Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007838.1 Hibiscus syriacus cultivar Beakdansim tig00110187_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3429202
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 13
Found at i:969326 original size:34 final size:34
Alignment explanation
Indices: 969250--969327 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 34
969240 CAAAATATTA
*
969250 ATTAT-TAAAAT-ATTTAAAATATATTTATTAAT
1 ATTATATAAAATAATATAAAATATATTTATTAAT
*
969282 ATT-TAT--AATAATATAATATAATATTT-TTAAT
1 ATTATATAAAATAATATAAAAT-ATATTTATTAAT
969313 ATTATATAAAATAAT
1 ATTATATAAAATAAT
969328 CAATTATATT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
30 3 0.08
31 16 0.42
32 13 0.34
34 6 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (34 bp):
ATTATATAAAATAATATAAAATATATTTATTAAT
Found at i:969394 original size:54 final size:52
Alignment explanation
Indices: 969283--969394 Score: 129
Period size: 54 Copynumber: 2.1 Consensus size: 52
969273 TTTATTAATA
*
969283 TTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATCAATTAT
1 TTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATAAATTAT
* * * *
969335 ATTATAATAATATAAGATATTATATTTTT-ATTTTA-ATAATATATAATAAATTTT
1 TTTATAATAATAT-A-ATATAATATTTTTAATATTATATAA-A-ATAATAAATTAT
969389 TTTATA
1 TTTATA
969395 TATTTAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
52 16 0.32
53 7 0.14
54 27 0.54
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (52 bp):
TTTATAATAATATAATATAATATTTTTAATATTATATAAAATAATAAATTAT
Found at i:969627 original size:20 final size:20
Alignment explanation
Indices: 969602--969671 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
969592 TTTCCAGATG
*
969602 TTTTCCAGAAATGTAATTAA
1 TTTTCCAGAAATGTAATTCA
969622 TTTTCCAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
969642 TTTTACAGAAATGTAATTCA
1 TTTTCCAGAAATGTAATTCA
*
969662 TTTTTCAGAA
1 TTTTCCAGAA
969672 TTCAAATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.37, C:0.11, G:0.10, T:0.41
Consensus pattern (20 bp):
TTTTCCAGAAATGTAATTCA
Found at i:969675 original size:14 final size:15
Alignment explanation
Indices: 969654--969740 Score: 104
Period size: 15 Copynumber: 5.9 Consensus size: 15
969644 TTACAGAAAT
*
969654 GTAATTCATTTTTCA
1 GTAATTCATTTTCCA
**
969669 G-AATTCAAATTCCA
1 GTAATTCATTTTCCA
969683 GTAATTCATTTTCCA
1 GTAATTCATTTTCCA
**
969698 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
**
969713 GTAATTCAAATTCCA
1 GTAATTCATTTTCCA
969728 GTAATTCATTTTC
1 GTAATTCATTTTC
969741 TGGAAAACCA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 11 0.18
15 51 0.82
ACGTcount: A:0.33, C:0.18, G:0.07, T:0.41
Consensus pattern (15 bp):
GTAATTCATTTTCCA
Found at i:969679 original size:20 final size:20
Alignment explanation
Indices: 969602--969680 Score: 59
Period size: 20 Copynumber: 4.0 Consensus size: 20
969592 TTTCCAGATG
* ** *
969602 TTTTCCAGAAATGTAATTAA
1 TTTTACAGAAATCAAATTCA
* **
969622 TTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATCAAATTCA
**
969642 TTTTACAGAAATGTAATTCA
1 TTTTACAGAAATCAAATTCA
* *
969662 TTTTTCAGAATTCAAATTC
1 TTTTACAGAAATCAAATTC
969681 CAGTAATTCA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (20 bp):
TTTTACAGAAATCAAATTCA
Found at i:969680 original size:40 final size:40
Alignment explanation
Indices: 969602--969680 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
969592 TTTCCAGATG
* **
969602 TTTTCCAGAAATGTAATTAATTTTCCAGAAATGTAATTCA
1 TTTTACAGAAATGTAATTAATTTTCCAGAAATCAAATTCA
* * *
969642 TTTTACAGAAATGTAATTCATTTTTCAGAATTCAAATTC
1 TTTTACAGAAATGTAATTAATTTTCCAGAAATCAAATTC
969681 CAGTAATTCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (40 bp):
TTTTACAGAAATGTAATTAATTTTCCAGAAATCAAATTCA
Found at i:969690 original size:15 final size:15
Alignment explanation
Indices: 969670--969735 Score: 114
Period size: 15 Copynumber: 4.4 Consensus size: 15
969660 CATTTTTCAG
969670 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
**
969685 AATTCATTTTCCAGT
1 AATTCAAATTCCAGT
969700 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
969715 AATTCAAATTCCAGT
1 AATTCAAATTCCAGT
969730 AATTCA
1 AATTCA
969736 TTTTCTGGAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 47 1.00
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (15 bp):
AATTCAAATTCCAGT
Found at i:969706 original size:30 final size:30
Alignment explanation
Indices: 969654--969735 Score: 130
Period size: 30 Copynumber: 2.8 Consensus size: 30
969644 TTACAGAAAT
*
969654 GTAATTCATTTTTCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
969683 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
**
969713 GTAATTCAAATTCCAGTAATTCA
1 GTAATTCATTTTCCAGTAATTCA
969736 TTTTCTGGAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 15 0.31
30 34 0.69
ACGTcount: A:0.35, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:979864 original size:2 final size:2
Alignment explanation
Indices: 979857--979889 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
979847 TTGATATGTT
979857 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
979890 TAAATTGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:984747 original size:22 final size:23
Alignment explanation
Indices: 984720--984763 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
984710 ACAATATTAT
* *
984720 TTTAATCATTAA-ATTATAAAAA
1 TTTAATAATTAAGATAATAAAAA
984742 TTTAATAATTAAGATAATAAAA
1 TTTAATAATTAAGATAATAAAA
984764 TCATTTCGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
TTTAATAATTAAGATAATAAAAA
Found at i:985037 original size:22 final size:24
Alignment explanation
Indices: 985009--985054 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
984999 TGAATATAAG
985009 TTTTAAAAAAT-AA-ATTTAAATA
1 TTTTAAAAAATAAATATTTAAATA
*
985031 TTTTAAAAATTAAATATTTAAATA
1 TTTTAAAAAATAAATATTTAAATA
985055 ATGTTAGATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.48
23 2 0.10
24 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
TTTTAAAAAATAAATATTTAAATA
Found at i:985851 original size:2 final size:2
Alignment explanation
Indices: 985844--985868 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
985834 AACACAAAGG
985844 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
985869 GAGGGCCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:986757 original size:2 final size:2
Alignment explanation
Indices: 986750--986802 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
986740 AATTTCATGA
986750 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
986792 AT AT AT AT AT A
1 AT AT AT AT AT A
986803 CGCGCGCGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:990489 original size:2 final size:2
Alignment explanation
Indices: 990482--990511 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
990472 ATTTGGTTTC
990482 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
990512 TGGGCATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:997114 original size:14 final size:14
Alignment explanation
Indices: 997095--997121 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
997085 TTTATCAAAA
997095 AAATATAGAATAAC
1 AAATATAGAATAAC
997109 AAATATAGAATAA
1 AAATATAGAATAA
997122 TAATAAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (14 bp):
AAATATAGAATAAC
Found at i:1003899 original size:2 final size:2
Alignment explanation
Indices: 1003877--1003924 Score: 69
Period size: 2 Copynumber: 22.5 Consensus size: 2
1003867 TTGTGTAACA
1003877 AT AT CAT AT CAT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT -AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1003920 AT AT A
1 AT AT A
