Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015270.1 Kokia drynarioides strain JFW-HI SEQ_130315, 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: 1190338
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 752 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:62 original size:7 final size:7
Alignment explanation
Indices: 50--83 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
40 TTCTCTTTTT
50 TTATTAA
1 TTATTAA
57 TTATTAA
1 TTATTAA
*
64 TTAATAA
1 TTATTAA
71 TTATT-A
1 TTATTAA
77 TTATTAA
1 TTATTAA
84 AACATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
TTATTAA
Found at i:718 original size:15 final size:15
Alignment explanation
Indices: 688--758 Score: 70
Period size: 15 Copynumber: 4.7 Consensus size: 15
678 GGCACTTTAC
* *
688 AATTGGACCATTTGT
1 AATTGGGCCATCTGT
* *
703 ATTTGGGCCGTCTGT
1 AATTGGGCCATCTGT
* *
718 AACTGGGCCATTTGT
1 AATTGGGCCATCTGT
*
733 ACTTGGGCCATCTGT
1 AATTGGGCCATCTGT
*
748 AACTGGGCCAT
1 AATTGGGCCAT
759 TTGTTTTGGA
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
15 43 1.00
ACGTcount: A:0.18, C:0.21, G:0.27, T:0.34
Consensus pattern (15 bp):
AATTGGGCCATCTGT
Found at i:731 original size:30 final size:30
Alignment explanation
Indices: 695--767 Score: 121
Period size: 30 Copynumber: 2.5 Consensus size: 30
685 TACAATTGGA
*
695 CCATTTGTATTTGGGCCGTCTGTAACTGGG
1 CCATTTGTATTTGGGCCATCTGTAACTGGG
*
725 CCATTTGTACTTGGGCCATCTGTAACTGGG
1 CCATTTGTATTTGGGCCATCTGTAACTGGG
755 CCATTTGT-TTTGG
1 CCATTTGTATTTGG
768 ATTTTTATTG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 4 0.10
30 36 0.90
ACGTcount: A:0.14, C:0.21, G:0.27, T:0.38
Consensus pattern (30 bp):
CCATTTGTATTTGGGCCATCTGTAACTGGG
Found at i:827 original size:17 final size:17
Alignment explanation
Indices: 793--854 Score: 88
Period size: 17 Copynumber: 3.6 Consensus size: 17
783 GGACTTTTCT
* *
793 AATTTTAATTTTATAATA
1 AATTTAAATTTCA-AATA
811 AATTTAAATTTCAAATA
1 AATTTAAATTTCAAATA
828 AATTTAAATTTCAAATA
1 AATTTAAATTTCAAATA
*
845 AACTTAAATT
1 AATTTAAATT
855 CAATTTCCAA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 30 0.73
18 11 0.27
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTAAATTTCAAATA
Found at i:11845 original size:20 final size:20
Alignment explanation
Indices: 11820--11870 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
11810 TAGAAAATGA
11820 TTTCTGGAAAAT-AAGTTACT
1 TTTCTGGAAAATGAA-TTACT
*
11840 TTTCTGTAAAATGAATTACT
1 TTTCTGGAAAATGAATTACT
*
11860 TTTTTGGAAAA
1 TTTCTGGAAAA
11871 GTTAATATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.43
Consensus pattern (20 bp):
TTTCTGGAAAATGAATTACT
Found at i:12072 original size:13 final size:13
Alignment explanation
Indices: 12039--12078 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
12029 TTAATAATTT
12039 TATATTTTACAT-
1 TATATTTTACATA
*
12051 TGT-TTTTACATA
1 TATATTTTACATA
12063 TATATTTTACATA
1 TATATTTTACATA
12076 TAT
1 TAT
12079 TGCAATGATT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 8 0.33
12 4 0.17
13 12 0.50
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (13 bp):
TATATTTTACATA
Found at i:16100 original size:123 final size:125
Alignment explanation
Indices: 15960--16185 Score: 330
Period size: 123 Copynumber: 1.8 Consensus size: 125
15950 GTTAAACATT
* *
15960 AAAACATGAAAGATAATATCCTTTTGGGAATGATATAATGTTTTAATAAACCTTCCATAGATTTC
1 AAAACATGAAAGATAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCATAGATTTC
* * * *
16025 TTTAAAG-GA-ATATTTCCGTTTTTATATTAGATATTATATAAAAGGAAATTGAATATTA
66 TATAAAGAGATATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTGAATATTA
* * * * *
16083 AAAACATGGAAGTTAATATCTTTTTGGAAAGGATATAATGTTTTAATAAATCTTCCATATATTTC
1 AAAACATGAAAGATAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCATAGATTTC
*
16148 TATAAAGATATATATTTCCATTTTAATATGAGATATTA
66 TATAAAGAGATATATTTCCATTTTAATATGAGATATTA
16186 ATCAAATGAA
Statistics
Matches: 89, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
123 64 0.72
124 1 0.01
125 24 0.27
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (125 bp):
AAAACATGAAAGATAATATCCTTTTGGAAAGGATATAATGTTTTAATAAACCTTCCATAGATTTC
TATAAAGAGATATATTTCCATTTTAATATGAGATATTATATAAAAGGAAATTGAATATTA
Found at i:18897 original size:26 final size:25
Alignment explanation
Indices: 18868--18925 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 25
18858 TTTATCAAGG
18868 TTATTAGTTATAGATAAATGAATATT
1 TTATTAGTTATAGATAAATGAATA-T
* * *
18894 TTATTAATTTATCGATAAATTAATAT
1 TTATT-AGTTATAGATAAATGAATAT
18920 TTATTA
1 TTATTA
18926 ATTTAGAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 1 0.04
26 11 0.39
27 16 0.57
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (25 bp):
TTATTAGTTATAGATAAATGAATAT
Found at i:18910 original size:27 final size:26
Alignment explanation
Indices: 18875--18930 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 26
18865 AGGTTATTAG
18875 TTATAGATAAATGAATATTTTATTAAT
1 TTATAGATAAATGAATA-TTTATTAAT
* *
18902 TTATCGATAAATTAATATTTATTAAT
1 TTATAGATAAATGAATATTTATTAAT
18928 TTA
1 TTA
18931 GAGAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 12 0.44
27 15 0.56
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (26 bp):
TTATAGATAAATGAATATTTATTAAT
Found at i:20174 original size:20 final size:20
Alignment explanation
Indices: 20144--20193 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
20134 ATTAACATGA
*
20144 GTTATATTAAGTA-TAAATAGG
1 GTTA-ATTAAG-ACTAAAAAGG
*
20165 TTTAATTAAGACTAAAAAGG
1 GTTAATTAAGACTAAAAAGG
20185 GTTAATTAA
1 GTTAATTAA
20194 AGCTTAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 1 0.04
20 21 0.84
21 3 0.12
ACGTcount: A:0.46, C:0.02, G:0.16, T:0.36
Consensus pattern (20 bp):
GTTAATTAAGACTAAAAAGG
Found at i:27018 original size:82 final size:83
Alignment explanation
Indices: 26858--27022 Score: 287
Period size: 82 Copynumber: 2.0 Consensus size: 83
26848 GACACACAAG
*
26858 CTTTCAACGTCATCTTCAGTATCAGAAAGAATATTTTTCACAAAGTATACACCATTATCATATGC
1 CTTTCAACGTCATCTTCAGTATCAGAAAGAATATTTTTCACAAAGTATACACCATTAGCATATGC
26923 AAGTTCACAGCATTGAAT
66 AAGTTCACAGCATTGAAT
* *
26941 CTTTCAACGTCATCTTCAGTATCAGAAAGAATA-TTTTCACAAAGTATGCTCCATTAGCATATGC
1 CTTTCAACGTCATCTTCAGTATCAGAAAGAATATTTTTCACAAAGTATACACCATTAGCATATGC
*
27005 AAGTTCACTGCATTGAAT
66 AAGTTCACAGCATTGAAT
27023 TTCTTCATCA
Statistics
Matches: 78, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 45 0.58
83 33 0.42
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.33
Consensus pattern (83 bp):
CTTTCAACGTCATCTTCAGTATCAGAAAGAATATTTTTCACAAAGTATACACCATTAGCATATGC
AAGTTCACAGCATTGAAT
Found at i:31079 original size:212 final size:212
Alignment explanation
Indices: 30706--31130 Score: 841
Period size: 212 Copynumber: 2.0 Consensus size: 212
30696 AAGCGGCCTC
*
30706 ATTGATGCAAGTTCAGCTTGTATTTCCAAAGCATAGGTTGTTTTAACTGAACGTATTACAGCAGG
1 ATTGAAGCAAGTTCAGCTTGTATTTCCAAAGCATAGGTTGTTTTAACTGAACGTATTACAGCAGG
30771 TGGCAGCTCAGTTTTGTAGTACCAGGACAGCCTGCCATGATACGCATCTTACACTGTGGGAAGTT
66 TGGCAGCTCAGTTTTGTAGTACCAGGACAGCCTGCCATGATACGCATCTTACACTGTGGGAAGTT
30836 TATTGATCTCATTATTTTACAATAATATCTCTCACCATATCCTATATTTCAAACCCATCAACGGT
131 TATTGATCTCATTATTTTACAATAATATCTCTCACCATATCCTATATTTCAAACCCATCAACGGT
30901 GGGTGCCGTAGCCCTTA
196 GGGTGCCGTAGCCCTTA
30918 ATTGAAGCAAGTTCAGCTTGTATTTCCAAAGCATAGGTTGTTTTAACTGAACGTATTACAGCAGG
1 ATTGAAGCAAGTTCAGCTTGTATTTCCAAAGCATAGGTTGTTTTAACTGAACGTATTACAGCAGG
30983 TGGCAGCTCAGTTTTGTAGTACCAGGACAGCCTGCCATGATACGCATCTTACACTGTGGGAAGTT
66 TGGCAGCTCAGTTTTGTAGTACCAGGACAGCCTGCCATGATACGCATCTTACACTGTGGGAAGTT
31048 TATTGATCTCATTATTTTACAATAATATCTCTCACCATATCCTATATTTCAAACCCATCAACGGT
131 TATTGATCTCATTATTTTACAATAATATCTCTCACCATATCCTATATTTCAAACCCATCAACGGT
31113 GGGTGCCGTAGCCCTTA
196 GGGTGCCGTAGCCCTTA
31130 A
1 A
31131 CAGTGACTAG
Statistics
Matches: 212, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
212 212 1.00
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.32
Consensus pattern (212 bp):
ATTGAAGCAAGTTCAGCTTGTATTTCCAAAGCATAGGTTGTTTTAACTGAACGTATTACAGCAGG
TGGCAGCTCAGTTTTGTAGTACCAGGACAGCCTGCCATGATACGCATCTTACACTGTGGGAAGTT
TATTGATCTCATTATTTTACAATAATATCTCTCACCATATCCTATATTTCAAACCCATCAACGGT
GGGTGCCGTAGCCCTTA
Found at i:34409 original size:7 final size:7
Alignment explanation
Indices: 34399--34425 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
34389 CCTAGGAAAT
