Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008086.1 Hibiscus syriacus cultivar Beakdansim tig00110596_pilon, 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: 756749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1102 original size:19 final size:21
Alignment explanation
Indices: 1074--1116 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1064 AAATAAGTAT
*
1074 TTTTTTAA-TTTT-TTATTAG
1 TTTTTCAATTTTTATTATTAG
1093 TTTTTCAATTTTTATTATTAG
1 TTTTTCAATTTTTATTATTAG
1114 TTT
1 TTT
1117 CAGTTAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 7 0.33
20 4 0.19
21 10 0.48
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (21 bp):
TTTTTCAATTTTTATTATTAG
Found at i:20323 original size:2 final size:2
Alignment explanation
Indices: 20316--20354 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
20306 CATGATAGTT
20316 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20355 TAGAGCGATG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:21899 original size:24 final size:21
Alignment explanation
Indices: 21854--21900 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
21844 GATTCATATG
*
21854 ATATGTGATAGAAGAAAAGAC
1 ATATGTGATACAAGAAAAGAC
21875 ATATGTGATTACAAGAGAAATGAC
1 ATATGTGA-TACAAGA-AAA-GAC
21899 AT
1 AT
21901 GAATACATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 8 0.36
22 6 0.27
23 3 0.14
24 5 0.23
ACGTcount: A:0.49, C:0.06, G:0.21, T:0.23
Consensus pattern (21 bp):
ATATGTGATACAAGAAAAGAC
Found at i:22638 original size:21 final size:21
Alignment explanation
Indices: 22612--22654 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
22602 TGCTGAAAGT
22612 ATTGTAGCAATGCATCGATAC
1 ATTGTAGCAATGCATCGATAC
*
22633 ATTGTAGCAGTGCATCGATAC
1 ATTGTAGCAATGCATCGATAC
22654 A
1 A
22655 CATTTTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.28
Consensus pattern (21 bp):
ATTGTAGCAATGCATCGATAC
Found at i:22786 original size:19 final size:20
Alignment explanation
Indices: 22743--22792 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
22733 CTGTTCATAG
* * *
22743 TACTATTTAAACAGTATCGA
1 TACTATTCATACAGTATCAA
22763 TACTATTCATACAGTAT-AA
1 TACTATTCATACAGTATCAA
22782 TACTATTCATA
1 TACTATTCATA
22793 AATACGTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.40, C:0.16, G:0.06, T:0.38
Consensus pattern (20 bp):
TACTATTCATACAGTATCAA
Found at i:23740 original size:23 final size:24
Alignment explanation
Indices: 23705--23750 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
23695 CCACTAGGGG
*
23705 CTATGAATTTGTCCCGAAGGACCA
1 CTATGAATATGTCCCGAAGGACCA
*
23729 CTATGAA-ATGTCCCGAATGACC
1 CTATGAATATGTCCCGAAGGACC
23751 TATGAACCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (24 bp):
CTATGAATATGTCCCGAAGGACCA
Found at i:25528 original size:25 final size:25
Alignment explanation
Indices: 25473--25530 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
25463 ATAAGTCTAG
* *
25473 ATTCAATATTTTGATACATGATCACA
1 ATTC-ATATTATGATACATGATCAAA
*
25499 TTTCATATTATGATACATGA-CATAA
1 ATTCATATTATGATACATGATCA-AA
25524 ATTCATA
1 ATTCATA
25531 CCATATGCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 2 0.07
25 22 0.81
26 3 0.11
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.40
Consensus pattern (25 bp):
ATTCATATTATGATACATGATCAAA
Found at i:25862 original size:23 final size:23
Alignment explanation
Indices: 25836--25894 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
25826 TGGCACTATA
*
25836 GTGCAATTCTACGCGGCACTCCG
1 GTGCAATTCTACGCGACACTCCG
* *
25859 GTGCAATTCTACGTGACACTTCG
1 GTGCAATTCTACGCGACACTCCG
*
25882 GTGCAATTATACG
1 GTGCAATTCTACG
25895 AGCTGTGGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (23 bp):
GTGCAATTCTACGCGACACTCCG
Found at i:26658 original size:20 final size:20
Alignment explanation
Indices: 26633--26670 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
26623 TCCCCTTTGA
26633 AGTGCATCGATACATTCTAT
1 AGTGCATCGATACATTCTAT
*
26653 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
26671 TTAACATGTG
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:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAT
Found at i:26782 original size:45 final size:44
Alignment explanation
Indices: 26698--26799 Score: 116
Period size: 45 Copynumber: 2.3 Consensus size: 44
26688 GCACCACCCA
* * *
26698 TGCATCGATACACCAATCACCTTCGATGTTTTCATTTTAAGGGGG
1 TGCATCGATACACCAATCACATTCGATGTTTTCATTTTAA-AGAG
* * * *
26743 TGCATCGATGCACTAATTACATTCGATG-TTTCTTCTTTAAAGAG
1 TGCATCGATACACCAATCACATTCGATGTTTTCAT-TTTAAAGAG
26787 TGCATCGATACAC
1 TGCATCGATACAC
26800 ATTGAGTGTG
Statistics
Matches: 48, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
44 19 0.40
45 29 0.60
ACGTcount: A:0.26, C:0.22, G:0.18, T:0.34
Consensus pattern (44 bp):
TGCATCGATACACCAATCACATTCGATGTTTTCATTTTAAAGAG
Found at i:28640 original size:409 final size:409
Alignment explanation
Indices: 27875--28699 Score: 1596
Period size: 409 Copynumber: 2.0 Consensus size: 409
27865 TTAACCAAGA
*
27875 ACACAGCCTTAAATCTTCTTTAAATATGATTCAACATACACTTTAAAGAATCTTTTCACATCACC
1 ACACAACCTTAAATCTTCTTTAAATATGATTCAACATACACTTTAAAGAATCTTTTCACATCACC
27940 TTGCACACTTTTCTTACTTCTATATCAAAATTATCATCTACACTTCCATATAACCTTTATCGTAT
66 TTGCACACTTTTCTTACTTCTATATCAAAATTATCATCTACACTTCCATATAACCTTTATCGTAT
28005 CTGATCCTTTAATTCAATCCCTTTCATTTCTTTATTCCATTATTCCTTTATTTATTCCTTATACA
131 CTGATCCTTTAATTCAATCCCTTTCATTTCTTTATTCCATTATTCCTTTATTTATTCCTTATACA
*
28070 CAAATCATATATTTCCTTTCATGTTCACATACTATTGTCTTATCACCTATACTCATCTCTATGTA
196 CAAATCATATATTTACTTTCATGTTCACATACTATTGTCTTATCACCTATACTCATCTCTATGTA
*
28135 CTAATCTTCATTGCATCCTCATAACTTTGATAACCCATTTCTTATACAGAGCTTTATTCTTTATC
261 CTAATCTTCATTGCATCCTCATAACTTTGATAACCCATTTCTTATACAGAGCTTCATTCTTTATC
*
28200 ATTTTTTATACTTGTATTTTTCTTCCTTAAGTTTTCATGCAAATAATTATCTCCTTTTCTACATC
326 ATTTCTTATACTTGTATTTTTCTTCCTTAAGTTTTCATGCAAATAATTATCTCCTTTTCTACATC
28265 ATAGCTATCTGATCAGAAT
391 ATAGCTATCTGATCAGAAT
28284 ACACAACCTTAAATCTTCTTTAAATATGATTCAACATACACTTTAAAGAATCTTTTCACATCACC
1 ACACAACCTTAAATCTTCTTTAAATATGATTCAACATACACTTTAAAGAATCTTTTCACATCACC
28349 TTGCACACTTTTCTTACTTCTATATCAAAATTATCATCTACACTTCCATATAACCTTTATCGTAT
66 TTGCACACTTTTCTTACTTCTATATCAAAATTATCATCTACACTTCCATATAACCTTTATCGTAT
*
28414 CTGATCCTTTAATTCAATCCCTTTCATTTCTTTATTCCATTTTTCCTTTATTTATTCCTTATACA
131 CTGATCCTTTAATTCAATCCCTTTCATTTCTTTATTCCATTATTCCTTTATTTATTCCTTATACA
28479 CAAATCATATATTTACTTTCATGTTCACATACTATTGTCTTATCACCTATACTCATCTCTATGTA
196 CAAATCATATATTTACTTTCATGTTCACATACTATTGTCTTATCACCTATACTCATCTCTATGTA
28544 CTAATCTTCATTGCATCCTCATAACTTTGATAACCCATTTCTTATACAGAGCTTCATTCTTTATC
261 CTAATCTTCATTGCATCCTCATAACTTTGATAACCCATTTCTTATACAGAGCTTCATTCTTTATC
*
28609 ATTTCTTATACTTGTATTTTTCTTCCTTAAGTTTTCATGCAAATACTTATCTCCTTTTCTACATC
326 ATTTCTTATACTTGTATTTTTCTTCCTTAAGTTTTCATGCAAATAATTATCTCCTTTTCTACATC
28674 ATAGCTATCTGATCAGAAT
391 ATAGCTATCTGATCAGAAT
28693 ACACAAC
1 ACACAAC
28700 TATATTCAGA
Statistics
Matches: 410, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
409 410 1.00
ACGTcount: A:0.28, C:0.24, G:0.04, T:0.44
Consensus pattern (409 bp):
ACACAACCTTAAATCTTCTTTAAATATGATTCAACATACACTTTAAAGAATCTTTTCACATCACC
TTGCACACTTTTCTTACTTCTATATCAAAATTATCATCTACACTTCCATATAACCTTTATCGTAT
CTGATCCTTTAATTCAATCCCTTTCATTTCTTTATTCCATTATTCCTTTATTTATTCCTTATACA
CAAATCATATATTTACTTTCATGTTCACATACTATTGTCTTATCACCTATACTCATCTCTATGTA
CTAATCTTCATTGCATCCTCATAACTTTGATAACCCATTTCTTATACAGAGCTTCATTCTTTATC
ATTTCTTATACTTGTATTTTTCTTCCTTAAGTTTTCATGCAAATAATTATCTCCTTTTCTACATC
ATAGCTATCTGATCAGAAT
Found at i:34203 original size:24 final size:20
Alignment explanation
Indices: 34150--34207 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
34140 TCCCCTTTGA
*
34150 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
34170 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
34193 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
34208 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:39456 original size:29 final size:29
Alignment explanation
Indices: 39414--39473 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
39404 TGAATACTTA
39414 ATTATAATCAAAGTAATTAATTAGTAGGT
1 ATTATAATCAAAGTAATTAATTAGTAGGT
39443 ATTATAATCAAAGTAATTAATTAGTAGGT
1 ATTATAATCAAAGTAATTAATTAGTAGGT
39472 AT
1 AT
39474 ATACTTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.13, T:0.38
Consensus pattern (29 bp):
ATTATAATCAAAGTAATTAATTAGTAGGT
Found at i:42412 original size:31 final size:31
Alignment explanation
Indices: 42376--42436 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
42366 ATAGTAATAT
* *
42376 TATTCTCATATACAACTCATATTCCATATCA
1 TATTCTAATATACAACTCATATGCCATATCA
* *
42407 TATTCTAATGTACATCTCATATGCCATATC
1 TATTCTAATATACAACTCATATGCCATATC
42437 TTATATTTGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.33, C:0.25, G:0.03, T:0.39
Consensus pattern (31 bp):
TATTCTAATATACAACTCATATGCCATATCA
Found at i:47379 original size:20 final size:20
Alignment explanation
Indices: 47354--47401 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
47344 TATATATTAC
* *
47354 TTAATTTTATTTTTTTAGGT
1 TTAATTTTATTATTTTACGT
* *
47374 TTAATTTCATTATTTTACTT
1 TTAATTTTATTATTTTACGT
47394 TTAATTTT
1 TTAATTTT
47402 TTTAAAAAAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (20 bp):
TTAATTTTATTATTTTACGT
Found at i:53469 original size:3 final size:3
Alignment explanation
Indices: 53461--53493 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
53451 CCTACTATCT
53461 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
53494 AATACATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:56057 original size:21 final size:21
Alignment explanation
Indices: 56033--56075 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
56023 TTCATATTCG
* *
56033 TTGAGGGGGTATCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
56054 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
