
*
239662 CTTTACGTACAACGCTTATGG
1 CTTTACGTACAACGCTTATGA
* * *
239683 CTTTGCGTACAACGCTTCTTA
1 CTTTACGTACAACGCTTATGA
*
239704 CTTTATGTACA
1 CTTTACGTACA
239715 GTGCTTCATT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.23, C:0.25, G:0.15, T:0.38
Consensus pattern (21 bp):
CTTTACGTACAACGCTTATGA
Found at i:243632 original size:21 final size:21
Alignment explanation
Indices: 243584--243640 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
243574 AGCAATTTAG
**
243584 AACTTCTACCGATACTTGAGA
1 AACTTCTACCGATACAAGAGA
* * *
243605 AAATTCTACCGATACAAGTGT
1 AACTTCTACCGATACAAGAGA
*
243626 AACTTCTACCAATAC
1 AACTTCTACCGATAC
243641 TAAAAACTCC
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.25, G:0.11, T:0.28
Consensus pattern (21 bp):
AACTTCTACCGATACAAGAGA
Found at i:245124 original size:7 final size:7
Alignment explanation
Indices: 245114--245146 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
245104 CAAAAAATCC
245114 AAAAAT-
1 AAAAATA
245120 AAAAATA
1 AAAAATA
245127 AAAAATAA
1 AAAAAT-A
245135 AAAAATA
1 AAAAATA
245142 AAAAA
1 AAAAA
245147 ACCTTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAATA
Found at i:245131 original size:21 final size:21
Alignment explanation
Indices: 245105--245145 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
245095 AAGCAAATCC
**
245105 AAAAAATCCAAAAATAAAAAT
1 AAAAAATAAAAAAATAAAAAT
245126 AAAAAATAAAAAAATAAAAA
1 AAAAAATAAAAAAATAAAAA
245146 AACCTTTTAA
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:0.83, C:0.05, G:0.00, T:0.12
Consensus pattern (21 bp):
AAAAAATAAAAAAATAAAAAT
Found at i:252735 original size:49 final size:49
Alignment explanation
Indices: 252613--252796 Score: 185
Period size: 49 Copynumber: 3.7 Consensus size: 49
252603 ACCAAGGAAA
** * * *
252613 CATGAAGATATGAAGGGAATGG-TTGAGGTTGCAACGACGAACCCGGTAC
1 CATGAAGATATGAAGGGAA-GGATTGAGGCCGCGACGACAAAGCCGGTAC
* * * * * * *
252662 CTTAAAAGATGTGATGGGAAGGATTGAGACCGCGACGACAAATCCTGTAC
1 CAT-GAAGATATGAAGGGAAGGATTGAGGCCGCGACGACAAAGCCGGTAC
* *
252712 CATGAAGATAT-AGAGGGAAGGATTGAGGCCGTGACGACGAAGCCGGTAC
1 CATGAAGATATGA-AGGGAAGGATTGAGGCCGCGACGACAAAGCCGGTAC
252761 CATGAAGATATGAAGGGAAAGG-TTGAGGCCGCGACG
1 CATGAAGATATGAAGGG-AAGGATTGAGGCCGCGACG
252797 GTGAACTCGA
Statistics
Matches: 109, Mismatches: 21, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
48 1 0.01
49 68 0.62
50 40 0.37
ACGTcount: A:0.33, C:0.16, G:0.34, T:0.17
Consensus pattern (49 bp):
CATGAAGATATGAAGGGAAGGATTGAGGCCGCGACGACAAAGCCGGTAC
Found at i:252899 original size:45 final size:43
Alignment explanation
Indices: 252834--253113 Score: 284
Period size: 45 Copynumber: 6.4 Consensus size: 43
252824 AAGACCTTCC
* *
252834 AGTCAATAGGAGTTGATTGAAGCCACATTCCAATCTTTTACCCCTA
1 AGTCAAGAGG-GTAGATTGAAG--ACATTCCAATCTTTTACCCCTA
* *
252880 AGTCAAGAGGGCATATTGAAGTCACATTCCAATCTTTTACCCCTA
1 AGTCAAGAGGGTAGATTGAAG--ACATTCCAATCTTTTACCCCTA
* * * *
252925 AGTCAAAAGGGGCAGATTGAAGTCATTCCAATCTTTTACCCTTA
1 AGTCAAGA-GGGTAGATTGAAGACATTCCAATCTTTTACCCCTA
252969 A-TCAAGAAGGGTAGATTGAAG--ATTCCAATCTTTTACCCCTA
1 AGTCAAG-AGGGTAGATTGAAGACATTCCAATCTTTTACCCCTA
* *
253010 AGTCAAGAGGGGTAGATTGAAGTC-TTCCAATATTTTACCCCTA
1 AGTCAAGA-GGGTAGATTGAAGACATTCCAATCTTTTACCCCTA
* ** *
253053 A-TCAAGAAGGTTAGATTGAAGACACATTCTGATCTTTTA-CCCTT
1 AGTCAAG-AGGGTAGATTGAAG--ACATTCCAATCTTTTACCCCTA
253097 AGTCAAGAGGGGTAGAT
1 AGTCAAGA-GGGTAGAT
253114 CAAACCCCAT
Statistics
Matches: 202, Mismatches: 20, Indels: 25
0.82 0.08 0.10
Matches are distributed among these distances:
41 21 0.10
42 35 0.17
43 36 0.18
44 29 0.14
45 60 0.30
46 21 0.10
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.30
Consensus pattern (43 bp):
AGTCAAGAGGGTAGATTGAAGACATTCCAATCTTTTACCCCTA