34399 AGGAGAA
1 AGGAGAA
34406 AGGAGAA
1 AGGAGAA
34413 AGGAGAA
1 AGGAGAA
34420 AGGAGA
1 AGGAGA
34426 GTTGAGGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (7 bp):
AGGAGAA
Found at i:48581 original size:21 final size:21
Alignment explanation
Indices: 48553--48605 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
48543 GAGTTTATTT
**
48553 TATCGGTAGAAGTGTTACTTG
1 TATCGGTAGAAGTCATACTTG
* *
48574 TTTCGGTAGTAGTCATACTTG
1 TATCGGTAGAAGTCATACTTG
48595 TATCGGTAGAA
1 TATCGGTAGAA
48606 CCATCACAAC
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:0.25, C:0.11, G:0.26, T:0.38
Consensus pattern (21 bp):
TATCGGTAGAAGTCATACTTG
Found at i:53399 original size:26 final size:26
Alignment explanation
Indices: 53368--53545 Score: 137
Period size: 26 Copynumber: 6.8 Consensus size: 26
53358 AGCGTTATTC
53368 TATCTGGGCTCGAATGAGCTAAACTT
1 TATCTGGGCTCGAATGAGCTAAACTT
* * * * *
53394 TGTCTGGGCTAGAGTGGGCTAAACTC
1 TATCTGGGCTCGAATGAGCTAAACTT
* *
53420 TATATGGGCTCGAATAAGCTAAA-TAT
1 TATCTGGGCTCGAATGAGCTAAACT-T
* ** * *
53446 TTTCTAAGCTCGTATGAGTTAAACTT
1 TATCTGGGCTCGAATGAGCTAAACTT
*
53472 TATCTGGGCT-TATATGAGCTAAACTT
1 TATCTGGGCTCGA-ATGAGCTAAACTT
* * * *
53498 TGTTTAGGCTCGTATGAGCTAAACTT
1 TATCTGGGCTCGAATGAGCTAAACTT
*
53524 TATTCTGGTCTCGAGA-GAGCTA
1 TA-TCTGGGCTCGA-ATGAGCTA
53546 TATTTTTGTA
Statistics
Matches: 111, Mismatches: 35, Indels: 11
0.71 0.22 0.07
Matches are distributed among these distances:
25 1 0.01
26 95 0.86
27 14 0.13
28 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (26 bp):
TATCTGGGCTCGAATGAGCTAAACTT
Found at i:53508 original size:78 final size:78
Alignment explanation
Indices: 53375--53520 Score: 177
Period size: 78 Copynumber: 1.9 Consensus size: 78
53365 TTCTATCTGG
* * *
53375 GCTCGAATGAGCTAAACTTTGTCTGGGCTAGAGTGGGCTAAACTCTATATGGGCTCGAATAAGCT
1 GCTCGAATGAGCTAAACTTTATCTGGGCTAGAGTGAGCTAAACTCTATATAGGCTCGAATAAGCT
53440 AAATATTTTCTAA
66 AAATATTTTCTAA
* * * * * * * *
53453 GCTCGTATGAGTTAAACTTTATCTGGGCTTATA-TGAGCTAAACTTTGTTTAGGCTCGTATGAGC
1 GCTCGAATGAGCTAAACTTTATCTGGGC-TAGAGTGAGCTAAACTCTATATAGGCTCGAATAAGC
53517 TAAA
65 TAAA
53521 CTTTATTCTG
Statistics
Matches: 56, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
78 53 0.95
79 3 0.05
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.34
Consensus pattern (78 bp):
GCTCGAATGAGCTAAACTTTATCTGGGCTAGAGTGAGCTAAACTCTATATAGGCTCGAATAAGCT
AAATATTTTCTAA
Found at i:63598 original size:58 final size:59
Alignment explanation
Indices: 63516--63626 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 59
63506 TAAACAACCT
* *
63516 ACCTTGCTACTATAAGCCTTACTTCTATTGCAGTCATTTTTTGTTAGATTCTATACTTA
1 ACCTTGCTACTATAAGCCTTACTTCTATTGCAGACATTCTTTGTTAGATTCTATACTTA
* * *
63575 ACCTT-CTACTATAAGCCTTACTTCTGTTGTAGACCTTCTTTGTTAGATTCTA
1 ACCTTGCTACTATAAGCCTTACTTCTATTGCAGACATTCTTTGTTAGATTCTA
63627 GGCATAATAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
58 42 0.89
59 5 0.11
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.45
Consensus pattern (59 bp):
ACCTTGCTACTATAAGCCTTACTTCTATTGCAGACATTCTTTGTTAGATTCTATACTTA
Found at i:72094 original size:30 final size:31
Alignment explanation
Indices: 72028--72098 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
72018 CATAAAAATC
*
72028 AGTGATTGTTCTGTCACTTTTCGATAACGTT
1 AGTGACTGTTCTGTCACTTTTCGATAACGTT
*
72059 AGTGACTGTTTTGTCACATTTTC-A-AA-GTT
1 AGTGACTGTTCTGTCAC-TTTTCGATAACGTT
72088 GAGTGACTGTT
1 -AGTGACTGTT
72099 GTGTTAAATG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.33
31 16 0.44
32 5 0.14
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (31 bp):
AGTGACTGTTCTGTCACTTTTCGATAACGTT
Found at i:73956 original size:38 final size:36
Alignment explanation
Indices: 73907--73984 Score: 104
Period size: 38 Copynumber: 2.1 Consensus size: 36
73897 AGTCTGAAAC
73907 TAAAAAAGTAATTTTAAT-TGCTTCAAAATAAAAAAA
1 TAAAAAAGTAATTTT-ATCTGCTTCAAAATAAAAAAA
* *
73943 TAAAACAATGTAATTTTATCTGTTTCAAAATAAAAAAT
1 TAAAA-AA-GTAATTTTATCTGCTTCAAAATAAAAAAA
73981 TAAA
1 TAAA
73985 TAATTAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
36 5 0.14
37 4 0.11
38 28 0.76
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.33
Consensus pattern (36 bp):
TAAAAAAGTAATTTTATCTGCTTCAAAATAAAAAAA
Found at i:76063 original size:16 final size:17
Alignment explanation
Indices: 76042--76074 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
76032 AGCACGGCTC
76042 AAATTTT-TTCAAGTTT
1 AAATTTTCTTCAAGTTT
*
76058 AAATTTTCTTCTAGTTT
1 AAATTTTCTTCAAGTTT
76075 GATTTTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.27, C:0.09, G:0.06, T:0.58
Consensus pattern (17 bp):
AAATTTTCTTCAAGTTT
Found at i:79142 original size:14 final size:14
Alignment explanation
Indices: 79104--79146 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
79094 CAAAATGTAC
79104 AATATAATTAAA-T
1 AATATAATTAAATT
79117 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
79132 AA-ATAATTTAATT
1 AATATAATTAAATT
79145 AA
1 AA
79147 GTATTTACCC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:80561 original size:23 final size:25
Alignment explanation
Indices: 80526--80572 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
80516 ATTATTTCAT
*
80526 TTTCTTATCTATTTCATTTTCTTTG
1 TTTCTTATCTATTTCATGTTCTTTG
*
80551 TTTCTT-T-TATTTTATGTTCTTT
1 TTTCTTATCTATTTCATGTTCTTT
80573 AATTCAAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 1 0.05
25 6 0.30
ACGTcount: A:0.11, C:0.13, G:0.04, T:0.72
Consensus pattern (25 bp):
TTTCTTATCTATTTCATGTTCTTTG
Found at i:83947 original size:24 final size:24
Alignment explanation
Indices: 83878--83932 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
83868 TCGATTCATA
*
83878 TTTTTCTGTTGCTTTTGGATTGCT
1 TTTTTCTGTTGATTTTGGATTGCT
83902 TTTTTCTGTTGATTTTGGATTGCT
1 TTTTTCTGTTGATTTTGGATTGCT
83926 TTTTTCT
1 TTTTTCT
83933 TTTTTTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.05, C:0.11, G:0.18, T:0.65
Consensus pattern (24 bp):
TTTTTCTGTTGATTTTGGATTGCT
Found at i:84853 original size:18 final size:20
Alignment explanation
Indices: 84817--84856 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
84807 GGATTTCTTT
*
84817 TATTTTTTGTGGTTATATTC
1 TATTTTTGGTGGTTATATTC
84837 TATTTTTGGT-GTT-TATTC
1 TATTTTTGGTGGTTATATTC
84855 TA
1 TA
84857 GCAATTATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.15, C:0.05, G:0.15, T:0.65
Consensus pattern (20 bp):
TATTTTTGGTGGTTATATTC
Found at i:90892 original size:40 final size:40
Alignment explanation
Indices: 90837--90930 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 40
90827 CCATTGCTTG
* * * *
90837 GCTTGTATTTTAACACTGGCCCATAGCTTGCTAAGTCATA
1 GCTTGAATTTTAACACCGACCCATAGCTTGCTAAGCCATA
* *
90877 GCTTGAATTTTAACACCGACTCATAGCTTGCTAAGCCGTA
1 GCTTGAATTTTAACACCGACCCATAGCTTGCTAAGCCATA
90917 GCTTGAA-TTTAACA
1 GCTTGAATTTTAACA
90931 TTTCATGCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
39 7 0.15
40 41 0.85
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (40 bp):
GCTTGAATTTTAACACCGACCCATAGCTTGCTAAGCCATA
Found at i:92456 original size:13 final size:13
Alignment explanation
Indices: 92440--92511 Score: 99
Period size: 13 Copynumber: 5.5 Consensus size: 13
92430 ATATAACTTA
92440 TTCATATAACCAT
1 TTCATATAACCAT
**
92453 TTCATATATTCAT
1 TTCATATAACCAT
*
92466 TTTATATAACCAT
1 TTCATATAACCAT
*
92479 TTCAAATAACCAT
1 TTCATATAACCAT
*
92492 ATCATATAACCAT
1 TTCATATAACCAT
92505 TTCATAT
1 TTCATAT
92512 TACAGTTAAT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 49 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (13 bp):
TTCATATAACCAT
Found at i:92472 original size:26 final size:26
Alignment explanation
Indices: 92424--92511 Score: 97
Period size: 26 Copynumber: 3.3 Consensus size: 26
92414 TTATATAATT
*
92424 ATTTCCATATAA-CTTATTCATATAACC
1 ATTT-CATATAACCATA-TCATATAACC
** * *
92451 ATTTCATATATTCATTTTATATAACC
1 ATTTCATATAACCATATCATATAACC
*
92477 ATTTCAAATAACCATATCATATAACC
1 ATTTCATATAACCATATCATATAACC
92503 ATTTCATAT
1 ATTTCATAT
92512 TACAGTTAAT
Statistics
Matches: 50, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
26 44 0.88
27 6 0.12
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (26 bp):
ATTTCATATAACCATATCATATAACC
Found at i:92810 original size:45 final size:46
Alignment explanation
Indices: 92737--93037 Score: 314
Period size: 45 Copynumber: 6.7 Consensus size: 46