56075 T
1 T
56076 AGCCCAGAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:62083 original size:23 final size:23
Alignment explanation
Indices: 62057--62101 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
62047 CACCACAGCT
*
62057 CGTATAAATGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCG
* *
62080 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACCGAAGTGCC
62102 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCG
Found at i:62794 original size:21 final size:21
Alignment explanation
Indices: 62770--62812 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
62760 TTCATATTCG
* *
62770 TTGAGGGGGTATCAATTCCCC
1 TTGAAGGGGTACCAATTCCCC
* *
62791 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCAATTCCCC
62812 T
1 T
62813 AGCCCAGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCAATTCCCC
Found at i:63954 original size:20 final size:20
Alignment explanation
Indices: 63926--63974 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
63916 CGTCAAGGGA
63926 TGCATCGATACATGGTGTAG
1 TGCATCGATACATGGTGTAG
*
63946 TGTATCGATACATGGTGTAG
1 TGCATCGATACATGGTGTAG
63966 TGCATCGAT
1 TGCATCGAT
63975 GCATACCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (20 bp):
TGCATCGATACATGGTGTAG
Found at i:64645 original size:23 final size:23
Alignment explanation
Indices: 64601--64645 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
64591 AATAGAACTT
* *
64601 TGGTGCATTTCTACGCGGCACTA
1 TGGTGCAATTCTACGCGACACTA
*
64624 TGGTGCAATTCTACGTGACACT
1 TGGTGCAATTCTACGCGACACT
64646 TCAGTGCATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
TGGTGCAATTCTACGCGACACTA
Found at i:68059 original size:17 final size:17
Alignment explanation
Indices: 68019--68060 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
68009 GGAAGAATAT
68019 ATTTAAAATATATACGA
1 ATTTAAAATATATACGA
*
68036 A-TTAAAATATATATGA
1 ATTTAAAATATATACGA
68052 ATTTAAAAT
1 ATTTAAAAT
68061 TTTCAAGTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (17 bp):
ATTTAAAATATATACGA
Found at i:70879 original size:39 final size:39
Alignment explanation
Indices: 70781--70881 Score: 157
Period size: 39 Copynumber: 2.6 Consensus size: 39
70771 TCCAGTGGAG
** * *
70781 AGTTCATAATGAGAAGAACTCATCTGATGAGGGAGAAGA
1 AGTTCATAATGAGAAGAACTTGTCCGACGAGGGAGAAGA
70820 AGTTCATAATGAGAAGAACTTGTCCGACGAGGGAGAAGA
1 AGTTCATAATGAGAAGAACTTGTCCGACGAGGGAGAAGA
*
70859 AGTTTATAATGAGAAGAACTTGT
1 AGTTCATAATGAGAAGAACTTGT
70882 TCAACCTTGG
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.40, C:0.10, G:0.28, T:0.23
Consensus pattern (39 bp):
AGTTCATAATGAGAAGAACTTGTCCGACGAGGGAGAAGA
Found at i:71767 original size:23 final size:23
Alignment explanation
Indices: 71733--71801 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
71723 CACCACAGCT
*
71733 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
71756 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
71779 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
71802 TATAAGGTTG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:72884 original size:21 final size:21
Alignment explanation
Indices: 72842--72884 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
72832 TTTTTAGGCT
* *
72842 AGGGGAATCGATACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
72863 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
72884 A
1 A
72885 ACGAACTAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.30, G:0.23, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:76914 original size:23 final size:23
Alignment explanation
Indices: 76881--76948 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
76871 ATTATTATAT
*
76881 GGCACTACGGTGAAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
76904 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* * *
76927 GACACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
76949 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.24, C:0.26, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:78917 original size:24 final size:20
Alignment explanation
Indices: 78860--78937 Score: 70
Period size: 20 Copynumber: 3.8 Consensus size: 20
78850 TTTCCCTTGA
*
78860 AGTGCATCGATGCATTCTAC
1 AGTGCATCGATGCATCCTAC
*
78880 AGTGTATCGATGCATCCCTTAAC
1 AGTGCATCGATGCAT-CC-T-AC
*
78903 ATGTGCATCGATGCACTCCT-T
1 A-GTGCATCGATGCA-TCCTAC
78924 A-TGCATCGATGCAT
1 AGTGCATCGATGCAT
78938 TAATTGCATT
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
18 1 0.02
19 12 0.24
20 14 0.29
21 2 0.04
22 1 0.02
23 4 0.08
24 14 0.29
25 1 0.02
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATCCTAC
Found at i:83093 original size:35 final size:35
Alignment explanation
Indices: 82972--83095 Score: 101
Period size: 35 Copynumber: 3.5 Consensus size: 35
82962 ATTTACTCAA
* **
82972 AATAATATGATCTTTTAATATTCAAATTTAAATGGAT
1 AATAA-AT-ATCTTTTAACATTCAAATTTAAAAAGAT
* * *
83009 AATAAATATATTTTAGC-TTGAACATTTTAAAATA-AT
1 AATAAATATCTTTTAACATTCAA-A-TTTAAAA-AGAT
* *
83045 -ATAATTATCCTTTTAACATTCAAACTTAAAAAGAT
1 AATAAATAT-CTTTTAACATTCAAATTTAAAAAGAT
83080 AATAAATATCTTTTAA
1 AATAAATATCTTTTAA
83096 TTTAGAATGT
Statistics
Matches: 68, Mismatches: 12, Indels: 16
0.71 0.12 0.17
Matches are distributed among these distances:
34 5 0.07
35 30 0.44
36 24 0.35
37 9 0.13
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (35 bp):
AATAAATATCTTTTAACATTCAAATTTAAAAAGAT
Found at i:83118 original size:71 final size:71
Alignment explanation
Indices: 82983--83119 Score: 161
Period size: 71 Copynumber: 1.9 Consensus size: 71
82973 ATAATATGAT
* * ** * * *
82983 CTTTTAATATTCAAATTTAAATGGATAATAAATATATTTTAGCTTGAACATTTTAAAATAATATA
1 CTTTTAACATTCAAACTTAAAAAGATAATAAATATATTTTAACTTGAACATGTTAAAAAAATATA
83048 ATTATC
66 ATTATC
* *
83054 CTTTTAACATTCAAACTTAAAAAGATAATAAATATCTTTTAA-TTTAGA-ATGTTAAAAAATATA
1 CTTTTAACATTCAAACTTAAAAAGATAATAAATATATTTTAACTTGA-ACATGTTAAAAAA-ATA
83117 TAA
64 TAA
83120 AATTAATTTA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
70 12 0.22
71 43 0.78
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (71 bp):
CTTTTAACATTCAAACTTAAAAAGATAATAAATATATTTTAACTTGAACATGTTAAAAAAATATA
ATTATC
Found at i:98061 original size:11 final size:11
Alignment explanation
Indices: 98045--98075 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
98035 TGGATGTGGG
98045 GCGGGGCGGAT
1 GCGGGGCGGAT
98056 GCGGGGCGGAT
1 GCGGGGCGGAT
98067 GCGGGGCGG
1 GCGGGGCGG
98076 GTAATGTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.06, C:0.19, G:0.68, T:0.06
Consensus pattern (11 bp):
GCGGGGCGGAT
Found at i:99198 original size:38 final size:35
Alignment explanation
Indices: 99154--99238 Score: 102
Period size: 38 Copynumber: 2.3 Consensus size: 35
99144 TTTTTGGGCC
99154 ACCCGACCCGACCCGA-GAAGA-AAGGGTTTTCACCCGTG
1 ACCCGACCCGACCCGACGAA-ATAA-GG-TTTCACCC--G
99192 ACCCGACCCGACCCGACGAAATTAAGGTTTCACCCG
1 ACCCGACCCGACCCGACGAAA-TAAGGTTTCACCCG
99228 ACCCGACCCGA
1 ACCCGACCCGA
99239 ATATATGACT
Statistics
Matches: 44, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
36 12 0.27
38 25 0.57
39 5 0.11
40 2 0.05
ACGTcount: A:0.27, C:0.39, G:0.22, T:0.12
Consensus pattern (35 bp):
ACCCGACCCGACCCGACGAAATAAGGTTTCACCCG
Found at i:109167 original size:20 final size:20
Alignment explanation
Indices: 109142--109180 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
109132 TAAATTAAAT
*
109142 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
109162 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
109181 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:109262 original size:53 final size:52
Alignment explanation
Indices: 109141--109290 Score: 266
Period size: 53 Copynumber: 2.9 Consensus size: 52
109131 ATAAATTAAA
*
109141 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
109193 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTCTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGT-TTTTATTCTATTAGT
*
109246 TATTAGATAGGGTCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
109291 GTTGCTAATT
Statistics
Matches: 95, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
51 9 0.09
52 37 0.39
53 49 0.52
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:109272 original size:20 final size:20
Alignment explanation
Indices: 109247--109286 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
109237 TCTATTAGTT
**
109247 ATTAGATAGGGTCATTTTTA
1 ATTAGATAGAATCATTTTTA
109267 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
109287 TTCTGTTGCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:113885 original size:20 final size:20
Alignment explanation
Indices: 113860--113898 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
113850 TAAATTAAAT
*
113860 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
113880 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAGTTTT
113899 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:113978 original size:53 final size:52
Alignment explanation
Indices: 113859--114006 Score: 262
Period size: 53 Copynumber: 2.8 Consensus size: 52
113849 CTAAATTAAA
*
113859 TATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
*
113911 TATTAGATATGATCATTTTTAATTAGATAGAATCAGTCTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGT-TTTTATTCTATTAGT
113964 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATT
114007 ATGTTGCTAA
Statistics
Matches: 92, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 7 0.08
52 36 0.39
53 49 0.53
ACGTcount: A:0.33, C:0.06, G:0.13, T:0.48
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:114007 original size:19 final size:19
Alignment explanation
Indices: 113963--114007 Score: 72
Period size: 20 Copynumber: 2.3 Consensus size: 19
113953 ATTCTATTAG
*
113963 TTATTAGATAGGATCATTT
1 TTATTAGATAGAATCATTT
113982 TTAATTAGATAGAATCATTT
1 TT-ATTAGATAGAATCATTT
114002 TTATTA
1 TTATTA
