Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015133.1 Corchorus olitorius cultivar O-4 contig15166, 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: 61913
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:926 original size:58 final size:58
Alignment explanation
Indices: 831--943 Score: 174
Period size: 58 Copynumber: 1.9 Consensus size: 58
821 ATTAATCAAA
* *
831 TATCAAGTGACATGTTCTTTATTAGATGCATTAAAAAAGACGTTTTCGGACCGAGACT
1 TATCAAGTGACATGTTCTTTATTAGATGCACTAAAAAAGACGTTTTAGGACCGAGACT
* *
889 TATCGAGTGACATGTTTTTTTATTAGATGC-CTAAAAAAGACGTTTTAGGACCGAG
1 TATCAAGTGACATG-TTCTTTATTAGATGCACTAAAAAAGACGTTTTAGGACCGAG
944 GCATGATGCT
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
58 36 0.72
59 14 0.28
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (58 bp):
TATCAAGTGACATGTTCTTTATTAGATGCACTAAAAAAGACGTTTTAGGACCGAGACT
Found at i:2725 original size:12 final size:12
Alignment explanation
Indices: 2681--2728 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
2671 AGCAAGGCGC
2681 GGCCCAAGCGCTT
1 GGCCC-AGCGCTT
**
2694 GGCCCAGGCGCGC
1 GGCCCA-GCGCTT
*
2707 GGGCCAGCGCTT
1 GGCCCAGCGCTT
2719 GGCCCAGCGC
1 GGCCCAGCGC
2729 CAAGCCAGGC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
12 14 0.50
13 14 0.50
ACGTcount: A:0.10, C:0.42, G:0.40, T:0.08
Consensus pattern (12 bp):
GGCCCAGCGCTT
Found at i:2728 original size:24 final size:24
Alignment explanation
Indices: 2677--2815 Score: 88
Period size: 24 Copynumber: 5.8 Consensus size: 24
2667 GGCCAGCAAG
*
2677 GCGCGGCCCAAGCGCTTGGCCCAGGC
1 GCGCGGGCC-AGCGCTTGGCCCA-GC
2703 GCGCGGGCCAGCGCTTGGCCCAGC
1 GCGCGGGCCAGCGCTTGGCCCAGC
** * ** *
2727 GC-CAAGCCAGGCACGCGGGCCAGC
1 GCGCGGGCCA-GCGCTTGGCCCAGC
** * **
2751 GCTTGGCCCAGCGCCAGG-CCAGGC
1 GCGCGGGCCAGCGCTTGGCCCA-GC
*
2775 GCGCGGGCCAGTGCTTGGCCCAGC
1 GCGCGGGCCAGCGCTTGGCCCAGC
2799 GC-CTGGGCCAG-GCTTGG
1 GCGC-GGGCCAGCGCTTGG
2816 GCCCTAAGCT
Statistics
Matches: 88, Mismatches: 20, Indels: 13
0.73 0.17 0.11
Matches are distributed among these distances:
23 15 0.17
24 46 0.52
25 19 0.22
26 8 0.09
ACGTcount: A:0.12, C:0.40, G:0.40, T:0.09
Consensus pattern (24 bp):
GCGCGGGCCAGCGCTTGGCCCAGC
Found at i:2738 original size:36 final size:36
Alignment explanation
Indices: 2697--2801 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
2687 AGCGCTTGGC
2697 CCAGGCGCGCGGGCCAGCGCTTGGCCCAGCGCCAAG
1 CCAGGCGCGCGGGCCAGCGCTTGGCCCAGCGCCAAG
* *
2733 CCAGGCACGCGGGCCAGCGCTTGGCCCAGCGCCAGG
1 CCAGGCGCGCGGGCCAGCGCTTGGCCCAGCGCCAAG
*
2769 CCAGGCGCGCGGGCCAGTGCTTGGCCCAGCGCC
1 CCAGGCGCGCGGGCCAGCGCTTGGCCCAGCGCC
2802 TGGGCCAGGC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 65 1.00
ACGTcount: A:0.12, C:0.42, G:0.39, T:0.07
Consensus pattern (36 bp):
CCAGGCGCGCGGGCCAGCGCTTGGCCCAGCGCCAAG
Found at i:2818 original size:11 final size:12
Alignment explanation
Indices: 2743--2818 Score: 57
Period size: 12 Copynumber: 6.4 Consensus size: 12
2733 CCAGGCACGC
2743 GGGCCAGCGCTT
1 GGGCCAGCGCTT
* *
2755 GGCCCAGCGC-C
1 GGGCCAGCGCTT
* **
2766 AGGCCAGGCGCGC
1 GGGCCA-GCGCTT
*
2779 GGGCCAGTGCTT
1 GGGCCAGCGCTT
* *
2791 GGCCCAGCGCCT
1 GGGCCAGCGCTT
2803 GGGCCAG-GCTT
1 GGGCCAGCGCTT
2814 GGGCC
1 GGGCC
2819 CTAAGCTCAA
Statistics
Matches: 49, Mismatches: 13, Indels: 5
0.73 0.19 0.07
Matches are distributed among these distances:
11 12 0.24
12 31 0.63
13 6 0.12
ACGTcount: A:0.09, C:0.38, G:0.42, T:0.11
Consensus pattern (12 bp):
GGGCCAGCGCTT
Found at i:5713 original size:36 final size:36
Alignment explanation
Indices: 5666--5735 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
5656 TTCAATAACC
* *
5666 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
5702 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
5736 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:6604 original size:207 final size:200
Alignment explanation
Indices: 6246--6657 Score: 646
Period size: 207 Copynumber: 2.0 Consensus size: 200
6236 GCTTAATAAC
*
6246 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAG
1 TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAA
* * * *
6311 ATACAACACATTATTATTATATATAAAACTATATCAAAAAAATTAGTTGAATATTAGTGGTTGAT
66 ATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATAGTTGAACATTAGTGGTTGAT
*
6376 TTATTAAATTAAATCAGATCAATGTC-AAACAAAATTTCAAAATTATAAAAGATATTAAAGATCC
131 TTATTAAATTAAATCAGATCAATGTCAAAAAAAAATTT-AAAATTATAAAAGATATTAAAGATCC
6440 GATTTA
195 GATTTA
* * *
6446 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGGTTGCTATCAAAAGTTGTAGTGAATA
1 TTTATCAATGGTGAATGTTATTAA-TTTTTAAGTCTAAGATTACTAAC-AAAGTTGTAGTGAATA
6511 AAATACAACACATTACTATTATATATATAGAACTATACCAAAAAAAAAAATAGTTGAACATTAGT
64 AAATACAACACATTACTATTATATATA-A-AACTATACC---AAAAAAAATAGTTGAACATTAGT