Found at i:253014 original size:85 final size:85
Alignment explanation
Indices: 252859--253074 Score: 310
Period size: 85 Copynumber: 2.5 Consensus size: 85
252849 ATTGAAGCCA
* *
252859 CATTCCAATCTTTTACCCCTAAGTCAAG-AGGGCATATTGAAGTCACATTCCAATCTTTTACCCC
1 CATTCCAATCTTTTACCCCTAA-TCAAGAAGGGTAGATTGAAG----ATTCCAATCTTTTACCCC
252923 TAAGTCAAAAGGGGCAGATTGAAGT
61 TAAGTCAAAAGGGGCAGATTGAAGT
*
252948 CATTCCAATCTTTTACCCTTAATCAAGAAGGGTAGATTGAAGATTCCAATCTTTTACCCCTAAGT
1 CATTCCAATCTTTTACCCCTAATCAAGAAGGGTAGATTGAAGATTCCAATCTTTTACCCCTAAGT
* *
253013 CAAGAGGGGTAGATTGAAGT
66 CAAAAGGGGCAGATTGAAGT
* *
253033 C-TTCCAATATTTTACCCCTAATCAAGAAGGTTAGATTGAAGA
1 CATTCCAATCTTTTACCCCTAATCAAGAAGGGTAGATTGAAGA
253075 CACATTCTGA
Statistics
Matches: 118, Mismatches: 8, Indels: 7
0.89 0.06 0.05
Matches are distributed among these distances:
84 38 0.32
85 42 0.36
88 5 0.04
89 33 0.28
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (85 bp):
CATTCCAATCTTTTACCCCTAATCAAGAAGGGTAGATTGAAGATTCCAATCTTTTACCCCTAAGT
CAAAAGGGGCAGATTGAAGT
Found at i:253514 original size:134 final size:134
Alignment explanation
Indices: 253344--253611 Score: 394
Period size: 134 Copynumber: 2.0 Consensus size: 134
253334 CTTGATGAGA
* *
253344 TACAGAGAAGTGGATTGAAACAAAGAGGCGGTCATCTTCTTGATGAGATACAGAGAAATAGACCA
1 TACAGAGAAGTGGATTGAAACAAAGAGGCGGCCATCTTCATGATGAGATACAGAGAAATAGACCA
* * * * * *
253409 AATCAATGAAGCGAAGCTCAATATGAATGAGATTTCAAACACCATCTTCTTAATGAGATATAAAG
66 AATCAACGAACCGAAGCTCAATACGAATGAGACTTCAAACACCAGCTTCCTAATGAGATATAAAG
253474 AAGT
131 AAGT
* * *
253478 TACAGAGAAGTGGATTGAAATAATA-AGGCGGCCATCTTCATGATGAGATATAGAGAAGTAGACC
1 TACAGAGAAGTGGATTGAAACAA-AGAGGCGGCCATCTTCATGATGAGATACAGAGAAATAGACC
* * *
253542 AAATCAACGAACCGAAGCTCAATACGAATGAGACTTCAAACCCCAGCTTCCTGATGAGATATAGA
65 AAATCAACGAACCGAAGCTCAATACGAATGAGACTTCAAACACCAGCTTCCTAATGAGATATAAA
253607 GAAGT
130 GAAGT
253612 GGATCAAAGC
Statistics
Matches: 119, Mismatches: 14, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
134 118 0.99
135 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (134 bp):
TACAGAGAAGTGGATTGAAACAAAGAGGCGGCCATCTTCATGATGAGATACAGAGAAATAGACCA
AATCAACGAACCGAAGCTCAATACGAATGAGACTTCAAACACCAGCTTCCTAATGAGATATAAAG
AAGT
Found at i:253996 original size:37 final size:38
Alignment explanation
Indices: 253946--254018 Score: 121
Period size: 37 Copynumber: 1.9 Consensus size: 38
253936 AAATGAGACT
253946 TCAAACCCTATCTTCCTGAAGAGATACAGAGAAGTGGA
1 TCAAACCCTATCTTCCTGAAGAGATACAGAGAAGTGGA
* *
253984 TCAAATCC-ATCTTCCTGAAGAGATATAGAGAAGTG
1 TCAAACCCTATCTTCCTGAAGAGATACAGAGAAGTG
254019 AATTAAAACA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
37 26 0.79
38 7 0.21
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (38 bp):
TCAAACCCTATCTTCCTGAAGAGATACAGAGAAGTGGA
Found at i:254043 original size:160 final size:159
Alignment explanation
Indices: 253633--254141 Score: 585
Period size: 160 Copynumber: 3.2 Consensus size: 159
253623 ATAAAGCGGT
* **
253633 CATCTTCTTAATGAGATACAGAGAAGTGGATCAAATTTGTCTTCCTGATA-AGAT-TCAGAGAAG
1 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAATCCGTCTTCCTGA-AGAGATAT-AGAGAAG
* * * * * *
253696 TGGATTAAAACAATGAGATGATTATCTT-TCTAATGAGATACAGAGAAGTAGACTAAAACGATGA
64 TGGATTAAAACAATGAGATGGTCATCTTCT-TGATGAGATACAGAGAAGTAGACCAAATCAATGA
* * * *
253760 AGTGAAGCTCAATGTGAGTGAAACTTCAAACCCC
128 AGCGAAGCTCAATGCGAATGAGACTTCAAA--CC
* * * * * *
253794 CATCTTCTTGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCT-AATGAGATACAAAGCAGT
1 CATCTTCTTGATGAGATACAGAGAAGTGGATCAAATCCGTCTTCCTGAA-GAGATATAGAGAAGT
* * * * * * *
253858 GGATTGAAATAAAGAGGTTGTCATCTTCTTGATGAGATACAGAGAAATAAACCAAATCAATGAAG
65 GGATTAAAACAATGAGATGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAG
* * *
253923 CAAAGCTCAATACAAATGAGACTTCAAACC
130 CGAAGCTCAATGCGAATGAGACTTCAAACC
* * *
253953 CTATCTTCCTGAAGAGATACAGAGAAGTGGATCAAATCCATCTTCCTGAAGAGATATAGAGAAGT
1 C-ATCTTCTTGATGAGATACAGAGAAGTGGATCAAATCCGTCTTCCTGAAGAGATATAGAGAAGT
* * * *
254018 GAATTAAAACAATGAGATGGTCATCTTCCTGATGAGATACATAGAAGTAGACCAAATCAACGAAG
65 GGATTAAAACAATGAGATGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAG
*
254083 CGAAGCTCAATGCGAATGAGACTTTAAAACC
130 CGAAGCTCAATGCGAATGAGAC-TTCAAACC
254114 CATCTTCTTGATGAGATACAGAGAAGTG
1 CATCTTCTTGATGAGATACAGAGAAGTG
254142 AGTCAAAGCA
Statistics
Matches: 286, Mismatches: 55, Indels: 15
0.80 0.15 0.04
Matches are distributed among these distances:
159 4 0.01
160 150 0.52
161 131 0.46
162 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (159 bp):
CATCTTCTTGATGAGATACAGAGAAGTGGATCAAATCCGTCTTCCTGAAGAGATATAGAGAAGTG
GATTAAAACAATGAGATGGTCATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGC
GAAGCTCAATGCGAATGAGACTTCAAACC
Found at i:254262 original size:208 final size:209
Alignment explanation
Indices: 253958--254350 Score: 536
Period size: 208 Copynumber: 1.9 Consensus size: 209
253948 AAACCCTATC
* * *
253958 TTCCTGAAGAGATACAGAGAAGTGGATCAAATCCATCTTCCTGAAGAGATATAGAGAAGTGAATT
1 TTCCTGAAGAGATACAGAGAAGTGGACCAAATCCATCTTCCTGAAGAGATACAAAGAAGTGAATT
*
254023 AAAACAATGAGATGGTCATCTTCCTGATGAGATACATAGAAGTAGACCAAATCAACGAAGCGAAG
66 AAAACAATGAGATGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCAACGAAGCGAAG
* * * *
254088 CTCAATGCGAATGAGACTTTAAAACC-CATCTTCTTGATGAGATACAGAGAAGTGAGTCAAAGCA
131 CTCAATACGAATGAAACTTCAAAACCTCATCTTCCTGATGAGATACAGAGAAGTGAGTCAAAGCA
254152 ATAAAGCGGTCATA
196 ATAAAGCGGTCATA
* * * * * * *
254166 TTCCTGATGAGATACAGAGAAGTGGACCAAATCTATGTTCTTGATGAGATACAAATAAGTGGATT
1 TTCCTGAAGAGATACAGAGAAGTGGACCAAATCCATCTTCCTGAAGAGATACAAAGAAGTGAATT
* * * * * * *
254231 AAAATAATGAGATGGTTATCTTCTTGATGAGATACAAAGAAGTAGACTAAATCGATGAAGTGAAG
66 AAAACAATGAGATGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCAACGAAGCGAAG
* * * * *
254296 CTCAATATGAGTGAAACTTCAAACCCTCATTTTCCTGATGAGATATAGAGAAGTG
131 CTCAATACGAATGAAACTTCAAAACCTCATCTTCCTGATGAGATACAGAGAAGTG
254351 GACTAAATCC
Statistics
Matches: 157, Mismatches: 27, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
208 132 0.84
209 25 0.16
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.25
Consensus pattern (209 bp):
TTCCTGAAGAGATACAGAGAAGTGGACCAAATCCATCTTCCTGAAGAGATACAAAGAAGTGAATT
AAAACAATGAGATGGTCATCTTCCTGATGAGATACAAAGAAGTAGACCAAATCAACGAAGCGAAG
CTCAATACGAATGAAACTTCAAAACCTCATCTTCCTGATGAGATACAGAGAAGTGAGTCAAAGCA
ATAAAGCGGTCATA
Found at i:254352 original size:161 final size:161
Alignment explanation
Indices: 254161--254511 Score: 425
Period size: 161 Copynumber: 2.2 Consensus size: 161
254151 AATAAAGCGG
* * * * *
254161 TCATATTCCTGATGAGATACAGAGAAGTGGACCAAATCTATGTTCTTGATGAGATACAAATAAGT
1 TCATATTCCTGATGAGATACAGAGAAGTGGACCAAATCCATCTTCCTGATAAGATACAAAGAAGT
* * * * * * * * * *
254226 GGATTAAAATAATGAGATGGTTATCTTCTTGATGAGATACAAAGAAGTAGACTAAATCGATGAAG
66 GGATTAAAAGAAAGAGACGGTCATCTTCCTGATGAGATACAAAGAAATAAACCAAATCAATGAAC
* *
254291 TGAAGCTCAATATGAGTGAAACTTCAAACCC
131 CGAAGCTCAATATGAATGAAACTTCAAACCC
* * * *
254322 TCATTTTCCTGATGAGATATAGAGAAGTGGACTAAATCCATCTTCCTGATAAGATACAGAGAAGT
1 TCATATTCCTGATGAGATACAGAGAAGTGGACCAAATCCATCTTCCTGATAAGATACAAAGAAGT
* * *
254387 GGATTGAAAGAAAGAGGCGGTCATCTTCCTGATGAGATACAGAGAAATAAACCAAATCAATGAAC
66 GGATTAAAAGAAAGAGACGGTCATCTTCCTGATGAGATACAAAGAAATAAACCAAATCAATGAAC
*
254452 CGAAGCTCAATATGAATGAGACTTCAAACCC
131 CGAAGCTCAATATGAATGAAACTTCAAACCC
* ** * *
254483 -CATCTTTTTTATGAGATACAAAGAAGTGG
1 TCATATTCCTGATGAGATACAGAGAAGTGG
254512 GTCAAAGCAA
Statistics
