Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold51
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: 3712191
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.32
Warning! 131352 characters in sequence are not A, C, G, or T
File 10 of 23
Found at i:1386340 original size:62 final size:62
Alignment explanation
Indices: 1385943--1386640 Score: 683
Period size: 62 Copynumber: 11.4 Consensus size: 62
1385933 AAATAAAATA
* * * * *
1385943 CGTCCTACTCTTTGAGGACTAGAAGGTGCCACCAACTTGTGTGGG-TTTTAAGAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
* * * * * *
1386004 CATCTTGCTCTTTGAGGATTGAAAGGTGCCACCAACTTGTATGGGCTTT-AAAAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
** * * *
1386065 CGTCCTGCTCTTTGAAAACTGAAAA-GTGTCACGAACTTGTGTGAGCTTTAAAAAG-AAAAGG
1 CGTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
* * * * * *
1386126 TGTCTTGCTCTTTAAGGACCGAAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAGGAATAA-G
1 CGTCCTGCTCTTTGAGGA-CTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
* * ** * * * *
1386187 CGTCCTGCTCTTTGAGGATTGGAAA-GTGCCATAAACTTGGGTGGCCTTT-AAAAGGAAAAGA
1 CGTCCTGCTCTTTGAGGACT-AAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
*
1386248 CATCCTGCTCTTTGAGGACTAGAAA-GTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
1 CGTCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
* * * *
1386310 TGTCCTGCTCTTTAAGGACTAAAAGATGCCACCAACTCGTGTGGGC-TT----AGAAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
* * * * *
1386367 CGTCTTGCTCTTTGAGGA-TAAAAGGGTGCCACAAACTCGTGTGGGCTTTGAAAAGAAAAAGA
1 CGTCCTGCTCTTTGAGGACTAAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
* * * * *
1386429 CATCCTACTCTTTGAGGACT-AAAGGATGCCACCAACTCGTGTGGGCTTTGAAAAGAAAAAAG
1 CGTCCTGCTCTTTGAGGACTAAAAGG-TGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
* * * ** * * *
1386491 CATCCTACTCTTTAAGGAC-AAAAGGGTGCCACCAACCCGTATGGGCTTTGAAAAGAAAAAGA
1 CGTCCTGCTCTTTGAGGACTAAAA-GGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
* * * *
1386553 TGTCCTGCTCTTTGAGGACTAAAAGGTGCTACCAACTCGTGTGGGCTTTAAAAAGGAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
**
1386615 TATCCTGCTCTTTGAGGACTAAAAGG
1 CGTCCTGCTCTTTGAGGACTAAAAGG
1386641 GCTAAAAGGG
Statistics
Matches: 531, Mismatches: 85, Indels: 41
0.81 0.13 0.06
Matches are distributed among these distances:
56 5 0.01
57 44 0.08
58 2 0.00
60 7 0.01
61 220 0.41
62 246 0.46
63 7 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (62 bp):
CGTCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTGTGTGGGCTTTAAAAAGAAAAAGG
Found at i:1395101 original size:1 final size:1
Alignment explanation
Indices: 1395091--1395174 Score: 78
Period size: 1 Copynumber: 84.0 Consensus size: 1
1395081 TGGCAATTGG
* * * ** * * **
1395091 AAAAAGAAAAAAACAAAACAAAAAAAAGGAAAAAGAAAAAAAAAACAAAACCAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
1395156 AAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAA
1395175 GTGAAGATTT
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 67 1.00
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:1395138 original size:32 final size:29
Alignment explanation
Indices: 1395091--1395174 Score: 109
Period size: 28 Copynumber: 2.9 Consensus size: 29
1395081 TGGCAATTGG
*
1395091 AAAAAGAAAAAAACAAAACAAAAAAAAGGAA
1 AAAAAAAAAAAAACAAAACAAAAAAAA--AA
*
1395122 AAAGAAAAAAAAAACAAAAC-CAAAAAAAA
1 AAA-AAAAAAAAAACAAAACAAAAAAAAAA
1395151 AAAAAAAAAAAAACAAAA-AAAAAA
1 AAAAAAAAAAAAACAAAACAAAAAA
1395175 GTGAAGATTT
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
28 19 0.40
29 5 0.10
31 9 0.19
32 15 0.31
ACGTcount: A:0.88, C:0.07, G:0.05, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAAAACAAAACAAAAAAAAAA
Found at i:1400700 original size:79 final size:79
Alignment explanation
Indices: 1400626--1400816 Score: 183
Period size: 79 Copynumber: 2.4 Consensus size: 79
1400616 GAAAAGTTTG
* * ** * *
1400626 ATATTTTGGAGATAAAATCGGGGTTGGAGTATC-CTCTCAGAAATAACGGGGTTAGAGTATCCTC
1 ATATTTTGAAAATAAAATCAAGGTTAGAGTATCTC-CTCAGAAATAACGAGGTTAGAGTATCCTC
1400690 GATTGTAAAAGATCA
65 GATTGTAAAAGATCA
* * *
1400705 ATGTTTTGAAAATAAAATCAAGGTTAGAGTATCTCCTCAGAAATAATGAGGTTGGAGTAT-CTCC
1 ATATTTTGAAAATAAAATCAAGGTTAGAGTATCTCCTCAGAAATAACGAGGTTAGAGTATCCT-C
*
1400769 GATTATGT-AAA-ATCG
65 GA-T-TGTAAAAGATCA
* * * * *
1400784 GTGTTTTGAAAATAAAATTAGGGTTGGAGTATC
1 ATATTTTGAAAATAAAATCAAGGTTAGAGTATC
1400817 CCCGTTTATG
Statistics
Matches: 94, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.02
79 84 0.89
80 5 0.05
81 3 0.03
ACGTcount: A:0.35, C:0.10, G:0.24, T:0.31
Consensus pattern (79 bp):
ATATTTTGAAAATAAAATCAAGGTTAGAGTATCTCCTCAGAAATAACGAGGTTAGAGTATCCTCG
ATTGTAAAAGATCA
Found at i:1400903 original size:51 final size:51
Alignment explanation
Indices: 1400753--1400903 Score: 176
Period size: 51 Copynumber: 3.0 Consensus size: 51
1400743 AGAAATAATG
* * * **
1400753 AGGTTGGAGTATCTCCGATTATGTAAAATCGGTGTTTTGAAAATAAAATTA
1 AGGTTGGAGTATCTCCGATTATGAAAAATCAGTGTTTTGGAAATAAAACCA
* * * * *
1400804 GGGTTGGAGTATCCCCGTTTATGGAAAATCAGTGTTTTTGAAATAAAACCA
1 AGGTTGGAGTATCTCCGATTATGAAAAATCAGTGTTTTGGAAATAAAACCA
* * * *
1400855 AGGTTAGAGTATCTTCGATTGTGAAAAATTAGTGTTTTGGAAATAAAAC
1 AGGTTGGAGTATCTCCGATTATGAAAAATCAGTGTTTTGGAAATAAAAC
1400904 TAAAGTTGAT
Statistics
Matches: 82, Mismatches: 18, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 82 1.00
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (51 bp):
AGGTTGGAGTATCTCCGATTATGAAAAATCAGTGTTTTGGAAATAAAACCA
Found at i:1403273 original size:51 final size:49
Alignment explanation
Indices: 1403148--1403282 Score: 182
Period size: 51 Copynumber: 2.7 Consensus size: 49
1403138 AAAAATACCT
* *
1403148 GAATGTATCGATATATTG-AGAAATGTATCGATACATCTGGGTAAACCCA
1 GAATGTATTGATATAATGAAG-AATGTATCGATACATCTGGGTAAACCCA
* * *
1403197 GAATGTATTGATACAACGAATAATGTATCGATACATCTAGGGTAAATCCCA
1 GAATGTATTGATATAATGAAGAATGTATCGATACATCT-GGGTAAA-CCCA
*
1403248 TAATGTATTGATATAATGAAGAATGTATCGATACA
1 GAATGTATTGATATAATGAAGAATGTATCGATACA
1403283 AATTGTGGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
49 31 0.42
50 8 0.11
51 35 0.47
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.30
Consensus pattern (49 bp):
GAATGTATTGATATAATGAAGAATGTATCGATACATCTGGGTAAACCCA
Found at i:1403903 original size:21 final size:20
Alignment explanation
Indices: 1403873--1403911 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
1403863 CACATTTTTG
1403873 TCCAAATGTATCGATACATT
1 TCCAAATGTATCGATACATT
1403893 TCCAGAATGTATCGATACA
1 TCCA-AATGTATCGATACA
1403912 AGGTCCCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.31
Consensus pattern (20 bp):
TCCAAATGTATCGATACATT
Found at i:1403922 original size:21 final size:20
Alignment explanation
Indices: 1403872--1403922 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
1403862 TCACATTTTT
*
1403872 GTCCAAATGTATCGATACAT
1 GTCCAAATGTATCGATACAG
*
1403892 TTCCAGAATGTATCGATACAAG
1 GTCCA-AATGTATCGATAC-AG
*
1403914 GTCCCAATG
1 GTCCAAATG
1403923 GTCAAAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
20 4 0.16
21 17 0.68
22 4 0.16
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.27
Consensus pattern (20 bp):
GTCCAAATGTATCGATACAG
Found at i:1404017 original size:32 final size:32
Alignment explanation
Indices: 1403976--1404045 Score: 113
Period size: 32 Copynumber: 2.2 Consensus size: 32
1403966 TAATTGTATT
*
1403976 GATACATAAGTGTTGTATCGATAGAATATATC
1 GATACATAAGTGTTGTATCGATACAATATATC
*
1404008 GATACATAAGTGTTGTATCGATACAATGTATC
1 GATACATAAGTGTTGTATCGATACAATATATC
*
1404040 GCTACA
1 GATACA
1404046 AAGCTACTGC
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:0.13, G:0.19, T:0.33
Consensus pattern (32 bp):
GATACATAAGTGTTGTATCGATACAATATATC
Found at i:1404028 original size:19 final size:19
Alignment explanation
Indices: 1403948--1404032 Score: 65
Period size: 19 Copynumber: 4.7 Consensus size: 19
1403938 ATTCAACAAT
* *
1403948 TTGTATCGATACAAACAGTAA
1 TTGTATCGATACATA-AGT-G
*
1403969 TTGTATTGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
1403988 TTGTATCGAT--AGAA---
1 TTGTATCGATACATAAGTG
*
1404002 -TATATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
1404020 TTGTATCGATACA
1 TTGTATCGATACA
1404033 ATGTATCGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
13 8 0.16
15 3 0.06
17 3 0.06
19 20 0.40
20 3 0.06
21 13 0.26
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:1405053 original size:20 final size:20
Alignment explanation
Indices: 1405008--1405053 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1404998 CTTAACAGCC
*
1405008 CATGATTCATGCATTTTAAG
1 CATGTTTCATGCATTTTAAG
1405028 CAATGTTTCATGCA-TTTACAG
1 C-ATGTTTCATGCATTTTA-AG
1405049 CATGT
1 CATGT
1405054 CCAGCACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 9 0.39
21 14 0.61
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.39
Consensus pattern (20 bp):
CATGTTTCATGCATTTTAAG
Found at i:1407517 original size:18 final size:18
Alignment explanation
Indices: 1407496--1407530 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1407486 TGATTGATGA
*
1407496 AAAAATTAGTAATTTTTT
1 AAAAATAAGTAATTTTTT
*
1407514 AAAAATAAGTTATTTTT
1 AAAAATAAGTAATTTTT
1407531 GGGTATTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (18 bp):
AAAAATAAGTAATTTTTT
Found at i:1414673 original size:21 final size:21
Alignment explanation
Indices: 1414649--1414697 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1414639 GTTAGGGCCT
*
1414649 TGTATCGATATATT-AGTGAAA
1 TGTATCGATACATTGAGTG-AA
* *
1414670 TGTATTGATACCTTGAGTGAA
1 TGTATCGATACATTGAGTGAA
1414691 TGTATCG
1 TGTATCG
1414698 TTACCCTAGC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.31, C:0.08, G:0.22, T:0.39
Consensus pattern (21 bp):
TGTATCGATACATTGAGTGAA
Found at i:1415645 original size:20 final size:20
Alignment explanation
Indices: 1415620--1415744 Score: 106
Period size: 20 Copynumber: 5.8 Consensus size: 20
1415610 TTTTACCCAG
1415620 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
1415640 ATGTATCGATACATTCTATCTTTTATCCAA
1 ATGTATCGAT--A--C-A--TTTT-T-C-A
*
1415670 ATGTATCGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1415690 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1415710 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
1415730 ATGTATCGATGCATT
1 ATGTATCGATACATT
1415745 CTTTTTACCC
Statistics
Matches: 85, Mismatches: 10, Indels: 20
0.74 0.09 0.17
Matches are distributed among these distances:
20 57 0.67
21 1 0.01
22 2 0.02
23 4 0.05
24 1 0.01
25 2 0.02
27 4 0.05
28 2 0.02
29 1 0.01
30 11 0.13
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1427385 original size:13 final size:13
Alignment explanation
Indices: 1427305--1427386 Score: 69
Period size: 13 Copynumber: 6.2 Consensus size: 13
1427295 CAATTCGCCA
*
1427305 TTTGTTAAGAAAT
1 TTTGTCAAGAAAT
*
1427318 GGTTGTCAAGAAAT
1 -TTTGTCAAGAAAT
* *
1427332 TATCGTCAAGAACT
1 T-TTGTCAAGAAAT
*
1427346 TATGTCAAG-AAT
1 TTTGTCAAGAAAT
*
1427358 GTTTGT-TAGAAAT
1 -TTTGTCAAGAAAT
1427371 TTTGTCAAGAAAT
1 TTTGTCAAGAAAT
1427384 TTT
1 TTT
1427387 CACCCACAAG
Statistics
Matches: 53, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
12 9 0.17
13 22 0.42
14 22 0.42
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.39
Consensus pattern (13 bp):
TTTGTCAAGAAAT
Found at i:1427422 original size:28 final size:28
Alignment explanation
Indices: 1427389--1427998 Score: 533
Period size: 28 Copynumber: 21.0 Consensus size: 28
1427379 GAAATTTTCA
1427389 CCCACAAGTCAGTGGCATCTTTTCAAAG
