Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2136
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: 134634
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:1019 original size:2 final size:2
Alignment explanation
Indices: 1014--1072 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
1004 ACCCACACAC
1014 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1056 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
1073 CATGCAATTG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1577 original size:336 final size:333
Alignment explanation
Indices: 1168--1830 Score: 937
Period size: 336 Copynumber: 2.0 Consensus size: 333
1158 TTAGAAAACC
* *
1168 TATTTCATATTAAATGCTTTAAATGAATTAGTTTAAATAAAAGAAAAATATGACAATTTCATATT
1 TATTTCATATTAAATGCTTTAAATAAATTAGTTTAAATAAAAGAAAAATATGAAAATTTCATATT
* * * *
1233 AATTAATTTCAATGTTTTA-CAAGCATTAATTTT-TAAAAGTTAATATTAA-CAAAAATAAAATA
66 AATTAATTTCAAT-ATTTAGCAAGCATTAATTTTGAAAAAGTTAATAGTAATAAAAAATAAAATA
*
1295 TGAAACTTTATTATATTAGTTTAATATTTTT-CATATTTCACAAACTATTGATTTGAACATAAAT
130 TGAAACTTTATTATATTAGTTT--T-TTTTTCCATATTTCACAAACTA-TGATTTGAAAATAAAT
*
1359 ATTT-AAATAT-AAAAATAAACTTTTCATGTTTTTATTCAACCA-ATTTTAATTGAAAAGACAAA
191 ATTTAAAATATAAAAAAT-AACTTTTCATATTTTTATTCAACCATA-TTTAATTGAAAAGACAAA
* *
1421 AAAAAAAAGTTTATAAAATCTTTCCATATTAATTTCA-ATTTTCTCATAATCAATTTATGTTGAA
254 AAAAAAAAGTTTATAAAATATTTCCATATTAATTTCATATTTTCTCACAATCAATTTATGTTGAA
1485 ACTTTTTTTATAAAA
319 ACTTTTTTTATAAAA
*
1500 TATTTCCATATTAAATGTTTTTAAATAAAATTAGTTTAAATAAAAAGAAAAATATGAAAATTTCA
1 TATTT-CATATTAAATG-CTTTAAAT-AAATTAGTTTAAAT-AAAAGAAAAATATGAAAATTTCA
* *
1565 TATTAATTAATTTCAATATTTAGCAAGTATTAATTTTGAAAAAGTTACTAGTAATAAAAAATAAA
62 TATTAATTAATTTCAATATTTAGCAAGCATTAATTTTGAAAAAGTTAATAGTAATAAAAAATAAA
* * **
1630 ATATGAAACTTTATTATATTAGTTTTTTTTTCCATATTTTACGAGGTATGATTTGAAAATAAATA
127 ATATGAAACTTTATTATATTAGTTTTTTTTTCCATATTTCACAAACTATGATTTGAAAATAAATA
* * * **
1695 TTTAAAATATAAAAAATAACTTTTCATATTTTTATTCTACCATATTTAATTGAAATGATAGGAAA
192 TTTAAAATATAAAAAATAACTTTTCATATTTTTATTCAACCATATTTAATTGAAAAGACAAAAAA
* * * *
1760 TAAAAGTTTATAAAATATTTCCATATTAATTTCATTTTTTTTCACAATCAATTTATTTTGAAACT
257 AAAAAGTTTATAAAATATTTCCATATTAATTTCATATTTTCTCACAATCAATTTATGTTGAAACT
1825 TTTTTT
322 TTTTTT
1831 TTATATTCTA
Statistics
Matches: 293, Mismatches: 26, Indels: 19
0.87 0.08 0.06
Matches are distributed among these distances:
332 5 0.02
333 11 0.04
334 7 0.02
335 41 0.14
336 143 0.49
337 52 0.18
338 34 0.12
ACGTcount: A:0.43, C:0.08, G:0.06, T:0.43
Consensus pattern (333 bp):
TATTTCATATTAAATGCTTTAAATAAATTAGTTTAAATAAAAGAAAAATATGAAAATTTCATATT
AATTAATTTCAATATTTAGCAAGCATTAATTTTGAAAAAGTTAATAGTAATAAAAAATAAAATAT
GAAACTTTATTATATTAGTTTTTTTTTCCATATTTCACAAACTATGATTTGAAAATAAATATTTA
AAATATAAAAAATAACTTTTCATATTTTTATTCAACCATATTTAATTGAAAAGACAAAAAAAAAA
AGTTTATAAAATATTTCCATATTAATTTCATATTTTCTCACAATCAATTTATGTTGAAACTTTTT
TTATAAAA
Found at i:2647 original size:13 final size:13
Alignment explanation
Indices: 2629--2683 Score: 56
Period size: 13 Copynumber: 3.8 Consensus size: 13
2619 CAACGATTTA
2629 TATCGATACAATG
1 TATCGATACAATG
2642 TATCGATACATAAGTGTTG
1 TATCGATAC--AA----TG
2661 TATCGATACAATG
1 TATCGATACAATG
2674 TATCGATACA
1 TATCGATACA
2684 TAAGTTTTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
13 21 0.58
15 2 0.06
17 2 0.06
19 11 0.31
ACGTcount: A:0.36, C:0.15, G:0.16, T:0.33
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:2664 original size:19 final size:18
Alignment explanation
Indices: 2640--2702 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
2630 ATCGATACAA
2640 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
2659 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
2672 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
2691 TGTATCGATACA
1 TGTATCGATACA
2703 ATGTATCGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:2670 original size:32 final size:32
Alignment explanation
Indices: 2629--2710 Score: 155
Period size: 32 Copynumber: 2.6 Consensus size: 32
2619 CAACGATTTA
2629 TATCGATACAATGTATCGATACATAAGTGTTG
1 TATCGATACAATGTATCGATACATAAGTGTTG
*
2661 TATCGATACAATGTATCGATACATAAGTTTTG
1 TATCGATACAATGTATCGATACATAAGTGTTG
2693 TATCGATACAATGTATCG
1 TATCGATACAATGTATCG
2711 CTATGAAGCT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.35
Consensus pattern (32 bp):
TATCGATACAATGTATCGATACATAAGTGTTG
Found at i:2756 original size:21 final size:19
Alignment explanation
Indices: 2730--2783 Score: 60
Period size: 21 Copynumber: 2.9 Consensus size: 19
2720 TACTCTAAGA
2730 AAATGTATCGATACATTACT
1 AAATGTATCGATACATTA-T
*
2750 CAAATGTATCAATACA--AT
1 -AAATGTATCGATACATTAT
2768 -AATGTATCGATACATT
1 AAATGTATCGATACATT
2784 GTATCGATAC
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
16 13 0.45
18 1 0.03
19 1 0.03
21 14 0.48
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (19 bp):
AAATGTATCGATACATTAT
Found at i:2788 original size:13 final size:13
Alignment explanation
Indices: 2770--2794 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2760 AATACAATAA
2770 TGTATCGATACAT
1 TGTATCGATACAT
2783 TGTATCGATACA
1 TGTATCGATACA
2795 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:8783 original size:27 final size:27
Alignment explanation
Indices: 8726--8783 Score: 62
Period size: 27 Copynumber: 2.1 Consensus size: 27
8716 AAAAGTCACC
* * * * *
8726 CTTTATGTTTATTAAAATTGGTGGTTA
1 CTTTATATTTATAAAAAATGATGATTA
*
8753 CTTTATATTTATAAAAAATGATGATTT
1 CTTTATATTTATAAAAAATGATGATTA
8780 CTTT
1 CTTT
8784 TTGTTTGTCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (27 bp):
CTTTATATTTATAAAAAATGATGATTA
Found at i:13321 original size:27 final size:27
Alignment explanation
Indices: 13291--13387 Score: 101
Period size: 27 Copynumber: 3.7 Consensus size: 27
13281 AAAGCCACCC
*
13291 TTTGTGTTTGTCAAAATTGGTGGTTAT
1 TTTGTATTTGTCAAAATTGGTGGTTAT
* * *
13318 TTTGTATTTGTCAAAAATGGTGATTCT
1 TTTGTATTTGTCAAAATTGGTGGTTAT
* *
13345 TTTTTATTTGTCAAAAATT-GTGG-CAT
1 TTTGTATTTGTC-AAAATTGGTGGTTAT
*
13371 GTTGT-TTTGTCAAAATT
1 TTTGTATTTGTCAAAATT
13388 AGTGACTAAT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
24 6 0.10
25 6 0.10
26 4 0.07
27 37 0.64
28 5 0.09
ACGTcount: A:0.24, C:0.06, G:0.20, T:0.51
Consensus pattern (27 bp):
TTTGTATTTGTCAAAATTGGTGGTTAT
Found at i:14207 original size:16 final size:16
Alignment explanation
Indices: 14182--14212 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14172 AATTAATATC
14182 TTTATATTTTTAAATT
1 TTTATATTTTTAAATT
*
14198 TTTATTTTTTTAAAT
1 TTTATATTTTTAAAT
14213 ATATGTTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTATATTTTTAAATT
Found at i:15195 original size:56 final size:52
Alignment explanation
Indices: 15133--15236 Score: 129
Period size: 52 Copynumber: 1.9 Consensus size: 52
15123 AGATTGTGTT
15133 TTCAATAGGAA-ATTAATAATAAACATCAAAATAATTTAAATTAAAATTTTAATATC
1 TTCAATA-GAAGATTAATAAT-AA-A--AAAATAATTTAAATTAAAATTTTAATATC
* * *
15189 TTCAATAGAAGTTTAATAATAAAAAAGTAATTTAATTTAAAATTTTAA
1 TTCAATAGAAGATTAATAATAAAAAAATAATTTAAATTAAAATTTTAA
15237 AAAGAGGTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
52 23 0.52
54 1 0.02
55 5 0.11
56 15 0.34
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.38
Consensus pattern (52 bp):
TTCAATAGAAGATTAATAATAAAAAAATAATTTAAATTAAAATTTTAATATC
Found at i:15820 original size:11 final size:12
Alignment explanation
Indices: 15801--15853 Score: 58
Period size: 12 Copynumber: 4.6 Consensus size: 12
15791 GTTCTTACAT
15801 ATATAAAAAATA
1 ATATAAAAAATA
15813 AT-T-AAAAATA
1 ATATAAAAAATA
*
15823 ATATAAAATAT-
1 ATATAAAAAATA
*