1003925 ATTTGAATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
2 37 0.86
3 6 0.14
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1027914 original size:15 final size:15
Alignment explanation
Indices: 1027894--1027922 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1027884 ATGAAACAAA
1027894 ACATGGGCGGCTATG
1 ACATGGGCGGCTATG
1027909 ACATGGGCGGCTAT
1 ACATGGGCGGCTAT
1027923 CAAAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.21, G:0.38, T:0.21
Consensus pattern (15 bp):
ACATGGGCGGCTATG
Found at i:1044995 original size:21 final size:21
Alignment explanation
Indices: 1044969--1045009 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
1044959 GGTTAATTAT
1044969 TTTTAAAGACCCATTTAGTTA
1 TTTTAAAGACCCATTTAGTTA
1044990 TTTTAAAGACCCATTTAGTT
1 TTTTAAAGACCCATTTAGTT
1045010 TTAAAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.32, C:0.15, G:0.10, T:0.44
Consensus pattern (21 bp):
TTTTAAAGACCCATTTAGTTA
Found at i:1047422 original size:46 final size:48
Alignment explanation
Indices: 1047371--1047480 Score: 116
Period size: 46 Copynumber: 2.3 Consensus size: 48
1047361 ACTCTTCATA
*
1047371 TTATAAATTATCTACAAGTTAATAATAGAATAATAATA-TATTAA-CT
1 TTATAAATTATCTACAAGTTAACAATAGAATAATAATATTATTAATCT
** * ** ** *
1047417 TTATAAAACATATTTATTTTAACAATAGAATAATAATATTATTAATTT
1 TTATAAATTATCTACAAGTTAACAATAGAATAATAATATTATTAATCT
1047465 TATATAAATTATCTAC
1 T-TATAAATTATCTAC
1047481 TTATTAATTT
Statistics
Matches: 47, Mismatches: 14, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
46 30 0.64
47 6 0.13
48 2 0.04
49 9 0.19
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (48 bp):
TTATAAATTATCTACAAGTTAACAATAGAATAATAATATTATTAATCT
Found at i:1048439 original size:10 final size:10
Alignment explanation
Indices: 1048395--1048446 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
1048385 ATATAGGTGG
1048395 AATAATAAAA
1 AATAATAAAA
* *
1048405 TATATATATAA
1 AATA-ATAAAA
* **
1048416 AATATTAATT
1 AATAATAAAA
1048426 AATAATAAAA
1 AATAATAAAA
1048436 AATAATAAAA
1 AATAATAAAA
1048446 A
1 A
1048447 TATCATATCA
Statistics
Matches: 31, Mismatches: 10, Indels: 2
0.72 0.23 0.05
Matches are distributed among these distances:
10 23 0.74
11 8 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATAATAAAA
Found at i:1058693 original size:24 final size:24
Alignment explanation
Indices: 1058666--1058736 Score: 63
Period size: 24 Copynumber: 3.0 Consensus size: 24
1058656 AAACGGATAT
*
1058666 ATCAGAAATCAAAACAGAATTTAG
1 ATCAGAAATCAAAACAGAATTCAG
* * ** * *
1058690 ATCATATATCTTAACAGAATCCAT
1 ATCAGAAATCAAAACAGAATTCAG
*
1058714 ATCAGAAATCAGAACA-AATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
1058737 GTCATGTATC
Statistics
Matches: 34, Mismatches: 13, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
23 5 0.15
24 29 0.85
ACGTcount: A:0.49, C:0.17, G:0.10, T:0.24
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1063027 original size:24 final size:24
Alignment explanation
Indices: 1063000--1063094 Score: 77
Period size: 24 Copynumber: 4.0 Consensus size: 24
1062990 AAACGGAGAT
*
1063000 ATCATAAATCAAAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * * *
1063024 ATCAGATATCATAACATAA-TCTAT
1 ATCAGAAATCAAAACAGAATTC-AG
*
1063048 ATCAGAAATCAGAACAGAATTCAG
1 ATCAGAAATCAAAACAGAATTCAG
* * *
1063072 GTCATG-TATCAAAACAAAATTCA
1 ATCA-GAAATCAAAACAGAATTCA
1063095 AGTCGAAAAT
Statistics
Matches: 55, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
23 2 0.04
24 50 0.91
25 3 0.05
ACGTcount: A:0.49, C:0.17, G:0.09, T:0.24
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAG
Found at i:1066152 original size:2 final size:2
Alignment explanation
Indices: 1066145--1066178 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1066135 TCTATACAAC
1066145 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1066179 TCTCTATTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1067378 original size:20 final size:20
Alignment explanation
Indices: 1067350--1067387 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1067340 TTCCCCTTAA
1067350 AGTGCATCGATACATTCTAT
1 AGTGCATCGATACATTCTAT
* *
1067370 AGTGTATCGATGCATTCT
1 AGTGCATCGATACATTCT
1067388 TTAACATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAT
Found at i:1067484 original size:64 final size:62
Alignment explanation
Indices: 1067395--1067556 Score: 157
Period size: 64 Copynumber: 2.5 Consensus size: 62
1067385 TCTTTAACAT
* * * *
1067395 GTGCATCGATACACTACCCATGCATCGATACACAGATCACCTTCAATGTTT-TAATTTTAAGGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACA-ATCACATTCAATGTTTCCAATTTTAAGGG
* * * *
1067458 AGTGCATCGATGCACTCCTTATGCATCGATGA-ACTAATTACATTCGATGTTTCCATTTTTAATG
1 -GTGCATCGATGCACTCC-TATGCATCGAT-ACAC-AATCACATTCAATGTTTCCAATTTTAAGG
1067522 G
62 G
* *
1067523 GTGCATCGATGCACTTCATGTGCATCGATACACA
1 GTGCATCGATGCAC-TCCTATGCATCGATACACA
1067557 CTGAACAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 13
0.78 0.10 0.12
Matches are distributed among these distances:
63 4 0.05
64 65 0.79
65 13 0.16
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (62 bp):
GTGCATCGATGCACTCCTATGCATCGATACACAATCACATTCAATGTTTCCAATTTTAAGGG
Found at i:1080402 original size:15 final size:15
Alignment explanation
Indices: 1080379--1080412 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1080369 TATAATCTTT
1080379 TAAATA-AAAATAT-
1 TAAATATAAAATATA
1080392 TAAATATAAAATATA
1 TAAATATAAAATATA
1080407 TAAATA
1 TAAATA
1080413 ATTATACGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 7 0.37
15 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
TAAATATAAAATATA
Found at i:1080575 original size:35 final size:35
Alignment explanation
Indices: 1080522--1080617 Score: 147
Period size: 35 Copynumber: 2.7 Consensus size: 35
1080512 GGTTCAAGAA
* * *
1080522 ACACGTGTACGCTACGATTATCGTTACGTAAACGG
1 ACACGTGTACGCTGCGATTATCGTTAAGTAAAAGG
* *
1080557 ACACGTGTAAGCTGCGATTATTGTTAAGTAAAAGG
1 ACACGTGTACGCTGCGATTATCGTTAAGTAAAAGG
1080592 ACACGTGTACGCTGCGATTATCGTTA
1 ACACGTGTACGCTGCGATTATCGTTA
1080618 GGAAAACGCA
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 54 1.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (35 bp):
ACACGTGTACGCTGCGATTATCGTTAAGTAAAAGG
Found at i:1083617 original size:3 final size:3
Alignment explanation
Indices: 1083609--1083637 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
1083599 TGCAGAAGAT
1083609 GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GA
1083638 TGATGTAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.34, T:0.00
Consensus pattern (3 bp):
GAC
Found at i:1089173 original size:12 final size:12
Alignment explanation
Indices: 1089156--1089189 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
1089146 CAAACAATAC
1089156 AAATAAGAGAAA
1 AAATAAGAGAAA
1089168 AAATAAGAGAAA
1 AAATAAGAGAAA
*
1089180 AAAAAAGAGA
1 AAATAAGAGA
1089190 GACGAAGATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (12 bp):
AAATAAGAGAAA
Found at i:1097438 original size:24 final size:22
Alignment explanation
Indices: 1097406--1097465 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
1097396 TATATATTTA
* * *
1097406 AAATTTTAAGAATTTTTATTTTT
1 AAATGTTAAGAATATTT-TCTTT
1097429 ATAATGTTAA-AATATTTTCTTT
1 A-AATGTTAAGAATATTTTCTTT
*
1097451 AATTGTTAAGAATAT
1 AAATGTTAAGAATAT
1097466 AGTAAATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
21 7 0.23
22 10 0.32
23 7 0.23
24 7 0.23
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (22 bp):
AAATGTTAAGAATATTTTCTTT
Found at i:1100352 original size:2 final size:2
Alignment explanation