92727 TTGTACAAAA
* * * ** *
92737 GATGACATAGTGTCTTTCAACCACGGTCTTACACACTTCTGAT-AT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGATCAT
* * *
92782 GATGCCATAGTGTCTTTCAATTATGGTCTTATTTATTTCCGA-CAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGATCAT
* *
92827 GATGCCATAGTTTCTTTCAACTACGGTCTTATTCATTT-TCGA-CAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCT-GATCAT
* * *
92872 GATGTCATAGTGTCTTTCAACTATGGCCTTATTCATTTC-CATCAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGATCAT
*
92917 G-TAGCCATAGTGTCTTTCAACTATGATCTTATTCATTTCTG-TCAT
1 GAT-GCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGATCAT
* * * * *
92962 GTTGTCATACTGTCTTTCAACTATGGTCTTACTC--GTCTGAATCAT
1 GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTG-ATCAT
**
93007 GATGCCATAGCATCTTTCAACTATGGTCTTA
1 GATGCCATAGTGTCTTTCAACTATGGTCTTA
93038 CTCGTTATAT
Statistics
Matches: 214, Mismatches: 33, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
43 4 0.02
44 2 0.01
45 207 0.97
46 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.41
Consensus pattern (46 bp):
GATGCCATAGTGTCTTTCAACTATGGTCTTATTCATTTCTGATCAT
Found at i:114121 original size:25 final size:25
Alignment explanation
Indices: 114071--114203 Score: 162
Period size: 25 Copynumber: 5.4 Consensus size: 25
114061 TTACATATTA
*
114071 ATCACATTAACAC--ATAAGCATTT
1 ATCACATTAACACATATAAGCATAT
* *
114094 ATCACATTAACACCTATAAGCATGT
1 ATCACATTAACACATATAAGCATAT
*
114119 ATCACATTAACACATATAAGCGTAT
1 ATCACATTAACACATATAAGCATAT
* *
114144 ATCACGTTGACACATATAAGCATAT
1 ATCACATTAACACATATAAGCATAT
* * * *
114169 ACCATATTAACACATATGAGTATAT
1 ATCACATTAACACATATAAGCATAT
114194 ATCACATTAA
1 ATCACATTAA
114204 TCAATAGTCA
Statistics
Matches: 93, Mismatches: 15, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
23 13 0.14
25 80 0.86
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.29
Consensus pattern (25 bp):
ATCACATTAACACATATAAGCATAT
Found at i:118019 original size:27 final size:27
Alignment explanation
Indices: 117989--118041 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
117979 TTAGCGACAC
* *
117989 TGAAAGTTCCCTTTTAAAGGGCGGCAT
1 TGAAAGTGCCCTTCTAAAGGGCGGCAT
* *
118016 TGAACGTGCCCTTCTAATGGGCGGCA
1 TGAAAGTGCCCTTCTAAAGGGCGGCA
118042 CAAGTGTGCC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.26
Consensus pattern (27 bp):
TGAAAGTGCCCTTCTAAAGGGCGGCAT
Found at i:119935 original size:14 final size:14
Alignment explanation
Indices: 119918--119963 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
119908 AATAAGTATT
119918 TTTAAAAAATTTAA
1 TTTAAAAAATTTAA
* *
119932 TTTAAATAATAT-A
1 TTTAAAAAATTTAA
119945 TATTAAAAAA-TTAA
1 T-TTAAAAAATTTAA
119959 TTTAA
1 TTTAA
119964 TTTAAGTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
13 7 0.27
14 19 0.73
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAAAAAATTTAA
Found at i:119936 original size:28 final size:28
Alignment explanation
Indices: 119905--119978 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
119895 TAAATCATAA
*
119905 TTAAATAAGTAT-TTTTAAAAAATTTAAT
1 TTAAATAAGTATATATTAAAAAA-TTAAT
119933 TTAAATAA-TATATATTAAAAAATTAAT
1 TTAAATAAGTATATATTAAAAAATTAAT
* *
119960 TTAATTTAAGTATAAATTA
1 TTAA-ATAAGTATATATTA
119979 GTGTAAAAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
27 12 0.30
28 20 0.50
29 8 0.20
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (28 bp):
TTAAATAAGTATATATTAAAAAATTAAT
Found at i:121060 original size:15 final size:16
Alignment explanation
Indices: 121034--121068 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
121024 TTTTAGAATA
121034 AAAATAATTTTTAATT
1 AAAATAATTTTTAATT
*
121050 AAAAT-ATTTTTATTT
1 AAAATAATTTTTAATT
121065 AAAA
1 AAAA
121069 ATGATAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAATAATTTTTAATT
Found at i:121069 original size:16 final size:17
Alignment explanation
Indices: 121032--121070 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
121022 TTTTTTAGAA
121032 TAAAAATAATTTTTAAT
1 TAAAAATAATTTTTAAT
*
121049 T-AAAAT-ATTTTTATT
1 TAAAAATAATTTTTAAT
121064 TAAAAAT
1 TAAAAAT
121071 GATAAATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 9 0.45
16 10 0.50
17 1 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAAATAATTTTTAAT
Found at i:122124 original size:15 final size:15
Alignment explanation
Indices: 122104--122133 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
122094 CTTATTAAAC
122104 AAAGTATGAAGGGTT
1 AAAGTATGAAGGGTT
122119 AAAGTATGAAGGGTT
1 AAAGTATGAAGGGTT
122134 TAATAGTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.33, T:0.27
Consensus pattern (15 bp):
AAAGTATGAAGGGTT
Found at i:122405 original size:30 final size:31
Alignment explanation
Indices: 122371--122434 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
122361 TAAAAATATA
* *
122371 ATTTTTAAAGA-ATTAAATTAAAATTTTATC
1 ATTTTTAAAGAGATCAAAGTAAAATTTTATC
*
122401 ATTTTTAGAGAGATCAAAGTAAAATTTTATC
1 ATTTTTAAAGAGATCAAAGTAAAATTTTATC
122432 ATT
1 ATT
122435 ACTAAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
30 10 0.33
31 20 0.67
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.44
Consensus pattern (31 bp):
ATTTTTAAAGAGATCAAAGTAAAATTTTATC
Found at i:125271 original size:21 final size:20
Alignment explanation
Indices: 125232--125278 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 20
125222 TTATTTCTAA
125232 ATATTTTTATAATCTTGTAT
1 ATATTTTTATAATCTTGTAT
125252 ATATTTTT-TAATC-T-TAT
1 ATATTTTTATAATCTTGTAT
*
125269 GTATTTTTAT
1 ATATTTTTAT
125279 CAAAAAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 2 0.08
19 5 0.20
20 8 0.32
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (20 bp):
ATATTTTTATAATCTTGTAT
Found at i:125388 original size:60 final size:60
Alignment explanation
Indices: 125322--125443 Score: 149
Period size: 58 Copynumber: 2.0 Consensus size: 60
125312 TTTTTTAATT
* * *
125322 TTGAATTCTTAAGAATTAAGACTAAATTGACATAATGTGTAAATA-TG-AGGGTTAAATTTG
1 TTGAATT-TTAAGAATT-AGACCAAATTGACAAAATCTGTAAATATTGAAGGGTTAAATTTG
* * * *
125382 TTGAATTTTTAGAGTTGGACCAAATTGATAAAATCTGTAAATATTGAAGGGTTAAATTTG
1 TTGAATTTTAAGAATTAGACCAAATTGACAAAATCTGTAAATATTGAAGGGTTAAATTTG
125442 TT
1 TT
125444 ATTATGCCAA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 22 0.42
59 9 0.17
60 22 0.42
ACGTcount: A:0.38, C:0.05, G:0.19, T:0.39
Consensus pattern (60 bp):
TTGAATTTTAAGAATTAGACCAAATTGACAAAATCTGTAAATATTGAAGGGTTAAATTTG
Found at i:131430 original size:10 final size:10
Alignment explanation
Indices: 131416--131502 Score: 58
Period size: 9 Copynumber: 9.0 Consensus size: 10
131406 TTAAAATGAT
131416 TAAAAAA-TA
1 TAAAAAATTA
131425 TAAAAAATTA
1 TAAAAAATTA
*
131435 TTAAAAATTA
1 TAAAAAATTA
* *
131445 T-AAATATCA
1 TAAAAAATTA
*
131454 TGAAAAA-TA
1 TAAAAAATTA
* *
131463 TTAAAGATTA
1 TAAAAAATTA
131473 T-AAAAATTA
1 TAAAAAATTA
*
131482 -AAAAAAATA
1 TAAAAAATTA
131491 TTAAAAACATTA
1 -TAAAAA-ATTA
131503 AAATTGATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 11
0.74 0.12 0.13
Matches are distributed among these distances:
9 34 0.56
10 19 0.31
11 5 0.08
12 3 0.05
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:131440 original size:19 final size:18
Alignment explanation
Indices: 131408--131497 Score: 65
Period size: 19 Copynumber: 4.8 Consensus size: 18
131398 ATTTTCTATT
*
131408 AAAATGATTAAAAAATATAA
1 AAAATTATT-AAAAAT-TAA
131428 AAAATTATTAAAAATTATA
1 AAAATTATTAAAAATTA-A
* * * *
131447 AATATCATGAAAAATATTA
1 AAAATTATTAAAAAT-TAA
*
131466 AAGATTA-TAAAAATTAAA
1 AAAATTATTAAAAATT-AA
*
131484 AAAAATATTAAAAA
1 AAAATTATTAAAAA
131498 CATTAAAATT
Statistics
Matches: 55, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
17 1 0.02
18 14 0.25
19 31 0.56
20 9 0.16
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.29
Consensus pattern (18 bp):
AAAATTATTAAAAATTAA
Found at i:131496 original size:8 final size:9
Alignment explanation
Indices: 131404--131505 Score: 57
Period size: 9 Copynumber: 10.9 Consensus size: 9
131394 TAATATTTTC
131404 TATT-AAAA
1 TATTAAAAA
131412 TGATTAAAAAA
1 T-ATT-AAAAA
*
131423 TATAAAAAA
1 TATTAAAAA
131432 TTATTAAAAA
1 -TATTAAAAA
*
131442 T-TATAAATA
1 TAT-TAAAAA
*
131451 TCATGAAAAA
1 T-ATTAAAAA
*
131461 TATTAAAGA
1 TATTAAAAA
131470 T-TATAAAAA
1 TAT-TAAAAA
**
131479 TTAAAAAAAA
1 -TATTAAAAA
131489 TATTAAAAA
1 TATTAAAAA
*
131498 CATTAAAA