15834 ATCACAAAAAATA
1 AT-ATAAAAAATA
15847 ATATAAA
1 ATATAAA
15854 TATAAATATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
10 9 0.27
11 4 0.12
12 18 0.55
13 2 0.06
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (12 bp):
ATATAAAAAATA
Found at i:15821 original size:10 final size:11
Alignment explanation
Indices: 15801--15875 Score: 55
Period size: 12 Copynumber: 6.5 Consensus size: 11
15791 GTTCTTACAT
15801 ATATAAAAAATA
1 ATAT-AAAAATA
15813 AT-TAAAAATA
1 ATATAAAAATA
15823 ATAT-AAAATA
1 ATATAAAAATA
*
15833 TATCACAAAAAATA
1 -AT-A-TAAAAATA
*
15847 ATATAAATATAA
1 ATATAAAAAT-A
*
15859 ATATAAATATAA
1 ATATAAAAAT-A
15871 ATATA
1 ATATA
15876 TATTAAATAT
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
10 15 0.28
11 9 0.17
12 22 0.41
13 2 0.04
14 6 0.11
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
ATATAAAAATA
Found at i:15861 original size:12 final size:12
Alignment explanation
Indices: 15846--15958 Score: 81
Period size: 12 Copynumber: 9.2 Consensus size: 12
15836 CACAAAAAAT
15846 AATATAAATATA
1 AATATAAATATA
15858 AATATAAATATA
1 AATATAAATATA
*
15870 AATATATAT-TA
1 AATATAAATATA
15881 AATAT--ATATA
1 AATATAAATATA
15891 AATTATTAATATATA
1 AA-TA-TAA-ATATA
* **
15906 AAAATTTATATA
1 AATATAAATATA
15918 ATATATAATATATTA
1 A-ATATAA-ATA-TA
*
15933 AATGT-AATATA
1 AATATAAATATA
*
15944 ATATATAAAAATA
1 A-ATATAAATATA
15957 AA
1 AA
15959 AAATCATAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
9 2 0.03
10 4 0.05
11 12 0.15
12 34 0.43
13 11 0.14
14 7 0.09
15 10 0.12
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (12 bp):
AATATAAATATA
Found at i:15902 original size:26 final size:26
Alignment explanation
Indices: 15850--15951 Score: 93
Period size: 26 Copynumber: 3.8 Consensus size: 26
15840 AAAAATAATA
*
15850 TAAATATAAATATAAATATAAATATATAT
1 TAAATAT--ATATAAATATATA-ATATAT
15879 TAAATATATATAAAT-TATTAATATA-
1 TAAATATATATAAATATA-TAATATAT
* *
15904 TAAAAATTTATATAATATATAATATAT
1 TAAATATATATA-AATATATAATATAT
*
15931 TAAATGTA-ATATAATATATAA
1 TAAATATATATA-AATATATAA
15952 AAATAAAAAA
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
25 10 0.16
26 30 0.48
27 16 0.25
29 7 0.11
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (26 bp):
TAAATATATATAAATATATAATATAT
Found at i:17463 original size:101 final size:101
Alignment explanation
Indices: 17288--17487 Score: 382
Period size: 101 Copynumber: 2.0 Consensus size: 101
17278 ATAATTGTTA
* *
17288 ATAAGGTCACTGATTAATCCAATATTCATAGTCAGAAATGATTGCATTATTCTCTTCTAATATGG
1 ATAAGGTCACTGATTAATCCAATATTCATACTCAGAAATGATTGCATTATTCTCCTCTAATATGG
17353 CTAGAAATAAGCTTGAAGAACCTTCTCAATCACACC
66 CTAGAAATAAGCTTGAAGAACCTTCTCAATCACACC
17389 ATAAGGTCACTGATTAATCCAATATTCATACTCAGAAATGATTGCATTATTCTCCTCTAATATGG
1 ATAAGGTCACTGATTAATCCAATATTCATACTCAGAAATGATTGCATTATTCTCCTCTAATATGG
17454 CTAGAAATAAGCTTGAAGAACCTTCTCAATCACA
66 CTAGAAATAAGCTTGAAGAACCTTCTCAATCACA
17488 TCCTGCTAAT
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
101 97 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (101 bp):
ATAAGGTCACTGATTAATCCAATATTCATACTCAGAAATGATTGCATTATTCTCCTCTAATATGG
CTAGAAATAAGCTTGAAGAACCTTCTCAATCACACC
Found at i:19137 original size:19 final size:19
Alignment explanation
Indices: 19113--19160 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
19103 GAAAAAAGAC
19113 AGAAAGAGAAAGAAGGAAA
1 AGAAAGAGAAAGAAGGAAA
* *
19132 AGAAAGA-ATAGGAGGGAAA
1 AGAAAGAGA-AAGAAGGAAA
*
19151 GGAAAGAGAA
1 AGAAAGAGAA
19161 TAAAAATTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.04
19 22 0.92
20 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.35, T:0.02
Consensus pattern (19 bp):
AGAAAGAGAAAGAAGGAAA
Found at i:19248 original size:41 final size:41
Alignment explanation
Indices: 19189--19272 Score: 109
Period size: 40 Copynumber: 2.0 Consensus size: 41
19179 TTTTGTATTA
**
19189 ATTTTTAGTATGTTTAAAATATTAAAATTT-TATTTATTTTTT
1 ATTTTTAGTATGGATAAAATATT-AAATTTATA-TTATTTTTT
*
19231 ATTTTTA-TATGGATAAAATATTATATTTATATTATTTTTT
1 ATTTTTAGTATGGATAAAATATTAAATTTATATTATTTTTT
19271 AT
1 AT
19273 GTCATATTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
40 16 0.42
41 15 0.39
42 7 0.18
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.61
Consensus pattern (41 bp):
ATTTTTAGTATGGATAAAATATTAAATTTATATTATTTTTT
Found at i:19279 original size:28 final size:28
Alignment explanation
Indices: 19248--19308 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
19238 TATGGATAAA
*
19248 ATATTA-TATTTATATTATTTTTTATGTC
1 ATATTATTATTTAAATTATTTTTT-TGTC
* *
19276 ATATTATTTTTTAAATTATTTTTTTGTT
1 ATATTATTATTTAAATTATTTTTTTGTC
19304 ATATT
1 ATATT
19309 TTAATTCATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (28 bp):
ATATTATTATTTAAATTATTTTTTTGTC
Found at i:22876 original size:13 final size:13
Alignment explanation
Indices: 22858--22908 Score: 61
Period size: 13 Copynumber: 4.0 Consensus size: 13
22848 ATTTTTCATC
22858 TAATATTTATTAT
1 TAATATTTATTAT
22871 TAATATTTATT-T
1 TAATATTTATTAT
* *
22883 TAATTAATTA-TAA
1 TAA-TATTTATTAT
22896 TAATATTTATTAT
1 TAATATTTATTAT
22909 ATTAATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 10 0.32
13 21 0.68
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TAATATTTATTAT
Found at i:22957 original size:19 final size:21
Alignment explanation
Indices: 22906--22961 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
22896 TAATATTTAT
22906 TATATTAATAATTATAAGAAA
1 TATATTAATAATTATAAGAAA
22927 TATA--ACATAATTA-AA-AAA
1 TATATTA-ATAATTATAAGAAA
*
22945 TATATTTATAATTATAA
1 TATATTAATAATTATAA
22962 TTTAAATGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 9
0.75 0.03 0.22
Matches are distributed among these distances:
18 7 0.23
19 10 0.33
20 9 0.30
21 4 0.13
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (21 bp):
TATATTAATAATTATAAGAAA
Found at i:23052 original size:50 final size:50
Alignment explanation
Indices: 22993--23330 Score: 451
Period size: 50 Copynumber: 6.7 Consensus size: 50
22983 TGGAAAGAAC
* * *
22993 CTTTGACAATAGAGGGAGGTGGCTATAATTGTTGACGATTCTTCACCAAA
1 CTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAAA
* *
23043 CTTTGACAATAGAGAGAGGTGGCCATAATTGTTGACAATTCTTCACCAATA
1 CTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAA-A
* * * *
23094 TTTTTGACAATAGAGGGAAGTGACCATAATTGTTGACGATTCTTCACCAAC
1 -CTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAAA
* ** *
23145 CTTTGATAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCATCAAA
1 CTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAAA
23195 CTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAAA
1 CTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAAA
* * * *
23245 CTTTGACAATAGAGAGATGTGACAATAATTGTTGACGATTCTTCACTAAC
1 CTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAAA
* * * * **
23295 CTTTGATAATGGAAAAAGGTGGTCATAATTGTTGAC
1 CTTTGACAATAGAGAGAGGTGACCATAATTGTTGAC
23331 TCTAAGTATA
Statistics
Matches: 253, Mismatches: 33, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
50 208 0.82
51 1 0.00
52 44 0.17
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (50 bp):
CTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAAA
Found at i:27768 original size:50 final size:50
Alignment explanation
Indices: 27708--27972 Score: 413
Period size: 50 Copynumber: 5.3 Consensus size: 50
27698 GGGTGAAAAG
* *
27708 AACCTTTGACAATAAAGGGAGGTGACCATAATTGTTGACGATTCTTCACC
1 AACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACC
*
27758 AAACTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACC
1 AACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACC
* * *
27808 AACCTTTGACAATAGAGGGAGATGGCCATAATTGTTGACGATTCTTCACC
1 AACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACC
* *
27858 AACCTTTGATAATAGAGAGAGGTGACCATAATTGTTTTTACGATTCTTCACC
1 AACCTTTGACAATAGAGAGAGGTGACCATAATTG--TTGACGATTCTTCACC
* **
27910 AAACTTTGACAATAGAGAGAGGTGGTCATAATTGTTGACGATTCTTCACC
1 AACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACC
27960 AACCTTTGACAAT
1 AACCTTTGACAAT
27973 GGAAAAAGGT
Statistics
Matches: 195, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
50 150 0.77
52 45 0.23
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (50 bp):
AACCTTTGACAATAGAGAGAGGTGACCATAATTGTTGACGATTCTTCACC
Found at i:27990 original size:152 final size:150
Alignment explanation
Indices: 27708--27995 Score: 441
Period size: 152 Copynumber: 1.9 Consensus size: 150
27698 GGGTGAAAAG
*
27708 AACCTTTGACAATAAAGGGAGGTGACCATAATTGTTGACGATTCTTCACCAAACTTTGACAATAG
1 AACCTTTGACAATAAAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAAACTTTGACAATAG
*** *
27773 AGAGAGGTGACCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAGGGAGATGGCCATA
66 AGAGAGGTGACCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAAAGATAGCCATA
27838 ATTGTTGACGATTCTTCACC
131 ATTGTTGACGATTCTTCACC
* * *
27858 AACCTTTGATAATAGAGAGAGGTGACCATAATTGTTTTTACGATTCTTCACCAAACTTTGACAAT
1 AACCTTTGACAATAAAGAGAGGTGACCATAATTG--TTGACGATTCTTCACCAAACTTTGACAAT
** * * *
27923 AGAGAGAGGTGGTCATAATTGTTGACGATTCTTCACCAACCTTTGACAATGGAAAAAGGTAGTCA
64 AGAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAAAGATAGCCA
27988 TAATTGTT
129 TAATTGTT
27996 AACTCTAAGT
Statistics
Matches: 123, Mismatches: 13, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
150 31 0.25
152 92 0.75
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (150 bp):
AACCTTTGACAATAAAGAGAGGTGACCATAATTGTTGACGATTCTTCACCAAACTTTGACAATAG
AGAGAGGTGACCATAATTGTTGACGATTCTTCACCAACCTTTGACAATAGAAAAAGATAGCCATA
ATTGTTGACGATTCTTCACC
Found at i:29455 original size:23 final size:24
Alignment explanation
Indices: 29424--29479 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
29414 TTTATTTAAA
*
29424 ATAAGTAAAT-TTATTTATAAATAT
1 ATAAATAAATATT-TTTATAAATAT
*
29448 -TAAATAAATATTTTTATTAATAT
1 ATAAATAAATATTTTTATAAATAT
*
29471 ATAATTAAA
1 ATAAATAAA
29480 CACGTTTACA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 18 0.67
24 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (24 bp):
ATAAATAAATATTTTTATAAATAT
Found at i:30326 original size:15 final size:16
Alignment explanation
Indices: 30306--30339 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30296 TCTACCTTTC
*
30306 AAAT-AAAATTAAAAA
1 AAATAAAAAATAAAAA
30321 AAATAAAAAATAAAAA
1 AAATAAAAAATAAAAA
30337 AAA
1 AAA
30340 AGGAAAAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (16 bp):
AAATAAAAAATAAAAA
Found at i:30513 original size:2 final size:2
Alignment explanation
Indices: 30506--30534 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
30496 TTTGATCGGC
30506 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
30535 AAGGGGAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:30766 original size:19 final size:19
Alignment explanation
Indices: 30742--30779 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
30732 TTTAAGAAAG
30742 TTAAAAATTATAAAA-AATA
1 TTAAAAATT-TAAAATAATA
30761 TTAAAAATTTAAAATAATA
1 TTAAAAATTTAAAATAATA
30780 ATATAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TTAAAAATTTAAAATAATA
Found at i:31336 original size:15 final size:16
Alignment explanation
Indices: 31298--31339 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
31288 TGCTGGATGA
*
31298 TAAATTAATTTTGAGT
1 TAAATTAATTTAGAGT
31314 TAAATTAATTTAGA-T
1 TAAATTAATTTAGAGT
*
31329 TGAATTAATTT
1 TAAATTAATTT
31340 TAATTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (16 bp):
TAAATTAATTTAGAGT
Found at i:38795 original size:38 final size:39
Alignment explanation
Indices: 38705--38815 Score: 95
Period size: 38 Copynumber: 2.8 Consensus size: 39
38695 TCTTCTTTTA
* * *
38705 TTTAATTAATT-ATTATT-ATTTTATGTATATATATTTATTT
1 TTTAATT-ATTAATTATTAATTTT-TATATTTTTA-TTATTT
*
38745 TTTAATTATTAATTATTGATTTTTAT-TTTTTATTATTCT
1 TTTAATTATTAATTATTAATTTTTATATTTTTATTATT-T
* * *
38784 TTT-ATTTTTAATTTTTAATTTTTTTATTTTTA
1 TTTAATTATTAATTATTAATTTTTATATTTTTA
38816 AATTAGTCCG
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
38 23 0.38
39 17 0.28
40 15 0.25
41 5 0.08
ACGTcount: A:0.27, C:0.01, G:0.02, T:0.70
Consensus pattern (39 bp):
TTTAATTATTAATTATTAATTTTTATATTTTTATTATTT
Found at i:38819 original size:16 final size:15
Alignment explanation
Indices: 38741--38816 Score: 59
Period size: 14 Copynumber: 5.1 Consensus size: 15
38731 ATATATATTT
*
38741 ATTTTTTAATTATTA
1 ATTTTTTAATTTTTA
* *
38756 A-TTATTGATTTTT-
1 ATTTTTTAATTTTTA
*
38769 ATTTTTTATTATTCTTTT
1 ATTTTTTA--ATT-TTTA
38787 A-TTTTTAATTTTTA
1 ATTTTTTAATTTTTA
*
38801 ATTTTTTTATTTTTA
1 ATTTTTTAATTTTTA
38816 A
1 A
38817 ATTAGTCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
13 1 0.02
14 17 0.35
15 17 0.35
16 3 0.06
17 9 0.19
18 1 0.02
ACGTcount: A:0.25, C:0.01, G:0.01, T:0.72
Consensus pattern (15 bp):
ATTTTTTAATTTTTA
Found at i:59292 original size:13 final size:12
Alignment explanation
Indices: 59271--59331 Score: 59
Period size: 13 Copynumber: 4.6 Consensus size: 12
59261 TAAATGTTTT
*
59271 AAAATTATTATTA
1 AAAAATATTA-TA
59284 AAAAATATTATA
1 AAAAATATTATA
59296 AAAAATTAATATATA
1 AAAAA-T-AT-TATA
59311 AAAAATATGTATA
1 AAAAATAT-TATA
59324 AAATAATA
1 AAA-AATA
59332 AAAAACTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
12 7 0.17
13 19 0.45
14 7 0.17
15 9 0.21
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (12 bp):
AAAAATATTATA
Found at i:59306 original size:16 final size:15
Alignment explanation
Indices: 59271--59316 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
59261 TAAATGTTTT
*
59271 AAAATTATTAT-TAA
1 AAAATTAATATATAA
59285 AAAA-T-AT-TATAA
1 AAAATTAATATATAA
59297 AAAATTAATATATAA
1 AAAATTAATATATAA
59312 AAAAT
1 AAAAT
59317 ATGTATAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
11 1 0.04
12 8 0.30
13 2 0.07
14 6 0.22
15 10 0.37
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AAAATTAATATATAA
Found at i:59313 original size:26 final size:27
Alignment explanation
Indices: 59271--59326 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
59261 TAAATGTTTT
*
59271 AAAATTATTATTAAAAAATAT-TATAA
1 AAAATTAATATTAAAAAATATGTATAA
59297 AAAATTAATATATAAAAAATATGTATAA
1 AAAATTAATAT-TAAAAAATATGTATAA
59325 AA
1 AA
59327 TAATAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 10 0.37
27 10 0.37
28 7 0.26
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (27 bp):
AAAATTAATATTAAAAAATATGTATAA
Found at i:60871 original size:39 final size:40
Alignment explanation
Indices: 60824--60899 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
60814 ATACATTATC
60824 ATTTATCTTTTAATTATTTATCAA-ATAAATATATTATAT
1 ATTTATCTTTTAATTATTTATCAAGATAAATATATTATAT
* * *
60863 ATTTATCTTTTGATTATTTATTAAGATTAATATATTA
1 ATTTATCTTTTAATTATTTATCAAGATAAATATATTA
60900 ATTTTAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 22 0.67
40 11 0.33
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (40 bp):
ATTTATCTTTTAATTATTTATCAAGATAAATATATTATAT
Found at i:61386 original size:14 final size:14
Alignment explanation
Indices: 61352--61380 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
61342 TAAAAACTAG
61352 TTAAAATTAAATAA
1 TTAAAATTAAATAA
61366 TTAAAATTAAA-AA
1 TTAAAATTAAATAA
61379 TT
1 TT