Indices: 1100345--1100380 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1100335 TAAATATCTT
1100345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1100381 GTTTCGATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1100706 original size:28 final size:29
Alignment explanation
Indices: 1100648--1100708 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
1100638 AAAATTTATT
1100648 TATTTTTATAAAAGAAAATCATTTTTAAA
1 TATTTTTATAAAAGAAAATCATTTTTAAA
1100677 TATTTTTATAAAAGAAAATCATTTTT-AA
1 TATTTTTATAAAAGAAAATCATTTTTAAA
1100705 TATT
1 TATT
1100709 AATTTTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 6 0.19
29 26 0.81
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (29 bp):
TATTTTTATAAAAGAAAATCATTTTTAAA
Found at i:1101723 original size:3 final size:3
Alignment explanation
Indices: 1101715--1101739 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1101705 ACTATTATAT
1101715 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
1101740 AAAATAGGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1101902 original size:17 final size:20
Alignment explanation
Indices: 1101846--1101893 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1101836 TAAACTATTC
1101846 ATATGATTACTAAATTTTTA
1 ATATGATTACTAAATTTTTA
1101866 ATATGATTACTAAATTTTTA
1 ATATGATTACTAAATTTTTA
1101886 ATAT-ATTA
1 ATATGATTA
1101894 TCATTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (20 bp):
ATATGATTACTAAATTTTTA
Found at i:1104410 original size:16 final size:16
Alignment explanation
Indices: 1104389--1104421 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1104379 CCTAAGTTCT
1104389 AATTCTCAATTTATAA
1 AATTCTCAATTTATAA
*
1104405 AATTCTTAATTTATAA
1 AATTCTCAATTTATAA
1104421 A
1 A
1104422 TTATCGGTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (16 bp):
AATTCTCAATTTATAA
Found at i:1109724 original size:12 final size:13
Alignment explanation
Indices: 1109707--1109735 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1109697 ATGTTAAAAT
1109707 CTAAACT-TAACC
1 CTAAACTATAACC
1109719 CTAAACTATAACC
1 CTAAACTATAACC
1109732 CTAA
1 CTAA
1109736 GCCCTATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (13 bp):
CTAAACTATAACC
Found at i:1114056 original size:29 final size:27
Alignment explanation
Indices: 1113998--1114060 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 27
1113988 ATACTTAGCA
1113998 TAAA-AAAAACTTGAAAAATAAAGAAG
1 TAAATAAAAACTTGAAAAATAAAGAAG
1114024 -AAATAAAAACTTTGAAAAATAAA-AAG
1 TAAATAAAAAC-TTGAAAAATAAAGAAG
1114050 CTTAAATAAAA
1 --TAAATAAAA
1114061 CAAGAGAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
25 3 0.09
26 9 0.28
27 12 0.38
29 8 0.25
ACGTcount: A:0.68, C:0.05, G:0.08, T:0.19
Consensus pattern (27 bp):
TAAATAAAAACTTGAAAAATAAAGAAG
Found at i:1123824 original size:18 final size:18
Alignment explanation
Indices: 1123803--1123841 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
1123793 CATTCTCGAA
1123803 TATTATATAAA-ATAATTT
1 TATTAT-TAAAGATAATTT
*
1123821 TATTCTTAAAGATAATTT
1 TATTATTAAAGATAATTT
1123839 TAT
1 TAT
1123842 ATTTCATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (18 bp):
TATTATTAAAGATAATTT
Found at i:1131382 original size:2 final size:2
Alignment explanation
Indices: 1131375--1131399 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1131365 CTATATTCAA
1131375 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1131400 AACTCCTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1133580 original size:23 final size:23
Alignment explanation
Indices: 1133550--1133605 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1133540 TTAATAATAT
1133550 TATTATGTAAAATGTTTCGATTA
1 TATTATGTAAAATGTTTCGATTA
1133573 TATTATGTAAAATGTTTCGATTA
1 TATTATGTAAAATGTTTCGATTA
1133596 TA--ATGTAAAA
1 TATTATGTAAAA
1133606 ATTATAACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 8 0.24
23 25 0.76
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.45
Consensus pattern (23 bp):
TATTATGTAAAATGTTTCGATTA
Found at i:1133639 original size:11 final size:12
Alignment explanation
Indices: 1133619--1133652 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1133609 ATAACTAATA
1133619 ATATTAAATATT
1 ATATTAAATATT
*
1133631 ATA-TAAATAAT
1 ATATTAAATATT
1133642 ATATTAAATAT
1 ATATTAAATAT
1133653 ATTTATGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
ATATTAAATATT
Found at i:1136631 original size:8 final size:8
Alignment explanation
Indices: 1136618--1136658 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1136608 CTCATTTTCA
1136618 GAGAATTT
1 GAGAATTT
1136626 GAGAATTT
1 GAGAATTT
*
1136634 -AGAGTTT
1 GAGAATTT
*
1136641 GGGAATTT
1 GAGAATTT
1136649 GAGAATTT
1 GAGAATTT
1136657 GA
1 GA
1136659 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1136946 original size:122 final size:124
Alignment explanation
Indices: 1136726--1137072 Score: 603
Period size: 122 Copynumber: 2.8 Consensus size: 124
1136716 CTATAATCGG
1136726 TTCACTATTCACGTGAAGGCGCGTTCCC-GGGGCGCG-CTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCC--TATTTCGTCAGAGAATATTA
1136789 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
64 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
1136850 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCC-ATTTCGTCAGAGAATATTATC
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCTATTTCGTCAGAGAATATTATC
*
1136914 A-TGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 ATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
*
1136972 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGACGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCC--TATTTCGTCAGAGAATATTA
*
1137037 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
64 TCATTGCCCTATTATGTCATTCATGTCCCTCGGGGA
1137073 ATAACTTAAA
Statistics
Matches: 214, Mismatches: 3, Indels: 10
0.94 0.01 0.04
Matches are distributed among these distances:
122 98 0.46
123 22 0.10
124 28 0.13
125 30 0.14
126 36 0.17
ACGTcount: A:0.22, C:0.27, G:0.20, T:0.31
Consensus pattern (124 bp):
TTCACTATTCACGTGAAGGCGCGTTCCCGGGGGCGCGCCTTCCTATTTCGTCAGAGAATATTATC
ATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTACTAT
Found at i:1138166 original size:21 final size:21
Alignment explanation
Indices: 1138059--1138160 Score: 145
Period size: 21 Copynumber: 4.9 Consensus size: 21
1138049 ATAAAACCCT
*
1138059 GCGGGTTAGGCATGTAA-CTG
1 GCGGGCTAGGCATGTAACCTG
1138079 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGCATGTAACCTG
1138100 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGCATGTAACCTG
*
1138121 GCGGGCTAGGAATGTAACCCT-
1 GCGGGCTAGGCATGTAA-CCTG
* *
1138142 GCGGGCTCGGAATGTAACC
1 GCGGGCTAGGCATGTAACC
1138161 CTGCGGAGAT
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
20 18 0.23
21 56 0.73
22 3 0.04
ACGTcount: A:0.21, C:0.23, G:0.37, T:0.20
Consensus pattern (21 bp):
GCGGGCTAGGCATGTAACCTG
Found at i:1138196 original size:21 final size:21
Alignment explanation
Indices: 1138170--1138217 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1138160 CCTGCGGAGA
*
1138170 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
1138191 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
1138212 GGGCAT
1 TGGCAT
1138218 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:1139724 original size:31 final size:33
Alignment explanation
Indices: 1139677--1139740 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1139667 TCTAAAATAC
1139677 GATCAGCATCCTAAT-A-ATATATTATAAAAAG
1 GATCAGCATCCTAATAATATATATTATAAAAAG
1139708 GATCAG-ATCCTAAATAATATATATTATAAAAAG
1 GATCAGCATCCT-AATAATATATATTATAAAAAG
1139741 TAAAAATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 5 0.17
31 9 0.30