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
* *
1427417 CCCACAAGTCAGTGGCATCATTTCAAAA
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
* *
1427445 CCCACAAGTCAGTGGCACCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
1427473 CCCACAAGTCAGTGGCACTCTTTTCAAAG
1 CCCACAAGTCAGTGGCA-TCTTTTCAAAG
*
1427502 CCCACAAGTCAATGGCAACTCTTTTCAAAG
1 CCCACAAGTCAGTGGC-A-TCTTTTCAAAG
*
1427532 TCCACACAAGTTAGTGGCAACTCTTTTCAAAG
1 -CC-CACAAGTCAGTGGC-A-TCTTTTCAAAG
* * * * * *
1427564 CCCACACAAATCGGTGGCACCCTTCCAAAA
1 -CC-CACAAGTCAGTGGCATCTTTTCAAAG
* * * *
1427594 CTCACAAGTCAGTGGCACCTTTTCACAC
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
* *
1427622 CCCACAA-ACAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
*
1427649 CCCACAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
* *
1427677 CCCACAAGTTAGTGGCATCCTTTTAAAACCCACTGAG
1 CCCACAAGTCAGTGGCAT-CTTTT------CA--AAG
** * *
1427714 CCCACAAGTTGGTAGCATCATTTCAAAG
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
* * * *
1427742 CCCACAAGTCAATAGCACCATTTCAAAG
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
* *
1427770 CCCATAAGTCAGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
* * *
1427798 CCCATAAGTCGGTGGCATCCTTTCAAAG
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
* * *
1427826 CCCACAAGTTAGTGGCATCCTTCCAAAG
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
* *
1427854 CCCACAAGTTAGTGGCATCATTTCAAAG
1 CCCACAAGTCAGTGGCATCTTTTCAAAG
*
1427882 CCCACAAGTCAGTGGCACCATTTT-AAAG
1 CCCACAAGTCAGTGGCATC-TTTTCAAAG
** * *
1427910 CTAACAAGTCAGTGGCACCATTTT-AAAA
1 CCCACAAGTCAGTGGCATC-TTTTCAAAG
* * *
1427938 CCCACAAGTTAATGGCATACCCTTTCAAAG
1 CCCACAAGTCAGTGGCAT--CTTTTCAAAG
*
1427968 CCCACACAAGTCGGTGGCAACTCTTTTCAAA
1 -CC-CACAAGTCAGTGGC-A-TCTTTTCAAA
1427999 ACTCATACAA
Statistics
Matches: 488, Mismatches: 72, Indels: 40
0.81 0.12 0.07
Matches are distributed among these distances:
27 22 0.05
28 315 0.65
29 35 0.07
30 26 0.05
31 5 0.01
32 59 0.12
33 1 0.00
34 1 0.00
35 2 0.00
36 4 0.01
37 18 0.04
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.23
Consensus pattern (28 bp):
CCCACAAGTCAGTGGCATCTTTTCAAAG
Found at i:1427732 original size:37 final size:37
Alignment explanation
Indices: 1427675--1427746 Score: 99
Period size: 37 Copynumber: 1.9 Consensus size: 37
1427665 ATCCTTTCAA
* * *
1427675 AGCCCACAAGTTAGTGGCATCCTTTTAAAACCCACTG
1 AGCCCACAAGTTAGTAGCATCATTTCAAAACCCACTG
* *
1427712 AGCCCACAAGTTGGTAGCATCATTTCAAAGCCCAC
1 AGCCCACAAGTTAGTAGCATCATTTCAAAACCCAC
1427747 AAGTCAATAG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.22
Consensus pattern (37 bp):
AGCCCACAAGTTAGTAGCATCATTTCAAAACCCACTG
Found at i:1427807 original size:149 final size:146
Alignment explanation
Indices: 1427415--1427973 Score: 604
Period size: 149 Copynumber: 3.8 Consensus size: 146
1427405 ATCTTTTCAA
*
1427415 AGCCCACAAGTCAGTGGCATCATTTCAAAACCCACAAGTCAGTGGCACCCTTTCAAAGCCCACAA
1 AGCCCACAAGTCAGTGGCATCATTTCAAAACCCACAAGTCAGTGGCACCATTTCAAAGCCCACAA
* *
1427480 GTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCAACTCTTTTCAAAGTCCACACAAGTTA
66 GTCAGTGGCA-TCCTTTCAAAGCCCACAAGTCAATGGC-A-TCCTTTCAAAG-CC-CACAAGTTA
*
1427545 GTGGCAACTCTTTTCAAAGCCCAC
126 GTGGCATC-CTTTT-AAA-CCCAC
* * * * * * * *
1427569 A---CA-AA-TCGGTGGCACCCTTCCAAAACTCACAAGTCAGTGGCACCTTTTCACACCCCACAA
1 AGCCCACAAGTCAGTGGCATCATTTCAAAACCCACAAGTCAGTGGCACCATTTCAAAGCCCACAA
* *
1427629 -ACAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGC
66 GTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAGCCCACAAGTTAGTGGC
1427693 ATCCTTTTAAAACCCAC
131 ATCCTTTT-AAACCCAC
** * * * * *
1427710 TGAGCCCACAAGTTGGTAGCATCATTTCAAAGCCCACAAGTCAATAGCACCATTTCAAAGCCCAT
1 --AGCCCACAAGTCAGTGGCATCATTTCAAAACCCACAAGTCAGTGGCACCATTTCAAAGCCCAC
* **
1427775 AAGTCAGTGGCATCCTTTCAAAGCCCATAAGTCGGTGGCATCCTTTCAAAGCCCACAAGTTAGTG
64 AAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAGCCCACAAGTTAGTG
*
1427840 GCATCC--TT----CCAA
129 GCATCCTTTTAAACCCAC
* * * **
1427852 AGCCCACAAGTTAGTGGCATCATTTCAAAGCCCACAAGTCAGTGGCACCATTTTAAAGCTAACAA
1 AGCCCACAAGTCAGTGGCATCATTTCAAAACCCACAAGTCAGTGGCACCATTTCAAAGCCCACAA
* * *
1427917 GTCAGTGGCA-CCATTTTAAAACCCACAAGTTAATGGCATACCCTTTCAAAGCCCACA
66 GTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAATGGCAT--CCTTTCAAAGCCCACA
1427974 CAAGTCGGTG
Statistics
Matches: 349, Mismatches: 45, Indels: 34
0.82 0.11 0.08
Matches are distributed among these distances:
139 2 0.01
140 87 0.25
141 5 0.01
142 27 0.08
143 17 0.05
144 2 0.01
145 10 0.03
146 3 0.01
147 29 0.08
148 50 0.14
149 112 0.32
150 2 0.01
151 2 0.01
154 1 0.00
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (146 bp):
AGCCCACAAGTCAGTGGCATCATTTCAAAACCCACAAGTCAGTGGCACCATTTCAAAGCCCACAA
GTCAGTGGCATCCTTTCAAAGCCCACAAGTCAATGGCATCCTTTCAAAGCCCACAAGTTAGTGGC
ATCCTTTTAAACCCAC
Found at i:1427842 original size:177 final size:175
Alignment explanation
Indices: 1427389--1427973 Score: 584
Period size: 177 Copynumber: 3.4 Consensus size: 175
1427379 GAAATTTTCA
* * *
1427389 CCCACAAGTCAGTGGCATCTTTTCAAAGCCCACAAGTCAGTGGCATCATTTCAAAACCCACAAGT
1 CCCACAAGTCAGTGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAACCCACAAGT
* * * *
1427454 CAGTGGCACCCTTTCAAAGCCCACAAGTCAGTGGCACTCTTTTCAAAGCCCACAAGTCAATGGCA
66 CAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTTCAAAGCCCACAAGTTAGTGGCA
* * ** * *
1427519 ACTCTTTTCAAAGTC-CACACAAGTTAGTGGCAACTCTTTTCAAAGC
130 TC-CTTTTAAAACCCACACACAAGTTAGTAGCAACTCATTTCAAAGC
* * * * * * * *
1427565 CCACACAAATCGGTGGCACCCTTCCAAAACTCACAAGTCAGTGGCA-CCTTTTCACACCCCACAA
1 CC-CACAAGTCAGTGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAACCCACAA
*
1427629 -ACAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGC
64 GTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGC
*
1427693 ATCCTTTTAAAACCCACTGAGCCCACAAGTTGGTAGC-A-TCATTTCAAAG-
129 ATCCTTTTAAAACCCAC--A---CACAAGTTAGTAGCAACTCATTTCAAAGC
* * * * *
1427742 CCCACAAGTCAATAGCACCATTTCAAAGCCCATAAGTCAGTGGCATCCTTTCAAAGCCCATAAGT
1 CCCACAAGTCAGTGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAACCCACAAGT
* * *
1427807 CGGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCATCCTTCCAAAGCCCACAAGTTAGTGGCAT
66 CAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCAT
* * * * * *
1427872 -CATTTCAAA-GC-C-CACAAGTCAGTGGC-AC-CATTTTAAAG-
131 CCTTTTAAAACCCACACACAAGTTAGTAGCAACTCATTTCAAAGC
** * * * * *
1427910 CTAACAAGTCAGTGGCACCATTTTAAAACCCACAAGTTAATGGCATACCCTTTCAAAGCCCACA
1 CCCACAAGTCAGTGGCACCATTTCAAAGCCCACAAGTCAGTGGCAT--CCTTTCAAAACCCACA
1427974 CAAGTCGGTG
Statistics
Matches: 341, Mismatches: 55, Indels: 32
0.80 0.13 0.07
Matches are distributed among these distances:
168 58 0.17
170 15 0.04
174 10 0.03
175 28 0.08
176 91 0.27
177 116 0.34
178 10 0.03
179 1 0.00
180 12 0.04
ACGTcount: A:0.31, C:0.30, G:0.16, T:0.22
Consensus pattern (175 bp):
CCCACAAGTCAGTGGCACCATTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAACCCACAAGT
CAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCAT
CCTTTTAAAACCCACACACAAGTTAGTAGCAACTCATTTCAAAGC
Found at i:1428148 original size:45 final size:47
Alignment explanation
Indices: 1428097--1428216 Score: 145
Period size: 49 Copynumber: 2.6 Consensus size: 47
1428087 TCCGATATCA
*
1428097 CTGGCATTGAATCAGCATATTGGCAC-CTT-TATTAGCCCAATGTCG
1 CTGGCATTGAATCAGCACATTGGCACACTTCTATTAGCCCAATGTCG
* * *
1428142 CTGGCATTGAATCAGTACATTGGTACACATTTCTCTTAGCCCAATGTCG
1 CTGGCATTGAATCAGCACATTGG--CACACTTCTATTAGCCCAATGTCG
* * *
1428191 CTGGCCTTGAATTAGCACATTAGCAC
1 CTGGCATTGAATCAGCACATTGGCAC
1428217 TCCTCTCATC
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
45 21 0.33
47 6 0.10
48 2 0.03
49 34 0.54
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (47 bp):
CTGGCATTGAATCAGCACATTGGCACACTTCTATTAGCCCAATGTCG
Found at i:1429018 original size:20 final size:20
Alignment explanation
Indices: 1428993--1429070 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
1428983 CTTTTATCCA
*
1428993 AATGTATCAATACATTTTTT
1 AATGTATCAATACATTTTTC
* * * *
1429013 AATGTATCGATACATGTATG
1 AATGTATCAATACATTTTTC
*
1429033 AATGTAT-AGATACATTCTTC
1 AATGTATCA-ATACATTTTTC
* *
1429053 AATGTATCGATATATTTT
1 AATGTATCAATACATTTT
1429071 ATCTTTTTAT
Statistics
Matches: 44, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.44
Consensus pattern (20 bp):
AATGTATCAATACATTTTTC
Found at i:1429117 original size:91 final size:90
Alignment explanation
Indices: 1428952--1429118 Score: 244
Period size: 91 Copynumber: 1.8 Consensus size: 90
1428942 AAATATACCA
* * *
1428952 ATACATTTTTTAATGTATCGATACATTCTATCTTTTATCCAAATGTATCAATACATTTTTTAATG
1 ATACATTCTTCAATGTATCGATACATTCTATCTTTTATCCAAATGTATCAATACATTTTTCAATG
*
1429017 TATCGATACATGTATGAATGTATAG
66 TATCAATACATGTATGAATGTATAG
* * * * *
1429042 ATACATTCTTCAATGTATCGATATATTTTATCTTTTTATCCAGATTTATCGATACATTTTTCAAT
1 ATACATTCTTCAATGTATCGATACATTCTATC-TTTTATCCAAATGTATCAATACATTTTTCAAT
1429107 GTATCAATACAT
65 GTATCAATACAT
1429119 CTAGTTAAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
90 28 0.42
91 39 0.58
ACGTcount: A:0.32, C:0.14, G:0.08, T:0.46
Consensus pattern (90 bp):
ATACATTCTTCAATGTATCGATACATTCTATCTTTTATCCAAATGTATCAATACATTTTTCAATG
TATCAATACATGTATGAATGTATAG
Found at i:1429974 original size:20 final size:22
Alignment explanation
Indices: 1429934--1429974 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
1429924 TCGCCTTTGA
*
1429934 CCATGCATTTTTTTACTATGTT
1 CCATGCATTTTTTAACTATGTT
1429956 CCATGCA-TTTTTAAC-ATGT
1 CCATGCATTTTTTAACTATGT
1429975 CTAGCATCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 7 0.39
22 7 0.39
ACGTcount: A:0.22, C:0.20, G:0.10, T:0.49
Consensus pattern (22 bp):
CCATGCATTTTTTAACTATGTT
Found at i:1435556 original size:13 final size:13
Alignment explanation
Indices: 1435538--1435562 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1435528 ATAATGCACA
1435538 GTATCGATACATT
1 GTATCGATACATT
1435551 GTATCGATACAT
1 GTATCGATACAT
1435563 GACCACTGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1435672 original size:32 final size:33
Alignment explanation
Indices: 1435631--1435698 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1435621 CCTTAACTGT
1435631 TTGTATCGATACAT-A-CAAGATGTATCAATACA
1 TTGTATCGATACATGACCAA-ATGTATCAATACA
*
1435663 TTGTATCGATACATGACCAAATGTATCGATACA
1 TTGTATCGATACATGACCAAATGTATCAATACA
1435696 TTG
1 TTG
1435699 GCTTGTAACG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
32 14 0.42
33 16 0.48
34 3 0.09
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (33 bp):
TTGTATCGATACATGACCAAATGTATCAATACA
Found at i:1444360 original size:13 final size:13
Alignment explanation
Indices: 1444342--1444366 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1444332 ATAATGTACA
1444342 GTATCGATACATT
1 GTATCGATACATT
1444355 GTATCGATACAT
1 GTATCGATACAT
1444367 GACCACTGTA
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1445986 original size:57 final size:57
Alignment explanation
Indices: 1445895--1446006 Score: 206
Period size: 57 Copynumber: 2.0 Consensus size: 57
1445885 TAGTACCAAG
*
1445895 TGTAGTGAAAGCACTAAGTCCTTAACTTGATATAGCATGTCTTGTCGCTTTTGGTAA
1 TGTAGTGAAAGCACTAAGTCCTTAACTTGATATAGCATGTCTTGTCACTTTTGGTAA
*
1445952 TGTAGTGAAAGCACTAAGTCCTTAACTTGGTATAGCATGTCTTGTCACTTTTGGT
1 TGTAGTGAAAGCACTAAGTCCTTAACTTGATATAGCATGTCTTGTCACTTTTGGT
1446007 TAGTATATTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (57 bp):
TGTAGTGAAAGCACTAAGTCCTTAACTTGATATAGCATGTCTTGTCACTTTTGGTAA
Found at i:1446579 original size:13 final size:13
Alignment explanation