* *
6576 GGTTGATTTATTAAATTAAATTAGATCAATGTCAAAAAAAAATTTTAAATTATAAAAGATATTAA
124 GGTTGATTTATTAAATTAAATCAGATCAATGTCAAAAAAAAATTTAAAATTATAAAAGATATTAA
6641 AGATCCGATTTA
189 AGATCCGATTTA
6653 TTTAT
1 TTTAT
6658 TATTAAGAAA
Statistics
Matches: 193, Mismatches: 11, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
200 24 0.12
201 20 0.10
202 41 0.21
203 1 0.01
204 8 0.04
207 89 0.46
208 10 0.05
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (200 bp):
TTTATCAATGGTGAATGTTATTAATTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAAA
ATACAACACATTACTATTATATATAAAACTATACCAAAAAAAATAGTTGAACATTAGTGGTTGAT
TTATTAAATTAAATCAGATCAATGTCAAAAAAAAATTTAAAATTATAAAAGATATTAAAGATCCG
ATTTA
Found at i:6845 original size:18 final size:18
Alignment explanation
Indices: 6786--6846 Score: 50
Period size: 18 Copynumber: 3.2 Consensus size: 18
6776 TTAATATAAG
*
6786 TATTTCAGTTATTATAGTA
1 TATTTTAGTTATTATA-TA
* * * *
6805 TTATATTTAATTAATGTAAA
1 -TAT-TTTAGTTATTATATA
6825 TATTTTAGTTATTATATA
1 TATTTTAGTTATTATATA
6843 TATT
1 TATT
6847 ACATAGAAAT
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
18 15 0.48
19 3 0.10
20 4 0.13
21 9 0.29
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (18 bp):
TATTTTAGTTATTATATA
Found at i:7078 original size:2 final size:2
Alignment explanation
Indices: 7066--7120 Score: 56
Period size: 2 Copynumber: 26.5 Consensus size: 2
7056 AGTTTAGACT
* * * *
7066 TA TA TA GTA TA TA GA TA TA TA GTA TA TA GA TA TA GA TA GA TA TA
1 TA TA TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
7110 TA TA TA TA TA T
1 TA TA TA TA TA T
7121 TTCACCCTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
2 39 0.91
3 4 0.09
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (2 bp):
TA
Found at i:9207 original size:123 final size:124
Alignment explanation
Indices: 8984--9241 Score: 439
Period size: 123 Copynumber: 2.1 Consensus size: 124
8974 AATGAAACCA
8984 AAATA-ATGTAAAATAATGCACTTATAAATATGATCTACTACTTTCTCGTTTCAAAAAAAAAAAT
1 AAATATATGTAAAATAATGCACTTATAAATATGATCTACTACTTTCTCGTTT---AAAAAAAAAT
*
9048 CATCTAAACTTTTGCATTTAATGAATTGATTTATTTGGTAACCAACATTTTGAAGAGAAAAT
63 CATCTAAACTTTTGCATTTAATGAAATGATTTATTTGGTAACCAACATTTTGAAGAGAAAAT
* *
9110 AAATGTATGTAAAATAATGTACTTATAAATATGATCTACTACTTTCTCGTTT-AAAAAAAATCAT
1 AAATATATGTAAAATAATGCACTTATAAATATGATCTACTACTTTCTCGTTTAAAAAAAAATCAT
*
9174 CTAAACTTTTGCATTTAATGAAATGATTTATTTGGTAACCATCATTTTGAAGAGAAAAT
66 CTAAACTTTTGCATTTAATGAAATGATTTATTTGGTAACCAACATTTTGAAGAGAAAAT
9233 AAATATATG
1 AAATATATG
9242 ATTAAATGAG
Statistics
Matches: 126, Mismatches: 5, Indels: 5
0.93 0.04 0.04
Matches are distributed among these distances:
123 77 0.61
126 4 0.03
127 45 0.36
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (124 bp):
AAATATATGTAAAATAATGCACTTATAAATATGATCTACTACTTTCTCGTTTAAAAAAAAATCAT
CTAAACTTTTGCATTTAATGAAATGATTTATTTGGTAACCAACATTTTGAAGAGAAAAT
Found at i:9535 original size:12 final size:12
Alignment explanation
Indices: 9498--9538 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
9488 ATCTACCGAT
* *
9498 ATATATCCGTCA
1 ATATATCTGTCG
9510 ATATATCTGTTCG
1 ATATATCTG-TCG
9523 ATATATCTGTCG
1 ATATATCTGTCG
9535 ATAT
1 ATAT
9539 CTGGATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.41
Consensus pattern (12 bp):
ATATATCTGTCG
Found at i:11778 original size:36 final size:37
Alignment explanation
Indices: 11726--11800 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 37
11716 TTATCTAGAT
* *
11726 AAGATGGTGGAAATACGGG-AAGAAAAA-AAGAGGAAG
1 AAGATGGCGGAAATACGGGCAA-AAAAAGAAGAAGAAG
*
11762 AAGATGGCGGAGATACGGGCAAAAAAAGAAGAAGAAG
1 AAGATGGCGGAAATACGGGCAAAAAAAGAAGAAGAAG
11799 AA
1 AA
11801 CCGTAAGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
36 22 0.65
37 12 0.35
ACGTcount: A:0.53, C:0.05, G:0.35, T:0.07
Consensus pattern (37 bp):
AAGATGGCGGAAATACGGGCAAAAAAAGAAGAAGAAG
Found at i:13967 original size:22 final size:23
Alignment explanation
Indices: 13933--13975 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
13923 TTGGTGGGTG
13933 ATCTCTAAATACCATG-CCTGTA
1 ATCTCTAAATACCATGTCCTGTA
* *
13955 ATCTGTAAGTACCATGTCCTG
1 ATCTCTAAATACCATGTCCTG
13976 ACCTTGGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (23 bp):
ATCTCTAAATACCATGTCCTGTA
Found at i:14096 original size:26 final size:26
Alignment explanation
Indices: 14066--14118 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
14056 TGTGAGCTCA
14066 TGCTTAATTTGTTTTATTTGACATGG
1 TGCTTAATTTGTTTTATTTGACATGG
14092 TGCTTAATTTGTTTTATTTGACATGG
1 TGCTTAATTTGTTTTATTTGACATGG
14118 T
1 T
14119 TAGCTTGTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.19, C:0.08, G:0.19, T:0.55
Consensus pattern (26 bp):
TGCTTAATTTGTTTTATTTGACATGG