32 1 0.03
33 15 0.50
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (33 bp):
GATCAGCATCCTAATAATATATATTATAAAAAG
Found at i:1141988 original size:21 final size:21
Alignment explanation
Indices: 1141947--1141989 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
1141937 AGGTACGGAT
* *
1141947 TTTTAAGATGATATATTAAAA
1 TTTTAAGATGATAAATAAAAA
1141968 TTTTAAGAAT-ATAAATAAAAA
1 TTTTAAG-ATGATAAATAAAAA
1141989 T
1 T
1141990 ATAAAAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTTAAGATGATAAATAAAAA
Found at i:1142683 original size:17 final size:16
Alignment explanation
Indices: 1142661--1142700 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 16
1142651 AAAATAAATT
1142661 TATTTTATTCTAATTTA
1 TATTTTATTC-AATTTA
1142678 TATTTTATTCAATTTA
1 TATTTTATTCAATTTA
1142694 T-TTTTAT
1 TATTTTAT
1142701 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 6 0.26
16 7 0.30
17 10 0.43
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TATTTTATTCAATTTA
Found at i:1142700 original size:15 final size:16
Alignment explanation
Indices: 1142657--1142700 Score: 65
Period size: 15 Copynumber: 2.8 Consensus size: 16
1142647 AGGTAAAATA
1142657 AATTTA-TTTTATTCT
1 AATTTATTTTTATTCT
1142672 AATTTATATTTTATTC-
1 AATTTAT-TTTTATTCT
1142688 AATTTATTTTTAT
1 AATTTATTTTTAT
1142701 ATATTTTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 12 0.44
16 7 0.26
17 8 0.30
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (16 bp):
AATTTATTTTTATTCT
Found at i:1147570 original size:141 final size:142
Alignment explanation
Indices: 1147312--1147588 Score: 529
Period size: 141 Copynumber: 2.0 Consensus size: 142
1147302 CTCTTCTGGC
*
1147312 TTGGCTTAACGATGCTCACTGCTGCCAACGCCGATCAGCTATTGCACAACACGATGATCCCATGC
1 TTGGCTTAACGATGCTCACTGCTGCCAACGCCGACCAGCTATTGCACAACACGATGATCCCATGC
1147377 TGTGTTTTTCAATAACTTTGAAATCAGCTGCTCGAGTCCCGAAATAAATCCAATTCACTTGAACA
66 TGTGTTTTTCAATAACTTTGAAATCAGCTGCTCGAGTCCCGAAATAAATCCAATTCACTTGAACA
1147442 TGAATATTTTTT
131 TGAATATTTTTT
1147454 TTGGCTTAACGATGCTCACTGCTGCCAACGCCGACCAGCTATTGCACAACACGATGAT-CCATGC
1 TTGGCTTAACGATGCTCACTGCTGCCAACGCCGACCAGCTATTGCACAACACGATGATCCCATGC
*
1147518 TGTGTTTTTCAATAACTTTGAAATCAGCTGCTCGAGTCCCGAAATAAATCCAATTCACTTGTACA
66 TGTGTTTTTCAATAACTTTGAAATCAGCTGCTCGAGTCCCGAAATAAATCCAATTCACTTGAACA
1147583 TGAATA
131 TGAATA
1147589 CGGTATTGAA
Statistics
Matches: 133, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
141 76 0.57
142 57 0.43
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (142 bp):
TTGGCTTAACGATGCTCACTGCTGCCAACGCCGACCAGCTATTGCACAACACGATGATCCCATGC
TGTGTTTTTCAATAACTTTGAAATCAGCTGCTCGAGTCCCGAAATAAATCCAATTCACTTGAACA
TGAATATTTTTT
Found at i:1158153 original size:10 final size:10
Alignment explanation
Indices: 1158138--1158180 Score: 59
Period size: 10 Copynumber: 4.1 Consensus size: 10
1158128 CATTTAATAA
1158138 ATAAACGAAC
1 ATAAACGAAC
1158148 ATAAACGAAC
1 ATAAACGAAC
*
1158158 ACGAACACGAAC
1 A-TAA-ACGAAC
1158170 ATAAACGAAC
1 ATAAACGAAC
1158180 A
1 A
1158181 CGAACATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 18 0.62
11 4 0.14
12 7 0.24
ACGTcount: A:0.58, C:0.23, G:0.12, T:0.07
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:1158163 original size:16 final size:16
Alignment explanation
Indices: 1158158--1158208 Score: 75
Period size: 16 Copynumber: 3.2 Consensus size: 16
1158148 ATAAACGAAC
1158158 ACGAACACGAACATAA
1 ACGAACACGAACATAA
1158174 ACGAACACGAACATAA
1 ACGAACACGAACATAA
** *
1158190 TTGAACGCGAACATAA
1 ACGAACACGAACATAA
1158206 ACG
1 ACG
1158209 TTGGAGACCC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.51, C:0.24, G:0.16, T:0.10
Consensus pattern (16 bp):
ACGAACACGAACATAA
Found at i:1158170 original size:22 final size:22
Alignment explanation
Indices: 1158142--1158186 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
1158132 TAATAAATAA
1158142 ACGAACATAAACGAACACGAAC
1 ACGAACATAAACGAACACGAAC
1158164 ACGAACATAAACGAACACGAAC
1 ACGAACATAAACGAACACGAAC
1158186 A
1 A
1158187 TAATTGAACG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.56, C:0.27, G:0.13, T:0.04
Consensus pattern (22 bp):
ACGAACATAAACGAACACGAAC
Found at i:1172468 original size:23 final size:23
Alignment explanation
Indices: 1172442--1172506 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
1172432 CAGCTCGTAT
1172442 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATGTAG
* * **
1172465 AATTGCACCGGAGTACCGCGTAG
1 AATTGCACCGAAGTGCCATGTAG
1172488 AATTGCACC-ATAGTGCCAT
1 AATTGCACCGA-AGTGCCAT
1172507 ATAAAAATGT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAG
Found at i:1173360 original size:2 final size:2
Alignment explanation
Indices: 1173353--1173384 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1173343 TCTTATATTC
1173353 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1173385 GTCATGATTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1173889 original size:27 final size:27
Alignment explanation
Indices: 1173851--1173904 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
1173841 ACTTAATAAA
1173851 CCAATATTCTTTTCTTCATTAGGGGGG
1 CCAATATTCTTTTCTTCATTAGGGGGG
1173878 CCAATATTCTTTTCTTCATTAGGGGGG
1 CCAATATTCTTTTCTTCATTAGGGGGG
1173905 AATCGGTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.41
Consensus pattern (27 bp):
CCAATATTCTTTTCTTCATTAGGGGGG
Found at i:1174484 original size:87 final size:88
Alignment explanation
Indices: 1174374--1174548 Score: 327
Period size: 87 Copynumber: 2.0 Consensus size: 88
1174364 TTCTTATCAC
1174374 CCCAAGAATCAAAATTAATTTAAAACTCAAGAATTAACCAGTTGAAATT-AACTTACCTTTGCCA
1 CCCAAGAATCAAAATTAATTTAAAACTCAAGAATTAACCAGTTGAAATTAAACTTACCTTTGCCA
1174438 TGGAGCTTACGGGAAGAGAAGAA
66 TGGAGCTTACGGGAAGAGAAGAA
1174461 CCCAAGAATC-AAATTAAGTTTAAAACTCAAGAATTAACCAGTTGAAATTAAACTTACCTTTGCC
1 CCCAAGAATCAAAATTAA-TTTAAAACTCAAGAATTAACCAGTTGAAATTAAACTTACCTTTGCC
1174525 ATGGAGCTTACGGGAAGAGAAGAA
65 ATGGAGCTTACGGGAAGAGAAGAA
1174549 TAAGAAGGTT
Statistics
Matches: 86, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
86 7 0.08
87 41 0.48
88 38 0.44
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.24
Consensus pattern (88 bp):
CCCAAGAATCAAAATTAATTTAAAACTCAAGAATTAACCAGTTGAAATTAAACTTACCTTTGCCA
TGGAGCTTACGGGAAGAGAAGAA
Found at i:1178558 original size:30 final size:29
Alignment explanation
Indices: 1178501--1178574 Score: 112
Period size: 30 Copynumber: 2.5 Consensus size: 29
1178491 GAAAACCGAA
* *
1178501 TTAAACGGAGACGGGGAAAACCATTTATG
1 TTAAACGGGGACGGGAAAAACCATTTATG
*
1178530 TTAAACGGGGACGGAGAAAAACCGTTTATG
1 TTAAACGGGGACGG-GAAAAACCATTTATG
1178560 TTAAACGGGGACGGG
1 TTAAACGGGGACGGG
1178575 TTTAGTAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 14 0.34
30 27 0.66
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.19
Consensus pattern (29 bp):
TTAAACGGGGACGGGAAAAACCATTTATG
Found at i:1184933 original size:5 final size:5
Alignment explanation
Indices: 1184923--1184952 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1184913 ACATTAATTA
1184923 TATAT TATAT TATAT TATAT TATAT T-TAT T
1 TATAT TATAT TATAT TATAT TATAT TATAT T
1184953 TACTGTATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TATAT
Found at i:1185676 original size:14 final size:12
Alignment explanation
Indices: 1185642--1185666 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1185632 TCAAGCAACT
1185642 AGAATCAAAGAG
1 AGAATCAAAGAG
1185654 AGAATCAAAGAG
1 AGAATCAAAGAG
1185666 A
1 A
1185667 AAGCATCAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.24, T:0.08
Consensus pattern (12 bp):
AGAATCAAAGAG
Found at i:1187843 original size:51 final size:51
Alignment explanation