Indices: 1446540--1446573 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1446530 TAAGTACTTT
1446540 AATTTAATTAAA-A
1 AATTT-ATTAAATA
1446553 AATTTATTAAATA
1 AATTTATTAAATA
1446566 AATTTATT
1 AATTTATT
1446574 TTATAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 14 0.70
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATTTATTAAATA
Found at i:1447043 original size:23 final size:22
Alignment explanation
Indices: 1447012--1447056 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1447002 CTTATTAATT
*
1447012 TTATTTATTCATAAAATATATAA
1 TTATATATTCA-AAAATATATAA
* *
1447035 TTATATATTTAAAAATCTATAA
1 TTATATATTCAAAAATATATAA
1447057 AACAACTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (22 bp):
TTATATATTCAAAAATATATAA
Found at i:1447433 original size:6 final size:6
Alignment explanation
Indices: 1447412--1447470 Score: 63
Period size: 6 Copynumber: 10.5 Consensus size: 6
1447402 TGTTTTTTAA
* **
1447412 TTAAA- TTAAA- TTAAAT TTAAAT TTAAAT TT--AT TTAAAT ATATTT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
1447456 TTAAAT TTAAAT TTA
1 TTAAAT TTAAAT TTA
1447471 TTAAATCACC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
4 4 0.09
5 10 0.22
6 31 0.69
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (6 bp):
TTAAAT
Found at i:1447438 original size:22 final size:22
Alignment explanation
Indices: 1447412--1447468 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
1447402 TGTTTTTTAA
*
1447412 TTAAATTAAATTAAATTTAAAT
1 TTAAATTAAATTAAATATAAAT
* * **
1447434 TTAAATTTATTTAAATATATTT
1 TTAAATTAAATTAAATATAAAT
1447456 TTAAATTTAAATT
1 TTAAA-TTAAATT
1447469 TATTAAATCA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
22 22 0.81
23 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAATTAAATTAAATATAAAT
Found at i:1448173 original size:23 final size:23
Alignment explanation
Indices: 1448147--1448198 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
1448137 TAAGTAATTT
* *
1448147 TTATTA-TATACATATATAAAATA
1 TTATTAGTATAAATAT-TAAAAAA
1448170 TTA-TAGTATAAATATTAAAAAA
1 TTATTAGTATAAATATTAAAAAA
1448192 TATATTA
1 T-TATTA
1448199 AGTTATTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
22 9 0.38
23 13 0.54
24 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TTATTAGTATAAATATTAAAAAA
Found at i:1448246 original size:15 final size:15
Alignment explanation
Indices: 1448214--1448259 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1448204 TTTAACTTTT
*
1448214 AAAATTTAA-TA-AA
1 AAAATTTAATTATTA
1448227 AAAATTTAATTATTA
1 AAAATTTAATTATTA
*
1448242 AAAATTTAATTTTTA
1 AAAATTTAATTATTA
1448257 AAA
1 AAA
1448260 TATATTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 9 0.31
14 2 0.07
15 18 0.62
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AAAATTTAATTATTA
Found at i:1448357 original size:11 final size:10
Alignment explanation
Indices: 1448329--1448389 Score: 56
Period size: 10 Copynumber: 6.2 Consensus size: 10
1448319 TTATTCACTT
*
1448329 ATAAATATAA
1 ATAAATTTAA
1448339 ATAAATTTAA
1 ATAAATTTAA
*
1448349 ATAAAATTTAC
1 AT-AAATTTAA
1448360 AT---TTTAA
1 ATAAATTTAA
1448367 ATTAAATTTAA
1 A-TAAATTTAA
*
1448378 ATAAATATAA
1 ATAAATTTAA
1448388 AT
1 AT
1448390 TATATTAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
7 5 0.12
8 1 0.02
10 21 0.50
11 15 0.36
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (10 bp):
ATAAATTTAA
Found at i:1449652 original size:115 final size:114
Alignment explanation
Indices: 1449441--1449657 Score: 289
Period size: 115 Copynumber: 1.9 Consensus size: 114
1449431 TTATAATTTT
*
1449441 AATTTTTTTATTATTAATACTCATGATTAATATTTATTATAATTACTTATCATAATATTTATTAT
1 AATTTTTTTATTATCAATACTCATGATTAATATTTATTATAATTACTTATCATAATATTTATTAT
* * * *
1449506 GTTTATAATTATAATTATCATGATAAGATTAAAAATATATTCATAATTA
66 ATTCATAATTACAATTATCATAATAAGATTAAAAATATATTCATAATTA
* * *
1449555 AATTTTTATTATTATCAATATTCATTG-TTAATATTTATTGTAATTA-TCTATCATGATATTTAT
1 AATTTTT-TTATTATCAATACTCA-TGATTAATATTTATTATAATTACT-TATCATAATATTTAT
1449618 TATATTCATAATTACAATTAAT-ATAATATA-ATTAAAAATA
63 TATATTCATAATTACAATT-ATCATAATA-AGATTAAAAATA
1449658 CATCTATCGC
Statistics
Matches: 90, Mismatches: 8, Indels: 9
0.84 0.07 0.08
Matches are distributed among these distances:
114 8 0.09
115 77 0.86
116 5 0.06
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (114 bp):
AATTTTTTTATTATCAATACTCATGATTAATATTTATTATAATTACTTATCATAATATTTATTAT
ATTCATAATTACAATTATCATAATAAGATTAAAAATATATTCATAATTA
Found at i:1450172 original size:24 final size:24
Alignment explanation
Indices: 1450112--1450177 Score: 71
Period size: 28 Copynumber: 2.6 Consensus size: 24
1450102 TTATATTAAA
1450112 TTATTTTT-AATATAAATAAAATT
1 TTATTTTTAAATATAAATAAAATT
* *
1450135 TTAATAATTATTAAATATAAGTATAATT
1 TT-AT--TT-TTAAATATAAATAAAATT
1450163 TTATTTTTAAATATA
1 TTATTTTTAAATATA
1450178 TATTTTATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
23 2 0.06
24 11 0.31
25 2 0.06
26 2 0.06
27 4 0.11
28 15 0.42
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTATTTTTAAATATAAATAAAATT
Found at i:1450184 original size:19 final size:18
Alignment explanation
Indices: 1450156--1450197 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
1450146 TAAATATAAG
1450156 TATAATTTTATT-TTTAAA
1 TATAATTTTATTATTT-AA
1450174 TATATATTTTATTATTTAA
1 TATA-ATTTTATTATTTAA
1450193 TATAA
1 TATAA
1450198 ATATAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.23
19 14 0.64
20 3 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TATAATTTTATTATTTAA
Found at i:1450185 original size:80 final size:80
Alignment explanation
Indices: 1450119--1450321 Score: 204
Period size: 73 Copynumber: 2.6 Consensus size: 80
1450109 AAATTATTTT
* *
1450119 TAATATAAATAAAATTTTAATAATTATTAAATATAAGTATAATTTTATTTTTAAATATATATTTT
1 TAAT-TAAAT-AAATTTTAATAATTATTAAACATAAATATAATTTTATTTTTAAATATATATTTT
*
1450184 ATTATTTAATATAAATA
64 ATTATTAAATATAAATA
* * * *
1450201 TAATTTAATAATTTTTAATTATTATTCAACATAAATATAATTTTA--TTT--AT-T-TA-TTTAT
1 TAATTAAATAAATTTTAATAATTATTAAACATAAATATAATTTTATTTTTAAATATATATTTTAT
* **
1450259 TATTTAATATAGGTA
66 TATTAAATATAAATA
* * * * *
1450274 TAATTTAATAATTTTTAATTATTATTCAACATAAATATAAATTTATTT
1 TAATTAAATAAATTTTAATAATTATTAAACATAAATATAATTTTATTT
1450322 ACATTTTATT
Statistics
Matches: 110, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
73 62 0.56
74 2 0.02
75 2 0.02
76 2 0.02
78 3 0.03
80 31 0.28
81 4 0.04
82 4 0.04
ACGTcount: A:0.44, C:0.02, G:0.01, T:0.52
Consensus pattern (80 bp):
TAATTAAATAAATTTTAATAATTATTAAACATAAATATAATTTTATTTTTAAATATATATTTTAT
TATTAAATATAAATA
Found at i:1450223 original size:37 final size:37
Alignment explanation
Indices: 1450182--1450364 Score: 178
Period size: 37 Copynumber: 5.0 Consensus size: 37
1450172 AATATATATT
1450182 TTATTATTTAATATAAATATAATTTAATAATTTTTAA
1 TTATTATTTAATATAAATATAATTTAATAATTTTTAA
* * * *
1450219 TTATTATTCAACATAAATATAATTT--TATTTATTTAT
1 TTATTATTTAATATAAATATAATTTAATAATT-TTTAA
**
1450255 TTATTATTTAATATAGGTATAATTTAATAATTTTTAA
1 TTATTATTTAATATAAATATAATTTAATAATTTTTAA
* * * ** *
1450292 TTATTATTCAACATAAATATAAATT--T-ATTTACATT
1 TTATTATTTAATATAAATATAATTTAATAATTTTTA-A
* *
1450327 TTATTATTTAATATAAATAGAGTTTTAATAATTTTTAA
1 TTATTATTTAATATAAATATA-ATTTAATAATTTTTAA
1450365 CACTTATTTT
Statistics
Matches: 112, Mismatches: 26, Indels: 15
0.73 0.17 0.10
Matches are distributed among these distances:
34 5 0.04
35 23 0.21
36 27 0.24
37 47 0.42
38 5 0.04
39 5 0.04
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (37 bp):
TTATTATTTAATATAAATATAATTTAATAATTTTTAA
Found at i:1450384 original size:73 final size:72
Alignment explanation
Indices: 1450179--1450364 Score: 291
Period size: 73 Copynumber: 2.6 Consensus size: 72
1450169 TTAAATATAT
*
1450179 ATTTTATTATTTAATATAAATATAATTTAATAATTTTTAATTATTATTCAACATAAATATAATTT
1 ATTTTATTATTTAATATAAATATAATTTAATAATTTTTAATTATTATTCAACATAAATATAAATT
*
1450244 TATTTAT
66 TATTTAC
* **
1450251 TTATTTATTATTTAATATAGGTATAATTTAATAATTTTTAATTATTATTCAACATAAATATAAAT
1 AT-TTTATTATTTAATATAAATATAATTTAATAATTTTTAATTATTATTCAACATAAATATAAAT
1450316 TTATTTAC
65 TTATTTAC
* *
1450324 ATTTTATTATTTAATATAAATAGAGTTTTAATAATTTTTAA
1 ATTTTATTATTTAATATAAATATA-ATTTAATAATTTTTAA
1450365 CACTTATTTT
Statistics
Matches: 102, Mismatches: 10, Indels: 3
0.89 0.09 0.03
Matches are distributed among these distances:
72 20 0.20
73 82 0.80
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (72 bp):
ATTTTATTATTTAATATAAATATAATTTAATAATTTTTAATTATTATTCAACATAAATATAAATT
TATTTAC
Found at i:1450402 original size:73 final size:72
Alignment explanation
Indices: 1450167--1450404 Score: 243
Period size: 73 Copynumber: 3.3 Consensus size: 72
1450157 ATAATTTTAT
1450167 TTTTAA-ATATATATTTTATTATTTAATATAAATATAATTTAATAATTTTTAATTATTATTCAAC
1 TTTTAATA-ATAT-TTTTATTATTTAATATAAATATAATTTAATAATTTTTAATTATTATTCAAC
1450231 ATAAATATAA
64 ATAAATAT-A
* * **
1450241 TTTTATTTAT-TTATTTATTATTTAATATAGGTATAATTTAATAATTTTTAATTATTATTCAACA
1 TTTTAATAATATT-TTTATTATTTAATATAAATATAATTTAATAATTTTTAATTATTATTCAACA
1450305 TAAATATAA
65 TAAATAT-A
* * * * * * * **
1450314 ATTTATTTACA-TTTTATTATTTAATATAAATAGAGTTTTAATAATTTTTAA-CACTTATTTTAC
1 TTTTAATAATATTTTTATTATTTAATATAAATATA-ATTTAATAATTTTTAATTA-TTATTCAAC
*
1450377 TTAAATAT-
64 ATAAATATA
1450385 TTTTAATAATCATTTTTATT
1 TTTTAATAAT-ATTTTTATT
1450405 CCATCATCAT
Statistics
Matches: 139, Mismatches: 18, Indels: 15
0.81 0.10 0.09
Matches are distributed among these distances:
71 6 0.04
72 22 0.16
73 104 0.75
74 7 0.05
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (72 bp):
TTTTAATAATATTTTTATTATTTAATATAAATATAATTTAATAATTTTTAATTATTATTCAACAT
AAATATA
Found at i:1451020 original size:21 final size:21
Alignment explanation
Indices: 1450965--1451054 Score: 100
Period size: 21 Copynumber: 4.4 Consensus size: 21
1450955 ATTATTAATT
*
1450965 TTAATTTTATTATCATAATAA
1 TTAATTTTATTATTATAATAA
*
1450986 TTAATCTTATTATTATAATAA
1 TTAATTTTATTATTATAATAA
1451007 TTAATTTTATTATTAT--T-A
1 TTAATTTTATTATTATAATAA
*
1451025 TTATTTTTAATT-TTAATAA-AA
1 TTAATTTT-ATTATT-ATAATAA
1451046 TTAATTTTA
1 TTAATTTTA
1451055 CCGTAGATCT
Statistics
Matches: 59, Mismatches: 5, Indels: 11
0.79 0.07 0.15
Matches are distributed among these distances:
18 10 0.17
19 6 0.10
20 1 0.02
21 42 0.71
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTAATTTTATTATTATAATAA
Found at i:1451034 original size:24 final size:24
Alignment explanation
Indices: 1450958--1451039 Score: 78
Period size: 24 Copynumber: 3.4 Consensus size: 24
1450948 ATATCTTATT
*
1450958 ATTAATTTTAATT-TTATTATCATA
1 ATTAATTTT-ATTATTATTATAATA
* *
1450982 A-TAATTAATCTTATTATTATAATA
1 ATTAATT-TTATTATTATTATAATA
* *
1451006 ATTAATTTTATTATTATTATTATT
1 ATTAATTTTATTATTATTATAATA
*
1451030 TTTAATTTTA
1 ATTAATTTTA
1451040 ATAAAATTAA
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
23 7 0.15
24 35 0.74
25 5 0.11
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTAATTTTATTATTATTATAATA
Found at i:1455998 original size:20 final size:20
Alignment explanation
Indices: 1455973--1456043 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
1455963 TGAAGCAATA
*
1455973 TATCGATACAAT-TCATCATG
1 TATCGATACAATAT-ACCATG
1455993 TATCGATACAATATACCATG
1 TATCGATACAATATACCATG
*
1456013 TATCGATATAATATACCATG
1 TATCGATACAATATACCATG
1456033 TATCGATACAA
1 TATCGATACAA
1456044 ACAGTGGTAG
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
20 46 0.98
21 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.10, T:0.32
Consensus pattern (20 bp):
TATCGATACAATATACCATG
Found at i:1456097 original size:20 final size:19