1 TATTAAAA
131506 TTGATATAAA
Statistics
Matches: 71, Mismatches: 13, Indels: 19
0.69 0.13 0.18
Matches are distributed among these distances:
8 3 0.04
9 41 0.58
10 21 0.30
11 6 0.08
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (9 bp):
TATTAAAAA
Found at i:131504 original size:28 final size:27
Alignment explanation
Indices: 131404--131505 Score: 71
Period size: 28 Copynumber: 3.6 Consensus size: 27
131394 TAATATTTTC
* * *
131404 TATTAAAATGATTAAAAAATATAAAAAAT
1 TATTAAAA-AATTAAAAATTA-AAAAAAA
* **
131433 TATTAAAA-ATTATAAATATCATGAAAAA
1 TATTAAAAAATTA-AAA-ATTAAAAAAAA
* *
131461 TATTAAAGATTATAAAAATTAAAAAAAA
1 TATTAAAAAAT-TAAAAATTAAAAAAAA
131489 TATTAAAAACATTAAAA
1 TATTAAAAA-ATTAAAA
131506 TTGATATAAA
Statistics
Matches: 56, Mismatches: 12, Indels: 11
0.71 0.15 0.14
Matches are distributed among these distances:
27 4 0.07
28 35 0.62
29 15 0.27
30 2 0.04
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (27 bp):
TATTAAAAAATTAAAAATTAAAAAAAA
Found at i:131676 original size:28 final size:27
Alignment explanation
Indices: 131628--131698 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 27
131618 AAACCTATAA
* * *
131628 AAATCATAAAAATTATTAAATGTTAT-T
1 AAATTATAAAAAATATTAAAT-TGATGT
131655 AAA-TATTAAAAAATATTAAAATTGATGT
1 AAATTA-TAAAAAATATT-AAATTGATGT
131683 AAATTATAAAAAATAT
1 AAATTATAAAAAATAT
131699 AATAATACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
26 1 0.03
27 16 0.43
28 18 0.49
29 2 0.05
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (27 bp):
AAATTATAAAAAATATTAAATTGATGT
Found at i:132536 original size:10 final size:9
Alignment explanation
Indices: 132512--132610 Score: 60
Period size: 10 Copynumber: 10.6 Consensus size: 9
132502 GAAATTTTGT
132512 ATTTTTATA
1 ATTTTTATA
132521 AGTTTTTATCA
1 A-TTTTTAT-A
*
132532 ATTTTAAT-
1 ATTTTTATA
132540 A-TTTTA-A
1 ATTTTTATA
*
132547 ATTTTCAATA
1 ATTTT-TATA
* *
132557 AATTTTAAA
1 ATTTTTATA
*
132566 ATTTTTTATG
1 A-TTTTTATA
*
132576 ATTTTTTTA
1 ATTTTTATA
132585 ATTTTTTATGA
1 A-TTTTTAT-A
132596 ATTTTTTATA
1 A-TTTTTATA
132606 ATTTT
1 ATTTT
132611 AATAGAAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
7 5 0.07
8 4 0.06
9 16 0.23
10 32 0.46
11 12 0.17
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
ATTTTTATA
Found at i:132581 original size:19 final size:20
Alignment explanation
Indices: 132559--132601 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
132549 TTTCAATAAA
132559 TTTTAAAATTTTTTATG-AT
1 TTTTAAAATTTTTTATGAAT
**
132578 TTTTTTAATTTTTTATGAAT
1 TTTTAAAATTTTTTATGAAT
132598 TTTT
1 TTTT
132602 TATAATTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.70
Consensus pattern (20 bp):
TTTTAAAATTTTTTATGAAT
Found at i:132602 original size:19 final size:19
Alignment explanation
Indices: 132565--132603 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
132555 TAAATTTTAA
*
132565 AATTTTTTATGATTTTTTT
1 AATTTTTTATGAATTTTTT
132584 AATTTTTTATGAATTTTTT
1 AATTTTTTATGAATTTTTT
132603 A
1 A
132604 TAATTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (19 bp):
AATTTTTTATGAATTTTTT
Found at i:135387 original size:20 final size:21
Alignment explanation
Indices: 135364--135411 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
135354 TAGTTGTTCT
* *
135364 AGTAGAAGC-ATATTTGTATC
1 AGTAGAAGCTATAATTGTATA
135384 AGTAGAA-CTATAATTGTATA
1 AGTAGAAGCTATAATTGTATA
135404 AGTAGAAG
1 AGTAGAAG
135412 AGGTGTTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.42, C:0.06, G:0.21, T:0.31
Consensus pattern (21 bp):
AGTAGAAGCTATAATTGTATA
Found at i:135643 original size:20 final size:20
Alignment explanation
Indices: 135618--135671 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
135608 AGTCTTCAAG
*
135618 GTATCGGTAAAAGTGGAGTT
1 GTATCGGTAGAAGTGGAGTT
135638 GTATCGGTAGAAGTGGAGTT
1 GTATCGGTAGAAGTGGAGTT
* *
135658 CTACCGGTAGAAGT
1 GTATCGGTAGAAGT
135672 CTCACTGGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.09, G:0.35, T:0.28
Consensus pattern (20 bp):
GTATCGGTAGAAGTGGAGTT
Found at i:139213 original size:28 final size:28
Alignment explanation
Indices: 139180--139266 Score: 102
Period size: 28 Copynumber: 3.0 Consensus size: 28
139170 AAAAATTATC
139180 AACTTTTAAGAGCCCAAAATTTTTTTTT
1 AACTTTTAAGAGCCCAAAATTTTTTTTT
* * *
139208 AGCTTTTAAGGGCCCAAAATTTTTTTTACA
1 AACTTTTAAGAGCCCAAAATTTTTTTT--T
* *
139238 AACTTTTAAGAGACCTAAAACTTTTTTTT
1 AACTTTTAAGAG-CCCAAAATTTTTTTTT
139267 CTCTAACTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
28 25 0.52
30 10 0.21
31 13 0.27
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.44
Consensus pattern (28 bp):
AACTTTTAAGAGCCCAAAATTTTTTTTT
Found at i:139482 original size:16 final size:16
Alignment explanation
Indices: 139449--139500 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
139439 TGGTTTGATA
* * *
139449 TAATGGAATATAGTTG
1 TAATGGAACAGAGCTG
*
139465 TAATGTAACAGAGCTG
1 TAATGGAACAGAGCTG
* *
139481 TAATGGAATAGGGCTG
1 TAATGGAACAGAGCTG
139497 TAAT
1 TAAT
139501 AAGTATTTCA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.31
Consensus pattern (16 bp):
TAATGGAACAGAGCTG
Found at i:139576 original size:44 final size:46
Alignment explanation
Indices: 139482--139576 Score: 124
Period size: 44 Copynumber: 2.1 Consensus size: 46
139472 ACAGAGCTGT
* *
139482 AATGGAATAGGGCTGTAATAAGTATTTCAGTTGTTTAGTTGCATGG
1 AATGGAATAGAGCTGTAATAAGTATTTCAGTTGTTTAGTTGAATGG
* *
139528 AATGGAATAGAGCTGTAAT-AGTA-TTC-TTGTGTTTGGTTGAATGG
1 AATGGAATAGAGCTGTAATAAGTATTTCAGT-TGTTTAGTTGAATGG
139572 AATGG
1 AATGG
139577 TGCTGTAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.48
45 4 0.09
46 18 0.41
ACGTcount: A:0.28, C:0.05, G:0.29, T:0.37
Consensus pattern (46 bp):
AATGGAATAGAGCTGTAATAAGTATTTCAGTTGTTTAGTTGAATGG
Found at i:139775 original size:38 final size:37
Alignment explanation
Indices: 139710--139783 Score: 112
Period size: 38 Copynumber: 2.0 Consensus size: 37
139700 AAAATAATAA
* *
139710 ATAATTTAATTATATTTTAACATAATTATTATTAAAT
1 ATAATTTAATAACATTTTAACATAATTATTATTAAAT
*
139747 ATAATTTAATAACATTTTTAATATAATTATTATTAAA
1 ATAATTTAATAACA-TTTTAACATAATTATTATTAAA
139784 ATATGAATGA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
37 12 0.36
38 21 0.64
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (37 bp):
ATAATTTAATAACATTTTAACATAATTATTATTAAAT
Found at i:139808 original size:39 final size:38
Alignment explanation
Indices: 139731--139810 Score: 90
Period size: 39 Copynumber: 2.1 Consensus size: 38
139721 ATATTTTAAC
* * * **
139731 ATAATTATTATTAAATATAATTTAATAACATTTTTAAT
1 ATAATTATTATTAAATATAATTGAATAAAAATCATAAT
139769 ATAATTATTATTAAAATATGAA-TGAATAAAAATCATAAT
1 ATAATTATTATT-AAATAT-AATTGAATAAAAATCATAAT
139808 ATA
1 ATA
139811 TAACCAACTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
38 12 0.34
39 21 0.60
40 2 0.06
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (38 bp):
ATAATTATTATTAAATATAATTGAATAAAAATCATAAT
Found at i:141508 original size:27 final size:27
Alignment explanation
Indices: 141478--141541 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
141468 TAGAATTTTA
141478 AATTTTGCCTTAACTTTTAAGGCGCTC
1 AATTTTGCCTTAACTTTTAAGGCGCTC
*
141505 AATTTTGCCTTAGCTTTTAAGGCGCTC
1 AATTTTGCCTTAACTTTTAAGGCGCTC
141532 AATTTTGCCT
1 AATTTTGCCT
141542 AAGCCTTAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (27 bp):
AATTTTGCCTTAACTTTTAAGGCGCTC
Found at i:154668 original size:2 final size:2
Alignment explanation
Indices: 154661--154700 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
154651 AAAGATACCC
154661 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
154701 GAATTCTTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:155798 original size:3 final size:3
Alignment explanation
Indices: 155790--155821 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
155780 CTTTTCTGAC
155790 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
155822 TTATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:157365 original size:135 final size:135
Alignment explanation
Indices: 157123--157392 Score: 468
Period size: 135 Copynumber: 2.0 Consensus size: 135
157113 TTGAATTCAT
*
157123 ACATGTGTTTTCAAATAGATGGATCCTTTATCATTCTTGACTTTCAATCAAATAGCATTCTCCAC
1 ACATGTGTTTTCAAATAAATGGATCCTTTATCATTCTTGACTTTCAATCAAATAGCATTCTCCAC
* *
157188 TATTCTCGTACCAAAAACTACTTCGAGTGTGGGTTCGAATGATTTAAATCAAGACACAGTACTAA
