Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008136.1 Hibiscus syriacus cultivar Beakdansim tig00110691_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: 1585607
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 9
Found at i:948384 original size:2 final size:2
Alignment explanation
Indices: 948377--948410 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
948367 TAGTTTTTGA
948377 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
948411 GTTTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:948454 original size:37 final size:40
Alignment explanation
Indices: 948343--948538 Score: 153
Period size: 37 Copynumber: 5.0 Consensus size: 40
948333 CCGAGGCTTA
* * *
948343 TTTAG-TATATATAT-TAATTTAGTATAGTTTTTGAATATA-
1 TTTAGATATATATATAT-ATATA-TATAGTTTTTGAAAACAT
* * *
948382 TATATATATATATATATATATAATATA-TAGTTTTTTAAAACAT
1 TTTAGATATATATATATATAT-ATATAGT--TTTT-GAAAACAT
948425 TTTAGATATATATATATATA-ATAT-GTTTTTGAAAACAT
1 TTTAGATATATATATATATATATATAGTTTTTGAAAACAT
* * * *
948463 TTT-GAAAGCATATATATA-ATATATAGTGTTTGAAAATAT
1 TTTAGATA-TATATATATATATATATAGTTTTTGAAAACAT
*
948502 TTT-GA-AAATATATATA-ATATATAGTTTTTGAAAACAT
1 TTTAGATATATATATATATATATATAGTTTTTGAAAACAT
948539 ATATATAATA
Statistics
Matches: 130, Mismatches: 16, Indels: 24
0.76 0.09 0.14
Matches are distributed among these distances:
37 32 0.25
38 24 0.18
39 25 0.19
40 16 0.12
41 11 0.08
42 4 0.03
43 18 0.14
ACGTcount: A:0.43, C:0.02, G:0.08, T:0.47
Consensus pattern (40 bp):
TTTAGATATATATATATATATATATAGTTTTTGAAAACAT
Found at i:948504 original size:39 final size:38
Alignment explanation
Indices: 948395--948743 Score: 229
Period size: 39 Copynumber: 9.6 Consensus size: 38
948385 ATATATATAT
*
948395 ATATATATAATATATAGTTTTTTAAAACATTTT---AG
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAG
948430 ATATATATATATATAATATGTTTTTGAAAACATTTTGAAAG
1 ATATATATA-ATAT-ATA-GTTTTTGAAAACATTTTGAAAG
* *
948471 CATATATATAATATATAGTGTTTGAAAATATTTTGAAA-
1 -ATATATATAATATATAGTTTTTGAAAACATTTTGAAAG
948509 ATATATATAATATATAGTTTTTGAAAAC----------
1 ATATATATAATATATAGTTTTTGAAAACATTTTGAAAG
*
948537 ATATATATAATAAATAG-TTTTGAAAACATTTTTTTG-AAG
1 ATATATATAATATATAGTTTTTGAAAACA---TTTTGAAAG
* **
948576 ATACATATATATTATATAG-TTTTGAAAACGATTTTTTAA-
1 AT--ATATATAATATATAGTTTTTGAAAAC-ATTTTGAAAG
948615 A-ATATAT--TATATAG-TTTTGAAAACGATTTTTG-AA-
1 ATATATATAATATATAGTTTTTGAAAAC-A-TTTTGAAAG
948649 A-ATATAT--TATATAG-TTTTGAAAATCAATTTTTGAAA-
1 ATATATATAATATATAGTTTTTGAAAA-C-A-TTTTGAAAG
* * *
948685 ACATATATATTATATAG-TTTTGAAAATAATTTTTGAAA-
1 ATATATATAATATATAGTTTTTGAAAA-CA-TTTTGAAAG
*
948723 ATATATATATTATATAGTTTT
1 ATATATATAATATATAGTTTT
948744 AAAAATGATT
Statistics
Matches: 271, Mismatches: 13, Indels: 56
0.80 0.04 0.16
Matches are distributed among these distances:
27 10 0.04
28 16 0.06
34 44 0.16
35 21 0.08
36 13 0.05
37 35 0.13
38 42 0.15
39 46 0.17
40 5 0.02
41 29 0.11
42 10 0.04
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (38 bp):
ATATATATAATATATAGTTTTTGAAAACATTTTGAAAG
Found at i:948504 original size:77 final size:76
Alignment explanation
Indices: 948395--948743 Score: 243
Period size: 77 Copynumber: 4.8 Consensus size: 76
948385 ATATATATAT
* * *
948395 ATATATATAATATATAGTTTTTTAAAACATTTT--AGATATATATATATATAATATGTTTTTGAA
1 ATATATATAATATATAGTGTTTGAAAACATTTTGAAAATATATATA-ATAT-ATA-GTTTTTGAA
948458 AACATTTTGAAAGC
63 AACATTTTGAAAGC
*
948472 ATATATATAATATATAGTGTTTGAAAATATTTTGAAAATATATATAATATATAGTTTTTG-----
1 ATATATATAATATATAGTGTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
948532 A-----AAA-C
66 ATTTTGAAAGC
* * *
948537 ATATATATAATAAATAGT-TTTGAAAACATTTTTTTGAAGATACATATATATTATATAG-TTTTG
1 ATATATATAATATATAGTGTTTGAAAACA---TTTTGAA-A-ATATATATAATATATAGTTTTTG
**
948600 AAAACGATTTTTTAA--
61 AAAAC-ATTTTGAAAGC
948615 A-ATATAT--TATATAGT-TTTGAAAACGATTTTTG-AAA-ATATAT--TATATAG-TTTTGAAA
1 ATATATATAATATATAGTGTTTGAAAAC-A-TTTTGAAAATATATATAATATATAGTTTTTGAAA
*
948671 ATCAATTTTTGAAAAC
64 A-C-A-TTTTGAAAGC
* *
948687 ATATATAT--TATATAGT-TTTGAAAATAATTTTTGAAAATATATATATTATATAGTTTT
1 ATATATATAATATATAGTGTTTGAAAA-CA-TTTTGAAAATATATATAATATATAGTTTT
948744 AAAAATGATT
Statistics
Matches: 228, Mismatches: 14, Indels: 59
0.76 0.05 0.20
Matches are distributed among these distances:
64 9 0.04
65 18 0.08
66 3 0.01
67 7 0.03
68 22 0.10
69 17 0.07
70 12 0.05
71 2 0.01
72 2 0.01
73 30 0.13
74 10 0.04
75 22 0.10
76 8 0.04
77 46 0.20
78 8 0.04
79 12 0.05
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (76 bp):
ATATATATAATATATAGTGTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTTGAAAAC
ATTTTGAAAGC
Found at i:948540 original size:28 final size:27
Alignment explanation
Indices: 948496--948565 Score: 101
Period size: 28 Copynumber: 2.7 Consensus size: 27
948486 TAGTGTTTGA
948496 AAATA-TTTTG-AAA-ATATATATAAT
1 AAATAGTTTTGAAAACATATATATAAT
*
948520 ATATAGTTTTTGAAAACATATATATAAT
1 AAATAG-TTTTGAAAACATATATATAAT
948548 AAATAGTTTTGAAAACAT
1 AAATAGTTTTGAAAACAT
948566 TTTTTTGAAG
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
24 4 0.10
26 5 0.12
27 15 0.38
28 16 0.40
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (27 bp):
AAATAGTTTTGAAAACATATATATAAT
Found at i:948625 original size:34 final size:36
Alignment explanation
Indices: 948533--948756 Score: 215
Period size: 34 Copynumber: 6.0 Consensus size: 36
948523 TAGTTTTTGA
*
948533 AAACATATATATAATAAATAGTTTTGAAAAC-ATTTTTTT
1 AAACATATATAT--TATATAGTTTTGAAAACGA--TTTTT
948572 GAAGATACATATATATTATATAGTTTTGAAAACGATTTTT
1 --A-A-ACATATATATTATATAGTTTTGAAAACGATTTTT
*
948612 TAA-A-ATATATTATATAGTTTTGAAAACGATTTTT
1 AAACATATATATTATATAGTTTTGAAAACGATTTTT
* *
948646 GAA-A-ATATATTATATAGTTTTGAAAATCAATTTTT
1 AAACATATATATTATATAGTTTTGAAAA-CGATTTTT
**
948681 GAAAACATATATATTATATAGTTTTGAAAATAATTTTT
1 --AAACATATATATTATATAGTTTTGAAAACGATTTTT
* * *
948719 GAAAATATATATATTATATAGTTTTAAAAATGATTTTT
1 --AAACATATATATTATATAGTTTTGAAAACGATTTTT
948757 TTTAAAACAT
Statistics
Matches: 166, Mismatches: 9, Indels: 19
0.86 0.05 0.10
Matches are distributed among these distances:
34 55 0.33
35 8 0.05
36 1 0.01
37 3 0.02
38 43 0.26
39 22 0.13
40 5 0.03
41 17 0.10
42 2 0.01
43 10 0.06
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (36 bp):
AAACATATATATTATATAGTTTTGAAAACGATTTTT
Found at i:948680 original size:109 final size:110
Alignment explanation
Indices: 948541--948756 Score: 296
Period size: 107 Copynumber: 2.0 Consensus size: 110
948531 GAAAACATAT
* *
948541 ATATAATAAATAGTTTTGAAAACATTTTTTTGAAGATACATATATATTATATAGTTTTGAAAACG
1 ATATAATAAATAGTTTTGAAAACATATTTTTGAA-A-ACATATATATTATATAGTTTTGAAAACA
* *
948606 ATTTTT-TAA-A-ATATATTATATAGTTTTGAAAACGATTTTTGAAA
64 ATTTTTAAAATATATATATTATATAGTTTTAAAAACGATTTTTGAAA
* * *
948650 ATATATTATATAGTTTTGAAAATCA-ATTTTTGAAAACATATATATTATATAGTTTTGAAAATAA
1 ATATAATAAATAGTTTTGAAAA-CATATTTTTGAAAACATATATATTATATAGTTTTGAAAACAA
*
948714 TTTTTGAAAATATATATATTATATAGTTTTAAAAATGATTTTT
65 TTTTT-AAAATATATATATTATATAGTTTTAAAAACGATTTTT
948757 TTTAAAACAT
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
107 32 0.34
108 1 0.01
109 30 0.32
110 3 0.03
111 28 0.30
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (110 bp):
ATATAATAAATAGTTTTGAAAACATATTTTTGAAAACATATATATTATATAGTTTTGAAAACAAT
TTTTAAAATATATATATTATATAGTTTTAAAAACGATTTTTGAAA
Found at i:948771 original size:15 final size:16
Alignment explanation
Indices: 948740--948773 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
948730 TATTATATAG
948740 TTTTAAAAATGATTTT
1 TTTTAAAAATGATTTT
948756 TTTTAAAACAT-ATTTT
1 TTTTAAAA-ATGATTTT
948772 TT
1 TT
948774 AATTTTAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.88
17 2 0.12
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTTAAAAATGATTTT
Found at i:953742 original size:2 final size:2
Alignment explanation
Indices: 953735--953767 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
953725 AAAAGAGTGT
953735 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 T
953768 TAATATTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:963778 original size:13 final size:13
Alignment explanation
Indices: 963760--963788 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
963750 ACTTTCATCT
963760 TCAGAAATGAAGA
1 TCAGAAATGAAGA
963773 TCAGAAATGAAGA
1 TCAGAAATGAAGA
963786 TCA
1 TCA
963789 ACAGATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.52, C:0.10, G:0.21, T:0.17
Consensus pattern (13 bp):
TCAGAAATGAAGA
Found at i:964432 original size:22 final size:23
Alignment explanation
Indices: 964404--964448 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
964394 GACCTCAAAG
964404 AATGTGAAT-AATTTTATTTATA
1 AATGTGAATGAATTTTATTTATA
964426 AATGTGAATGAATTTTATTTATA
1 AATGTGAATGAATTTTATTTATA
964449 TTTGTAATCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (23 bp):
AATGTGAATGAATTTTATTTATA
Found at i:966822 original size:2 final size:2
Alignment explanation
Indices: 966815--966839 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
966805 TTTTGATGAC
966815 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 T
966840 TATTTCTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:966988 original size:14 final size:14
Alignment explanation
Indices: 966969--966995 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
966959 TTATTTATTA
966969 TTTTTTTCTTTTTC
1 TTTTTTTCTTTTTC
966983 TTTTTTTCTTTTT
1 TTTTTTTCTTTTT
966996 ATTCCTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (14 bp):
TTTTTTTCTTTTTC
Found at i:967007 original size:49 final size:48
Alignment explanation
Indices: 966909--967074 Score: 131
Period size: 49 Copynumber: 3.3 Consensus size: 48
966899 TATTTTAATT
* ** * * *
966909 TTTATTTTTATTTTATTTTCTTTATCTTCGTTTC-ATTTATTCATATTTA
1 TTTATTTTTA-TTT-TTTTCTTTTTCTTTTTTTCTTTTTATTCCTTTTTA
966958 TTTATTTATTATTTTTTTCTTTTTCTTTTTTTCTTTTTATTCCTTTTTA
1 TTTATTT-TTATTTTTTTCTTTTTCTTTTTTTCTTTTTATTCCTTTTTA
* * * *
967007 TTT-TCTTTATCTTTTTC-TCTTCATGTTATTTTCTTTGTTTTTCTCTATTTTA
1 TTTATTTTTATTTTTTTCTTTTTC-T-TT-TTTTCTTT-TTATTC-CT-TTTTA
*
967059 TTTATTTTCATTTTTT
1 TTTATTTTTATTTTTT
967075 CTCTAACACG
Statistics
Matches: 95, Mismatches: 13, Indels: 14
0.78 0.11 0.11
Matches are distributed among these distances:
46 4 0.04
47 11 0.12
48 20 0.21
49 33 0.35
50 8 0.08
51 2 0.02
52 8 0.08
53 9 0.09
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (48 bp):
TTTATTTTTATTTTTTTCTTTTTCTTTTTTTCTTTTTATTCCTTTTTA
Found at i:972448 original size:83 final size:83
Alignment explanation
Indices: 972307--972492 Score: 239
Period size: 83 Copynumber: 2.2 Consensus size: 83
972297 TTTTTTCCCT
* * * *
972307 ATTTGCAGCATAGCTCAAGGAAAGAAGGACTATCTGCCAATAAAGACTTTCGAGTTTGATTACAC
1 ATTTGCAGCATAGCTCAAGGAAAGAAGGACTATATGCCAACAAAGACCTTCGACTTTGATTACAC
* *
972372 TCAGCTCAAAGGTACATC
66 TCAACTCAAAGGCACATC
* ** *
972390 ATTTGCAGTATAGCTCAAGGTAAA-AAGGGTTATATGCTAACAAAGACCTTCGACTTTGATTACA
1 ATTTGCAGCATAGCTCAAGG-AAAGAAGGACTATATGCCAACAAAGACCTTCGACTTTGATTACA
972454 CTCAACTCAAAGGCACATC
65 CTCAACTCAAAGGCACATC
* * *
972473 ATTTACAACATAACTCAAGG
1 ATTTGCAGCATAGCTCAAGG
972493 CTATAATGGT
Statistics
Matches: 88, Mismatches: 14, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
83 85 0.97
84 3 0.03
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (83 bp):
ATTTGCAGCATAGCTCAAGGAAAGAAGGACTATATGCCAACAAAGACCTTCGACTTTGATTACAC
TCAACTCAAAGGCACATC
Found at i:972567 original size:60 final size:60
