Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015360.1 Kokia drynarioides strain JFW-HI SEQ_130407, 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: 850717
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 109 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:795 original size:39 final size:39
Alignment explanation
Indices: 751--834 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 39
741 TGGGACAAGT
*
751 CTCTTCCAAGAGGTAT-GTCCAATATGAAAAGGATTGTGA
1 CTCTTCCAAGAGGTATCATCCAATATG-AAAGGATTGTGA
* * *
790 CTCTT-CAATAGGTGTCCATCCAATTTGAAAGGATTGTGA
1 CTCTTCCAAGAGGTAT-CATCCAATATGAAAGGATTGTGA
*
829 TTCTTC
1 CTCTTC
835 AAAATGTGTC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
38 8 0.22
39 21 0.57
40 8 0.22
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (39 bp):
CTCTTCCAAGAGGTATCATCCAATATGAAAGGATTGTGA
Found at i:835 original size:39 final size:40
Alignment explanation
Indices: 768--847 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
758 AAGAGGTATG
*
768 TCCAATATGAAAAGGATTGTGACTCTTCAATAGGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
* * *
808 TCCAATTTG-AAAGGATTGTGATTCTTCAAAATGTGTCCA
1 TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
847 T
1 T
848 TGAGTGCATA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 28 0.78
40 8 0.22
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (40 bp):
TCCAATATGAAAAGGATTGTGACTCTTCAAAAGGTGTCCA
Found at i:13504 original size:6 final size:6
Alignment explanation
Indices: 13495--13519 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13485 CCCTACTCCA
13495 ACACCC ACACCC ACACCC ACACCC A
1 ACACCC ACACCC ACACCC ACACCC A
13520 ACGCCGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.64, G:0.00, T:0.00
Consensus pattern (6 bp):
ACACCC
Found at i:14214 original size:28 final size:29
Alignment explanation
Indices: 14183--14242 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
14173 AGAAAAATAA
*
14183 ATTTTAATTTGTATATA-A-GAGTAATAGG
1 ATTTTAATTTGTAGATAGAGGAGTAA-AGG
*
14211 ATTTTAATTTTTAGATAGAGGAGTAAAGG
1 ATTTTAATTTGTAGATAGAGGAGTAAAGG
14240 ATT
1 ATT
14243 AAATTTTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 15 0.54
29 7 0.25
30 6 0.21
ACGTcount: A:0.38, C:0.00, G:0.20, T:0.42
Consensus pattern (29 bp):
ATTTTAATTTGTAGATAGAGGAGTAAAGG
Found at i:29740 original size:52 final size:54
Alignment explanation
Indices: 29667--29913 Score: 274
Period size: 52 Copynumber: 4.7 Consensus size: 54
29657 CATACAAGCC
* * *
29667 AAACAAAATTACGCTCATACGAGCCA-AA-CAGAATTACGCTCTTACGAGCCAA
1 AAACAGAATTAAGCTCTTACGAGCCAGAATCAGAATTACGCTCTTACGAGCCAA
* * * *
29719 AAACAGAATTAAGCTTTTACGAGCTAGAATCAGAATTATGCTCTTACAAGCC-A
1 AAACAGAATTAAGCTCTTACGAGCCAGAATCAGAATTACGCTCTTACGAGCCAA
* * *
29772 AAA-AGAATTACA-CTCTTATGAGCCAGAATCAGAATTATGCTCTTACGAGCCAG
1 AAACAGAATTA-AGCTCTTACGAGCCAGAATCAGAATTACGCTCTTACGAGCCAA
* ** *
29825 AATCAGAATTATTCTCTTACGAGCCA-AA-CAGAATTACGCTCTTACGAGCCAG
1 AAACAGAATTAAGCTCTTACGAGCCAGAATCAGAATTACGCTCTTACGAGCCAA
* * * *
29877 AATCAGAATTACGCTCTTACGAGCTAGAATTAGAATT
1 AAACAGAATTAAGCTCTTACGAGCCAGAATCAGAATT
29914 TCTTTGTCTT
Statistics
Matches: 167, Mismatches: 20, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
52 109 0.65
53 13 0.08
54 45 0.27
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.24
Consensus pattern (54 bp):
AAACAGAATTAAGCTCTTACGAGCCAGAATCAGAATTACGCTCTTACGAGCCAA
Found at i:29779 original size:79 final size:79
Alignment explanation
Indices: 29673--29913 Score: 356
Period size: 79 Copynumber: 3.1 Consensus size: 79
29663 AGCCAAACAA
* * * * *
29673 AATTACGCTCATACGAGCCAAACAGAATTACGCTCTTACGAGCCAAAAACAGAATTAAGCTTTTA
1 AATTATGCTCTTACGAGCCAAACAGAATTACGCTCTTACGAGCCAGAATCAGAATTAAGCTCTTA
29738 CGAGCTAGAATCAG
66 CGAGCTAGAATCAG
* * * * *
29752 AATTATGCTCTTACAAGCCAAAAAGAATTACACTCTTATGAGCCAGAATCAGAATTATGCTCTTA
1 AATTATGCTCTTACGAGCCAAACAGAATTACGCTCTTACGAGCCAGAATCAGAATTAAGCTCTTA
*
29817 CGAGCCAGAATCAG
66 CGAGCTAGAATCAG
* *
29831 AATTATTCTCTTACGAGCCAAACAGAATTACGCTCTTACGAGCCAGAATCAGAATTACGCTCTTA
1 AATTATGCTCTTACGAGCCAAACAGAATTACGCTCTTACGAGCCAGAATCAGAATTAAGCTCTTA
*
29896 CGAGCTAGAATTAG
66 CGAGCTAGAATCAG
29910 AATT
1 AATT
29914 TCTTTGTCTT
Statistics
Matches: 143, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 143 1.00
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (79 bp):
AATTATGCTCTTACGAGCCAAACAGAATTACGCTCTTACGAGCCAGAATCAGAATTAAGCTCTTA
CGAGCTAGAATCAG
Found at i:29906 original size:27 final size:27
Alignment explanation
Indices: 29673--29913 Score: 296
Period size: 27 Copynumber: 9.1 Consensus size: 27
29663 AGCCAAACAA
*
29673 AATTACGCTCATACGAGCCA-AA-CAG
1 AATTACGCTCTTACGAGCCAGAATCAG
* *
29698 AATTACGCTCTTACGAGCCAAAAACAG
1 AATTACGCTCTTACGAGCCAGAATCAG
* * *
29725 AATTAAGCTTTTACGAGCTAGAATCAG
1 AATTACGCTCTTACGAGCCAGAATCAG
* * *
29752 AATTATGCTCTTACAAGCCA-AA-AAG
1 AATTACGCTCTTACGAGCCAGAATCAG
* *
29777 AATTACACTCTTATGAGCCAGAATCAG
1 AATTACGCTCTTACGAGCCAGAATCAG
*
29804 AATTATGCTCTTACGAGCCAGAATCAG
1 AATTACGCTCTTACGAGCCAGAATCAG
**
29831 AATTATTCTCTTACGAGCCA-AA-CAG
1 AATTACGCTCTTACGAGCCAGAATCAG
29856 AATTACGCTCTTACGAGCCAGAATCAG
1 AATTACGCTCTTACGAGCCAGAATCAG
* *
29883 AATTACGCTCTTACGAGCTAGAATTAG
1 AATTACGCTCTTACGAGCCAGAATCAG
29910 AATT
1 AATT
29914 TCTTTGTCTT
Statistics
Matches: 186, Mismatches: 24, Indels: 10
0.85 0.11 0.05
Matches are distributed among these distances:
25 58 0.31
26 10 0.05
27 118 0.63
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (27 bp):
AATTACGCTCTTACGAGCCAGAATCAG
Found at i:37177 original size:48 final size:47
Alignment explanation
Indices: 37116--37210 Score: 181
Period size: 48 Copynumber: 2.0 Consensus size: 47
37106 AGTATAAACT
37116 TTTAAATTTTCTCATGTAATTTTCTCTTTCGCCTTACCAGTATATAG
1 TTTAAATTTTCTCATGTAATTTTCTCTTTCGCCTTACCAGTATATAG
37163 TTTAAATTTTTCTCATGTAATTTTCTCTTTCGCCTTACCAGTATATAG
1 TTTAAA-TTTTCTCATGTAATTTTCTCTTTCGCCTTACCAGTATATAG
37211 CTTGTATCTT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
47 6 0.13
48 41 0.87
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.49
Consensus pattern (47 bp):
TTTAAATTTTCTCATGTAATTTTCTCTTTCGCCTTACCAGTATATAG
Found at i:37393 original size:23 final size:22
Alignment explanation
Indices: 37362--37456 Score: 100
Period size: 23 Copynumber: 4.2 Consensus size: 22
37352 CTTGGGAAAT
* *
37362 AGTAAGCACACACAGTGCAATCC
1 AGTAGGCACACATAGTGCAAT-C
37385 AGTAGGCACACATAGTGCAATC
1 AGTAGGCACACATAGTGCAATC
* * *
37407 AGTAGACGCACATAGCGCAAATC
1 AGTAGGCACACATAGTGC-AATC
* *
37430 AGTAGGCACACAAAGTGCGAAAC
1 AGTAGGCACACATAGTGC-AATC
37453 AGTA
1 AGTA
37457 AGCGCGCTAG
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 16 0.27
23 44 0.73
ACGTcount: A:0.40, C:0.24, G:0.22, T:0.14
Consensus pattern (22 bp):
AGTAGGCACACATAGTGCAATC
Found at i:45026 original size:25 final size:25
Alignment explanation
Indices: 44991--45040 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
44981 AATGATGAGA
44991 AAATTTAAATTTCAA-AAAATTGTTC
1 AAATTTAAA-TTCAATAAAATTGTTC
* *
45016 AAATTTTAATTCAATGAAATTGTTC
1 AAATTTAAATTCAATAAAATTGTTC
45041 GAGTTTTCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (25 bp):
AAATTTAAATTCAATAAAATTGTTC
Found at i:45054 original size:25 final size:27
Alignment explanation
Indices: 45007--45063 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 27
44997 AAATTTCAAA
45007 AAATTGTTCAAATTTTAATTC-AAT-G
1 AAATTGTTCAAATTTTAATTCAAATCG
* *
45032 AAATTGTTCGAGTTTTCAA-TCAAATCG
1 AAATTGTTCAAATTTT-AATTCAAATCG
45059 AAATT
1 AAATT
45064 TCTTCTATCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
25 16 0.59
26 5 0.19
27 6 0.22
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.40
Consensus pattern (27 bp):
AAATTGTTCAAATTTTAATTCAAATCG
Found at i:53316 original size:20 final size:21
Alignment explanation
Indices: 53274--53320 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
53264 TAAAAATATG
53274 AAAATATAAAATATCATCATA
1 AAAATATAAAATATCATCATA
* * *
53295 AAAATATTAATTATCAT-TTA
1 AAAATATAAAATATCATCATA
53315 AAAATA
1 AAAATA
53321 AATATAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (21 bp):
AAAATATAAAATATCATCATA
Found at i:58583 original size:28 final size:29
Alignment explanation
Indices: 58521--58575 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
58511 TGCTATAGAT
* *
58521 TATTGTATTATTTATAAATTTGATTTTTA
1 TATTTTATTATTTAGAAATTTGATTTTTA
58550 TATTTTATT-TTTAGAAATTT-ATTTTT
1 TATTTTATTATTTAGAAATTTGATTTTT
58576 TCTATTTTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 10 0.42
29 8 0.33
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.65
Consensus pattern (29 bp):
TATTTTATTATTTAGAAATTTGATTTTTA
Found at i:59242 original size:13 final size:13
Alignment explanation
Indices: 59224--59248 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
59214 GTTAAACCGA
59224 AAGATTATATTCG
1 AAGATTATATTCG
59237 AAGATTATATTC
1 AAGATTATATTC
59249 ACTTAAACGC
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:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
AAGATTATATTCG
Found at i:63804 original size:24 final size:24
Alignment explanation
Indices: 63777--63824 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
63767 TTTTTTTTCC
63777 TATAGTAATAAAAGAATAGATAAA
1 TATAGTAATAAAAGAATAGATAAA
63801 TATAGTAATAAAAGAATAGATAAA
1 TATAGTAATAAAAGAATAGATAAA
63825 CTACATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (24 bp):
TATAGTAATAAAAGAATAGATAAA
Found at i:67433 original size:40 final size:40
Alignment explanation
Indices: 67378--67581 Score: 266
Period size: 40 Copynumber: 5.1 Consensus size: 40
67368 TTGTTAAATT
* *
67378 CGGTGTTAATATTCAAGCTTTAGCTTAGCATGCTATGAGC
1 CGGTGTTAATATTCAAGCTTCAGCTTAGCAGGCTATGAGC
67418 CGGTGTTAATATTCAAGCTTCAGCTTAGCAGGCTATGAGC
1 CGGTGTTAATATTCAAGCTTCAGCTTAGCAGGCTATGAGC
* * *