Alignment explanation
Indices: 1456072--1456144 Score: 76
Period size: 20 Copynumber: 3.7 Consensus size: 19
1456062 TTGCCAGTTT
**
1456072 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
*
1456092 CATGTATCGATATAATGAA
1 CATGTATCGATACAATGAA
*
1456111 CATGTATCGATACAAAGCATA
1 CATGTATCGATACAATG-A-A
1456132 -ATGTATCGATACA
1 CATGTATCGATACA
1456145 TCTGGATGTG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
19 17 0.37
20 28 0.61
21 1 0.02
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1456116 original size:19 final size:20
Alignment explanation
Indices: 1456072--1456125 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
1456062 TTGCCAGTTT
**
1456072 CATGTATCGATACAATTGTC
1 CATGTATCGATACAATTGAA
*
1456092 CATGTATCGATATAA-TGAA
1 CATGTATCGATACAATTGAA
1456111 CATGTATCGATACAA
1 CATGTATCGATACAA
1456126 AGCATAATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1458671 original size:13 final size:13
Alignment explanation
Indices: 1458653--1458689 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1458643 ATAGTAACCC
1458653 ATGTATCGATACA
1 ATGTATCGATACA
1458666 ATGTATCGATACA
1 ATGTATCGATACA
*
1458679 ATGTATGGATA
1 ATGTATCGATA
1458690 TGAGGAATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1462418 original size:13 final size:13
Alignment explanation
Indices: 1462400--1462424 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1462390 CAAAAAATGT
1462400 TGTATCGATACAA
1 TGTATCGATACAA
1462413 TGTATCGATACA
1 TGTATCGATACA
1462425 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1462508 original size:13 final size:13
Alignment explanation
Indices: 1462490--1462514 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1462480 ATTACTCACA
1462490 TGTATCGATACAT
1 TGTATCGATACAT
1462503 TGTATCGATACA
1 TGTATCGATACA
1462515 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1462651 original size:52 final size:52
Alignment explanation
Indices: 1462523--1462643 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1462513 CACTGATCTT
*
1462523 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1462575 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1462627 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
1462644 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1469917 original size:14 final size:14
Alignment explanation
Indices: 1469898--1469936 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1469888 TAATCTTCAC
* *
1469898 AAAAAAAGATGAAA
1 AAAAAAAAAAGAAA
1469912 AAAAAAAAAAGAAA
1 AAAAAAAAAAGAAA
1469926 AAAAAGAAAAA
1 AAAAA-AAAAA
1469937 CCCCTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 17 0.77
15 5 0.23
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAAGAAA
Found at i:1469920 original size:17 final size:15
Alignment explanation
Indices: 1469898--1469936 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1469888 TAATCTTCAC
1469898 AAAAAAAGATGAAAAAA
1 AAAAAAAGA--AAAAAA
1469915 AAAAAAAGAAAAAAA
1 AAAAAAAGAAAAAAA
*
1469930 AGAAAAA
1 AAAAAAA
1469937 CCCCTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 12 0.57
17 9 0.43
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (15 bp):
AAAAAAAGAAAAAAA
Found at i:1469921 original size:9 final size:9
Alignment explanation
Indices: 1469898--1469936 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
1469888 TAATCTTCAC
1469898 AAAAAAAGA
1 AAAAAAAGA
**
1469907 TGAAAAA-A
1 AAAAAAAGA
1469915 AAAAAAAGA
1 AAAAAAAGA
1469924 AAAAAAAGA
1 AAAAAAAGA
1469933 AAAA
1 AAAA
1469937 CCCCTTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
8 6 0.24
9 19 0.76
ACGTcount: A:0.87, C:0.00, G:0.10, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:1470912 original size:30 final size:31
Alignment explanation
Indices: 1470876--1470942 Score: 109
Period size: 30 Copynumber: 2.2 Consensus size: 31
1470866 CCTTTTTAAC
1470876 GTCCACGACTCAGTGGCATTTTGTC-TCAAA
1 GTCCACGACTCAGTGGCATTTTGTCTTCAAA
*
1470906 GTCCACGACTCAGTGGCATTTTTTCTTCAAA
1 GTCCACGACTCAGTGGCATTTTGTCTTCAAA
*
1470937 GCCCAC
1 GTCCAC
1470943 AGCTTCGTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 24 0.71
31 10 0.29
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (31 bp):
GTCCACGACTCAGTGGCATTTTGTCTTCAAA
Found at i:1471082 original size:103 final size:103
Alignment explanation
Indices: 1470901--1471573 Score: 840
Period size: 103 Copynumber: 6.5 Consensus size: 103
1470891 GCATTTTGTC
* * * ** *
1470901 TCAAAGTCCACGACTCAGTGGCA-TTTTTTCTTCAAAGCCCACAGCT-TCGTGGCAC-C-TTTTC
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAGCCCACAACTCT-GTGGCACACTTTTTC
* *
1470962 -CTTTAAAGCCCACAACTCCGTGGCAC-CTTCTT-CTTT
65 TTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTT
* *
1470998 TCAAAGCCCACAACTCCGTGGCACTTTTTTCATCTTTAAGTCCACAACTCCGTGGCACACTTTTT
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTC-T-TTTAAGCCCACAACTCTGTGGCACACTTTTT
1471063 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTT
64 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTT
*
1471104 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTGAAGCCCACAACTCTGTGGCACAC-TTTT-
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT-AAGCCCACAACTCTGTGGCACACTTTTTC
* * *
1471167 TTTGTAAAGCCCACAACTCTGTGGCCCTCTTTTTCCCTTT
65 TTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTT
*
1471207 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCTGTGGCACACTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTT-AAGCCCACAACTCTGTGGCACACTTTTTC
*
1471272 TTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTT
65 TTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CCTTT
* *
1471312 TCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTC-TTTT-AAGCCCACAACTCTGTGGCACACTTTTT
*
1471377 CCCTTTTCAAAGCCCACAACTCCGTGGCACTC-TTTTCC-TT
64 --CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTT
* * *
1471417 T-AAAGCCCACAACTACGTGGCACTCTTTTCCTTCTAAGCCCACAACTCTGTGGCACTA-TTTTT
1 TCAAAGCCCACAACTCCGTGGCACT-TTTTTCTTTTAAGCCCACAACTCTGTGGCAC-ACTTTTT
* *
1471480 CCTTCT-AAGCCCACAACTCCGTGGCACT-TTTTT-CTTT
64 CTTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTT
* *
1471517 T-AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTAAGTCCACAACTCCGTGGCA
1 TCAAAGCCCACAACTCCGTGGCACT-TTTTT--CTTTTAAGCCCACAACTCTGTGGCA
1471574 TCTTTTTTCC
Statistics
Matches: 519, Mismatches: 35, Indels: 39
0.88 0.06 0.07
Matches are distributed among these distances:
97 20 0.04
98 7 0.01
99 2 0.00
100 74 0.14
101 4 0.01
102 27 0.05
103 146 0.28
104 40 0.08
105 99 0.19
106 68 0.13
107 4 0.01
108 28 0.05
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.33
Consensus pattern (103 bp):
TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAGCCCACAACTCTGTGGCACACTTTTTCT
TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCTTT
Found at i:1471149 original size:33 final size:34
Alignment explanation
Indices: 1470903--1471580 Score: 789
Period size: 33 Copynumber: 19.9 Consensus size: 34
1470893 ATTTTGTCTC
* * * *
1470903 AAAGTCCACGACTCAGTGGCA-T-TTTTTC-TTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
* * *
1470934 AAAGCCCACAGCTTCGTGGCAC-C-TTTTCCTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
*
1470966 AAAGCCCACAACTCCGTGGCAC-CTTCTTCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
1470999 CAAAGCCCACAACTCCGTGGCACT-TTTTTCATCTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTC-T-TTT
* *
1471035 -AAGTCCACAACTCCGTGGCACACTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTT
1471069 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--CTTTT
1471105 CAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
* * * *
1471139 GAAGCCCACAACTCTGTGGCACACTTTTT-TTGT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
* *
1471172 AAAGCCCACAACTCTGTGGCCCTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--CTTTT
1471208 CAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
* *
1471242 AAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTT
*
1471277 AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--CTTTT
1471313 CAAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTC-TTTT
*
1471348 AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--CTTTT
*
1471384 CAAAGCCCACAACTCCGTGGCACTC-TTTTCCTTT
1 -AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
* * *
1471418 AAAGCCCACAACTACGTGGCACTCTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
* * *
1471452 -AAGCCCACAACTCTGTGGCACTATTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT-CTTTT
1471486 -AAGCCCACAACTCCGTGGCACT-TTTTTCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
1471518 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT--CTTTT
*
1471554 -AAGTCCACAACTCCGTGGCA-TCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTT
1471581 TCCTTCCCAA
Statistics
Matches: 571, Mismatches: 42, Indels: 65
0.84 0.06 0.10
Matches are distributed among these distances:
31 21 0.04
32 27 0.05
33 151 0.26
34 143 0.25
35 95 0.17
36 45 0.08
37 89 0.16
ACGTcount: A:0.21, C:0.33, G:0.12, T:0.34
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCTTTT
Found at i:1471624 original size:33 final size:34
Alignment explanation
Indices: 1471587--1471652 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 34
1471577 TTTTTCCTTC
1471587 CCAAAGCCCACACAAGTCGGTGGCAA-CCTTCTT
1 CCAAAGCCCACACAAGTCGGTGGCAACCCTTCTT
1471620 CCAAAGCCCACACAAGTCGGTGGCAACCCTTCT
1 CCAAAGCCCACACAAGTCGGTGGCAACCCTTCT
1471653 AAGCCCAATA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
33 26 0.81
34 6 0.19
ACGTcount: A:0.27, C:0.38, G:0.18, T:0.17
Consensus pattern (34 bp):
CCAAAGCCCACACAAGTCGGTGGCAACCCTTCTT
Found at i:1471716 original size:49 final size:49
Alignment explanation
Indices: 1471652--1472016 Score: 475
Period size: 49 Copynumber: 7.6 Consensus size: 49
1471642 GCAACCCTTC
*
1471652 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* *
1471701 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* *
1471744 TAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* *
1471793 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA----C--CTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
*
1471836 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
* * * * *
1471885 TAAGTCCAATGTAGTTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
*
1471934 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTT
* *
1471986 TAAGTTCAATGTAGCTGGCCTTGAATCAGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCA
1472017 CGTTGACATC
Statistics
Matches: 273, Mismatches: 28, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
43 77 0.28
45 2 0.01
47 2 0.01
49 155 0.57
51 2 0.01
52 35 0.13
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTT
Found at i:1471809 original size:92 final size:92
Alignment explanation
Indices: 1471647--1472017 Score: 580
Period size: 92 Copynumber: 3.9 Consensus size: 92
1471637 CGGTGGCAAC
1471647 CCTTCTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1 CCTT-TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATG
1471712 TAGCTGGCCTTGAATCAGCACATTGGCA
65 TAGCTGGCCTTGAATCAGCACATTGGCA
*
1471740 CCTTTAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1471805 AGCTGGCCTTGAATCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
1471832 CCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
1 CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
* *
1471897 AGTTGGCCTTGACTCAGCACATTGGCA
66 AGCTGGCCTTGAATCAGCACATTGGCA
* *
1471924 CCTTCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAA
1 ----C--CTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAA
*
1471989 GTTCAATGTAGCTGGCCTTGAATCAGCAC
57 GTCCAATGTAGCTGGCCTTGAATCAGCAC
1472018 GTTGACATCC
Statistics
Matches: 258, Mismatches: 11, Indels: 10
0.92 0.04 0.04
Matches are distributed among these distances:
92 174 0.67
93 4 0.02
96 1 0.00
98 41 0.16
100 3 0.01
101 35 0.14
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (92 bp):
CCTTTAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGT
AGCTGGCCTTGAATCAGCACATTGGCA
Found at i:1471914 original size:141 final size:135
Alignment explanation
Indices: 1471652--1471977 Score: 427
Period size: 141 Copynumber: 2.3 Consensus size: 135
1471642 GCAACCCTTC
* *
1471652 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGCT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA----C--CTTTAAGTCCAATATAGCT
*
1471717 GGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATAGCTGGCCCTGAATCAGCATATTGGC
60 GGCCTTGAATCAGCACATTGGCACCTTTAAGCCCAATATAGCTGGCCCTGAATCAGCACATTGGC
*
1471782 ATCTTCATCTT
125 ACCTTCATCTT
* * *
1471793 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATCGCTGGCCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
* * * * * *
1471858 GAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAGTTGGCCTTGACTCAGCACATTGGC
66 GAATCAGCACATTGGCA----C--CTTTAAGCCCAATATAGCTGGCCCTGAATCAGCACATTGGC
1471923 ACCTTCATCTT
125 ACCTTCATCTT
1471934 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTT
1471978 TCCATCTTTA
Statistics
Matches: 164, Mismatches: 15, Indels: 12
0.86 0.08 0.06
Matches are distributed among these distances:
135 39 0.24
137 1 0.01
139 1 0.01
141 123 0.75
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (135 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTAAGTCCAATATAGCTGGCCTT
GAATCAGCACATTGGCACCTTTAAGCCCAATATAGCTGGCCCTGAATCAGCACATTGGCACCTTC
ATCTT
Found at i:1472074 original size:107 final size:99
Alignment explanation
Indices: 1471652--1472093 Score: 470
Period size: 92 Copynumber: 4.5 Consensus size: 99
1471642 GCAACCCTTC
*
1471652 TAAGCCCAATAT-AGCTGGCCTTGAATCAGCATATTGGCA-TCTTCATCTTTAAGTCCAATGTAG
1 TAAGCCCAATATCA-CTGGCCTTGAATCAGCATATTGGCACTTTTCATCTTTAAGTCCAATGTAG
*
1471715 CTGGCCTTGAATCAGCACATTGGCA----C--CTT
65 CTGGCCTTGAATCAGCACATTGACACCTTCATCTT
* *
1471744 TAAGCCCAATAT-AGCTGGCCCTGAATCAGCATATTGGCA-TCTTCATCTTTAAGTCCAATGTAG
1 TAAGCCCAATATCA-CTGGCCTTGAATCAGCATATTGGCACTTTTCATCTTTAAGTCCAATGTAG
*
1471807 CTGGCCTTGAATCAGCACATTGGCA----C--CTT
65 CTGGCCTTGAATCAGCACATTGACACCTTCATCTT
* * * *
1471836 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-TCTTCATCTTTAAGTCCAATGTAGT
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACTTTTCATCTTTAAGTCCAATGTAGC
* *
1471900 TGGCCTTGACTCAGCACATTGGCACCTTCATCTT
66 TGGCCTTGAATCAGCACATTGACACCTTCATCTT
* *
1471934 TAAGTCCAATAT-AGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTTCAATGT
1 TAAGCCCAATATCA-CTGGCCTTGAATCAGCATATTGGCA-CTTTT-CATCTTTAAGTCCAATGT
*
1471998 AGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTT
63 AGCTGGCCTTGAATCAGCACATTGACA-CC----T-TCATCTT
* * * *
1472041 TAGGCCCAATATCATTGGCCATGAATCAACATATTGGCATCTTTATCACTCTT
1 TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCA-CTTT-TCA-TCTT
1472094 CTCATCATCA
Statistics
Matches: 311, Mismatches: 19, Indels: 24
0.88 0.05 0.07
Matches are distributed among these distances:
92 173 0.56
96 1 0.00
98 40 0.13
100 3 0.01
101 40 0.13
102 2 0.01
106 1 0.00
107 45 0.14
108 6 0.02
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (99 bp):
TAAGCCCAATATCACTGGCCTTGAATCAGCATATTGGCACTTTTCATCTTTAAGTCCAATGTAGC
TGGCCTTGAATCAGCACATTGACACCTTCATCTT
Found at i:1472221 original size:171 final size:171
Alignment explanation
Indices: 1471927--1472325 Score: 672
Period size: 171 Copynumber: 2.3 Consensus size: 171
1471917 ATTGGCACCT
*
1471927 TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTTTAAGTT
1 TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA--TCTT-CATCTTTAAGTT
* *
1471992 CAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTTAGGCCCAATATCATT
63 CAATGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTCAAGCCCAATATCATT
1472057 GGCCATGAATCAACATATTGGCATCTTTATCACTCTTCTCATCA
128 GGCCATGAATCAACATATTGGCATCTTTATCACTCTTCTCATCA
* *
1472101 TCATTTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAA
1 TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAA
*
1472166 TGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTCAAGCCCAATATCGTTGGC
66 TGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTCAAGCCCAATATCATTGGC
* *
1472231 CATGAATCAACATATTGGCATCTTTATCACTTTTCTCATCT
131 CATGAATCAACATATTGGCATCTTTATCACTCTTCTCATCA
* * *
1472272 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTAGCACCTTCATC
1 TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1472326 ATCTTTAAAA
Statistics
Matches: 213, Mismatches: 12, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
171 166 0.78
172 3 0.01
174 44 0.21
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.37
Consensus pattern (171 bp):
TCATCTTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTTCAA
TGTAGCTGGCCTTGAATCAGCACGTTGACATCCTTTTTCTCATCTTCAAGCCCAATATCATTGGC
CATGAATCAACATATTGGCATCTTTATCACTCTTCTCATCA
Found at i:1472313 original size:67 final size:68
Alignment explanation
Indices: 1472205--1472331 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 68
1472195 ATCCTTTTTC
* * * *
1472205 TCATCTTCAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCATCTTTATCA-CTTTTCTCA
1 TCATCTTCAAGCCCAATATCGCTGGCCATGAATCAACATATTAGCACCTTCATCATCTTTTCTCA
1472269 TCT
66 TCT
* * * * *
1472272 TCATCTTTAAGTCCAATATTGCTGGCCTTGAATCAGCATATTAGCACCTTCATCATCTTT
1 TCATCTTCAAGCCCAATATCGCTGGCCATGAATCAACATATTAGCACCTTCATCATCTTT
1472332 AAAACCCAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
67 46 0.92
68 4 0.08
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (68 bp):
TCATCTTCAAGCCCAATATCGCTGGCCATGAATCAACATATTAGCACCTTCATCATCTTTTCTCA
TCT
Found at i:1473164 original size:13 final size:13
Alignment explanation
Indices: 1473146--1473170 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1473136 CAAAAAATGT
1473146 TGTATCGATACAA
1 TGTATCGATACAA
1473159 TGTATCGATACA
1 TGTATCGATACA
1473171 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1473254 original size:13 final size:13
Alignment explanation
Indices: 1473236--1473260 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1473226 ATTACTCACA
1473236 TGTATCGATACAT
1 TGTATCGATACAT
1473249 TGTATCGATACA
1 TGTATCGATACA
1473261 CTAATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1473397 original size:52 final size:52
Alignment explanation
Indices: 1473249--1473389 Score: 228
Period size: 52 Copynumber: 2.7 Consensus size: 52
1473239 ATCGATACAT
* ***
1473249 TGTATCGATACACTAATCTTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
1473301 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1473353 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1473390 ATAAATTTTC
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 81 1.00
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (52 bp):
TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:1479227 original size:20 final size:20
Alignment explanation
Indices: 1479202--1479255 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
1479192 GTTAGAAGCA
* *
1479202 ATGTATCGATATAAT-TCATC
1 ATGTATCGATACAATGT-ACC
*
1479222 ATGTATTGATACAATGTACC
1 ATGTATCGATACAATGTACC
1479242 ATGTATCGATACAA
1 ATGTATCGATACAA
1479256 ACAGTGGTAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:1480037 original size:13 final size:13
Alignment explanation
Indices: 1480019--1480044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1480009 CAATTTTTTG
1480019 TGTATCGATACAT
1 TGTATCGATACAT
1480032 TGTATCGATACAT
1 TGTATCGATACAT
1480045 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1482443 original size:21 final size:21
Alignment explanation
Indices: 1482419--1482465 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1482409 TTTGATGCTG
1482419 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
1482439 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
1482460 ATTTTG
1 ATTTTG
1482466 CAAAATATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:1482604 original size:13 final size:13
Alignment explanation
Indices: 1482586--1482624 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1482576 ATAATCACCC
*
1482586 TGTATCGATACAG
1 TGTATCGATACAA
1482599 TGTATCGATACAA
1 TGTATCGATACAA
1482612 TGTATCGATACAA
1 TGTATCGATACAA
1482625 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1482635 original size:20 final size:20
Alignment explanation
Indices: 1482610--1482688 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
1482600 GTATCGATAC
1482610 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1482630 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
1482655 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
1482675 CATGTATCGATACA
1 AATGTATCGATACA
1482689 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1486567 original size:21 final size:21
Alignment explanation
Indices: 1486538--1486582 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1486528 AAGTTTTCAT
*
1486538 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1486558 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1486580 TTT
1 TTT
1486583 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1488819 original size:13 final size:13
Alignment explanation
Indices: 1488801--1488826 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1488791 CAATTTTTTG
1488801 TGTATCGATACAT
1 TGTATCGATACAT
1488814 TGTATCGATACAT
1 TGTATCGATACAT
1488827 ACTTGCTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1490045 original size:39 final size:39
Alignment explanation
Indices: 1489983--1490071 Score: 135
Period size: 39 Copynumber: 2.3 Consensus size: 39
1489973 GGTATCTAAA
*
1489983 CTTTCTCCTTTCACTTTTCAGTCCTCAAAGAGCAGGACG
1 CTTTCTCCTTTCACCTTTCAGTCCTCAAAGAGCAGGACG
*
1490022 CTTTCTCCTTTCACCCTTT-AGTCCTCAAAGAGTAGGACG
1 CTTTCTCCTTTCA-CCTTTCAGTCCTCAAAGAGCAGGACG
*
1490061 CTTTTTCCTTT
1 CTTTCTCCTTT
1490072 TAAAGGCCCA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
39 42 0.91
40 4 0.09
ACGTcount: A:0.18, C:0.30, G:0.13, T:0.38
Consensus pattern (39 bp):
CTTTCTCCTTTCACCTTTCAGTCCTCAAAGAGCAGGACG
Found at i:1490194 original size:61 final size:61
Alignment explanation
Indices: 1490036--1490685 Score: 807
Period size: 61 Copynumber: 10.6 Consensus size: 61
1490026 CTCCTTTCAC
* *
1490036 CCTTT-AGTCCTCAAAGAGTAGGACGCTTTTTCCTTTTAAAGGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAA-GCCCACACAAGTTGGTGGCA
* * * * *
1490097 CTTTTCTAGTACTCAAAGAGCAGGACGCCTTCTCCTTTTAAAGCCTATACAAGTTGGTGGCA
1 CCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1490159 CCTTTCAGTCCTCAAGGAGCAGGACGTCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * *
1490220 CTTTTCTAGTCCTCAAAGAGCAAGACG-CTTTCTCCTTTTAAAGCCTACACAAGTTGGTGGCA
1 CCTTTC-AGTCCTCAAAGAGCAGGACGCCTTT-TCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1490282 CC-TTCTAGTCCTCAAAGAGAAGGACGCTTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
1 CCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* * * *
1490343 CC-TTCTAGTCTTCAAAGAGCAGGACGCCTTTTCTTTTTAAAGCCCACACAAGCTAGTGGCA
1 CCTTTC-AGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
* *
1490404 CC-TTCAGTCCTCAAAGAGCAGGATGCCTTTTCCTTTTTAAAGCCCACACATGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCC-TTTTAAAGCCCACACAAGTTGGTGGCA