Alignment explanation
Indices: 972449--972567 Score: 166
Period size: 60 Copynumber: 2.0 Consensus size: 60
972439 TCGACTTTGA
* * * *
972449 TTACACTCAACTCAAAGGCACATCATTTACAACATAACTCAAGGCTATAATGGTTATCTG
1 TTACACTCAACTCAAAGGCACATCATTTACAACATAACTCAAGGCAAGAAAGGCTATCTG
* * * *
972509 TTACACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAGGGCAAGAAAGGCTATCT
1 TTACACTCAACTCAAAGGCACATCATTTACAACATAACTCAAGGCAAGAAAGGCTATCT
972568 ACCAACAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.25
Consensus pattern (60 bp):
TTACACTCAACTCAAAGGCACATCATTTACAACATAACTCAAGGCAAGAAAGGCTATCTG
Found at i:972657 original size:84 final size:84
Alignment explanation
Indices: 972509--973235 Score: 919
Period size: 84 Copynumber: 8.7 Consensus size: 84
972499 TGGTTATCTG
* * * *
972509 TTACACTCAGCTCAAAGGCACATCATTTGCAACATAGCTCAGGGCAAGAAAGGCTATCTACCAAC
1 TTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATCTGCCAAC
*
972574 AAAAAACCTTCGAGTTCGA
66 AAAAGACCTTCGAGTTCGA
* ** * * *
972593 TTACACTCAGCTCAAAGGCACACCATTTTTAGCATAGCTCCAGGCAAGAAGGGCTATATGCCAAC
1 TTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATCTGCCAAC
* *
972658 CAAAGACCTTCGAGTTTGA
66 AAAAGACCTTCGAGTTCGA
* ** * *** * *
972677 TTACACTCAGTTCAAAGATACATCATTTGCTGTATAGCTCAAGGTAAGAAGGGTTATCTGCCAAC
1 TTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATCTGCCAAC
*
972742 CAAAGACCTTCGAGTTCGA
66 AAAAGACCTTCGAGTTCGA
* * * * *
972761 TTACACTCAGCTCAAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAAC
1 TTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATCTGCCAAC
*
972826 -AAAGACATTCGAGTTCGA
66 AAAAGACCTTCGAGTTCGA
* *
972844 TTACACTTAGCTCAAAGGTACATCATTTGCAGCATA-ACTAGCTCAAGGCAAGAA-GGCTATCTG
1 TTACACTCAGCTCAAAGGCACATCATTT--A-CA-ACA-TAGCTCAAGGCAAGAAGGGCTATCTG
*
972907 CCAATAAAAGACCTTCGAGTTCGA
61 CCAACAAAAGACCTTCGAGTTCGA
* * * * * **
972931 TTACACTCATCTCAAAGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATTTATCAAC
1 TTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATCTGCCAAC
972996 -AAAGACCTTCGAGTTCGA
66 AAAAGACCTTCGAGTTCGA
* *
973014 TTACACTCAGCTCAAAGGCACATCATTTACAACATATCTCAAGGCAAGAAGGGATATCTGCCAAC
1 TTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATCTGCCAAC
973079 AAAAGACCTTCGAGTTCGA
66 AAAAGACCTTCGAGTTCGA
* * * ** * *
973098 TTACACTAAACTTAAAGGCGTATCATTTGCAACATAACTCAAGGCAAGAAGGGCTATCTGCCAAC
1 TTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATCTGCCAAC
*
973163 AAATGACCTTCGAGTTCGA
66 AAAAGACCTTCGAGTTCGA
973182 TTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAA---AAGAAGGGCTAT
1 TTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTAT
973236 ATGTTAACAA
Statistics
Matches: 554, Mismatches: 80, Indels: 21
0.85 0.12 0.03
Matches are distributed among these distances:
81 12 0.02
83 133 0.24
84 336 0.61
85 2 0.00
86 14 0.03
87 57 0.10
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (84 bp):
TTACACTCAGCTCAAAGGCACATCATTTACAACATAGCTCAAGGCAAGAAGGGCTATCTGCCAAC
AAAAGACCTTCGAGTTCGA
Found at i:973736 original size:2 final size:2
Alignment explanation
Indices: 973729--973753 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
973719 CATATAACAT
973729 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 T
973754 TATCTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:975177 original size:18 final size:17
Alignment explanation
Indices: 975154--975211 Score: 64
Period size: 18 Copynumber: 3.4 Consensus size: 17
975144 ATATATATTA
975154 TTTCTTTACTATTATTTT
1 TTTCTTTA-TATTATTTT
*
975172 TTTC-TTATCTTATTTAT
1 TTTCTTTATATTATTT-T
* *
975189 TTTATTTATTTTATTTT
1 TTTCTTTATATTATTTT
975206 TTTCTT
1 TTTCTT
975212 CTCTTTATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.21
17 13 0.38
18 14 0.41
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTCTTTATATTATTTT
Found at i:975190 original size:4 final size:4
Alignment explanation
Indices: 975176--975288 Score: 70
Period size: 4 Copynumber: 26.5 Consensus size: 4
975166 TATTTTTTTC
* * *
975176 TTAT CTTAT TTATT TTAT TTATT TTAT TTTT TTCT TCTCT TTAT TTAT
1 TTAT -TTAT TTA-T TTAT TTA-T TTAT TTAT TTAT T-TAT TTAT TTAT
* *
975224 TT-T TAGTAT CTT-T ATAT TTGT TTCAT TTAT TCATAT TTAT TTAT TTAT
1 TTAT T--TAT -TTAT TTAT TTAT TT-AT TTAT T--TAT TTAT TTAT TTAT
975272 TTA- TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TT
975289 TTATTTCTAT
Statistics
Matches: 89, Mismatches: 7, Indels: 25
0.74 0.06 0.21
Matches are distributed among these distances:
3 6 0.07
4 56 0.63
5 21 0.24
6 5 0.06
7 1 0.01
ACGTcount: A:0.20, C:0.06, G:0.02, T:0.72
Consensus pattern (4 bp):
TTAT
Found at i:975193 original size:9 final size:9
Alignment explanation
Indices: 975176--975392 Score: 88
Period size: 9 Copynumber: 23.2 Consensus size: 9
975166 TATTTTTTTC
*
975176 TTATCTTAT
1 TTATTTTAT
975185 TTATTTTAT
1 TTATTTTAT
975194 TTATTTTAT
1 TTATTTTAT
*
975203 TT-TTTTCT
1 TTATTTTAT
*
975211 TCT-CTTTAT
1 T-TATTTTAT
975220 TTATTTTTAGT
1 TTA-TTTTA-T
* *
975231 ATCTTTATAT
1 TTATTT-TAT
* *
975241 TTGTTTCAT
1 TTATTTTAT
*
975250 TTATTCATAT
1 TTATT-TTAT
975260 TTA-TTTAT
1 TTATTTTAT
975268 TTATTTATTAT
1 TTA-TT-TTAT
*
975279 TTATTTATTT
1 TTATTT-TAT
975289 TTATTTCTAT
1 TTATTT-TAT
975299 TT-TTCTT-T
1 TTATT-TTAT
975307 TTATTCCTT-T
1 TTATT--TTAT
*
975317 TTATTTTCT
1 TTATTTTAT
*
975326 TTATCTT-T
1 TTATTTTAT
* *
975334 TTCTCTTCAT
1 TTAT-TTTAT
*
975344 GTTATTTTCT
1 -TTATTTTAT
*
975354 TTATTTTCT
1 TTATTTTAT
* *
975363 TTGTTTTCT
1 TTATTTTAT
*
975372 CTATTTTAT
1 TTATTTTAT
975381 TTATTTTCAT
1 TTATTTT-AT
975391 TT
1 TT
975393 TTTCTCTAAC
Statistics
Matches: 161, Mismatches: 29, Indels: 35
0.72 0.13 0.16
Matches are distributed among these distances:
8 22 0.14
9 75 0.47
10 50 0.31
11 14 0.09
ACGTcount: A:0.16, C:0.10, G:0.02, T:0.72
Consensus pattern (9 bp):
TTATTTTAT
Found at i:975240 original size:91 final size:91
Alignment explanation
Indices: 975145--975329 Score: 195
Period size: 91 Copynumber: 2.0 Consensus size: 91
975135 TATATATATA
975145 TATATATTATTTC-TTTACT-ATTATTT-TTT-TCTTATCTTATTTATTTTATTTA-TTTTATTT
1 TATAT-TTATTTCATTTACTCA-TATTTATTTAT-TTAT-TTA-TTA-TTTATTTATTTTTATTT
*
975205 -T-TTTCTTCTCTTTATTTATTTTTAGTATCTT
60 CTATTT-TTCTCTTTATTCATTTTTAGTATCTT
* *
975236 TATATTTGTTTCATTTATTCATATTTATTTATTTATTTATTATTTATTTATTTTTATTTCTATTT
1 TATATTTATTTCATTTACTCATATTTATTTATTTATTTATTATTTATTTATTTTTATTTCTATTT
* * * *
975301 TTCTTTTTATTCCTTTTTATTTTCTT
66 TTCTCTTTATTCATTTTTAGTATCTT
975327 TAT
1 TAT
975330 CTTTTTCTCT
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
89 8 0.10
90 17 0.21
91 43 0.54
92 11 0.14
93 1 0.01
ACGTcount: A:0.19, C:0.08, G:0.01, T:0.72
Consensus pattern (91 bp):
TATATTTATTTCATTTACTCATATTTATTTATTTATTTATTATTTATTTATTTTTATTTCTATTT
TTCTCTTTATTCATTTTTAGTATCTT
Found at i:975261 original size:19 final size:18
Alignment explanation
Indices: 975237--975288 Score: 68
Period size: 19 Copynumber: 2.8 Consensus size: 18
975227 TAGTATCTTT
*
975237 ATATTTGTTTCATTTATTC
1 ATATTTATTT-ATTTATTC
*
975256 ATATTTATTTATTTATTT
1 ATATTTATTTATTTATTC
975274 ATTATTTATTTATTT
1 A-TATTTATTTATTT
975289 TTATTTCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 8 0.27
19 22 0.73
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.69
Consensus pattern (18 bp):
ATATTTATTTATTTATTC
Found at i:975280 original size:15 final size:14
Alignment explanation
Indices: 975165--975294 Score: 72
Period size: 14 Copynumber: 8.9 Consensus size: 14
975155 TTCTTTACTA
*
975165 TTATTTTTTTCTTAT
1 TTATTTTTAT-TTAT
*
975180 CTTATTTAT-TTTAT
1 -TTATTTTTATTTAT
975194 TTA-TTTTATTT-T
1 TTATTTTTATTTAT
* *
975206 TT-TCTTCTCTTTAT
1 TTAT-TTTTATTTAT
975220 TTATTTTTAGTATCT-T
1 TTATTTTTA-T-T-TAT
975236 TATATTTGTTTCATTTAT
1 T-TA-TT-TTT-ATTTAT
* *
975254 TCATATTTATTTAT
1 TTATTTTTATTTAT
975268 TTATTTATTATTTAT
1 TTATTT-TTATTTAT
975283 TTATTTTTATTT
1 TTATTTTTATTT
975295 CTATTTTTCT
Statistics
Matches: 90, Mismatches: 10, Indels: 30
0.69 0.08 0.23
Matches are distributed among these distances:
12 6 0.07
13 12 0.13
14 26 0.29
15 20 0.22
16 11 0.12
17 5 0.06
18 5 0.06
19 4 0.04
20 1 0.01
ACGTcount: A:0.19, C:0.06, G:0.02, T:0.73
Consensus pattern (14 bp):
TTATTTTTATTTAT
Found at i:975384 original size:27 final size:26
Alignment explanation
Indices: 975346--975400 Score: 83
Period size: 27 Copynumber: 2.1 Consensus size: 26
975336 CTCTTCATGT
* *
975346 TATTTTCTTTATTTTCTTTGTTTTCTC
1 TATTTTATTTATTTTCATT-TTTTCTC
975373 TATTTTATTTATTTTCATTTTTTCTC
1 TATTTTATTTATTTTCATTTTTTCTC
975399 TA
1 TA
975401 ACACGTTTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.73
Consensus pattern (26 bp):
TATTTTATTTATTTTCATTTTTTCTC
Found at i:975479 original size:6 final size:6
Alignment explanation
Indices: 975468--975495 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
975458 GAATCGGATT
975468 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTA
975496 CGCAATTAAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:977823 original size:26 final size:26
Alignment explanation
Indices: 977785--977847 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
977775 GCTTTTGTTT
* *
977785 GTGAATTTTGTCAATTTTCATGAATA
1 GTGAATTTCGTCAAATTTCATGAATA
977811 GTGAATTTCGTCAAATTTCATGAATA
1 GTGAATTTCGTCAAATTTCATGAATA
977837 GTGAATTTCGT
1 GTGAATTTCGT
977848 GAATAGTGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (26 bp):
GTGAATTTCGTCAAATTTCATGAATA
Found at i:977845 original size:16 final size:16
Alignment explanation
Indices: 977824--977857 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
977814 AATTTCGTCA
977824 AATTTCATGAATAGTG
1 AATTTCATGAATAGTG
*
977840 AATTTCGTGAATAGTG
1 AATTTCATGAATAGTG
977856 AA
1 AA
977858 ATTTGGTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (16 bp):
AATTTCATGAATAGTG
Found at i:979703 original size:18 final size:18
Alignment explanation
Indices: 979680--979714 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
979670 CACTGAAATT
979680 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
979698 TGTCCCGTAGGACCACT
1 TGTCCCGAAGGACCACT
979715 GTAACCCTCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.34, G:0.23, T:0.20
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:986720 original size:21 final size:20
Alignment explanation
Indices: 986681--986730 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 20
986671 TTTATTATTA
986681 TTATTACATATATTTTTTAT
1 TTATTACATATATTTTTTAT
*
986701 TTATTAC-TATA--TTATAT
1 TTATTACATATATTTTTTAT
*
986718 TTATTATATATAT
1 TTATTACATATAT
986731 ATGTTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 11 0.42
18 4 0.15
19 4 0.15
20 7 0.27
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTACATATATTTTTTAT
Found at i:986868 original size:47 final size:47
Alignment explanation
Indices: 986769--986886 Score: 143
Period size: 47 Copynumber: 2.5 Consensus size: 47
986759 GTGGGTTTGA
* *
986769 TTTGATTAGTTTTAATATGTTGT-GTTGATTATTTTAATAGGTAGTGG
1 TTTGATTA-TTTTAATAGGTAGTGGTTGATTATTTTAATAGGTAGTGG
* *
986816 TTTGATTATTTTAATAGGTAGTGGTTTGATTTTTTTTAATATGTAGT-G
1 TTTGATTATTTTAATAGGTAGTGG-TTGA-TTATTTTAATAGGTAGTGG
*
986864 -TTGATTATTTTATTAGGTAGTGG
1 TTTGATTATTTTAATAGGTAGTGG
986887 GCCAATTATT
Statistics
Matches: 63, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
46 12 0.19
47 31 0.49
48 5 0.08
49 15 0.24
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (47 bp):
TTTGATTATTTTAATAGGTAGTGGTTGATTATTTTAATAGGTAGTGG