67458 TGGTGTTAATATTCAAGCTTCAGCTTAGTAGGCTATGAGT
1 CGGTGTTAATATTCAAGCTTCAGCTTAGCAGGCTATGAGC
* * ** * * **
67498 AGGTGTTAGTATTCAAGCTTTGGCTTAGCAAGCCATGAAT
1 CGGTGTTAATATTCAAGCTTCAGCTTAGCAGGCTATGAGC
* *
67538 CAGTG-TAATATTCAAGCTTCGGCTTAGCAGGCTATGAGC
1 CGGTGTTAATATTCAAGCTTCAGCTTAGCAGGCTATGAGC
67577 CGGTG
1 CGGTG
67582 AATATGTAAG
Statistics
Matches: 142, Mismatches: 22, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
39 32 0.23
40 110 0.77
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (40 bp):
CGGTGTTAATATTCAAGCTTCAGCTTAGCAGGCTATGAGC
Found at i:76379 original size:34 final size:34
Alignment explanation
Indices: 76341--76408 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
76331 GACACACGTT
*
76341 GAGGCTTCATAAACCTCAAGCGGGCTTTTTAATG
1 GAGGCTTCATAAACCTCAAGCGAGCTTTTTAATG
*
76375 GAGGCTTCATAAACCTCAAGCGATCTTTTTAATG
1 GAGGCTTCATAAACCTCAAGCGAGCTTTTTAATG
76409 AAGAAAGTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (34 bp):
GAGGCTTCATAAACCTCAAGCGAGCTTTTTAATG
Found at i:80522 original size:3 final size:3
Alignment explanation
Indices: 80514--80550 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
80504 AGCAAGAGAA
80514 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
80551 ATGTGGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:81968 original size:19 final size:18
Alignment explanation
Indices: 81930--81968 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
81920 TAATGTTCAT
* *
81930 TTAACAAAATTAATCGAA
1 TTAACAAAATTAACCAAA
81948 TTAACCAAAATTAACCAAA
1 TTAA-CAAAATTAACCAAA
81967 TT
1 TT
81969 CGTAATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.54, C:0.15, G:0.03, T:0.28
Consensus pattern (18 bp):
TTAACAAAATTAACCAAA
Found at i:83539 original size:4 final size:4
Alignment explanation
Indices: 83530--83585 Score: 76
Period size: 4 Copynumber: 14.0 Consensus size: 4
83520 TACACTGTTG
* * *
83530 GTAT GTAT GTGT GTAT GTAT GTAT GTAT GTAT GTAT GTGT GTAT GCAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
*
83578 GCAT GTAT
1 GTAT GTAT
83586 CACATTCATA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.21, C:0.04, G:0.29, T:0.46
Consensus pattern (4 bp):
GTAT
Found at i:90017 original size:19 final size:19
Alignment explanation
Indices: 89981--90017 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
89971 ATAATCACTG
89981 TTATCCACTGTAATCAAAT
1 TTATCCACTGTAATCAAAT
*
90000 TTATTCACTGTAATCAAA
1 TTATCCACTGTAATCAAA
90018 ATTGTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (19 bp):
TTATCCACTGTAATCAAAT
Found at i:92958 original size:195 final size:195
Alignment explanation
Indices: 92587--93034 Score: 542
Period size: 195 Copynumber: 2.3 Consensus size: 195
92577 GAAATCGATG
* * *
92587 CGATGGTTGAGGTATCGCATATGTTGCGAGACCTCGACAGCTCGTGTGAGCAGCATCGTGAGTCG
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTAAGTCG
* * ** *
92652 AAAAATGAGTAAATGAACCAAGAATGGATTACAGGCCCTACGATGATTGAGATTTATGCATAAGT
66 AAAAAAGAGTAAATGAACCAAGAATAGATTACAGGCCCTACGATGACGGAGACTTATGCATAAGT
* ** * * * * * *
92717 GTATATTCTCGACAGATCGTGTGAGCAGCATCATTAGGGAATAGTTATATACATAGATACTGTAT
131 GCATAACCTCAACAGATCGTGTAAGCAGCATCATTAGGGAATAGTTATATACACAAACACCGTAT
* * *
92782 CGATGGTTGAGGTACCGCACATGTTACGAGTCCTCGACAGCTCGTGTGAGTAGCATCGTAAGTCG
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTAAGTCG
* * * * * *
92847 AAAAAAGAG-ATATGAATCCTAGAATAGATTATAGGCCTTGCGATGGCGGAGACTTATGCATAAG
66 AAAAAAGAGTAAATGAA-CCAAGAATAGATTACAGGCCCTACGATGACGGAGACTTATGCATAAG
* * * * *
92911 TGCATACACCT-AATAGCTCGTGTAAGCATCATCGTTA-GGAGATAGTTATATAGACAAACACCG
130 TGCATA-ACCTCAACAGATCGTGTAAGCAGCATCATTAGGGA-ATAGTTATATACACAAACACCG
92974 TAT
193 TAT
* * *
92977 TGATGGTTGGGGTACCGCATATGTTGCGAGTCCTCGATAGCTCGTGTGAGCAGCATCG
1 CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCG
93035 GGTACTAGTA
Statistics
Matches: 213, Mismatches: 37, Indels: 6
0.83 0.14 0.02
Matches are distributed among these distances:
194 9 0.04
195 202 0.95
196 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (195 bp):
CGATGGTTGAGGTACCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTAAGTCG
AAAAAAGAGTAAATGAACCAAGAATAGATTACAGGCCCTACGATGACGGAGACTTATGCATAAGT
GCATAACCTCAACAGATCGTGTAAGCAGCATCATTAGGGAATAGTTATATACACAAACACCGTAT
Found at i:107013 original size:12 final size:12
Alignment explanation
Indices: 106998--107036 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
106988 AGAGAAGGAT
106998 GAAGAAAAAGAA
1 GAAGAAAAAGAA
* *
107010 GAAGGAAAGGAA
1 GAAGAAAAAGAA
*
107022 GAAGAGAAAGAA
1 GAAGAAAAAGAA
107034 GAA
1 GAA
107037 ACAAAACCTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (12 bp):
GAAGAAAAAGAA
Found at i:112643 original size:5 final size:5
Alignment explanation
Indices: 112633--112657 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
112623 AACAAAAGCA
112633 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
112658 TACGTAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:119012 original size:11 final size:11
Alignment explanation
Indices: 118996--119025 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
118986 CAGCGTTTAG
118996 AAAAGAAATGT
1 AAAAGAAATGT
119007 AAAAGAAATGT
1 AAAAGAAATGT
119018 AAAAGAAA
1 AAAAGAAA
119026 CAAGTGGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.70, C:0.00, G:0.17, T:0.13
Consensus pattern (11 bp):
AAAAGAAATGT
Found at i:123897 original size:14 final size:14
Alignment explanation
Indices: 123878--123905 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
123868 CTCTCTTAAC
123878 AAAAAAATTCAAAA
1 AAAAAAATTCAAAA
123892 AAAAAAATTCAAAA
1 AAAAAAATTCAAAA
123906 TAATTTTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.07, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAAAAATTCAAAA
Found at i:123951 original size:20 final size:19
Alignment explanation
Indices: 123895--123944 Score: 75
Period size: 18 Copynumber: 2.6 Consensus size: 19
123885 TTCAAAAAAA
*
123895 AAAATTCAAAATAATT-TT
1 AAAATTCAAAATATTTATT
123913 AAAATTCAAAATATTTATT
1 AAAATTCAAAATATTTATT
123932 AAAATTTCAAAAT
1 AAAA-TTCAAAAT
123945 TTGTATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 15 0.52
19 6 0.21
20 8 0.28
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.38
Consensus pattern (19 bp):
AAAATTCAAAATATTTATT
Found at i:123996 original size:29 final size:29
Alignment explanation
Indices: 123949--124020 Score: 87
Period size: 27 Copynumber: 2.5 Consensus size: 29
123939 CAAAATTTGT
123949 ATTT-TAAAAAATATAAAAATAT-AAAAA
1 ATTTCTAAAAAATATAAAAATATAAAAAA
*
123976 A-TTCTAAAAAATATATTAAAATTTAAAAAA
1 ATTTCTAAAAAATATA--AAAATATAAAAAA
124006 ATTTCTAAAATAATA
1 ATTTCTAAAA-AATA
124021 ATTTTAGGGG
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
26 2 0.05
27 12 0.32
29 6 0.16
30 6 0.16
31 8 0.21
32 4 0.11
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (29 bp):
ATTTCTAAAAAATATAAAAATATAAAAAA
Found at i:124016 original size:19 final size:20
Alignment explanation
Indices: 123963--124005 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
123953 TAAAAAATAT
*
123963 AAAAATATA-AAAAATTCTA
1 AAAAATATATTAAAATTCTA
123982 AAAAATATATTAAAATT-TA
1 AAAAATATATTAAAATTCTA
124001 AAAAA
1 AAAAA
124006 ATTTCTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (20 bp):
AAAAATATATTAAAATTCTA
Found at i:128759 original size:14 final size:14
Alignment explanation
Indices: 128740--128768 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
128730 TGTACCAAAA
128740 ATTTTTAGATTTTT
1 ATTTTTAGATTTTT
128754 ATTTTTAGATTTTT
1 ATTTTTAGATTTTT
128768 A
1 A
128769 ATTGTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (14 bp):
ATTTTTAGATTTTT
Found at i:137257 original size:21 final size:21
Alignment explanation
Indices: 137215--137265 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
137205 ATGACTTGTT
**
137215 TCGGTAGAAGTTACACTTGTA
1 TCGGTAGAAGTTACACAAGTA
137236 TCGGTAGAAGTGT-CACAAGTA
1 TCGGTAGAAGT-TACACAAGTA
137257 TCGGTAGAA
1 TCGGTAGAA
137266 ATTTGTTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.27
Consensus pattern (21 bp):
TCGGTAGAAGTTACACAAGTA
Found at i:143135 original size:16 final size:18
Alignment explanation
Indices: 143096--143137 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
143086 GTTTATAATA
143096 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
143113 ATTTTTATATATTATG-T
1 ATATTTATATATTATGTT
143130 A-ATTTATA
1 ATATTTATA
143138 ACACATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 6 0.27
17 7 0.32
18 9 0.41
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:145232 original size:8 final size:8
Alignment explanation
Indices: 145216--145251 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
145206 ACAACCCAAA
*
145216 TATTCAAT
1 TATTTAAT
145224 TATTTAAT
1 TATTTAAT
*
145232 TATTTAAA
1 TATTTAAT
145240 TATTTAAT
1 TATTTAAT
145248 TATT
1 TATT
145252 AACAGTAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (8 bp):
TATTTAAT
Found at i:145306 original size:40 final size:40
Alignment explanation
Indices: 145237--145314 Score: 106
Period size: 40 Copynumber: 1.9 Consensus size: 40
145227 TTAATTATTT
**
145237 AAATATTTAATTATTAACAGTAACTCAAATATTTAATTCA
1 AAATATTTAATTATTAACAACAACTCAAATATTTAATTCA
145277 AAATATTTAATTACTTAA-AACAA-TCCAAATATTTAATT
1 AAATATTTAATTA-TTAACAACAACT-CAAATATTTAATT
145315 ATTAAAAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 1 0.03
40 29 0.85
41 4 0.12
ACGTcount: A:0.49, C:0.10, G:0.01, T:0.40
Consensus pattern (40 bp):
AAATATTTAATTATTAACAACAACTCAAATATTTAATTCA
Found at i:145312 original size:26 final size:26
Alignment explanation
Indices: 145277--145340 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
145267 ATTTAATTCA
145277 AAATATTTAATTACTT-AAAACAATCC
1 AAATATTTAATTA-TTAAAAACAATCC
* *
145303 AAATATTTAATTATTAAAAATAATCT
1 AAATATTTAATTATTAAAAACAATCC
145329 AAATATTTAATT
1 AAATATTTAATT