* ** *
1490465 CCCTTT-AGTCCTAAAAGATTAGGACGCCTTTT-CTTTTCAAAGCCCACACATGTTGGTGGCA
1 -CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
* * * **
1490526 CCCTTT-AGTCCCCAAAGAGCATGACGCCTTTT-CTTTTCGAAGCCCACATGAGTTGGTGGCA
1 -CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
* * * *
1490587 CCTTTTAGTCCTTAAAGAGCAGGATGCC-TTTCCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT-AAAGCCCACACAAGTTGGTGGCA
* *
1490648 CCTTGCAGTCCTCAAAGAGCAGGAAGCCTTTTCCTTTT
1 CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTT
1490686 CTCCTTTGCC
Statistics
Matches: 519, Mismatches: 58, Indels: 23
0.87 0.10 0.04
Matches are distributed among these distances:
60 37 0.07
61 342 0.66
62 107 0.21
63 33 0.06
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (61 bp):
CCTTTCAGTCCTCAAAGAGCAGGACGCCTTTTCCTTTTAAAGCCCACACAAGTTGGTGGCA
Found at i:1490832 original size:46 final size:45
Alignment explanation
Indices: 1490681--1490862 Score: 144
Period size: 45 Copynumber: 4.1 Consensus size: 45
1490671 AAGCCTTTTC
* * ** * *
1490681 CTTTTCTCCTTT-GCCCTCAAAGAGCAGGACATATTTCATTTCATT
1 CTTTTC-CCTTTAGTCCTCAAAGAGCAAGACGCACTTCATTTCCTT
* * * *
1490726 CTTTTCCCTTTTGTCCTCAAAGAGCAAGATG--CTT-TTTTTCTT
1 CTTTTCCCTTTAGTCCTCAAAGAGCAAGACGCACTTCATTTCCTT
*
1490768 -TTTT-CTTTTA-TCCTCAAAGAGCAAGACGCACTTCATTTCCTT
1 CTTTTCCCTTTAGTCCTCAAAGAGCAAGACGCACTTCATTTCCTT
* * * *
1490810 CTTTTCCCTTCTAGTTCTCAAAGAGCAGGACGCATTTTATTCTCCTT
1 CTTTTCCCTT-TAGTCCTCAAAGAGCAAGACGCACTTCATT-TCCTT
*
1490857 TTTTTC
1 CTTTTC
1490863 TTTGTCCTAA
Statistics
Matches: 109, Mismatches: 19, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
39 17 0.16
40 4 0.04
41 7 0.06
42 11 0.10
43 6 0.06
44 8 0.07
45 23 0.21
46 23 0.21
47 10 0.09
ACGTcount: A:0.20, C:0.26, G:0.11, T:0.43
Consensus pattern (45 bp):
CTTTTCCCTTTAGTCCTCAAAGAGCAAGACGCACTTCATTTCCTT
Found at i:1490998 original size:83 final size:86
Alignment explanation
Indices: 1490654--1491006 Score: 309
Period size: 84 Copynumber: 4.2 Consensus size: 86
1490644 GGCACCTTGC
* * * *
1490654 AGTCCTCAAAGAGCAGGAAGC---CT-TTTCCTTTTCTCCTTTGCCCTCAAAGAGCAGGACATAT
1 AGTCCTCAAAGAGCAGGATGCATTTTATTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACAT
*
1490715 TTCATTTCATTCTTTTCCCTTT
66 TTCATTTC-TCCTTTTCCCTTT
* * * * * * * *
1490737 TGTCCTCAAAGAGCAAGATGC-TTTT-TTT-CTTTTTTCTTTTATCCTCAAAGAGCAAGACGCAC
1 AGTCCTCAAAGAGCAGGATGCATTTTATTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACAT
*
1490799 TTCATTTCCTTCTTTTCCCTTCT
66 TTCATTT-CTCCTTTTCCCTT-T
* * * * * * * *
1490822 AGTTCTCAAAGAGCAGGACGCATTTTATTCTCCTTTTTTTCTTTGTCCTAAAAAAGCACGACACG
1 AGTCCTCAAAGAGCAGGATGCATTTTATT-TCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACA
* *
1490887 TTT-AATT-TCCTTTTTCCTTT
65 TTTCATTTCTCCTTTTCCCTTT
* * * * *
1490907 -GTCTTCAAAGGGTAGGATGCATTTTATTTCCTTTTCTCCTTTGTCCTCAAGGAGCAGGACCCAT
1 AGTCCTCAAAGAGCAGGATGCATTTTATTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACAT
1490971 TTCA-TTCTCCTTTT-CC-TT
66 TTCATTTCTCCTTTTCCCTTT
*
1490989 AATCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
1491007 CGCTCCCTTC
Statistics
Matches: 214, Mismatches: 45, Indels: 22
0.76 0.16 0.08
Matches are distributed among these distances:
82 2 0.01
83 65 0.30
84 76 0.36
85 24 0.11
86 14 0.07
87 2 0.01
88 4 0.02
89 27 0.13
ACGTcount: A:0.22, C:0.25, G:0.13, T:0.40
Consensus pattern (86 bp):
AGTCCTCAAAGAGCAGGATGCATTTTATTTCCTTTTCTCCTTTGTCCTCAAAGAGCAGGACACAT
TTCATTTCTCCTTTTCCCTTT
Found at i:1491674 original size:20 final size:20
Alignment explanation
Indices: 1491646--1491696 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1491636 TACCCAGATG
* * *
1491646 TATCAATACATCGTTTATTA
1 TATCGATACATCATTCATTA
* *
1491666 TATCGATACATTATTCATTG
1 TATCGATACATCATTCATTA
1491686 TATCGATACAT
1 TATCGATACAT
1491697 TATATCGATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (20 bp):
TATCGATACATCATTCATTA
Found at i:1491697 original size:13 final size:13
Alignment explanation
Indices: 1491681--1491710 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1491671 ATACATTATT
*
1491681 CATTGTATCGATA
1 CATTATATCGATA
1491694 CATTATATCGATA
1 CATTATATCGATA
1491707 CATT
1 CATT
1491711 CTGGGTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:1491769 original size:29 final size:29
Alignment explanation
Indices: 1491699--1491770 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
1491689 CGATACATTA
*
1491699 TATCGATACATTCTGGGTTTACCCAGATG
1 TATCGATACATTTTGGGTTTACCCAGATG
1491728 TATCGATACATTTTGGGTTTACCCAGATG
1 TATCGATACATTTTGGGTTTACCCAGATG
1491757 TATCGATACATTTT
1 TATCGATACATTTT
1491771 TCAATGTATC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 42 1.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (29 bp):
TATCGATACATTTTGGGTTTACCCAGATG
Found at i:1495128 original size:52 final size:52
Alignment explanation
Indices: 1495050--1495198 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 52
1495040 CGAAATATGA
*
1495050 AAATTTGCCTGCATGTATTGATACATTTAATAGTGTATCGATACATCAGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCAGGGC
* *
1495102 AAATTTGCCTGCATGTATCGATACATTATAA-AATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATT-TAATAGTGTATCGATACATCAGGGC
*** *
1495154 AAATTTGCCTGCATGTATCGATACAAAGATTAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACA
1495199 ATATATCGAT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 1 0.01
52 83 0.95
53 3 0.03
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAGTGTATCGATACATCAGGGC
Found at i:1495291 original size:13 final size:13
Alignment explanation
Indices: 1495273--1495297 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1495263 ACAAAACTTA
1495273 TGTATCGATACAT
1 TGTATCGATACAT
1495286 TGTATCGATACA
1 TGTATCGATACA
1495298 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1495293 original size:32 final size:33
Alignment explanation
Indices: 1495252--1495317 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
1495242 AGTAGCTTAA
1495252 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
1495284 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
1495317 A
1 A
1495318 AATCGTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:1497887 original size:79 final size:78
Alignment explanation
Indices: 1497745--1498093 Score: 357
Period size: 79 Copynumber: 4.4 Consensus size: 78
1497735 TACTCCAACC
* *
1497745 TTTCATAATCGGGGATACTCCAATCCC-GTTATTTCTGAGGGGATACTCCAACCCC-AGCTTTAT
1 TTTCACAATCGGGGATACTCCAA-CCCTGTTATTT-TGAGGGGATACTCCAACCCCGATC-TTAT
* **
1497808 TTCTAAAATATTGATT
63 TTCTAAAACACCGATT
* * *
1497824 TCTCACAATCGGGGATACTCCAACCCTATTATTTTG-GTAGGGATAATCCAACCCCGATCTTATT
1 TTTCACAATCGGGGATACTCCAACCCTGTTATTTTGAG--GGGATACTCCAACCCCGATCTTATT
* **
1497888 TCTAAAGCTTCGATT
64 TCTAAAACACCGATT
* * * * *
1497903 TTTCACGATCAGGGATACTCTAACCCTGTTATTTTTGAAGGGATACTCCAACCCCGATTTTATTT
1 TTTCACAATCGGGGATACTCCAACCCTGTTA-TTTTGAGGGGATACTCCAACCCCGATCTTATTT
1497968 -TCAAAACACCGA-T
65 CT-AAAACACCGATT
* ** * *
1497981 TTTCTATAATCAAGGATACTCCAACCCTGTTATTTTCGAGGGGATACTCCAACCTCGATTTTATT
1 TTTC-ACAATCGGGGATACTCCAACCCTGTTATTTT-GAGGGGATACTCCAACCCCGATCTTATT
*
1498046 TCCAAAACACCGATT
64 TCTAAAACACCGATT
* * *
1498061 TTTCATAATCGGGGATACTCCAGCCCCGTTATT
1 TTTCACAATCGGGGATACTCCAACCCTGTTATT
1498094 ATCCCCACAA
Statistics
Matches: 228, Mismatches: 31, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
77 1 0.00
78 15 0.07
79 200 0.88
80 12 0.05
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.34
Consensus pattern (78 bp):
TTTCACAATCGGGGATACTCCAACCCTGTTATTTTGAGGGGATACTCCAACCCCGATCTTATTTC
TAAAACACCGATT
Found at i:1503406 original size:32 final size:32
Alignment explanation
Indices: 1503370--1503431 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
1503360 CATTATGACA
* *
1503370 TCTTTAATTAGATTTCA-TAAATCTAATTTATG
1 TCTTTAATAAGATTTAACTAAA-CTAATTTATG
*
1503402 TCTTTAATAATATTTAACTAAACTAATTTA
1 TCTTTAATAAGATTTAACTAAACTAATTTA
1503432 GTTAAGTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 22 0.85
33 4 0.15
ACGTcount: A:0.39, C:0.10, G:0.03, T:0.48
Consensus pattern (32 bp):
TCTTTAATAAGATTTAACTAAACTAATTTATG
Found at i:1505435 original size:33 final size:32
Alignment explanation
Indices: 1505398--1505462 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
1505388 CTACACTGTT
1505398 TGTATCGATACATG-GCACATTGTATCGATACAA
1 TGTATCGATACATGAG-A-ATTGTATCGATACAA
1505431 TGTATCGATACATGATGAATTGTATCGATACA
1 TGTATCGATACATGA-GAATTGTATCGATACA
1505463 TTGCTTCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 28 0.93
34 1 0.03
35 1 0.03
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATACAA
Found at i:1505436 original size:13 final size:13
Alignment explanation
Indices: 1505418--1505442 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1505408 CATGGCACAT
1505418 TGTATCGATACAA
1 TGTATCGATACAA
1505431 TGTATCGATACA
1 TGTATCGATACA
1505443 TGATGAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1510851 original size:13 final size:13
Alignment explanation
Indices: 1510833--1510857 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1510823 CATTATGCTT
1510833 TGTATCGATACAA
1 TGTATCGATACAA
1510846 TGTATCGATACA
1 TGTATCGATACA
1510858 TGTTCATTGT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1510888 original size:20 final size:20
Alignment explanation
Indices: 1510842--1510898 Score: 64
Period size: 19 Copynumber: 3.0 Consensus size: 20
1510832 TTGTATCGAT
*
1510842 ACAA-TGTATCGATACATGT
1 ACAATTGTATCGATACATGG
* *
1510861 TC-ATTGTATCGATCCATGG
1 ACAATTGTATCGATACATGG
*
1510880 ACAATTGTAACGATACATG
1 ACAATTGTATCGATACATG
1510899 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
18 1 0.03
19 15 0.50
20 14 0.47
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Consensus pattern (20 bp):
ACAATTGTATCGATACATGG
Found at i:1510952 original size:20 final size:19
Alignment explanation
Indices: 1510927--1510980 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 19
1510917 CTACCACTAT
1510927 TTGTATCGATACATG-GCACA
1 TTGTATCGATACATGAG-A-A
1510947 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGA-GAA
1510967 TTGTATCGATACAT
1 TTGTATCGATACAT
1510981 TACTTCAAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 30 0.94
21 1 0.03
22 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGAGAA
Found at i:1512199 original size:30 final size:31
Alignment explanation
Indices: 1512159--1512227 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
1512149 TAATTGAATA
* *
1512159 GAGCTCAAATAGTTAGA-TTTATCTCGAGCT
1 GAGCTCAAATAGTTAGATTTTATCTCAAGAT
* *
1512189 GAGCTTAAATAGTTTGATTTTATCTCAAGAT
1 GAGCTCAAATAGTTAGATTTTATCTCAAGAT
1512220 GAGCTCAA
1 GAGCTCAA
1512228 GCTTAGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
30 15 0.45
31 18 0.55
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (31 bp):
GAGCTCAAATAGTTAGATTTTATCTCAAGAT
Found at i:1514905 original size:16 final size:15
Alignment explanation
Indices: 1514859--1514910 Score: 59
Period size: 16 Copynumber: 3.3 Consensus size: 15
1514849 TCAATTTTAA
*
1514859 GTCATTTTGAGTTTGC
1 GTCATTTTG-GTTTGG
*
1514875 GTTATTTTGGTTTTGG
1 GTCATTTTGG-TTTGG
1514891 GTCATTTTAGGTTTGG
1 GTCATTTT-GGTTTGG
1514907 GTCA
1 GTCA
1514911 ATCGGGTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 1 0.03
16 28 0.90
17 2 0.06
ACGTcount: A:0.12, C:0.08, G:0.29, T:0.52
Consensus pattern (15 bp):
GTCATTTTGGTTTGG
Found at i:1516146 original size:16 final size:17
Alignment explanation
Indices: 1516120--1516160 Score: 68