Indices: 1187767--1187869 Score: 206
Period size: 51 Copynumber: 2.0 Consensus size: 51
1187757 AGGAGAATTG
1187767 ACTTTGGTGATAATTCAAAAGGTCACATTGAAGGTATTGGTACTATTGGTA
1 ACTTTGGTGATAATTCAAAAGGTCACATTGAAGGTATTGGTACTATTGGTA
1187818 ACTTTGGTGATAATTCAAAAGGTCACATTGAAGGTATTGGTACTATTGGTA
1 ACTTTGGTGATAATTCAAAAGGTCACATTGAAGGTATTGGTACTATTGGTA
1187869 A
1 A
1187870 TACCTCTTCC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.32, C:0.10, G:0.23, T:0.35
Consensus pattern (51 bp):
ACTTTGGTGATAATTCAAAAGGTCACATTGAAGGTATTGGTACTATTGGTA
Found at i:1191069 original size:22 final size:19
Alignment explanation
Indices: 1191043--1191098 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
1191033 ATAGGGTAGA
1191043 GGGAATCGATACCCCCTTGAAG
1 GGGAATCGATACCCCC-T--AG
* *
1191065 GGGAACCGATTCCCCCTAG
1 GGGAATCGATACCCCCTAG
1191084 GGGAATCGATACCCC
1 GGGAATCGATACCCC
1191099 ATGAGGGTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 15 0.50
21 1 0.03
22 14 0.47
ACGTcount: A:0.25, C:0.32, G:0.27, T:0.16
Consensus pattern (19 bp):
GGGAATCGATACCCCCTAG
Found at i:1199155 original size:50 final size:50
Alignment explanation
Indices: 1199030--1199155 Score: 148
Period size: 50 Copynumber: 2.5 Consensus size: 50
1199020 GTAGTAGTAA
* * *
1199030 AACGCGCCCCCTGAAT-CGCGCTATACGCTGATTTGGCGCCACGTGGATAT
1 AACGCGCCCCCTG-ATCCGCGCTATACGATGATCTGACGCCACGTGGATAT
* * * * *
1199080 AGCGCGCCCCCTG-CCCTGCGATATACGATGATCTGACGCCATGTGGGTAT
1 AACGCGCCCCCTGATCC-GCGCTATACGATGATCTGACGCCACGTGGATAT
1199130 AACGCGCCCCCTGATCCGCGCTATAC
1 AACGCGCCCCCTGATCCGCGCTATAC
1199156 CTGGGTATCT
Statistics
Matches: 62, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
49 1 0.02
50 59 0.95
51 2 0.03
ACGTcount: A:0.19, C:0.35, G:0.25, T:0.21
Consensus pattern (50 bp):
AACGCGCCCCCTGATCCGCGCTATACGATGATCTGACGCCACGTGGATAT
Found at i:1199290 original size:10 final size:10
Alignment explanation
Indices: 1199275--1199314 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
1199265 TTTATCACAC
1199275 CAAATTCTCT
1 CAAATTCTCT
1199285 CAAATTCTCT
1 CAAATTCTCT
1199295 -AAATTTCTCT
1 CAAA-TTCTCT
*
1199305 CAAATACTCT
1 CAAATTCTCT
1199315 ATCTTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1199635 original size:111 final size:111
Alignment explanation
Indices: 1199441--1199773 Score: 585
Period size: 111 Copynumber: 3.0 Consensus size: 111
1199431 TGGAAATCAT
* *
1199441 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTGTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
1199506 TATTTAGTTGATTTATTTAATACATTATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
* *
1199552 ATATCTCGATACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1199617 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
1199663 ATATCTTGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1199728 TAATTAGTTGATTTATTTAATGCATGATTATTAGAGTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1199774 TTTTTGTAAT
Statistics
Matches: 211, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 211 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1200533 original size:16 final size:16
Alignment explanation
Indices: 1200512--1200542 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1200502 CTGAGGTAAT
*
1200512 TATATTACTAATTTTG
1 TATATTAATAATTTTG
1200528 TATATTAATAATTTT
1 TATATTAATAATTTT
1200543 ATACAGCGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (16 bp):
TATATTAATAATTTTG
Found at i:1201660 original size:9 final size:9
Alignment explanation
Indices: 1201646--1201693 Score: 69
Period size: 9 Copynumber: 5.3 Consensus size: 9
1201636 TGCTCAGGAC
1201646 GACGACGAT
1 GACGACGAT
1201655 GACGACGAT
1 GACGACGAT
* *
1201664 GACGATGGT
1 GACGACGAT
1201673 GACGACGAT
1 GACGACGAT
*
1201682 GACGATGAT
1 GACGACGAT
1201691 GAC
1 GAC
1201694 AGCGAGGAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.31, C:0.19, G:0.35, T:0.15
Consensus pattern (9 bp):
GACGACGAT
Found at i:1201675 original size:18 final size:18
Alignment explanation
Indices: 1201646--1201693 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
1201636 TGCTCAGGAC
*
1201646 GACGACGATGACGACGAT
1 GACGATGATGACGACGAT
*
1201664 GACGATGGTGACGACGAT
1 GACGATGATGACGACGAT
1201682 GACGATGATGAC
1 GACGATGATGAC
1201694 AGCGAGGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.31, C:0.19, G:0.35, T:0.15
Consensus pattern (18 bp):
GACGATGATGACGACGAT
Found at i:1206046 original size:7 final size:7
Alignment explanation
Indices: 1206034--1206071 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
1206024 TTAAGCCATC
1206034 AATTTAA
1 AATTTAA
1206041 AATTTAA
1 AATTTAA
1206048 AATTTAA
1 AATTTAA
1206055 AATTTAA
1 AATTTAA
1206062 AATTTAA
1 AATTTAA
1206069 AAT
1 AAT
1206072 AGAGTGGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AATTTAA
Found at i:1206770 original size:36 final size:36
Alignment explanation
Indices: 1206730--1206803 Score: 105
Period size: 36 Copynumber: 2.1 Consensus size: 36
1206720 ATATGTAGAT
1206730 TTAATTTTGAGATGATGACATG-GTTTAATTTAAATA
1 TTAATTTTGAGATGATGACA-GAGTTTAATTTAAATA
* * *
1206766 TTAATTTTTAGGTGATGATAGAGTTTAATTTAAATA
1 TTAATTTTGAGATGATGACAGAGTTTAATTTAAATA
1206802 TT
1 TT
1206804 TTTTGAAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.35, C:0.01, G:0.16, T:0.47
Consensus pattern (36 bp):
TTAATTTTGAGATGATGACAGAGTTTAATTTAAATA
Found at i:1208569 original size:2 final size:2
Alignment explanation
Indices: 1208562--1208601 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1208552 AAGTCCATTA
* *
1208562 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT GT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1208602 GGTCGAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1215405 original size:26 final size:26
Alignment explanation
Indices: 1215376--1215438 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
1215366 TGAGTTTTTG
1215376 TAATTGTTTACCACATATAATTCTTA
1 TAATTGTTTACCACATATAATTCTTA
1215402 TAATTGTTTACCACATATAATTCTTA
1 TAATTGTTTACCACATATAATTCTTA
*
1215428 AAATTGTTTAC
1 TAATTGTTTAC
1215439 ATTCTCTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (26 bp):
TAATTGTTTACCACATATAATTCTTA
Found at i:1218791 original size:37 final size:37
Alignment explanation
Indices: 1218701--1218805 Score: 111
Period size: 37 Copynumber: 2.8 Consensus size: 37
1218691 CTTTTTCGTC
*
1218701 CTACTAAGATTCAAACTCCTAAAAATATGATAAAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * * * * *
1218738 TTGCTAGGATTCAAACTCCTAAAAATGGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
1218775 CTACTATGATTTAAACTCTTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
1218806 CCACAAGCAC
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.41, C:0.14, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:1219219 original size:2 final size:2
Alignment explanation
Indices: 1219214--1219260 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
1219204 TTAGTGTTAT
*
1219214 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1219256 TA TA T
1 TA TA T
1219261 TTCCTATTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1219340 original size:20 final size:20
Alignment explanation
Indices: 1219315--1219352 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1219305 TTTATTATTA
1219315 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
1219335 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
1219353 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:1223698 original size:14 final size:14
Alignment explanation
Indices: 1223679--1223711 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1223669 AAAGAAGAAG
*