145341 CAAAATATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 2 0.06
26 33 0.94
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.41
Consensus pattern (26 bp):
AAATATTTAATTATTAAAAACAATCC
Found at i:145317 original size:66 final size:66
Alignment explanation
Indices: 145237--145380 Score: 220
Period size: 66 Copynumber: 2.2 Consensus size: 66
145227 TTAATTATTT
* *
145237 AAATATTTAATTATTAACAGTAA-CTCAAATATTTAATTCAAAATATTTAATTACTT-AAAACAA
1 AAATATTTAATTATTAAAAATAATCT-AAATATTTAATTCAAAATATTTAATTA-TTAAAAACAA
145300 TCC
64 TCC
*
145303 AAATATTTAATTATTAAAAATAATCTAAATATTTAATTCAAAATATTTAATTATTAAAAATAATC
1 AAATATTTAATTATTAAAAATAATCTAAATATTTAATTCAAAATATTTAATTATTAAAAACAATC
*
145368 T
66 C
145369 AAATATTTAATT
1 AAATATTTAATT
145381 TAAAATATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
65 2 0.03
66 68 0.94
67 2 0.03
ACGTcount: A:0.51, C:0.08, G:0.01, T:0.41
Consensus pattern (66 bp):
AAATATTTAATTATTAAAAATAATCTAAATATTTAATTCAAAATATTTAATTATTAAAAACAATC
C
Found at i:145347 original size:40 final size:40
Alignment explanation
Indices: 145303--145415 Score: 199
Period size: 40 Copynumber: 2.8 Consensus size: 40
145293 AAAACAATCC
145303 AAATATTTAATTATTAAAAATAATCTAAATATTTAATTCA
1 AAATATTTAATTATTAAAAATAATCTAAATATTTAATTCA
*
145343 AAATATTTAATTATTAAAAATAATCTAAATATTTAATTTA
1 AAATATTTAATTATTAAAAATAATCTAAATATTTAATTCA
* *
145383 AAATATTTAATTATTAAAAACAATCCAAATATT
1 AAATATTTAATTATTAAAAATAATCTAAATATT
145416 CGGTTCAAAT
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 70 1.00
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (40 bp):
AAATATTTAATTATTAAAAATAATCTAAATATTTAATTCA
Found at i:145348 original size:14 final size:14
Alignment explanation
Indices: 145329--145394 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
145319 AAAATAATCT
145329 AAATATTTAATTCA
1 AAATATTTAATTCA
145343 AAATATTTAATT-A
1 AAATATTTAATTCA
* *
145356 TTAAA-A-ATAA-TCT
1 --AAATATTTAATTCA
*
145369 AAATATTTAATTTA
1 AAATATTTAATTCA
145383 AAATATTTAATT
1 AAATATTTAATT
145395 ATTAAAAACA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
11 3 0.07
12 2 0.05
13 7 0.17
14 26 0.63
15 3 0.07
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
AAATATTTAATTCA
Found at i:146891 original size:66 final size:68
Alignment explanation
Indices: 146818--146962 Score: 201
Period size: 66 Copynumber: 2.2 Consensus size: 68
146808 ATAAAATAAA
* *
146818 AAATAAATAATAAAACATAATTAATATTATT-TTACATTTA-TTATTTACATTCAT-ACAATAAC
1 AAATAAATAATAAAACAAAATTAATATTATTATT-CATTTATTTATTTACATTCATAAAAATAAC
146880 AAAT
65 AAAT
* * *
146884 AAATAAATAATAAAACAAAATTAATATTATTATTTATTTATTTATTTATATTCATAAAAATAATA
1 AAATAAATAATAAAACAAAATTAATATTATTATTCATTTATTTATTTACATTCATAAAAATAACA
146949 AAT
66 AAT
146952 -AA-AAATAATAA
1 AAATAAATAATAA
146963 GAAAAATGGA
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
66 44 0.62
67 17 0.24
68 10 0.14
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (68 bp):
AAATAAATAATAAAACAAAATTAATATTATTATTCATTTATTTATTTACATTCATAAAAATAACA
AAT
Found at i:146968 original size:13 final size:13
Alignment explanation
Indices: 146937--146962 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
146927 ATTTATATTC
146937 ATAAAAATAATAA
1 ATAAAAATAATAA
146950 ATAAAAATAATAA
1 ATAAAAATAATAA
146963 GAAAAATGGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
ATAAAAATAATAA
Found at i:147548 original size:40 final size:40
Alignment explanation
Indices: 147502--147875 Score: 310
Period size: 40 Copynumber: 9.3 Consensus size: 40
147492 ATTAGATTGT
* * * *
147502 TTCAATTTGCCCCATGGTCGGGGTAAGAGATCGAATAGTA
1 TTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTC
* * ** * * *
147542 TTCAATTTGCCTTC-TGGTTAGGGTAAAAGATTGGATTG-C
1 TTCAATCTGCC-CCATGGTCGGGGTAAGAGATCGGATGGTC
* *
147581 TTCAATCTACCCCATGGTCGGGGTAAGAGATCGAATGGTC
1 TTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTC
** * * *
147621 TTCAATCTGCCCTC-TGGTTAGGGTAAAAGATTGGATTG-C
1 TTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGGATGGTC
* *** * ** *
147660 TTCAATCTGCCCTATGGTTAAGGTAAAAGATTAGATTG-C
1 TTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTC
* *
147699 TTCAATCTGCCTCATGGTCGGGGTAAGAGATCGGATGGTT
1 TTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTC
* * * *
147739 TTCAATTTGCCCTC-TAGTTGGGGTAAAAGATCGGATGGTC
1 TTCAATCTGCCC-CATGGTCGGGGTAAGAGATCGGATGGTC
147779 TTCGATTTGATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTC
1 TTC-A----ATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTC
* ** *
147824 TTCAATCTGTCCTTTGGTCGGGGTAAGAGATCAGATGGTC
1 TTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTC
147864 TTCAATCTGCCC
1 TTCAATCTGCCC
147876 ATTTCATCTT
Statistics
Matches: 269, Mismatches: 52, Indels: 26
0.78 0.15 0.07
Matches are distributed among these distances:
38 1 0.00
39 92 0.34
40 137 0.51
41 4 0.01
44 2 0.01
45 33 0.12
ACGTcount: A:0.23, C:0.18, G:0.27, T:0.31
Consensus pattern (40 bp):
TTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTC
Found at i:147685 original size:79 final size:80
Alignment explanation
Indices: 147483--147875 Score: 341
Period size: 79 Copynumber: 4.9 Consensus size: 80
147473 ATAGTTTTAG
* * * * * *
147483 GGGTAAAAGATTAGATTGTTTCAATTTGCCCCATGGTCGGGGTAAGAGATCGAATAGTATTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
* * *
147548 TTGCCTTC-TGGTTA
66 CTGCCCTCATGGTCA
* *
147562 GGGTAAAAGATTGGATTGCTTCAATCTACCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
*
147627 CTGCCCTC-TGGTTA
66 CTGCCCTCATGGTCA
*** * * *
147641 GGGTAAAAGATTGGATTGCTTCAATCTGCCCTATGGTTAAGGTAAAAGAT-TAGATTG-CTTCAA
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATCGA-ATGGTCTTCAA
*
147704 TCTG-CCTCATGGTCG
65 TCTGCCCTCATGGTCA
* * * * * * * * * *
147719 GGGTAAGAGATCGGATGGTTTTCAATTTGCCCTCTAGTTGGGGTAAAAGATCGGATGGTCTTCGA
1 GGGTAAAAGATTGGATTG-CTTCAATCTGCCCTATGGTCGGGGTAAGAGATCGAATGGTCTTC-A
*
147784 TTTGATCTGCCC-CATGGTCG
64 ----ATCTGCCCTCATGGTCA
* * * * *
147804 GGGTAAGAGATCGGATGGTCTTCAATCTGTCCTTTGGTCGGGGTAAGAGATC-AGATGGTCTTCA
1 GGGTAAAAGATTGGATTG-CTTCAATCTGCCCTATGGTCGGGGTAAGAGATCGA-ATGGTCTTCA
147868 ATCTGCCC
64 ATCTGCCC
147876 ATTTCATCTT
Statistics
Matches: 264, Mismatches: 38, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
77 4 0.02
78 30 0.11
79 147 0.56
80 12 0.05
81 1 0.00
84 1 0.00
85 67 0.25
86 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (80 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCTATGGTCGGGGTAAGAGATCGAATGGTCTTCAAT
CTGCCCTCATGGTCA
Found at i:147685 original size:118 final size:119
Alignment explanation
Indices: 147522--147875 Score: 388
Period size: 118 Copynumber: 2.9 Consensus size: 119
147512 CCCATGGTCG
* * * * * * *
147522 GGGTAAGAGATCGAATAGTATTCAATTTGCCTTCTGGTTAGGGTAAAAGATTGGATTGCTTCAAT
1 GGGTAAAAGATCGGATGGTCTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTGCTTCAAT
* *
147587 CTACCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAATCTGCCCTCTGGTTA
66 CTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAATCTGCCCTCTAGTTA
* * * *
147641 GGGTAAAAGATTGGATTG-CTTCAATCTGCCCTATGGTTAAGGTAAAAGATTAGATTGCTTCAAT
1 GGGTAAAAGATCGGATGGTCTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTGCTTCAAT
* * * * *
147705 CTGCCTCATGGTCGGGGTAAGAGATCGGATGGTTTTCAATTTGCCCTCTAGTTG
66 CTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAATCTGCCCTCTAGTTA
* ** * * *
147759 GGGTAAAAGATCGGATGGTCTTCGATTTGATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTC
1 GGGTAAAAGATCGGATGGTCTTC-A----ATCTGCCCTATGGTTAGGGTAAAAGATTGGATTG-C
* **
147824 TTCAATCTGTCCTTTGGTCGGGGTAAGAGATC-AGATGGTCTTCAATCTGCCC
60 TTCAATCTGCCCCATGGTCGGGGTAAGAGATCGA-ATGGTCTTCAATCTGCCC
147876 ATTTCATCTT
Statistics
Matches: 193, Mismatches: 34, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
118 103 0.53
119 18 0.09
120 1 0.01
124 26 0.13
125 45 0.23
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (119 bp):
GGGTAAAAGATCGGATGGTCTTCAATCTGCCCTATGGTTAGGGTAAAAGATTGGATTGCTTCAAT
CTGCCCCATGGTCGGGGTAAGAGATCGAATGGTCTTCAATCTGCCCTCTAGTTA
Found at i:147810 original size:85 final size:85
Alignment explanation
Indices: 147703--147866 Score: 247
Period size: 85 Copynumber: 1.9 Consensus size: 85
147693 GATTGCTTCA
* * * *
147703 ATCTGCCTCATGGTCGGGGTAAGAGATCGGATGGTTTTCAATTTGCCCTCTAGTTGGGGTAAAAG
1 ATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAGTCGGGGTAAAAG
*
147768 ATCGGATGGTCTTCGATTTG
66 ATCAGATGGTCTTCGATTTG
* * * *
147788 ATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAATCTGTCCTTTGGTCGGGGTAAGAG
1 ATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAGTCGGGGTAAAAG
147853 ATCAGATGGTCTTC
66 ATCAGATGGTCTTC
147867 AATCTGCCCA
Statistics
Matches: 70, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (85 bp):
ATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAATCTGCCCTCTAGTCGGGGTAAAAG
ATCAGATGGTCTTCGATTTG
Found at i:148006 original size:50 final size:50
Alignment explanation
Indices: 147925--148020 Score: 122
Period size: 50 Copynumber: 1.9 Consensus size: 50
147915 CAATTTGCCC
* *
147925 CTCTACAGCTTTAGGTGAATGAAATTCGTCATTACGGATTCAATCTACCG
1 CTCTACAACTTTAGGTGAATGAAATTCGTCATCACGGATTCAATCTACCG
* * * *
147975 CTCTACAACTTTAGGT-ATATGAGATTTGTCATCATGGTTTCAATCT
1 CTCTACAACTTTAGGTGA-ATGAAATTCGTCATCACGGATTCAATCT
148021 GTTCCTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 1 0.03
50 38 0.97
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (50 bp):
CTCTACAACTTTAGGTGAATGAAATTCGTCATCACGGATTCAATCTACCG
Found at i:155224 original size:63 final size:64
Alignment explanation
Indices: 155156--155326 Score: 244
Period size: 63 Copynumber: 2.7 Consensus size: 64
155146 TTTGTTATTT
*
155156 ATTTATTTATCTTAT-TT-ATTTAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
1 ATTTATTTAT-TTATATTCATTAAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