61381 TTAAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.27
14 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAAATTAAATAA
Found at i:61415 original size:29 final size:30
Alignment explanation
Indices: 61383--61450 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
61373 TAAAAATTTT
* *
61383 AAATATTATATAATC-GATAT-AAATTAATA
1 AAATATTATATAAACTAATATAAAATTAA-A
61412 AAAT-TTATATAAACTAATATAAAATTAAA
1 AAATATTATATAAACTAATATAAAATTAAA
61441 AATATATTAT
1 AA-ATATTAT
61451 TATATCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 9 0.27
29 11 0.33
30 9 0.27
31 4 0.12
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (30 bp):
AAATATTATATAAACTAATATAAAATTAAA
Found at i:61959 original size:16 final size:14
Alignment explanation
Indices: 61937--61988 Score: 61
Period size: 15 Copynumber: 3.6 Consensus size: 14
61927 ACCAAACTAG
61937 TATTATTTTAAAAA
1 TATTATTTTAAAAA
*
61951 T-TAATTATTAAATAA
1 TATTATT-TTAAA-AA
61966 TATTATTTTAAAATA
1 TATTATTTTAAAA-A
61981 TATTATTT
1 TATTATTT
61989 AAATTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
13 4 0.12
14 7 0.22
15 17 0.53
16 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (14 bp):
TATTATTTTAAAAA
Found at i:61980 original size:13 final size:13
Alignment explanation
Indices: 61937--62000 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 13
61927 ACCAAACTAG
61937 TATTATTTTAAAA
1 TATTATTTTAAAA
61950 -ATTAATTATTAAATAA
1 TATT-ATT-TT-AA-AA
61966 TATTATTTTAAAA
1 TATTATTTTAAAA
*
61979 TA-TATTATTTAAA
1 TATTATT-TTAAAA
*
61992 TTTTATTTT
1 TATTATTTT
62001 TTATTAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 14
0.72 0.03 0.24
Matches are distributed among these distances:
12 7 0.17
13 15 0.36
14 8 0.19
15 4 0.10
16 5 0.12
17 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TATTATTTTAAAA
Found at i:62575 original size:20 final size:20
Alignment explanation
Indices: 62521--62595 Score: 53
Period size: 19 Copynumber: 3.5 Consensus size: 20
62511 AGAACAACGT
* *
62521 AAATTCACATTTATTATTTAA
1 AAATTCATATTT-TTATTTTA
* **
62542 AAAAT-ATAAATTTATTTTA
1 AAATTCATATTTTTATTTTA
62561 AAATTCATATTTTTACTATTTA
1 AAATTCATATTTTTA-T-TTTA
62583 ATGAATTCATATT
1 A--AATTCATATT
62596 AAAAATCTAA
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
19 11 0.27
20 10 0.24
21 5 0.12
22 5 0.12
24 10 0.24
ACGTcount: A:0.43, C:0.07, G:0.01, T:0.49
Consensus pattern (20 bp):
AAATTCATATTTTTATTTTA
Found at i:62960 original size:82 final size:80
Alignment explanation
Indices: 62840--62988 Score: 210
Period size: 82 Copynumber: 1.8 Consensus size: 80
62830 TTTTTATGTA
* *
62840 TTCATATTATTTTTATATCATGTAATATTTTAGGTCATGTTATTTT-TTATATATTTGTGTTATT
1 TTCATATTATTTTTATATCATGTAATATTTTAGGTCATGTTATTTTATTATACATTAGTGTTATT
62904 TTATTTGTATTATAT
66 TTATTTGTATTATAT
* ** *
62919 TTCATATTATTTTTTTCATGCCATGTCGTATTTTAGGTCATGTTATTTTATTATGCATTAGTGTT
1 TTCATATTATTTTTAT-AT--CATGTAATATTTTAGGTCATGTTATTTTATTATACATTAGTGTT
62984 ATTTT
63 ATTTT
62989 TTCCAGTCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
79 15 0.25
80 2 0.03
82 26 0.43
83 17 0.28
ACGTcount: A:0.23, C:0.07, G:0.11, T:0.60
Consensus pattern (80 bp):
TTCATATTATTTTTATATCATGTAATATTTTAGGTCATGTTATTTTATTATACATTAGTGTTATT
TTATTTGTATTATAT
Found at i:63526 original size:29 final size:29
Alignment explanation
Indices: 63484--63555 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
63474 CAAAAATAGT
* *
63484 ATTATTTTGGTAATATATTT-AGATACAAC
1 ATTATTTTGATAATATATTTCA-AAACAAC
* * *
63513 ATTATTTTAATAATATGTTTCAAAACAAT
1 ATTATTTTGATAATATATTTCAAAACAAC
63542 ATTATTTTGATAAT
1 ATTATTTTGATAAT
63556 TAATTTTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
29 35 0.97
30 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (29 bp):
ATTATTTTGATAATATATTTCAAAACAAC
Found at i:63755 original size:2 final size:2
Alignment explanation
Indices: 63748--63773 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63738 TATTTAATAC
63748 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
63774 GAGTTCATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:66220 original size:11 final size:11
Alignment explanation
Indices: 66185--66239 Score: 58
Period size: 11 Copynumber: 4.9 Consensus size: 11
66175 AAAGTTAGAT
66185 AAGAAAGAAAG
1 AAGAAAGAAAG
*
66196 AAGGAAGATGAAG
1 AAGAAAGA--AAG
66209 AAGAAAGAAAG
1 AAGAAAGAAAG
*
66220 AA-AAAGAAAA
1 AAGAAAGAAAG
*
66230 AAAAAAGAAA
1 AAGAAAGAAA
66240 AAATATGAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 9 0.24
11 19 0.50
13 10 0.26
ACGTcount: A:0.75, C:0.00, G:0.24, T:0.02
Consensus pattern (11 bp):
AAGAAAGAAAG
Found at i:66226 original size:17 final size:17
Alignment explanation
Indices: 66206--66241 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
66196 AAGGAAGATG
* *
66206 AAGAAGAAAGAAAGAAA
1 AAGAAAAAAAAAAGAAA
66223 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
66240 AA
1 AA
66242 ATATGAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:68879 original size:2 final size:2
Alignment explanation
Indices: 68872--68902 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
68862 AATCATAATT
*
68872 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
68903 GAATCCTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 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):
TA
Found at i:69867 original size:15 final size:15
Alignment explanation
Indices: 69833--69876 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
69823 ATAAAATAAA
69833 AATAAATTAATAAATT
1 AATAAATTAA-AAATT
*
69849 -ATAAATTAAATATT
1 AATAAATTAAAAATT
*
69863 AATAAAATAAAAAT
1 AATAAATTAAAAAT
69877 ATTTATATCT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AATAAATTAAAAATT
Found at i:70191 original size:25 final size:23
Alignment explanation
Indices: 70158--70203 Score: 65
Period size: 25 Copynumber: 1.9 Consensus size: 23
70148 TGTGTTTATA
70158 TATAATAAATAATTAAAAATATATT
1 TATAATAAATAA-T-AAAATATATT
*
70183 TATATTAAATAATAAAATATA
1 TATAATAAATAATAAAATATA
70204 AATAAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 8 0.40
24 1 0.05
25 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TATAATAAATAATAAAATATATT
Found at i:70216 original size:35 final size:36
Alignment explanation
Indices: 70166--70262 Score: 110
Period size: 35 Copynumber: 2.8 Consensus size: 36
70156 TATATAATAA
* *
70166 ATAATTAAAAATATATTTATATTAAATAA-TAAAAT
1 ATAAATAAAATTATATTTATATTAAATAATTAAAAT
* *
70201 ATAAATAAAATTATATTTATGTTCAATAATTAAAAT
1 ATAAATAAAATTATATTTATATTAAATAATTAAAAT
* * *
70237 -T-ACTAAAATGATACTTATATTAAATA
1 ATAAATAAAATTATATTTATATTAAATA
70263 GTAATTTAAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
34 20 0.38
35 26 0.50
36 6 0.12
ACGTcount: A:0.55, C:0.03, G:0.02, T:0.40
Consensus pattern (36 bp):
ATAAATAAAATTATATTTATATTAAATAATTAAAAT
Found at i:70373 original size:25 final size:24
Alignment explanation
Indices: 70345--70424 Score: 83
Period size: 24 Copynumber: 3.3 Consensus size: 24
70335 TATTTATTGT
*
70345 TAATTAATTCATATTAATTTTATAA
1 TAATAAATT-ATATTAATTTTATAA
*
70370 TAATAAATTATATAATATTTTATAA
1 TAATAAATTATATTA-ATTTTATAA
*
70395 -AATAAAATATATCT-ATTTTATAA
1 TAATAAATTATAT-TAATTTTATAA
*
70418 TAGTAAA
1 TAATAAA
70425 ATTGAATTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
23 9 0.19
24 21 0.45
25 17 0.36
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (24 bp):
TAATAAATTATATTAATTTTATAA
Found at i:70424 original size:24 final size:25
Alignment explanation
Indices: 70361--70426 Score: 91
Period size: 24 Copynumber: 2.7 Consensus size: 25
70351 ATTCATATTA
*
70361 ATTTTATAATAATAAATTATATAAT