Found at i:15805 original size:54 final size:54
Alignment explanation
Indices: 15722--15827 Score: 167
Period size: 54 Copynumber: 2.0 Consensus size: 54
15712 GGTTCCATCA
15722 TCATTCTCCAAACTCAAGAGCTTGAGAGAGTCTTCCAAACATTCTGCAGAAATT
1 TCATTCTCCAAACTCAAGAGCTTGAGAGAGTCTTCCAAACATTCTGCAGAAATT
** * * *
15776 TCATTCTCCAATTTCAAGAGCTTGGGAGAGTCTTCCAGAGATTCTGCAGAAA
1 TCATTCTCCAAACTCAAGAGCTTGAGAGAGTCTTCCAAACATTCTGCAGAAA
15828 ATTGGCTCGT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (54 bp):
TCATTCTCCAAACTCAAGAGCTTGAGAGAGTCTTCCAAACATTCTGCAGAAATT
Found at i:22315 original size:24 final size:25
Alignment explanation
Indices: 22265--22316 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 25
22255 TTAATGATCT
22265 AAGTTTATTATCTTGTTGAATTCAAAA
1 AAGTTTATTATCTTGTT--ATTCAAAA
*
22292 AAGTTTATTATCTTGTT-TTTAAAA
1 AAGTTTATTATCTTGTTATTCAAAA
22316 A
1 A
22317 TTAATTATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
27 17 0.71
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.48
Consensus pattern (25 bp):
AAGTTTATTATCTTGTTATTCAAAA
Found at i:34865 original size:1 final size:1
Alignment explanation
Indices: 34818--34848 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
34808 TTCTGATTTC
34818 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
34849 CTGGTCTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:39902 original size:11 final size:11
Alignment explanation
Indices: 39888--39912 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39878 ATTCATTCAA
39888 TAACCATTTTG
1 TAACCATTTTG
39899 TAACCATTTTG
1 TAACCATTTTG
39910 TAA
1 TAA
39913 ACAAGAAAAA
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:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (11 bp):
TAACCATTTTG
Found at i:43103 original size:69 final size:69
Alignment explanation
Indices: 42891--43082 Score: 375
Period size: 69 Copynumber: 2.8 Consensus size: 69
42881 GGGACTAAAG
*
42891 GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTGATCTATCATCGACAGACAT
1 GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTCATCTATCATCGACAGACAT
42956 TGAA
66 TGAA
42960 GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTCATCTATCATCGACAGACAT
1 GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTCATCTATCATCGACAGACAT
43025 TGAA
66 TGAA
43029 GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTCATCTATCA
1 GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTCATCTATCA
43083 CGGACAAGGA
Statistics
Matches: 122, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
69 122 1.00
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (69 bp):
GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTCATCTATCATCGACAGACAT
TGAA
Found at i:43139 original size:138 final size:138
Alignment explanation
Indices: 42891--43139 Score: 308
Period size: 138 Copynumber: 1.8 Consensus size: 138
42881 GGGACTAAAG
*
42891 GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTGATCTATCATCGACAGACAT
1 GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTCATCTATCATCGACAGACAT
* ****** *
42956 TGAAGAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTCATCTATCATCGACAG
66 TGAAGAGTTGCCAGAAGGAACTTCAAATTTAACAAAACTAAAATGTCTTCATCTATCATCGACAG
43021 ACATTGAA
131 ACATTGAA
*
43029 GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTCATCTATCA-CGGACA-AGG
1 GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTCATCTATCATC-GACAGA-C
* * * *
43092 ATTGGAGAGTTGTC-GATGGAGCTT-AAGAGTTTAACAAAACTAAAATGT
64 ATTGAAGAGTTGCCAGAAGGAACTTCAA-A-TTTAACAAAACTAAAATGT
43140 TTGGACTTGT
Statistics
Matches: 93, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
136 2 0.02
137 10 0.11
138 81 0.87
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (138 bp):
GAGTTGCCAGAAGGAATTTCAAATTTGGTTTCACTAGAATGTCTTCATCTATCATCGACAGACAT
TGAAGAGTTGCCAGAAGGAACTTCAAATTTAACAAAACTAAAATGTCTTCATCTATCATCGACAG
ACATTGAA
Found at i:45375 original size:66 final size:66
Alignment explanation
Indices: 45264--45460 Score: 238
Period size: 66 Copynumber: 3.0 Consensus size: 66
45254 CTTTAGAGGA
* * * * * **
45264 AGAATCCTTGGAAGATTCCCCCAAAGCTCTTGAATTTGGAAAATGATGATGGAAGCCAAATTTCT
1 AGAATCTTTGAAAGAATCTCCC-AAGCTCTTGAATTTGGAGAATGATGATGGAAGCCAAATGCCT
45329 GC
65 GC
* *
45331 AGAATGTTTGAAAGACTCTCCCAAGCTCTTGAATTTGGAGAATGATGATGGAAGCCAAATGCCTG
1 AGAATCTTTGAAAGAATCTCCCAAGCTCTTGAATTTGGAGAATGATGATGGAAGCCAAATGCCTG
45396 C
66 C
* * * * *
45397 AGAATCTTTGGAAGAATCTCTCAAGCTCTTGAGTCTAGAG-A--ATGATGGAAGCCAAATGCCTG
1 AGAATCTTTGAAAGAATCTCCCAAGCTCTTGAATTTGGAGAATGATGATGGAAGCCAAATGCCTG
45459 C
66 C
45460 A
1 A
45461 AGTGCAACTT
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
63 23 0.20
65 1 0.01
66 74 0.64
67 17 0.15
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (66 bp):