*
155219 ATTTATTTATTTATATTCA-TACAAT-AATAAATAAATAATAAAACAAAATTAATATTATTTTAT
1 ATTTATTTATTTATATTCATTA-AATAAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
*
155282 ATTTATTTATTTATATTCA-TAAAAATAATAAATAAATAAATAAAA
1 ATTTATTTATTTATATTCATTAAATA-AATAAATAAAT-AATAAAA
155327 ATAATAAGAA
Statistics
Matches: 99, Mismatches: 3, Indels: 10
0.88 0.03 0.09
Matches are distributed among these distances:
62 6 0.06
63 71 0.72
64 15 0.15
65 7 0.07
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (64 bp):
ATTTATTTATTTATATTCATTAAATAAATAAATAAATAATAAAACAAAATTAATATTATTTTAC
Found at i:155346 original size:21 final size:21
Alignment explanation
Indices: 155300--155341 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
155290 ATTTATATTC
*
155300 ATAAAAATAATAAATAAATAA
1 ATAAAAATAATAAAAAAATAA
155321 ATAAAAATAATAAGAAAAATA
1 ATAAAAATAATAA-AAAAATA
155342 GTAAACTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (21 bp):
ATAAAAATAATAAAAAAATAA
Found at i:159675 original size:145 final size:146
Alignment explanation
Indices: 159448--159926 Score: 732
Period size: 149 Copynumber: 3.3 Consensus size: 146
159438 TGATTAAAAC
* * *
159448 AAAATCAGTACTTTACTTCAAAATCAAAACTTTTATTTCGAAATAGTTTAAAAAAATCAAACTTT
1 AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTTAAAAAAATAAAACTTT
*
159513 GTTTAAAAATTTAAATTTTTTCTTTAAAATCACT-AAAAACATATTTTTATTTTTTAAAAATCTA
66 GTTTAAAAATTTAAATTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTTAAAAATCTA
*
159577 AACTTTTTTTTTAATG
131 AACTTTTTTTTTAAAG
* *
159593 AAAATCACTACTTTACTTAAAAATCCAAACTTTTATTTCGAAATAGTTTTAAAAAATAAAACTTT
1 AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTTAAAAAAATAAAACTTT
* * * **
159658 GTTTAAAAATTTTAATTTTTTCTTTAAAATGACTAAAAAACAGATTTTTATTTTTAAAAAAAAAT
66 GTTTAAAAATTTAAATTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTT-TAAAAATCT
* *
159723 AAACTTTCTTTTTAAAAAA
130 AAACTTT-TTTTT-TAAAG
*
159742 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAG-TTAAAAAAATAAAAACTT
1 AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTTAAAAAAAT-AAAACTT
*
159806 TATTTAAAAATTTAAATTTTTTCTTTAAAATGACTAAAAAACATATTTTTA-TTTTTAAAAATCT
65 TGTTTAAAAATTTAAATTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTTAAAAATCT
159870 AAAC-TTTTTTTTAAAG
130 AAACTTTTTTTTTAAAG
* *
159886 AAAATCACTATTTTTCTTAAAAATCAAAACTTTTATTTCGA
1 AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGA
159927 TTTTTAAAAA
Statistics
Matches: 303, Mismatches: 26, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
144 43 0.14
145 97 0.32
146 21 0.07
147 23 0.08
148 18 0.06
149 101 0.33
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (146 bp):
AAAATCACTACTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTTAAAAAAATAAAACTTT
GTTTAAAAATTTAAATTTTTTCTTTAAAATGACTAAAAAACATATTTTTATTTTTTAAAAATCTA
AACTTTTTTTTTAAAG
Found at i:160390 original size:9 final size:9
Alignment explanation
Indices: 160378--160429 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
160368 AATAATATTT
160378 AATAATAAC
1 AATAATAAC
160387 AATAATAAC
1 AATAATAAC
* *
160396 AACAACAAC
1 AATAATAAC
* *
160405 AACAACAAC
1 AATAATAAC
*
160414 AATAATAAT
1 AATAATAAC
160423 AATAATA
1 AATAATA
160430 TAATTGTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 38 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.17
Consensus pattern (9 bp):
AATAATAAC
Found at i:163464 original size:20 final size:21
Alignment explanation
Indices: 163441--163484 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
163431 ATTAAATTTT
163441 AAATAT-AAATA-ATAAAACAA
1 AAATATAAAATATATAAAA-AA
*
163461 AAATCTAAAATATATAAAAAA
1 AAATATAAAATATATAAAAAA
163482 AAA
1 AAA
163485 AACTTGTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (21 bp):
AAATATAAAATATATAAAAAA
Found at i:166688 original size:31 final size:31
Alignment explanation
Indices: 166653--166711 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
166643 AGTCCCTTAT
* *
166653 TTTATTTGTTTTTATTCA-TTTATTTTATTTA
1 TTTATTTATTTTTA-ACATTTTATTTTATTTA
166684 TTTATTTATTTTTAACATTTTATTTTAT
1 TTTATTTATTTTTAACATTTTATTTTAT
166712 GATATTTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 2 0.08
31 23 0.92
ACGTcount: A:0.22, C:0.03, G:0.02, T:0.73
Consensus pattern (31 bp):
TTTATTTATTTTTAACATTTTATTTTATTTA
Found at i:167554 original size:20 final size:20
Alignment explanation
Indices: 167514--167555 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
167504 TTACCTGTAA
* *
167514 AACTTCACTTCTAGCGGTAC
1 AACTTCACTTCTACCGATAC
*
167534 AACTTCAGTTCTACCGATAC
1 AACTTCACTTCTACCGATAC
167554 AA
1 AA
167556 GTATGCTTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (20 bp):
AACTTCACTTCTACCGATAC
Found at i:173800 original size:26 final size:26
Alignment explanation
Indices: 173762--173900 Score: 108
Period size: 26 Copynumber: 5.5 Consensus size: 26
173752 CCAGCTTGCG
* *
173762 CACGTTTATGCTCGTCAGCTTATTTA
1 CACGTTTACGCTCGTCAGCTTATTCA
* * *
173788 CACATTTACGCTCGCCAGC-T-TGCGA
1 CACGTTTACGCTCGTCAGCTTATTC-A
173813 -ACGTTTACGCTCGTCAGCTTATTCA
1 CACGTTTACGCTCGTCAGCTTATTCA
** * * *
173838 CGTGTTTACACTCGCCAGC-T-TGCA
1 CACGTTTACGCTCGTCAGCTTATTCA
* *
173862 CATGTTTACGCTCGTCAGCTTATTTA
1 CACGTTTACGCTCGTCAGCTTATTCA
* *
173888 CATGTTTATGCTC
1 CACGTTTACGCTC
173901 ACCAGGTTGT
Statistics
Matches: 88, Mismatches: 19, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
24 36 0.41
25 6 0.07
26 46 0.52
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (26 bp):
CACGTTTACGCTCGTCAGCTTATTCA
Found at i:173824 original size:24 final size:24
Alignment explanation
Indices: 173742--173882 Score: 77
Period size: 24 Copynumber: 5.7 Consensus size: 24
173732 TAATTATGCA
* * *
173742 TTTATGCTTGCCAGCTTGCGCACG
1 TTTACGCTCGCCAGCTTGCGAACG
* * *** *
173766 TTTATGCTCGTCAGCTTATTTACACA
1 TTTACGCTCGCCAGCTT-GCGA-ACG
173792 TTTACGCTCGCCAGCTTGCGAACG
1 TTTACGCTCGCCAGCTTGCGAACG
* ****
173816 TTTACGCTCGTCAGCTTATTCACGTG
1 TTTACGCTCGCCAGCTTGCGAAC--G
* *
173842 TTTACACTCGCCAGCTTGC-ACATG
1 TTTACGCTCGCCAGCTTGCGA-ACG
*
173866 TTTACGCTCGTCAGCTT
1 TTTACGCTCGCCAGCTT
173883 ATTTACATGT
Statistics
Matches: 86, Mismatches: 26, Indels: 10
0.70 0.21 0.08
Matches are distributed among these distances:
24 51 0.59
25 1 0.01
26 34 0.40
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (24 bp):
TTTACGCTCGCCAGCTTGCGAACG
Found at i:173894 original size:50 final size:50
Alignment explanation
Indices: 173751--173895 Score: 202
Period size: 50 Copynumber: 2.9 Consensus size: 50
173741 ATTTATGCTT
* * ** *
173751 GCCAGCTTGCGCACGTTTATGCTCGTCAGCTTATTTACACATTTACGCTC
1 GCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTACATGTTTACACTC
* *
173801 GCCAGCTTGCGA-ACGTTTACGCTCGTCAGCTTATTCACGTGTTTACACTC
1 GCCAGCTTGC-ACACGTTTACGCTCGTCAGCTTATTTACATGTTTACACTC
*
173851 GCCAGCTTGCACATGTTTACGCTCGTCAGCTTATTTACATGTTTA
1 GCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTACATGTTTA
173896 TGCTCACCAG
Statistics
Matches: 83, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
49 1 0.01
50 82 0.99
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (50 bp):
GCCAGCTTGCACACGTTTACGCTCGTCAGCTTATTTACATGTTTACACTC
Found at i:192403 original size:20 final size:20
Alignment explanation
Indices: 192378--192415 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
192368 TTTAAGTCAT
192378 TTAATTTCAAAAAATTAAAA
1 TTAATTTCAAAAAATTAAAA
*
192398 TTAATTTCAAAAAGTTAA
1 TTAATTTCAAAAAATTAA
192416 GAAAAAATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
TTAATTTCAAAAAATTAAAA
Found at i:214082 original size:233 final size:233
Alignment explanation
Indices: 213668--214134 Score: 718
Period size: 233 Copynumber: 2.0 Consensus size: 233
213658 TTGATGCGAC
** * * *
213668 ACAATGAGGGATCAAGCTAAGCACATGCTCAAAGCGGTTGTTACATTTTGACTAAAACAATCCCT
1 ACAATGAGGGATCAAGCTAAGCACATGCTCAAAGCAATTATTACATTATAACTAAAACAATCCCT
*
213733 TGAAATACTTACAAGCCACCTCACAAATTCCTCAAGTATCACTGATCCATCTCCCCCTATCATCA
66 TGAAATACTCACAAGCCACCTCACAAATTCCTCAAGTATCACTGATCCATCTCCCCCTATCATCA
*
213798 CGTAAGCCCTCAATGTGATTCTTCCTCACCCGATGTGTAGCACGCACGTGAAAGAATCTCATATT
131 CGTAAGCCCTCAATGTGATTCTTCCTCACCCGATGTGTAGCACGCACGTGAAAGAATCTCACATT
*
213863 TCTGCCACCCTCTTTCATCCATCTAATGTAGGATCTCT
196 TCTGCCACCCTCTTTCATCCATCTAATGCAGGATCTCT
* * * *
213901 ACAATGTGGGATCAAGTTAAGCACATTCTCAAAGCAATTATTACATTATAACTTAAACAATCCCT
1 ACAATGAGGGATCAAGCTAAGCACATGCTCAAAGCAATTATTACATTATAACTAAAACAATCCCT
* * * * *
213966 TGAAATACTCACAAGCTACCTCACAAATTCCTCGAGTATTACTGATCCATCTCCTCCTATCATCT
66 TGAAATACTCACAAGCCACCTCACAAATTCCTCAAGTATCACTGATCCATCTCCCCCTATCATCA
* * * * **
214031 CGTAAGCCCTCAATGTGATTCTTCCTCGCCTGATGTGTGGCGCGCACGTGAAAGAATCTGGCATT
131 CGTAAGCCCTCAATGTGATTCTTCCTCACCCGATGTGTAGCACGCACGTGAAAGAATCTCACATT
*
214096 TCTGCCACCCTCTTTCATTCATCTAATGCAGGATCTCT
196 TCTGCCACCCTCTTTCATCCATCTAATGCAGGATCTCT
214134 A
1 A
214135 AGTCGAATAA
Statistics
Matches: 210, Mismatches: 24, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
233 210 1.00
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (233 bp):
ACAATGAGGGATCAAGCTAAGCACATGCTCAAAGCAATTATTACATTATAACTAAAACAATCCCT
TGAAATACTCACAAGCCACCTCACAAATTCCTCAAGTATCACTGATCCATCTCCCCCTATCATCA
CGTAAGCCCTCAATGTGATTCTTCCTCACCCGATGTGTAGCACGCACGTGAAAGAATCTCACATT
TCTGCCACCCTCTTTCATCCATCTAATGCAGGATCTCT
Found at i:217269 original size:51 final size:51
Alignment explanation
Indices: 217193--217337 Score: 254
Period size: 51 Copynumber: 2.8 Consensus size: 51
217183 ATACCAACCG
* *
217193 AACATCAACGGGTATATGCTCACACTCTACAAGCAATTATTTTAACATTTT
1 AACATAAATGGGTATATGCTCACACTCTACAAGCAATTATTTTAACATTTT
* *
217244 AACATAAATGGGTTTATGCTCACACTCTACAAGCAGTTATTTTAACATTTT
1 AACATAAATGGGTATATGCTCACACTCTACAAGCAATTATTTTAACATTTT
217295 AACATAAATGGGTATATGCTCACACTCTACAAGCAATTATTTT
1 AACATAAATGGGTATATGCTCACACTCTACAAGCAATTATTTT
217338 TGGGAAATAC
Statistics