1 ATTTTATAATAATAAAATATATAAT
*
70386 ATTTTATAA-AATAAAATATAT-CT
1 ATTTTATAATAATAAAATATATAAT
*
70409 ATTTTATAATAGTAAAAT
1 ATTTTATAATAATAAAAT
70427 TGAATTTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.27
24 18 0.49
25 9 0.24
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
ATTTTATAATAATAAAATATATAAT
Found at i:71412 original size:16 final size:16
Alignment explanation
Indices: 71379--71412 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
71369 TACATTTAGC
*
71379 ATGATACGAGTTCAAA
1 ATGATACGAATTCAAA
*
71395 ATGATACGAATTCGAA
1 ATGATACGAATTCAAA
71411 AT
1 AT
71413 AGTTCAAACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (16 bp):
ATGATACGAATTCAAA
Found at i:72131 original size:16 final size:16
Alignment explanation
Indices: 72070--72135 Score: 71
Period size: 16 Copynumber: 4.1 Consensus size: 16
72060 CTTGAATTTC
* *
72070 ACTTCAAACTTAAAATG
1 ACTTGAAAC-TAAAGTG
72087 ACTTGAAACTAAAGTG
1 ACTTGAAACTAAAGTG
* * *
72103 ATTTAAAATTAAAGTG
1 ACTTGAAACTAAAGTG
72119 ACTTGAAACTAAA-TG
1 ACTTGAAACTAAAGTG
72134 AC
1 AC
72136 GTAAATTCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 4 0.10
16 29 0.71
17 8 0.20
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (16 bp):
ACTTGAAACTAAAGTG
Found at i:73137 original size:16 final size:16
Alignment explanation
Indices: 73112--73145 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
73102 CTATGGCATC
73112 TTTCCTTTTCTC-TCT
1 TTTCCTTTTCTCTTCT
73127 TTTCTCTTTTCTCTTCT
1 TTTC-CTTTTCTCTTCT
73144 TT
1 TT
73146 ATTTCTCCCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 8 0.47
17 5 0.29
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTCCTTTTCTCTTCT
Found at i:74969 original size:25 final size:24
Alignment explanation
Indices: 74941--75011 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 24
74931 GTAGATTTGA
74941 ATATTTAAATTTGATATTT-ATTTAT
1 ATATTTAAATTT-ATATTTAATTT-T
*
74966 ATATTT-AATTTTTATTTAATTTT
1 ATATTTAAATTTATATTTAATTTT
*
74989 ATATTT-AATTT-T-TTTAAATTT
1 ATATTTAAATTTATATTTAATTTT
75010 AT
1 AT
75012 TTAATAAATT
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
21 10 0.23
22 1 0.02
23 17 0.40
24 9 0.21
25 6 0.14
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.65
Consensus pattern (24 bp):
ATATTTAAATTTATATTTAATTTT
Found at i:74971 original size:12 final size:12
Alignment explanation
Indices: 74941--75000 Score: 79
Period size: 12 Copynumber: 5.0 Consensus size: 12
74931 GTAGATTTGA
*
74941 ATATTTAAATTTG
1 ATATTT-AATTTT
74954 ATATTT-ATTTAT
1 ATATTTAATTT-T
74966 ATATTTAATTTT
1 ATATTTAATTTT
74978 -TATTTAATTTT
1 ATATTTAATTTT
74989 ATATTTAATTTT
1 ATATTTAATTTT
75001 TTTAAATTTA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
11 15 0.35
12 18 0.42
13 10 0.23
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (12 bp):
ATATTTAATTTT
Found at i:74981 original size:11 final size:11
Alignment explanation
Indices: 74967--75001 Score: 61
Period size: 11 Copynumber: 3.1 Consensus size: 11
74957 TTTATTTATA
74967 TATTTAATTTT
1 TATTTAATTTT
74978 TATTTAATTTT
1 TATTTAATTTT
74989 ATATTTAATTTT
1 -TATTTAATTTT
75001 T
1 T
75002 TTAAATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (11 bp):
TATTTAATTTT
Found at i:75010 original size:21 final size:23
Alignment explanation
Indices: 74965--75011 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
74955 TATTTATTTA
*
74965 TATATTTAATTTTTATTTAATTT
1 TATATTTAATTTTTATTTAAATT
74988 TATATTTAA-TTTT-TTTAAATT
1 TATATTTAATTTTTATTTAAATT
75009 TAT
1 TAT
75012 TTAATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 10 0.43
22 4 0.17
23 9 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (23 bp):
TATATTTAATTTTTATTTAAATT
Found at i:75031 original size:17 final size:17
Alignment explanation
Indices: 75009--75045 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
74999 TTTTTAAATT
*
75009 TATTTAATAAATTTAAA
1 TATTTAAAAAATTTAAA
*
75026 TATTTAAAAAATTTCAA
1 TATTTAAAAAATTTAAA
75043 TAT
1 TAT
75046 CTGATGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTTAAAAAATTTAAA
Found at i:75136 original size:26 final size:24
Alignment explanation
Indices: 75093--75142 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
75083 AGATAATACG
75093 TGGATAATAAATAAATTTAAATTT
1 TGGATAATAAATAAATTTAAATTT
*
75117 TGGATAAATTAAATATATTTAAATTT
1 TGGAT-AA-TAAATAAATTTAAATTT
75143 AAATATTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.22
25 2 0.09
26 16 0.70
ACGTcount: A:0.48, C:0.00, G:0.08, T:0.44
Consensus pattern (24 bp):
TGGATAATAAATAAATTTAAATTT
Found at i:75150 original size:14 final size:15
Alignment explanation
Indices: 75121--75153 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
75111 AAATTTTGGA
75121 TAAATTAAATATATT
1 TAAATTAAATATATT
*
75136 TAAATTTAA-ATATT
1 TAAATTAAATATATT
75150 TAAA
1 TAAA
75154 AATTGTAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TAAATTAAATATATT
Found at i:75455 original size:29 final size:29
Alignment explanation
Indices: 75422--75482 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
75412 CCAAGCAAAG
75422 AAAAAAAAAACTCAAAA-AGACTTAAATCT
1 AAAAAAAAAACTCAAAATA-ACTTAAATCT
* *
75451 AAAAAAAAAATTCAAAATAATTTAAATCT
1 AAAAAAAAAACTCAAAATAACTTAAATCT
75480 AAA
1 AAA
75483 TAATTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (29 bp):
AAAAAAAAAACTCAAAATAACTTAAATCT
Found at i:76291 original size:2 final size:2
Alignment explanation
Indices: 76284--76311 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
76274 TGTGTTAATA
76284 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
76312 GGGGTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:83558 original size:37 final size:37
Alignment explanation
Indices: 83517--83597 Score: 126
Period size: 37 Copynumber: 2.2 Consensus size: 37
83507 ATTTTTCGTA
* * * *
83517 GATTGGCGCTGTCACCCAAATTCTAACAATTATAGTG
1 GATTGGCACTGCCACCCAAATACTAACAATCATAGTG
83554 GATTGGCACTGCCACCCAAATACTAACAATCATAGTG
1 GATTGGCACTGCCACCCAAATACTAACAATCATAGTG
83591 GATTGGC
1 GATTGGC
83598 CAAGCCACCA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (37 bp):
GATTGGCACTGCCACCCAAATACTAACAATCATAGTG
Found at i:83605 original size:37 final size:37
Alignment explanation
Indices: 83529--83612 Score: 116
Period size: 37 Copynumber: 2.3 Consensus size: 37
83519 TTGGCGCTGT
* * *
83529 CACCCAAATTCTAACAATTATAGTGGATTGGCACTGC
1 CACCCAAATACTAACAATCATAGTGGATTGGCACAGC
83566 CACCCAAATACTAACAATCATAGTGGATTGGC-CAAGC
1 CACCCAAATACTAACAATCATAGTGGATTGGCAC-AGC
*
83603 CACCAAAATA
1 CACCCAAATA
83613 TTACTTGTCG
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
36 1 0.02
37 41 0.98
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.21
Consensus pattern (37 bp):
CACCCAAATACTAACAATCATAGTGGATTGGCACAGC
Found at i:86241 original size:20 final size:20
Alignment explanation
Indices: 86216--86261 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
86206 AAATAGAGGC
*
86216 TCCCTCCTCCATCTCAAGTA
1 TCCCTCATCCATCTCAAGTA
* **
86236 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCATCTCAAGTA
86256 TCCCTC
1 TCCCTC
86262 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.48, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCATCTCAAGTA
Found at i:88678 original size:20 final size:20
Alignment explanation
Indices: 88653--88698 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
88643 AAATAGAGGC
*
88653 TCCCTCCTCCATCTCAAGTA
1 TCCCTCATCCATCTCAAGTA
* **
88673 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCATCTCAAGTA
88693 TCCCTC
1 TCCCTC