Found at i:986874 original size:25 final size:24
Alignment explanation
Indices: 986769--986886 Score: 145
Period size: 24 Copynumber: 5.0 Consensus size: 24
986759 GTGGGTTTGA
* *
986769 TTTGATTAGTTTTAATATGTTGT-G
1 TTTGATTA-TTTTAATAGGTAGTGG
986793 -TTGATTATTTTAATAGGTAGTGG
1 TTTGATTATTTTAATAGGTAGTGG
986816 TTTGATTATTTTAATAGGTAGTGG
1 TTTGATTATTTTAATAGGTAGTGG
* *
986840 TTTGATTTTTTTTAATATGTAGT-G
1 TTTGA-TTATTTTAATAGGTAGTGG
*
986864 -TTGATTATTTTATTAGGTAGTGG
1 TTTGATTATTTTAATAGGTAGTGG
986887 GCCAATTATT
Statistics
Matches: 83, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
22 26 0.31
23 13 0.16
24 29 0.35
25 15 0.18
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (24 bp):
TTTGATTATTTTAATAGGTAGTGG
Found at i:986937 original size:26 final size:26
Alignment explanation
Indices: 986903--986975 Score: 80
Period size: 26 Copynumber: 2.8 Consensus size: 26
986893 TATTTAGTTG
* *
986903 TTTTGTTAATTTCGTTTTTTTCT-TTT
1 TTTTTTTAATTTC-TTTTTTTATATTT
986929 TTTTTTTAATTTCATTTTTTTATATTT
1 TTTTTTTAATTTC-TTTTTTTATATTT
986956 TGTTTTTT--TTTCTTTTTTTA
1 T-TTTTTTAATTTCTTTTTTTA
986976 AATTGTTAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
25 8 0.19
26 24 0.57
27 4 0.10
28 6 0.14
ACGTcount: A:0.11, C:0.05, G:0.04, T:0.79
Consensus pattern (26 bp):
TTTTTTTAATTTCTTTTTTTATATTT
Found at i:986973 original size:40 final size:40
Alignment explanation
Indices: 986903--986979 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
986893 TATTTAGTTG
* *
986903 TTTTGTTAATTTCGTTTTTTTCTTTTTTTTTTTAATTTCA
1 TTTTGTTAATTTCGTTTTTTTCTTCTTTTTTTAAATTTCA
* *
986943 TTTTTTTATATTTTGTTTTTTT-TTCTTTTTTTAAATT
1 TTTTGTTA-ATTTCGTTTTTTTCTTCTTTTTTTAAATT
986980 GTTAAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 20 0.62
41 12 0.38
ACGTcount: A:0.13, C:0.05, G:0.04, T:0.78
Consensus pattern (40 bp):
TTTTGTTAATTTCGTTTTTTTCTTCTTTTTTTAAATTTCA
Found at i:987051 original size:2 final size:2
Alignment explanation
Indices: 987046--987084 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
987036 TTCTTTTTCT
987046 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
987085 GTTTTCAATC
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:998307 original size:106 final size:106
Alignment explanation
Indices: 998122--999511 Score: 2118
Period size: 106 Copynumber: 13.2 Consensus size: 106
998112 AAGTTTTAGC
* * * *
998122 CAGAGTCAATTTCAAATTCACAACGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
998187 ACGAAGGGATCGCTGGTTGTCAATAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
998228 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
998293 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
998334 CAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
998399 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
998440 CAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
998505 ATGAAGGGACCACTGGTTGTCAACAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
998546 CGGAGCCAATTTCAACTTCACAGTGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
998611 ACGAAGAGACCGCTGGTTGTCAACAAACAATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
998652 CGGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * * *
998717 AGGAAGCGACCACTGGTTGTCAACAAACAAATTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
998758 CAGAGCAAATTTCAACTTCACAACGAAAGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
998823 ATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
998864 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
998929 ACGAAGGGACCGCTGGTTGTCAAC-AATAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
998969 CAGAGCCAATCTCAACTTCACAGCGAAGGATATTGGACTCCACACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
999034 ACGAATGGACAGTTGGTTGTCAAC-AACAACCTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
*
999074 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
999139 ATGAAGGGACCACTGGTTGTCAAC-AACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * *
999179 TAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCATACAACGCAAG-T----TTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
999239 ACGAAGGGACCACTGGTTGTCAAC-AACAACTACCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* *
999279 CAGAGCCAATTTCAACTTCACAGTGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
999344 ACGAAGGGACCGCTGGTTGTCAAC-AACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
* * * *
999384 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCAACTTCAC-
1 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * ** * * *
999448 AGTGAAGGGGCGGCTGACTGTCAACAAACAATTTCCCAGTTC
66 A-CGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
** *
999490 CAGATACAATTCCAACTTCACA
1 CAGAGCCAATTTCAACTTCACA
999512 AATGAATTGA
Statistics
Matches: 1186, Mismatches: 91, Indels: 14
0.92 0.07 0.01
Matches are distributed among these distances:
100 92 0.08
101 1 0.00
104 2 0.00
105 377 0.32
106 714 0.60
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (106 bp):
CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTT
Found at i:1000974 original size:37 final size:38
Alignment explanation
Indices: 1000915--1000990 Score: 93
Period size: 37 Copynumber: 2.0 Consensus size: 38
1000905 TATTTATTAT
* *
1000915 TTTTTTATATATTCCGTTTATTAT-TATTATTACATATA
1 TTTTTTATATATTACGTATATTATAT-TTATTACATATA
* *
1000953 TTTTTTATTTATTAC-TATATTATATTTATTATATATA
1 TTTTTTATATATTACGTATATTATATTTATTACATATA
1000990 T
1 T
1000991 ATGTTCTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 19 0.58
38 14 0.42
ACGTcount: A:0.30, C:0.05, G:0.01, T:0.63
Consensus pattern (38 bp):
TTTTTTATATATTACGTATATTATATTTATTACATATA
Found at i:1000980 original size:21 final size:20
Alignment explanation
Indices: 1000941--1000990 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 20
1000931 TTTATTATTA
1000941 TTATTACATATATTTTTTAT
1 TTATTACATATATTTTTTAT
*
1000961 TTATTAC-TATA--TTATAT
1 TTATTACATATATTTTTTAT
*
1000978 TTATTATATATAT
1 TTATTACATATAT
1000991 ATGTTCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 11 0.42
18 4 0.15
19 4 0.15
20 7 0.27
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (20 bp):
TTATTACATATATTTTTTAT
Found at i:1001106 original size:47 final size:46
Alignment explanation
Indices: 1001028--1001170 Score: 178
Period size: 47 Copynumber: 3.0 Consensus size: 46
1001018 GTGGGTTTGA
* *
1001028 TTTGATTAGTTTTAATATGTTGTGTTGATTATTTTAATAGGTAGTGG
1 TTTGATTA-TTTTTATATGTAGTGTTGATTATTTTAATAGGTAGTGG
* *
1001075 TTTGATTATTTTTATAGGTAGTGGTTTATTATTTTAATAGGTAGTGG
1 TTTGATTATTTTTATATGTAGT-GTTGATTATTTTAATAGGTAGTGG
* * *
1001122 TTTGGTTTTTTTCTTAATATGTAGTGTTGATTATTTTATTAGGTAGTGG
1 TTT-GATTATTT-TT-ATATGTAGTGTTGATTATTTTAATAGGTAGTGG
1001171 GCCAATTATT
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
46 11 0.13
47 34 0.41
48 6 0.07
49 24 0.29
50 8 0.10
ACGTcount: A:0.22, C:0.01, G:0.23, T:0.55
Consensus pattern (46 bp):
TTTGATTATTTTTATATGTAGTGTTGATTATTTTAATAGGTAGTGG
Found at i:1001109 original size:23 final size:24
Alignment explanation
Indices: 1001028--1001170 Score: 152
Period size: 23 Copynumber: 6.0 Consensus size: 24
1001018 GTGGGTTTGA
* *
1001028 TTTGATTAGTTTTAATATGTTGT-G
1 TTTGATTA-TTTTAATAGGTAGTGG
1001052 -TTGATTATTTTAATAGGTAGTGG
1 TTTGATTATTTTAATAGGTAGTGG
*
1001075 TTTGATTATTTTTATAGGTAGTGG
1 TTTGATTATTTTAATAGGTAGTGG
1001099 TTT-ATTATTTTAATAGGTAGTGG
1 TTTGATTATTTTAATAGGTAGTGG
* * *
1001122 TTTGGTTTTTTTCTTAATATGTAGT-G
1 TTT-G-ATTATT-TTAATAGGTAGTGG
*
1001148 -TTGATTATTTTATTAGGTAGTGG
1 TTTGATTATTTTAATAGGTAGTGG
1001171 GCCAATTATT
Statistics
Matches: 101, Mismatches: 11, Indels: 15
0.80 0.09 0.12
Matches are distributed among these distances:
22 22 0.22
23 35 0.35
24 26 0.26
25 2 0.02
26 5 0.05
27 11 0.11
ACGTcount: A:0.22, C:0.01, G:0.23, T:0.55
Consensus pattern (24 bp):
TTTGATTATTTTAATAGGTAGTGG
Found at i:1001208 original size:9 final size:8
Alignment explanation
Indices: 1001196--1001255 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
1001186 ATTTTGTTAA
1001196 TTTCGTTTT
1 TTTC-TTTT
1001205 TTTCTTTT
1 TTTCTTTT
* *
1001213 TTTATTTA
1 TTTCTTTT
*
1001221 TTTCATTT
1 TTTCTTTT
* *
1001229 TTT-TATA
1 TTTCTTTT
1001236 TTTCGTTTT
1 TTTC-TTTT
1001245 TTTCTTTT
1 TTTCTTTT
1001253 TTT
1 TTT
1001256 AAATTGTTAA
Statistics
Matches: 39, Mismatches: 10, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
7 4 0.10
8 25 0.64
9 10 0.26
ACGTcount: A:0.08, C:0.08, G:0.03, T:0.80
Consensus pattern (8 bp):
TTTCTTTT
Found at i:1001237 original size:15 final size:15
Alignment explanation
Indices: 1001205--1001247 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 15
1001195 ATTTCGTTTT
1001205 TTTCTTTTTTTATTTA
1 TTTCTTTTTTTA-TTA
1001221 TTTCATTTTTTTA-TA
1 TTTC-TTTTTTTATTA
1001236 TTTCGTTTTTTT
1 TTTC-TTTTTTT
1001248 CTTTTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 13 0.52
16 4 0.16
17 8 0.32
ACGTcount: A:0.12, C:0.07, G:0.02, T:0.79
Consensus pattern (15 bp):
TTTCTTTTTTTATTA
Found at i:1001241 original size:40 final size:38
Alignment explanation
Indices: 1001176--1001256 Score: 126
Period size: 40 Copynumber: 2.1 Consensus size: 38
1001166 AGTGGGCCAA
1001176 TTATTTAGTTATTTTGTTAATTTCGTTTTTTTCTTTTT
1 TTATTTAGTTATTTTGTTAATTTCGTTTTTTTCTTTTT
* *
1001214 TTATTTATTTCATTTTTTTATATTTCGTTTTTTTCTTTTT
1 TTATTTAGTT-ATTTTGTTA-ATTTCGTTTTTTTCTTTTT
1001254 TTA
1 TTA
1001257 AATTGTTAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
38 9 0.23
39 8 0.21
40 22 0.56
ACGTcount: A:0.14, C:0.06, G:0.05, T:0.75
Consensus pattern (38 bp):
TTATTTAGTTATTTTGTTAATTTCGTTTTTTTCTTTTT
Found at i:1001331 original size:2 final size:2
Alignment explanation
Indices: 1001326--1001378 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
1001316 TCTTTTTTCT
1001326 TA TA TA TA TA TA 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
1001368 TA TA TA TA TA T
1 TA TA TA TA TA T
1001379 GTTTTCAATC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1001744 original size:21 final size:20
Alignment explanation
Indices: 1001718--1001765 Score: 64
Period size: 18 Copynumber: 2.5 Consensus size: 20
1001708 CGGTTACGAC
1001718 ACCACTGTATTGTCCCGAAGG
1 ACCACTGTA-TGTCCCGAAGG
*
1001739 ACCAC--TATGTCCCGTAGG
1 ACCACTGTATGTCCCGAAGG
1001757 ACCACTGTA
1 ACCACTGTA
1001766 ACCCTCGACC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 15 0.62
19 2 0.08
20 2 0.08
21 5 0.21
ACGTcount: A:0.25, C:0.31, G:0.21, T:0.23
Consensus pattern (20 bp):
ACCACTGTATGTCCCGAAGG
Found at i:1002012 original size:22 final size:21
Alignment explanation
Indices: 1001973--1002044 Score: 65
Period size: 22 Copynumber: 3.3 Consensus size: 21
1001963 ATGTAGTTTA
1001973 TTTTCATATAATTCATATCAC
1 TTTTCATATAATTCATATCAC
*
1001994 TTTTCATATGATTTCATATC-C
1 TTTTCATAT-AATTCATATCAC
* * * *
1002015 ATATGTCACATAGTTCGTATCAC
1 -T-TTTCATATAATTCATATCAC
1002038 TTTTCAT
1 TTTTCAT
1002045 GAATTCACAT
Statistics
Matches: 40, Mismatches: 7, Indels: 8
0.73 0.13 0.15
Matches are distributed among these distances:
21 14 0.35
22 19 0.47
23 7 0.17
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (21 bp):
TTTTCATATAATTCATATCAC
Found at i:1010972 original size:20 final size:20
Alignment explanation
Indices: 1010949--1010994 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
1010939 CAGGTATCAG
1010949 TACACCCCTTAATGTATCGA
1 TACACCCCTTAATGTATCGA