AGAATCTTTGAAAGAATCTCCCAAGCTCTTGAATTTGGAGAATGATGATGGAAGCCAAATGCCTG
C
Found at i:55733 original size:52 final size:54
Alignment explanation
Indices: 55643--55747 Score: 169
Period size: 52 Copynumber: 2.0 Consensus size: 54
55633 GATTGTATGT
*
55643 GAGAACTCATGGAAACCAACGATTTGTTTTCAATGTAAGCTGTCAAAGTTCTTGA
1 GAGAACTCATCGAAACCAAC-ATTTGTTTTCAATGTAAGCTGTCAAAGTTCTTGA
*
55698 GAGAACTCATCGAAACC-AC-TTTGTTTTCAATGTAAGGTGTCAAAGTTCTT
1 GAGAACTCATCGAAACCAACATTTGTTTTCAATGTAAGCTGTCAAAGTTCTT
55748 CATGATACTC
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
52 30 0.62
54 2 0.04
55 16 0.33
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Consensus pattern (54 bp):
GAGAACTCATCGAAACCAACATTTGTTTTCAATGTAAGCTGTCAAAGTTCTTGA
Found at i:57728 original size:15 final size:16
Alignment explanation
Indices: 57703--57732 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
57693 AATAATTATT
57703 TTTAGATTATAATATA
1 TTTAGATTATAATATA
57719 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
57733 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:58021 original size:60 final size:60
Alignment explanation
Indices: 57870--58033 Score: 253
Period size: 59 Copynumber: 2.8 Consensus size: 60
57860 GCTAATTGCT
* * *
57870 CAAATAAGAGCCTAACGTT-TGCCAAATTGCTCAAATAAGGGTCC-GATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTAT-CGAAAATGCTCAAATAAGGG-CCTGATCTTTTAATTTGGC
*
57930 C-AATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGAGCCTGATCTTTTAATTTGGC
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
57989 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTG
1 CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTG
58034 GCGTCAGTTT
Statistics
Matches: 96, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
58 2 0.02
59 50 0.52
60 44 0.46
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (60 bp):
CAAATAAGGGCCTAACGTTATCGAAAATGCTCAAATAAGGGCCTGATCTTTTAATTTGGC
Found at i:58025 original size:31 final size:31
Alignment explanation
Indices: 57931--58032 Score: 113
Period size: 31 Copynumber: 3.4 Consensus size: 31
57921 TAATTTGGCC
57931 AATAAGGGCCTAACGTTATCGAAAATGCTCA
1 AATAAGGGCCTAACGTTATCGAAAATGCTCA
* * * **
57962 AATAAGAGCCTGATC-TT-T-TAATTTGGC-CA
1 AATAAGGGCCT-AACGTTATCGAAAAT-GCTCA
57991 AATAAGGGCCTAACGTTATCGAAAATGCTCA
1 AATAAGGGCCTAACGTTATCGAAAATGCTCA
58022 AATAAGGGCCT
1 AATAAGGGCCT
58033 GGCGTCAGTT
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 2 0.04
29 17 0.31
30 6 0.11
31 28 0.51
32 2 0.04
ACGTcount: A:0.36, C:0.19, G:0.20, T:0.25
Consensus pattern (31 bp):
AATAAGGGCCTAACGTTATCGAAAATGCTCA
Found at i:58113 original size:31 final size:31
Alignment explanation
Indices: 58077--58238 Score: 108
Period size: 31 Copynumber: 5.4 Consensus size: 31
58067 CGCCAGACCT
*
58077 TTATTTGAGCATTTTGGCAAACGTTAGGCCC
1 TTATTTGAGCATTTTGGCAAAAGTTAGGCCC
** *
58108 TTATTTG-GCCAAATT---AAGAGATT-GTGCCC
1 TTATTTGAG-CATTTTGGCAAAAG-TTAG-GCCC
* * *
58137 TTATTTGAGTATTTTGGCAAACGTTAGGCTC
1 TTATTTGAGCATTTTGGCAAAAGTTAGGCCC
** * *
58168 TTATTTG-GTCAAATT---AAAAGATCAGACCC
1 TTATTTGAG-CATTTTGGCAAAAG-TTAGGCCC
*
58197 TTATTTGAGCATTTTGGCAAAAATTAGGCCC
1 TTATTTGAGCATTTTGGCAAAAGTTAGGCCC
58228 TTATTTGAGCA
1 TTATTTGAGCA
58239 ATTAGCCTAT
Statistics
Matches: 95, Mismatches: 22, Indels: 28
0.66 0.15 0.19
Matches are distributed among these distances:
28 8 0.08
29 32 0.34
30 4 0.04
31 43 0.45
32 8 0.08
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (31 bp):
TTATTTGAGCATTTTGGCAAAAGTTAGGCCC
Found at i:58171 original size:60 final size:60
Alignment explanation
Indices: 58070--58234 Score: 233
Period size: 60 Copynumber: 2.8 Consensus size: 60
58060 TTTTCGACGC
* *
58070 CAGACCTTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAGAGAT
1 CAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
* * * * *
58130 -TGTGCCCTTATTTGAGTATTTTGGCAAACGTTAGGCTCTTATTTGGTCAAATTAAAAGAT
1 CAG-ACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
**
58190 CAGACCCTTATTTGAGCATTTTGGCAAAAATTAGGCCCTTATTTG
1 CAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
58235 AGCAATTAGC
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 1 0.01
60 88 0.98
61 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.36
Consensus pattern (60 bp):
CAGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGAT
Found at i:60792 original size:328 final size:329
Alignment explanation
Indices: 58486--61784 Score: 2373
Period size: 328 Copynumber: 10.0 Consensus size: 329
58476 ATACTTTACA
* * * * * * * *
58486 TCATCTAACCAAATCTCAGCAACATTGGATTTAAGAATTTATTTTTACGTGCATCTAAATCTTAT
1 TCATCTAATCAAA--TCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * * * *
58551 TTTGATTTAATTAGAAATTAATTTAGAAAAGATAAGAAATATGATATTAAAAGCGTAAAAAGCCC
64 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * *
58616 TCCAATCTTTTTGGCGTTGAATTATATAT-TTTTATTAGTATTTTAGCCAAACATTGA-GAAGAA
129 TCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAA-AA
* * * * * *
58679 ATATTTCATGT-AAATTTTTGCAAAATTTTA-GCGGAAATCGTGTACTAACAAACCATCACGGTT
193 TTTTTTC-GGTCATA-TTTTGCAAAATTTTAGGC-GAAATCGTG---TAA-TAATCATCACGGTT
* * * * * * * * * * * *
58742 TTTAGCTAAAAACACGTTCCGGGGACCCGGCTCAATTTCGCATGATTTCTGGCTCCGAGACTACT
251 TTTGGCTAAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAACTCCT
58807 TGAAATATCTATAT
316 TGAAATATCTATAT
* * * * *
58821 TAATCTAATCAAATCTCATCCACATTAG-ATTTAAGGATTTGTCTTTACGAGCATCTGAATTTTA
1 TCATCTAATCAAA--TCAGCCACATT-GCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
** * * *
58885 TTTCGATTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACGATATTAGAAA-CGTCAAAAGC
63 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTA-AAAGCGTGAAAAGT
* * * * * *
58949 CCTTCAATCTTTTTGGGCTTTTGACGTTGAGTTATATATTTTTTATAATTAATTTAGCTAAAAAT
127 CCTCCAATCTTTTT--G-----G-CGTTGAATTATATATATTTTATGAGTATTTTAGCTAAAAAT
* * * * *
59014 TGAGG-AAA-TCTTTCGGATCA-ATTTTTACAACATTTT-GGCCGAAATCATGTAATAACCATCA
184 TGAGGAAAATTTTTTCGG-TCATA-TTTTGCAAAATTTTAGG-CGAAATCGTGTAATAATCATCA
* * ** * * * *
59075 CAGTTTTTGGATAAAAAAACGTTTTATGGCCCC-G----G-TTTGCATGATTTTTGGCACCAAGA
246 CGGTTTTTGGCTAAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAA
* *
59134 CTCCTTGAGATATCTATAC
311 CTCCTTGAAATATCTATAT
* * * ** * *
59153 TCATTTAATCAAATCACATCCACATTGGATTTAAAAATTTGTTTTT-CCACGCATCTAAATCTTG
1 TCATCTAATCAAAT--CAGCCACATTGCATTTAAGGATTTGTTTTTACGA-GCATCTGAATCTTG
* * *
59217 TTTCGATTTAATTAGAAATTAATACAG-AAAAATATGAAAAACGATATTAAAAACATGAAAAGTC
63 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTC
** * * * *
59281 CTCCAATCTTTTTACCATTAAATTATATATATATATATATTAGGAGTATTTTATCCAAAAATTGA
128 CTCCAATCTTTTTGGCGTTGAATTATATATAT-T-T-TA-T--GAGTATTTTAGCTAAAAATTGA
* * * * * * *
59346 AGACAAA-TTTTTCAGGTTATATTTTACAAAAGTTTAGGCAAAATCGTGTACTAACCATCACGGT
187 GGA-AAATTTTTTC-GGTCATATTTTGCAAAATTTTAGGCGAAATCGTGTAATAATCATCACGGT
* * * * * * * *
59410 TTTTGACTAAAAACGCGTTTCGGGGCACCAGTTCAGTTTTGCATTATTTTTGGCACCGAAACTCC
250 TTTTGGCTAAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAACTCC
*
59475 TTGAAATAACTATAT
315 TTGAAATATCTATAT
*
59490 TCATCTAATAAAATCTTAGCCACATTGCATTTAA-GATTTTTTTTTGTTTTTAACGAGCATCTGA
1 TCATCTAATCAAATC--AGCCACATTGCATTTAAGGA------TTTGTTTTT-ACGAGCATCTGA
* * * * *
59554 ATCATGTTTCGATTTAATTATAAATTAATTTAGAAAAAATATGAAAAACAATATTAAAAGCGTCA
57 ATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGA
* * * * * * * * *
59619 CAAGTCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTTATGAATATTATGGATAAAAATTA
122 AAAGTCCTCCAATCTTTTTGGCGTTGAATTATATA-TATTTTATGAGTATTTTAGCTAAAAATTG
* * * * * *
59684 AGGAATA-TCTATCGGGTCA-ATTTTTGCAAAATTTTAGCCGGAATCGTGTAATAATCATCATGA
186 AGGAAAATTTTTTC-GGTCATA-TTTTGCAAAATTTTAGGCGAAATCGTGTAATAATCATCACG-
* * *** * * * * *
59747 G-TTTTGGCTAAAAACG-GGTTCCGAGG-CCCATTTCAGATTT-AATGGTTTTTGGCGCCGAGAC
248 GTTTTTGGCTAAAAACGCGTTTCAG-GGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAAC
*
59808 TCCTGGAAATATCTATAT
312 TCCTTGAAATATCTATAT
* * * * * *
59826 TCATCTGACCAAAT----CTCA--GCCA-TT---G--TT-TTTATA--AGCATTTGAATCATGTT
1 TCATCTAATCAAATCAGCCACATTG-CATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
** * * * * * *
59876 TCTTTTTAATTAGAAATTAATTC-GGAAAAATAGGAAAAACGGTATTAGAAGCATGAAAAGCCCT
65 TCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* * * *
59940 TCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTGT-GACTAAAATTTGAGGAAAAG
130 CCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAG-CTAAAAATTGAGGAAAAT
* * * * * ** *
60003 TATTTCGCGTCATTTTTTGCAAAATATTAGTCGAAATCGTG---CAA-CATCACTTTTTTTTGCT
194 TTTTTCG-GTCATATTTTGCAAAATTTTAGGCGAAATCGTGTAATAATCATCACGGTTTTTGGCT
* * * * * *
60064 AAAAACGCGTTCCAGGACCCCGGGTCAGTATTGCATGATTTTTGACGCCAAAACTCCTTGAACTA
258 AAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAACTCCTTGAAATA
*
60129 TTTATAT
323 TCTATAT
* * * * * *
60136 TAAACTAATCAAATCTCAGCCACATTGGATTTAAGGAATTGTTTTTACGAGCATCTAAATCTTCT
1 TCATCTAATCAAA--TCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * * * * *
60201 TTCGTTTTAATTAGAAACTAATTCA-AAAACAGTAGGAAAAACTATATTAGAAGCATAAAAATTC
64 TTCGATTTAATTAGAAATTAATTCAGAAAA-AATATGAAAAACGATATTAAAAGCGTGAAAAGTC
* * ** * * *
60265 CTTCAATATTTTTGGCGTAAAATTATATTATTTTTTATGA-TAATTTAGCAAAAAATTGAGGAAA
128 CTCCAATCTTTTTGGCGTTGAATTATA-TATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAA
* * * * * *
60329 TATATTTCCGGTCATTTTTTGCAAAATTTTAGCCGAAATCATGTAAAAATCATCACGGTTTTTGG