88699 TTCAATTCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.48, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCATCTCAAGTA
Found at i:91113 original size:2 final size:2
Alignment explanation
Indices: 91106--91133 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
91096 TTTCTAAATA
91106 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
91134 GCAATTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92309 original size:35 final size:33
Alignment explanation
Indices: 92252--92317 Score: 96
Period size: 35 Copynumber: 1.9 Consensus size: 33
92242 ATTTAACATG
92252 AATAATAAAAAAAATAAAAATAAAAAAGTAAGA
1 AATAATAAAAAAAATAAAAATAAAAAAGTAAGA
* *
92285 AATAATAATAAAAATATAATAATAAAATAGTAA
1 AATAATAA-AAAAA-ATAAAAATAAAAAAGTAA
92318 TAGTTAATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 8 0.28
34 5 0.17
35 16 0.55
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (33 bp):
AATAATAAAAAAAATAAAAATAAAAAAGTAAGA
Found at i:92319 original size:14 final size:14
Alignment explanation
Indices: 92264--92311 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
92254 TAATAAAAAA
*
92264 AATAAAAATA-AAA
1 AATAAAAATATAAT
*
92277 AAGTAAGAA-ATAAT
1 AA-TAAAAATATAAT
92291 AATAAAAATATAAT
1 AATAAAAATATAAT
92305 AATAAAA
1 AATAAAA
92312 TAGTAATAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 8 0.28
14 21 0.72
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (14 bp):
AATAAAAATATAAT
Found at i:93002 original size:22 final size:22
Alignment explanation
Indices: 92953--93002 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
92943 GAAACCGATG
* * *
92953 CAGCAATGAAGATATCAATGGG
1 CAGCAATGAAGACATCAACGGA
*
92975 CTGCAATGAAGACATCAACGGA
1 CAGCAATGAAGACATCAACGGA
92997 CAGCAA
1 CAGCAA
93003 AGAATGCAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (22 bp):
CAGCAATGAAGACATCAACGGA
Found at i:94665 original size:163 final size:162
Alignment explanation
Indices: 94394--95171 Score: 980
Period size: 163 Copynumber: 4.8 Consensus size: 162
94384 TTTTTATATT
* * * * * * *
94394 AAAATGGT-TTTTTATGCTCACTCGAGTCATATTTTTATATTCTTATGATTTTTTATTA-GGGTA
1 AAAATGGTCGTTTT-TGCCCACTCGAGTCATGTTCTCATATTCCTATGATTTTTCA-TAGGGGTA
* * * * *
94457 TAAAAATTTTTAAAACCTTTCATAT-CTCTTAATTTTCTATCGGGTACGAAACGTAATTTTCAAA
64 TAAAAATTTTTAAAACCTTTCGTATCCCCTGATTTTTC-GTCGGGTACGAAACGTAATTTTCAAA
*
94521 ATTTAGAAGTGTTTGGCCCATTTACATTGATATAAA
128 ATTTAAAAGTGTTTGGCCC-TTTACATTGATATAAA
* *
94557 AAAATGGTCGATTTTGCCCACTCAAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATA
1 AAAATGGTCGTTTTTGCCCACTCGAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATA
* *
94622 AAAATTTTTAAAACCTTTCGTATCCCCT-AGTTTTTCGTCGGGTACGAAATGTAATTTTTAAAAT
66 AAAATTTTTAAAACCTTTCGTATCCCCTGA-TTTTTCGTCGGGTACGAAACGTAATTTTCAAAAT
*
94686 TTAAAAGTTTTTGGCCCCTTTTACATTGATATAAA
130 TTAAAAGTGTTTGG-CCC-TTTACATTGATATAAA
** *
94721 AAAAT-GTCGTTTTTGCCCACTTAAGTCATGTACTCATATTCCTATGATTTTTCATAGGGGTATA
1 AAAATGGTCGTTTTTGCCCACTCGAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATA
* * *
94785 AAAATGTTTAAAACCTTTTGTATCCCCTGATTTTTCGTCGGGTACGAAACGTAATTTTTAAAATT
66 AAAATTTTTAAAACCTTTCGTATCCCCTGATTTTTCGTCGGGTACGAAACGTAATTTTCAAAATT
*
94850 TAAAAGTATTTGGCCTCTTTACATTGATATAAA
131 TAAAAGTGTTTGGCC-CTTTACATTGATATAAA
* ** * *
94883 AAAAGGGTCGTTTTTGCTTACTCGAGTCATGTTCTTATATTCCTATGATTTTTCATAGAGGTATA
1 AAAATGGTCGTTTTTGCCCACTCGAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATA
* * *
94948 AAAATTTTTAAAACTTTTCGTATCCCCTGATTTTTCGTCGGATATGAAACGTAATTTTCAAAATT
66 AAAATTTTTAAAACCTTTCGTATCCCCTGATTTTTCGTCGGGTACGAAACGTAATTTTCAAAATT
* *
95013 TAGAAGTGTTCTGCCCCTTTACATTGATATAAA
131 TAAAAGTGTT-TGGCCCTTTACATTGATATAAA
* * * * * * * *
95046 AGAAAAGATCGTTTTTGCCCATTCGAGTCATGTTTTCATATTCCTATGGTTTTCCGTAGGAGTAT
1 A-AAATGGTCGTTTTTGCCCACTCGAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTAT
* * * *
95111 AAAATTTTTTAAAA-CATT--TATCCCCTGATATTTCGTCGGGTACGAAACATAATTTT-AAAAT
65 AAAAATTTTTAAAACCTTTCGTATCCCCTGATTTTTCGTCGGGTACGAAACGTAATTTTCAAAAT
95172 AAAATAAATT
Statistics
Matches: 544, Mismatches: 61, Indels: 23
0.87 0.10 0.04
Matches are distributed among these distances:
160 5 0.01
161 34 0.06
162 24 0.04
163 377 0.69
164 104 0.19
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (162 bp):
AAAATGGTCGTTTTTGCCCACTCGAGTCATGTTCTCATATTCCTATGATTTTTCATAGGGGTATA
AAAATTTTTAAAACCTTTCGTATCCCCTGATTTTTCGTCGGGTACGAAACGTAATTTTCAAAATT
TAAAAGTGTTTGGCCCTTTACATTGATATAAA
Found at i:96961 original size:2 final size:2
Alignment explanation
Indices: 96954--96996 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
96944 TGCCTTTTTC
96954 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96996 A
1 A
96997 AAAGTCATTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:97594 original size:167 final size:168
Alignment explanation
Indices: 97369--97691 Score: 479
Period size: 167 Copynumber: 1.9 Consensus size: 168
97359 CTAAAAGTTG
* *
97369 AGGCTATCCACGAGTCAACTATTTTTTTTTTTTCATTTTTCCTTTGGTTGCCGTGTAGTCATTTC
1 AGGCTATCCACGAGTCAACTATTTATTTTTTTTCATTTTTCCGTTGGTTGCCGTGTAGTCATTTC
*
97434 TATTACTTTTTTTCCATTCTTTGTACTTAACCTATTTGT-TCAAGTTAAAAAACTGATGAGTTTA
66 TATTACTTTTTTTCCATTCTTTGTACTCAACCTATTTGTCT-AAGTTAAAAAACTGATGAGTTTA
* *
97498 GAAAAGATTTTACAGAGATATTAAAAGATTTAATAGCTA
130 AAAAAAATTTTACAGAGATATTAAAAGATTTAATAGCTA
* * * *
97537 AGGCTATCCATGTGTCAACTA-TTATTTTTTTTCATTTTTCCGTTGGTTGCTGTGTAGTTATTTC
1 AGGCTATCCACGAGTCAACTATTTATTTTTTTTCATTTTTCCGTTGGTTGCCGTGTAGTCATTTC
* * * * ** *
97601 TATTGCTTTTTTTTCATTCTTTGTACTCAGCCTTTTTGTCTAAGTTAAAAAGTTTATGAGTTTAA
66 TATTACTTTTTTTCCATTCTTTGTACTCAACCTATTTGTCTAAGTTAAAAAACTGATGAGTTTAA
97666 AAAAAATTTTACAGAGATATTAAAAG
131 AAAAAATTTTACAGAGATATTAAAAG
97692 CTTTTATGTA
Statistics
Matches: 138, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
167 118 0.86
168 20 0.14
ACGTcount: A:0.27, C:0.13, G:0.14, T:0.46
Consensus pattern (168 bp):
AGGCTATCCACGAGTCAACTATTTATTTTTTTTCATTTTTCCGTTGGTTGCCGTGTAGTCATTTC
TATTACTTTTTTTCCATTCTTTGTACTCAACCTATTTGTCTAAGTTAAAAAACTGATGAGTTTAA
AAAAAATTTTACAGAGATATTAAAAGATTTAATAGCTA
Found at i:98443 original size:13 final size:12
Alignment explanation
Indices: 98421--98455 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
98411 TTCTTAATAC
98421 TTTTTTTTTATT
1 TTTTTTTTTATT
98433 TTTTGTTTTTATT
1 TTTT-TTTTTATT
98446 TTTATTTTTT
1 TTT-TTTTTT
98456 TTACTTTCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.19
13 16 0.76
14 1 0.05
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.89
Consensus pattern (12 bp):
TTTTTTTTTATT
Found at i:99835 original size:20 final size:22
Alignment explanation
Indices: 99810--99866 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 22
99800 CATTATTTAA
99810 TATTGGCATG-G-CTATTATTC
1 TATTGGCATGTGACTATTATTC
99830 TATTGGCATGTGTAATCTATTATTC
1 TATTGGCATGTG--A-CTATTATTC
99855 TATTGGCATGTG
1 TATTGGCATGTG
99867 TAATTTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.31
21 1 0.03
25 21 0.66
ACGTcount: A:0.21, C:0.12, G:0.21, T:0.46
Consensus pattern (22 bp):
TATTGGCATGTGACTATTATTC
Found at i:99850 original size:25 final size:25
Alignment explanation
Indices: 99821--99870 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
99811 ATTGGCATGG
99821 CTATTATTCTATTGGCATGTGTAAT
1 CTATTATTCTATTGGCATGTGTAAT
99846 CTATTATTCTATTGGCATGTGTAAT
1 CTATTATTCTATTGGCATGTGTAAT
99871 TTTTGTGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (25 bp):
CTATTATTCTATTGGCATGTGTAAT
Found at i:102325 original size:19 final size:19
Alignment explanation
Indices: 102293--102347 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
102283 TTATATTATT
102293 TATATAATTA-TAAATATAA