1010969 TACACCCCTTAATGTATCGA
1 TACACCCCTTAATGTATCGA
1010989 TACACC
1 TACACC
1010995 ATGAAGATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.33, G:0.09, T:0.28
Consensus pattern (20 bp):
TACACCCCTTAATGTATCGA
Found at i:1018838 original size:35 final size:35
Alignment explanation
Indices: 1018785--1018859 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
1018775 CGTCACGAAC
*
1018785 AGTAAGGTCCTGACCACAAATCCAAGGAGCCTACA
1 AGTAAGGTCCTGACCACAAAGCCAAGGAGCCTACA
* * *
1018820 AGTAAGG-CCATGAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGTCC-TGACCACAAAGCCAAGGAGCCTACA
1018855 AGTAA
1 AGTAA
1018860 TCTTCCTCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 2 0.06
35 33 0.94
ACGTcount: A:0.37, C:0.27, G:0.24, T:0.12
Consensus pattern (35 bp):
AGTAAGGTCCTGACCACAAAGCCAAGGAGCCTACA
Found at i:1018986 original size:24 final size:24
Alignment explanation
Indices: 1018959--1019071 Score: 85
Period size: 24 Copynumber: 4.8 Consensus size: 24
1018949 AGAAATCAGG
1018959 TCAAGTGA-CAGATCAAAATCCAAT
1 TCAAGT-ATCAGATCAAAATCCAAT
*
1018983 TCAAGTATCAGATCAGAATCC-AT
1 TCAAGTATCAGATCAAAATCCAAT
* *
1019006 GTC-AGATATCGGATCAGAATCC-AT
1 -TCAAG-TATCAGATCAAAATCCAAT
* * *
1019030 GTCAAGTATCAGATCAGAATTCAAA
1 -TCAAGTATCAGATCAAAATCCAAT
*
1019055 TCAA-AATCAGAT-AAAAT
1 TCAAGTATCAGATCAAAAT
1019072 ATTCATGTTA
Statistics
Matches: 77, Mismatches: 7, Indels: 12
0.80 0.07 0.12
Matches are distributed among these distances:
22 4 0.05
23 12 0.16
24 58 0.75
25 3 0.04
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (24 bp):
TCAAGTATCAGATCAAAATCCAAT
Found at i:1019079 original size:48 final size:48
Alignment explanation
Indices: 1018967--1019079 Score: 113
Period size: 48 Copynumber: 2.4 Consensus size: 48
1018957 GGTCAAGTGA
* ** *
1018967 CAGATCAAAATCCAAT-TCAAGTATCAGATCAGAATCCATGTCAGATAT
1 CAGATAAAAATCC-ATGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
* * * *
1019015 CGGATCAGAATCCATGTCAAGTATCAGATCAGAATTCAAATCA-AAAT
1 CAGATAAAAATCCATGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
*
1019062 CAGATAAAATATTCATGT
1 CAGATAAAA-ATCCATGT
1019080 TAGTAGGGAA
Statistics
Matches: 53, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
47 11 0.21
48 42 0.79
ACGTcount: A:0.42, C:0.19, G:0.13, T:0.26
Consensus pattern (48 bp):
CAGATAAAAATCCATGTCAAGTATCAGATCAGAATCCAAATCAGAAAT
Found at i:1021515 original size:18 final size:18
Alignment explanation
Indices: 1021492--1021543 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
1021482 GGTGAACGCA
*
1021492 GGTCAACGGATCGGGTCG
1 GGTCAACGGGTCGGGTCG
**
1021510 GGTCAACGGGTCAAGTCG
1 GGTCAACGGGTCGGGTCG
*
1021528 GGTCAGCGGGTCGGGT
1 GGTCAACGGGTCGGGT
1021544 TATGACTGGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.17
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:1023673 original size:24 final size:24
Alignment explanation
Indices: 1023611--1023726 Score: 112
Period size: 24 Copynumber: 4.8 Consensus size: 24
1023601 CATAATTCAA
* * *
1023611 GTCAAGTATCATATTAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAT
* * *
1023635 GTCAAGTAACAGATCAAAACCCAAT
1 GTCAAGTATCAGATCAGAATCC-AT
*
1023660 -TCAAGTATCCGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
1023683 GTC-AGATATCCGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
1023707 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
1023727 TCAAATCAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
23 6 0.08
24 67 0.88
25 3 0.04
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:1026212 original size:23 final size:23
Alignment explanation
Indices: 1026186--1026230 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1026176 GTAGGTCAAC
*
1026186 GGTCAACGGATCGGGTCGGGTCG
1 GGTCAACGGATCGGGTCAGGTCG
* *
1026209 GGTCAGCGGGTCGGGTCAGGTC
1 GGTCAACGGATCGGGTCAGGTC
1026231 AACGATTTGG
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:0.11, C:0.22, G:0.49, T:0.18
Consensus pattern (23 bp):
GGTCAACGGATCGGGTCAGGTCG
Found at i:1026218 original size:13 final size:13
Alignment explanation
Indices: 1026202--1026227 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1026192 CGGATCGGGT
1026202 CGGGTCGGGTCAG
1 CGGGTCGGGTCAG
1026215 CGGGTCGGGTCAG
1 CGGGTCGGGTCAG
1026228 GTCAACGATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.54, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTCAG
Found at i:1026218 original size:18 final size:18
Alignment explanation
Indices: 1026197--1026231 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1026187 GTCAACGGAT
*
1026197 CGGGTCGGGTCGGGTCAG
1 CGGGTCGGGTCAGGTCAG
1026215 CGGGTCGGGTCAGGTCA
1 CGGGTCGGGTCAGGTCA
1026232 ACGATTTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.09, C:0.23, G:0.51, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAGGTCAG
Found at i:1027360 original size:32 final size:32
Alignment explanation
Indices: 1027323--1027392 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
1027313 GTTTTTTGTT
* *
1027323 AGATGAAAGGAGTTTGTTTTGTAAGAGATTGA
1 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
*
1027355 AGATGAAAGGAGTGTGTTATGTGAGAGATTGA
1 AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
1027387 AGATGA
1 AGATGA
1027393 TGTGCACAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.36, C:0.00, G:0.34, T:0.30
Consensus pattern (32 bp):
AGATGAAAGGAGTGTGTTATGTAAGAGATTGA
Found at i:1031357 original size:11 final size:11
Alignment explanation
Indices: 1031312--1031359 Score: 51
Period size: 12 Copynumber: 4.0 Consensus size: 11
1031302 CCTTTGTTAC
1031312 TATTATTATTTAT
1 TATT-TTATTT-T
1031325 CTATTTTATTTT
1 -TATTTTATTTT
*
1031337 TACTTGTATTTT
1 TA-TTTTATTTT
1031349 TATTTTATTTT
1 TATTTTATTTT
1031360 ATTACAGGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 10 0.32
12 11 0.35
13 6 0.19
14 4 0.13
ACGTcount: A:0.21, C:0.04, G:0.02, T:0.73
Consensus pattern (11 bp):
TATTTTATTTT
Found at i:1031870 original size:13 final size:13
Alignment explanation
Indices: 1031840--1031864 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1031830 ATTCGAAATA
1031840 AAAAGAGGAAAAC
1 AAAAGAGGAAAAC
1031853 AAAAGAGGAAAA
1 AAAAGAGGAAAA
1031865 GGAAAGTTCT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.24, T:0.00
Consensus pattern (13 bp):
AAAAGAGGAAAAC
Found at i:1038186 original size:38 final size:37
Alignment explanation
Indices: 1038090--1038210 Score: 118
Period size: 38 Copynumber: 3.2 Consensus size: 37
1038080 TTATACCCCA
* * * *
1038090 AGAAACCTTAATCTTGAT-TTTCTTAGGCTCATTTTTCT
1 AGAAACCTCAA-CTT-ATCTTTCTTAAGATCATTTCTCT
* *
1038128 AGAAACCTCAATTTAGTCTTTCTTAAGATCATTTCCCT
1 AGAAACCTCAACTTA-TCTTTCTTAAGATCATTTCTCT
* **
1038166 AGAAACCTCAACCTTATCTTTCATAAGATTGTTTCTCT
1 AGAAACCTCAA-CTTATCTTTCTTAAGATCATTTCTCT
1038204 AGAAACC
1 AGAAACC
1038211 AACTTTATCT
Statistics
Matches: 69, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
36 1 0.01
37 3 0.04
38 62 0.90
39 3 0.04
ACGTcount: A:0.29, C:0.22, G:0.09, T:0.40
Consensus pattern (37 bp):
AGAAACCTCAACTTATCTTTCTTAAGATCATTTCTCT
Found at i:1038796 original size:131 final size:132
Alignment explanation
Indices: 1038564--1038808 Score: 339
Period size: 131 Copynumber: 1.9 Consensus size: 132
1038554 AGCCTATTCC
* * * *
1038564 TTTTTCTATATTTGATCTTCTCTGAAGAGTAGTGAATAAAATCTACCCCGATTCAATCTTCCCTG
1 TTTTTCCAGATTTGATCTTCTCTGAAGAGTAGTGAAGAAAATCTACCCCGATTCAATCTTCCCTA
*** * * *
1038629 AAGAATGGTGAAGTGAATCAGAGGTTCCAGATCTGATATACCCTAGAACACAACGGAGTAGATCC
66 AAGAACACTGAAGTAAATCAAAGGTTACAGATCTGATATACCCTAGAACACAACGGAGTAGATCC
1038694 CT
131 CT
* *
1038696 TTTTTCCAGATTTGATCTTCTTTGAAGAG-AGTGAAGAAAATCTACCCTGATTCAATCTTCCCTA
1 TTTTTCCAGATTTGATCTTCTCTGAAGAGTAGTGAAGAAAATCTACCCCGATTCAATCTTCCCTA
* * * *
1038760 AAGAGCACTGAAGTAAATCAAAGTTTACAGATCTGATCTACCCTGGAAC
66 AAGAACACTGAAGTAAATCAAAGGTTACAGATCTGATATACCCTAGAAC
1038809 GCAGTTGAGC
Statistics
Matches: 97, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
131 71 0.73
132 26 0.27
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (132 bp):
TTTTTCCAGATTTGATCTTCTCTGAAGAGTAGTGAAGAAAATCTACCCCGATTCAATCTTCCCTA
AAGAACACTGAAGTAAATCAAAGGTTACAGATCTGATATACCCTAGAACACAACGGAGTAGATCC
CT
Found at i:1039221 original size:130 final size:130
Alignment explanation
Indices: 1038874--1039933 Score: 803
Period size: 131 Copynumber: 8.1 Consensus size: 130
1038864 TACCCAATTC
* ** * ** * *
1038874 ATCTT-CTGAAGAGCATTGAAGCAAATTTACCCTGATTCAATCTTATCTGAAGAACAGTGAAGT-
1 ATCTTCCTGAAGAGCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAGTG
* * * ** * *
1038937 AACTCAATA-T-TTCTAGATCTGATCTACCTTGGAACGTGA-AGTAG---ATCCCTTTTTTCATA
66 AA-TCAA-AGTCTTC-AAATCTGATCTACCCTAGAACGCAACAG-AGCATATCCCTTTTTTTAGA
1038996 TTTG
127 TTTG
* * * * * *
1039000 ATCTTCTATGAAGAGCAGTGAAGCAAATCTACCCCGATTCAATCTTCCCTGAGGAACAGTAAAGT
1 ATCTTC-CTGAAGAGCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAGT
* * * *
1039065 GAATCAAAGTTTTCATAA-ATGATCTACCCTAGAACGCAGCAGAGCAAATCCCTTTTTTTAGATT
65 GAATCAAAGTCTTCA-AATCTGATCTACCCTAGAACGCAACAGAGCATATCCCTTTTTTTAGATT
1039129 TG
129 TG
* * * *
1039131 ATCTTTCCTGAAGAGTAGTGAAGCAAAT-AAACCCGATTCAATCTTCCCTAAAGAGCAATGAATT
1 ATC-TTCCTGAAGAGCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAGT
* * * * * * *
1039195 GAATCGAACTTTTCAAATATGCTCTACCCTAGAACGCAACA-AGACATATCTCTTTTTTCAGATT
65 GAATCAAAGTCTTCAAATCTGATCTACCCTAGAACGCAACAGAG-CATATCCCTTTTTTTAGATT
1039259 TG
129 TG
* * *
1039261 ATCTTCCTTGAAGAGCAGTGAAGCAAATCAACCCTGATTCAATCTACCCTGAAGAGCAGTGAAGT
1 ATCTTCC-TGAAGAGCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAGT
* * * * * * *
1039326 GAATCGAACTTTTCAAATCTGATCTACCCTAGAAAGCAACATAACATAT-ACTTTTTTTCAGATT
65 GAATCAAAGTCTTCAAATCTGATCTACCCTAGAACGCAACAGAGCATATCCCTTTTTTT-AGATT
1039390 TG
129 TG
* * ** * * *
1039392 ATCTTCTCTGAAGAACAATGAATTAAATCAACCCCGATTTAATCTTCCCTAAATAACAGTGAAGT
1 ATCTTC-CTGAAGAGCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAGT
* * * * * * * * *
1039457 GAATCAAAGTCTCCAGATCTGGTTTGCCTTGGAACACAACAGAGTATAT---TTTTTTCTCAGAT
65 GAATCAAAGTCTTCAAATCTGATCTACCCTAGAACGCAACAGAGCATATCCCTTTTTT-T-AGAT
1039519 TTG
128 TTG
* * * * * * *
1039522 ATCTTCTATAAATAACAATGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAGCATTGAAGT
1 ATCTTC-CTGAAGAGCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAGT
* * * ** *
1039587 GAATCAAAGTCTCCATAA-CTAATCTA-CCTTGAAACGCAATGGAGCATAT--CTTTTTTCTCAT
65 GAATCAAAGTCTTCA-AATCTGATCTACCCTAG-AACGCAACAGAGCATATCCCTTTTTT-T-AG
1039648 ATTTG
126 ATTTG
* * * *
1039653 ATCTTCCCTGAAGATCGGTGAAGCAAATCAACCCCGATTCAATCTTCACTAAAGAGCAGTGAAAT
1 ATCTT-CCTGAAGAGCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAGT
* * * * * * * * * * *
1039718 TAATCAAAGTCTTCAGATCTGATCTA-CTTTGTAATGTAGCAGAGAAAATCCCTTTTTTCATA-T
65 GAATCAAAGTCTTCAAATCTGATCTACCCTAG-AACGCAACAGAGCATATCCCTTTTTTTAGATT
1039781 TG
129 TG
** * **
1039783 ATCTTCCTTGAAGAATAGCGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAAAAGTGAAGT
1 ATCTTCC-TGAAGAGCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAGT
* * * * * * *** * * * *
1039848 GAATCAAAGTGTCCAGATCTAATCTACCCTGGGACGCAGTGGAGCAAAACTCTTTTTTGAGATTT
65 GAATCAAAGTCTTCAAATCTGATCTACCCTAGAACGCAACAGAGCATATCCCTTTTTTTAGATTT
1039913 G
130 G
1039914 ATCTTTCCTGAAGAGCAGTG
1 ATC-TTCCTGAAGAGCAGTG
1039934 GAGAAAATAT
Statistics
Matches: 759, Mismatches: 145, Indels: 55
0.79 0.15 0.06
Matches are distributed among these distances:
126 5 0.01
127 1 0.00
128 73 0.10
129 27 0.04
130 306 0.40
131 330 0.43
132 10 0.01
133 7 0.01
ACGTcount: A:0.33, C:0.21, G:0.16, T:0.30
Consensus pattern (130 bp):
ATCTTCCTGAAGAGCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAGTG
AATCAAAGTCTTCAAATCTGATCTACCCTAGAACGCAACAGAGCATATCCCTTTTTTTAGATTTG
Found at i:1039519 original size:261 final size:260
Alignment explanation
Indices: 1038878--1039857 Score: 921
Period size: 261 Copynumber: 3.8 Consensus size: 260
1038868 CAATTCATCT
* * ** * ** * * *
1038878 TCTGAAGAGCATTGAAGCAAATTTACCCTGATTCAATCTTATCTGAAGAACAGTGAAGT-AACTC
1 TCTGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAATGAA-TC
** * * *
1038942 AATA-T-TTCTAGATCTGATCTACCTTGGAACGTGA-AGTAG-AT-CCCTTTTTTCATATTTGAT
65 AA-AGTCTTC-AGATCTGATCTACCTTGGAACGCAACAG-AGAATATCTTTTTTTCAGATTTGAT
* * * *
1039002 CTTCTATGAAGAGCAGTGAAGCAAATCTACCCCGATTCAATCTTCCCTGAGGAACAGTAAAGTGA
127 CTTCTATGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAACAGTGAAGTGA
* * * *
1039067 ATCAAAGTTTTCATAAATGATCTACCCTAGAACGCAGCAGAGCAAATCCCTTTTTTT-AGATTTG
192 ATCAAAGTTTTCATAACTGATCTACCCTAGAAAGCAACAGAGCATAT--CTTTTTTTCAGATTTG
1039131 ATCTT-
255 ATCTTC
** * * *
1039136 TCCTGAAGAGTAGTGAAGCAAAT-AAACCCGATTCAATCTTCCCTAAAGAGCAATGAATTGAATC
1 T-CTGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAATGAATC
* * * * * * * *
1039200 GAACTTTTCAAATATGCTCTACCCTAGAACGCAACA-AGACATATCTCTTTTTTCAGATTTGATC
65 AAAGTCTTCAGATCTGATCTACCTTGGAACGCAACAGAGA-ATATCT-TTTTTTCAGATTTGATC
* * * *
1039264 TTCCT-TGAAGAGCAGTGAAGCAAATCAACCCTGATTCAATCTACCCTGAAGAGCAGTGAAGTGA
128 TT-CTATGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAACAGTGAAGTGA
* * * *
1039328 ATCGAACTTTTCA-AATCTGATCTACCCTAGAAAGCAACATAACATATACTTTTTTTCAGATTTG
192 ATCAAAGTTTTCATAA-CTGATCTACCCTAGAAAGCAACAGAGCATAT-CTTTTTTTCAGATTTG
1039392 ATCTTC
255 ATCTTC
* ** * * * *
1039398 TCTGAAGAACAATGAATTAAATCAACCCCGATTTAATCTTCCCTAAATAACAGTGAAGTGAATCA
1 TCTGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAATGAATCA
* * * * * *
1039463 AAGTCTCCAGATCTGGTTTGCCTTGGAACACAACAGAGTATAT-TTTTTTCTCAGATTTGATCTT
66 AAGTCTTCAGATCTGATCTACCTTGGAACGCAACAGAGAATATCTTTTTT-TCAGATTTGATCTT
* * * * *
1039527 CTATAAATAACAATGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAGCATTGAAGTGAATC
130 CTATGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAACAGTGAAGTGAATC
* * * * ** *
1039592 AAAGTCTCCATAACTAATCTA-CCTTGAAACGCAATGGAGCATATCTTTTTTCTCATATTTGATC
195 AAAGTTTTCATAACTGATCTACCCTAGAAA-GCAACAGAGCATATCTTTTTT-TCAGATTTGATC
1039656 TTC
258 TTC
* * * * *
1039659 CCTGAAGATCGGTGAAGCAAATCAACCCCGATTCAATCTTCACTAAAGAGCAGTGAAATTAATCA
1 TCTGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAATGAATCA
* * * * * * * *
1039724 AAGTCTTCAGATCTGATCTACTTTGTAATGTAGCAGAGAAAATCCCTTTTTTCATA-TTGATCTT
66 AAGTCTTCAGATCTGATCTACCTTGGAACGCAACAGAGAATAT-CTTTTTTTCAGATTTGATCTT
* * * *
1039788 CCT-TGAAGAATAGCGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAAAAGTGAAGTGAAT
130 -CTATGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAACAGTGAAGTGAAT
1039852 CAAAGT
194 CAAAGT
1039858 GTCCAGATCT
Statistics
Matches: 585, Mismatches: 114, Indels: 43
0.79 0.15 0.06
Matches are distributed among these distances:
257 3 0.01
258 50 0.09
259 27 0.05
260 32 0.05
261 392 0.67
262 74 0.13
263 7 0.01
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.30
Consensus pattern (260 bp):
TCTGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAATGAATCA
AAGTCTTCAGATCTGATCTACCTTGGAACGCAACAGAGAATATCTTTTTTTCAGATTTGATCTTC
TATGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAACAGTGAAGTGAATCA
AAGTTTTCATAACTGATCTACCCTAGAAAGCAACAGAGCATATCTTTTTTTCAGATTTGATCTTC
Found at i:1039872 original size:261 final size:261
Alignment explanation
Indices: 1038879--1039985 Score: 912
Period size: 261 Copynumber: 4.2 Consensus size: 261
1038869 AATTCATCTT
* * ** * ** * * *
1038879 CTGAAGAGCATTGAAGCAAATTTACCCTGATTCAATCTTATCTGAAGAACAGTG-AAGTAACTCA
1 CTGAAGATCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAATTAA-TCA
** *
1038943 ATA-T-TTCTAGATCTGATCTACCTTGGAACGTGA-AGTAG---ATCCCTTTTTTCATATTTGAT
65 A-AGTCTTC-AGATCTGATCTACCTT-GAACGCAACAG-AGAATATCCCTTTTTTCAGATTTGAT
* * * *
1039002 CTTCTATGAAGAGCAGTGAAGCAAATCTACCCCGATTCAATCTTCCCTGAGGAACAGTAAAGTGA
126 CTTCTATGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAACAGTGAAGTGA
* * * *
1039067 ATCAAAGTTTTCATAAATGATCTACCCT-AGAACGCAGCAGAGCAAATCCCTTTTTTT-AGATTT
191 ATCAAAGTTTCCATAACTAATCTACCCTGA-AACGCAACAGAGCAAAT-CCTTTTTTTCAGATTT
*
1039130 GATCTTTC
254 GATCTTCC
* *
1039138 CTGAAGAGT-AGTGAAGCAAAT-AAACCCGATTCAATCTTCCCTAAAGAGCAATG-AATTGAATC
1 CTGAAGA-TCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAATT-AATC
* * * * * * * *
1039200 GAACTTTTCAAATATGCTCTACCCTAGAACGCAACA-AGACATATCTCTTTTTTCAGATTTGATC
64 AAAGTCTTCAGATCTGATCTA-CCTTGAACGCAACAGAGA-ATATCCCTTTTTTCAGATTTGATC
* * * *
1039264 TTCCT-TGAAGAGCAGTGAAGCAAATCAACCCTGATTCAATCTACCCTGAAGAGCAGTGAAGTGA
127 TT-CTATGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAACAGTGAAGTGA
* * * * * * * *
1039328 ATCGAACTTTTCA-AATCTGATCTACCCTAGAAA-GCAACATAACATATACTTTTTTTCAGATTT
191 ATCAAAGTTTCCATAA-CTAATCTACCCT-GAAACGCAACAGAGCAAATCCTTTTTTTCAGATTT
*
1039391 GATCTTCT
254 GATCTTCC
* * ** * * * * *
1039399 CTGAAGAACAATGAATTAAATCAACCCCGATTTAATCTTCCCTAAATAACAGTGAAGTGAATCAA
1 CTGAAGATCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAATTAATCAA
* * * * * * *
1039464 AGTCTCCAGATCTGGTTTGCCTTGGAACACAACAGAGTATAT--TTTTTTCTCAGATTTGATCTT
66 AGTCTTCAGATCTGATCTACCTT-GAACGCAACAGAGAATATCCCTTTTT-TCAGATTTGATCTT
* * * * *
1039527 CTATAAATAACAATGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAGCATTGAAGTGAATC
129 CTATGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAACAGTGAAGTGAATC
* * ** * *
1039592 AAAGTCTCCATAACTAATCTACCTTGAAACGCAATGGAGCATAT-CTTTTTTCTCATATTTGATC
194 AAAGTTTCCATAACTAATCTACCCTGAAACGCAACAGAGCAAATCCTTTTTT-TCAGATTTGATC
1039656 TTCC
258 TTCC
* *
1039660 CTGAAGATCGGTGAAGCAAATCAACCCCGATTCAATCTTCACTAAAGAGCAGTGAAATTAATCAA
1 CTGAAGATCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAATTAATCAA
* * * * * *
1039725 AGTCTTCAGATCTGATCTACTTTGTAATGTAGCAGAGAAAATCCCTTTTTTCATA-TTGATCTTC
66 AGTCTTCAGATCTGATCTACCTTG-AACGCAACAGAGAATATCCCTTTTTTCAGATTTGATCTT-
* * * *
1039789 CT-TGAAGAATAGCGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAAAAGTGAAGTGAATC
129 CTATGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAACAGTGAAGTGAATC
* * * ** *** * *
1039853 AAAGTGTCCAGATCTAATCTACCCTGGGACGCAGTGGAGCAAA-ACTCTTTTTTGAGATTTGATC
194 AAAGTTTCCATAACTAATCTACCCTGAAACGCAACAGAGCAAATCCT-TTTTTTCAGATTTGATC
*
1039917 TTTC
258 TTCC
* * * * * * * * *
1039921 CTGAAGAGCAGTGGAGAAAAT-ATACCTCAATTCAAGCTTCCTTAGAGAACAGT-AAAGTTAATC
1 CTGAAGATCAGTGAAGCAAATCA-ACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAA-TTAATC
1039984 AA
64 AA
1039986 TATTCCAGAT
Statistics
Matches: 681, Mismatches: 134, Indels: 64
0.77 0.15 0.07
Matches are distributed among these distances:
257 3 0.00
258 46 0.07
259 27 0.04
260 33 0.05
261 489 0.72
262 73 0.11
263 10 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.30
Consensus pattern (261 bp):
CTGAAGATCAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTAAAGAGCAGTGAAATTAATCAA
AGTCTTCAGATCTGATCTACCTTGAACGCAACAGAGAATATCCCTTTTTTCAGATTTGATCTTCT
ATGAAGAACAGTGAAGCAAATCAACCCCGATTCAATCTTCCCTGAAGAACAGTGAAGTGAATCAA
AGTTTCCATAACTAATCTACCCTGAAACGCAACAGAGCAAATCCTTTTTTTCAGATTTGATCTTC
C
Found at i:1040241 original size:3 final size:3
Alignment explanation
Indices: 1040233--1040284 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
1040223 ATTTTGTTTA
1040233 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1040279 TAT TAT
1 TAT TAT
1040285 AGGCCCTTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:1045072 original size:21 final size:21
Alignment explanation
Indices: 1045046--1045145 Score: 73
Period size: 21 Copynumber: 4.8 Consensus size: 21
1045036 ATCAGTTCCC
1045046 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
*
1045067 AGAATCGCAATGCGA-TA-GTA
1 AGAATCGCAACGCGATTATG-A
** * **
1045087 CA-AATTCGCATTGCGATTTTCC
1 -AGAA-TCGCAACGCGATTATGA
* *
1045109 AGAATCGCAACGCAAATATGA
1 AGAATCGCAACGCGATTATGA
1045130 A-AATCGCAACGCGATT
1 AGAATCGCAACGCGATT
1045146 CTGACTATCG
Statistics
Matches: 59, Mismatches: 14, Indels: 13
0.69 0.16 0.15
Matches are distributed among these distances:
19 1 0.02
20 18 0.31
21 37 0.63
22 3 0.05
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATGA
Found at i:1045196 original size:20 final size:20
Alignment explanation
Indices: 1045152--1045324 Score: 204
Period size: 20 Copynumber: 8.6 Consensus size: 20
1045142 GATTCTGACT
*
1045152 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
1045173 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1045193 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
1045213 ATCGCAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
1045233 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
1045253 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
1045273 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
1045294 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
*
1045314 ATCTCAACGCG
1 ATCGCAACGCG
1045325 ATTTTTAAAG
Statistics
Matches: 127, Mismatches: 22, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
20 93 0.73
21 34 0.27
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:1045215 original size:81 final size:79
Alignment explanation
Indices: 1045111--1045322 Score: 275
Period size: 81 Copynumber: 2.6 Consensus size: 79
1045101 GATTTTCCAG
* * * * *
1045111 AATCGCAACGCAAATATGAAAATCGCAACGCG-ATTCTG-ACTATCGCAACGAGTATCCGTAAAA
1 AATCGCAACG-AAATACGTAAATCGCAACGCGTA-TCTGTA-AATCGCAACGAGAATACGT-AAA
1045174 TCGCAACGCGTATCCGTA
62 TCGCAACGCGTATCCGTA
1045192 AATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCG
1 AATCGCAACGA-AATACGTAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCG
*
1045257 CAATGCGTATCCGTA
65 CAACGCGTATCCGTA
* *
1045272 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATCTCAACG
1 AATCGCAACGA-AATACGT-AAATCGCAACGCGTATCTGTAAATCGCAACG
1045323 CGATTTTTAA
Statistics
Matches: 118, Mismatches: 9, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
80 39 0.33
81 77 0.65
82 2 0.02
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (79 bp):
AATCGCAACGAAATACGTAAATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGC
AACGCGTATCCGTA
Found at i:1045226 original size:40 final size:41
Alignment explanation
Indices: 1045111--1045322 Score: 274
Period size: 40 Copynumber: 5.2 Consensus size: 41
1045101 GATTTTCCAG
* *
1045111 AATCGCAACGCA-AATATG-AAAATCGCAACGCG-ATTC-TGA
1 AATCGCAACG-AGAATACGTAAAATCGCAACGCGTATCCGT-A
* * *
1045150 CTATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
1045192 AATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
1045232 AATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
1045272 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
1045313 AATCTCAACG
1 AATCGCAACG
1045323 CGATTTTTAA
Statistics
Matches: 153, Mismatches: 14, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 1 0.01
40 88 0.58
41 59 0.39
42 4 0.03
43 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
Found at i:1045942 original size:21 final size:19
Alignment explanation
Indices: 1045881--1045993 Score: 103