Matches: 159, Mismatches: 31, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
160 23 0.14
161 136 0.86
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.26
Consensus pattern (161 bp):
TCATATTCCTGATGAGATACAGAGAAGTGGACCAAATCCATCTTCCTGATAAGATACAAAGAAGT
GGATTAAAAGAAAGAGACGGTCATCTTCCTGATGAGATACAAAGAAATAAACCAAATCAATGAAC
CGAAGCTCAATATGAATGAAACTTCAAACCC
Found at i:254479 original size:529 final size:529
Alignment explanation
Indices: 253510--254517 Score: 1489
Period size: 529 Copynumber: 1.9 Consensus size: 529
253500 ATAAGGCGGC
*
253510 CATCTTCATGATGAGATATAGAGAAGTAGACCAAATCAACGAACCGAAGCTCAATACGAATGAGA
1 CATCTTCATGATGAGATACAGAGAAGTAGACCAAATCAACGAACCGAAGCTCAATACGAATGAGA
* * *
253575 CTTCAAACCCCAGCTTCCTGATGAGATATAGAGAAGTGGATCAAAGCAATAAAGCGGTCATCTTC
66 CTTCAAAACCCAGCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGGTCATATTC
* * * * * *
253640 TTAATGAGATACAGAGAAGTGGATCAAATTTGTCTTCCTGATAAGATTCAGAGAAGTGGATTAAA
131 CTAATGAGATACAGAGAAGTGGACCAAATCTATCTTCCTGATAAGATACAAAGAAGTGGATTAAA
*
253705 ACAATGAGATGATTATCTTTCTAATGAGATACAGAGAAGTAGACTAAAACGATGAAGTGAAGCTC
196 ACAATGAGATGATTATCTTTCTAATGAGATACAAAGAAGTAGACTAAAACGATGAAGTGAAGCTC
* * *
253770 AATGTGAGTGAAACTTCAAACCCCCATCTTCTTGATGAGATACAAAGAAGTGAACCAAATCCGTC
261 AATATGAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCATC
* * * ** *
253835 TTCCTAATGAGATACAAAGCAGTGGATTGAAATAAAGAGGTTGTCATCTTCTTGATGAGATACAG
326 TTCCTAATAAGATACAAAGAAGTGGATTGAAAGAAAGAGGCGGTCATCTTCCTGATGAGATACAG
* *
253900 AGAAATAAACCAAATCAATGAAGCAAAGCTCAATACAAATGAGACTTCAAACCCTATCTTCCTGA
391 AGAAATAAACCAAATCAATGAACCAAAGCTCAATACAAATGAGACTTCAAACCCCATCTTCCTGA
*
253965 AGAGATACAGAGAAGTGGATCAAATCCATCTTCCTGAAGAGATATAGAGAAGTGAATTAAAACAA
456 AGAGATACAAAGAAGTGGATCAAATCCATCTTCCTGAAGAGATATAGAGAAGTGAATTAAAACAA
254030 TGAGATGGT
521 TGAGATGGT
* * * *
254039 CATCTTCCTGATGAGATACATAGAAGTAGACCAAATCAACGAAGCGAAGCTCAATGCGAATGAGA
1 CATCTTCATGATGAGATACAGAGAAGTAGACCAAATCAACGAACCGAAGCTCAATACGAATGAGA
* * *
254104 CTTTAAAACCCATCTTCTTGATGAGATACAGAGAAGT-GAGTCAAAGCAATAAAGCGGTCATATT
66 CTTCAAAACCCAGCTTCCTGATGAGATACAGAGAAGTGGA-TCAAAGCAATAAAGCGGTCATATT
* * * * *
254168 CCTGATGAGATACAGAGAAGTGGACCAAATCTATGTTCTTGATGAGATACAAATAAGTGGATTAA
130 CCTAATGAGATACAGAGAAGTGGACCAAATCTATCTTCCTGATAAGATACAAAGAAGTGGATTAA
* * * *
254233 AATAATGAGATGGTTATC-TTCTTGATGAGATACAAAGAAGTAGACTAAATCGATGAAGTGAAGC
195 AACAATGAGATGATTATCTTTC-TAATGAGATACAAAGAAGTAGACTAAAACGATGAAGTGAAGC
* * * * * *
254297 TCAATATGAGTGAAACTTCAAACCCTCATTTTCCTGATGAGATATAGAGAAGTGGACTAAATCCA
259 TCAATATGAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCA
* *
254362 TCTTCCTGATAAGATACAGAGAAGTGGATTGAAAGAAAGAGGCGGTCATCTTCCTGATGAGATAC
324 TCTTCCTAATAAGATACAAAGAAGTGGATTGAAAGAAAGAGGCGGTCATCTTCCTGATGAGATAC
* ** **
254427 AGAGAAATAAACCAAATCAATGAACCGAAGCTCAATATGAATGAGACTTCAAACCCCATCTTTTT
389 AGAGAAATAAACCAAATCAATGAACCAAAGCTCAATACAAATGAGACTTCAAACCCCATCTTCCT
* * *
254492 TATGAGATACAAAGAAGTGGGTCAAA
454 GAAGAGATACAAAGAAGTGGATCAAA
254518 GCAATAAAAT
Statistics
Matches: 422, Mismatches: 55, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
528 5 0.01
529 417 0.99
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.24
Consensus pattern (529 bp):
CATCTTCATGATGAGATACAGAGAAGTAGACCAAATCAACGAACCGAAGCTCAATACGAATGAGA
CTTCAAAACCCAGCTTCCTGATGAGATACAGAGAAGTGGATCAAAGCAATAAAGCGGTCATATTC
CTAATGAGATACAGAGAAGTGGACCAAATCTATCTTCCTGATAAGATACAAAGAAGTGGATTAAA
ACAATGAGATGATTATCTTTCTAATGAGATACAAAGAAGTAGACTAAAACGATGAAGTGAAGCTC
AATATGAGTGAAACTTCAAACCCCCATCTTCCTGATGAGATACAAAGAAGTGAACCAAATCCATC
TTCCTAATAAGATACAAAGAAGTGGATTGAAAGAAAGAGGCGGTCATCTTCCTGATGAGATACAG
AGAAATAAACCAAATCAATGAACCAAAGCTCAATACAAATGAGACTTCAAACCCCATCTTCCTGA