1 TATA-AATTATTAAATATAA
* *
102312 TATAAATTATTAAATTTAT
1 TATAAATTATTAAATATAA
*
102331 TA-AAATT-TTAAAAATAA
1 TATAAATTATTAAATATAA
102348 ATGTTATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
17 7 0.23
18 10 0.33
19 13 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TATAAATTATTAAATATAA
Found at i:102399 original size:17 final size:17
Alignment explanation
Indices: 102379--102430 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
102369 ATAATATTTA
102379 TTATAATATTTTTATAT
1 TTATAATATTTTTATAT
* * *
102396 TTATAAAAATTTAATAT
1 TTATAATATTTTTATAT
*
102413 TTATATTATATTTTATAT
1 TTATAATAT-TTTTATAT
102431 AGTATATAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 20 0.74
18 7 0.26
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TTATAATATTTTTATAT
Found at i:102442 original size:37 final size:37
Alignment explanation
Indices: 102368--102460 Score: 104
Period size: 37 Copynumber: 2.5 Consensus size: 37
102358 TGGATAATTA
* *
102368 TATAATATTTATTATAATATTTTTATATTTATAAAAAT
1 TATAATATTTA-TATTATATTTTTATATATATAAAAAT
102406 T-TAATATTTATATTATA-TTTTATATAGTATATAAAAT
1 TATAATATTTATATTATATTTTTATATA-TATA-AAAAT
102443 TATCAA-ATTTA-ATTATAT
1 TAT-AATATTTATATTATAT
102461 GATATAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
35 8 0.17
36 10 0.21
37 21 0.44
38 7 0.15
39 2 0.04
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (37 bp):
TATAATATTTATATTATATTTTTATATATATAAAAAT
Found at i:103795 original size:24 final size:26
Alignment explanation
Indices: 103768--103818 Score: 70
Period size: 24 Copynumber: 2.0 Consensus size: 26
103758 ATGATATGTA
103768 TTAAATATATCATATTA-ATT-GTGT
1 TTAAATATATCATATTATATTGGTGT
* *
103792 TTAAATATGTTATATTATATTGGTGT
1 TTAAATATATCATATTATATTGGTGT
103818 T
1 T
103819 GATTAAATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 15 0.65
25 3 0.13
26 5 0.22
ACGTcount: A:0.33, C:0.02, G:0.12, T:0.53
Consensus pattern (26 bp):
TTAAATATATCATATTATATTGGTGT
Found at i:106192 original size:2 final size:2
Alignment explanation
Indices: 106187--106217 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
106177 GTTTTTTGGT
106187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
106218 GCATATGTAG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:109679 original size:27 final size:26
Alignment explanation
Indices: 109642--109692 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
109632 TTTCTTGATT
*
109642 GAAAAATGGGGTTGGAGTATCCCCTC
1 GAAAAATGGGGTTAGAGTATCCCCTC
109668 GAAAGAATGGGGTTAGAGTATCCCC
1 GAAA-AATGGGGTTAGAGTATCCCC
109693 GATGATGACA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 4 0.17
27 19 0.83
ACGTcount: A:0.29, C:0.18, G:0.31, T:0.22
Consensus pattern (26 bp):
GAAAAATGGGGTTAGAGTATCCCCTC
Found at i:112021 original size:20 final size:19
Alignment explanation
Indices: 111992--112063 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 19
111982 AAAAAGACAT
111992 AATGTATCGATATATTGTA
1 AATGTATCGATATATTGTA
* * *
112011 GAATATATCGATACATTCATA
1 -AATGTATCGATATATT-GTA
* *
112032 CATGTATCGATATATTGAAA
1 AATGTATCGATATATTG-TA
112052 AATGTATCGATA
1 AATGTATCGATA
112064 CATCAAGGTA
Statistics
Matches: 41, Mismatches: 9, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
20 39 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (19 bp):
AATGTATCGATATATTGTA
Found at i:112048 original size:40 final size:39
Alignment explanation
Indices: 111989--112066 Score: 120
Period size: 40 Copynumber: 2.0 Consensus size: 39
111979 GGTAAAAAGA
* *
111989 CATAATGTATCGATATATTGTAGAATATATCGATACATT
1 CATAATGTATCGATATATTGAAAAATATATCGATACATT
*
112028 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATATATTGAAAAATATATCGATACAT
112067 CAAGGTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 4 0.11
40 31 0.89
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATATATTGAAAAATATATCGATACATT
Found at i:112950 original size:16 final size:16
Alignment explanation
Indices: 112889--112969 Score: 74
Period size: 16 Copynumber: 5.1 Consensus size: 16
112879 CAGGTTCAGA
* *
112889 TTATTTTGGGTTCAGG
1 TTATTTTGAGTTCGGG
** *
112905 TCCTTTCGAGTTCGGG
1 TTATTTTGAGTTCGGG
* *
112921 TCATTTCG-GATTCGGG
1 TTATTTTGAG-TTCGGG
*
112937 TTGTTTTGAGTTCGGG
1 TTATTTTGAGTTCGGG
112953 TTATTTTGAGTTCGGG
1 TTATTTTGAGTTCGGG
112969 T
1 T
112970 CAATCGGGTT
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
15 1 0.02
16 51 0.96
17 1 0.02
ACGTcount: A:0.10, C:0.12, G:0.32, T:0.46
Consensus pattern (16 bp):
TTATTTTGAGTTCGGG
Found at i:112967 original size:32 final size:31
Alignment explanation
Indices: 112889--112970 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 31
112879 CAGGTTCAGA
*
112889 TTATTTTGGGTTCAGGTCCTTTCGAGTTCGGG
1 TTATTTT-GGTTCGGGTCCTTTCGAGTTCGGG
* * ** *
112921 TCATTTCGGATTCGGGTTGTTTTGAGTTCGGG
1 TTATTTTGG-TTCGGGTCCTTTCGAGTTCGGG
112953 TTATTTTGAGTTCGGGTC
1 TTATTTTG-GTTCGGGTC
112971 AATCGGGTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
31 2 0.05
32 36 0.92
33 1 0.03
ACGTcount: A:0.10, C:0.13, G:0.32, T:0.45
Consensus pattern (31 bp):
TTATTTTGGTTCGGGTCCTTTCGAGTTCGGG
Found at i:113023 original size:44 final size:45
Alignment explanation
Indices: 112973--113057 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
112963 TTCGGGTCAA
* **
112973 TCGGGTTTAACACTCAGGTT-AATTGGGTTCGGGTCATTTTGGAT
1 TCGGGTTTAACACTCAGGTTAAATTAGGTTCAAGTCATTTTGGAT
* *
113017 TCGGGTTTAACATTCGGGTTAAATTAGGTTCAAGTCATTTT
1 TCGGGTTTAACACTCAGGTTAAATTAGGTTCAAGTCATTTT
113058 AAATTTAGAT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 18 0.51
45 17 0.49
ACGTcount: A:0.21, C:0.13, G:0.26, T:0.40
Consensus pattern (45 bp):
TCGGGTTTAACACTCAGGTTAAATTAGGTTCAAGTCATTTTGGAT
Found at i:114421 original size:15 final size:15
Alignment explanation
Indices: 114403--114453 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
114393 ATCTTCTTCT
114403 TTCTTCTTCTCTTGC
1 TTCTTCTTCTCTTGC
*
114418 TTCTTCATATTTTCTT-C
1 TTCTTC---TTCTCTTGC
114435 TTTCTTCTTCTCTTGC
1 -TTCTTCTTCTCTTGC
114451 TTC
1 TTC
114454 CTCCAACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 15 0.52
16 1 0.03
17 1 0.03
18 12 0.41
ACGTcount: A:0.04, C:0.29, G:0.04, T:0.63
Consensus pattern (15 bp):
TTCTTCTTCTCTTGC
Found at i:114426 original size:33 final size:33
Alignment explanation
Indices: 114389--114453 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
114379 TTGGAGTTGC
114389 TCATATCTTCTTCTTTCTTCTTCTCTTGCTTCT
1 TCATATCTTCTTCTTTCTTCTTCTCTTGCTTCT
*
114422 TCATATTTTCTTCTTTCTTCTTCTCTTGCTTC
1 TCATATCTTCTTCTTTCTTCTTCTCTTGCTTC
114454 CTCCAACCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.06, C:0.29, G:0.03, T:0.62
Consensus pattern (33 bp):
TCATATCTTCTTCTTTCTTCTTCTCTTGCTTCT
Found at i:114439 original size:18 final size:18
Alignment explanation
Indices: 114389--114441 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
114379 TTGGAGTTGC
*
114389 TCATATCTTCTTCTTTCT
1 TCATATTTTCTTCTTTCT
*
114407 TC---TTCTCTTGC-TTCT
1 TCATATTTTCTT-CTTTCT
114422 TCATATTTTCTTCTTTCT
1 TCATATTTTCTTCTTTCT
114440 TC
1 TC
114442 TTCTCTTGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 10
0.68 0.08 0.25
Matches are distributed among these distances:
15 11 0.41
16 1 0.04
17 1 0.04
18 14 0.52
ACGTcount: A:0.08, C:0.28, G:0.02, T:0.62
Consensus pattern (18 bp):
TCATATTTTCTTCTTTCT
Found at i:116200 original size:114 final size:112
Alignment explanation
Indices: 115976--116195 Score: 343
Period size: 114 Copynumber: 1.9 Consensus size: 112
115966 TCCAAGGCCA
** *
115976 AAATCTTTTATCATCTTTTTAGCATCCTTACAAGACTTAGGAATTTTCGTAAAAAGAAACATTTC