192 -ATTTTTTCGGTCATATTTTGCAAAATTTTAGGCGAAATCGTGTAATAATCATCACGGTTTTTGG
* * * * * * * * * *
60394 CTAAAAATGCGTTCCAAGGCCCTGGGTTAGTTTTGCATGATTTTTGGCGCTAAGACTACTTGAGA
256 CTAAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAACTCCTTGAAA
*
60459 TATCCATAT
321 TATCTATAT
* * * * *
60468 TCATCTAATCAAATCAGACACAATGCATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTATTT
1 TCATCTAATCAAATCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTT
* * * * * *
60533 CGATTAAATTAAAAAATAATTCAGAAAAAATTATGAAAAACGATATGAAAATCGTGAAACGTCCT
66 CGATTTAATTAGAAATTAATTCAGAAAAAA-TATGAAAAACGATATTAAAAGCGTGAAAAGTCCT
* * * *
60598 CCAATCTTTTTGGTGTTAAATTATATATATTTAATGAGTATTTTAGCCAAAAATTGAGGAAAATT
130 CCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAATT
* * * *
60663 TTTTTGGT-ATATTTTGTAAAATTTTAGGCG-CATCGTGTAATAATCATCACGGTTTTTGGTTAA
195 TTTTCGGTCATATTTTGCAAAATTTTAGGCGAAATCGTGTAATAATCATCACGGTTTTTGGCTAA
* * * * * *
60726 AAACACGTTTCAGGGCCCCGGCTAAGTTTTGCATGATTTTTGGCGTCAAAAATCTTTGACATATC
260 AAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAACTCCTTGAAATATC
*
60791 CATAT
325 TATAT
* * * * * *
60796 TCATCTAATTAAATCTCATCTACATTGGATTTAAGAATTTGATTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAA--TCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
60861 TTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAACACGATATT---A-----AAAATTCC
64 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCC
* * * * ** *
60917 CCCAATCCTTTTGGTGTTAAATTATATATATTTTATGAGTA-TTTATG-GGAAAATTGACAGAAA
129 TCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTA-GCTAAAAATTG--AGGAA
* * ** * **
60980 AATTTTTTGGGTCACT-TTTTACAAAATTTTAGTTGAAATCGTGTACTAATCATCACAATTTTTT
191 AATTTTTTCGGTCA-TATTTTGCAAAATTTTAGGCGAAATCGTGTAATAATCATCAC---GGTTT
* * * *
61044 TTTGCTAAAAACGCGTTTC-GGAACCCCGGCTTAGTTTTGCATGATTTTTGGCACCAAAACTCCT
252 TTGGCTAAAAACGCGTTTCAGG-GCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAACTCCT
61108 TGAAATATCTATAT
316 TGAAATATCTATAT
*
61122 TTATCTAATCAAATCTTAGCCACATT-CAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
1 TCATCTAATCAAATC--AGCCACATTGC-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * **
61186 TTT-GATTTAATTAGAAATTAATTCAG-AAAAATATAAAAAATGATATTAAAAGCGTGAAGGGTC
63 TTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTC
* * * * * * * *
61249 CTCCAATATTTTTGGCTTTTAATTATATATATTCTATAAGTATTGTGGCTAAAAATGGAGGAAAA
128 CTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGG-AAA
* * * * * *
61314 ATATTTTGGGTCA-ATTTTTGGAAAATATTAGCCGAAATCGTGTACT-AT-A--ACGGTTTTTTT
192 ATTTTTTCGGTCATA-TTTTGCAAAATTTTAGGCGAAATCGTGTAATAATCATCACGG--TTTTT
** * * * * * * *
61374 GGCTAAAAACGCGTTTTGGGGCTCCGGGTCAGTTTTGCATGATTTTTAGAGGCAACATTCCTTGA
254 GGCTAAAAACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAACTCCTTGA
61439 AATATCTATAT
319 AATATCTATAT
* * * *
61450 TCATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGT
1 TCATCTAATCAAATC--AGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
61515 TTCAATTTAATTAGAAATTAATT-TGAAAACAAATAGGAAAAACGATATTAGAAGCGTGAGAAGC
64 TTCGATTTAATTAGAAATTAATTCAG-AAA-AAATATGAAAAACGATATTAAAAGCGTGAAAAGT
* * * * * *
61579 CCTTCAATTTTTTTGGCGTGGAATTATATATATTTTTATGAGTATTATGGCTAAAAATTGAGAAA
127 CCTCCAATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATTTTAGCTAAAAATTGAG-GA
* * * * * * * * ** * *
61644 AAAATATTTCTGATCA-ATTTTTGTAAAATTTTAGCCGAAATTGTATACCATATTGGT--TGTTT
190 AAATTTTTTC-GGTCATA-TTTTGCAAAATTTTAGGCGAAATCGTGTA--ATAATCATCACGGTT
* * * * ** *
61706 TTTTGCTAAAAAAGCGTTCCGGGGCTCTAGG-TCAGTTTTGCATGATTTTTGGCGCCAACACTCC
251 TTTGGCTAAAAACGCGTTTCAGGGC-CCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAACTCC
*
61770 TT-AATATATATATAT
315 TTGAA-ATATCTATAT
61785 ATATATATAT
Statistics
Matches: 2369, Mismatches: 457, Indels: 276
0.76 0.15 0.09
Matches are distributed among these distances:
308 20 0.01
309 15 0.01
310 41 0.02
311 27 0.01
312 34 0.01
313 58 0.02
314 35 0.01
316 4 0.00
317 5 0.00
318 5 0.00
319 11 0.00
320 45 0.02
321 16 0.01
322 16 0.01
323 34 0.01
324 8 0.00
325 45 0.02
326 162 0.07
327 53 0.02
328 294 0.12
329 81 0.03
330 156 0.07
331 237 0.10
332 232 0.10
333 111 0.05
334 10 0.00
335 183 0.08
336 52 0.02
337 84 0.04
338 91 0.04
339 21 0.01
341 2 0.00
342 41 0.02
343 55 0.02
344 82 0.03
345 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (329 bp):
TCATCTAATCAAATCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTT
CGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTC
CAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCTAAAAATTGAGGAAAATTT
TTTCGGTCATATTTTGCAAAATTTTAGGCGAAATCGTGTAATAATCATCACGGTTTTTGGCTAAA
AACGCGTTTCAGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAAACTCCTTGAAATATCT
ATAT