Period size: 20 Copynumber: 5.9 Consensus size: 19
1045871 TTCTAAACTT
1045881 AAAATCGCAACATGAAAATG
1 AAAATCGCAACA-GAAAATG
1045901 AAAATCGCAACACGAAAATG
1 AAAATCGCAACA-GAAAATG
**
1045921 ACTATCGCAACTAGAGAAATG
1 AAAATCGCAAC-AGA-AAATG
1045942 AAAATCGCAAC-G---A-G
1 AAAATCGCAACAGAAAATG
*
1045956 AAAATCGCAAC-GCGAAATG
1 AAAATCGCAACAG-AAAATG
1045975 AAAATCGCAACGAGAAAAT
1 AAAATCGCAAC-AGAAAAT
1045994 CGCAACGAGA
Statistics
Matches: 78, Mismatches: 6, Indels: 18
0.76 0.06 0.18
Matches are distributed among these distances:
14 13 0.17
15 1 0.01
18 1 0.01
19 13 0.17
20 34 0.44
21 16 0.21
ACGTcount: A:0.51, C:0.19, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAACAGAAAATG
Found at i:1045944 original size:41 final size:40
Alignment explanation
Indices: 1045884--1045960 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 40
1045874 TAAACTTAAA
1045884 ATCGCAACATGAAAATGAAAATCGCAAC-ACGAAAATGACT
1 ATCGCAACATGAAAATGAAAATCGCAACGA-GAAAATGACT
1045924 ATCGCAAC-TAGAGAAATGAAAATCGCAACGAGAAAAT
1 ATCGCAACAT-GA-AAATGAAAATCGCAACGAGAAAAT
1045961 CGCAACGCGA
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
39 1 0.03
40 10 0.29
41 22 0.65
42 1 0.03
ACGTcount: A:0.51, C:0.18, G:0.17, T:0.14
Consensus pattern (40 bp):
ATCGCAACATGAAAATGAAAATCGCAACGAGAAAATGACT
Found at i:1045960 original size:14 final size:14
Alignment explanation
Indices: 1045941--1046019 Score: 95
Period size: 14 Copynumber: 5.3 Consensus size: 14
1045931 CTAGAGAAAT
1045941 GAAAATCGCAACGA
1 GAAAATCGCAACGA
1045955 GAAAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
1045973 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
1045988 GAAAATCGCAACGA
1 GAAAATCGCAACGA
* *
1046002 GATAATCGCAACGT
1 GAAAATCGCAACGA
1046016 GAAA
1 GAAA
1046020 CCAAAATCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
14 40 0.70
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 11 0.19
ACGTcount: A:0.48, C:0.20, G:0.22, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1045976 original size:33 final size:33
Alignment explanation
Indices: 1045936--1046000 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
1045926 CGCAACTAGA
1045936 GAAATGAAAATCGCAACGAGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAAAATCGCAACGC
1045969 GAAATGAAAATCGCAACGAGAAAATCGCAACG
1 GAAATGAAAATCGCAACGAGAAAATCGCAACG
1046001 AGATAATCGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.49, C:0.20, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAAAATCGCAACGC
Found at i:1045992 original size:47 final size:47
Alignment explanation
Indices: 1045941--1046030 Score: 144
Period size: 47 Copynumber: 1.9 Consensus size: 47
1045931 CTAGAGAAAT
**
1045941 GAAAATCGCAACGAGAAAATCGCAACGCGAAATGAAAATCGCAACGA
1 GAAAATCGCAACGAGAAAATCGCAACGCGAAACCAAAATCGCAACGA
* *
1045988 GAAAATCGCAACGAGATAATCGCAACGTGAAACCAAAATCGCA
1 GAAAATCGCAACGAGAAAATCGCAACGCGAAACCAAAATCGCA
1046031 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.10
Consensus pattern (47 bp):
GAAAATCGCAACGAGAAAATCGCAACGCGAAACCAAAATCGCAACGA
Found at i:1046048 original size:19 final size:19
Alignment explanation
Indices: 1046026--1046185 Score: 107
Period size: 19 Copynumber: 9.1 Consensus size: 19
1046016 GAAACCAAAA
*
1046026 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1046045 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
1046059 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTCATT
1046078 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1046092 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1046111 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
1046125 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
1046144 TCCGCATTGCGATATTCATT
1 T-CGCGTTGCGATTTTCATT
*
1046164 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1046184 TC
1 TC
1046186 AACCAAAAGA
Statistics
Matches: 109, Mismatches: 15, Indels: 34
0.69 0.09 0.22
Matches are distributed among these distances:
14 30 0.28
16 7 0.06
17 8 0.07
19 33 0.30
20 30 0.28
21 1 0.01
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1046067 original size:14 final size:14
Alignment explanation
Indices: 1046048--1046136 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
1046038 TTTCATTTCG
1046048 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
1046062 CGTTGCGATTTTAATTTCG
1 CGTTGCGA---T--TCTCT
1046081 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1046095 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1046114 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1046128 CGTTGCGAT
1 CGTTGCGAT
1046137 AGTCATTTCC
Statistics
Matches: 59, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 30 0.51
16 4 0.07
17 4 0.07
19 21 0.36
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1046073 original size:33 final size:33
Alignment explanation
Indices: 1046031--1046185 Score: 211
Period size: 33 Copynumber: 4.5 Consensus size: 33
1046021 CAAAATCGCA
1046031 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1046064 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1046097 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
1046130 TTGCGATAGTCATTTCCGCATTGCGATATTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
1046170 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1046186 AACCAAAAGA
Statistics
Matches: 108, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
33 77 0.71
34 8 0.07
39 1 0.01
40 22 0.20
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1046173 original size:20 final size:20
Alignment explanation
Indices: 1046121--1046183 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 20
1046111 TCGCGTTGCG
*
1046121 ATTCTCTCGTTGCGATAGTC
1 ATTCTCTCGTTGCGATATTC
1046141 ATT-TC-CGCATTGCGATATTC
1 ATTCTCTCG--TTGCGATATTC
*
1046161 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATATTC
1046181 ATT
1 ATT
1046184 TCAACCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 2 0.05
19 2 0.05
20 29 0.78
21 2 0.05
22 2 0.05
ACGTcount: A:0.16, C:0.24, G:0.16, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATATTC
Found at i:1047986 original size:94 final size:94
Alignment explanation
Indices: 1047825--1048203 Score: 613
Period size: 94 Copynumber: 4.1 Consensus size: 94
1047815 TAGATTGCTT
* * * *
1047825 AGTAAATTTACTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTAAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1047890 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
* *
1047919 AGTAAATTTATTCAGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1047984 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
1048013 AGTAAATTTGTTCGGTTGCTGCCAATTATGCTAAACTGTGTATTCTTTAACACTGTGAAGTTA-T
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1048077 A-TTGTCTTTGTTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTG-TTTTGTCTTTTGGTTGAA
* * *
1048106 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1048171 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1048199 AGTAA
1 AGTAA
1048204 TGCAATCCAT
Statistics
Matches: 268, Mismatches: 13, Indels: 9
0.92 0.04 0.03
Matches are distributed among these distances:
92 9 0.03
93 106 0.40
94 144 0.54
95 9 0.03
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1048167 original size:187 final size:187
Alignment explanation
Indices: 1047825--1048203 Score: 613
Period size: 187 Copynumber: 2.0 Consensus size: 187
1047815 TAGATTGCTT
*
1047825 AGTAAATTTACTCGGTTGCTGCCAATACTGCTAAACTGTTTATTCTTTAACACTGTAAAGTTAGT
1 AGTAAATTTACTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTAAAGTTAGT
1047890 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCAGTTGCTGCCAATTCTGCTAAAC
66 ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCAGTTGCTGCCAATTCTGCTAAAC
*
1047955 TATGTATTCTTTAACACTGTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 TATGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTG-A
** *
1048013 AGTAAATTTGTTCGGTTGCTGCCAATTA-TGCTAAACTGTGTATTCTTTAACACTGTGAAGTTA-
1 AGTAAATTTACTCGGTTGCTGCCAA-TACTGCTAAACTGTGTATTCTTTAACACTGTAAAGTTAG
* *
1048076 TA-TTGTC-TTTGTTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTA
65 TATTTGTCTTTTG-TTTTGTCTTTTGGTTG-AAGTAAATTTATTCAGTTGCTGCCAATTCTGCTA
* *
1048139 AACTGTGTATTCTTTAATACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
128 AACTATGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
1048199 AGTAA
1 AGTAA
1048204 TGCAATCCAT
Statistics
Matches: 179, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
185 4 0.02
186 27 0.15
187 90 0.50
188 56 0.31
189 2 0.01
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (187 bp):
AGTAAATTTACTCGGTTGCTGCCAATACTGCTAAACTGTGTATTCTTTAACACTGTAAAGTTAGT
ATTTGTCTTTTGTTTTGTCTTTTGGTTGAAGTAAATTTATTCAGTTGCTGCCAATTCTGCTAAAC
TATGTATTCTTTAACACTCTGAAGTTAGTATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:1048325 original size:14 final size:14
Alignment explanation
Indices: 1048306--1048332 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1048296 AACGCGAAAC
1048306 CAAAATCGCAACGA
1 CAAAATCGCAACGA
1048320 CAAAATCGCAACG
1 CAAAATCGCAACG
1048333 CGAAACCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.48, C:0.30, G:0.15, T:0.07
Consensus pattern (14 bp):
CAAAATCGCAACGA
Found at i:1048366 original size:19 final size:19
Alignment explanation
Indices: 1048291--1048357 Score: 99
Period size: 19 Copynumber: 3.8 Consensus size: 19
1048281 AAAAATGACT
1048291 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAACCAAA
1048310 ATCGCAA--CG--A-CAAA
1 ATCGCAACGCGAAACCAAA
1048324 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAACCAAA
1048343 ATCGCAACGCGAAAC
1 ATCGCAACGCGAAAC
1048358 TATAATCGCG
Statistics
Matches: 43, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 2 0.05
17 2 0.05
18 1 0.02
19 26 0.60
ACGTcount: A:0.46, C:0.31, G:0.16, T:0.06
Consensus pattern (19 bp):
ATCGCAACGCGAAACCAAA
Found at i:1048430 original size:20 final size:20
Alignment explanation
Indices: 1048405--1048527 Score: 183
Period size: 20 Copynumber: 6.2 Consensus size: 20
1048395 CTCTCGTTGT
** *
1048405 GATAGTCAAATTCGTATTGC
1 GATAGTCATTTTCGCATTGC
*
1048425 GATAGTCATTTTCACATTGC
1 GATAGTCATTTTCGCATTGC
1048445 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
1048465 GATAGTCATTTTCGCATTGC
1 GATAGTCATTTTCGCATTGC
* *
1048485 GATAGTCATTTTCACGTTGC
1 GATAGTCATTTTCGCATTGC
*
1048505 GATAGTCATTTTCGCGTTGC
1 GATAGTCATTTTCGCATTGC
1048525 GAT
1 GAT
1048528 TTTAAGTTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 95 1.00
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (20 bp):
GATAGTCATTTTCGCATTGC
Found at i:1049043 original size:18 final size:19
Alignment explanation
Indices: 1049004--1049045 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1048994 CTCACCTGTC
1049004 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1049025 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1049043 ATC
1 ATC
1049046 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1050405 original size:33 final size:34
Alignment explanation
Indices: 1050358--1050426 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
1050348 TGTTTTGCTG
1050358 CGAGAGAATCGCAATGC-AAAATGAAAATCGCAA
1 CGAGAGAATCGCAATGCGAAAATGAAAATCGCAA
*
1050391 CGAGTGAATCGCAATGCGAAAATGAAAATCGCAA
1 CGAGAGAATCGCAATGCGAAAATGAAAATCGCAA
1050425 CG
1 CG
1050427 TGAAACTCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 16 0.47