Matches: 88, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 88 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.34
Consensus pattern (51 bp):
AACATAAATGGGTATATGCTCACACTCTACAAGCAATTATTTTAACATTTT
Found at i:217558 original size:16 final size:16
Alignment explanation
Indices: 217537--217570 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
217527 TAGCTAGATT
217537 AAGCTAATACGAACTC
1 AAGCTAATACGAACTC
* *
217553 AAGCTAATGCGCACTC
1 AAGCTAATACGAACTC
217569 AA
1 AA
217571 AAACAAAGAT
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:0.41, C:0.26, G:0.15, T:0.18
Consensus pattern (16 bp):
AAGCTAATACGAACTC
Found at i:240735 original size:15 final size:16
Alignment explanation
Indices: 240711--240745 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
240701 GAGATAAGTG
240711 TTTTTAAGACTT-TAA
1 TTTTTAAGACTTGTAA
*
240726 TTTTTTAGACTTGTAA
1 TTTTTAAGACTTGTAA
240742 TTTT
1 TTTT
240746 GGATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.60
Consensus pattern (16 bp):
TTTTTAAGACTTGTAA
Found at i:241051 original size:13 final size:14
Alignment explanation
Indices: 241017--241051 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
241007 TTTTTGCATA
241017 TAGTTTTTAATTTT
1 TAGTTTTTAATTTT
*
241031 TAGTTTTT-CTTTT
1 TAGTTTTTAATTTT
241044 TAGTTTTT
1 TAGTTTTT
241052 TTTGGGTGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (14 bp):
TAGTTTTTAATTTT
Found at i:271487 original size:22 final size:21
Alignment explanation
Indices: 271456--271542 Score: 92
Period size: 22 Copynumber: 4.2 Consensus size: 21
271446 GGTACTATTT
271456 TTTTTACTGTTTTGGTTGCTA
1 TTTTTACTGTTTTGGTTGCTA
* *
271477 TTTATTACTGTTTTAGTGTTGTTG
1 TTT-TTACTGTTTT-G-GTTGCTA
*
271501 TTTTT-CTGTTTT-GTT--TT
1 TTTTTACTGTTTTGGTTGCTA
271518 TTTTTACTGTTTTGGTTGCTA
1 TTTTTACTGTTTTGGTTGCTA
271539 TTTT
1 TTTT
271543 GGTTTTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
17 6 0.11
18 7 0.13
19 6 0.11
21 8 0.15
22 17 0.31
23 3 0.05
24 8 0.15
ACGTcount: A:0.08, C:0.07, G:0.17, T:0.68
Consensus pattern (21 bp):
TTTTTACTGTTTTGGTTGCTA
Found at i:271549 original size:30 final size:29
Alignment explanation
Indices: 271453--271562 Score: 87
Period size: 30 Copynumber: 3.6 Consensus size: 29
271443 TTTGGTACTA
271453 TTTTTTTTACTGTTTTGGTTGCTATTTAT-
1 TTTTTTTTACTGTTTTGGTTGCTATTT-TG
* * * * * *
271482 TACTGTTTTAGTGTTGTTGTTTTTCTGTTTTG
1 T-TTTTTTTACTGTT-TTG-GTTGCTATTTTG
271514 TTTTTTTTTACTGTTTTGGTTGCTATTTTGG
1 -TTTTTTTTACTGTTTTGGTTGCTATTTT-G
*
271545 TTTTTTTTAACTATTTTG
1 TTTTTTTT-ACTGTTTTG
271563 ATAATGTTAT
Statistics
Matches: 61, Mismatches: 13, Indels: 12
0.71 0.15 0.14
Matches are distributed among these distances:
29 1 0.02
30 26 0.43
31 16 0.26
32 17 0.28
33 1 0.02
ACGTcount: A:0.09, C:0.06, G:0.16, T:0.68
Consensus pattern (29 bp):
TTTTTTTTACTGTTTTGGTTGCTATTTTG
Found at i:271551 original size:31 final size:30
Alignment explanation
Indices: 271453--271562 Score: 96
Period size: 31 Copynumber: 3.6 Consensus size: 30
271443 TTTGGTACTA
271453 TTTTTTTTACTGTTTTGGTTGCTATTTAT-T
1 TTTTTTTTACTGTTTTGGTTGCTATTT-TGT
** * * * * *
271483 ACTGTTTTAGTGTTGTTGTTTTTCTGTTTTGT
1 TTTTTTTTACTGTT-TTG-GTTGCTATTTTGT
271515 TTTTTTTTACTGTTTTGGTTGCTATTTTGGT
1 TTTTTTTTACTGTTTTGGTTGCTATTTT-GT
* *
271546 TTTTTTTAACTATTTTG
1 TTTTTTTTACTGTTTTG
271563 ATAATGTTAT
Statistics
Matches: 60, Mismatches: 16, Indels: 7
0.72 0.19 0.08
Matches are distributed among these distances:
30 18 0.30
31 24 0.40
32 18 0.30
ACGTcount: A:0.09, C:0.06, G:0.16, T:0.68
Consensus pattern (30 bp):
TTTTTTTTACTGTTTTGGTTGCTATTTTGT
Found at i:271596 original size:24 final size:23
Alignment explanation
Indices: 271569--271639 Score: 79
Period size: 24 Copynumber: 3.0 Consensus size: 23
271559 TTTGATAATG
*
271569 TTATTTTTGTAGTTGTTTTTGTTA
1 TTATTTTTGT-GTTATTTTTGTTA
271593 TTATTTTTGCTGTTATTTTTGTTA
1 TTATTTTTG-TGTTATTTTTGTTA
* * *
271617 CTGTTTTTGTTTCTATTTTTGTT
1 TTATTTTTGTGT-TATTTTTGTT
271640 GTTTTGTTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.05
24 38 0.93
25 1 0.02
ACGTcount: A:0.10, C:0.04, G:0.14, T:0.72
Consensus pattern (23 bp):
TTATTTTTGTGTTATTTTTGTTA
Found at i:271599 original size:12 final size:12
Alignment explanation
Indices: 271569--271653 Score: 68
Period size: 12 Copynumber: 7.2 Consensus size: 12
271559 TTTGATAATG
271569 TTATTTTTG-TA
1 TTATTTTTGTTA
*
271580 GTTGTTTTTGTTA
1 -TTATTTTTGTTA
* *
271593 TTATTTTTGCTG
1 TTATTTTTGTTA
271605 TTATTTTTGTTA
1 TTATTTTTGTTA
* *
271617 CTGTTTTTGTT-
1 TTATTTTTGTTA
*
271628 TCTATTTTTGTTG
1 T-TATTTTTGTTA
*
271641 TT-TTGTTGTTA
1 TTATTTTTGTTA
271652 TT
1 TT
271654 TTGGTTGTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
11 9 0.16
12 46 0.79
13 3 0.05
ACGTcount: A:0.09, C:0.04, G:0.15, T:0.72
Consensus pattern (12 bp):
TTATTTTTGTTA
Found at i:271607 original size:36 final size:36
Alignment explanation
Indices: 271567--271651 Score: 104
Period size: 36 Copynumber: 2.4 Consensus size: 36
271557 ATTTTGATAA
*
271567 TGTTATTTTTG-TAGTTGTTTTTGTTAT-TATTTTTGC
1 TGTTATTTTTGTTA-CTGTTTTTGTT-TCTATTTTTGC
*
271603 TGTTATTTTTGTTACTGTTTTTGTTTCTATTTTTGT
1 TGTTATTTTTGTTACTGTTTTTGTTTCTATTTTTGC
*
271639 TGTT-TTGTTGTTA
1 TGTTATTTTTGTTA
271652 TTTTGGTTGT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
35 9 0.20
36 33 0.75
37 2 0.05
ACGTcount: A:0.09, C:0.04, G:0.16, T:0.71
Consensus pattern (36 bp):
TGTTATTTTTGTTACTGTTTTTGTTTCTATTTTTGC
Found at i:271646 original size:20 final size:20
Alignment explanation
Indices: 271621--271675 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
271611 TTGTTACTGT
*
271621 TTTTGTT-TCTATTTTTGTTG
1 TTTTGTTGT-TATTTTGGTTG
271641 TTTTGTTGTTATTTTGGTTG
1 TTTTGTTGTTATTTTGGTTG
* *
271661 TTTGGATGTTATTTT
1 TTTTGTTGTTATTTT
271676 TATGCGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.07, C:0.02, G:0.20, T:0.71
Consensus pattern (20 bp):
TTTTGTTGTTATTTTGGTTG
Found at i:290138 original size:18 final size:18
Alignment explanation
Indices: 290115--290151 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
290105 CTTTGTTGAG
290115 GGGGAAGATGAGCATACC
1 GGGGAAGATGAGCATACC
290133 GGGGAAGATGAGCATACC
1 GGGGAAGATGAGCATACC
290151 G
1 G
290152 CCTTCCTAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.41, T:0.11
Consensus pattern (18 bp):
GGGGAAGATGAGCATACC
Found at i:292771 original size:4 final size:4
Alignment explanation
Indices: 292762--292797 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
292752 TATTCTATAT
292762 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC -TTTC TTT
292798 TATGCGACTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:303473 original size:26 final size:26
Alignment explanation
Indices: 303444--303538 Score: 102
Period size: 26 Copynumber: 3.7 Consensus size: 26
303434 CAGTTAGAAA
* *
303444 ATTGCTTCTACGAGCCAGTACAGTAT
1 ATTGCTTCTACAAGCCAATACAGTAT
303470 ATTG-TTCCTACAAGCCAATACAGTAT
1 ATTGCTT-CTACAAGCCAATACAGTAT
* *** *
303496 ATTGCTCCTGTGAGCCAACACAGTAT
1 ATTGCTTCTACAAGCCAATACAGTAT
*
303522 ATTGCTTTTACAAGCCA
1 ATTGCTTCTACAAGCCA
303539 GTATTGTTCT
Statistics
Matches: 55, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
25 2 0.04
26 52 0.95
27 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (26 bp):
ATTGCTTCTACAAGCCAATACAGTAT
Found at i:303551 original size:19 final size:19
Alignment explanation
Indices: 303529--303565 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
303519 TATATTGCTT
303529 TTACAAGCCAGTATTGTTC
1 TTACAAGCCAGTATTGTTC
*
303548 TTACGAGCCAGTATTGTT
1 TTACAAGCCAGTATTGTT
303566 GATTCCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (19 bp):
TTACAAGCCAGTATTGTTC
Found at i:304945 original size:19 final size:19
Alignment explanation
Indices: 304883--304948 Score: 87
Period size: 19 Copynumber: 3.5 Consensus size: 19
304873 CCAATACTGT
304883 ATATTGCTCTTACGAGCCA
1 ATATTGCTCTTACGAGCCA
** *
304902 ATATCACTCTTACGAGCGA
1 ATATTGCTCTTACGAGCCA
*
304921 ATATTGCTCTTACGAGCTA
1 ATATTGCTCTTACGAGCCA
*
304940 ACATTGCTC
1 ATATTGCTC
304949 ATGTGAGCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (19 bp):
ATATTGCTCTTACGAGCCA
Found at i:312082 original size:11 final size:11
Alignment explanation
Indices: 312058--312093 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
312048 TTAATTATTC
*
312058 AATT-TTAAAA
1 AATTATTAAAT
312068 AATTATTAAAT
1 AATTATTAAAT
312079 AATTATTAAAT
1 AATTATTAAAT
312090 AATT
1 AATT
312094 TAAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 4 0.17
11 20 0.83
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AATTATTAAAT
Found at i:314236 original size:20 final size:20
Alignment explanation
Indices: 314142--314227 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
314132 TTGGTTCTAT
*
314142 TTTTTACTGTTTTGGT-TGT-
1 TTTTTACTGTTTTGATAT-TA
*
314161 TTTTTA-T-TTTTTATA-T-
1 TTTTTACTGTTTTGATATTA
** *
314177 TTTTTACTGTTTTGATGCTC
1 TTTTTACTGTTTTGATATTA
314197 TTTTTACTGTTTTGATATTA
1 TTTTTACTGTTTTGATATTA
314217 TTTTTACTGTT
1 TTTTTACTGTT
314228 ATTTTATTAC
Statistics
Matches: 55, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
16 7 0.13
17 6 0.11
18 7 0.13
19 7 0.13
20 28 0.51
ACGTcount: A:0.13, C:0.07, G:0.12, T:0.69
Consensus pattern (20 bp):
TTTTTACTGTTTTGATATTA
Found at i:314496 original size:19 final size:19
Alignment explanation
Indices: 314444--314500 Score: 57
Period size: 19 Copynumber: 3.0 Consensus size: 19
314434 TTTTAATCCA
*
314444 TTTTAAATTTATTT-AT-T
1 TTTTAAATGTATTTAATAT
314461 TTTT-AATGTTTATTTTAATAT
1 TTTTAAATG--TA-TTTAATAT
314482 TTTTAAATGTATTTAATAT
1 TTTTAAATGTATTTAATAT
314501 ATTATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 3 0.09
17 4 0.12
18 2 0.06
19 11 0.33
20 4 0.12
21 5 0.15
22 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.65
Consensus pattern (19 bp):
TTTTAAATGTATTTAATAT