114008 TGTTGCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 6 0.25
20 18 0.75
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (19 bp):
TTATTAGATAGAATCATTT
Found at i:123052 original size:123 final size:123
Alignment explanation
Indices: 122833--123090 Score: 507
Period size: 123 Copynumber: 2.1 Consensus size: 123
122823 TAAACACCAT
122833 TACAAAAAACATAATCACCTAAAGCTCTCACCTTCTCGACCACAAAAATCAAGAGGCAATCACCC
1 TACAAAAAACATAATCACCTAAAGCTCTCACCTTCTCGACCACAAAAATCAAGAGGCAATCACCC
122898 TATACCTAAGATAAACCTCCATCAATAGGAAAACAACCCAACATTTAATGACATAACA
66 TATACCTAAGATAAACCTCCATCAATAGGAAAACAACCCAACATTTAATGACATAACA
122956 TACAAAAAACATAATCACCTAAAGCTCTCACCTTCTCGACCACAAAAATCAAGAGGCAATCACCC
1 TACAAAAAACATAATCACCTAAAGCTCTCACCTTCTCGACCACAAAAATCAAGAGGCAATCACCC
123021 TATACCTAAGATAAACCTCCATCAATAGGAAAACAACCCAACATTTAATGACATAACA
66 TATACCTAAGATAAACCTCCATCAATAGGAAAACAACCCAACATTTAATGACATAACA
123079 TACATAAAAACA
1 TACA-AAAAACA
123091 AAACCTAAAA
Statistics
Matches: 134, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
123 127 0.95
124 7 0.05
ACGTcount: A:0.47, C:0.28, G:0.07, T:0.19
Consensus pattern (123 bp):
TACAAAAAACATAATCACCTAAAGCTCTCACCTTCTCGACCACAAAAATCAAGAGGCAATCACCC
TATACCTAAGATAAACCTCCATCAATAGGAAAACAACCCAACATTTAATGACATAACA
Found at i:135035 original size:15 final size:15
Alignment explanation
Indices: 135015--135051 Score: 65
Period size: 15 Copynumber: 2.4 Consensus size: 15
135005 GAAGAGATAT
135015 GATTAAATGTTTAAC
1 GATTAAATGTTTAAC
135030 GATTAAATGTTTAAC
1 GATTAAATGTTTAAC
135045 GAGTTAA
1 GA-TTAA
135052 GCAGTTCGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 17 0.81
16 4 0.19
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (15 bp):
GATTAAATGTTTAAC
Found at i:137608 original size:21 final size:21
Alignment explanation
Indices: 137578--137620 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
137568 TATAACACAT
137578 ATGTCCCGAAGGACCGCGTAG
1 ATGTCCCGAAGGACCGCGTAG
*
137599 ATGTCTCGAAGGACCGCGTAG
1 ATGTCCCGAAGGACCGCGTAG
137620 A
1 A
137621 CCCTCGACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.16
Consensus pattern (21 bp):
ATGTCCCGAAGGACCGCGTAG
Found at i:138453 original size:20 final size:20
Alignment explanation
Indices: 138428--138466 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
138418 TTCCCATTGA
*
138428 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
138448 AGTGCATCGATGCATTCTT
1 AGTGCATCGATGCATTCTT
138467 TAACATGTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:140559 original size:21 final size:21
Alignment explanation
Indices: 140517--140559 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
140507 TTTCTGGGCT
*
140517 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
140538 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
140559 A
1 A
140560 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:140632 original size:23 final size:22
Alignment explanation
Indices: 140584--140632 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
140574 ACAGAATGTC
*
140584 AAGG-GGGAATCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
140605 CAGGAGGGAACCGATTCCCCCTA
1 AAGGAGGGAACCGATACCCCC-A
140628 AAGGA
1 AAGGA
140633 AAATTGTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 14 0.64
23 5 0.23
ACGTcount: A:0.33, C:0.29, G:0.29, T:0.10
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:142280 original size:103 final size:103
Alignment explanation
Indices: 142096--142307 Score: 370
Period size: 103 Copynumber: 2.1 Consensus size: 103
142086 GTTGAGGGTT
*
142096 TATGTGGTCGTTCGGGACATATATGTATTCTTTGGAACATGCGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGCGTGAAGTCTGGTGAGACACATAC
* *
142161 TTGATCCTTGGCATATGTATATGATTCATAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCATAAGGAATGA
*
142199 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGCGTGAAGTCTGGTGAGACACATAC
* *
142264 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATGTATATGATTCATAAGGAATGA
142302 TATGTG
1 TATGTG
142308 ATCCTTATGG
Statistics
Matches: 103, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.27, C:0.13, G:0.25, T:0.35
Consensus pattern (103 bp):
TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGCGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCATAAGGAATGA
Found at i:142360 original size:23 final size:23
Alignment explanation
Indices: 142330--142381 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 23
142320 ATTATTATAT
142330 GGCACTACGGTACAATTCTACGC
1 GGCACTACGGTACAATTCTACGC
* * *
142353 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTACAATTCTACGC
142376 GGCACT
1 GGCACT
142382 TCAGTGCATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTACAATTCTACGC
Found at i:142388 original size:23 final size:23
Alignment explanation
Indices: 142330--142389 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
142320 ATTATTATAT
* *
142330 GGCACTACGGTACAATTCTACGC
1 GGCACTACAGTGCAATTCTACGC
* * *
142353 GGCACTACGGTGCAATTCTATGT
1 GGCACTACAGTGCAATTCTACGC
*
142376 GGCACTTCAGTGCA
1 GGCACTACAGTGCA
142390 TTTATATGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACAGTGCAATTCTACGC
Found at i:142397 original size:23 final size:23
Alignment explanation
Indices: 142320--142397 Score: 57
Period size: 23 Copynumber: 3.3 Consensus size: 23
142310 CCTTATGGAC
* * *
142320 ATTATTATATGGCACTACGGTACA
1 ATTA-TATGTGGCACTACAGTGCA
* * * *
142344 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACAGTGCA
* *
142367 ATTCTATGTGGCACTTCAGTGCA
1 ATTATATGTGGCACTACAGTGCA
*
142390 TTTATATG
1 ATTATATG
142398 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 40 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACAGTGCA
Found at i:145660 original size:21 final size:21
Alignment explanation
Indices: 145618--145660 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
145608 TTTCTGGGCT
*
145618 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
145639 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
145660 A
1 A
145661 ACGAACCAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:147325 original size:103 final size:103
Alignment explanation
Indices: 147141--147358 Score: 373
Period size: 103 Copynumber: 2.1 Consensus size: 103
147131 GTCGAGGGTC
*
147141 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGCGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGCGTGAAGTCTGATGAGACACATAC
* *
147206 TTGATCATTGGCATATGTATATGATTCTTAAGGAATGA
66 TTGATCACTAGCATATGTATATGATTCTTAAGGAATGA
* *
147244 TATGTGGTCCTTCGGGCCATATATGTATTCTTTGGAACATGTGTGAAGTCTGATGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGCGTGAAGTCTGATGAGACACATAC
* *
147309 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCACTAGCATATGTATATGATTCTTAAGGAATGA
147347 TATGTGGTCCTT
1 TATGTGGTCCTT
147359 ATGGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGCGTGAAGTCTGATGAGACACATAC
TTGATCACTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:147431 original size:23 final size:23
Alignment explanation
Indices: 147375--147434 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
147365 ATTATTATAT
* *
147375 GGCACTACGATACAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
147398 GGCACTACGGTGCAATTCTATGT
1 GGCACTACGGTGCAATTCTACGC
*
147421 GGCACTTCGGTGCA
1 GGCACTACGGTGCA
147435 TTTATATGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:147442 original size:23 final size:23
Alignment explanation
Indices: 147365--147442 Score: 66
Period size: 23 Copynumber: 3.3 Consensus size: 23
147355 CCTTATGGAC
* * *
147365 ATTATTATATGGCACTACGATACA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
147389 ATTCTACGCGGCACTACGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
147412 ATTCTATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
147435 TTTATATG
1 ATTATATG
147443 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 11, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
23 40 0.93
24 3 0.07
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:149303 original size:23 final size:23
Alignment explanation
Indices: 149277--149321 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
149267 CACCACAGCT
*
149277 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
149300 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
149322 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:149542 original size:149 final size:149
Alignment explanation
Indices: 149289--149603 Score: 544
Period size: 149 Copynumber: 2.1 Consensus size: 149
149279 TATAATTGCA
*
149289 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAA
149353 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTT
* *
149418 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
*
149438 CCGAAGGACCGCATAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
*
149503 TCCTTAAGAATCATATACATATGCTAGGGATCATA-TATGTGTCTTTCAAGACTTCACACATGTT
66 TCCTTAAGAATCATATACATATGCTAGGGATCA-AGTATGTGTCTCTCAAGACTTCACACATGTT
*
149567 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATATC
149587 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
149604 CCCTCGACTC
Statistics
Matches: 157, Mismatches: 7, Indels: 4
0.93 0.04 0.02
Matches are distributed among these distances:
148 1 0.01
149 155 0.99
150 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.18, T:0.26
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATCAAGTATGTGTCTCTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:151138 original size:21 final size:21
Alignment explanation
Indices: 151114--151158 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
151104 TGTTGTTCGT
* *
151114 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
151135 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
151156 TTG
1 TTG
151159 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:153373 original size:18 final size:18
Alignment explanation