66 TATTCTCGTACCAAAAACTACTTCGAGTGTGGGCTCGAATGATTTAAATCAAAACACAGTACTAA
157253 AAATA
131 AAATA
* * * *
157258 ACATGTGTTTTCAAATAAATGGATCCTTTATCGTTCTTGGCTTTCAATCAAATAGCCTTCTCCGC
1 ACATGTGTTTTCAAATAAATGGATCCTTTATCATTCTTGACTTTCAATCAAATAGCATTCTCCAC
*
157323 TATTCTCGTACCAAAAACTACTTCGAGTGTGGGCTCGAATGATTTAAATCAAAACACAGTACTAG
66 TATTCTCGTACCAAAAACTACTTCGAGTGTGGGCTCGAATGATTTAAATCAAAACACAGTACTAA
157388 AAATA
131 AAATA
157393 GTTTTCTTTG
Statistics
Matches: 127, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
135 127 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (135 bp):
ACATGTGTTTTCAAATAAATGGATCCTTTATCATTCTTGACTTTCAATCAAATAGCATTCTCCAC
TATTCTCGTACCAAAAACTACTTCGAGTGTGGGCTCGAATGATTTAAATCAAAACACAGTACTAA
AAATA
Found at i:157657 original size:24 final size:24
Alignment explanation
Indices: 157630--157678 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
157620 CGAACTCTTA
157630 GTCTATCTAGGAGTATAGGAGGCG
1 GTCTATCTAGGAGTATAGGAGGCG
157654 GTCTATCTAGGAGTATAGGAGGCG
1 GTCTATCTAGGAGTATAGGAGGCG
157678 G
1 G
157679 CAGCCTTAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.12, G:0.39, T:0.24
Consensus pattern (24 bp):
GTCTATCTAGGAGTATAGGAGGCG
Found at i:157908 original size:11 final size:11
Alignment explanation
Indices: 157892--157916 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
157882 AATTCTAATT
157892 ATGTTAAAATC
1 ATGTTAAAATC
157903 ATGTTAAAATC
1 ATGTTAAAATC
157914 ATG
1 ATG
157917 ACGATTTTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.08, G:0.12, T:0.36
Consensus pattern (11 bp):
ATGTTAAAATC
Found at i:158131 original size:12 final size:13
Alignment explanation
Indices: 158109--158137 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
158099 ATGATTCCAT
158109 TTTTTCATTTTCA
1 TTTTTCATTTTCA
158122 TTTTTC-TTTTCA
1 TTTTTCATTTTCA
158134 TTTT
1 TTTT
158138 GGAGAAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTCATTTTCA
Found at i:158185 original size:64 final size:64
Alignment explanation
Indices: 158053--158195 Score: 166
Period size: 63 Copynumber: 2.2 Consensus size: 64
158043 TCCAAGTCAT
* * *
158053 TTTCATTTTTTATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGATTCCATTTTTTCAT
1 TTTCATTTTTTATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCATTTTCTCAG
* * *
158117 TTTCA-TTTTTCTTTTCATTTTGGAGAAAACTATAATCATTTCCAAAT-ATTTCTCA-TTTCTCT
1 TTTCATTTTTTATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGA-TTC-CATTTTCTC-
158179 AG
63 AG
158181 TTTCACTATTTTTAT
1 TTTCA-T-TTTTTAT
158196 CTATTTCTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
62 1 0.02
63 46 0.70
64 13 0.20
67 6 0.09
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.52
Consensus pattern (64 bp):
TTTCATTTTTTATTTTCATTTTGGAGAAAACCACAATCATTTCCAAATGATTCCATTTTCTCAG
Found at i:165986 original size:24 final size:24
Alignment explanation
Indices: 165922--165989 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
165912 TCAAACTTTG
* * *
165922 TCTGGGCTTGCATGAGCTAACTTA
1 TCTGGGCTAGTATGAGCTAACCTA
* * * *
165946 TATGGGTTAATAAGAGCTAACCTA
1 TCTGGGCTAGTATGAGCTAACCTA
*
165970 TCTGGGCTCGTATGAGCTAA
1 TCTGGGCTAGTATGAGCTAA
165990 TTTTGTTTGG
Statistics
Matches: 32, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.31
Consensus pattern (24 bp):
TCTGGGCTAGTATGAGCTAACCTA
Found at i:166281 original size:11 final size:11
Alignment explanation
Indices: 166265--166289 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
166255 ATGGCATGTA
166265 TTAGGATTGTG
1 TTAGGATTGTG
166276 TTAGGATTGTG
1 TTAGGATTGTG
166287 TTA
1 TTA
166290 CTTGAGTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (11 bp):
TTAGGATTGTG
Found at i:176017 original size:16 final size:16
Alignment explanation
Indices: 175996--176026 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
175986 TTTAATTAAG
175996 GTAAAAGAAGTAAAAT
1 GTAAAAGAAGTAAAAT
*
176012 GTAAAAGAGGTAAAA
1 GTAAAAGAAGTAAAA
176027 GTTAATTACT
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:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (16 bp):
GTAAAAGAAGTAAAAT
Found at i:177484 original size:26 final size:26
Alignment explanation
Indices: 177403--177512 Score: 121
Period size: 26 Copynumber: 4.2 Consensus size: 26
177393 TGTAGAAATG
* *
177403 ACTGTACTAGCTCGTAAGAGTGATAT
1 ACTGTACTAGCTCATAAGAGCGATAT
* * *
177429 ACTATACTAGCTCGTAAGAGTGATAT
1 ACTGTACTAGCTCATAAGAGCGATAT
* *
177455 ACTGCACTGGCTCATAAGAGCGATAT
1 ACTGTACTAGCTCATAAGAGCGATAT
* * *
177481 ACTGAATTGGCTCATAAGAGCGATAT
1 ACTGTACTAGCTCATAAGAGCGATAT
*
177507 AATGTA
1 ACTGTA
177513 TTGGGAGCAA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (26 bp):
ACTGTACTAGCTCATAAGAGCGATAT
Found at i:177515 original size:26 final size:26
Alignment explanation
Indices: 177412--177690 Score: 106
Period size: 26 Copynumber: 11.2 Consensus size: 26
177402 GACTGTACTA
* * * *
177412 GCTCGTAAGAGTGATATACT-ATACTA
1 GCTCATAAGAGCGATATACTGA-ATTG
* * * *
177438 GCTCGTAAGAGTGATATACTGCACTG
1 GCTCATAAGAGCGATATACTGAATTG
177464 GCTCATAAGAGCGATATACTGAATTG
1 GCTCATAAGAGCGATATACTGAATTG
* *
177490 GCTCATAAGAGCGATATAATGTATTG
1 GCTCATAAGAGCGATATACTGAATTG
* *
177516 G-------GAGCAATATACTGCATTG
1 GCTCATAAGAGCGATATACTGAATTG
* *
177535 GCTCGTAAAAGCGATATACT-ATATTG
1 GCTCATAAGAGCGATATACTGA-ATTG
* * * *
177561 G-------GATCGATACACTAAACTG
1 GCTCATAAGAGCGATATACTGAATTG
* **
177580 GCTCGTAAGAGCGATATACTTTATTG
1 GCTCATAAGAGCGATATACTGAATTG
* * * *
177606 GCTCGGA-AGAGNAGTGATATACTAAACTA
1 GCTC--ATA-AG-AGCGATATACTGAATTG
* *
177635 GCTCATAAGAGCGATATACTGTACTG
1 GCTCATAAGAGCGATATACTGAATTG
* * * *
177661 GCTCGTAAGAGCGATTTTCTGAATGG
1 GCTCATAAGAGCGATATACTGAATTG
177687 GCTC
1 GCTC
177691 GTATGAGCTA
Statistics
Matches: 192, Mismatches: 39, Indels: 44
0.70 0.14 0.16
Matches are distributed among these distances:
19 29 0.15
20 1 0.01
26 139 0.72
27 4 0.02
28 3 0.02
29 16 0.08
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (26 bp):
GCTCATAAGAGCGATATACTGAATTG
Found at i:177527 original size:45 final size:45
Alignment explanation
Indices: 177472--177606 Score: 171
Period size: 45 Copynumber: 3.0 Consensus size: 45
177462 TGGCTCATAA
* * *
177472 GAGCGATATACTGAATTGGCTCATAAGAGCGATATAATGTATTGG
1 GAGCGATATACTGAATTGGCTCGTAAGAGCGATATACTATATTGG
* * *
177517 GAGCAATATACTGCATTGGCTCGTAAAAGCGATATACTATATTGG
1 GAGCGATATACTGAATTGGCTCGTAAGAGCGATATACTATATTGG
* * * * *
177562 GATCGATACACTAAACTGGCTCGTAAGAGCGATATACTTTATTGG
1 GAGCGATATACTGAATTGGCTCGTAAGAGCGATATACTATATTGG
177607 CTCGGAAGAG
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.29
Consensus pattern (45 bp):
GAGCGATATACTGAATTGGCTCGTAAGAGCGATATACTATATTGG
Found at i:177663 original size:55 final size:54
Alignment explanation
Indices: 177566--177671 Score: 149
Period size: 55 Copynumber: 1.9 Consensus size: 54
177556 TATTGGGATC
* * * *
177566 GATACACTAAACTGGCTCGTAAGAGCGATATACTTTATTGGCTCGGAAGAGNAGT
1 GATACACTAAACTAGCTCATAAGAGCGATATACTGTACTGGCTCGGAAGAG-AGT
* *
177621 GATATACTAAACTAGCTCATAAGAGCGATATACTGTACTGGCTCGTAAGAG
1 GATACACTAAACTAGCTCATAAGAGCGATATACTGTACTGGCTCGGAAGAG
177672 CGATTTTCTG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.33, C:0.17, G:0.24, T:0.25
Consensus pattern (54 bp):
GATACACTAAACTAGCTCATAAGAGCGATATACTGTACTGGCTCGGAAGAGAGT
Found at i:204500 original size:9 final size:9
Alignment explanation
Indices: 204483--204528 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
204473 TGAGTTTTCG
204483 AATTCGAAT
1 AATTCGAAT
*
204492 AACTCGAAT
1 AATTCGAAT
204501 AATTCGAAT
1 AATTCGAAT
204510 AATTCGAAT
1 AATTCGAAT
*
204519 AAATCGAAT
1 AATTCGAAT
204528 A
1 A
204529 TTAAATTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.48, C:0.13, G:0.11, T:0.28
Consensus pattern (9 bp):
AATTCGAAT
Found at i:204581 original size:21 final size:22
Alignment explanation
Indices: 204541--204593 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
204531 AAATTATAAT
* *
204541 TTTTTATATTTTTACCTCAAACA
1 TTTTTATTTTTTTA-CTCAAAAA
204564 TTTTTATTTTTTTA-TCAAAAA
1 TTTTTATTTTTTTACTCAAAAA
*
204585 CTTTTATTT
1 TTTTTATTT
204594 CTTCCCACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 14 0.52
23 13 0.48
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTTATTTTTTTACTCAAAAA
Found at i:204585 original size:23 final size:22
Alignment explanation