Period size: 16 Copynumber: 2.5 Consensus size: 17
1516110 TCATTTCAGA
1516120 TCACTTT-AAGTTCATG
1 TCACTTTCAAGTTCATG
1516136 TCA-TTTCAAGTTCATG
1 TCACTTTCAAGTTCATG
1516152 TCACTTTCA
1 TCACTTTCA
1516161 GATTTGGATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.13
16 15 0.65
17 5 0.22
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (17 bp):
TCACTTTCAAGTTCATG
Found at i:1520999 original size:30 final size:30
Alignment explanation
Indices: 1520965--1521026 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
1520955 TTTGAATGCT
1520965 TTGATCTCTTGATGTTTCTTGATTGTTCTC
1 TTGATCTCTTGATGTTTCTTGATTGTTCTC
1520995 TTGATCTCTTGATGTTTCTTGATTGTTCTC
1 TTGATCTCTTGATGTTTCTTGATTGTTCTC
1521025 TT
1 TT
1521027 CTTCTTCAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.10, C:0.16, G:0.16, T:0.58
Consensus pattern (30 bp):
TTGATCTCTTGATGTTTCTTGATTGTTCTC
Found at i:1521006 original size:20 final size:18
Alignment explanation
Indices: 1520981--1521017 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
1520971 TCTTGATGTT
1520981 TCTTGATTGTTCTCTTGATC
1 TCTTGA-TGTT-TCTTGATC
1521001 TCTTGATGTTTCTTGAT
1 TCTTGATGTTTCTTGAT
1521018 TGTTCTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 4 0.24
20 6 0.35
ACGTcount: A:0.11, C:0.16, G:0.16, T:0.57
Consensus pattern (18 bp):
TCTTGATGTTTCTTGATC
Found at i:1521023 original size:10 final size:10
Alignment explanation
Indices: 1520971--1521017 Score: 53
Period size: 10 Copynumber: 4.7 Consensus size: 10
1520961 TGCTTTGATC
1520971 TCTTGATGTT
1 TCTTGATGTT
1520981 TCTTGATTGTT
1 TCTTGA-TGTT
*
1520992 CTCTTGA--TC
1 -TCTTGATGTT
1521001 TCTTGATGTT
1 TCTTGATGTT
1521011 TCTTGAT
1 TCTTGAT
1521018 TGTTCTCTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
8 6 0.19
9 1 0.03
10 14 0.45
11 4 0.13
12 6 0.19
ACGTcount: A:0.11, C:0.15, G:0.17, T:0.57
Consensus pattern (10 bp):
TCTTGATGTT
Found at i:1521579 original size:20 final size:20
Alignment explanation
Indices: 1521554--1521610 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
1521544 TTTTACCCAG
1521554 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
1521574 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTCTTCA
*
1521594 ATGTATCAATACATTCT
1 ATGTATCGATACATTCT
1521611 ATCTTTTACC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.09, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTCTTCA
Found at i:1527512 original size:31 final size:31
Alignment explanation
Indices: 1527477--1527543 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
1527467 TGATGAAGAT
*
1527477 TTTGAAGAAAAATG-AAAGGAAAAGATGCAAA
1 TTTGAAGAAAAATGAAAAAGAAAAGAT-CAAA
* ** *
1527508 TTTGATGAAATTTGAAAAAGAAATGATCAAA
1 TTTGAAGAAAAATGAAAAAGAAAAGATCAAA
1527539 TTTGA
1 TTTGA
1527544 GATTGAAAAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 20 0.67
32 10 0.33
ACGTcount: A:0.52, C:0.03, G:0.19, T:0.25
Consensus pattern (31 bp):
TTTGAAGAAAAATGAAAAAGAAAAGATCAAA
Found at i:1527650 original size:13 final size:13
Alignment explanation
Indices: 1527632--1527657 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1527622 AATAGTGCCC
1527632 TTGTATCGATACA
1 TTGTATCGATACA
1527645 TTGTATCGATACA
1 TTGTATCGATACA
1527658 ATGATCATTG
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1529924 original size:21 final size:21
Alignment explanation
Indices: 1529900--1529940 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1529890 ACTCGTGTAG
*
1529900 TATTTA-AACAAATATGCATAA
1 TATTTAGAA-AAAAATGCATAA
1529921 TATTTAGAAAAAAATGCATA
1 TATTTAGAAAAAAATGCATA
1529941 TTTGCATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.54, C:0.07, G:0.07, T:0.32
Consensus pattern (21 bp):
TATTTAGAAAAAAATGCATAA
Found at i:1530426 original size:6 final size:6
Alignment explanation
Indices: 1530417--1530466 Score: 84
Period size: 6 Copynumber: 8.3 Consensus size: 6
1530407 TTTATGATTA
1530417 TTAATT TTAATT TTAATT TTAATT TTAATT TT-ATT TTAATT TTAGATT
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTAATT TTA-ATT
1530465 TT
1 TT
1530467 GTTTTATTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.12
6 32 0.76
7 5 0.12
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (6 bp):
TTAATT
Found at i:1530438 original size:18 final size:17
Alignment explanation
Indices: 1530417--1530472 Score: 85
Period size: 18 Copynumber: 3.2 Consensus size: 17
1530407 TTTATGATTA
1530417 TTAATTTTAATTTTAATT
1 TTAATTTTAATTTT-ATT
1530435 TTAATTTTAATTTTATT
1 TTAATTTTAATTTTATT
*
1530452 TTAATTTTAGATTTTGTT
1 TTAATTTTA-ATTTTATT
1530470 TTA
1 TTA
1530473 TTCTTTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
17 12 0.33
18 24 0.67
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.68
Consensus pattern (17 bp):
TTAATTTTAATTTTATT
Found at i:1536310 original size:14 final size:14
Alignment explanation
Indices: 1536287--1536316 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1536277 TTCATTTTTC
*
1536287 ATTTTTTTTTTAAA
1 ATTTTATTTTTAAA
1536301 ATTTTATTTTTAAA
1 ATTTTATTTTTAAA
1536315 AT
1 AT
1536317 ACGAAGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTATTTTTAAA
Found at i:1536392 original size:164 final size:164
Alignment explanation
Indices: 1536222--1536578 Score: 406
Period size: 165 Copynumber: 2.2 Consensus size: 164
1536212 AAATTCTATT
* * * *
1536222 AATATTATCATTTAATATTAGTTTTAAAT-TAGTTT-AAAAAATTCATTCATTTTCATTCATTTT
1 AATATTATTATTTAAT-TCA-TATTAAATCTA-TTTAAAAAAATTCATTCATTTTCA-TCAGTTT
* * * * *
1536285 TCATTTTTTTTTTAAAATT-TTA-TTT-TTAAA-ATACGAAGTTTTCTACTCCGTAAATATTTTT
62 TCAATTTTTCTTTAAAATTCCTAGTTTCTGAAATATA-G-AGTTTTCTACTCCGTAAATATTTTC
* *
1536346 GGAGGGATTTTTCTTCA-TTTTTAA-TTTTTAGAATTCATCA
125 GGAGGGATCTTTCTT-AGTTTTTAATTTTTTA-AATTCATAA
** * * *
1536386 AATATTATTATTTAATTCATATTAAATCTATTTAAAAAAATTTGTTTATTTTCATGAGTTTTGAA
1 AATATTATTATTTAATTCATATTAAATCTATTTAAAAAAATTCATTCATTTTCATCAGTTTTCAA
* * *
1536451 TTTTTCTTTGAAATTCCCTAGTTTCTGAAATATAGAGTTTTCTACTTCGTAAATGTTTTCGGAGG
66 TTTTTCTTTAAAATT-CCTAGTTTCTGAAATATAGAGTTTTCTACTCCGTAAATATTTTCGGAGG
1536516 GATCTTTCTTAGTTTTTAATTTTTTAAATTCATAA
130 GATCTTTCTTAGTTTTTAATTTTTTAAATTCATAA
1536551 AATATTATTATTTAATTCATATTAAATC
1 AATATTATTATTTAATTCATATTAAATC
1536579 AGTTTTCAAA
Statistics
Matches: 165, Mismatches: 19, Indels: 17
0.82 0.09 0.08
Matches are distributed among these distances:
162 30 0.18
163 21 0.13
164 18 0.11
165 82 0.50
166 11 0.07
167 3 0.02
ACGTcount: A:0.32, C:0.09, G:0.08, T:0.52
Consensus pattern (164 bp):
AATATTATTATTTAATTCATATTAAATCTATTTAAAAAAATTCATTCATTTTCATCAGTTTTCAA
TTTTTCTTTAAAATTCCTAGTTTCTGAAATATAGAGTTTTCTACTCCGTAAATATTTTCGGAGGG
ATCTTTCTTAGTTTTTAATTTTTTAAATTCATAA
Found at i:1536517 original size:165 final size:164
Alignment explanation
Indices: 1536321--1536629 Score: 437
Period size: 165 Copynumber: 1.9 Consensus size: 164
1536311 TAAAATACGA
* *
1536321 AGTTTTCTACTCCGTAAATATTTTTGGAGGGATTTTTCTTCA-TTTTTAA-TTTTTAGAATTCAT
1 AGTTTTCTACTCCGTAAATATTTTCGGAGGGATCTTTCTT-AGTTTTTAATTTTTTA-AATTCAT
* *** * *
1536384 CAAATATTATTATTTAATTCATATTAAATCTA-TTTAAAAAAATTTGTTTATTTTCATGAGTTTT
64 AAAATATTATTATTTAATTCATATTAAATC-AGTTT-AAAAAATTAAATTATTTTCATGAGATTG
1536448 GAA-TTTTTCTTTGAAATTCCCTAGTTTCTGAAATATAG
127 GAATTTTTTC-TTGAAATTCCCTAGTTTCTGAAATATAG
* *
1536486 AGTTTTCTACTTCGTAAATGTTTTCGGAGGGATCTTTCTTAGTTTTTAATTTTTTAAATTCATAA
1 AGTTTTCTACTCCGTAAATATTTTCGGAGGGATCTTTCTTAGTTTTTAATTTTTTAAATTCATAA
**
1536551 AATATTATTATTTAATTCATATTAAATCAGTTTTCAAAATTAAATTATTTTCATGAGATTGGAAT
66 AATATTATTATTTAATTCATATTAAATCAGTTTAAAAAATTAAATTATTTTCATGAGATTGGAAT
1536616 TTTTTCTTGAAATT
131 TTTTTCTTGAAATT
1536630 TTTCTATTTT
Statistics
Matches: 128, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
164 34 0.27
165 88 0.69
166 6 0.05
ACGTcount: A:0.31, C:0.09, G:0.10, T:0.50
Consensus pattern (164 bp):
AGTTTTCTACTCCGTAAATATTTTCGGAGGGATCTTTCTTAGTTTTTAATTTTTTAAATTCATAA
AATATTATTATTTAATTCATATTAAATCAGTTTAAAAAATTAAATTATTTTCATGAGATTGGAAT
TTTTTCTTGAAATTCCCTAGTTTCTGAAATATAG
Found at i:1537117 original size:19 final size:17
Alignment explanation
Indices: 1537083--1537130 Score: 69
Period size: 19 Copynumber: 2.7 Consensus size: 17
1537073 AAAAATGGAG
1537083 AGAAAAAAAAAAGAAAA
1 AGAAAAAAAAAAGAAAA
*
1537100 AGAAAGAAAATAAGGAAAA
1 AGAAA-AAAA-AAAGAAAA
1537119 AGAAAAAAAAAA
1 AGAAAAAAAAAA
1537131 ACAAGCTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.26
18 8 0.30
19 12 0.44
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (17 bp):
AGAAAAAAAAAAGAAAA
Found at i:1545978 original size:145 final size:140
Alignment explanation
Indices: 1545674--1546003 Score: 355
Period size: 145 Copynumber: 2.3 Consensus size: 140
1545664 TTTCTATAGG
* * * ** ** * *
1545674 GGTATAGAAATCATTAAAACTTTTCGTATCTTTTCACTTCTCCATTAAAG-TACGAAATGAATTT
1 GGTATAGAAATCTTTAAAACATATCGTATCTTTTCGGTTCTTTATT-AAGTTGCAAAATGAATTT
* * *
1545738 TTAAAAAATAAAAATTAAATAAAAATTATTGTCTTAATTTTTTAAGATTTTTAGTATTCCTATGG
65 TTAAAAAATAAAAATTAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAGTATTCCTATGG
*
1545803 TTTTTTGTAGA
130 TTTTTCGTAGA
*
1545814 GGTATAGAAATCTTTAAAACATATCGTATCTTTTTGGTTCTTTATTAAGTTGCAAAATGAATTTT
1 GGTATAGAAATCTTTAAAACATATCGTATCTTTTCGGTTCTTTATTAAGTTGCAAAATGAATTTT
** *
1545879 TTTAAAATCAAAAAATTAAATAAGAATTATTATTATCTTAATTTTTCAATATTTCTA-TCATTCC
66 TAAAAAAT--AAAAATTAAATAA-AA--ATTATTATCTTAATTTTTCAAGATTTCTAGT-ATTCC
1545943 TATAGG-TTTTCGTAG-
125 TAT-GGTTTTTCGTAGA
* * *
1545958 GGATATAGAAAT-TTTCAAAACCTTTCGTATCTTTTCGGTTTTTTAT
1 GG-TATAGAAATCTTT-AAAACATATCGTATCTTTTCGGTTCTTTAT
1546004 CATATATTAA
Statistics
Matches: 159, Mismatches: 21, Indels: 15
0.82 0.11 0.08
Matches are distributed among these distances:
139 3 0.02
140 57 0.36
142 13 0.08
143 2 0.01
144 6 0.04
145 76 0.48
146 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (140 bp):
GGTATAGAAATCTTTAAAACATATCGTATCTTTTCGGTTCTTTATTAAGTTGCAAAATGAATTTT
TAAAAAATAAAAATTAAATAAAAATTATTATCTTAATTTTTCAAGATTTCTAGTATTCCTATGGT
TTTTCGTAGA
Found at i:1546686 original size:155 final size:154
Alignment explanation
Indices: 1546257--1546686 Score: 438
Period size: 155 Copynumber: 2.8 Consensus size: 154
1546247 ATAGGTTCAT
* ** *
1546257 TAATCCTTTTTAAGTCCTTTA-GGAGTATCGAGCACTTTTAAGTCGAAGGTATCCTGTAGAGGCA
1 TAATCCTTTTTAAGTCCTTTAGGGA-TATCGAGCACTTCTAAGTCGAAGGTATCCCATAGGGGCA
* * * * * ** *
1546321 TTTTCTTAATTTTTCAAAAACAAAGTCTTAGGTTGTCA-CTATGTCCACTTTTATACTGAATGTT
65 TTTTCATAATTTTTCAAAATC-GAGTCTTAGGTTGTCATCGA-GT-CACTTTTATGCCAAATGTG
1546385 GGTATTTAGGATAGGTTCATCCCATCTA
127 GGTATTTAGGATAGGTTCATCCCATCTA
* * ** * * **
1546413 TAATCTTTTTTAAGTCCTTTAGGGGTATCGA-CACTTCTAAGTCGAAAATATCCCTTAAGGATAT
1 TAATCCTTTTTAAGTCCTTTAGGGATATCGAGCACTTCTAAGTCGAAGGTATCCCATAGGGGCAT
* ** *
1546477 TTTCATAAATATTTCAGAAAT-GAGTCTTAGGTCATCATCGGGTC-CGTTTTTATGCCAAATGTG
66 TTTCAT-AATTTTTCA-AAATCGAGTCTTAGGTTGTCATCGAGTCAC--TTTTATGCCAAATGTG
*
1546540 GGTATTTAGGATAGTTTCATCCCATCTA
127 GGTATTTAGGATAGGTTCATCCCATCTA
* * *
1546568 TAATCCTTTTTAAGCCCTTTAGGGATATCAAGCACTTCTAAGTTGAAGGTATCCCATAGGGGCAT
1 TAATCCTTTTTAAGTCCTTTAGGGATATCGAGCACTTCTAAGTCGAAGGTATCCCATAGGGGCAT
* * * ** *
1546633 TTTCATATTTTTTCTATAATCGAGTCCTAATTTGTCATCGAGTCACTTCTATGC
66 TTTCATAATTTTTC-AAAATCGAGTCTTAGGTTGTCATCGAGTCACTTTTATGC
1546687 TGAGGGTACA
Statistics
Matches: 219, Mismatches: 45, Indels: 21
0.77 0.16 0.07
Matches are distributed among these distances:
153 1 0.00
154 1 0.00
155 126 0.58
156 85 0.39
157 6 0.03
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.39
Consensus pattern (154 bp):
TAATCCTTTTTAAGTCCTTTAGGGATATCGAGCACTTCTAAGTCGAAGGTATCCCATAGGGGCAT