AGAGATACAAAGAAGTGGATCAAATCCATCTTCCTGAAGAGATATAGAGAAGTGAATTAAAACAA
TGAGATGGT
Found at i:254487 original size:369 final size:368
Alignment explanation
Indices: 253802--254718 Score: 1172
Period size: 369 Copynumber: 2.5 Consensus size: 368
253792 CCCATCTTCT
* * * *
253802 TGATGAGATACAAAGAAGTGAACCAAATCCGTCTTCCTAATGAGATACAAAGCAGTGGATTGAAA
1 TGATGAGATACAAAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAAAGAAGTGGATTGAAA
* * * * * *
253867 TAAAGAGGTTGTCATCTTCTTGATGAGATACAGAGAAATAAACCAAATCAATGAAGCAAAGCTCA
66 TAATGAGGTGGTTATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCA
**
253932 ATACAAATGAGACTTCAAACCCTATCTTCCTGAAGAGATACAGAGAAGTGGATCAAATCCATCTT
131 ATATGAATGAGACTTCAAACCCTATCTTCCTGAAGAGATACAGAGAAGTGGATCAAATCCATCTT
* * * *
253997 CCTGAAGAGATATAGAGAAGTGAATTAAAACAATGAGATGGTCATCTTCCTGATGAGATACATAG
196 CCTGAAGAGATACAGAGAAGTGAATTAAAACAAAGAGACGGTCATCTTCCTGATGAGATACAGAG
* * * * *
254062 AAGTAGACCAAATCAACGAAGCGAAGCTCAATGCGAATGAGACTTTAAAACCCATCTTCTTGATG
261 AAATAAACCAAATCAACGAACCGAAGCTCAATACGAATGAGACTTCAAAACCCATCTTCTTGATG
* * *
254127 AGATACAGAGAAGTGAGTCAAAGCAATAAAGCGGTCATATTCC
326 AGATACAAAGAAGTGAGTCAAAGCAATAAAACGATCATATTCC
* ** * * *
254170 TGATGAGATACAGAGAAGTGGACCAAATCTATGTTCTTGATGAGATACAAATAAGTGGATTAAAA
1 TGATGAGATACAAAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAAAGAAGTGGATTGAAA
* * * * *
254235 TAATGAGATGGTTATCTTCTTGATGAGATACAAAGAAGTAGACTAAATCGATGAAGTGAAGCTCA
66 TAATGAGGTGGTTATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCA
* * * * *
254300 ATATGAGTGAAACTTCAAACCCTCATTTTCCTGATGAGATATAGAGAAGTGGA-CTAAATCCATC
131 ATATGAATGAGACTTCAAACCCT-ATCTTCCTGAAGAGATACAGAGAAGTGGATC-AAATCCATC
* * * *
254364 TTCCTGATA-AGATACAGAGAAGTGGATTGAAAGAAAGAGGCGGTCATCTTCCTGATGAGATACA
194 TTCCTGA-AGAGATACAGAGAAGTGAATTAAAACAAAGAGACGGTCATCTTCCTGATGAGATACA
* * * * *
254428 GAGAAATAAACCAAATCAATGAACCGAAGCTCAATATGAATGAGACTTCAAACCCCATCTTTTTT
258 GAGAAATAAACCAAATCAACGAACCGAAGCTCAATACGAATGAGACTTCAAAACCCATCTTCTTG
* * *
254493 ATGAGATACAAAGAAGTGGGTCAAAGCAATAAAATGATCATCTTCC
323 ATGAGATACAAAGAAGTGAGTCAAAGCAATAAAACGATCATATTCC
* *
254539 TTATGAGATACAAAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAGAGAAGTGGATTGAAA
1 TGATGAGATACAAAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAAAGAAGTGGATTGAAA
* * * * * * * * *
254604 GAATGTGGTGGTTATCTTCCTGATGTGATATAGAGAAGTAGCCCAAATCAACGAAACGATGCTCA
66 TAATGAGGTGGTTATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCA
** * * * *
254669 ATATGAATGAGACTTCAAACATTATCTTCTTGAAAAGATTCAGAAAAGTG
131 ATATGAATGAGACTTCAAACCCTATCTTCCTGAAGAGATACAGAGAAGTG
254719 AGTCAAAGCA
Statistics
Matches: 461, Mismatches: 85, Indels: 6
0.84 0.15 0.01
Matches are distributed among these distances:
368 149 0.32
369 311 0.67
370 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.25
Consensus pattern (368 bp):
TGATGAGATACAAAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAAAGAAGTGGATTGAAA
TAATGAGGTGGTTATCTTCTTGATGAGATACAGAGAAGTAGACCAAATCAATGAAGCGAAGCTCA
ATATGAATGAGACTTCAAACCCTATCTTCCTGAAGAGATACAGAGAAGTGGATCAAATCCATCTT
CCTGAAGAGATACAGAGAAGTGAATTAAAACAAAGAGACGGTCATCTTCCTGATGAGATACAGAG
AAATAAACCAAATCAACGAACCGAAGCTCAATACGAATGAGACTTCAAAACCCATCTTCTTGATG
AGATACAAAGAAGTGAGTCAAAGCAATAAAACGATCATATTCC
Found at i:254726 original size:208 final size:208
Alignment explanation
Indices: 254322--254801 Score: 635
Period size: 208 Copynumber: 2.3 Consensus size: 208
254312 CTTCAAACCC
* * * *
254322 TCATTTTCCTGATGAGATATAGAGAAGTGGACTAAATCCATCTTCCTGATAAGATACAGAGAAGT
1 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCATCTTCCTGATGAGATACAGAGAAGT
* *
254387 GGATTGAAAGAAAGAGGCGGTCATCTTCCTGATGAGATACAGAGAAATAAACCAAATCAATGAAC
66 GGATTGAAAGAAAGAGGCGGTCATCTTCCTGATGAGATACAGAGAAATAAACCAAATCAACGAAA