Indices: 204541--204593 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
204531 AAATTATAAT
* **
204541 TTTTTATATTTTTACCTCAAAC
1 TTTTTATTTTTTTACCAAAAAC
*
204563 ATTTTTATTTTTTTATCAAAAAC
1 -TTTTTATTTTTTTACCAAAAAC
204586 -TTTTATTT
1 TTTTTATTT
204594 CTTCCCACTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 8 0.31
23 18 0.69
ACGTcount: A:0.28, C:0.11, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTTATTTTTTTACCAAAAAC
Found at i:205054 original size:18 final size:18
Alignment explanation
Indices: 205033--205078 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 18
205023 CTATTTATAT
*
205033 TATTGAATTTTTTAATAA
1 TATTGAATTTTATAATAA
*
205051 TATTGAATATTTATATTAA
1 TATTGAAT-TTTATAATAA
*
205070 AATTGAATT
1 TATTGAATT
205079 ATTAATCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (18 bp):
TATTGAATTTTATAATAA
Found at i:237748 original size:24 final size:24
Alignment explanation
Indices: 237720--237770 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
237710 AGAAATAATC
* *
237720 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTAGTTG
237744 TTTCAATTAAACTCTGTTTAGTTG
1 TTTCAATTAAACTCTGTTTAGTTG
237768 TTT
1 TTT
237771 AAGTCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.22, C:0.12, G:0.12, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTAGTTG
Found at i:241171 original size:27 final size:27
Alignment explanation
Indices: 241120--241174 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
241110 CTGAATATTC
*
241120 AAATTGGGCTTTTAAGAGCCACCAAAA
1 AAATTGGGCTTTTAAGAGCAACCAAAA
*
241147 AAATTGGGCTTTTAA-ATCAATCCAAAA
1 AAATTGGGCTTTTAAGAGCAA-CCAAAA
241174 A
1 A
241175 GGTAATTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (27 bp):
AAATTGGGCTTTTAAGAGCAACCAAAA
Found at i:241755 original size:20 final size:20
Alignment explanation
Indices: 241727--241765 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
241717 AAATAATATG
241727 ATTTATTAACTCGACTTGAA
1 ATTTATTAACTCGACTTGAA
* * *
241747 ATTTTTTAATTCGATTTGA
1 ATTTATTAACTCGACTTGA
241766 CTCGACTTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (20 bp):
ATTTATTAACTCGACTTGAA
Found at i:242101 original size:28 final size:28
Alignment explanation
Indices: 242045--242112 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
242035 TCATCGTTAT
* * *
242045 TTTTTTTAATAAAAAATTATAAATTAAA
1 TTTTTTTATTAAAAAAATATAAATAAAA
242073 TTTTTTTATTAAAAAAATATTAAA-AAAA
1 TTTTTTTATTAAAAAAATA-TAAATAAAA
*
242101 TTTAATTTATTA
1 TTT-TTTTATTA
242113 TTTTTCTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 23 0.68
29 11 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTTTTTATTAAAAAAATATAAATAAAA
Found at i:247328 original size:17 final size:18
Alignment explanation
Indices: 247300--247338 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
247290 GAATTATTAT
247300 TTAAGCAAATAG-TTAAA
1 TTAAGCAAATAGATTAAA
247317 GTTAAG-AAATAGATTAAA
1 -TTAAGCAAATAGATTAAA
247335 TTAA
1 TTAA
247339 TTGGTCATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 10 0.50
18 10 0.50
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.31
Consensus pattern (18 bp):
TTAAGCAAATAGATTAAA
Found at i:247464 original size:16 final size:17
Alignment explanation
Indices: 247431--247472 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
247421 ACGAAATTAG
247431 AATTGAATTGAGAAAATT
1 AATT-AATTGAGAAAATT
*
247449 ATTTAATTGA-AAAATT
1 AATTAATTGAGAAAATT
247465 AATTAATT
1 AATTAATT
247473 TAGTAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 13 0.59
17 6 0.27
18 3 0.14
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (17 bp):
AATTAATTGAGAAAATT
Found at i:248245 original size:21 final size:23
Alignment explanation
Indices: 248197--248247 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
248187 TGATATAAAT
248197 AAAACATGCTTAAAAATGATCCAC
1 AAAACATGC-TAAAAATGATCCAC
*
248221 -AAACATG-TAAAAAT-ATCCTC
1 AAAACATGCTAAAAATGATCCAC
248241 AAAACAT
1 AAAACAT
248248 ATTCAACCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 5 0.20
21 13 0.52
23 7 0.28
ACGTcount: A:0.53, C:0.20, G:0.06, T:0.22
Consensus pattern (23 bp):
AAAACATGCTAAAAATGATCCAC
Found at i:255046 original size:2 final size:2
Alignment explanation
Indices: 255041--255067 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
255031 TATATATATA
255041 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
255068 CTAATCTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:264847 original size:19 final size:20
Alignment explanation
Indices: 264811--264856 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
264801 CTCTAAAAAA
264811 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAATAATTTAT
264830 CAAAAATTCAAAAT-ATTTAT
1 -AAAAATTCAAAATAATTTAT
264850 AAAAATT
1 AAAAATT
264857 TCCAAAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTAT
Found at i:264900 original size:20 final size:20
Alignment explanation
Indices: 264871--264908 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
264861 AAATTTAGAT
* *
264871 ATTTTTAAAAATTGTAAAAA
1 ATTTTAAAAAATTCTAAAAA
264891 ATTTTAAAAAATTCTAAA
1 ATTTTAAAAAATTCTAAA
264909 GAAAATATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (20 bp):
ATTTTAAAAAATTCTAAAAA
Found at i:265738 original size:17 final size:17
Alignment explanation
Indices: 265718--265750 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
265708 TTTAAGGACT
265718 TTTTAATTTTA-TTTAAG
1 TTTT-ATTTTAGTTTAAG
265735 TTTTATTTTAGTTTAA
1 TTTTATTTTAGTTTAA
265751 CAAGTGATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (17 bp):
TTTTATTTTAGTTTAAG
Found at i:266131 original size:17 final size:17
Alignment explanation
Indices: 266100--266134 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
266090 CAAACACTTA
266100 TTAAACTAAAATAAAAG
1 TTAAACTAAAATAAAAG
266117 TTAAA-TAAAATTAAAAG
1 TTAAACTAAAA-TAAAAG
266134 T
1 T
266135 CCTTTAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.63, C:0.03, G:0.06, T:0.29
Consensus pattern (17 bp):
TTAAACTAAAATAAAAG
Found at i:266725 original size:22 final size:22
Alignment explanation
Indices: 266697--266750 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
266687 CTTAGCTACA
266697 TATTATTTTTCCTCAACCTCAC
1 TATTATTTTTCCTCAACCTCAC
266719 TATTATTTTTCCTCAACCTCAC
1 TATTATTTTTCCTCAACCTCAC
* *
266741 TTTTTTTTTT
1 TATTATTTTT
266751 TTAAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.19, C:0.26, G:0.00, T:0.56
Consensus pattern (22 bp):
TATTATTTTTCCTCAACCTCAC
Found at i:274675 original size:45 final size:45
Alignment explanation
Indices: 274609--274698 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
274599 TTATAAAGGG
* *
274609 ATTTTAATTGAAACAATGAAGGAGGGACCAAAGGGGGTAATTTCC
1 ATTTTAATTGAAACAAAGAAGGAGGGACCAAAAGGGGTAATTTCC
*
274654 ATTTTAATTGAAACAAAGAAGGAGGGACCAAAAGGGGTATTTTCC
1 ATTTTAATTGAAACAAAGAAGGAGGGACCAAAAGGGGTAATTTCC
274699 CCTTCAAAGC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.39, C:0.11, G:0.26, T:0.24
Consensus pattern (45 bp):
ATTTTAATTGAAACAAAGAAGGAGGGACCAAAAGGGGTAATTTCC
Found at i:278974 original size:6 final size:6
Alignment explanation
Indices: 278948--279025 Score: 57
Period size: 6 Copynumber: 13.0 Consensus size: 6
278938 CCACCTCGTT
* * * * *
278948 CACGTC CACGTC CACGTC CTCGAC CTCGAC CACGAC CACGAC CACGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC CACGAC
* * * * * *
278996 CATGGC CACGGC CATGTC CTCGAC CACGAC
1 CACGAC CACGAC CACGAC CACGAC CACGAC
279026 TACTAGTGTG
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 60 1.00
ACGTcount: A:0.22, C:0.47, G:0.19, T:0.12
Consensus pattern (6 bp):
CACGAC
Found at i:280656 original size:3 final size:3
Alignment explanation
Indices: 280648--280687 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
280638 TTCATGTTTA
280648 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC T
280688 CATTAATCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TAC
Found at i:282081 original size:27 final size:27
Alignment explanation
Indices: 282039--282215 Score: 200
Period size: 27 Copynumber: 6.7 Consensus size: 27
282029 GGAGATATTT
* *
282039 TGATTCTTGCTTGTAAGAGCGTAATTC
1 TGATTCTGGCTCGTAAGAGCGTAATTC
282066 TGATTCTGGCTCGTAAGAGCGTAATTC
1 TGATTCTGGCTCGTAAGAGCGTAATTC
* * *
282093 TAATTCTGGCTCGTAAGAACGTAATTT
1 TGATTCTGGCTCGTAAGAGCGTAATTC
*
282120 TGATTCTGGCTCGTAGGAGCGTAATTC