Found at i:320586 original size:5 final size:6
Alignment explanation
Indices: 320571--320596 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
320561 GTTAGAGCAG
320571 AAAAAT AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AA
320597 GATATGATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAAAT
Found at i:320762 original size:27 final size:25
Alignment explanation
Indices: 320709--320765 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
320699 TTTTTAATTT
*
320709 TTTTATAATTTTATAAAACTATAAA
1 TTTTAGAATTTTATAAAACTATAAA
* *
320734 TTTTAGAATTTTTATAAATACTTTGAA
1 TTTTAGAA-TTTTATAAA-ACTATAAA
320761 TTTTA
1 TTTTA
320766 AAAATTATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 7 0.26
26 9 0.33
27 11 0.41
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (25 bp):
TTTTAGAATTTTATAAAACTATAAA
Found at i:320763 original size:19 final size:20
Alignment explanation
Indices: 320739--320784 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
320729 ATAAATTTTA
*
320739 GAATTTTTATAAA-TACTTT
1 GAATTTTTAAAAATTACTTT
*
320758 GAA-TTTTAAAAATTATTTT
1 GAATTTTTAAAAATTACTTT
320777 GAATTTTT
1 GAATTTTT
320785 TTTGTAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 8 0.35
19 11 0.48
20 4 0.17
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (20 bp):
GAATTTTTAAAAATTACTTT
Found at i:322853 original size:18 final size:18
Alignment explanation
Indices: 322816--322855 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
322806 ACTACCGGAT
*
322816 AGATTTGCACTTTCATTA
1 AGATTTGCACTTTCAGTA
322834 AGATTTGCAC-TTCTAGTA
1 AGATTTGCACTTTC-AGTA
322852 AGAT
1 AGAT
322856 GATTATCTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (18 bp):
AGATTTGCACTTTCAGTA
Found at i:323932 original size:17 final size:16
Alignment explanation
Indices: 323894--323933 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
323884 CAATCTTGGG
323894 AATT-TTTATAAAAAT
1 AATTATTTATAAAAAT
*
323909 AATTATTTATCAAAAT
1 AATTATTTATAAAAAT
323925 AATATATTT
1 AAT-TATTT
323934 TCCGTATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 13 0.59
17 5 0.23
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTATTTATAAAAAT
Found at i:324470 original size:30 final size:30
Alignment explanation
Indices: 324436--324492 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
324426 TTGTTTTGTT
324436 TTAATTTAAATTTTAAAGAAATGTTGTTTG
1 TTAATTTAAATTTTAAAGAAATGTTGTTTG
* **
324466 TTAATTTAATTTTTAATTAAATGTTGT
1 TTAATTTAAATTTTAAAGAAATGTTGT
324493 ATTATGTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (30 bp):
TTAATTTAAATTTTAAAGAAATGTTGTTTG
Found at i:327199 original size:27 final size:27
Alignment explanation
Indices: 327150--327204 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
327140 GATACCACAG
* * *
327150 CAGTACTCTACTCCTTTCAACCCGTTA
1 CAGTACTCCACTCCTATCAACCCATTA
327177 CAGTACTCCACTCCTCATC-ACCCATTA
1 CAGTACTCCACTCCT-ATCAACCCATTA
327204 C
1 C
327205 TGCCTCAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 22 0.92
28 2 0.08
ACGTcount: A:0.24, C:0.42, G:0.05, T:0.29
Consensus pattern (27 bp):
CAGTACTCCACTCCTATCAACCCATTA
Found at i:327499 original size:26 final size:26
Alignment explanation
Indices: 327447--327499 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
327437 ATGAATTTGG
* * *
327447 AATTAATTGTGTTTATGTTTGTATTT
1 AATTAATTATATTTATGTTTATATTT
*
327473 AATTAATTATATTTATGTTTATGTTT
1 AATTAATTATATTTATGTTTATATTT
327499 A
1 A
327500 GGGTTTAAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.60
Consensus pattern (26 bp):
AATTAATTATATTTATGTTTATATTT
Found at i:327534 original size:21 final size:21
Alignment explanation
Indices: 327510--327549 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
327500 GGGTTTAAGA
*
327510 TTTAAAGTTTTTGGTGTATGG
1 TTTAAAGTTTTTGATGTATGG
**
327531 TTTAGGGTTTTTGATGTAT
1 TTTAAAGTTTTTGATGTAT
327550 AGTTAGGATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.55
Consensus pattern (21 bp):
TTTAAAGTTTTTGATGTATGG
Found at i:327589 original size:21 final size:21
Alignment explanation
Indices: 327564--327616 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
327554 AGGATTGGGG
*
327564 TTTGGGTTTAAGGTTTTAGGT
1 TTTGGGTTTAAGGTTTAAGGT
* *
327585 TTTGGATTTATGGTTTAAGGT
1 TTTGGGTTTAAGGTTTAAGGT
*
327606 TTAAGGGTTTA
1 TT-TGGGTTTA
327617 GGGTACTTAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.19, C:0.00, G:0.30, T:0.51
Consensus pattern (21 bp):
TTTGGGTTTAAGGTTTAAGGT
Found at i:327720 original size:29 final size:28
Alignment explanation
Indices: 327640--327722 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 28
327630 ATGGAGTTAG
*
327640 AACCTTAAAACCCTAAAGCCCTAAACCTTA
1 AACCTTAAAA--CTAAAACCCTAAACCTTA
* **
327670 ATCTCTATATCACTAAAA-CCTAAACCTTA
1 AAC-CT-TAAAACTAAAACCCTAAACCTTA
327699 AACCTTAAAACTTAAAACCCTAAA
1 AACCTTAAAAC-TAAAACCCTAAA
327723 AACCTAAATC
Statistics
Matches: 42, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
27 4 0.10
28 7 0.17
29 19 0.45
30 7 0.17
31 2 0.05
32 3 0.07
ACGTcount: A:0.46, C:0.29, G:0.01, T:0.24
Consensus pattern (28 bp):
AACCTTAAAACTAAAACCCTAAACCTTA
Found at i:327722 original size:8 final size:7
Alignment explanation
Indices: 327682--327738 Score: 53
Period size: 7 Copynumber: 7.9 Consensus size: 7
327672 CTCTATATCA
327682 CTAAAAC
1 CTAAAAC
327689 CT-AAAC
1 CTAAAAC
*
327695 CTTAAAC
1 CTAAAAC
327702 CTTAAAAC
1 C-TAAAAC
*
327710 TTAAAACC
1 CTAAAA-C
327718 CTAAAAAC
1 CT-AAAAC
*
327726 CTAAATC
1 CTAAAAC
327733 CTAAAA
1 CTAAAA
327739 TGAGTTTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
6 6 0.15
7 21 0.51
8 10 0.24
9 4 0.10
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (7 bp):
CTAAAAC
Found at i:327833 original size:23 final size:24
Alignment explanation
Indices: 327808--327872 Score: 96
Period size: 23 Copynumber: 2.8 Consensus size: 24
327798 CAATTTATGT
* *
327808 AAAAGCCTTAACCTTAAAATCTTA
1 AAAAGCATAAACCTTAAAATCTTA
*
327832 AAAATCATAAACCTT-AAATCTTA
1 AAAAGCATAAACCTTAAAATCTTA
327855 AAAAGCATAAACCTTAAA
1 AAAAGCATAAACCTTAAA
327873 CCAAAATACA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 22 0.61
24 14 0.39
ACGTcount: A:0.52, C:0.18, G:0.03, T:0.26
Consensus pattern (24 bp):
AAAAGCATAAACCTTAAAATCTTA
Found at i:331025 original size:27 final size:27
Alignment explanation
Indices: 330995--331066 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
330985 ACTAGTACTG
330995 CCTACCCAATAGGCACCATTGGTGCCA
1 CCTACCCAATAGGCACCATTGGTGCCA
* * *
331022 CCTACCCAACAAGCACCATTGGTGTCA
1 CCTACCCAATAGGCACCATTGGTGCCA
* *
331049 CTTACCCCATAGGCACCA
1 CCTACCCAATAGGCACCA
331067 CCCGAAATTT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.28, C:0.39, G:0.15, T:0.18
Consensus pattern (27 bp):
CCTACCCAATAGGCACCATTGGTGCCA
Found at i:332460 original size:49 final size:48
Alignment explanation
Indices: 332395--332500 Score: 160
Period size: 49 Copynumber: 2.2 Consensus size: 48
332385 AATTCGTTTA
*
332395 ATTTAATTATGCTATTTTTAGTTT-TATAATTTAATTATTTTTTAATAAT
1 ATTTAATTATGCTATTTTTA-TTTGTATAATTTAATT-GTTTTTAATAAT
**
332444 ATTTAATTATTTTATTTTTATTTGTATAATTTAATTGTTTTTAATAAT
1 ATTTAATTATGCTATTTTTATTTGTATAATTTAATTGTTTTTAATAAT
332492 ATTTAATTA
1 ATTTAATTA
332501 ATTTGTGTCG
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
48 23 0.43
49 30 0.57
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (48 bp):
ATTTAATTATGCTATTTTTATTTGTATAATTTAATTGTTTTTAATAAT
Found at i:336317 original size:21 final size:21
Alignment explanation
Indices: 336271--336313 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
336261 CATAATCCTC
* *
336271 AATTTAAAATGCCTACACCCT
1 AATTTAAAATACCTAAACCCT
*
336292 TATTTAAAATACC-AAACCCT
1 AATTTAAAATACCTAAACCCT
336312 AA
1 AA
336314 ATTTCCTACA
Statistics
Matches: 18, Mismatches: 4, Indels: 1
0.78 0.17 0.04
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.44, C:0.26, G:0.02, T:0.28
Consensus pattern (21 bp):
AATTTAAAATACCTAAACCCT
Found at i:336571 original size:30 final size:29
Alignment explanation
Indices: 336537--336595 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
336527 TAAGCACGTT
* *
336537 TTTACAAAATTGATCCATTCCCGTCAATAA
1 TTTACAAAATAG-TCCATTCCCGTAAATAA
* *
336567 TTTACAATATAGTCCATTTCCGTAAATAA
1 TTTACAAAATAGTCCATTCCCGTAAATAA
336596 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 15 0.60
30 10 0.40
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (29 bp):
TTTACAAAATAGTCCATTCCCGTAAATAA
Found at i:337014 original size:3 final size:3
Alignment explanation
Indices: 337006--337044 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
336996 CAATCACTTC
337006 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
337045 CAGCAACAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:337052 original size:6 final size:6
Alignment explanation
Indices: 337043--337417 Score: 471
Period size: 6 Copynumber: 62.5 Consensus size: 6
337033 TAATAATAAT
* *
337043 AACAGC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAT AACAAC
1 AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC
* * *
337091 AACAAT AACAAC AACAAC AACAGC AACAAC AGCAAC AACAAC AACAAC
1 AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC
* * * *
337139 AACAAC AACAAT AACAAC AATAAC AACAAC AACAAT AACAAT AACAAC
1 AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC
337187 AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC
1 AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC
* * *
337235 AACAAC AACAAC AACAAC AACAAC AACAAC AATAAC AATAAC AATAAC
1 AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC
* * * * * * * *
337283 AATAAC AACAAT AATAAT AACAAT AACAAT AACAAT AACAAC AACAAT
1 AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC
** * * * * *
337331 AATGAC AACAAC AACAAT AACAAT AACAAT AACAAT AACAAC AACAAT
1 AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC
* * * *
337379 AACAAC AACAAT AACAAC AATAAT AACAAC AATAAC AAC
1 AACAAC AACAAC AACAAC AACAAC AACAAC AACAAC AAC
337418 TCGAAATGAG
Statistics
Matches: 330, Mismatches: 39, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 330 1.00
ACGTcount: A:0.66, C:0.26, G:0.01, T:0.07
Consensus pattern (6 bp):
AACAAC
Found at i:337055 original size:9 final size:9
Alignment explanation
Indices: 337043--337417 Score: 471
Period size: 9 Copynumber: 41.7 Consensus size: 9
337033 TAATAATAAT
*
337043 AACAGCAAC
1 AACAACAAC
337052 AACAACAAC
1 AACAACAAC
337061 AACAACAAC
1 AACAACAAC
337070 AACAACAAC
1 AACAACAAC
*
337079 AACAATAAC
1 AACAACAAC
*
337088 AACAACAAT
1 AACAACAAC
337097 AACAACAAC
1 AACAACAAC
*
337106 AACAACAGC
1 AACAACAAC
*
337115 AACAACAGC
1 AACAACAAC
337124 AACAACAAC
1 AACAACAAC
337133 AACAACAAC
1 AACAACAAC
*
337142 AACAACAAT
1 AACAACAAC
*
337151 AACAACAAT
1 AACAACAAC
337160 AACAACAAC
1 AACAACAAC
*
337169 AACAATAAC
1 AACAACAAC
*
337178 AATAACAAC
1 AACAACAAC
337187 AACAACAAC
1 AACAACAAC
337196 AACAACAAC
1 AACAACAAC
337205 AACAACAAC
1 AACAACAAC
337214 AACAACAAC
1 AACAACAAC
337223 AACAACAAC
1 AACAACAAC
337232 AACAACAAC
1 AACAACAAC
337241 AACAACAAC
1 AACAACAAC
337250 AACAACAAC
1 AACAACAAC
*
337259 AACAACAAT
1 AACAACAAC
*
337268 AACAATAAC
1 AACAACAAC
* *
337277 AATAACAAT
1 AACAACAAC
*
337286 AACAACAAT
1 AACAACAAC
* *
337295 AATAATAAC
1 AACAACAAC
* *
337304 AATAACAAT
1 AACAACAAC
*
337313 AACAATAAC
1 AACAACAAC
*
337322 AACAACAAT
1 AACAACAAC
**
337331 AATGACAAC
1 AACAACAAC
*
337340 AACAACAAT
1 AACAACAAC
*
337349 AACAATAAC
1 AACAACAAC
* *
337358 AATAACAAT
1 AACAACAAC
337367 AACAACAAC
1 AACAACAAC
*
337376 AATAACAAC
1 AACAACAAC
*
337385 AACAATAAC
1 AACAACAAC
* *
337394 AACAATAAT
1 AACAACAAC
*
337403 AACAACAAT
1 AACAACAAC
337412 AACAAC
1 AACAAC
337418 TCGAAATGAG
Statistics
Matches: 318, Mismatches: 48, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 318 1.00
ACGTcount: A:0.66, C:0.26, G:0.01, T:0.07
Consensus pattern (9 bp):
AACAACAAC
Found at i:337479 original size:44 final size:44
Alignment explanation
Indices: 337416--337628 Score: 255
Period size: 44 Copynumber: 5.0 Consensus size: 44
337406 AACAATAACA
*
337416 ACTCGAAATGAGCGTGAGAATATGTTTAAAAAGGAAGACTCATG
1 ACTCGAAATGAGCATGAGAATATGTTTAAAAAGGAAGACTCATG
*
337460 ACTCGAAATGAGCATGAGAATATATTTAAAAAGGAAGACTCATG
1 ACTCGAAATGAGCATGAGAATATGTTTAAAAAGGAAGACTCATG
*
337504 ACTCGAAATGAGCATGAGAATATGTTTAAAAAGGAAGACTTATG
1 ACTCGAAATGAGCATGAGAATATGTTTAAAAAGGAAGACTCATG
* * * *
337548 ACTC--AGTACAGCATAAG-AT-TG-TTAAAAAGGAAGACTTATG
1 ACTCGAAAT-GAGCATGAGAATATGTTTAAAAAGGAAGACTCATG
** * *
337588 ACTCGGTA-GAGCATAAG-AT-TG-TTAAAAAGGAAGACACATG
1 ACTCGAAATGAGCATGAGAATATGTTTAAAAAGGAAGACTCATG
337628 A
1 A
337629 ACCTATGCAG
Statistics
Matches: 154, Mismatches: 12, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
40 53 0.34
41 2 0.01
42 4 0.03
43 7 0.05
44 88 0.57
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (44 bp):
ACTCGAAATGAGCATGAGAATATGTTTAAAAAGGAAGACTCATG
Found at i:344693 original size:17 final size:17
Alignment explanation
Indices: 344648--344694 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
344638 CGGTCACATG
344648 GCATTGATATGGTCAGT
1 GCATTGATATGGTCAGT
344665 G-A-TG-TA---TCAGT
1 GCATTGATATGGTCAGT
344676 GCATTGATATGGTCAGT
1 GCATTGATATGGTCAGT
344693 GC
1 GC
344695 CACATGGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 12
0.67 0.00 0.33
Matches are distributed among these distances:
11 6 0.25
12 1 0.04
13 2 0.08
14 4 0.17
15 2 0.08
16 1 0.04
17 8 0.33
ACGTcount: A:0.23, C:0.13, G:0.30, T:0.34
Consensus pattern (17 bp):
GCATTGATATGGTCAGT
Found at i:352140 original size:18 final size:20
Alignment explanation
Indices: 352096--352141 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
352086 TCTTTTGAAA
352096 TCTATTTTTACTATTTTTAT
1 TCTATTTTTACTATTTTTAT
*
352116 TCT-TTTTTCCTA-TTTTAT
1 TCTATTTTTACTATTTTTAT
352134 T-TATTTTT
1 TCTATTTTT
352142 TTAAAACCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 1 0.04
18 12 0.50
19 8 0.33
20 3 0.12
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (20 bp):
TCTATTTTTACTATTTTTAT
Found at i:352140 original size:19 final size:19
Alignment explanation
Indices: 352100--352142 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
352090 TTGAAATCTA
*
352100 TTTTTACTATTTTTATTCT
1 TTTTTACTATTTTTATTAT
*
352119 TTTTTCCTA-TTTTATTTAT
1 TTTTTACTATTTTTA-TTAT
352138 TTTTT
1 TTTTT
352143 TAAAACCTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTTACTATTTTTATTAT
Found at i:353858 original size:41 final size:41
Alignment explanation
Indices: 353698--353954 Score: 228
Period size: 41 Copynumber: 6.0 Consensus size: 41
353688 AAAATGTGGT
* * * *
353698 TTCAATCTACCCCTTTTGACTTAAGGGTAAAAGATTGAATAATGAT
1 TTCAATCTACCCCTCTT-AATTAAGGGTAAAAGATTG--GAAT--C
* * * * *
353744 TTCAATTTGCCCCTCTTAACTTAGGGGTATAAGATGGGATGATGAC
1 TTCAATCTACCCCTCTTAA-TTAAGGGTAAAAGATTGGA--AT--C
* * * *
353790 TTCAATCAACCCTTCTTTATTAGGGGTAAAAGATTGGAATC
1 TTCAATCTACCCCTCTTAATTAAGGGTAAAAGATTGGAATC
* *
353831 TTCAATCTTCCCCTCTTGATTAAGGGTAAAAGATTGGAATC
1 TTCAATCTACCCCTCTTAATTAAGGGTAAAAGATTGGAATC
* *
353872 TTCAATCTGCCCCTCTTAATT-AGGGGAAAAGATTGGAATC
1 TTCAATCTACCCCTCTTAATTAAGGGTAAAAGATTGGAATC
* * * *
353912 TTTAATCTGCCCCTCTTAATTAGGGGTAAAAGATTGTAATC
1 TTCAATCTACCCCTCTTAATTAAGGGTAAAAGATTGGAATC
353953 TT
1 TT
353955 TAATTTGTTC
Statistics
Matches: 179, Mismatches: 28, Indels: 13
0.81 0.13 0.06
Matches are distributed among these distances:
40 38 0.21
41 74 0.41
43 2 0.01
44 1 0.01
45 18 0.10
46 46 0.26
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (41 bp):
TTCAATCTACCCCTCTTAATTAAGGGTAAAAGATTGGAATC
Found at i:353913 original size:81 final size:82
Alignment explanation
Indices: 353744--353954 Score: 253
Period size: 81 Copynumber: 2.5 Consensus size: 82
353734 GAATAATGAT
* * * * * *
353744 TTCAATTTGCCCCTCTTAACTTAGGGGTATAAGATGGGATGATGACTTCAATCAACCCTTCTTTA
1 TTCAATCTGCCCCTCTTAA-TTAAGGGTAAAAGATTGGA--AT--CTTCAATCAACCCCTCTTAA
353809 TTAGGGGTAAAAGATTGGAATC
61 TTAGGGGTAAAAGATTGGAATC
* * **
353831 TTCAATCTTCCCCTCTTGATTAAGGGTAAAAGATTGGAATCTTCAATCTGCCCCTCTTAATTAGG
1 TTCAATCTGCCCCTCTTAATTAAGGGTAAAAGATTGGAATCTTCAATCAACCCCTCTTAATTAGG
353896 GG-AAAAGATTGGAATC
66 GGTAAAAGATTGGAATC
* * *
353912 TTTAATCTGCCCCTCTTAATTAGGGGTAAAAGATTGTAATCTT
1 TTCAATCTGCCCCTCTTAATTAAGGGTAAAAGATTGGAATCTT
353955 TAATTTGTTC
Statistics
Matches: 109, Mismatches: 15, Indels: 6
0.84 0.12 0.05
Matches are distributed among these distances:
81 52 0.48
82 23 0.21
84 2 0.02
86 16 0.15
87 16 0.15
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (82 bp):
TTCAATCTGCCCCTCTTAATTAAGGGTAAAAGATTGGAATCTTCAATCAACCCCTCTTAATTAGG
GGTAAAAGATTGGAATC
Found at i:353958 original size:41 final size:41
Alignment explanation
Indices: 353744--353954 Score: 262
Period size: 41 Copynumber: 5.0 Consensus size: 41
353734 GAATAATGAT
* * *
353744 TTCAATTTGCCCCTCTTAACTTAGGGGTATAAGATGGGATGATGAC
1 TTCAATCTGCCCCTCTTAA-TTAGGGGTAAAAGATTGGA--AT--C
** * *
353790 TTCAATCAACCCTTCTTTATTAGGGGTAAAAGATTGGAATC
1 TTCAATCTGCCCCTCTTAATTAGGGGTAAAAGATTGGAATC
* * *
353831 TTCAATCTTCCCCTCTTGATTAAGGGTAAAAGATTGGAATC
1 TTCAATCTGCCCCTCTTAATTAGGGGTAAAAGATTGGAATC
353872 TTCAATCTGCCCCTCTTAATTAGGGG-AAAAGATTGGAATC
1 TTCAATCTGCCCCTCTTAATTAGGGGTAAAAGATTGGAATC
* *
353912 TTTAATCTGCCCCTCTTAATTAGGGGTAAAAGATTGTAATC
1 TTCAATCTGCCCCTCTTAATTAGGGGTAAAAGATTGGAATC
353953 TT
1 TT
353955 TAATTTGTTC
Statistics
Matches: 147, Mismatches: 17, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
40 39 0.27
41 75 0.51
43 2 0.01
45 17 0.12
46 14 0.10
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (41 bp):
TTCAATCTGCCCCTCTTAATTAGGGGTAAAAGATTGGAATC
Found at i:354296 original size:49 final size:49
Alignment explanation
Indices: 354231--354428 Score: 157
Period size: 49 Copynumber: 4.0 Consensus size: 49
354221 ATATTTCTAA
* * ** *
354231 GGTACTAGGTTTGTCGTTACAGCCTCAACCTTTCCATTCAAATCTTCAT
1 GGTACCAGGTTCGTCGTTGTAGCCTCAACCTTTCCCTTCAAATCTTCAT
* * * *
354280 GGTACCGGGTTCGTCGTTGTGGCCTCAACCTTTCCCGTCACATCTTC-T
1 GGTACCAGGTTCGTCGTTGTAGCCTCAACCTTTCCCTTCAAATCTTCAT
* ** * *
354328 GAGGTACTAGGTTCACCGTTGTAGTCTCAACCATTCCCTTCAAATCTTCAT
1 --GGTACCAGGTTCGTCGTTGTAGCCTCAACCTTTCCCTTCAAATCTTCAT
* * * * * * **
354379 GGTA-CAGAGTTTGCCGTTGTGGTCTTAACCTTTCCCATCGCATCTTCAT
1 GGTACCAG-GTTCGTCGTTGTAGCCTCAACCTTTCCCTTCAAATCTTCAT
354428 G
1 G
354429 TTTCCTTGGT
Statistics
Matches: 118, Mismatches: 27, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
48 3 0.03
49 76 0.64
50 38 0.32
51 1 0.01
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.35
Consensus pattern (49 bp):
GGTACCAGGTTCGTCGTTGTAGCCTCAACCTTTCCCTTCAAATCTTCAT
Found at i:354357 original size:50 final size:49
Alignment explanation
Indices: 354254--354428 Score: 158
Period size: 49 Copynumber: 3.6 Consensus size: 49
354244 TCGTTACAGC
* * * ** *
354254 CTCAACCTTT-CCATTCAAATCTTCATGGTACCGGGTTCGTCGTTGTGGC
1 CTCAACCTTTCCCA-TCACATCTTCATGGTACAGAGTTCACCGTTGTGGT
* *
354303 CTCAACCTTTCCCGTCACATCTTC-TGAGGTACTAG-GTTCACCGTTGTAGT
1 CTCAACCTTTCCCATCACATCTTCAT--GGTAC-AGAGTTCACCGTTGTGGT
* * * **
354353 CTCAACCATTCCCTTCAAATCTTCATGGTACAGAGTTTGCCGTTGTGGT
1 CTCAACCTTTCCCATCACATCTTCATGGTACAGAGTTCACCGTTGTGGT
* *
354402 CTTAACCTTTCCCATCGCATCTTCATG
1 CTCAACCTTTCCCATCACATCTTCATG
354429 TTTCCTTGGT
Statistics
Matches: 102, Mismatches: 18, Indels: 12
0.77 0.14 0.09
Matches are distributed among these distances:
48 3 0.03
49 58 0.57
50 39 0.38
51 2 0.02
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (49 bp):
CTCAACCTTTCCCATCACATCTTCATGGTACAGAGTTCACCGTTGTGGT
Found at i:358890 original size:14 final size:14
Alignment explanation
Indices: 358870--358906 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
358860 CATCTTTCTT
*