34 18 0.53
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (34 bp):
CGAGAGAATCGCAATGCGAAAATGAAAATCGCAA
Found at i:1050460 original size:19 final size:19
Alignment explanation
Indices: 1050436--1050500 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
1050426 GTGAAACTCG
1050436 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1050455 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
1050474 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1050493 TTGCGATT
1 TTGCGATT
1050501 CTCTCGTTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.15, C:0.18, G:0.17, T:0.49
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1050530 original size:20 final size:20
Alignment explanation
Indices: 1050505--1050593 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
1050495 GCGATTCTCT
1050505 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1050525 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
* * *
1050545 CATTGCGACAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
* *
1050565 TGTTGCGATAGTCATAAT-CG
1 CGTTGCGATAGTCAT-TTCCG
1050585 CGTTGCGAT
1 CGTTGCGAT
1050594 TTCCACGTTG
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
20 57 0.98
21 1 0.02
ACGTcount: A:0.19, C:0.22, G:0.25, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1053030 original size:24 final size:24
Alignment explanation
Indices: 1053003--1053049 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1052993 CAAAATCCGA
*
1053003 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGAACAAGATCAAAGTTCGG
*
1053027 GTATTGAACAAGATCAAATTTCG
1 GTATTGAACAAGATCAAAGTTCG
1053050 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGAACAAGATCAAAGTTCGG
Found at i:1053920 original size:19 final size:19
Alignment explanation
Indices: 1053896--1053947 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
1053886 CGATACCGGA
1053896 GATCGCGTTGCGAATTATC
1 GATCGCGTTGCGAATTATC
* *
1053915 GATCGCGTTGCGATTTATG
1 GATCGCGTTGCGAATTATC
1053934 GATACGCGTTGCGA
1 GAT-CGCGTTGCGA
1053948 TTTTACGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 20 0.67
20 10 0.33
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (19 bp):
GATCGCGTTGCGAATTATC
Found at i:1053943 original size:20 final size:20
Alignment explanation
Indices: 1053899--1054114 Score: 195
Period size: 20 Copynumber: 10.7 Consensus size: 20
1053889 TACCGGAGAT
*
1053899 CGCGTTGCGAATTATC-GAT-
1 CGCGTTGCGATTTA-CGGATA
*
1053918 CGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
* *
1053938 CGCGTTGCGATTTTACGTATT
1 CGCGTTGCGA-TTTACGGATA
** * * *
1053959 TTCGTTGTGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
1053979 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* * *
1053999 CGCGTTACGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
1054019 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1054039 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
1054059 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
1054080 TGCGTTGCGATTTTACGGATA
1 CGCGTTGCGA-TTTACGGATA
*
1054101 CTCGTTGCGATTTA
1 CGCGTTGCGATTTA
1054115 TATGTTCGCG
Statistics
Matches: 162, Mismatches: 28, Indels: 13
0.80 0.14 0.06
Matches are distributed among these distances:
19 16 0.10
20 96 0.59
21 50 0.31
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1054040 original size:101 final size:102
Alignment explanation
Indices: 1053920--1054114 Score: 295
Period size: 101 Copynumber: 1.9 Consensus size: 102
1053910 TTATCGATCG
* * * * *
1053920 CGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTTTCGTTGTGATTTACGTAT-TCTCGT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATAT-GCGT
1053984 TGCGA-TTTACAGATACGCGTTACGATTTACGTATTCT
65 TGCGATTTTACAGATACGCGTTACGATTTACGTATTCT
1054021 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATATGCGTT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATATGCGTT
* * *
1054086 GCGATTTTACGGATACTCGTTGCGATTTA
66 GCGATTTTACAGATACGCGTTACGATTTA
1054115 TATGTTCGCG
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
101 62 0.74
102 22 0.26
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.41
Consensus pattern (102 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATATGCGTT
GCGATTTTACAGATACGCGTTACGATTTACGTATTCT
Found at i:1054066 original size:41 final size:40
Alignment explanation
Indices: 1053901--1054114 Score: 234
Period size: 41 Copynumber: 5.3 Consensus size: 40
1053891 CCGGAGATCG
* * * * *
1053901 CGTTGCGAATTATC-GAT-CGCGTTGCGATTTATGGATACG
1 CGTTGCGATTTA-CGGATACGCGTTGCGATTTACGTATTCT
* *** *
1053940 CGTTGCGATTTTACGTATTTTCGTTGTGATTTACGTATTCT
1 CGTTGCGA-TTTACGGATACGCGTTGCGATTTACGTATTCT
* *
1053981 CGTTGCGATTTACAGATACGCGTTACGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
*
1054021 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
* * *
1054062 CGTTGCGATTTACGGATATGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
1054103 CGTTGCGATTTA
1 CGTTGCGATTTA
1054115 TATGTTCGCG
Statistics
Matches: 148, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
39 9 0.06
40 56 0.38
41 83 0.56
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:1054127 original size:61 final size:59
Alignment explanation
Indices: 1053920--1054133 Score: 218
Period size: 61 Copynumber: 3.5 Consensus size: 59
1053910 TTATCGATCG
* * * *
1053920 CGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTTTCGTTGTGATTTACGTATTCT
1 CGTTGCGATTTATAGATACGCGTTGCGA-TTTACGTA-TTTCGTTGCGATTTACGGATACT
* * *
1053981 CGTTGCGATTTACAGATACGCGTTACGATTTACGTATTCTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTATAGATACGCGTTGCGATTTACGTATT-TCGTTGCGATTTACGGATACT
* * *
1054041 CGTTGCGATTT-TACG-TATTGTCGTTGCGATTTACGGATATGCGTTGCGATTTTACGGATACT
1 CGTTGCGATTTATA-GATA-CG-CGTTGCGATTTACGTAT-TTCGTTGCGA-TTTACGGATACT
* *
1054103 CGTTGCGATTTATATG-TTCGCGTTGTGATTT
1 CGTTGCGATTTATA-GATACGCGTTGCGATTT
1054134 TCATATTAGC
Statistics
Matches: 129, Mismatches: 17, Indels: 14
0.81 0.11 0.09
Matches are distributed among these distances:
59 5 0.04
60 38 0.29
61 58 0.45
62 24 0.19
63 4 0.03
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (59 bp):
CGTTGCGATTTATAGATACGCGTTGCGATTTACGTATTTCGTTGCGATTTACGGATACT
Found at i:1063481 original size:10 final size:11
Alignment explanation
Indices: 1063453--1063556 Score: 62
Period size: 10 Copynumber: 9.7 Consensus size: 11
1063443 AAAAATGTAG
1063453 AGATAAAA-AA
1 AGATAAAAGAA
*
1063463 GAGAGAAAAGAA
1 -AGATAAAAGAA
1063475 A-ATAAAA-AA
1 AGATAAAAGAA
1063484 AGATAAAAGAA
1 AGATAAAAGAA
* *
1063495 AGATAAAACAT
1 AGATAAAAGAA
*
1063506 A-A-AAAAGAT
1 AGATAAAAGAA
1063515 AGA-AAATAGAAA
1 AGATAAA-AG-AA
*
1063527 AGATAGAA-AA
1 AGATAAAAGAA
1063537 AGA-AAATAGAAA
1 AGATAAA-AG-AA
1063549 AGATAAAA
1 AGATAAAA
1063557 AAAAAAGAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 21
0.72 0.08 0.20
Matches are distributed among these distances:
9 12 0.16
10 22 0.30
11 22 0.30
12 13 0.18
13 5 0.07
ACGTcount: A:0.74, C:0.01, G:0.15, T:0.10
Consensus pattern (11 bp):
AGATAAAAGAA
Found at i:1063491 original size:20 final size:20
Alignment explanation
Indices: 1063455--1063582 Score: 84
Period size: 20 Copynumber: 6.0 Consensus size: 20
1063445 AAATGTAGAG
1063455 ATAAAAAAGAGAGAAAAGAAA
1 ATAAAAAA-AGAGAAAAGAAA
*
1063476 ATAAAAAAAGATAAAAGAAA
1 ATAAAAAAAGAGAAAAGAAA
*
1063496 GATAAAACATAA-AAAAGATAGAAA
1 -ATAAAA-A-AAGAGAA-A-AGAAA
1063520 ATAGAAAAGATAGA-AAAAGAAA
1 ATA-AAAA-A-AGAGAAAAGAAA
* *
1063542 AT-AGAAAAGATAAAA-AAA
1 ATAAAAAAAGAGAAAAGAAA
*
1063560 AAAGAAAAAAGAGAAAAGGAAA
1 ATA-AAAAAAGAGAAAA-GAAA
1063582 A
1 A
1063583 GAAGGAAAAA
Statistics
Matches: 87, Mismatches: 7, Indels: 25
0.73 0.06 0.21
Matches are distributed among these distances:
18 7 0.08
19 5 0.06
20 25 0.29
21 14 0.16
22 15 0.17
23 9 0.10
24 11 0.13
25 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.16, T:0.08
Consensus pattern (20 bp):
ATAAAAAAAGAGAAAAGAAA
Found at i:1063491 original size:31 final size:31
Alignment explanation
Indices: 1063453--1063567 Score: 83
Period size: 31 Copynumber: 3.6 Consensus size: 31
1063443 AAAAATGTAG
1063453 AGATAAAAAAGAGAGAAAAGAAAATAAAAAA
1 AGATAAAAAAGAGAGAAAAGAAAATAAAAAA
* *
1063484 AGATAAAAGAA-AGATAAAACATAAA-AAAGATAGA
1 AGATAAAA-AAGAGAGAAAAGA-AAATAAA-A-A-A
* * * *
1063518 AAATAGAAAAGATAGAAAAAGAAAAT-AGAAA
1 AGATAAAAAAGAGAG-AAAAGAAAATAAAAAA
* *
1063549 AGATAAAAAAAAAAGAAAA
1 AGATAAAAAAGAGAGAAAA
1063568 AAGAGAAAAG
Statistics
Matches: 64, Mismatches: 12, Indels: 17
0.69 0.13 0.18
Matches are distributed among these distances:
30 4 0.06
31 31 0.48
32 7 0.11
33 4 0.06
34 13 0.20
35 5 0.08
ACGTcount: A:0.76, C:0.01, G:0.15, T:0.09
Consensus pattern (31 bp):
AGATAAAAAAGAGAGAAAAGAAAATAAAAAA
Found at i:1063583 original size:20 final size:20
Alignment explanation
Indices: 1063457--1063610 Score: 82
Period size: 20 Copynumber: 7.2 Consensus size: 20
1063447 ATGTAGAGAT
*
1063457 AAAAAAGAGAGAAAAGAAAAT
1 AAAAAAGAGA-AAAAGAAAAG
1063478 AAAAAA-AGATAAAAG-AAAG
1 AAAAAAGAGA-AAAAGAAAAG
* *
1063497 ATAAAACATA-AAAAAGATAGAAA
1 A-AAAA-AGAGAAAAAGA-A-AAG
*
1063520 ATAGAAAAGATAGAAAAAGAAAAT
1 A-A-AAAAG--AGAAAAAGAAAAG
* * *
1063544 AGAAAAGATAAAAAAAAAAG
1 AAAAAAGAGAAAAAGAAAAG
*
1063564 AAAAAAGAGAAAAGGAAAAG
1 AAAAAAGAGAAAAAGAAAAG
1063584 AAGGAAAA-AGAAAAATGAGAAAG
1 AA--AAAAGAGAAAAA-GA-AAAG
1063607 AAAA
1 AAAA
1063611 TAAATCAAGT
Statistics
Matches: 105, Mismatches: 14, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
19 4 0.04
20 45 0.43
21 16 0.15
22 13 0.12
23 12 0.11
24 6 0.06
25 2 0.02
26 7 0.07
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (20 bp):
AAAAAAGAGAAAAAGAAAAG
Found at i:1063606 original size:23 final size:23
Alignment explanation
Indices: 1063556--1063608 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1063546 AAAAGATAAA
* *
1063556 AAAAAAAGAAAAAAGAGAAAAGG
1 AAAAGAAGGAAAAAGAGAAAAGG
*
1063579 AAAAGAAGGAAAAAGA-AAAATG
1 AAAAGAAGGAAAAAGAGAAAAGG
1063601 AGAAAGAA
1 A-AAAGAA
1063609 AATAAATCAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 6 0.23
23 20 0.77
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.02
Consensus pattern (23 bp):
AAAAGAAGGAAAAAGAGAAAAGG
Found at i:1067425 original size:134 final size:134
Alignment explanation
Indices: 1067181--1067890 Score: 741
Period size: 134 Copynumber: 5.3 Consensus size: 134
1067171 AATCGAACTC
* *
1067181 GATTCAATCTTCCCTGAGGAACAGTGGAATGAATCAACATTTCC-AGATCTGATTTTCCCTCAAG
1 GATTCAATCTTCCCTGAGGAACAGTGGAATGAATCAACA-TCCCAAGATCTAATTTTCCCTCAAG
* * * *
1067245 AAGAAGCGGAACAGATCACTCTCTTTCAAGATTTGATATTCCCTGAGTAATAGTGGAACAAGTTT
65 AAGAAGCGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
1067310 GCCTCT
130 GCCT-T
* * ** * *
1067316 -ATTCAATATTCCCTAAGGAACA-TCGGAATGAATCAATGTCCTAATATCTAATTTTCCCTCAAG
1 GATTCAATCTTCCCTGAGGAACAGT-GGAATGAATCAACATCCCAAGATCTAATTTTCCCTCAAG
* * * *
1067379 AAGAAGCAGAACATATCCCTCTCTTTCAAGATTTGATATTCTCTGAGAAATAGTGGAACAAGTCT
65 AAGAAGCGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
* **
1067444 ACCAC
130 GCCTT
* * * *
1067449 GATTCAATCTTCCCTGAGGAATAGTGGAATGAATCAACGTACCCAA-ATCTAATTTACCCTCATG
1 GATTCAATCTTCCCTGAGGAACAGTGGAATGAATCAACAT-CCCAAGATCTAATTTTCCCTCAAG
* * * * * * *
1067513 AAGGAGCGGAACAAATCCTTCTCTTTTC-AGATTTTATATTCCTTGAGTAACAACT-GAATAAGT
65 AAGAAGCGGAACATATCCCTCTC-TTTCAAGATTTGATATTCCCTGAGTAAC-AGTGGAACAAGT
*
1067576 TTGCCTT
128 CTGCCTT