* * * ** *
254452 CGAAGCTCAATATGAATGAGACTTCAAACCCCATCTTTTTTATGAGATACAAAGAAGTGGGTCAA
131 CGAAGCTCAATATGAATGAGACTTCAAACACCATCTTCTTGAAAAGATACAAAGAAGTGAGTCAA
*
254517 AGCAATAAAATGA
196 AGCAATAAAACGA
* * * *
254530 TCATCTTCCTTATGAGATACAAAGAAGTGGACCAAATCCGTCTTCTTGATGAGATACAGAGAAGT
1 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCATCTTCCTGATGAGATACAGAGAAGT
* * * * * * * **
254595 GGATTGAAAGAATGTGGTGGTTATCTTCCTGATGTGATATAGAGAAGTAGCCCAAATCAACGAAA
66 GGATTGAAAGAAAGAGGCGGTCATCTTCCTGATGAGATACAGAGAAATAAACCAAATCAACGAAA
* ** *
254660 CGATGCTCAATATGAATGAGACTTCAAACATTATCTTCTTGAAAAGATTCAGAA-AAGTGAGTCA
131 CGAAGCTCAATATGAATGAGACTTCAAACACCATCTTCTTGAAAAGATACA-AAGAAGTGAGTCA
*
254724 AAGCAATAAAGCGA
195 AAGCAATAAAACGA
254738 TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAAAT-CATC-TCCTGATGAGAT-CAGAGAAG
1 TCATCTTCCTGATGAGATACAGAGAAGTGGACC-AAATCCATCTTCCTGATGAGATACAGAGAAG
254800 TG
65 TG
254802 AATTAAAATA
Statistics
Matches: 235, Mismatches: 35, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
206 10 0.04
207 11 0.05
208 208 0.89
209 6 0.03
ACGTcount: A:0.38, C:0.16, G:0.21, T:0.25
Consensus pattern (208 bp):
TCATCTTCCTGATGAGATACAGAGAAGTGGACCAAATCCATCTTCCTGATGAGATACAGAGAAGT
GGATTGAAAGAAAGAGGCGGTCATCTTCCTGATGAGATACAGAGAAATAAACCAAATCAACGAAA
CGAAGCTCAATATGAATGAGACTTCAAACACCATCTTCTTGAAAAGATACAAAGAAGTGAGTCAA
AGCAATAAAACGA
Found at i:255184 original size:85 final size:85
Alignment explanation
Indices: 255036--255202 Score: 183
Period size: 85 Copynumber: 2.0 Consensus size: 85
255026 CAAACCCCCA
* * * *
255036 TCTTTTTGATGAGATACAAAGAAGTGGGTCAAAGAAATAAAGCAGTCATCTTCTTGACGAGATAC
1 TCTTCTTGATGAGATACAAAGAAGTGGGTCAAACAAATAAAGCAGTCATCTTCCTAACGAGATAC
*
255101 AAAAAAGTGGACCAAATTCG
66 AAAAAAGTAGACCAAATTCG
* * * * * * *
255121 TCTTCTTGATGAGATACAAAGTAGTGGATTGAAACAAA-GAGGCGGTCATCTTCCTAATGAGATA
1 TCTTCTTGATGAGATACAAAGAAGTGG-GTCAAACAAATAAAGCAGTCATCTTCCTAACGAGATA
* * *
255185 TAGAGAAGTAGACCAAAT
65 CAAAAAAGTAGACCAAAT
255203 CAATGAGGCA
Statistics
Matches: 66, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
85 59 0.89
86 7 0.11
ACGTcount: A:0.39, C:0.14, G:0.22, T:0.25
Consensus pattern (85 bp):
TCTTCTTGATGAGATACAAAGAAGTGGGTCAAACAAATAAAGCAGTCATCTTCCTAACGAGATAC
AAAAAAGTAGACCAAATTCG
Found at i:255239 original size:209 final size:208
Alignment explanation
Indices: 254873--255269 Score: 490
Period size: 209 Copynumber: 1.9 Consensus size: 208
254863 TTCAAACCCC
* * * *
254873 CATCTTCTTGATGAGATATAAAGAAGTGGATCAAATTCAACTTCTTGATGAGATACAAAGAAGTG
1 CATCTTCTTGACGAGATACAAAAAAGTGGACCAAATTCAACTTCTTGATGAGATACAAAGAAGTG
* * * * * **
254938 GATTAAAATAATGACATGATCATCTTCCTGATAAGATACAGAGAAGTAGATCAAATTGATGAAGC
66 GATTAAAACAAAGACACGATCATCTTCCTAATAAGATACAGAGAAGTAGACCAAATCAATGAAGC
* ** *
255003 GAAGCTCAATGTGAGTGAAACTTCAAACCCCCATCTTTT-TGATGAGATACAAAGAAGTGGGTCA
131 AAAGCTCAATACGAATGAAACTTCAAA-CCCCAT-TTTTCTGATGAGATACAAAGAAGTGGGTCA
255067 AAGAAATAAAGCAGT
194 AAGAAATAAAGCAGT
** *
255082 CATCTTCTTGACGAGATACAAAAAAGTGGACCAAATTCGTCTTCTTGATGAGATACAAAGTAGTG
1 CATCTTCTTGACGAGATACAAAAAAGTGGACCAAATTCAACTTCTTGATGAGATACAAAGAAGTG
* ** * * * *
255147 GATTGAAACAAAGAGGCGGTCATCTTCCTAATGAGATATAGAGAAGTAGACCAAATCAATGAGGC
66 GATTAAAACAAAGACACGATCATCTTCCTAATAAGATACAGAGAAGTAGACCAAATCAATGAAGC
** * * * *
255212 AAAGCTCAATACGAATGGGAGTTCAAACCTCATTTTTCTGATGAGATATAGAGAAGTG
131 AAAGCTCAATACGAATGAAACTTCAAACCCCATTTTTCTGATGAGATACAAAGAAGTG
255270 AATTGAAACA
Statistics
Matches: 156, Mismatches: 31, Indels: 3
0.82 0.16 0.02
Matches are distributed among these distances:
207 4 0.03
208 23 0.15
209 129 0.83
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (208 bp):
CATCTTCTTGACGAGATACAAAAAAGTGGACCAAATTCAACTTCTTGATGAGATACAAAGAAGTG