1 AAATCTTTTATCATCTTTTTAGCATCCTTACAAGACTTAGGAATTTTCAAAAAAAAAAACATTTC
116041 TTTAAGAAACTCTAATAACAGTGTCAAAGAATTTCTTGTCTATCCACTC
66 TTTAAGAAACTCTAATAACAGTGTCAAAGAATTTC-T-TCTATCCACTC
116090 AAATCTTTTATCATCTTTTTAGCATCCTTACAAGACTTAGGAATTTTTGCAAAAAAAAAAAAAAC
1 AAATCTTTTATCATCTTTTTAGCATCCTTACAAGACTTAGGAA-TTTT-C---AAAAAAAAAAAC
116155 ATTT-TTTAAGAAACTCTAATAACAGTGTCAAAGAATTTCTT
61 ATTTCTTTAAGAAACTCTAATAACAGTGTCAAAGAATTTCTT
116196 ATCCATCCAC
Statistics
Matches: 98, Mismatches: 3, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
114 43 0.44
115 4 0.04
116 2 0.02
117 1 0.01
118 35 0.36
119 13 0.13
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (112 bp):
AAATCTTTTATCATCTTTTTAGCATCCTTACAAGACTTAGGAATTTTCAAAAAAAAAAACATTTC
TTTAAGAAACTCTAATAACAGTGTCAAAGAATTTCTTCTATCCACTC
Found at i:117175 original size:2 final size:2
Alignment explanation
Indices: 117168--117223 Score: 53
Period size: 2 Copynumber: 28.5 Consensus size: 2
117158 ATCTAACAAG
* * * *
117168 AT AT AT AT AT AT AT AT AT AT AT AC AA AT A- AT GT A- AT ACC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
117209 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
117224 ATTTTACTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
1 2 0.05
2 41 0.93
3 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:118442 original size:41 final size:40
Alignment explanation
Indices: 118378--118484 Score: 97
Period size: 42 Copynumber: 2.6 Consensus size: 40
118368 TAGTGGAGAT
* * * * * * *
118378 ATTTAGCAACGTTTTTTAGCAAAATGTTGCTGTATTGACAG
1 ATTTAGC-ACGTTTGTCACCAAAACGCTGCTATATGGACAG
* *
118419 CTTTAGCGACGTTTGTCACCAAAAACGCTGCTATATGGATAG
1 ATTTAGC-ACGTTTGTCACC-AAAACGCTGCTATATGGACAG
118461 ATTTAGCAGCGTTTGTCACCAAAA
1 ATTTAGCA-CGTTTGTCACCAAAA
118485 ATGCCATTAT
Statistics
Matches: 53, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
41 20 0.38
42 33 0.62
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (40 bp):
ATTTAGCACGTTTGTCACCAAAACGCTGCTATATGGACAG
Found at i:120262 original size:33 final size:33
Alignment explanation
Indices: 120215--120282 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
120205 TTTTGTCATA
* * * *
120215 AATTTAGTAGTATTAGAGATAAATATTGTTTTT
1 AATTTAATAATATTAGAGACAAATATTATTTTT
120248 AATTTAATAATATTAGAGACAAATATTATTTTT
1 AATTTAATAATATTAGAGACAAATATTATTTTT
120281 AA
1 AA
120283 AACTTTTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.43, C:0.01, G:0.10, T:0.46
Consensus pattern (33 bp):
AATTTAATAATATTAGAGACAAATATTATTTTT
Found at i:122121 original size:2 final size:2
Alignment explanation
Indices: 122114--122154 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
122104 CAAACAATAA
122114 TC TC TC TC TC 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 TC TC TC TC TC T
122155 ATATATATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:123445 original size:27 final size:28
Alignment explanation
Indices: 123384--123469 Score: 79
Period size: 27 Copynumber: 3.1 Consensus size: 28
123374 TTTTAAGGTA
*
123384 AAAAATAATAAAAATTTT-ATTTTTATCTT
1 AAAAAT-AT-AAAATTTTAATTTTGATCTT
* *
123413 AAAAAT-TTATATTTTAATTTTGATCTT
1 AAAAATATAAAATTTTAATTTTGATCTT
**
123440 TTAAATATAAAATTTTTAA-TTTGATCTT
1 AAAAATATAAAA-TTTTAATTTTGATCTT
123468 AA
1 AA
123470 TTACAAATAA
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
26 6 0.13
27 15 0.33
28 12 0.27
29 12 0.27
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.51
Consensus pattern (28 bp):
AAAAATATAAAATTTTAATTTTGATCTT
Found at i:123736 original size:3 final size:3
Alignment explanation
Indices: 123728--123753 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
123718 AAACAACTTC
123728 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
123754 GTATAGATTC
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:124189 original size:5 final size:5
Alignment explanation
Indices: 124179--124218 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
124169 GGCAAACATC
* *
124179 TATAT TATAT TATTT TATAT TACAT TATAT TATAT TATAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TATAT
124219 AAATTGCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (5 bp):
TATAT
Found at i:125460 original size:2 final size:2
Alignment explanation
Indices: 125453--125482 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
125443 AGCAATATGA
125453 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
125483 CATCTCAAAC
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):
AT
Found at i:125992 original size:10 final size:10
Alignment explanation
Indices: 125953--126025 Score: 60
Period size: 10 Copynumber: 7.2 Consensus size: 10
125943 ATAATTTTTA
*
125953 TTATATAAAT
1 TTATATATAT
125963 TT-TAATATAT
1 TTAT-ATATAT
*
125973 TT-TATTTAT
1 TTATATATAT
*
125982 TTATTTATAT
1 TTATATATAT
125992 TATATAATATAT
1 T-TAT-ATATAT
*
126004 ATATATATAT
1 TTATATATAT
*
126014 ATATATATAT
1 TTATATATAT
126024 TT
1 TT
126026 TTCATGTTTC
Statistics
Matches: 52, Mismatches: 7, Indels: 8
0.78 0.10 0.12
Matches are distributed among these distances:
9 8 0.15
10 33 0.63
11 6 0.12
12 5 0.10
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (10 bp):
TTATATATAT
Found at i:126003 original size:2 final size:2
Alignment explanation
Indices: 125987--126023 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
125977 TTTATTTATT
125987 TA TA T- TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
126024 TTTTCATGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:126636 original size:2 final size:2
Alignment explanation
Indices: 126631--126659 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
126621 AAGAATATAT
126631 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
126660 AATGCCATGA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:128469 original size:2 final size:2
Alignment explanation
Indices: 128464--128489 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
128454 TGTTTGGTGC
128464 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
128490 GAAGCACTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128874 original size:16 final size:18
Alignment explanation
Indices: 128844--128877 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
128834 GCATGTTATA
128844 ATTTTATATATAATTAAT
1 ATTTTATATATAATTAAT
128862 ATTTTA-ATA-AATTAAT
1 ATTTTATATATAATTAAT
128878 TATTAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTTATATATAATTAAT
Found at i:129593 original size:22 final size:22
Alignment explanation
Indices: 129552--129593 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
129542 TTTCATTTCT
* *
129552 TTTATTATTACCTTTTAATACA
1 TTTATTATTACCATTAAATACA
*
129574 TTTATTATTATCATTAAATA
1 TTTATTATTACCATTAAATA
129594 AAATTCTATG
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:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTATTATTACCATTAAATACA
Found at i:129954 original size:2 final size:2
Alignment explanation
Indices: 129947--129983 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
129937 TGCTTAATGC
129947 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
129984 TCATAGATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:132480 original size:26 final size:25
Alignment explanation
Indices: 132443--132492 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
132433 CATAAGTCAT
*
132443 TTTTTTTAATTATTCTTTATTTAAA
1 TTTTTTTAATTATTCTTTAATTAAA
*
132468 TTTTTTTATATTATTTTTTAATTAA
1 TTTTTTTA-ATTATTCTTTAATTAA
132493 TTTACTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (25 bp):
TTTTTTTAATTATTCTTTAATTAAA
Done.