Found at i:61415 original size:654 final size:646
Alignment explanation
Indices: 58514--61564 Score: 2083
Period size: 654 Copynumber: 4.6 Consensus size: 646
58504 GCAACATTGG
* * * * * * *
58514 ATTTAAGAATTTATTTTTACGTGCATCTAAATCTTATTTTGATTTAATTAGAAATTAATTTAGAA
1 ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAA
* * * * * * *
58579 AAGATAAGAAATATGATATTAAAAGCGTAAAAAGCCCTCCAATCTTTTTGGCGTTGAATTATATA
66 AA-ATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCTTTAAATTATATA
* * * * * * *** * *
58644 TTTTTATTAGTATTTTAGCCAAACATTGA-GAAGAAATATTTCATGTAAATTTTTGCAAAATTTT
130 TATTTATGAGTATTGTGGCTAAAAATTGAGGAA-AAATATTTTGGGTCAATTTTTGCAAAATATT
* * ** * * * * * * *
58708 AGCGGAAATCGTGTACTAACAAACCATCACGGTTTTTAGCTAAAAACACGTTCCGGGGACCCGGC
194 AGCCGAAATCGTGTACT-A-TAACGGT----TTTTTTGGCTAAAAACGCGTTTCAGGGCCCCGGG
* * * * * * * * *
58773 TCAATTTCGCATGATTTCTGGCTCCGAGACTACTTGAAATATCTATATTAATCTAATCAAATCTC
253 TCAGTTTTGCATGATTTTTGGCGCCAAAAATCCTTG-AATATCTATATTCATCTAATCAAATCTC
* * * * * *
58838 ATCCACATTAGATTTAAGGATTTGTCTTTACGAGCATCTGAATTTTATTTCGATTTAATTAGAAA
317 AGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAA
* **
58903 TTAATTTGGAAAAAATAGGAAAAACGATATTAGAAACGTCAAAAGCCCTTCAAT-CTTTTTGGGC
382 TTAA-TT-CAAAAAATAGGAAAAACGATATTA-AAAATTC-----CCC--CAATAC-TTTT-GGC
* * ** * * * * *
58967 TTTTGACGTTGAGTTATATATTTTTTATAATTAATTTAGCTAAAAATTG-AG-GAAATCTTT-CG
435 --GTAAAATT-A--TAT-TATATTTTATGA-TAATTTAGCAAAAAATTGAAGAAAAATATTTCCG
* * * * * * * **
59029 GATCAATTTTTACAACATTTTGGCCGAAATCATGTAATAACCATCACAGTTTTTGGATAAAAAAA
493 G-TCACTTTTTACAAAATTTTAGCCGAAATCATGTAAAAATCATCACGGTTTTTGGCTAAAAACG
** * * * * * *
59094 CGTTTTATGGCCCC-G----G-TTTGCATGATTTTTGGCACCAAGACTCCTTGAGATATCTATAC
557 CGTTCCA-AGCCCCGGCTTAGTTTTGCATGATTTTTGGCACCAAAACTACTTGAAATATCCATAT
* * * *
59153 TCATTTAATCAAATCACATCCACATTGG
621 TCATCTAATCAAATCAGA--CACAATGC
** * * *
59181 ATTTAAAAATTTGTTTTT-CCACGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATACAGA
1 ATTTAAGGATTTGTTTTTACGA-GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGA
* * ** *
59245 AAAATATGAAAAACGATATTAAAAACATGAAAAGTCCTCCAATCTTTTTACCATTAAATTATATA
65 AAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCTTTAAA-T-TATA
* ** * * * * * *
59310 TATATATATATTAGGAGTATTTTATCCAAAAATTGAAGACAAAT-TTTTCAGGT-TATATTTTAC
128 TATAT-T-TA-T--GAGTATTGTGGCTAAAAATTGAGGAAAAATATTTT-GGGTCAAT-TTTTGC
* * * * *
59373 AAAAGT-TTAGGCAAAATCGTGTACTAACCATCACGG--TTTTTGACTAAAAACGCGTTTCGGGG
186 AAAA-TATTAGCCGAAATCGTGTACT----ATAACGGTTTTTTTGGCTAAAAACGCGTTTCAGGG
* * * * * * * * *
59435 CACCAGTTCAGTTTTGCATTATTTTTGGCACCGAAACTCCTTGAAATAACTATATTCATCTAATA
246 CCCCGGGTCAGTTTTGCATGATTTTTGGCGCCAAAAATCCTTG-AATATCTATATTCATCTAATC
* * * *
59500 AAATCTTAGCCACATTGCATTTAAGATTTTTTTTTGTTTTTAACGAGCATCTGAATCATGTTTCG
310 AAATCTCAGCCACATTGGATTTAAGA-----ATTTGTTTTT-ACGAGCATCTGAATCTTGTTTCG
* * * * **
59565 ATTTAATTATAAATTAATTTAGAAAAAATATGAAAAACAATATTAAAAGCGTCACAAGTCCTTCA
369 ATTTAATTAGAAATTAA-TT-CAAAAAATAGGAAAAACGATATTAAAA-ATTC-C----CC--CA
* ** * * * *
59630 ATATTTTTGGCGTTGAATTATA-TAT-TTTT-TTATGAATATTATGGATAAAAATT-AAGGAATA
424 ATACTTTTGGCGTAAAATTATATTATATTTTATGAT-AAT-TTA-GCA-AAAAATTGAAGAAAAA
* * * * * * * * *
59691 TCTATCGGGTCAATTTTTGCAAAATTTTAGCCGGAATCGTGTAATAATCATCATGAG-TTTTGGC
485 TATTTCCGGTCACTTTTTACAAAATTTTAGCCGAAATCATGTAAAAATCATCACG-GTTTTTGGC
* * * ** * * * * * * * *
59755 TAAAAACGGGTTCCGAGGCCC-ATTTCAGATTT-AATGGTTTTTGGCGCCGAGACTCCTGGAAAT
549 TAAAAACGCGTTCCAAGCCCCGGCTT-AGTTTTGCATGATTTTTGGCACCAAAACTACTTGAAAT
* * * *
59818 ATCTATATTCATCTGACCAAAT----CTC-A-GCC
613 ATCCATATTCATCTAATCAAATCAGACACAATG-C
* * * ** *
59847 A-TT---G--TT-TTTATA--AGCATTTGAATCATGTTTCTTTTTAATTAGAAATTAATTCGGAA
1 ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAA
* * * * * * * *
59903 AAATAGGAAAAACGGTATTAGAAGCATGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT
66 AAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCTTTAAATTATATAT
* * * * * * *
59968 TTTTATGAGTATTGTGACTAAAATTTGAGGAAAAGTATTTCGCGTCATTTTTTGCAAAATATTAG
131 ATTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAATATTAG
* * * * * * *
60033 TCGAAATCGTGCAAC-ATCAC--TTTTTTTTGCTAAAAACGCGTTCCAGGACCCCGGGTCAGTAT
196 CCGAAATCGTG-TACTATAACGGTTTTTTTGGCTAAAAACGCGTTTCAGGGCCCCGGGTCAGTTT
* * * * *
60095 TGCATGATTTTTGACGCCAAAACTCCTTGAACTATTTATATTAAACTAATCAAATCTCAGCCACA
260 TGCATGATTTTTGGCGCCAAAAATCCTTGAA-TATCTATATTCATCTAATCAAATCTCAGCCACA
* * * *
60160 TTGGATTTAAGGAA-TTGTTTTTACGAGCATCTAAATCTTCTTTCGTTTTAATTAGAAACTAATT
324 TTGGATTTAA-GAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
* ** *
60224 CAAAAACAGTAGGAAAAACTATATTAGAAGCATAAAAATTCCTTCAATATTTTTGGCGTAAAATT
388 CAAAAA-A-TAGGAAAAACGATA-T-------TAAAAATTCCCCCAATACTTTTGGCGTAAAATT
* * * * *