GATTAAAACAAAGACACGATCATCTTCCTAATAAGATACAGAGAAGTAGACCAAATCAATGAAGC
AAAGCTCAATACGAATGAAACTTCAAACCCCATTTTTCTGATGAGATACAAAGAAGTGGGTCAAA
GAAATAAAGCAGT
Found at i:256179 original size:18 final size:19
Alignment explanation
Indices: 256153--256201 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
256143 ACATACATAC
*
256153 ATACATATATATA-T-ATAT
1 ATACTTATATATATTCAT-T
*
256171 ATACTTATATTTATTCATT
1 ATACTTATATATATTCATT
256190 ATA-TTATATATA
1 ATACTTATATATA
256202 AACATTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 19 0.73
19 5 0.19
20 2 0.08
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (19 bp):
ATACTTATATATATTCATT
Found at i:256232 original size:17 final size:17
Alignment explanation
Indices: 256175--256230 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
256165 ATATATATAC
256175 TTATATTTATTCATTATA
1 TTATATTTATTCATT-TA
* **
256193 TTATATATAAACATTTA
1 TTATATTTATTCATTTA
*
256210 TTATTTTTATTCATTTA
1 TTATATTTATTCATTTA
256227 TTAT
1 TTAT
256231 TTCGAAATCA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 19 0.61
18 12 0.39
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (17 bp):
TTATATTTATTCATTTA
Found at i:268088 original size:97 final size:98
Alignment explanation
Indices: 267913--268107 Score: 275
Period size: 97 Copynumber: 2.0 Consensus size: 98
267903 AACCTTGGAA
* * *
267913 AAGGATATTCGATTATCCCGATTTGAAGGAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCCCGATTTGAAGAAAACTCACGCCTAGTAAGTTAAGGCACAAATTTTCA
*
267978 AAACCAGAGATAAAGAAACATTGCCTCG-TTTT
66 AAACCAGAAATAAAGAAACATTGCCTCGATTTT
* * * *
268010 AAGGGTATTCGATTATCTCGGTTTGAAGAAAACTCACGCCTAGTTAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCCCGATTTGAAGAAAACTCACGCCTAGTAAGTTAAGGCACAAATTTTCA
* * * *
268075 AATCCCGAAATAAAGGAATATTGCCTCGATTTT
66 AAACCAGAAATAAAGAAACATTGCCTCGATTTT
268108 TAAATGTTTT
Statistics
Matches: 85, Mismatches: 12, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
97 81 0.95
98 4 0.05
ACGTcount: A:0.35, C:0.17, G:0.19, T:0.29
Consensus pattern (98 bp):
AAGGATATTCGATTATCCCGATTTGAAGAAAACTCACGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCAGAAATAAAGAAACATTGCCTCGATTTT
Found at i:268439 original size:28 final size:27
Alignment explanation
Indices: 268403--268516 Score: 104
Period size: 28 Copynumber: 4.1 Consensus size: 27
268393 AAGTTTTAAG
*
268403 GGTAAAAATGTCATTTTAGGAAATTCGA
1 GGTAAAAATGTCATTTT-GGAAGTTCGA
* * *
268431 GGTAGAAAT-ACGATTTTTGGAAGTTCTA
1 GGTAAAAATGTC-A-TTTTGGAAGTTCGA
* *
268459 GGGAAAAATGTGATTTTGGAAGTTCGA
1 GGTAAAAATGTCATTTTGGAAGTTCGA
* **
268486 GGCAAAAATGAAATTATTGGAAGTTCGA
1 GGTAAAAATGTCATT-TTGGAAGTTCGA
268514 GGT
1 GGT
268517 TGAAAATATA
Statistics
Matches: 69, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
27 26 0.38
28 39 0.57
29 4 0.06
ACGTcount: A:0.36, C:0.06, G:0.27, T:0.31
Consensus pattern (27 bp):
GGTAAAAATGTCATTTTGGAAGTTCGA
Found at i:268507 original size:55 final size:57
Alignment explanation
Indices: 268384--268511 Score: 138
Period size: 55 Copynumber: 2.2 Consensus size: 57
268374 GTTAAAACAT
* * *
268384 AATTTTGGAAAGTTTTAAGGGTAAAAATGTCATTTTAGGAAATTCGAGGTAGAAATAC
1 AATTTTGG-AAGTTCTAAGGGTAAAAATGTCATTTTAGGAAATTCGAGGCAAAAATAC
* * *
268442 GATTTTTGGAAGTTCT-AGGG-AAAAATGTGATTTT-GGAAGTTCGAGGCAAAAATGA-
1 -AATTTTGGAAGTTCTAAGGGTAAAAATGTCATTTTAGGAAATTCGAGGCAAAAAT-AC
268497 AATTATTGGAAGTTC
1 AATT-TTGGAAGTTC
268512 GAGGTTGAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
54 3 0.05
55 26 0.43
56 14 0.23
57 4 0.07
58 6 0.10
59 7 0.12
ACGTcount: A:0.37, C:0.05, G:0.25, T:0.33
Consensus pattern (57 bp):
AATTTTGGAAGTTCTAAGGGTAAAAATGTCATTTTAGGAAATTCGAGGCAAAAATAC
Found at i:268562 original size:30 final size:30