Indices: 153350--153449 Score: 81
Period size: 18 Copynumber: 5.8 Consensus size: 18
153340 ATATAACACA
153350 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
*
153368 TATGTCCCGAAGGACCGC
1 TATGTCCCGAAGGACCAC
153386 GTATATGTCCCGAAGGACCAC
1 ---TATGTCCCGAAGGACCAC
* * *
153407 -ATAT----AA-CA-TA-
1 TATGTCCCGAAGGACCAC
153417 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
153435 TATGTCCCGAAGGAC
1 TATGTCCCGAAGGAC
153450 TGCATAGACC
Statistics
Matches: 63, Mismatches: 8, Indels: 22
0.68 0.09 0.24
Matches are distributed among these distances:
11 4 0.06
12 1 0.02
13 2 0.03
15 2 0.03
16 1 0.02
17 4 0.06
18 32 0.51
21 17 0.27
ACGTcount: A:0.30, C:0.29, G:0.22, T:0.19
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:153394 original size:21 final size:19
Alignment explanation
Indices: 153346--153410 Score: 96
Period size: 18 Copynumber: 3.4 Consensus size: 19
153336 CCACATATAA
153346 CACATATGTCCCGAAGGAC
1 CACATATGTCCCGAAGGAC
153365 CAC-TATGTCCCGAAGGAC
1 CACATATGTCCCGAAGGAC
*
153383 CGCGTATATGTCCCGAAGGAC
1 CAC--ATATGTCCCGAAGGAC
153404 CACATAT
1 CACATAT
153411 AACATATATG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 17 0.41
19 7 0.17
21 17 0.41
ACGTcount: A:0.29, C:0.31, G:0.22, T:0.18
Consensus pattern (19 bp):
CACATATGTCCCGAAGGAC
Found at i:153394 original size:67 final size:67
Alignment explanation
Indices: 153303--153449 Score: 258
Period size: 67 Copynumber: 2.2 Consensus size: 67
153293 GCGTAGAATT
*
153303 TGTCCCGAAAGACCACGTAGATGTCCCGAAGGACCACATATAACACATATGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCACGTAGATGTCCCGAAGGACCACATATAACACATATGTCCCGAAGGACCAC
153368 TA
66 TA
* * *
153370 TGTCCCGAAGGACCGCGTATATGTCCCGAAGGACCACATATAACATATATGTCCCGAAGGACCAC
1 TGTCCCGAAGGACCACGTAGATGTCCCGAAGGACCACATATAACACATATGTCCCGAAGGACCAC
153435 TA
66 TA
153437 TGTCCCGAAGGAC
1 TGTCCCGAAGGAC
153450 TGCATAGACC
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
67 76 1.00
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (67 bp):
TGTCCCGAAGGACCACGTAGATGTCCCGAAGGACCACATATAACACATATGTCCCGAAGGACCAC
TA
Found at i:154318 original size:24 final size:20
Alignment explanation
Indices: 154265--154322 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
154255 TTCCCATTGA
*
154265 AGTGCATCGGTGCATTCTTC
1 AGTGCATCGATGCATTCTTC
154285 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TT--C
154308 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
154323 CTACCATGCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTTC
Found at i:158066 original size:20 final size:20
Alignment explanation
Indices: 158027--158066 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
158017 TTTGGTTCAC
* **
158027 GGAATGTAAGATTATTAGTG
1 GGAATATAAGATTACCAGTG
158047 GGAATATAAGATTACCAGTG
1 GGAATATAAGATTACCAGTG
158067 AATATGATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.05, G:0.28, T:0.30
Consensus pattern (20 bp):
GGAATATAAGATTACCAGTG
Found at i:172586 original size:3 final size:3
Alignment explanation
Indices: 172578--172613 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
172568 TTCTACAGGT
172578 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
172614 TGCAACAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:173471 original size:14 final size:15
Alignment explanation
Indices: 173446--173475 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
173436 AAAGAATTCA
173446 TTCTTCCCTTTCTTT
1 TTCTTCCCTTTCTTT
173461 TTCTT-CCTTTCTTT
1 TTCTTCCCTTTCTTT
173475 T
1 T
173476 CTTTTCTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (15 bp):
TTCTTCCCTTTCTTT
Found at i:174176 original size:63 final size:63
Alignment explanation
Indices: 174072--174322 Score: 334
Period size: 63 Copynumber: 4.0 Consensus size: 63
174062 TTGAACAGGT
* * * *
174072 GGAGCAGGTCCCTTGTGAGAGGAATTAGTAGTAGAGGTTGCCATTGGAGCTGGTGGCGGTGGC
1 GGAGCAGGTCCCTTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGTGGC
*
174135 GGAGTAGGTCCCTTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGTGGAGG
1 GGAGCAGGTCCCTTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGT---GG
174200 C
63 C
*
174201 GGTGGAGCAGGTCCCCTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGA------GGTGGTGG
1 ---GGAGCAGGTCCCTTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGTGG
174260 C
63 C
* *
174261 GGAGTAGGTCCCTTATGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGTGG
1 GGAGCAGGTCCCTTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGTGG
174323 AGGCGGTGTC
Statistics
Matches: 166, Mismatches: 10, Indels: 24
0.83 0.05 0.12
Matches are distributed among these distances:
57 45 0.27
60 3 0.02
63 69 0.42
66 3 0.02
69 46 0.28
ACGTcount: A:0.20, C:0.14, G:0.44, T:0.23
Consensus pattern (63 bp):
GGAGCAGGTCCCTTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGTGGC
Found at i:174280 original size:57 final size:57
Alignment explanation
Indices: 174204--174316 Score: 199
Period size: 57 Copynumber: 2.0 Consensus size: 57
174194 TGGAGGCGGT
*
174204 GGAGCAGGTCCCCTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGC
1 GGAGCAGGTCCCCTATGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGC
* *
174261 GGAGTAGGTCCCTTATGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGG
1 GGAGCAGGTCCCCTATGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGG
174317 TGGTGGAGGC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.22, C:0.15, G:0.42, T:0.21
Consensus pattern (57 bp):
GGAGCAGGTCCCCTATGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGC
Found at i:174310 original size:126 final size:128
Alignment explanation
Indices: 174069--174330 Score: 438
Period size: 126 Copynumber: 2.0 Consensus size: 128
174059 GCCTTGAACA
* * *
174069 GGTGGAGCAGGTCCCTTGTGAGAGGAATTAGTAGTAGAGGTTGCCATTGGAGCTGGTGGCGGTGG
1 GGTGGAGCAGGTCCCCTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGA-C-GGT-G-GGTGG
*
174134 CGGAGTAGGTCCCTTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGTGGAG
62 CGGAGTAGGTCCCTTATGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGTGGAG
174199 GC
127 GC
174201 GGTGGAGCAGGTCCCCTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGA-GGT-GGTGGCGGA
1 GGTGGAGCAGGTCCCCTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGACGGTGGGTGGCGGA
174264 GTAGGTCCCTTATGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGTGGAGGC
66 GTAGGTCCCTTATGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGTGGAGGC
174327 GGTG
1 GGTG
174331 TCAGTGTCGG
Statistics
Matches: 126, Mismatches: 4, Indels: 6
0.93 0.03 0.04
Matches are distributed among these distances:
126 75 0.60
129 3 0.02
132 48 0.38
ACGTcount: A:0.19, C:0.13, G:0.45, T:0.23
Consensus pattern (128 bp):
GGTGGAGCAGGTCCCCTGTGAGAGGAACTAGCAGTAGAGGTTGCCATTGGACGGTGGGTGGCGGA
GTAGGTCCCTTATGAGAGGAACTAGCAGTAGAGGTTGCCATTGGAGGTGGTGGTGGTGGAGGC
Found at i:174503 original size:24 final size:24
Alignment explanation
Indices: 174453--174505 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
174443 TCCCGACGAA
* * *
174453 GGTGGATGCAAGGATGGGGGTAGG
1 GGTGGAGGCAAGGATGGCGGCAGG
* *
174477 GGTGGAGGCAAGGGTGGCGGCATG
1 GGTGGAGGCAAGGATGGCGGCAGG
174501 GGTGG
1 GGTGG
174506 TGATAACAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.08, G:0.60, T:0.15
Consensus pattern (24 bp):
GGTGGAGGCAAGGATGGCGGCAGG
Found at i:174823 original size:9 final size:9
Alignment explanation
Indices: 174806--174835 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
174796 GGTAGATGCA
174806 GTGGAGGTG
1 GTGGAGGTG
*
174815 GTGGTGGTG
1 GTGGAGGTG
174824 GTGGAGGTG
1 GTGGAGGTG
174833 GTG
1 GTG
174836 CATGAGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.07, C:0.00, G:0.67, T:0.27
Consensus pattern (9 bp):
GTGGAGGTG
Found at i:177703 original size:17 final size:17
Alignment explanation
Indices: 177683--177715 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
177673 ATATTTATTT
*
177683 ATATAAAATATAATATA
1 ATATAAAAAATAATATA
177700 ATATAAAAAATAATAT
1 ATATAAAAAATAATAT
177716 TATGGTAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATAAAAAATAATATA
Found at i:178471 original size:33 final size:30
Alignment explanation
Indices: 178387--178483 Score: 99
Period size: 28 Copynumber: 3.1 Consensus size: 30
178377 AAAAAAATCA
178387 GGGTTCGGTCGGATTTTTTAAGTGTGATATTC
1 GGGTT-GG-CGGATTTTTTAAGTGTGATATTC
* *
178419 GGGTTGGC--CTTTTTTAAGTGTGATATTT
1 GGGTTGGCGGATTTTTTAAGTGTGATATTC
* *
178447 GGGTTGGATCGGGATTTTTAAAGTGTGCTATTC
1 GGGTTGG--C-GGATTTTTTAAGTGTGATATTC
178480 GGGT
1 GGGT
178484 GGAGTTCGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
28 25 0.46
30 2 0.04
31 2 0.04
32 5 0.09
33 20 0.37
ACGTcount: A:0.15, C:0.08, G:0.33, T:0.43
Consensus pattern (30 bp):
GGGTTGGCGGATTTTTTAAGTGTGATATTC
Found at i:182243 original size:45 final size:47
Alignment explanation
Indices: 182170--182275 Score: 153
Period size: 45 Copynumber: 2.3 Consensus size: 47
182160 TTTATTTTCG
* *
182170 TTTTTCGAATAAATGCATGCGAACTAGATATTATGCGGTTAGG-TTTA
1 TTTTTTGAAT-AATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
*
182217 TTTTTTGAATAA-GCATGCGAATTAGATATCATGCGGTTAGGATTTA
1 TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
182263 TTTTTGTGAATAA
1 TTTTT-TGAATAA
182276 CAAAGCAGAG
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
45 27 0.50
46 11 0.20
47 16 0.30
ACGTcount: A:0.30, C:0.08, G:0.21, T:0.41
Consensus pattern (47 bp):
TTTTTTGAATAATGCATGCGAACTAGATATCATGCGGTTAGGATTTA
Found at i:191940 original size:8 final size:8
Alignment explanation
Indices: 191927--192011 Score: 60
Period size: 8 Copynumber: 11.4 Consensus size: 8
191917 AATAAAAGAG
191927 AAAATGAA
1 AAAATGAA
191935 AAAATGAA
1 AAAATGAA
191943 AAAATGAA
1 AAAATGAA
191951 AATAAT--A
1 AA-AATGAA
*
191958 ATAAT--A
1 AAAATGAA
191964 AAAATGAGA
1 AAAATGA-A
*
191973 AGAA-G-A
1 AAAATGAA
191979 AAAA-GAA
1 AAAATGAA
*
191986 GAAATG-A