1223679 AATTCATCTGAAAT
1 AATTCATCCGAAAT
1223693 AATTCATCCGAAAT
1 AATTCATCCGAAAT
1223707 AATTC
1 AATTC
1223712 TATCATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.42, C:0.18, G:0.06, T:0.33
Consensus pattern (14 bp):
AATTCATCCGAAAT
Found at i:1224055 original size:9 final size:9
Alignment explanation
Indices: 1224022--1224069 Score: 60
Period size: 9 Copynumber: 5.0 Consensus size: 9
1224012 AGATCCAATC
1224022 AAGAAAAAA
1 AAGAAAAAA
1224031 AAGAAGCAAAA
1 AAGAA--AAAA
*
1224042 GAAGAAACAA
1 -AAGAAAAAA
1224052 AAGAAAAAA
1 AAGAAAAAA
1224061 AAGAAAAAA
1 AAGAAAAAA
1224070 GAAAGAACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 22 0.65
10 3 0.09
11 4 0.12
12 5 0.15
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:1224069 original size:28 final size:28
Alignment explanation
Indices: 1224022--1224095 Score: 89
Period size: 30 Copynumber: 2.6 Consensus size: 28
1224012 AGATCCAATC
1224022 AAGAAAAAAAAGAAGCAAAAG-AAGAAACAA
1 AAGAAAAAAAAGAA--AAAAGAAAG-AACAA
1224052 AAGAAAAAAAAGAAAAAAGAAAGAACAA
1 AAGAAAAAAAAGAAAAAAGAAAGAACAA
**
1224080 AA-ATCAAAAAGAAAAA
1 AAGAAAAAAAAGAAAAA
1224096 GGGATAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
27 12 0.29
28 12 0.29
29 3 0.07
30 14 0.34
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.01
Consensus pattern (28 bp):
AAGAAAAAAAAGAAAAAAGAAAGAACAA
Found at i:1224082 original size:21 final size:19
Alignment explanation
Indices: 1224022--1224082 Score: 70
Period size: 21 Copynumber: 3.1 Consensus size: 19
1224012 AGATCCAATC
1224022 AAGAAAAAAAAGAAGCAAAA
1 AAGAAAAAAAAGAA-CAAAA
*
1224042 GAAGAAACAAAAGAA-AAAA
1 -AAGAAAAAAAAGAACAAAA
1224061 AAGAAAAAAGAAAGAACAAAA
1 AAG-AAAAA-AAAGAACAAAA
1224082 A
1 A
1224083 TCAAAAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 3 0.09
19 8 0.23
20 6 0.17
21 18 0.51
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAAGAACAAAA
Found at i:1224088 original size:20 final size:20
Alignment explanation
Indices: 1224025--1224093 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
1224015 TCCAATCAAG
**
1224025 AAAAA-AAAGAAGCAAAAGA
1 AAAAAGAAAGAAAAAAAAGA
1224044 AGAAACA-AAAGAAAAAAAAGA
1 A-AAA-AGAAAGAAAAAAAAGA
* **
1224065 AAAAAGAAAGAACAAAAATC
1 AAAAAGAAAGAAAAAAAAGA
1224085 AAAAAGAAA
1 AAAAAGAAA
1224094 AAGGGATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
19 2 0.05
20 26 0.62
21 14 0.33
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAGAAAAAAAAGA
Found at i:1225772 original size:106 final size:106
Alignment explanation
Indices: 1225559--1226721 Score: 1628
Period size: 106 Copynumber: 11.0 Consensus size: 106
1225549 ATATCGTGCC
* * * *
1225559 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAAC-AACAATTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCC
* * *
1225622 CAATTTCGGAGCCAATTTCAACTTCACAGCGAAAGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1225664 ACTCCAGACAACGCAAGTTCAACTTCACAACGAATGGACCGTTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * *
1225729 AATTTTAGATCCAATTTCAACTTCACAACAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1225770 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTT-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAA-TTTCC
* *
1225834 GAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1225876 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1225941 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1225982 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
1226047 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1226088 ACTCCAGACAACGCAAGTTCAACTTCACAATGAAGGGATCGCTGGTTGTCAACAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
1226153 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATTTTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
1226194 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
*
1226259 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1226300 ACTCCAGAAAACGCAAGTTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAATAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
1226365 AATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * *
1226406 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGTGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * * *
1226471 AATTTCAGAGCCAATTTTAACTTCTCAACGAAGGATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
1226512 AC-CCAAGGCAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTATCAAC-AA-AATTT--
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCC
* * *
1226572 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGA
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
1226612 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAATAATTT-CC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* * ** *
1226676 AGGTTCCAGAGCCAATTTCAACTTCATGACGGAGGATATTGG
66 A-ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
1226718 ACTC
1 ACTC
1226722 AGAACAATGC
Statistics
Matches: 948, Mismatches: 98, Indels: 23
0.89 0.09 0.02
Matches are distributed among these distances:
100 77 0.08
101 4 0.00
102 6 0.01
103 1 0.00
104 4 0.00
105 50 0.05
106 803 0.85
107 3 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:1227505 original size:37 final size:37
Alignment explanation
Indices: 1227452--1227556 Score: 129
Period size: 37 Copynumber: 2.8 Consensus size: 37
1227442 CATTTTCGTC
* *
1227452 CTACTAGGATTCAAACTCCTAAAAATATGATAAAATT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
* * * *
1227489 TTGCTAGGATTTAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
* * *
1227526 CTACTATGATTTAAACTCCTCAAGATAGGAT
1 CTACTAGGATTTAAACTCCTAAAAATAGGAT
1227557 CCACAAGCAC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 57 1.00
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.31
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATAGGATAAAATT
Found at i:1228073 original size:20 final size:20
Alignment explanation
Indices: 1228048--1228085 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1228038 ATTATTATTA
1228048 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
1228068 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
1228086 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:1229795 original size:24 final size:24
Alignment explanation
Indices: 1229767--1229822 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
1229757 TAATATGTTT
1229767 TCTTCTTAGAATTTTAGAAATATA
1 TCTTCTTAGAATTTTAGAAATATA
1229791 TCTTCTTAGAATTTTAGAAATATA
1 TCTTCTTAGAATTTTAGAAATATA
1229815 TCTTCTTA
1 TCTTCTTA
1229823 ACATAAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (24 bp):
TCTTCTTAGAATTTTAGAAATATA
Found at i:1234528 original size:20 final size:20
Alignment explanation
Indices: 1234505--1234700 Score: 144
Period size: 20 Copynumber: 9.7 Consensus size: 20
1234495 GTTTCCAGAT
1234505 TCGCAATGCGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* * * *
1234525 TCGCATTGCGATTTTTTA-AA
1 TCGCAATGCGA-TTCTGACTA
*** *
1234545 TTCGTGTTGCGATTTTCCGACTA
1 -TCGCAATGCGA--TTCTGACTA
* * *
1234568 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGATTCTG-ACTA
*
1234588 TCGCAATGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
* *
1234608 TCGCAACGCGATTATGACTA
1 TCGCAATGCGATTCTGACTA
* *
1234628 TCGCAACGAGATTCTGACTA
1 TCGCAATGCGATTCTGACTA
* *
1234648 TCGCAACGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
* * *
1234668 TCTCAACGCGATGCTGACTA
1 TCGCAATGCGATTCTGACTA
1234688 TCGCAATGCGATT
1 TCGCAATGCGATT
1234701 TTCAAAGCGC
Statistics
Matches: 142, Mismatches: 28, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
19 1 0.01
20 114 0.80
21 14 0.10