Alignment explanation
Indices: 268443--268662 Score: 170
Period size: 30 Copynumber: 7.5 Consensus size: 30
268433 TAGAAATACG
**
268443 ATTTTTG-GAAGTTCT-AGGG-AAAAATGTG
1 ATTTTTGAGAAGTT-TGAGGGTAAAAATGAA
* *
268471 A-TTTTG-GAAGTTCGA-GGCAAAAATGAA
1 ATTTTTGAGAAGTTTGAGGGTAAAAATGAA
* * *
268498 ATTATTG-GAAGTTCGAGGTTGAAAATAT-AA
1 ATTTTTGAGAAGTTTGAGGGT-AAAA-ATGAA
*
268528 ATTTTTTAGAAGTTTGAGGGTAAAAATGAA
1 ATTTTTGAGAAGTTTGAGGGTAAAAATGAA
* * *
268558 ATTTTTGAGAAGTTCGAGGGTCAAAATGTA
1 ATTTTTGAGAAGTTTGAGGGTAAAAATGAA
* * * *
268588 ATTTTTGAGAAGTTTAAGTGTTAAAATGTA
1 ATTTTTGAGAAGTTTGAGGGTAAAAATGAA
* * *
268618 ATTTTTGAAAAGTTT-AGGGGTTAAAATGTA
1 ATTTTTGAGAAGTTTGA-GGGTAAAAATGAA
*
268648 ATTTTTGAAAAGTTT
1 ATTTTTGAGAAGTTT
268663 AGTGGTCAAA
Statistics
Matches: 163, Mismatches: 20, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.01
27 20 0.12
28 14 0.09
29 4 0.02
30 110 0.67
31 13 0.08
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.37
Consensus pattern (30 bp):
ATTTTTGAGAAGTTTGAGGGTAAAAATGAA
Found at i:268631 original size:90 final size:90
Alignment explanation
Indices: 268472--268674 Score: 213
Period size: 90 Copynumber: 2.3 Consensus size: 90
268462 AAAAATGTGA
*
268472 TTTTG-GAAGTTCGA-GG-CAAAAATGAAATTATTGGAAGTTCGAGGTTGAAAATATAAATTTTT
1 TTTTGAGAAGTTCGAGGGTC-AAAATGAAATTATTGGAAGTTCAAGGTTGAAAATATAAATTTTT
* *
268534 TAGAAGTTT-GAGGGTAAAAATGAAAT
65 GAAAAGTTTAG-GGGTAAAAATGAAAT
* * * *
268560 TTTTGAGAAGTTCGAGGGTCAAAATGTAATTTTTGAGAAGTTTAAGTGTT-AAAATGT-AATTTT
1 TTTTGAGAAGTTCGAGGGTCAAAATGAAATTATTG-GAAGTTCAAG-GTTGAAAATATAAATTTT
* *
268623 TGAAAAGTTTAGGGGTTAAAATGTAAT
64 TGAAAAGTTTAGGGGTAAAAATGAAAT
* *
268650 TTTTGAAAAGTT-TAGTGGTCAAAAT
1 TTTTGAGAAGTTCGAG-GGTCAAAAT
268675 ATGATTTATA
Statistics
Matches: 97, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
88 5 0.05
89 11 0.11
90 62 0.64
91 16 0.16
92 3 0.03
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.36
Consensus pattern (90 bp):
TTTTGAGAAGTTCGAGGGTCAAAATGAAATTATTGGAAGTTCAAGGTTGAAAATATAAATTTTTG
AAAAGTTTAGGGGTAAAAATGAAAT
Found at i:268692 original size:60 final size:60
Alignment explanation
Indices: 268575--268693 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
268565 AGAAGTTCGA
* * * *
268575 GGGTCAAAATGTAATTTTTGAGAAGTTTAAGTGTTAAAATGTAATTTTTGAAAAGTTTAG
1 GGGTCAAAATGTAATTTTTGAAAAGTTTAAGTGTCAAAATATAATTTATGAAAAGTTTAG
* *
268635 GGGTTAAAATGTAATTTTTGAAAAGTTT-AGTGGTCAAAATATGATTTAT-AAAGAGTTTA
1 GGGTCAAAATGTAATTTTTGAAAAGTTTAAGT-GTCAAAATATAATTTATGAAA-AGTTTA
268694 CGGACATTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
59 6 0.12
60 45 0.88
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.39
Consensus pattern (60 bp):
GGGTCAAAATGTAATTTTTGAAAAGTTTAAGTGTCAAAATATAATTTATGAAAAGTTTAG
Found at i:268692 original size:90 final size:90
Alignment explanation
Indices: 268527--268693 Score: 196
Period size: 90 Copynumber: 1.9 Consensus size: 90
268517 TGAAAATATA
* * * *
268527 AATTTTTTAGAAGTTTGAGGGTAAAAATGAAATTTTTGAGAAGTTCGAGGGTCAAAATGTAATTT
1 AATTTTTGAAAAGTTTGAGGGTAAAAATGAAATTTTTGAAAAGTTCGAGGGTCAAAATATAATTT
**
268592 TTGAGAAGTTTAAGTGTTAAAATGT
66 TAAAGAAGTTTAAGTGTTAAAATGT
* * * *
268617 AATTTTTGAAAAGTTT-AGGGGTTAAAATGTAATTTTTGAAAAGTT-TAGTGGTCAAAATATGAT
1 AATTTTTGAAAAGTTTGA-GGGTAAAAATGAAATTTTTGAAAAGTTCGAG-GGTCAAAATATAAT
268680 TTATAAAG-AGTTTA
64 TT-TAAAGAAGTTTA
268694 CGGACATTCT
Statistics
Matches: 64, Mismatches: 10, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
89 3 0.05
90 58 0.91
91 3 0.05
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.39
Consensus pattern (90 bp):
AATTTTTGAAAAGTTTGAGGGTAAAAATGAAATTTTTGAAAAGTTCGAGGGTCAAAATATAATTT
TAAAGAAGTTTAAGTGTTAAAATGT
Done.