TTTCATAATTTTTCAAAATCGAGTCTTAGGTTGTCATCGAGTCACTTTTATGCCAAATGTGGGTA
TTTAGGATAGGTTCATCCCATCTA
Found at i:1548108 original size:24 final size:24
Alignment explanation
Indices: 1548076--1548124 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
1548066 AAAAGAAGTA
1548076 AGTTTCTTCCCCAGCACACACACT
1 AGTTTCTTCCCCAGCACACACACT
1548100 AGTTTCTTCCCCAGCACACACACT
1 AGTTTCTTCCCCAGCACACACACT
1548124 A
1 A
1548125 TGCACATGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.27, C:0.41, G:0.08, T:0.24
Consensus pattern (24 bp):
AGTTTCTTCCCCAGCACACACACT
Found at i:1550450 original size:21 final size:22
Alignment explanation
Indices: 1550424--1550468 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1550414 TCCTCCAAAT
* *
1550424 AAGAAACAAC-CAAAAAGAGAA
1 AAGAAAAAACTCAAAAAAAGAA
*
1550445 AAGAAAAAACTGAAAAAAAGAA
1 AAGAAAAAACTCAAAAAAAGAA
1550467 AA
1 AA
1550469 ACACATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.76, C:0.09, G:0.13, T:0.02
Consensus pattern (22 bp):
AAGAAAAAACTCAAAAAAAGAA
Found at i:1552415 original size:89 final size:89
Alignment explanation
Indices: 1552259--1552509 Score: 301
Period size: 89 Copynumber: 2.8 Consensus size: 89
1552249 TTGATAAAGA
* * * * * **
1552259 GGCAAGGTGCAACTCACACATTCCTAATCATATCCCCTTT-ATCCAACCACTAGATGGTATTGGT
1 GGCAAGGTGCAGCACACATATTCCTAATCATAT-CCCTTTCATCTAATCACTAGATGGTATTAAT
1552323 GCATCACAAAACCTAATTTCCTTGG
65 GCATCACAAAACCTAATTTCCTTGG
* * * *
1552348 GGCAAGGTGCAGCCCATATATTCCTAATCATATCGCTTTCATCTAATCATTAGATGGTATTAATG
1 GGCAAGGTGCAGCACACATATTCCTAATCATATCCCTTTCATCTAATCACTAGATGGTATTAATG
*
1552413 CATCACAAAGCCTAATTTCCTTGG
66 CATCACAAAACCTAATTTCCTTGG
* **
1552437 GGCAAGGTGCAGTACACATATTCCTAATCATATCTTTTTC-T-TAATAGCCACTAGATGGTATTA
1 GGCAAGGTGCAGCACACATATTCCTAATCATATCCCTTTCATCTAAT---CACTAGATGGTATTA
*
1552500 ATACATCACA
63 ATGCATCACA
1552510 TGATTACAAA
Statistics
Matches: 140, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
87 4 0.03
88 6 0.04
89 107 0.76
90 23 0.16
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (89 bp):
GGCAAGGTGCAGCACACATATTCCTAATCATATCCCTTTCATCTAATCACTAGATGGTATTAATG
CATCACAAAACCTAATTTCCTTGG
Found at i:1553004 original size:47 final size:47
Alignment explanation
Indices: 1552934--1553153 Score: 212
Period size: 47 Copynumber: 4.7 Consensus size: 47
1552924 GACCTAGATA
* *
1552934 TCAAACTCTTTC-ACCTTCATTTAACTGTATTGGCATTAGGACCTGG
1 TCAAACTCTTTCTACCTTCGTTTAACTGTATTGGCATTAGGACATGG
* *
1552980 TCAAACTCTATCTACCTTCGTTTAACTATATTGGCATTAGGACATGG
1 TCAAACTCTTTCTACCTTCGTTTAACTGTATTGGCATTAGGACATGG
* * *
1553027 TCAAACTCTTTTTACTTTCGTTTGACTGTATTGGCATTAGG-CATGG
1 TCAAACTCTTTCTACCTTCGTTTAACTGTATTGGCATTAGGACATGG
* * * * * * * * * * *
1553073 TCAAAGTTTTTCCACCATCATTTGACTATATAGGTATTAGGACCTAG
1 TCAAACTCTTTCTACCTTCGTTTAACTGTATTGGCATTAGGACATGG
* * * *
1553120 TTAAACTCTTT-TCACCCTCGTTTGACTATATTGG
1 TCAAACTCTTTCT-ACCTTCGTTTAACTGTATTGG
1553154 TGTTAAAACC
Statistics
Matches: 143, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
46 47 0.33
47 96 0.67
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (47 bp):
TCAAACTCTTTCTACCTTCGTTTAACTGTATTGGCATTAGGACATGG
Found at i:1553101 original size:93 final size:94
Alignment explanation
Indices: 1552934--1553153 Score: 255
Period size: 93 Copynumber: 2.4 Consensus size: 94
1552924 GACCTAGATA
* * * * *
1552934 TCAAACTC-TTTCACCTTCATTTAACTGTATTGGCATTAGGACCTGGTCAAACTCTATCTACCTT
1 TCAAACTCTTTTCACCTTCGTTTGACTGTATTGGCATTAGGACATGGTCAAACTCTATCCACCAT
* * *
1552998 CGTTTAACTATATTGGCATTAGGACATGG
66 CATTTAACTATATAGGCATTAGGACATAG
* * * * *
1553027 TCAAACTCTTTTTACTTTCGTTTGACTGTATTGGCATTAGG-CATGGTCAAAGTTTTTCCACCAT
1 TCAAACTCTTTTCACCTTCGTTTGACTGTATTGGCATTAGGACATGGTCAAACTCTATCCACCAT
* * *
1553091 CATTTGACTATATAGGTATTAGGACCTAG
66 CATTTAACTATATAGGCATTAGGACATAG
* * *
1553120 TTAAACTCTTTTCACCCTCGTTTGACTATATTGG
1 TCAAACTCTTTTCACCTTCGTTTGACTGTATTGG
1553154 TGTTAAAACC
Statistics
Matches: 105, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
93 77 0.73
94 28 0.27
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.39
Consensus pattern (94 bp):
TCAAACTCTTTTCACCTTCGTTTGACTGTATTGGCATTAGGACATGGTCAAACTCTATCCACCAT
CATTTAACTATATAGGCATTAGGACATAG
Found at i:1553165 original size:47 final size:47
Alignment explanation
Indices: 1553093--1553312 Score: 169
Period size: 47 Copynumber: 4.9 Consensus size: 47
1553083 TCCACCATCA
* * * *
1553093 TTTGACTATATAGGTATTAGGACCTAGTTAAACTCTTTTCACCC-TCG
1 TTTGACTATATTGGTGTTAAGACCTAGTCAAACTCTTTTCACCCAT-G
* *
1553140 TTTGACTATATTGGTGTTAAAACCTAGTGAAACTC-TTTCTACCCATG
1 TTTGACTATATTGGTGTTAAGACCTAGTCAAACTCTTTTC-ACCCATG
* ***
1553187 TTTGACTGTATTAACGTTAAGACCTAGTCAAACTCTTTTCA-CCA--
1 TTTGACTATATTGGTGTTAAGACCTAGTCAAACTCTTTTCACCCATG
* * * *
1553231 -TTG----T-TTGGTATTAAGACCT-GATCAAACTTTTTTC-CCCCTCA
1 TTTGACTATATTGGTGTTAAGACCTAG-TCAAACTCTTTTCACCCAT-G
* *
1553272 TTTGACTATATTAGTGTTAGGACCTAGTCAAACTCTTTTCA
1 TTTGACTATATTGGTGTTAAGACCTAGTCAAACTCTTTTCA
1553313 TCATCATTTG
Statistics
Matches: 136, Mismatches: 21, Indels: 31
0.72 0.11 0.16
Matches are distributed among these distances:
37 1 0.01
38 25 0.18
39 1 0.01
42 3 0.02
43 3 0.02
46 8 0.06
47 89 0.65
48 6 0.04
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.39
Consensus pattern (47 bp):
TTTGACTATATTGGTGTTAAGACCTAGTCAAACTCTTTTCACCCATG
Found at i:1553390 original size:59 final size:60
Alignment explanation
Indices: 1553298--1553411 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 60
1553288 TTAGGACCTA
* * *
1553298 GTCAAACTCTTTTCATCATCATTTGGCTGCATCT-GTCAAACTCTTTTCATCATCGTTTG
1 GTCAAACTCTTTTCATCATCATTTAGCTACATCTGGTCAAAATCTTTTCATCATCGTTTG
* * *
1553357 GTCAAACTCTTTTCATTATTATTTAGCTACATCTGGTCAAAATCTTTTTATCATC
1 GTCAAACTCTTTTCATCATCATTTAGCTACATCTGGTCAAAATCTTTTCATCATC
1553412 TTGATTGCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
59 30 0.62
60 18 0.38
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.44
Consensus pattern (60 bp):
GTCAAACTCTTTTCATCATCATTTAGCTACATCTGGTCAAAATCTTTTCATCATCGTTTG
Found at i:1553403 original size:35 final size:35
Alignment explanation
Indices: 1553355--1553614 Score: 177
Period size: 35 Copynumber: 7.5 Consensus size: 35
1553345 CATCATCGTT
* *
1553355 TGGTCAAACTCTTTTCATTATTATTTAGCTACATC
1 TGGTCAAACTCTTTTCATCATTGTTTAGCTACATC
* * * * * *
1553390 TGGTCAAAATCTTTTTATCA-TCTTGA-TTGCATC
1 TGGTCAAACTCTTTTCATCATTGTTTAGCTACATC
* * * *
1553423 TGGTCAAACT-TTCTTCACCATTGTTTAGTTATATT
1 TGGTCAAACTCTT-TTCATCATTGTTTAGCTACATC
* ** * ***
1553458 TGGTCAAAATCTTTTCATCATCATTTGGCCGTATC
1 TGGTCAAACTCTTTTCATCATTGTTTAGCTACATC
* * * * * *
1553493 TGGTTAAACTATTTTCATCATCGTTTGGTTGCATC
1 TGGTCAAACTCTTTTCATCATTGTTTAGCTACATC
* *
1553528 TGGTCAAACTCTTTTCATCATTGTTTAACTATATC
1 TGGTCAAACTCTTTTCATCATTGTTTAGCTACATC
* * * **
1553563 TGGTGAAA-TCTTTTCATCATCGTTTGGCTGTATC
1 TGGTCAAACTCTTTTCATCATTGTTTAGCTACATC
* *
1553597 TAGTTAAACTCTTTTCAT
1 TGGTCAAACTCTTTTCAT
1553615 TATCGTTTGG
Statistics
Matches: 174, Mismatches: 46, Indels: 10
0.76 0.20 0.04
Matches are distributed among these distances:
32 2 0.01
33 19 0.11
34 36 0.21
35 115 0.66
36 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.45
Consensus pattern (35 bp):
TGGTCAAACTCTTTTCATCATTGTTTAGCTACATC
Found at i:1553603 original size:104 final size:105
Alignment explanation
Indices: 1553416--1553627 Score: 311
Period size: 104 Copynumber: 2.0 Consensus size: 105
1553406 ATCATCTTGA
** *
1553416 TTGCATCTGGTCAAACTTTCTTCACCATTGTTTAGTTATATTTGGTCAAAATCTTTTCATCATCA
1 TTGCATCTGGTCAAACTTTCTTCACCATTGTTTAACTATATCTGGTCAAAATCTTTTCATCATCA
*
1553481 TTTGGCCGTATCTGGTTAAACTATTTTCATCATCGTTTGG
66 TTTGGCCGTATCTAGTTAAACTATTTTCATCATCGTTTGG
* *
1553521 TTGCATCTGGTCAAACTCTT-TTCATCATTGTTTAACTATATCTGGT-GAAATCTTTTCATCATC
1 TTGCATCTGGTCAAACT-TTCTTCACCATTGTTTAACTATATCTGGTCAAAATCTTTTCATCATC
* * * *
1553584 GTTTGGCTGTATCTAGTTAAACTCTTTTCATTATCGTTTGG
65 ATTTGGCCGTATCTAGTTAAACTATTTTCATCATCGTTTGG
1553625 TTG
1 TTG
1553628 TATTTAGTTA
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
104 55 0.57
105 39 0.41
106 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.15, T:0.46
Consensus pattern (105 bp):
TTGCATCTGGTCAAACTTTCTTCACCATTGTTTAACTATATCTGGTCAAAATCTTTTCATCATCA
TTTGGCCGTATCTAGTTAAACTATTTTCATCATCGTTTGG
Found at i:1553620 original size:35 final size:35
Alignment explanation
Indices: 1553458--1553640 Score: 197
Period size: 35 Copynumber: 5.3 Consensus size: 35
1553448 TAGTTATATT
* * * *
1553458 TGGTCAAAATCTTTTCATCATCATTTGGCCGTATC
1 TGGTTAAACTCTTTTCATCATCGTTTGGCTGTATC
* * *
1553493 TGGTTAAACTATTTTCATCATCGTTTGGTTGCATC
1 TGGTTAAACTCTTTTCATCATCGTTTGGCTGTATC
* * ** *
1553528 TGGTCAAACTCTTTTCATCATTGTTTAACTATATC
1 TGGTTAAACTCTTTTCATCATCGTTTGGCTGTATC
*
1553563 TGGTGAAA-TCTTTTCATCATCGTTTGGCTGTATC
1 TGGTTAAACTCTTTTCATCATCGTTTGGCTGTATC
* * * *
1553597 TAGTTAAACTCTTTTCATTATCGTTTGGTTGTATT
1 TGGTTAAACTCTTTTCATCATCGTTTGGCTGTATC
*
1553632 TAGTTAAAC
1 TGGTTAAAC
1553641 CATTTCGTTC
Statistics
Matches: 122, Mismatches: 25, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
34 28 0.23
35 94 0.77
ACGTcount: A:0.22, C:0.17, G:0.15, T:0.45
Consensus pattern (35 bp):
TGGTTAAACTCTTTTCATCATCGTTTGGCTGTATC
Found at i:1553707 original size:46 final size:46
Alignment explanation
Indices: 1553654--1553751 Score: 110
Period size: 46 Copynumber: 2.1 Consensus size: 46
1553644 TTCGTTCTCG
* *
1553654 TTTGACTG-AATCGGTTACCAGCTTGGTCAAACCCCTTT-CATTCCCA
1 TTTGACTGCAA-CGATTACCACCTTGGTCAAA-CCCTTTCCATTCCCA
** *
1553700 TTTGACTGCAACGATTGTCACCTTGGTCAAACCCTTTCCATTCTCA
1 TTTGACTGCAACGATTACCACCTTGGTCAAACCCTTTCCATTCCCA
*
1553746 CTTGAC
1 TTTGAC
1553752 CTTATCAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
45 6 0.14
46 36 0.82
47 2 0.05
ACGTcount: A:0.21, C:0.31, G:0.14, T:0.34
Consensus pattern (46 bp):
TTTGACTGCAACGATTACCACCTTGGTCAAACCCTTTCCATTCCCA
Found at i:1555209 original size:165 final size:164
Alignment explanation
Indices: 1554917--1555327 Score: 574
Period size: 165 Copynumber: 2.5 Consensus size: 164
1554907 GAAATTTTCT
* * * * * **
1554917 AAATATTATCAATTAA-TCACTATTAAATCAGTTTTCAAAAATTCATTTATTTTTATGAGTTTTC
1 AAATATTATTATTTAATTCA-TATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAGTTTGA
* * *
1554981 ATTTTTCTTTGAAATTCTCCTGTTTCTGAAATATGGAGTTTTCTACTCTATAAATATTTTTGGAG
65 ATTTTTCTTTGAAATTCTCATGTTTCTGAAATACGGAGTTTTCTACTCCATAAATATTTTTGGAG
* * *
1555046 GGATTTTTCTTAGTTTTTAATTTTTAAAATTCATC
130 AGATTTTTCCTAGATTTTAATTTTTAAAATTCATC
* *
1555081 AAATGTTATTTTTTTAATTCATATTAAATCAGTTTTAAAAAATTAATTTA-TTTCATGAGTTATG
1 AAATATTA-TTATTTAATTCATATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAGTT-TG
*
1555145 AATTTTTCTTTGAAATTCTCATGTTTCTGAAATACGGAGTTTTCTACTCCATAAATGTTTTTGGA
64 AATTTTTCTTTGAAATTCTCATGTTTCTGAAATACGGAGTTTTCTACTCCATAAATATTTTTGGA
* *
1555210 GAGATTTTTCCTAGATTTTAATTTTTTAAATTCATT
129 GAGATTTTTCCTAGATTTTAATTTTTAAAATTCATC
* *
1555246 AAATATTATTATTTAATTCATATTAAATTAGTTTTGAAAAATTAATTTATTTTCATGAGTTTTGA
1 AAATATTATTATTTAATTCATATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAG-TTTGA
*
1555311 ATTTTTTTCTTGAAATT
65 ATTTTTCT-TTGAAATT
1555328 TTCTTATTTC
Statistics
Matches: 218, Mismatches: 23, Indels: 10
0.87 0.09 0.04
Matches are distributed among these distances:
164 55 0.25
165 150 0.69
166 13 0.06
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.51
Consensus pattern (164 bp):
AAATATTATTATTTAATTCATATTAAATCAGTTTTAAAAAATTAATTTATTTTCATGAGTTTGAA
TTTTTCTTTGAAATTCTCATGTTTCTGAAATACGGAGTTTTCTACTCCATAAATATTTTTGGAGA
GATTTTTCCTAGATTTTAATTTTTAAAATTCATC
Done.