1 AAAATGAA
191993 AAAATGAA
1 AAAATGAA
*
192001 AAAAAGAA
1 AAAATGAA
192009 AAA
1 AAA
192012 TGATGGAAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
6 13 0.21
7 12 0.19
8 31 0.49
9 7 0.11
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (8 bp):
AAAATGAA
Found at i:191945 original size:15 final size:15
Alignment explanation
Indices: 191927--192014 Score: 78
Period size: 15 Copynumber: 5.9 Consensus size: 15
191917 AATAAAAGAG
191927 AAAATGAAAAAATGAA
1 AAAATG-AAAAATGAA
191943 AAAATG-AAAAT-AA
1 AAAATGAAAAATGAA
191956 TAATAAT-AAAAATGAGA
1 -AA-AATGAAAAATGA-A
*
191973 AGAA-GAAAAA-GAA
1 AAAATGAAAAATGAA
*
191986 GAAATGAAAAATGAA
1 AAAATGAAAAATGAA
*
192001 AAAAAGAAAAATGA
1 AAAATGAAAAATGA
192015 TGGAAAAAAC
Statistics
Matches: 59, Mismatches: 5, Indels: 17
0.73 0.06 0.21
Matches are distributed among these distances:
13 5 0.08
14 15 0.25
15 30 0.51
16 8 0.14
17 1 0.02
ACGTcount: A:0.73, C:0.00, G:0.15, T:0.12
Consensus pattern (15 bp):
AAAATGAAAAATGAA
Found at i:191945 original size:29 final size:29
Alignment explanation
Indices: 191913--192075 Score: 85
Period size: 28 Copynumber: 5.6 Consensus size: 29
191903 TCGCTTGAAG
191913 AAAAAATAAAAGAGAAAATGAAAAAATG-
1 AAAAAATAAAAGAGAAAATGAAAAAATGA
* * *
191941 AAAAAATGAAAATA-ATAATAATAAAAATGA
1 AAAAAAT-AAAAGAGAAAATGA-AAAAATGA
*
191971 GAAGAAGA-AAAAGA-AGAAATG-AAAAATGA
1 -AA-AAAATAAAAGAGA-AAATGAAAAAATGA
* *
192000 AAAAAAGAAAA-ATG---ATGGAAAAAACGA
1 AAAAAATAAAAGA-GAAAAT-GAAAAAATGA
* *
192027 AAAGAAAAAAAAGAGAAAATG-GAAAATGGA
1 AAA-AAATAAAAGAGAAAATGAAAAAAT-GA
*
192057 AGAAAAATGAAAGAGAAAA
1 A-AAAAATAAAAGAGAAAA
192076 ACAAAAAGAG
Statistics
Matches: 103, Mismatches: 14, Indels: 34
0.68 0.09 0.23
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
27 14 0.14
28 26 0.25
29 25 0.24
30 23 0.22
31 9 0.09
32 3 0.03
ACGTcount: A:0.72, C:0.01, G:0.18, T:0.10
Consensus pattern (29 bp):
AAAAAATAAAAGAGAAAATGAAAAAATGA
Found at i:192052 original size:14 final size:15
Alignment explanation
Indices: 192035--192097 Score: 53
Period size: 14 Copynumber: 4.3 Consensus size: 15
192025 GAAAAGAAAA
192035 AAAAGAG-AAAATGG
1 AAAAGAGAAAAATGG
192049 AAAATGGAAGAAAAAT-G
1 AAAA--G-AGAAAAATGG
**
192066 -AAAGAGAAAAA-CA
1 AAAAGAGAAAAATGG
192079 AAAAGAGAAAAATGG
1 AAAAGAGAAAAATGG
192094 AAAA
1 AAAA
192098 AAGAGAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 13
0.71 0.05 0.24
Matches are distributed among these distances:
13 7 0.18
14 16 0.41
15 4 0.10
16 4 0.10
17 3 0.08
18 5 0.13
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.06
Consensus pattern (15 bp):
AAAAGAGAAAAATGG
Found at i:192220 original size:45 final size:45
Alignment explanation
Indices: 192108--192232 Score: 162
Period size: 45 Copynumber: 2.8 Consensus size: 45
192098 AAGAGAAATA
* *
192108 AAAGGAGGGTTCAAGACGAAAACCTGAAAAGGGCATCTTAGAACC
1 AAAGGAGGGTTCAAGACGAAAACCCGAAAAGGGCGTCTTAGAACC
* *
192153 AAAGGAGGGTACAAGACCAAAACCCGAAAAGGGCGTCTTAGAACC
1 AAAGGAGGGTTCAAGACGAAAACCCGAAAAGGGCGTCTTAGAACC
** * *
192198 AAAGGA-GGTCTCAAGTTGAAAACTCGCAAAGGGCG
1 AAAGGAGGGT-TCAAGACGAAAACCCGAAAAGGGCG
192233 ACTTGACTTG
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
44 3 0.04
45 66 0.96
ACGTcount: A:0.41, C:0.19, G:0.28, T:0.12
Consensus pattern (45 bp):
AAAGGAGGGTTCAAGACGAAAACCCGAAAAGGGCGTCTTAGAACC
Found at i:193549 original size:55 final size:54
Alignment explanation
Indices: 193414--194145 Score: 779
Period size: 55 Copynumber: 13.5 Consensus size: 54
193404 GTTGAAGTTT
* * * *
193414 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCAGTT-TTTGAAGATTGTTC
* * * * * *
193465 GAGTCCTATACTCTCTGAATGAATAGAGAGCGGACAAGTTTGTTGAAGATTGCTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCAGTTT-TTGAAGATTGTTC
* *
193520 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCA-TTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGA-CCAGTTTT-TGAAGATTGTTC
* * *
193575 GAGTTCTATACTCCCTGAACGAATAGGGAGTGGACCCGTTTATTGAAGATTGTTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCAGTTT-TTGAAGATTGTTC
* *
193630 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCA-TTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGA-CCAGTTTT-TGAAGATTGTTC
* *
193685 GAGTTCTATACTCCTTGAACGG-ATAGGGAGCGGACCCGTTTATTGAAGATTGTTC
1 GAGTTCTATACTCCCTGAA-GGAATAGGGAGCGGACCAGTTT-TTGAAGATTGTTC
* * * *
193740 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCAGTTTT-TGAAGATTGTTC
*
193795 AAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGACCCA-TTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAA-GGAATAGGGAGCGGA-CCAGTTTT-TGAAGATTGTTC
* *
193850 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCAGACCCGTTTATTGAAGATTGTTC
1 GAGTTCTATACTCCCTGAA-GGAATAGGGAGCGGACCAGTTT-TTGAAGATTGTTC
* * *
193905 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCAGTTTT-TGAAGATTGTTC
* * *
193960 GAGTTCTATACTCCCTGAACGG-ATAGAGAGCGAACCCGCTTTATT-AAGATTGTTC
1 GAGTTCTATACTCCCTGAA-GGAATAGGGAGCGGACCAG-TTT-TTGAAGATTGTTC
*
194015 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCGGATTCA-TTTTATGAAGATTGTTC
1 GAGTTCTATACTCCCTGAA-GGAATAGGGAGCGGA-CCAGTTTT-TGAAGATTGTTC
* *
194070 GAGTTCTATACTCCCTGAACGAATAGGGA---G--C--TTTATTGAAGATTGATC
1 GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCAGTTT-TTGAAGATTGTTC
194118 GAGTAT-TATACTCCCTGAAGGAATAGGG
1 GAGT-TCTATACTCCCTGAAGGAATAGGG
194146 GGCAGACTTA
Statistics
Matches: 604, Mismatches: 46, Indels: 65
0.84 0.06 0.09
Matches are distributed among these distances:
48 39 0.06
49 3 0.00
51 45 0.07
52 1 0.00
53 1 0.00
54 20 0.03
55 474 0.78
56 20 0.03
57 1 0.00
ACGTcount: A:0.28, C:0.17, G:0.25, T:0.30
Consensus pattern (54 bp):
GAGTTCTATACTCCCTGAAGGAATAGGGAGCGGACCAGTTTTTGAAGATTGTTC
Found at i:193636 original size:110 final size:110
Alignment explanation
Indices: 193414--194100 Score: 876
Period size: 110 Copynumber: 6.3 Consensus size: 110
193404 GTTGAAGTTT
* * * * *
193414 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGA-CAAGTTCGT-TGAAGA---TT-GAGTCCTA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCA-TT-TTATGAAGATTGTTCGAGTTCTA
* * * ** *
193473 TACTCTCTGAATGAATAGAGAGCGGACAAGTTTGT-TGAAGATTGCTC
64 TACTCCCTGAACGAATAGGGAGCGGACCCGTTT-TATGAAGATTGTTC
193520 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATA
*
193585 CTCCCTGAACGAATAGGGAGTGGACCCG-TTTATTGAAGATTGTTC
66 CTCCCTGAACGAATAGGGAGCGGACCCGTTTTA-TGAAGATTGTTC
193630 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATA
* *
193695 CTCCTTGAACGGATAGGGAGCGGACCCG-TTTATTGAAGATTGTTC
66 CTCCCTGAACGAATAGGGAGCGGACCCGTTTTA-TGAAGATTGTTC
* * *
193740 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTATGAAGATTGTTCAAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATA
* *
193805 CTCCCTGAACGGATAGGGAGCGGACCCATTTTATGAAGATTGTTC
66 CTCCCTGAACGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
* * * *
193850 GAGTTCTATACTCCCTGAACGG-ATAGGGAGCAGACCC-GTTTATTGAAGATTGTTCGAGTTCTA
1 GAGTTCTATACTCTCTGAA-GGAATAGAGAGCGGACCCATTTTA-TGAAGATTGTTCGAGTTCTA
* * *
193913 TACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTC
64 TACTCCCTGAACGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
* * ** *
193960 GAGTTCTATACTCCCTGAACGG-ATAGAGAGCGAACCCGCTTTATTAAGATTGTTCGAGTTCTAT
1 GAGTTCTATACTCTCTGAA-GGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTAT
* ** *
194024 ACTCCCTGAACGGATAGGGAGCGGATTCATTTTATGAAGATTGTTC
65 ACTCCCTGAACGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
* * *
194070 GAGTTCTATACTCCCTGAACGAATAGGGAGC
1 GAGTTCTATACTCTCTGAAGGAATAGAGAGC
194101 TTTATTGAAG
Statistics
Matches: 523, Mismatches: 45, Indels: 22
0.89 0.08 0.04
Matches are distributed among these distances:
105 1 0.00
106 40 0.08
107 2 0.00
108 1 0.00
109 9 0.02
110 460 0.88
111 10 0.02
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (110 bp):
GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATA
CTCCCTGAACGAATAGGGAGCGGACCCGTTTTATGAAGATTGTTC
Found at i:193689 original size:165 final size:164
Alignment explanation
Indices: 193414--194143 Score: 913
Period size: 165 Copynumber: 4.5 Consensus size: 164
193404 GTTGAAGTTT
* ** * *
193414 GAGTCCTATACTCTCTGAAGGAATAGGGAGCGGACAAGTTCGTTGAAGA---TT-GAGTCCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTT-TTTGAAGATTGTTCGAGTTCTATA
* * * * *
193475 CTCTCTGAATGAATAGAGAGCGGA-CAAGTTTGT-TGAAGATTGCTCGAGTTCTATACTCTCTGA
65 CTCCCTGAAGGAATAGAGAGCGGACCCA-TTT-TATGAAGATTGTTCGAGTTCTATACTCCCTGA
* *
193538 A-GGAATAGAGAGCGGACCCATTT-TATGAAGATTGTTC
128 ACGG-ATAGGGAGCGGACCCGTTTAT-TGAAGATTGTTC
* * *
193575 GAGTTCTATACTCCCTGAACGAATAGGGAGTGGACCCGTTTATTGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTT-TTGAAGATTGTTCGAGTTCTATA
* *
193640 CTCTCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATACTCCTTGAAC
65 CTCCCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAAC
193705 GGATAGGGAGCGGACCCGTTTATTGAAGATTGTTC
130 GGATAGGGAGCGGACCCGTTTATTGAAGATTGTTC
* * *
193740 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGAACCCGTTTTATGAAGATTGTTCAAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTT-TGAAGATTGTTCGAGTTCTATA
*
193805 CTCCCTGAACGG-ATAGGGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAA
65 CTCCCTGAA-GGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAA
*
193869 CGGATAGGGAGCAGACCCGTTTATTGAAGATTGTTC
129 CGGATAGGGAGCGGACCCGTTTATTGAAGATTGTTC
*
193905 GAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATGAAGATTGTTCGAGTTCTATA
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTT-TGAAGATTGTTCGAGTTCTATA
* ** *
193970 CTCCCTGAACGG-ATAGAGAGCGAACCCGCTTTATTAAGATTGTTCGAGTTCTATACTCCCTGAA
65 CTCCCTGAA-GGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAA
** *
194034 CGGATAGGGAGCGGATTCATTT-TATGAAGATTGTTC
129 CGGATAGGGAGCGGACCCGTTTAT-TGAAGATTGTTC
* * *
194070 GAGTTCTATACTCCCTGAACGAATAGGGA---G---C-TTTATTGAAGATTGATCGAGTAT-TAT