1 TGATTCTGGCTCGTAAGAGCGTAATTC
* * * *
282147 TAATTTTGGCTTGTAGGAGCGTAATTC
1 TGATTCTGGCTCGTAAGAGCGTAATTC
* * *
282174 TG--TCTAGCTAGTAAGAGTGTAATTC
1 TGATTCTGGCTCGTAAGAGCGTAATTC
*
282199 T-AAT-TGGCTCGTAAGAG
1 TGATTCTGGCTCGTAAGAG
282216 TGATATTCTA
Statistics
Matches: 128, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
25 30 0.23
26 1 0.01
27 97 0.76
ACGTcount: A:0.24, C:0.15, G:0.25, T:0.36
Consensus pattern (27 bp):
TGATTCTGGCTCGTAAGAGCGTAATTC
Found at i:282124 original size:54 final size:54
Alignment explanation
Indices: 282041--282215 Score: 223
Period size: 54 Copynumber: 3.3 Consensus size: 54
282031 AGATATTTTG
* *
282041 ATTCTTGCTTGTAAGAGCGTAATTCTGATTCTGGCTCGTAAGAGCGTAATTCTA
1 ATTCTGGCTCGTAAGAGCGTAATTCTGATTCTGGCTCGTAAGAGCGTAATTCTA
* * *
282095 ATTCTGGCTCGTAAGAACGTAATTTTGATTCTGGCTCGTAGGAGCGTAATTCTA
1 ATTCTGGCTCGTAAGAGCGTAATTCTGATTCTGGCTCGTAAGAGCGTAATTCTA
* * * * * *
282149 ATTTTGGCTTGTAGGAGCGTAATTCTG--TCTAGCTAGTAAGAGTGTAATTCTA
1 ATTCTGGCTCGTAAGAGCGTAATTCTGATTCTGGCTCGTAAGAGCGTAATTCTA
282201 A-T-TGGCTCGTAAGAG
1 ATTCTGGCTCGTAAGAG
282216 TGATATTCTA
Statistics
Matches: 105, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
50 11 0.10
51 1 0.01
52 22 0.21
54 71 0.68
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.36
Consensus pattern (54 bp):
ATTCTGGCTCGTAAGAGCGTAATTCTGATTCTGGCTCGTAAGAGCGTAATTCTA
Found at i:283339 original size:19 final size:20
Alignment explanation
Indices: 283317--283365 Score: 64
Period size: 22 Copynumber: 2.4 Consensus size: 20
283307 ATGTGCTAAA
283317 CAGAAGCACA-AGTGCTGAT
1 CAGAAGCACACAGTGCTGAT
283336 CAGAAGCACACACAGTGCTGAT
1 CAGAAG--CACACAGTGCTGAT
283358 CAGTAAGC
1 CAG-AAGC
283366 GCGCTAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.23
21 5 0.19
22 12 0.46
23 3 0.12
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.14
Consensus pattern (20 bp):
CAGAAGCACACAGTGCTGAT
Found at i:283355 original size:22 final size:22
Alignment explanation
Indices: 283323--283365 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
283313 TAAACAGAAG
283323 CACAAGTGCTGATCAG-AAGCA
1 CACAAGTGCTGATCAGTAAGCA
283344 CACACAGTGCTGATCAGTAAGC
1 CACA-AGTGCTGATCAGTAAGC
283366 GCGCTAGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 4 0.20
22 12 0.60
23 4 0.20
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (22 bp):
CACAAGTGCTGATCAGTAAGCA
Found at i:285842 original size:21 final size:21
Alignment explanation
Indices: 285818--285864 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
285808 TGTACTGGTT
*
285818 GAAGTATCAAAAGTATCGGTA
1 GAAGTATCAAAAGTATCGATA
*
285839 GAAGTATCACAAGTATCGATA
1 GAAGTATCAAAAGTATCGATA
285860 GAAGT
1 GAAGT
285865 TTGCACTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (21 bp):
GAAGTATCAAAAGTATCGATA
Found at i:296198 original size:25 final size:27
Alignment explanation
Indices: 296161--296210 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
296151 GATTTACTTT
*
296161 TAATTGCACTGAC-A-TTTAACTTTTA
1 TAATTACACTGACAATTTTAACTTTTA
*
296186 TAATTACATTGACAATTTTAACTTT
1 TAATTACACTGACAATTTTAACTTT
296211 CTTAGTGTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 11 0.52
26 1 0.05
27 9 0.43
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.46
Consensus pattern (27 bp):
TAATTACACTGACAATTTTAACTTTTA
Found at i:310607 original size:15 final size:16
Alignment explanation
Indices: 310587--310619 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
310577 AACTCTATAC
310587 TTTAAAT-TTTATTTA
1 TTTAAATGTTTATTTA
310602 TTTAAATGTTTATTTA
1 TTTAAATGTTTATTTA
310618 TT
1 TT
310620 ATTACTATCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (16 bp):
TTTAAATGTTTATTTA
Found at i:311252 original size:3 final size:3
Alignment explanation
Indices: 311244--311281 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
311234 ACATTTAATC
311244 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
311282 TTAAAAAGAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:316706 original size:27 final size:27
Alignment explanation
Indices: 316676--316757 Score: 123
Period size: 27 Copynumber: 3.1 Consensus size: 27
316666 CGACGGAGAT
316676 ATTTTGATTCTGGCTCATAGGAGCGTA
1 ATTTTGATTCTGGCTCATAGGAGCGTA
*
316703 ATTTTG--TCTGGCTCATAAGAGCGTA
1 ATTTTGATTCTGGCTCATAGGAGCGTA
* *
316728 ATTCTGATTCTGGCTCGTAGGAGCGTA
1 ATTTTGATTCTGGCTCATAGGAGCGTA
316755 ATT
1 ATT
316758 CTGTCTAGCT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
25 23 0.47
27 26 0.53
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.37
Consensus pattern (27 bp):
ATTTTGATTCTGGCTCATAGGAGCGTA
Found at i:316758 original size:27 final size:25
Alignment explanation
Indices: 316684--316802 Score: 130
Period size: 25 Copynumber: 4.7 Consensus size: 25
316674 ATATTTTGAT
* *
316684 TCTGGCTCATAGGAGCGTAATTTTG
1 TCTGGCTCATAAGAGCGTAATTCTG
316709 TCTGGCTCATAAGAGCGTAATTCTG
1 TCTGGCTCATAAGAGCGTAATTCTG
* *
316734 ATTCTGGCTCGTAGGAGCGTAATTCTG
1 --TCTGGCTCATAAGAGCGTAATTCTG
* * * *
316761 TCTAGCTCGTAAGAGTGTAATTCTA
1 TCTGGCTCATAAGAGCGTAATTCTG
* *
316786 ACTGGCTTATAAGAGCG
1 TCTGGCTCATAAGAGCG
316803 ATACTAAACT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
25 56 0.71
27 23 0.29
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.33
Consensus pattern (25 bp):
TCTGGCTCATAAGAGCGTAATTCTG
Found at i:316763 original size:52 final size:52
Alignment explanation
Indices: 316680--316784 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 52
316670 GGAGATATTT
* *
316680 TGATTCTGGCTCATAGGAGCGTAATTTTGTCTGGCTCATAAGAGCGTAATTC
1 TGATTCTGGCTCATAGGAGCGTAATTCTGTCTAGCTCATAAGAGCGTAATTC
* * *
316732 TGATTCTGGCTCGTAGGAGCGTAATTCTGTCTAGCTCGTAAGAGTGTAATTC
1 TGATTCTGGCTCATAGGAGCGTAATTCTGTCTAGCTCATAAGAGCGTAATTC
316784 T
1 T
316785 AACTGGCTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.35
Consensus pattern (52 bp):
TGATTCTGGCTCATAGGAGCGTAATTCTGTCTAGCTCATAAGAGCGTAATTC
Found at i:319604 original size:80 final size:80
Alignment explanation
Indices: 319471--319619 Score: 192
Period size: 80 Copynumber: 1.9 Consensus size: 80
319461 TAAACCGATG
** ** * * *
319471 ATCCTGGTTCCTAGTGCCTAACGGATAAACTGCGAAAGTGAGCCCAGCTCTAGTCGGTTAAACCG
1 ATCCTGGCACCTAGTGCCTAACAAATAAACTGCAAAAATGAGCCCAGCTCTAGTCAGTTAAACCG
319536 ACAAATATTCGTTAA
66 ACAAATATTCGTTAA
* * *
319551 ATCCTGGCACCTAGTGCCTAACAAATAAA-TCGCAAAAATGAGCCTAGCTCTAGTTAGTTAAACT
1 ATCCTGGCACCTAGTGCCTAACAAATAAACT-GCAAAAATGAGCCCAGCTCTAGTCAGTTAAACC
319615 GACAA
65 GACAA
319620 CATGAATAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
79 1 0.02
80 57 0.98
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (80 bp):
ATCCTGGCACCTAGTGCCTAACAAATAAACTGCAAAAATGAGCCCAGCTCTAGTCAGTTAAACCG
ACAAATATTCGTTAA
Found at i:332041 original size:12 final size:12
Alignment explanation
Indices: 332026--332050 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
332016 ATTAAAGAAT
332026 TAATAGCATTCA
1 TAATAGCATTCA
332038 TAATAGCATTCA
1 TAATAGCATTCA
332050 T
1 T
332051 CATGATAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.08, T:0.36
Consensus pattern (12 bp):
TAATAGCATTCA
Found at i:334909 original size:18 final size:18
Alignment explanation
Indices: 334888--334931 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
334878 CTCCACATGA
* *
334888 TCTTCTTCAGGATCTTTT
1 TCTTCTTCAGGATCCTCT
*
334906 TCTTCCTCAGGATCCTCT
1 TCTTCTTCAGGATCCTCT
334924 TCTTCTTC
1 TCTTCTTC
334932 TTCTTCTTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.32, G:0.09, T:0.50
Consensus pattern (18 bp):
TCTTCTTCAGGATCCTCT
Found at i:344739 original size:18 final size:18
Alignment explanation
Indices: 344708--344746 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
344698 GGAAGCACCC
344708 AAAAAGAAAGAAAAGG-G
1 AAAAAGAAAGAAAAGGAG
*
344725 AAAAAGGAAGAAAAAGGAG
1 AAAAAGAAAG-AAAAGGAG
344744 AAA
1 AAA
344747 TCAGACTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 6 0.32
19 4 0.21
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAGAAAAGGAG
Found at i:346436 original size:10 final size:9
Alignment explanation
Indices: 346423--346474 Score: 53
Period size: 8 Copynumber: 6.3 Consensus size: 9
346413 AAAAATCACA
346423 AAAAGAAAGG
1 AAAAGAAA-G
346433 AAAAGAAAG
1 AAAAGAAAG
346442 --AAG-AAG
1 AAAAGAAAG
346448 AAAAGAAA-
1 AAAAGAAAG
346456 AAAAGAAA-
1 AAAAGAAAG
346464 AAAA-AAAG
1 AAAAGAAAG
346472 AAA
1 AAA