358870 CGACCATATACACA
1 CGACCATATACAAA
*
358884 TGACCATATACAAA
1 CGACCATATACAAA
358898 CGACCATAT
1 CGACCATAT
358907 TATCTTCCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.43, C:0.30, G:0.08, T:0.19
Consensus pattern (14 bp):
CGACCATATACAAA
Found at i:360563 original size:119 final size:116
Alignment explanation
Indices: 360364--360706 Score: 345
Period size: 119 Copynumber: 2.9 Consensus size: 116
360354 AAAAATCGAG
*
360364 GGTTAAAATGTAATTTTGGGAAAGTTTAAGG-GTTAAAATGTAATCTT-GGAAAAGTTTAAGGGT
1 GGTTAAAATGTAATTTTGGGAAAGTTT--GGAGTTAAAATGTAATTTTAGG-AAAGTTT-AGGGT
* ** *
360427 CAAAATGAAATTTTGGAAAAGTTTGGGAGCTAAAATGTAATTTT-AGGAAAGTTTGGC
62 TAAAATGTGATTTTGGAAAAGTTTGGG-G-TAAAATGTAATTTTGAAG-AAGTTTGGC
** *
360484 GGTTAAAATACAATTTTGGGAAA-TTTGGTAGTTAAAATGCAATTTTAGGAAAGTTTAGGGGTTA
1 GGTTAAAATGTAATTTTGGGAAAGTTTGG-AGTTAAAATGTAATTTTAGGAAAGTTTA-GGGTTA
* * * *
360548 AAATGTGATTTTGGAAAAGTTCGAGGGTCAAAATGTGATTGTGAAGAAGTTTGGG
64 AAATGTGATTTTGGAAAAGTTTG-GGGT-AAAATGTAATTTTGAAGAAGTTTGGC
* ** * * *
360603 GGTCAAAATGTAATTTTAAGAAAGTTT-AAGGTTAAAATGTGATTTTAGAAAAGTTTAGGGTTAA
1 GGTTAAAATGTAATTTTGGGAAAGTTTGGA-GTTAAAATGTAATTTTAGGAAAGTTTAGGGTTAA
* * *
360667 AATATGATTTTAGAAAAGTTTGGGGTTAAAATATAATTTT
65 AATGTGATTTTGGAAAAGTTTGGGG-TAAAATGTAATTTT
360707 TAGATAAAAC
Statistics
Matches: 186, Mismatches: 27, Indels: 23
0.79 0.11 0.10
Matches are distributed among these distances:
117 15 0.08
118 30 0.16
119 111 0.60
120 30 0.16
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (116 bp):
GGTTAAAATGTAATTTTGGGAAAGTTTGGAGTTAAAATGTAATTTTAGGAAAGTTTAGGGTTAAA
ATGTGATTTTGGAAAAGTTTGGGGTAAAATGTAATTTTGAAGAAGTTTGGC
Found at i:360710 original size:30 final size:29
Alignment explanation
Indices: 360363--360706 Score: 289
Period size: 30 Copynumber: 11.6 Consensus size: 29
360353 AAAAAATCGA
* * *
360363 GGGTTAAAATGTAATTTTGGGAAAGTTTAA
1 GGGTTAAAATGTAATTTTAGAAAAGTTT-G
* * *
360393 GGGTTAAAATGTAATCTTGGAAAAGTTTAA
1 GGGTTAAAATGTAATTTTAGAAAAGTTT-G
* * *
360423 GGGTCAAAATGAAATTTTGGAAAAGTTTG
1 GGGTTAAAATGTAATTTTAGAAAAGTTTG
* *
360452 GGAGCTAAAATGTAATTTTAGGAAAGTTTG
1 GG-GTTAAAATGTAATTTTAGAAAAGTTTG
** * *
360482 GCGGTTAAAATACAATTTTGGGAAA-TTTG
1 G-GGTTAAAATGTAATTTTAGAAAAGTTTG
* * *
360511 GTAGTTAAAATGCAATTTTAGGAAAGTTTAG
1 G-GGTTAAAATGTAATTTTAGAAAAGTTT-G
* * *
360542 GGGTTAAAATGTGATTTTGGAAAAGTTCG
1 GGGTTAAAATGTAATTTTAGAAAAGTTTG
* * *
360571 AGGGTCAAAATGTGATTGT-GAAGAAGTTTGG
1 -GGGTTAAAATGTAATTTTAGAA-AAGTTT-G
* *
360602 GGGTCAAAATGTAATTTTA-AGAAAGTTTA
1 GGGTTAAAATGTAATTTTAGA-AAAGTTTG
* * *
360631 AGGTTAAAATGTGATTTTAGAAAAGTTTA
1 GGGTTAAAATGTAATTTTAGAAAAGTTTG
* *
360660 GGGTTAAAATATGATTTTAGAAAAGTTTG
1 GGGTTAAAATGTAATTTTAGAAAAGTTTG
*
360689 GGGTTAAAATATAATTTT
1 GGGTTAAAATGTAATTTT
360707 TAGATAAAAC
Statistics
Matches: 266, Mismatches: 38, Indels: 21
0.82 0.12 0.06
Matches are distributed among these distances:
29 98 0.37
30 163 0.61
31 5 0.02
ACGTcount: A:0.37, C:0.03, G:0.25, T:0.35
Consensus pattern (29 bp):
GGGTTAAAATGTAATTTTAGAAAAGTTTG
Found at i:362981 original size:17 final size:17
Alignment explanation
Indices: 362959--362992 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
362949 ATGTTCCCCA
362959 CATTGTGACAAACATGG
1 CATTGTGACAAACATGG
362976 CATTGTGACAAACATGG
1 CATTGTGACAAACATGG
362993 TTTTCTCTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (17 bp):
CATTGTGACAAACATGG
Found at i:372214 original size:3 final size:3
Alignment explanation
Indices: 372206--372234 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
372196 TTCGTATTCT
372206 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
372235 TAGTTGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:372480 original size:27 final size:28
Alignment explanation
Indices: 372431--372494 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
372421 ACATGCTTGC
*
372431 TTTTATTTAATTTTATTTATTTATG-TA
1 TTTTATTTAATTTTATATATTTATGCTA
*
372458 TTTTATTTATTTGTTATAT-TTTATGCTA
1 TTTTATTTAATT-TTATATATTTATGCTA
372486 TTTGTATTT
1 TTT-TATTT
372495 TTGCCTTAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 17 0.53
28 10 0.31
29 5 0.16
ACGTcount: A:0.22, C:0.02, G:0.06, T:0.70
Consensus pattern (28 bp):
TTTTATTTAATTTTATATATTTATGCTA
Found at i:376661 original size:30 final size:30
Alignment explanation
Indices: 376621--376842 Score: 137
Period size: 30 Copynumber: 7.4 Consensus size: 30
376611 TTTGGCCACC
*
376621 AAACTATCCAAAAATTATGTTTTAACCCTT
1 AAACTTTCCAAAAATTATGTTTTAACCCTT
* * ** *
376651 AAATTTTCC-AAAATTTTAAATTTGACCCTT
1 AAACTTTCCAAAAATTAT-GTTTTAACCCTT
* * *
376681 GAACTTTCTAAAAATTATCTTTTAACCCTT
1 AAACTTTCCAAAAATTATGTTTTAACCCTT
* * * * *
376711 AAACTTTCTAAAAATTAAGTTTTGATCCTC
1 AAACTTTCCAAAAATTATGTTTTAACCCTT
* * *
376741 GAACTTCCCAAAAATT-TGAATTTAACCCTT
1 AAACTTTCCAAAAATTATG-TTTTAACCCTT
* * * * ** *
376771 GAACTTT-CTAAAATTTTAGATTTGGCCCTC
1 AAACTTTCCAAAAATTAT-GTTTTAACCCTT
* * *
376801 GAACTTTCCAAAAACTATGTTTTAGCCC-T
1 AAACTTTCCAAAAATTATGTTTTAACCCTT
*
376830 AAACTTTCTAAAA
1 AAACTTTCCAAAA
376843 TTCTATTTTT
Statistics
Matches: 146, Mismatches: 40, Indels: 13
0.73 0.20 0.07
Matches are distributed among these distances:
29 26 0.18
30 105 0.72
31 15 0.10
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (30 bp):
AAACTTTCCAAAAATTATGTTTTAACCCTT
Found at i:376694 original size:60 final size:60
Alignment explanation
Indices: 376622--376844 Score: 263
Period size: 60 Copynumber: 3.7 Consensus size: 60
376612 TTGGCCACCA
* * * *
376622 AACTATCCAAAAATTATGTTTTAACCCTTAAATTTTCCAAAATTTTAAATTTGACCCTTG
1 AACTTTCCAAAAATTATGTTTTAACCCTTAAACTTTCTAAAATTTTAAATTTGACCCTCG
* * * * *
376682 AACTTTCTAAAAATTATCTTTTAACCCTTAAACTTTCTAAAA-ATTAAGTTTTGATCCTCG
1 AACTTTCCAAAAATTATGTTTTAACCCTTAAACTTTCTAAAATTTTAA-ATTTGACCCTCG
* * * * *
376742 AACTTCCCAAAAATT-TGAATTTAACCCTTGAACTTTCTAAAATTTTAGATTTGGCCCTCG
1 AACTTTCCAAAAATTATG-TTTTAACCCTTAAACTTTCTAAAATTTTAAATTTGACCCTCG
* *
376802 AACTTTCCAAAAACTATGTTTTAGCCC-TAAACTTTCTAAAATT
1 AACTTTCCAAAAATTATGTTTTAACCCTTAAACTTTCTAAAATT
376845 CTATTTTTGA
Statistics
Matches: 135, Mismatches: 24, Indels: 9
0.80 0.14 0.05
Matches are distributed among these distances:
59 20 0.15
60 110 0.81
61 5 0.04
ACGTcount: A:0.35, C:0.20, G:0.06, T:0.39
Consensus pattern (60 bp):
AACTTTCCAAAAATTATGTTTTAACCCTTAAACTTTCTAAAATTTTAAATTTGACCCTCG
Found at i:376806 original size:90 final size:90
Alignment explanation
Indices: 376658--376823 Score: 199
Period size: 90 Copynumber: 1.8 Consensus size: 90
376648 CTTAAATTTT
* * * * *
376658 CCAAAATTTTAAATTTGACCCTTGAACTTTCTAAAAATTATCTTTTAACCCTTAAACTTTCTAAA
1 CCAAAAATTTAAATTTAACCCTTGAACTTTCTAAAAATTATCATTTAACCCTCAAACTTTCCAAA
*
376723 AATTAAGTTTTGATCCTCGAACTTC
66 AACTAAGTTTTGATCCTCGAACTTC
* * * ** *
376748 CCAAAAATTTGAATTTAACCCTTGAACTTTCT-AAAATTTTAGATTTGGCCCTCGAACTTTCCAA
1 CCAAAAATTTAAATTTAACCCTTGAACTTTCTAAAAATTAT-CATTTAACCCTCAAACTTTCCAA
*
376812 AAACTATGTTTT
65 AAACTAAGTTTT
376824 AGCCCTAAAC
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
89 7 0.11
90 55 0.89
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (90 bp):
CCAAAAATTTAAATTTAACCCTTGAACTTTCTAAAAATTATCATTTAACCCTCAAACTTTCCAAA
AACTAAGTTTTGATCCTCGAACTTC
Found at i:376852 original size:29 final size:30
Alignment explanation
Indices: 376772--376852 Score: 76
Period size: 30 Copynumber: 2.7 Consensus size: 30
376762 TTAACCCTTG
* ** * *
376772 AACTTTCTAAAATTTTAGATTTGGCCCTCG
1 AACTTTCTAAAATTCTATTTTTAGCCCTCA
* *
376802 AACTTTCCAAAA-ACTATGTTTTAGCCCT-A
1 AACTTTCTAAAATTCTAT-TTTTAGCCCTCA
376831 AACTTTCTAAAATTCTATTTTT
1 AACTTTCTAAAATTCTATTTTT
376853 GACCCCATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.31, C:0.20, G:0.07, T:0.42
Consensus pattern (30 bp):
AACTTTCTAAAATTCTATTTTTAGCCCTCA
Found at i:378482 original size:5 final size:5
Alignment explanation
Indices: 378464--378501 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
378454 TGTTAAACTA
* *
378464 AAAAT AAGAC AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
378502 TCTTGTTGCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:379712 original size:19 final size:19
Alignment explanation
Indices: 379688--379726 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
379678 AAAAATACAC
379688 AAATAAAAATACTAAAATT
1 AAATAAAAATACTAAAATT
379707 AAATAAAAATACTAAAATT
1 AAATAAAAATACTAAAATT
379726 A
1 A
379727 TTTACTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (19 bp):
AAATAAAAATACTAAAATT
Found at i:381094 original size:12 final size:12
Alignment explanation
Indices: 381077--381102 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
381067 AATTTGTTTG
381077 TTGTTTTAATAT
1 TTGTTTTAATAT
381089 TTGTTTTAATAT
1 TTGTTTTAATAT
381101 TT
1 TT
381103 TTAAGTGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.08, T:0.69
Consensus pattern (12 bp):
TTGTTTTAATAT
Found at i:384293 original size:18 final size:18
Alignment explanation
Indices: 384254--384307 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
384244 GAGAAATTAA
*
384254 CTCTTACGATCAAGTAATG
1 CTCTTACGAGCAAGT-ATG
*
384273 CTCTTACGAGCTAGTATG
1 CTCTTACGAGCAAGTATG
** *
384291 CTCCAACGAGCCAGTAT
1 CTCTTACGAGCAAGTAT
384308 ACTAATCCTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.28
Consensus pattern (18 bp):
CTCTTACGAGCAAGTATG
Found at i:391256 original size:24 final size:24
Alignment explanation
Indices: 391165--391247 Score: 139
Period size: 24 Copynumber: 3.5 Consensus size: 24
391155 TTAAACTCTA
391165 TCTGGGCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
391189 TCTGGGCTCGTAAGAGCTAACCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
* *
391213 TCTGGGCTTGTAAGAGCTAATCAT
1 TCTGGGCTCGTAAGAGCTAACCAT
*
391237 TATGGGCTCGT
1 TCTGGGCTCGT
391248 GTAGGCTAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.29
Consensus pattern (24 bp):
TCTGGGCTCGTAAGAGCTAACCAT
Done.