1 GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTT-TTGAAGATTGTTCGAGT-TCTAT
194127 ACTCCCTGAAGGAATAG
64 ACTCCCTGAAGGAATAG
194144 GGGGCAGACT
Statistics
Matches: 514, Mismatches: 40, Indels: 33
0.88 0.07 0.06
Matches are distributed among these distances:
157 2 0.00
158 35 0.07
159 3 0.01
161 41 0.08
162 1 0.00
164 5 0.01
165 420 0.82
166 7 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (164 bp):
GAGTTCTATACTCTCTGAAGGAATAGGGAGCGGACCCGTTTTTGAAGATTGTTCGAGTTCTATAC
TCCCTGAAGGAATAGAGAGCGGACCCATTTTATGAAGATTGTTCGAGTTCTATACTCCCTGAACG
GATAGGGAGCGGACCCGTTTATTGAAGATTGTTC
Found at i:194128 original size:48 final size:47
Alignment explanation
Indices: 194054--194145 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 47
194044 GCGGATTCAT
*
194054 TTTATGAAGATTGTTCGAGTTCTATACTCCCTGAACGAATAGGGAGC
1 TTTATGAAGATTGATCGAGTTCTATACTCCCTGAACGAATAGGGAGC
*
194101 TTTATTGAAGATTGATCGAGTAT-TATACTCCCTGAAGGAATAGGG
1 TTTA-TGAAGATTGATCGAGT-TCTATACTCCCTGAACGAATAGGG
194146 GGCAGACTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
47 4 0.10
48 36 0.88
49 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (47 bp):
TTTATGAAGATTGATCGAGTTCTATACTCCCTGAACGAATAGGGAGC
Found at i:196913 original size:31 final size:31
Alignment explanation
Indices: 196887--197059 Score: 285
Period size: 31 Copynumber: 5.6 Consensus size: 31
196877 TCCATAGATT
* *
196887 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
196918 CCGAAGAACATAGGTAAACA-TCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
196948 CCAAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
* * *
196979 CCAAAGAATATAAGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
197010 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
197041 CCGAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
197060 CCTCGACCCT
Statistics
Matches: 133, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
30 29 0.22
31 104 0.78
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:198132 original size:21 final size:21
Alignment explanation
Indices: 198108--198148 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
198098 TGTTGTTCGT
* *
198108 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
198129 TTGAATGGGTACCGATTCCC
1 TTGAAGGGGTACCGATTCCC
198149 TTTGCCCAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.29, T:0.29
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:205486 original size:145 final size:145
Alignment explanation
Indices: 205218--205497 Score: 411
Period size: 145 Copynumber: 1.9 Consensus size: 145
205208 GTGCTCAAGC
* * * * * *
205218 CCTTAAAATTAATTTTTAATAACTTTATTTAGTTATTATTAAATTTTAATTAAATTTGTTATTTC
1 CCTTAAAATTAAATTTTAATAACTGTATCTAGTTATAATTAAATTTTAATTAAAATTATTATTTC
** * * *
205283 AGTCATCAAATGTGTAGCTCCTGAAACAGCCAAGTATTCTTCACCTTTTACCATAGAGGGAGATG
66 AGTCATCAAATCCGTAGCTCCTGAAACAGCAAAGTATTCTTCACCTTTTACCACAGAGGAAGATG
205348 AACATCCCTCGTACT
131 AACATCCCTCGTACT
205363 CCTTAAAATTAAATTTTAATAACTGTATCTAGGTT-TAATTAAATTTTAATTAAAATTATTATTT
1 CCTTAAAATTAAATTTTAATAACTGTATCTA-GTTATAATTAAATTTTAATTAAAATTATTATTT
* *
205427 CAGTCATCAAATCCGTAGCTCCTGAAAC-GGAAGAGTATTCTTCACCTTTTGCCACAGAGGAAGA
65 CAGTCATCAAATCCGTAGCTCCTGAAACAGCAA-AGTATTCTTCACCTTTTACCACAGAGGAAGA
205491 TGAACAT
129 TGAACAT
205498 TCATCATTCT
Statistics
Matches: 120, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
144 2 0.02
145 115 0.96
146 3 0.03
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (145 bp):
CCTTAAAATTAAATTTTAATAACTGTATCTAGTTATAATTAAATTTTAATTAAAATTATTATTTC
AGTCATCAAATCCGTAGCTCCTGAAACAGCAAAGTATTCTTCACCTTTTACCACAGAGGAAGATG
AACATCCCTCGTACT
Found at i:206072 original size:145 final size:144
Alignment explanation
Indices: 205799--206084 Score: 441
Period size: 145 Copynumber: 2.0 Consensus size: 144
205789 TGCTCAAAGC
* * * *
205799 CCTTGAAATTAATTTTTATAACTTTATTTAGTTATTATTAAATTTTAATTAAAATTGTTATCTCA
1 CCTTGAAATTAATTTTAATAACTTTATCTAGTTATAATTAAATTTTAATTAAAATTATTATCTCA
* * *
205864 GTCATCAAATGTGTAGCTCCTGAAACAGGCAGGTATTCTTCACCTTTTACCATAGAGGGAGATGA
66 GTCATCAAATCTGTAGCTCCTGAAACAGGAAGGTATTCTTCACCTTTTACCATAGAGGAAGATGA
*
205929 ACATCCCTCATACT
131 ACATCCATCATACT
*
205943 CCTTGAAATTAAATTTTAATAACTTTATCTAGGTT-TAATTAAATTTTAATTAAAATTATTATTT
1 CCTTGAAATT-AATTTTAATAACTTTATCTA-GTTATAATTAAATTTTAATTAAAATTATTATCT
*
206007 CAGTCATCAAATCTGTAGCTCCTGAAAC-GGAAGAGTATTCTTCACCTTTTGCCATAGAGGAAGA
64 CAGTCATCAAATCTGTAGCTCCTGAAACAGGAAG-GTATTCTTCACCTTTTACCATAGAGGAAGA
206071 TGAACATCCATCAT
128 TGAACATCCATCAT
206085 TCTCTCCCTC
Statistics
Matches: 129, Mismatches: 10, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
144 14 0.11
145 112 0.87
146 3 0.02
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (144 bp):
CCTTGAAATTAATTTTAATAACTTTATCTAGTTATAATTAAATTTTAATTAAAATTATTATCTCA
GTCATCAAATCTGTAGCTCCTGAAACAGGAAGGTATTCTTCACCTTTTACCATAGAGGAAGATGA
ACATCCATCATACT
Found at i:208134 original size:27 final size:27
Alignment explanation
Indices: 208099--208155 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
208089 TAGTCTTGAT
208099 TTTCATTATTATAAAC-CGTGCTACTGA
1 TTTCATTATTATAAACTC-TGCTACTGA
208126 TTTCATTATTATAAACTCTGCTACTGA
1 TTTCATTATTATAAACTCTGCTACTGA
208153 TTT
1 TTT
208156 GTTTAGGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 28 0.97
28 1 0.03
ACGTcount: A:0.28, C:0.18, G:0.09, T:0.46
Consensus pattern (27 bp):
TTTCATTATTATAAACTCTGCTACTGA
Found at i:214187 original size:66 final size:66
Alignment explanation
Indices: 214088--214211 Score: 167
Period size: 66 Copynumber: 1.9 Consensus size: 66
214078 ATGGTAATGC
* * *
214088 AGAGCATCCAAATAACGACGAGTCGAATAAAGAACAAAGCACTGAAGAAGAGGGACATCGTCACA
1 AGAGCATCCAAATAACAACGAGTCGAAGAAAGAACAAAGCACTGAAGAAGACGGACATCGTCACA
214153 G
66 G
* * * * * *
214154 AGAGCATCCAAATAATAATGAGTTGAAGGAAGAAGAAAGCCCTGAAGAAGACGGACAT
1 AGAGCATCCAAATAACAACGAGTCGAAGAAAGAACAAAGCACTGAAGAAGACGGACAT
214212 ACTAGAAAGA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 49 1.00
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (66 bp):
AGAGCATCCAAATAACAACGAGTCGAAGAAAGAACAAAGCACTGAAGAAGACGGACATCGTCACA
G
Found at i:214642 original size:11 final size:11
Alignment explanation
Indices: 214626--214692 Score: 66
Period size: 11 Copynumber: 5.9 Consensus size: 11
214616 CAAGGTTTAA
214626 CGTAAAATTAT
1 CGTAAAATTAT
*
214637 CGTAAAAATAAAT
1 CGT-AAAAT-TAT
214650 -GTAAAATTAT
1 CGTAAAATTAT
*
214660 CGTAAAAGTAAAT
1 CGTAAAA-T-TAT
214673 -GTAAAATTAT
1 CGTAAAATTAT
214683 CGTAAAATTA
1 CGTAAAATTA
214693 AATGTTTAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
10 4 0.09
11 24 0.52
12 14 0.30
13 4 0.09
ACGTcount: A:0.52, C:0.06, G:0.10, T:0.31
Consensus pattern (11 bp):
CGTAAAATTAT
Found at i:214653 original size:23 final size:23
Alignment explanation
Indices: 214627--214714 Score: 131
Period size: 23 Copynumber: 3.7 Consensus size: 23
214617 AAGGTTTAAC
214627 GTAAAATTATCGTAAAAATAAAT
1 GTAAAATTATCGTAAAAATAAAT
*
214650 GTAAAATTATCGTAAAAGTAAAT
1 GTAAAATTATCGTAAAAATAAAT
*
214673 GTAAAATTATCGTAAAATTAAAT
1 GTAAAATTATCGTAAAAATAAAT
*
214696 GTTTAAATTATACGTAAAA
1 G-TAAAATTAT-CGTAAAA
214715 TTAACTTTAG
Statistics
Matches: 60, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
23 45 0.75
24 8 0.13
25 7 0.12
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (23 bp):
GTAAAATTATCGTAAAAATAAAT
Found at i:218939 original size:51 final size:51
Alignment explanation
Indices: 218767--219272 Score: 679
Period size: 51 Copynumber: 9.9 Consensus size: 51
218757 TCATAAAATG
* * * * * *
218767 TGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACG
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGAC-T---CAATCTTCAACGAACT
* * * * * *
218822 TGTCTGCTCCCTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAACAAACG
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTC----AATCTTCAACGAACT
* * * ** *
218877 GGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAACG
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
218928 TGTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
218979 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAATT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
219030 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
219081 TGTCCGC-CCCT-TTCCTTCAGAGAGTATAGGA--CAATCTTC-ACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
219127 TGTCCGCT-CCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
219177 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
*
219228 TGTCCGCTCCCTATTCATTC--AGAGTATA-GACTCAATCTTCAACGA
1 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGA
219273 CGAATTGCTT
Statistics
Matches: 421, Mismatches: 20, Indels: 27
0.90 0.04 0.06
Matches are distributed among these distances:
46 17 0.04
47 28 0.07
48 17 0.04
49 36 0.09
50 19 0.05
51 225 0.53
54 1 0.00
55 78 0.19
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (51 bp):
TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
Found at i:219163 original size:198 final size:202
Alignment explanation
Indices: 218767--219272 Score: 684
Period size: 198 Copynumber: 2.5 Consensus size: 202
218757 TCATAAAATG
* * * * * *
218767 TGTCTGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAACAAACGTGTCTGCTCC
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGAC-T---CAATCTTCAACGAACTTGTCCGCTCC
* * *
218832 CTATTCGTTCAGGGAGTATAAGACTCGAATAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTC
62 CTATTCATTCAGAGAGTAT-AGACTC----AATCTTCAACGAACGGGTCCGCTCCCTATTCCTTC
* * *
218897 AGAGAGTATAAGACTCGATCTTCAATAAACGTGTTCGCTCCCTATTCCTTCAGAGAGTATAGGAC
122 AGAGAGTATAAGAC-CAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGAC
218962 TCAATCTTCAACGAACT
186 TCAATCTTCAACGAACT
* *
218979 TGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAATTTGTCCGCTCCCTAT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTAT
* **
219044 TCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGC-CCCT-TTCCTTCAGAGAGTA