346475 TATATTTCCA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
6 3 0.08
7 6 0.16
8 18 0.47
9 3 0.08
10 8 0.21
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (9 bp):
AAAAGAAAG
Found at i:346452 original size:15 final size:14
Alignment explanation
Indices: 346422--346473 Score: 61
Period size: 13 Copynumber: 3.6 Consensus size: 14
346412 AAAAAATCAC
346422 AAAAAGAAAGGAAAAG
1 AAAAAG-AA-GAAAAG
346438 AAAGAAGAAGAAAAG
1 AAA-AAGAAGAAAAG
*
346453 AAAAA-AAGAAAAA
1 AAAAAGAAGAAAAG
346466 AAAAAGAA
1 AAAAAGAA
346474 ATATATTTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
13 12 0.36
14 4 0.12
15 9 0.27
16 5 0.15
17 3 0.09
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGAAAAG
Found at i:346462 original size:19 final size:20
Alignment explanation
Indices: 346422--346474 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
346412 AAAAAATCAC
*
346422 AAAAAGAAAGGAAAAGAAAG
1 AAAAAGAAAAGAAAAGAAAG
*
346442 AAGAAGAAAAGAAAA-AAAG
1 AAAAAGAAAAGAAAAGAAAG
*
346461 AAAAAAAAAAGAAA
1 AAAAAGAAAAGAAA
346475 TATATTTCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAGAAAG
Found at i:348528 original size:19 final size:20
Alignment explanation
Indices: 348506--348553 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
348496 CAAACTCTTA
348506 ATAATAATTAATATA-AATT
1 ATAATAATTAATATATAATT
*
348525 ATAA-AATTTAATTTATAATT
1 ATAATAA-TTAATATATAATT
348545 -TAAT-ATTAA
1 ATAATAATTAA
348554 GAATAATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.24
19 15 0.60
20 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATAATTAATATATAATT
Found at i:356230 original size:22 final size:22
Alignment explanation
Indices: 356204--356277 Score: 69
Period size: 22 Copynumber: 3.4 Consensus size: 22
356194 CTCCAATTTT
356204 GTATGAAATTAGGTAAAAAAGG
1 GTATGAAATTAGGTAAAAAAGG
* * * * ***
356226 GTATGAAA-AAGTCTATATATTT
1 GTATGAAATTAG-GTAAAAAAGG
356248 GTATGAAATTAGGTAAAAAAGG
1 GTATGAAATTAGGTAAAAAAGG
356270 GTATGAAA
1 GTATGAAA
356278 AAGTCTATAT
Statistics
Matches: 36, Mismatches: 14, Indels: 4
0.67 0.26 0.07
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.47, C:0.01, G:0.23, T:0.28
Consensus pattern (22 bp):
GTATGAAATTAGGTAAAAAAGG
Found at i:356251 original size:44 final size:44
Alignment explanation
Indices: 356201--356291 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
356191 TTACTCCAAT
356201 TTTGTATGAAATTAGGTAAAAAAGGGTATGAAAAAGTCTATATA
1 TTTGTATGAAATTAGGTAAAAAAGGGTATGAAAAAGTCTATATA
356245 TTTGTATGAAATTAGGTAAAAAAGGGTATGAAAAAGTCTATATA
1 TTTGTATGAAATTAGGTAAAAAAGGGTATGAAAAAGTCTATATA
356289 TTT
1 TTT
356292 TCATCGTTCC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.44, C:0.02, G:0.20, T:0.34
Consensus pattern (44 bp):
TTTGTATGAAATTAGGTAAAAAAGGGTATGAAAAAGTCTATATA
Found at i:365727 original size:17 final size:17
Alignment explanation
Indices: 365701--365749 Score: 89
Period size: 17 Copynumber: 2.9 Consensus size: 17
365691 ACATACATCA
*
365701 CTAGCAGATAGTATCGC
1 CTAGCGGATAGTATCGC
365718 CTAGCGGATAGTATCGC
1 CTAGCGGATAGTATCGC
365735 CTAGCGGATAGTATC
1 CTAGCGGATAGTATC
365750 AACTGACGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.27, C:0.22, G:0.27, T:0.24
Consensus pattern (17 bp):
CTAGCGGATAGTATCGC
Found at i:367530 original size:24 final size:22
Alignment explanation
Indices: 367476--367521 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
367466 AGTTAGCACT
*
367476 TAGTTAATTTTTTAAGTTTTTA
1 TAGTTATTTTTTTAAGTTTTTA
*
367498 TAGTTATTTTTTTTAGTTTTTA
1 TAGTTATTTTTTTAAGTTTTTA
367520 TA
1 TA
367522 TCATCATTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (22 bp):
TAGTTATTTTTTTAAGTTTTTA
Found at i:368898 original size:15 final size:15
Alignment explanation
Indices: 368866--368906 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
368856 TATAACAATA
*
368866 TTTCTCTTTTTTCCT
1 TTTCTCTTTTTTCAT
368881 TTTCTC-TTTTTCTAT
1 TTTCTCTTTTTTC-AT
368896 TTTC-CTTTTTT
1 TTTCTCTTTTTT
368907 GTTTCTCGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTCTCTTTTTTCAT
Found at i:369678 original size:20 final size:20
Alignment explanation
Indices: 369655--369693 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
369645 CTCTCCTTCC
* *
369655 TCCTTGTGCTTCTTCTTTTG
1 TCCTTGCGCTTCCTCTTTTG
369675 TCCTTGCGCTTCCTCTTTT
1 TCCTTGCGCTTCCTCTTTT
369694 TATCCTTCGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.00, C:0.31, G:0.13, T:0.56
Consensus pattern (20 bp):
TCCTTGCGCTTCCTCTTTTG
Found at i:369699 original size:21 final size:20
Alignment explanation
Indices: 369655--369700 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
369645 CTCTCCTTCC
* * *
369655 TCCTTGTGCTTCTTCTTTTG
1 TCCTTGCGCTTCCTCTTTTA
369675 TCCTTGCGCTTCCTCTTTTTA
1 TCCTTGCGCTTCCTC-TTTTA
369696 TCCTT
1 TCCTT
369701 CGAACCAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.02, C:0.30, G:0.11, T:0.57
Consensus pattern (20 bp):
TCCTTGCGCTTCCTCTTTTA
Found at i:373550 original size:16 final size:16
Alignment explanation
Indices: 373529--373561 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
373519 TACTAGCATA
373529 ATAAATAGAATGAAAT
1 ATAAATAGAATGAAAT
373545 ATAAATAGAATGAAAT
1 ATAAATAGAATGAAAT
373561 A
1 A
373562 CCTTTTCTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (16 bp):
ATAAATAGAATGAAAT
Found at i:373834 original size:110 final size:110
Alignment explanation
Indices: 373641--373862 Score: 381
Period size: 110 Copynumber: 2.0 Consensus size: 110
373631 GTTGCGTCCA
* *
373641 ATCTAGTGCGACAATAATCAAAACTTGTACTAGCTATTTCTTTATTGTGATGAATACGTCTAGAC
1 ATCTAGTGCGACAACAATCAAAACTTGTACTAGCTACTTCTTTATTGTGATGAATACGTCTAGAC
* *
373706 AAGTGTCATCAAACACAAACTTATTATTCTTCTCTAGTAATGAGC
66 AAGTGTCATCAAACACAAACTTATTATTCTGCTCTAGCAATGAGC
*
373751 ATCTAGTGCGACAACAATCGAAACTTGTACTAGCTACTTCTTTATTGTGATGAATACGTCTAGAC
1 ATCTAGTGCGACAACAATCAAAACTTGTACTAGCTACTTCTTTATTGTGATGAATACGTCTAGAC
* *
373816 AGGTGTCATCAAACACAAACTTTTTATTCTGCTCTAGCAATGAGC
66 AAGTGTCATCAAACACAAACTTATTATTCTGCTCTAGCAATGAGC
373861 AT
1 AT
373863 AACGGTTTAG
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
110 105 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (110 bp):
ATCTAGTGCGACAACAATCAAAACTTGTACTAGCTACTTCTTTATTGTGATGAATACGTCTAGAC
AAGTGTCATCAAACACAAACTTATTATTCTGCTCTAGCAATGAGC
Found at i:377250 original size:54 final size:54
Alignment explanation
Indices: 377168--377275 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
377158 TTCACAGGTA
377168 AATGTCGAGACATCCATCTGTTGGGCTACATGGATAGGGGCAACATCACTTGAC
1 AATGTCGAGACATCCATCTGTTGGGCTACATGGATAGGGGCAACATCACTTGAC
377222 AATGTCGAGACATCCATCTGTTGGGCTACATGGATAGGGGCAACATCACTTGAC
1 AATGTCGAGACATCCATCTGTTGGGCTACATGGATAGGGGCAACATCACTTGAC
377276 CCCTTCATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (54 bp):
AATGTCGAGACATCCATCTGTTGGGCTACATGGATAGGGGCAACATCACTTGAC
Found at i:382172 original size:25 final size:25
Alignment explanation
Indices: 382113--382175 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
382103 ATATGAATTA
*
382113 TTATAATAAAATTTATTTAAATATT
1 TTATAATAAAAATTATTTAAATATT
** *
382138 GCATGA-AAAAATTATTTAAATATAT
1 TTATAATAAAAATTATTTAAATAT-T
382163 TTAT-ATAAAAATT
1 TTATAATAAAAATT
382176 TTAATATGCA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.51, C:0.02, G:0.03, T:0.44
Consensus pattern (25 bp):
TTATAATAAAAATTATTTAAATATT
Found at i:390190 original size:8 final size:8
Alignment explanation
Indices: 390177--390217 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
390167 TTATGTGATA
390177 ATAATAAT
1 ATAATAAT
390185 ATAAT-AT
1 ATAATAAT
390192 -TAATTAAT
1 ATAA-TAAT
390200 ATAATAAT
1 ATAATAAT
*
390208 ATATTAAT
1 ATAATAAT
390216 AT
1 AT
390218 GAAATTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
6 3 0.10
7 3 0.10
8 20 0.69
9 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (8 bp):
ATAATAAT
Found at i:390201 original size:15 final size:15
Alignment explanation
Indices: 390181--390230 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
390171 GTGATAATAA
390181 TAATATAATATTAAT
1 TAATATAATATTAAT
*
390196 TAATATAATAATATAT
1 TAATATAATATTA-AT
390212 TAATATGAA-ATTAAT
1 TAATAT-AATATTAAT
390227 TAAT
1 TAAT
390231 TTGATCATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 18 0.58
16 11 0.35
17 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (15 bp):
TAATATAATATTAAT
Done.