* * * * * * * *
1067583 GATTTAATCTTCCCTGAGCAACAGTGGAATAAATCAACATCCCCATATTTGATTTTCCCTCAGGA
1 GATTCAATCTTCCCTGAGGAACAGTGGAATGAATCAACATCCCAAGATCTAATTTTCCCTCAAGA
* * * * * * * * * *
1067648 AGAAGCGAAATAGATCCCCCTCTTTTC-AGATTTGATAATCTCTGAGTAACAGCGAAAAAAATCT
66 AGAAGCGGAACATATCCCTCTC-TTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
1067712 GCCTT
130 GCCTT
* * * *
1067717 GATTCAATCTTCCCTGAGTAACATTGGAATGAATCAACATCCCCAGATCTAATTTTCCCTCAAAA
1 GATTCAATCTTCCCTGAGGAACAGTGGAATGAATCAACATCCCAAGATCTAATTTTCCCTCAAGA
* * * * * *
1067782 AGAAGCGGAACATATCTCTCTTTTTCAAGATTTGATATTCCCTAAGTGACAGTGGAACAAATCTA
66 AGAAGCGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG
* *
1067847 ACTC
131 CCTT
* *
1067851 GATTCAATCTTCCCTGAAGAACAGTGAAATGAATCAACAT
1 GATTCAATCTTCCCTGAGGAACAGTGGAATGAATCAACAT
1067891 TTCTCGATCT
Statistics
Matches: 471, Mismatches: 94, Indels: 21
0.80 0.16 0.04
Matches are distributed among these distances:
133 12 0.03
134 448 0.95
135 11 0.02
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Consensus pattern (134 bp):
GATTCAATCTTCCCTGAGGAACAGTGGAATGAATCAACATCCCAAGATCTAATTTTCCCTCAAGA
AGAAGCGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTG
CCTT
Found at i:1068069 original size:3 final size:3
Alignment explanation
Indices: 1068061--1068104 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1068051 GCCTGGAACG
1068061 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1068105 TATTTCTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1076377 original size:20 final size:20
Alignment explanation
Indices: 1076352--1076390 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1076342 TTCACTTTGA
1076352 AGAACAAATTCTCCACCTTG
1 AGAACAAATTCTCCACCTTG
* *
1076372 AGAACATATTCTCTACCTT
1 AGAACAAATTCTCCACCTT
1076391 AACAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.28, G:0.08, T:0.31
Consensus pattern (20 bp):
AGAACAAATTCTCCACCTTG
Found at i:1078194 original size:2 final size:2
Alignment explanation
Indices: 1078189--1078216 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1078179 TTTAATTTTC
1078189 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
1078217 AAGATTGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1083902 original size:12 final size:12
Alignment explanation
Indices: 1083887--1083911 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1083877 ACCGTCACCC
1083887 TCATTATCTTCT
1 TCATTATCTTCT
1083899 TCATTATCTTCT
1 TCATTATCTTCT
1083911 T
1 T
1083912 TTAAGAACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.00, T:0.60
Consensus pattern (12 bp):
TCATTATCTTCT
Found at i:1085621 original size:23 final size:24
Alignment explanation
Indices: 1085578--1085622 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1085568 ATCATGTTTG
* *
1085578 TGTTTATTTTTTTATTTTTTAAAT
1 TGTTTATTTTTGTATTATTTAAAT
1085602 TGTTTATTTTTGT-TTATTTAA
1 TGTTTATTTTTGTATTATTTAA
1085623 TATTCGTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (24 bp):
TGTTTATTTTTGTATTATTTAAAT
Found at i:1085713 original size:23 final size:23
Alignment explanation
Indices: 1085664--1085714 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
1085654 AAAATATTTG
*
1085664 TTTAATATTTACGAATATGATCG
1 TTTAATATTTACGAATATGATCA
* *
1085687 TTTAATATTTACGAATATGTTTA
1 TTTAATATTTACGAATATGATCA
1085710 TTTAA
1 TTTAA
1085715 CGTTTGTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.49
Consensus pattern (23 bp):
TTTAATATTTACGAATATGATCA
Found at i:1092022 original size:2 final size:2
Alignment explanation
Indices: 1092015--1092042 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1092005 ATCCTATCTC
1092015 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1092043 GAGATAGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1092395 original size:2 final size:2
Alignment explanation
Indices: 1092388--1092444 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1092378 ACTAGGTGTA
1092388 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1092430 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
1092445 AGTACTTGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1093239 original size:32 final size:32
Alignment explanation
Indices: 1093220--1093297 Score: 156
Period size: 32 Copynumber: 2.4 Consensus size: 32
1093210 TTGGGGCGTG
1093220 AGAGCCTACCCAAGAGAGTACCTTAGGGCCTA
1 AGAGCCTACCCAAGAGAGTACCTTAGGGCCTA
1093252 AGAGCCTACCCAAGAGAGTACCTTAGGGCCTA
1 AGAGCCTACCCAAGAGAGTACCTTAGGGCCTA
1093284 AGAGCCTACCCAAG
1 AGAGCCTACCCAAG
1093298 GTCACCTTAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.32, C:0.29, G:0.24, T:0.14
Consensus pattern (32 bp):
AGAGCCTACCCAAGAGAGTACCTTAGGGCCTA
Found at i:1095780 original size:15 final size:15
Alignment explanation
Indices: 1095760--1095810 Score: 84
Period size: 15 Copynumber: 3.4 Consensus size: 15
1095750 CGCCCCGCAT
1095760 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCGC
1095775 CCGCCCCGCATCCGC
1 CCGCCCCGCATCCGC
* *
1095790 CTGCCCCACATCCGC
1 CCGCCCCGCATCCGC
1095805 CCGCCC
1 CCGCCC
1095811 AGCCAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.08, C:0.67, G:0.18, T:0.08
Consensus pattern (15 bp):
CCGCCCCGCATCCGC
Found at i:1095790 original size:11 final size:11
Alignment explanation
Indices: 1095749--1095776 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
1095739 GAGACATTAC
1095749 CCGCCCCGCAT
1 CCGCCCCGCAT
1095760 CCGCCCCGCAT
1 CCGCCCCGCAT
1095771 CCGCCC
1 CCGCCC
1095777 GCCCCGCATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.68, G:0.18, T:0.07
Consensus pattern (11 bp):
CCGCCCCGCAT
Found at i:1098938 original size:32 final size:33
Alignment explanation
Indices: 1098898--1099029 Score: 118
Period size: 32 Copynumber: 4.1 Consensus size: 33
1098888 GATCCAACCT
* * *
1098898 AAGG-AAGTATCTTGGGGCCTGAGAGCCTACCC
1 AAGGAAAGTACCTTAGGGCCTAAGAGCCTACCC
*
1098930 AA-GAAAGTACCTTAGAGCCTAAGAGCCTACCC
1 AAGGAAAGTACCTTAGGGCCTAAGAGCCTACCC
*
1098962 AATGG--AGTACCTT-GGGACCTTAGAGCCTACCC
1 AA-GGAAAGTACCTTAGGG-CCTAAGAGCCTACCC
*
1098994 AAGGAAATGT--CTTATGGCCTCAA-AGCCTACCC
1 AAGGAAA-GTACCTTAGGGCCT-AAGAGCCTACCC
1099026 AAGG
1 AAGG
1099030 TCACCTTAGG
Statistics
Matches: 83, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
31 5 0.06
32 71 0.86
33 4 0.05
34 3 0.04
ACGTcount: A:0.30, C:0.27, G:0.24, T:0.19
Consensus pattern (33 bp):
AAGGAAAGTACCTTAGGGCCTAAGAGCCTACCC
Found at i:1099021 original size:64 final size:63
Alignment explanation
Indices: 1098903--1099027 Score: 157
Period size: 64 Copynumber: 2.0 Consensus size: 63
1098893 AACCTAAGGA
* *
1098903 AGTATCTTGGGGCCTGAGAGCCTACCCAAGAAAGTACCTTAGAGCCTAAGAGCCTACCCAATGG
1 AGTACCTTGGGACCTGAGAGCCTACCCAAGAAAGTA-CTTAGAGCCTAAGAGCCTACCCAATGG
*
1098967 AGTACCTTGGGACCTTAGAGCCTACCCAAGGAAATGT-CTTATG-GCCTCAA-AGCCTACCCAA
1 AGTACCTTGGGACCTGAGAGCCTACCCAA-GAAA-GTACTTA-GAGCCT-AAGAGCCTACCCAA
1099028 GGTCACCTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
64 45 0.83
65 7 0.13
66 2 0.04
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (63 bp):
AGTACCTTGGGACCTGAGAGCCTACCCAAGAAAGTACTTAGAGCCTAAGAGCCTACCCAATGG
Found at i:1099578 original size:17 final size:17
Alignment explanation
Indices: 1099556--1099599 Score: 88
Period size: 17 Copynumber: 2.6 Consensus size: 17
1099546 CTGTTATATC
1099556 AGAATTTCTTAAGATTT
1 AGAATTTCTTAAGATTT
1099573 AGAATTTCTTAAGATTT
1 AGAATTTCTTAAGATTT
1099590 AGAATTTCTT
1 AGAATTTCTT
1099600 GGGGTTATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (17 bp):
AGAATTTCTTAAGATTT
Found at i:1100286 original size:21 final size:21
Alignment explanation
Indices: 1100262--1100345 Score: 123
Period size: 21 Copynumber: 4.0 Consensus size: 21
1100252 ACATAGAATT
* * *
1100262 TGTCCCTAATGACCATATATA
1 TGTCCCGAAAGACCACATATA
*
1100283 TGTCCCAAAAGACCACATATA
1 TGTCCCGAAAGACCACATATA
*
1100304 TGTCCCGAATGACCACATATA
1 TGTCCCGAAAGACCACATATA
1100325 TGTCCCGAAAGACCACATATA
1 TGTCCCGAAAGACCACATATA
1100346 ATTTGTAACA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (21 bp):
TGTCCCGAAAGACCACATATA
Found at i:1100315 original size:42 final size:42
Alignment explanation
Indices: 1100262--1100345 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
1100252 ACATAGAATT
* *
1100262 TGTCCCTAATGACCATATATATGTCCCAAAAGACCACATATA
1 TGTCCCGAATGACCACATATATGTCCCAAAAGACCACATATA
*
1100304 TGTCCCGAATGACCACATATATGTCCCGAAAGACCACATATA
1 TGTCCCGAATGACCACATATATGTCCCAAAAGACCACATATA
1100346 ATTTGTAACA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (42 bp):
TGTCCCGAATGACCACATATATGTCCCAAAAGACCACATATA
Found at i:1102012 original size:23 final size:23
Alignment explanation
Indices: 1101986--1102046 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
1101976 TTTTATATGG
1101986 CACTTCGGTGTATTTCTACAAGA
1 CACTTCGGTGTATTTCTACAAGA
* ** *
1102009 CACTTCGGTATATTTCTACGTGG
1 CACTTCGGTGTATTTCTACAAGA
*
1102032 CACTTCGGTGCATTT
1 CACTTCGGTGTATTT
1102047 TATACGAGCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.38
Consensus pattern (23 bp):
CACTTCGGTGTATTTCTACAAGA
Found at i:1108956 original size:21 final size:21
Alignment explanation
Indices: 1108926--1108966 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1108916 TTCTACGTGG
1108926 TCCTTCGGAACATATATGTAA
1 TCCTTCGGAACATATATGTAA
*
1108947 TCCTTTGGAACATATATGTA
1 TCCTTCGGAACATATATGTA
1108967 GTTCGTTGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.37
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:1108982 original size:23 final size:21
Alignment explanation
Indices: 1108932--1108984 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
1108922 GTGGTCCTTC
*
1108932 GGAACATATATGTAATCCTTT
1 GGAACATATATGTAATCCGTT
* *
1108953 GGAACATATATGTAGTTCGTT
1 GGAACATATATGTAATCCGTT
1108974 GAGACACATAT
1 G-GA-ACATAT
1108985 TTGGTCCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 19 0.70
22 2 0.07
23 6 0.22
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (21 bp):
GGAACATATATGTAATCCGTT
Found at i:1109111 original size:23 final size:23
Alignment explanation
Indices: 1109066--1109115 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1109056 ACTTTGGTGT
*
1109066 ATTTCTACGCGACACTTCGGTGC
1 ATTTCTACGCGACACTTCAGTGC
* * *
1109089 ATTTCTACGTGGCATTTCAGTGC
1 ATTTCTACGCGACACTTCAGTGC
1109112 ATTT
1 ATTT
1109116 TATACGAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.18, C:0.24, G:0.20, T:0.38
Consensus pattern (23 bp):
ATTTCTACGCGACACTTCAGTGC
Found at i:1114285 original size:21 final size:21
Alignment explanation
Indices: 1114237--1114286 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
1114227 ATTTGTCTGG
* *
1114237 AATGACCATATATATGTTCTA
1 AATGACCATATATATGTCCGA
1114258 AATGACCATATATATGTCCCGA
1 AATGACCATATATATGT-CCGA
1114280 AA-GACCA
1 AATGACCA
1114287 CATAGAATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 22 0.85
22 4 0.15
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (21 bp):
AATGACCATATATATGTCCGA
Found at i:1122397 original size:30 final size:30
Alignment explanation
Indices: 1122362--1122418 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
1122352 ACTATTATGT
1122362 TAACTATAACCACTTGGAAACTAAGAGTCA
1 TAACTATAACCACTTGGAAACTAAGAGTCA
1122392 TAACTATAACCACTTGGAAACTAAGAG
1 TAACTATAACCACTTGGAAACTAAGAG
1122419 ACAAGGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.23
Consensus pattern (30 bp):
TAACTATAACCACTTGGAAACTAAGAGTCA
Done.