66 TCATTCAGAGAGTATA-GACTCAATCTTCAACGAACGGGTCCGCTCCCTATTCCTTCAGAGAGTA
* * *
219107 TAGGA-CAATCTTC-ACGAACTTGTCCGCT-CCTATTCCTTCAGAGAGTATAGGACTCAATCTTC
130 TAAGACCAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTC
219169 AACGAACT
195 AACGAACT
219177 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTAT
1 TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTAT
219242 TCATTC--AGAGTATAGACTCAATCTTCAACGA
66 TCATTCAGAGAGTATAGACTCAATCTTCAACGA
219273 CGAATTGCTT
Statistics
Matches: 271, Mismatches: 22, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
195 17 0.06
196 8 0.03
198 110 0.41
199 11 0.04
200 7 0.03
202 19 0.07
203 4 0.01
204 19 0.07
207 1 0.00
208 44 0.16
211 1 0.00
212 30 0.11
ACGTcount: A:0.27, C:0.27, G:0.16, T:0.30
Consensus pattern (202 bp):
TGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCTAT
TCATTCAGAGAGTATAGACTCAATCTTCAACGAACGGGTCCGCTCCCTATTCCTTCAGAGAGTAT
AAGACCAATCTTCAACAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCA
ACGAACT
Found at i:219317 original size:147 final size:145
Alignment explanation
Indices: 218861--219256 Score: 443
Period size: 147 Copynumber: 2.7 Consensus size: 145
218851 AAGACTCGAA
* ** * * * **
218861 TAATCTTCAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAATAAA
1 TAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAA
* * * * * *
218926 CGTGTTCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCCGCTCCCT
66 CTTGTCCGC-CCCT-TTCATTCA-AGAGTATAGGA--CAATCTTC-ACGAAATTGTCCACT-ACT
* **
218991 ATTCCTTCAGAGAGTATAGGAC
124 ACTCCTGAAGAGAGTATAGGAC
* *
219013 TCAATCTTCAACGAATTTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGA
1 T-AATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGA
* * * * *
219078 ACTTGTCCGCCCCTTTCCTTCAGAGAGTATAGGACAATCTTCACGAACTTGTCCGCTCCTATTCC
65 ACTTGTCCGCCCCTTTCATTCA-AGAGTATAGGACAATCTTCACGAAATTGTCCACTACTACTCC
**
219143 TTCAGAGAGTATAGGAC
129 TGAAGAGAGTATAGGAC
219160 TCAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGA
1 T-AATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGA
219225 ACTTGTCCGCTCCCTATTCATTC-AGAGTATAG
65 ACTTGTCCGC-CCCT-TTCATTCAAGAGTATAG
219257 ACTCAATCTT
Statistics
Matches: 228, Mismatches: 13, Indels: 11
0.90 0.05 0.04
Matches are distributed among these distances:
147 107 0.47
148 19 0.08
149 14 0.06
151 20 0.09
152 5 0.02
153 63 0.28
ACGTcount: A:0.26, C:0.28, G:0.16, T:0.30
Consensus pattern (145 bp):
TAATCTTCAACGAACTTGTCCGCTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAA
CTTGTCCGCCCCTTTCATTCAAGAGTATAGGACAATCTTCACGAAATTGTCCACTACTACTCCTG
AAGAGAGTATAGGAC
Found at i:220610 original size:19 final size:19
Alignment explanation
Indices: 220582--220632 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
220572 CCTCCTTTTA
*
220582 TTTC-TTTTTTTTTTCACT
1 TTTCATTTTTTCTTTCACT
220600 TTTCATTTTTTCTTTCACT
1 TTTCATTTTTTCTTTCACT
*
220619 TTCCATTTTTTCTT
1 TTTCATTTTTTCTT
220633 CTTCTTCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 4 0.13
19 26 0.87
ACGTcount: A:0.08, C:0.20, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTCATTTTTTCTTTCACT
Found at i:220717 original size:14 final size:14
Alignment explanation
Indices: 220670--220724 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
220660 TTCCATAATT
*
220670 TTTTCATTTTTTCTC
1 TTTT-ATTTCTTCTC
*
220685 ATTTT-TTTC-TCTT
1 -TTTTATTTCTTCTC
220698 TTTTATTTCTTCTC
1 TTTTATTTCTTCTC
*
220712 TTTTATTTATTCT
1 TTTTATTTCTTCT
220725 TTAAGCAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
12 4 0.12
13 7 0.21
14 18 0.55
16 4 0.12
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (14 bp):
TTTTATTTCTTCTC
Found at i:230388 original size:41 final size:42
Alignment explanation
Indices: 230285--230406 Score: 158
Period size: 41 Copynumber: 2.9 Consensus size: 42
230275 TTGTTATCCA
* * *
230285 CAAAAAGAATCCTAACCTCATGATATCTA-TTCGCATGCTTATT
1 CAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC-T-TT
230328 CAGAAAATAAACCTAACCGCATGATATCTAGTTCGCATGC-TT
1 CA-AAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTT
*
230370 GAAAAATAAACCTAACCGCATGATATCTAGTTTCGCA
1 CAAAAATAAACCTAACCGCATGATATCTAG-TTCGCA
230407 ATTTATTCGA
Statistics
Matches: 72, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
41 28 0.39
42 9 0.12
43 2 0.03
44 24 0.33
45 9 0.12
ACGTcount: A:0.37, C:0.23, G:0.12, T:0.28
Consensus pattern (42 bp):
CAAAAATAAACCTAACCGCATGATATCTAGTTCGCATGCTTT
Found at i:235734 original size:3 final size:3
Alignment explanation
Indices: 235728--235763 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
235718 ACATTATTAT
235728 TAA TAA TAA -AA T-A TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
235764 TCCGGACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:246006 original size:2 final size:2
Alignment explanation
Indices: 245988--246038 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
245978 TATTACTATT
* *
245988 TA TA CA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
246030 TA TA TA TA T
1 TA TA TA TA T
246039 CACTCCCTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:247593 original size:64 final size:64
Alignment explanation
Indices: 247509--247661 Score: 161
Period size: 64 Copynumber: 2.4 Consensus size: 64
247499 AGGTGTATCT
* * ** * *
247509 ATGCACAGGTAGTGCATCGATGCA-CTCTTTTAA-AATAAAAAGATCGAATGCA-ATTAGTGCAT
1 ATGCACAAGCAGTGCATCGATGCATC-CCATTAATAAT-AAAACATCGAATGCATATTA-TGCAC
247571 CG
63 CG
* *
247573 ATGCATAAGGCA-TGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATTTTATGCACCG
1 ATGCACAA-GCAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGCACCG
*
247637 ATGCACAAGTAGTGCATCGATGCAT
1 ATGCACAAGCAGTGCATCGATGCAT
247662 ACCTCCATTA
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
63 2 0.03
64 63 0.85
65 9 0.12
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (64 bp):
ATGCACAAGCAGTGCATCGATGCATCCCATTAATAATAAAACATCGAATGCATATTATGCACCG
Found at i:247961 original size:29 final size:29
Alignment explanation
Indices: 247922--248031 Score: 195
Period size: 29 Copynumber: 3.8 Consensus size: 29
247912 TATGTGATAT
247922 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
247952 GAGAAATGACATGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
247981 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
248010 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
248032 ACATATAAAA
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
28 7 0.09
29 66 0.85
30 5 0.06
ACGTcount: A:0.45, C:0.16, G:0.21, T:0.17
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:254452 original size:106 final size:106
Alignment explanation
Indices: 254327--254537 Score: 278
Period size: 106 Copynumber: 2.0 Consensus size: 106
254317 GACCACATAT
* * *
254327 AAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCTCAAAAGACCTCATACAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
*
254392 GCTCCAAATAATACATATACGTCCCGAAGGACCACGTAGAA
66 GCTCCAAAGAATACATATACGTCCCGAAGGACCACGTAGAA
* * * * * *
254433 AAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATACGTGTCGCAAAGGACCTCATAGAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
* * * * * *
254498 GTTCCATAGGATACCTATATGTCCCGAAGGACCGCGTAGA
66 GCTCCAAAGAATACATATACGTCCCGAAGGACCACGTAGA
254538 CCTTCGACTC
Statistics
Matches: 89, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
106 89 1.00
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (106 bp):
AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
GCTCCAAAGAATACATATACGTCCCGAAGGACCACGTAGAA
Found at i:258632 original size:31 final size:31
Alignment explanation
Indices: 258594--258687 Score: 136
Period size: 31 Copynumber: 3.0 Consensus size: 31
258584 CCCGAAGGAC
* * *
258594 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATACG-TCCCGAAGAACATAGGTAAA
258625 CAGTCCATACGTCCCGAAGAACATAGGTAAA
1 CAGTCCATACGTCCCGAAGAACATAGGTAAA
*
258656 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATACGTCCCGAAGAACATAGGTAAA
258687 C
1 C
258688 CCTCGACCCT
Statistics
Matches: 58, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 57 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATACGTCCCGAAGAACATAGGTAAA
Found at i:259389 original size:21 final size:21
Alignment explanation
Indices: 259365--259409 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
259355 TTTTGTTCGT
* *
259365 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
259386 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
259407 TTG
1 TTG
259410 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:262683 original size:31 final size:31
Alignment explanation
Indices: 262560--262684 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
262550 CTCGAAGGAC
* * *
262560 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
262591 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
262622 TAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
262653 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
262684 C
1 C
262685 CCTCGACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 87 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:263405 original size:21 final size:21
Alignment explanation
Indices: 263362--263406 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
263352 TTTTTTTCGT
* *
263362 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
* *
263383 TTGAATGGGTACCGATTCTCC
1 TTGAAGGGGTACCGATTCCCC
263404 TTG
1 TTG
263407 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:265981 original size:106 final size:105
Alignment explanation
Indices: 265786--265995 Score: 267
Period size: 106 Copynumber: 2.0 Consensus size: 105
265776 GACCACATAT
* * *
265786 AAATTCCTTAAGAACCATATACATATACCAAGGATCAAGTAAGTGTCTCAAAAGACCTCATACAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
265851 GCTCCAAAGAATACATATACGTCCCAAAGGACCACGTAGAA