60289 ATATTATTTTTTATGATAATTTAGCAAAAAATTGAGGAAATATATTTCCGGTCATTTTTTGCAAA
443 ATATTATATTTTATGATAATTTAGCAAAAAATTGAAGAAAAATATTTCCGGTCACTTTTTACAAA
* *
60354 ATTTTAGCCGAAATCATGTAAAAATCATCACGGTTTTTGGCTAAAAATGCGTTCCAAGGCCCTGG
508 ATTTTAGCCGAAATCATGTAAAAATCATCACGGTTTTTGGCTAAAAACGCGTTCCAA-GCCCCGG
* * * * *
60419 GTTAGTTTTGCATGATTTTTGGCGCTAAGACTACTTGAGATATCCATATTCATCTAATCAAATCA
572 CTTAGTTTTGCATGATTTTTGGCACCAAAACTACTTGAAATATCCATATTCATCTAATCAAATCA
60484 GACACAATGC
637 GACACAATGC
* * * * * *
60494 ATTTGAGGATTTGTTTTTACGAGCATCTAAATCTTATTTCGATTAAATTAAAAAATAATTCAGAA
1 ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-A
* * *
60559 AAAATTATGAAAAACGATATGAAAATCGTGAAACGTCCTCCAATCTTTTTGG-TGTTAAATTATA
65 AAAA-TATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCT-TTAAATTATA
* * * * * *
60623 TATATTTAATGAGTATTTTAGCCAAAAATTGAGG-AAAATTTTTTTGGT--ATATTTTGTAAAAT
128 TATATTT-ATGAGTATTGTGGCTAAAAATTGAGGAAAAATATTTTGGGTCAAT-TTTTGCAAAAT
* * * * * *
60685 TTTAGGCG-CATCGTGTAATAATCATCACGG--TTTTTGGTTAAAAACACGTTTCAGGGCCCCGG
191 ATTAGCCGAAATCGTGTACT-AT-A--ACGGTTTTTTTGGCTAAAAACGCGTTTCAGGGCCCCGG
* * * * * *
60747 CTAAGTTTTGCATGATTTTTGGCGTCAAAAATCTTTGACATATCCATATTCATCTAATTAAATCT
252 GTCAGTTTTGCATGATTTTTGGCGCCAAAAATCCTTGA-ATATCTATATTCATCTAATCAAATCT
* * *
60812 CATCTACATTGGATTTAAGAATTTGATTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
316 CAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAA
* * * * *
60877 ATTAATTCAGAAAAATATGAAACACGATATTAAAAATTCCCCCAATCCTTTTGGTGTTAAATTAT
381 ATTAATTCA-AAAAATAGGAAAAACGATATTAAAAATTCCCCCAATACTTTTGGCGTAAAATTAT
** * **
60942 A-TATATTTTATGAGT-ATTTATG-GGAAAATTGACAGAAAAATTTTTTGGGTCACTTTTTACAA
445 ATTATATTTTATGA-TAATTTA-GCAAAAAATTGA-AGAAAAATATTTCCGGTCACTTTTTACAA
** * ** ** * *
61004 AATTTTAGTTGAAATCGTGTACTAATCATCACAATTTTTTTTTGCTAAAAACGCGTTTCGGAA-C
507 AATTTTAGCCGAAATCATGTAAAAATCATCAC---GGTTTTTGGCTAAAAACGCG-TTC-CAAGC
* * *
61068 CCCGGCTTAGTTTTGCATGATTTTTGGCACCAAAACTCCTTGAAATATCTATATTTATCTAATCA
567 CCCGGCTTAGTTTTGCATGATTTTTGGCACCAAAACTACTTGAAATATCCATATTCATCTAATCA
* *
61133 AATCTTAGCCAC-ATTC
632 AATC--AGACACAATGC
61149 AATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTT-GATTTAATTAGAAATTAATTCAGA
1 -ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGA
* * ** * *
61213 AAAATATAAAAAATGATATTAAAAGCGTGAAGGGTCCTCCAATATTTTTGGCTTTTAATTATATA
65 AAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCTTTAAATTATATA
* * *
61278 TATTCTATAAGTATTGTGGCTAAAAATGGAGGAAAAATATTTTGGGTCAATTTTTGGAAAATATT
130 TATT-TATGAGTATTGTGGCTAAAAATTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAATATT
** *
61343 AGCCGAAATCGTGTACTATAACGGTTTTTTTGGCTAAAAACGCGTTTTGGGGCTCCGGGTCAGTT
194 AGCCGAAATCGTGTACTATAACGGTTTTTTTGGCTAAAAACGCGTTTCAGGGCCCCGGGTCAGTT
* * * * * * *
61408 TTGCATGATTTTTAGAGGCAACATTCCTTGAAATATCTATATTCATCTAACCAAATCTTAGCCAC
259 TTGCATGATTTTTGGCGCCAAAAATCCTTG-AATATCTATATTCATCTAATCAAATCTCAGCCAC
* * * *
61473 ATTGGATTTAAGGATTTGTTTTTACGAGCATTTGAATCATGTTTCAATTTAATTAGAAATTAATT
323 ATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-T
*
61538 TGAAAACAAATAGGAAAAACGATATTA
387 T-CAAA-AAATAGGAAAAACGATATTA
61565 GAAGCGTGAG
Statistics
Matches: 1887, Mismatches: 375, Indels: 255
0.75 0.15 0.10
Matches are distributed among these distances:
638 5 0.00
639 11 0.01
640 143 0.08
641 23 0.01
642 52 0.03
643 3 0.00
645 2 0.00
646 100 0.05
647 7 0.00
648 8 0.00
649 1 0.00
650 70 0.04
651 88 0.05
652 5 0.00
653 80 0.04
654 244 0.13
655 58 0.03
656 113 0.06
657 106 0.06
658 64 0.03
659 39 0.02
660 146 0.08
661 5 0.00
664 1 0.00
665 8 0.00
666 53 0.03
667 64 0.03
668 21 0.01
669 156 0.08
670 5 0.00
671 3 0.00
672 8 0.00
673 95 0.05
674 20 0.01
675 79 0.04
676 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (646 bp):
ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAA
AAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCTTTAAATTATATAT
ATTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAATATTAG
CCGAAATCGTGTACTATAACGGTTTTTTTGGCTAAAAACGCGTTTCAGGGCCCCGGGTCAGTTTT
GCATGATTTTTGGCGCCAAAAATCCTTGAATATCTATATTCATCTAATCAAATCTCAGCCACATT
GGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAA
AAAATAGGAAAAACGATATTAAAAATTCCCCCAATACTTTTGGCGTAAAATTATATTATATTTTA
TGATAATTTAGCAAAAAATTGAAGAAAAATATTTCCGGTCACTTTTTACAAAATTTTAGCCGAAA
TCATGTAAAAATCATCACGGTTTTTGGCTAAAAACGCGTTCCAAGCCCCGGCTTAGTTTTGCATG
ATTTTTGGCACCAAAACTACTTGAAATATCCATATTCATCTAATCAAATCAGACACAATGC
Found at i:61780 original size:2 final size:2
Alignment explanation
Indices: 61773--61798 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
61763 ACACTCCTTA
61773 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
61799 TCATCTAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.