66 GCTCCAAAGAATACATATACGTCCCAAA-GACCACGTAGAA
* * * * * *
265892 AAATTCCTTAAGAATCATATACATATGCTAAGGACCAAATACGTGTCGCAAAGGACCTCATAGAT
1 AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
* * * * * * *
265957 GTTCCATAGGATACCTATATGTCCCGAAGACCGCGTAGA
66 GCTCCAAAGAATACATATACGTCCCAAAGACCACGTAGA
265996 CCCTCGACTC
Statistics
Matches: 88, Mismatches: 16, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
105 10 0.11
106 78 0.89
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (105 bp):
AAATTCCTTAAGAACCATATACATATACCAAGGACCAAATAAGTGTCGCAAAAGACCTCATACAT
GCTCCAAAGAATACATATACGTCCCAAAGACCACGTAGAA
Found at i:269112 original size:45 final size:46
Alignment explanation
Indices: 269026--269131 Score: 121
Period size: 45 Copynumber: 2.3 Consensus size: 46
269016 GATGCACAGG
* *
269026 TAGTGCATCGATGCACTCTTTTAAAATAAAAAGATCAAATGCA-AT
1 TAGTGCATCGATGCACTCTATTAAAATAAAAACATCAAATGCATAT
* *
269071 TAGTGCATCGATGCA-TCTCATTAATAAT-AAAACATCGAATGCATTT
1 TAGTGCATCGATGCACTCT-ATTAA-AATAAAAACATCAAATGCATAT
*
269117 TA-TGCACCGATGCAC
1 TAGTGCATCGATGCAC
269132 AAGTAGTGCA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
44 3 0.06
45 43 0.83
46 6 0.12
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (46 bp):
TAGTGCATCGATGCACTCTATTAAAATAAAAACATCAAATGCATAT
Found at i:269568 original size:29 final size:29
Alignment explanation
Indices: 269529--269638 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
269519 TATGTGAAAT
269529 GAGAACATGACATGAGCTACATGATCACAA
1 GAGAA-ATGACATGAGCTACATGATCACAA
*
269559 GAGAAATGACACGAGCTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
*
269588 GAGAAATGACATGAACTACATGATCACAA
1 GAGAAATGACATGAGCTACATGATCACAA
269617 GAGAAATGACATGAG-TACATGA
1 GAGAAATGACATGAGCTACATGA
269639 ACATATAAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
28 7 0.09
29 64 0.84
30 5 0.07
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.16
Consensus pattern (29 bp):
GAGAAATGACATGAGCTACATGATCACAA
Found at i:269741 original size:15 final size:15
Alignment explanation
Indices: 269723--269756 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
269713 AAGGGTATAA
*
269723 TAGTCCTTTGGGATG
1 TAGTCCTTCGGGATG
269738 TAGTCCTTCGGGATG
1 TAGTCCTTCGGGATG
269753 TAGT
1 TAGT
269757 GGTCCTACTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.15, C:0.15, G:0.32, T:0.38
Consensus pattern (15 bp):
TAGTCCTTCGGGATG
Found at i:270637 original size:26 final size:25
Alignment explanation
Indices: 270603--270651 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
270593 CTGAGGGAAA
270603 TATTAAAA-TTATTAAATAATTTTAAT
1 TATTAAAATTTATT-AAT-ATTTTAAT
*
270629 TATTCAAATTTATTAATATTTTA
1 TATTAAAATTTATTAATATTTTA
270652 TTAAATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 6 0.29
26 10 0.48
27 5 0.24
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (25 bp):
TATTAAAATTTATTAATATTTTAAT
Found at i:271751 original size:17 final size:17
Alignment explanation
Indices: 271729--271785 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 17
271719 TAAGGATTTC
*
271729 TTTTAAAAAAATTAATT
1 TTTTAAAAAAATTAATA
**
271746 TTTTAAGGAAATTAATA
1 TTTTAAAAAAATTAATA
271763 TTTT--AAAAA-TAATA
1 TTTTAAAAAAATTAATA
271777 TTTTAAAAA
1 TTTTAAAAA
271786 TATTTTTCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
14 9 0.27
15 3 0.09
16 3 0.09
17 18 0.55
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (17 bp):
TTTTAAAAAAATTAATA
Found at i:271787 original size:14 final size:15
Alignment explanation
Indices: 271735--271786 Score: 70
Period size: 14 Copynumber: 3.4 Consensus size: 15
271725 TTTCTTTTAA
*
271735 AAAAATTAATTTTTT
1 AAAAATTAATATTTT
271750 AAGGAAATTAATATTTT
1 AA--AAATTAATATTTT
271767 AAAAA-TAATATTTT
1 AAAAATTAATATTTT
271781 AAAAAT
1 AAAAAT
271787 ATTTTTCAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 14 0.42
15 5 0.15
17 14 0.42
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (15 bp):
AAAAATTAATATTTT
Found at i:276448 original size:15 final size:15
Alignment explanation
Indices: 276428--276466 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
276418 ATTTGGGAAA
276428 AACCGGTTTTTTTTT
1 AACCGGTTTTTTTTT
276443 AACCGGTTTTTTTTT
1 AACCGGTTTTTTTTT
276458 AACCGGTTT
1 AACCGGTTT
276467 GGAGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (15 bp):
AACCGGTTTTTTTTT
Found at i:278870 original size:21 final size:21
Alignment explanation
Indices: 278846--278885 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
278836 TTTATTTTAT
278846 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
278867 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
278886 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:278933 original size:33 final size:33
Alignment explanation
Indices: 278880--278978 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
278870 TTTGTTTCAA
278880 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
278912 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
278945 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
278978 T
1 T
278979 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:279007 original size:13 final size:13
Alignment explanation
Indices: 278964--279018 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
278954 TTGGAAGTAT
278964 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
278977 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
278991 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
279004 TTAAGTATTTGAA
1 TTAAGTATTTCAA
279017 TT
1 TT
279019 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:279240 original size:21 final size:21
Alignment explanation
Indices: 279214--279270 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
279204 AGGAGCTTGG
*
279214 GGGAATCGGTACCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
*
279235 GGGAATCGGTTTCCTCTCATA
1 GGGAATCGGTTCCCTCTCATA
279256 GGGAATCGGTTCCCT
1 GGGAATCGGTTCCCT
279271 AAGTGTAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (21 bp):
GGGAATCGGTTCCCTCTCATA
Found at i:279489 original size:15 final size:15
Alignment explanation
Indices: 279437--279492 Score: 58
Period size: 15 Copynumber: 3.6 Consensus size: 15
279427 ATCTGGAATA
*
279437 TTAAAATCGGTTTTT
1 TTAAAACCGGTTTTT
* *
279452 TTATAATCGGTTTTT
1 TTAAAACCGGTTTTT
*
279467 TAAAAAAACCGGTTTTT
1 T--TAAAACCGGTTTTT
279484 TTAAAACCG
1 TTAAAACCG
279493 AAACCGGTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 22 0.65
17 12 0.35
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:287263 original size:130 final size:130
Alignment explanation
Indices: 287076--287341 Score: 514
Period size: 130 Copynumber: 2.0 Consensus size: 130
287066 ATATGTCAAG
287076 AATTAGAAAGATAAAGCCTTAGCAACCTGTCTGGAGCAGATCTTTAAGATGTTCCTTTCAGATGG
1 AATTAGAAAGATAAAGCCTTAGCAACCTGTCTGGAGCAGATCTTTAAGATGTTCCTTTCAGATGG
287141 AAAAATCAGGCAAAAAGACAAAATGATAAATGAGCAGCTTAGGGGATCAATAAAGGTTCATTTAT
66 AAAAATCAGGCAAAAAGACAAAATGATAAATGAGCAGCTTAGGGGATCAATAAAGGTTCATTTAT
287206 AATTAGAAAGATAAAGCCTTAGCAACCTGTCTGGAGCAGATCTTTAAGATGTTCCTTTCAGATGG
1 AATTAGAAAGATAAAGCCTTAGCAACCTGTCTGGAGCAGATCTTTAAGATGTTCCTTTCAGATGG
* *
287271 AAAAATCAGGCAAAAAGACAAAATGATAAATGAGCAGCTTAGGGTATCAATAAAGGTTGATTTAT
66 AAAAATCAGGCAAAAAGACAAAATGATAAATGAGCAGCTTAGGGGATCAATAAAGGTTCATTTAT
287336 AATTAG
1 AATTAG
287342 GGTAATTCTT
Statistics
Matches: 134, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
130 134 1.00
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (130 bp):
AATTAGAAAGATAAAGCCTTAGCAACCTGTCTGGAGCAGATCTTTAAGATGTTCCTTTCAGATGG
AAAAATCAGGCAAAAAGACAAAATGATAAATGAGCAGCTTAGGGGATCAATAAAGGTTCATTTAT
Found at i:290842 original size:28 final size:29
Alignment explanation
Indices: 290801--290855 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
290791 TATAAACTTA
*
290801 ATTTATATTATTTAATT-TAATTATTTTTC
1 ATTTATATTATTTAGTTAT-ATTATTTTTC
290830 ATTT-TATTATTTAGTTATATTATTTT
1 ATTTATATTATTTAGTTATATTATTTT
290856 ATGTAGCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (29 bp):
ATTTATATTATTTAGTTATATTATTTTTC
Found at i:298855 original size:42 final size:42
Alignment explanation
Indices: 298798--298891 Score: 154
Period size: 43 Copynumber: 2.2 Consensus size: 42
298788 AAAATTTCAA
*
298798 ATTATCAGAGTCGGCTCTTAGG-GGGATATTTTATTTCAAATT
1 ATTATCAG-GTCGGCTCTTAGGAGGAATATTTTATTTCAAATT
298840 ATTATCAGGTCCGGCTCTTAGGAGGAATATTTTATTTCAAATT
1 ATTATCAGGT-CGGCTCTTAGGAGGAATATTTTATTTCAAATT
298883 ATTATCAGG
1 ATTATCAGG
298892 GCCACCTCGT
Statistics
Matches: 49, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
41 2 0.04
42 19 0.39
43 28 0.57
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (42 bp):
ATTATCAGGTCGGCTCTTAGGAGGAATATTTTATTTCAAATT
Found at i:303813 original size:18 final size:19
Alignment explanation
Indices: 303782--303818 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
303772 TTTGCCAAAA
*
303782 AAATACCTAAAATATTATT
1 AAATACCTAAAATAATATT
303801 AAATACC-AAAATAATATT
1 AAATACCTAAAATAATATT
303819 CTTTTGTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATACCTAAAATAATATT
Found at i:316169 original size:6 final size:6
Alignment explanation
Indices: 316158--316185 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
316148 AGACACGTAT
316158 GACCAC GACCAC GACCAC GACCAC GACC
1 GACCAC GACCAC GACCAC GACCAC GACC
316186 CGAGACGGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.32, C:0.50, G:0.18, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:316867 original size:21 final size:21
Alignment explanation
Indices: 316824--316867 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
316814 ACAACTGTAG
** *
316824 ACTATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
316845 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
316866 AC
1 AC
316868 GCGAATTTGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Done.