22 12 0.08
23 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.30
Consensus pattern (20 bp):
TCGCAATGCGATTCTGACTA
Found at i:1234631 original size:40 final size:40
Alignment explanation
Indices: 1234563--1234700 Score: 161
Period size: 40 Copynumber: 3.5 Consensus size: 40
1234553 GCGATTTTCC
* * * * *
1234563 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGATTAT
1 GACTATCGCAACGCGATTATG-ACTATCGCAACGCGATTCT
*
1234603 GACTATCGCAACGCGATTATGACTATCGCAACGAGATTCT
1 GACTATCGCAACGCGATTATGACTATCGCAACGCGATTCT
** * *
1234643 GACTATCGCAACGCGATGCTGACTATCTCAACGCGATGCT
1 GACTATCGCAACGCGATTATGACTATCGCAACGCGATTCT
*
1234683 GACTATCGCAATGCGATT
1 GACTATCGCAACGCGATT
1234701 TTCAAAGCGC
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 1 0.01
40 83 0.99
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (40 bp):
GACTATCGCAACGCGATTATGACTATCGCAACGCGATTCT
Found at i:1234903 original size:22 final size:22
Alignment explanation
Indices: 1234878--1234921 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1234868 ACATCCGTCC
*
1234878 CCATCTTCGACGAAATCAGTCT
1 CCATCTCCGACGAAATCAGTCT
* *
1234900 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGACGAAATCAGTCT
1234922 ACCTCCATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.23, C:0.36, G:0.16, T:0.25
Consensus pattern (22 bp):
CCATCTCCGACGAAATCAGTCT
Found at i:1235435 original size:20 final size:20
Alignment explanation
Indices: 1235313--1235428 Score: 135
Period size: 20 Copynumber: 5.8 Consensus size: 20
1235303 GCAATTTTAG
*
1235313 TTTCGCGTTGCGATTTTCA-
1 TTTCGTGTTGCGATTTTCAT
** ** *
1235332 TTTCACGTTGCGATAGTCAA
1 TTTCGTGTTGCGATTTTCAT
* * **
1235352 ATTCGCGTTGCGATAGTCAT
1 TTTCGTGTTGCGATTTTCAT
1235372 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
1235392 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTCAT
1235412 TTTCGTGTTGCGATTTT
1 TTTCGTGTTGCGATTTT
1235429 AAGTTTCAGA
Statistics
Matches: 86, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
19 16 0.19
20 70 0.81
ACGTcount: A:0.14, C:0.17, G:0.22, T:0.47
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTCAT
Found at i:1237186 original size:18 final size:18
Alignment explanation
Indices: 1237163--1237212 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
1237153 TTTACTCGTA
1237163 ATTTCACTTAGATTAACC
1 ATTTCACTTAGATTAACC
*
1237181 ATTTCACTTAGATAAACC
1 ATTTCACTTAGATTAACC
1237199 ATTTCACTTAGATT
1 ATTTCACTTAGATT
1237213 GCTTAGTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.34, C:0.20, G:0.06, T:0.40
Consensus pattern (18 bp):
ATTTCACTTAGATTAACC
Found at i:1237350 original size:30 final size:30
Alignment explanation
Indices: 1237315--1237374 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
1237305 GCAACGAAAG
1237315 AAGAATAGTTTACTTTCGCAACGCGAAAAT
1 AAGAATAGTTTACTTTCGCAACGCGAAAAT
*
1237345 AAGAATAGTTTACTTTCGCAACGTGAAAAT
1 AAGAATAGTTTACTTTCGCAACGCGAAAAT
1237375 GACTATTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (30 bp):
AAGAATAGTTTACTTTCGCAACGCGAAAAT
Found at i:1237459 original size:20 final size:20
Alignment explanation
Indices: 1237430--1237477 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1237420 GCGATTCTCT
*
1237430 CGTTGTGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
1237450 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTCCG
*
1237470 TGTTGCGA
1 CGTTGCGA
1237478 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.15, C:0.19, G:0.27, T:0.40
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:1237693 original size:20 final size:20
Alignment explanation
Indices: 1237668--1237715 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1237658 TAGTTTACTT
1237668 TCGCAACGCGAAAATAACTA
1 TCGCAACGCGAAAATAACTA
** *
1237688 TCGCAACGCGAATTTTACTA
1 TCGCAACGCGAAAATAACTA
1237708 TCGCAACG
1 TCGCAACG
1237716 AAATAATCGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (20 bp):
TCGCAACGCGAAAATAACTA
Found at i:1238332 original size:18 final size:19
Alignment explanation
Indices: 1238293--1238334 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1238283 CTCATATGCC
1238293 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
1238314 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
1238332 ATC
1 ATC
1238335 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:1239812 original size:14 final size:14
Alignment explanation
Indices: 1239776--1239837 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
1239766 TTGCTTGTTT
*
1239776 AATTGATTTATAAA
1 AATTGATTTGTAAA
1239790 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* * *
1239804 AGTTTATTTGTTTAA
1 AATTGATTTG-TAAA
* *
1239819 TATTGATGTGTAAA
1 AATTGATTTGTAAA
1239833 TAATT
1 -AATT
1239838 CTTATTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
14 24 0.67
15 12 0.33
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.48
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1239987 original size:20 final size:20
Alignment explanation
Indices: 1239936--1239989 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
1239926 AGGTACACTT
* **
1239936 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAAGACAAAA
* **
1239956 TTGCAATACGAAAGACAAAA
1 TCGCAACGCGAAAGACAAAA
1239976 TCGCAACGCGAAAG
1 TCGCAACGCGAAAG
1239990 TCAATTCGCG
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.46, C:0.24, G:0.17, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGAAAGACAAAA
Found at i:1240057 original size:20 final size:20
Alignment explanation
Indices: 1240032--1240236 Score: 191
Period size: 20 Copynumber: 10.8 Consensus size: 20
1240022 GCGATTTTCT
* *
1240032 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
*
1240052 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1240072 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1240092 CGTTGAGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
1240112 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
1240126 CGTTGCTATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
*
1240146 TGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1240166 CGTTGTGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
1240180 AGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
1240200 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
1240220 CGTTACGATATTCAAAT
1 CGTTGCGATAGTCAAAT
1240237 GAATGTGTAA
Statistics
Matches: 149, Mismatches: 24, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
14 21 0.14
16 2 0.01
18 1 0.01
20 125 0.84
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:1240087 original size:40 final size:40
Alignment explanation
Indices: 1239992--1240236 Score: 159
Period size: 34 Copynumber: 6.6 Consensus size: 40
1239982 CGCGAAAGTC
* *
1239992 AATTCGCGTTGCGATAGTCTAATACGCTTTGCGAT--T--
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATAATCA
* *
1240028 --TTCTCGTTGCGATAGTCAAATACCCGTTGCGATAATCA
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATAATCA
* *
1240066 AATTCGCGTTGCGATAGTCAAATTCGCGTTGAGATAGA-CA
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATA-ATCA
** * *
1240106 AATTCGCGTTGCGAT--T----TTTGCGTTGCTATAGTCA
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATAATCA
* * * *
1240140 TATTCGTGTTGCGATAGTCAAATTCGCGTTGTGAT--T--
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATAATCA
* * * * *
1240176 --TTTGAGTTGCGATAATCAAATTCGCGTTGCGATAGTCA
1 AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATAATCA
* *
1240214 AATTCGCGTTACGATATTCAAAT
1 AATTCGCGTTGCGATAGTCAAAT
1240237 GAATGTGTAA
Statistics
Matches: 164, Mismatches: 25, Indels: 36
0.73 0.11 0.16
Matches are distributed among these distances:
34 84 0.51
36 3 0.02
38 2 0.01
40 74 0.45
41 1 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (40 bp):
AATTCGCGTTGCGATAGTCAAATACGCGTTGCGATAATCA
Found at i:1240122 original size:94 final size:93
Alignment explanation
Indices: 1239983--1240170 Score: 243
Period size: 94 Copynumber: 2.0 Consensus size: 93
1239973 AAATCGCAAC
* * * *
1239983 GCGAAAGTCAATTCGCGTTGCGATAGTCTAATACGCTTTGCGATTTTCT-CGTTGCGATAGTCAA
1 GCGAAAGTCAATTCGCGTTGAGATAGACAAATACGCGTTGCGATTTT-TGCGTTGCGATAGTCAA
1240047 ATACCCGTTGCGATAATCAAATTCGCGTT
65 ATACCCGTTGCGATAATCAAATTCGCGTT
* * * *
1240076 GCGATAGTCAAATTCGCGTTGAGATAGACAAATTCGCGTTGCGATTTTTGCGTTGCTATAGTCAT
1 GCGAAAGTC-AATTCGCGTTGAGATAGACAAATACGCGTTGCGATTTTTGCGTTGCGATAGTCAA
* ** *
1240141 ATTCGTGTTGCGATAGTCAAATTCGCGTT
65 ATACCCGTTGCGATAATCAAATTCGCGTT
1240170 G
1 G
1240171 TGATTTTTGA
Statistics
Matches: 81, Mismatches: 12, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
93 9 0.11
94 72 0.89
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (93 bp):
GCGAAAGTCAATTCGCGTTGAGATAGACAAATACGCGTTGCGATTTTTGCGTTGCGATAGTCAAA
TACCCGTTGCGATAATCAAATTCGCGTT
Found at i:1240129 original size:54 final size:54
Alignment explanation
Indices: 1240071--1240228 Score: 235
Period size: 54 Copynumber: 2.9 Consensus size: 54
1240061 AATCAAATTC
* *
1240071 GCGTTGCGATAGTCAAATTCGCGTTGAGATAGACAAATTCGCGTTGCGATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
* * * *
1240125 GCGTTGCTATAGTCATATTCGTGTTGCGATAGTCAAATTCGCGTTGTGATTTTT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
* * *
1240179 GAGTTGCGATAATCAAATTCGCGTTGCGATAGTCAAATTCGCGTTACGAT
1 GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGAT
1240229 ATTCAAATGA
Statistics
Matches: 91, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 91 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.35
Consensus pattern (54 bp):
GCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATTTTT
Found at i:1240459 original size:140 final size:140
Alignment explanation
Indices: 1240207--1240476 Score: 495
Period size: 140 Copynumber: 1.9 Consensus size: 140
1240197 TCGCGTTGCG
*
1240207 ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACATATCA
1 ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCA
*
1240272 TAGCAATGTTCAAACTCAAGTTACTAGTACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1240337 AATACACATA
131 AATACACATA
* * *
1240347 ATAGTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAATAGATCA
1 ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCA
1240412 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
1240477 TACAACGTTT
Statistics
Matches: 125, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
140 125 1.00
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.29
Consensus pattern (140 bp):
ATAGTCAAATTCGCGTTACGATATTCAAATGAATGTGTAATAAGTGATAACAACTAAACAGATCA
TAGCAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
AATACACATA
Found at i:1242513 original size:14 final size:14
Alignment explanation
Indices: 1242494--1242530 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
1242484 TCCCGTAGCA
1242494 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
1242508 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
1242522 TTCTTCTTC
1 TT-TTCTTC
1242531 TTCTTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:1242754 original size:24 final size:24
Alignment explanation
Indices: 1242720--1242773 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
1242710 CTAAAACATC
1242720 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
1242744 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
1242768 ATCAAA
1 ATCAAA
1242774 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:1243620 original size:20 final size:20
Alignment explanation
Indices: 1243595--1243662 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
1243585 GAAATTCAGT
*
1243595 GTTGCGACAGTCAGAATCGC
1 GTTGCGATAGTCAGAATCGC
* *
1243615 GTTGCGATAGTCATAATCTC
1 GTTGCGATAGTCAGAATCGC
*
1243635 GTTGCGATAGTCAGAATCAC
1 GTTGCGATAGTCAGAATCGC
*
1243655 ATTGCGAT
1 GTTGCGAT
1243663 TTACATATTC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (20 bp):
GTTGCGATAGTCAGAATCGC
Found at i:1243680 original size:40 final size:40
Alignment explanation
Indices: 1243596--1243686 Score: 103
Period size: 40 Copynumber: 2.3 Consensus size: 40
1243586 AAATTCAGTG
* * * * *
1243596 TTGCGACAGTCAGAATCGCGTTGCGATAGTCATAATCTCG
1 TTGCGATAGTCAGAATCACATTGCGATAGTCATAATCGCA
* *
1243636 TTGCGATAGTCAGAATCACATTGCGAT-TTACATATTCGCA
1 TTGCGATAGTCAGAATCACATTGCGATAGT-CATAATCGCA
1243676 TTGCGATAGTC
1 TTGCGATAGTC
1243687 GGAAAATCGC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 1 0.02
40 42 0.98
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (40 bp):
TTGCGATAGTCAGAATCACATTGCGATAGTCATAATCGCA
Found at i:1243715 original size:21 final size:21
Alignment explanation
Indices: 1243689--1243745 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
1243679 CGATAGTCGG
*
1243689 AAAATCGCAACGCGAATTTAA
1 AAAATCGCAATGCGAATTTAA
*
1243710 AAAATCGCAATGCAAATTTAA
1 AAAATCGCAATGCGAATTTAA
1243731 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
1243746 TAGTAGAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (21 bp):
AAAATCGCAATGCGAATTTAA
Found at i:1245091 original size:21 final size:21
Alignment explanation
Indices: 1245065--1245113 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1245055 TTAGTTTGTT
1245065 TTCAACTGCTGTAAACGTTGC
1 TTCAACTGCTGTAAACGTTGC
*
1245086 TTCAACTGCTGTATACGTTGC
1 TTCAACTGCTGTAAACGTTGC
1245107 TTCAACT
1 TTCAACT
1245114 TATCTGTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (21 bp):
TTCAACTGCTGTAAACGTTGC
Found at i:1253643 original size:37 final size:37
Alignment explanation
Indices: 1253587--1253682 Score: 147
Period size: 37 Copynumber: 2.6 Consensus size: 37
1253577 AGTGCAACGG
* *
1253587 TGCAAGTGTTATAAAGGTACAATTTTATATTTACACA
1 TGCAAGTGTTATAACGGTACAATTTTACATTTACACA
*
1253624 TGCACGTGTTATAACGGTACAATTTTACATTTACACA
1 TGCAAGTGTTATAACGGTACAATTTTACATTTACACA
* *
1253661 TGCATGTGTTATAACAGTACAA
1 TGCAAGTGTTATAACGGTACAA
1253683 AATTAAAATA
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (37 bp):
TGCAAGTGTTATAACGGTACAATTTTACATTTACACA
Found at i:1254417 original size:3 final size:3
Alignment explanation
Indices: 1254409--1254441 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
1254399 TATAAATTGT
1254409 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1254442 ATAACGAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1254912 original size:37 final size:37
Alignment explanation
Indices: 1254862--1254951 Score: 162
Period size: 37 Copynumber: 2.4 Consensus size: 37
1254852 ACGGTGAAAG
1254862 TGTTATAACGGTACAATTTTATATTTACACATGCAAA
1 TGTTATAACGGTACAATTTTATATTTACACATGCAAA
**
1254899 TGTTATAACGGTACAATTTTATATTTACACATGCATG
1 TGTTATAACGGTACAATTTTATATTTACACATGCAAA
1254936 TGTTATAACGGTACAA
1 TGTTATAACGGTACAA
1254952 AATTAAAATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (37 bp):
TGTTATAACGGTACAATTTTATATTTACACATGCAAA
Found at i:1255758 original size:44 final size:44
Alignment explanation
Indices: 1255708--1255798 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
1255698 AAAGATGATG
* *
1255708 ATATGCTTGTGCCACTTTATGATTTGACTGACAATGATCATCCC
1 ATATGCTTGTGCCACTCTATGATTTGACTGACAATGACCATCCC
1255752 ATATGCTTGTGCCACTCTATGATTTGACTGACAATGACCATCCC
1 ATATGCTTGTGCCACTCTATGATTTGACTGACAATGACCATCCC
1255796 ATA
1 ATA
1255799 GAAGGTACTC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.34
Consensus pattern (44 bp):
ATATGCTTGTGCCACTCTATGATTTGACTGACAATGACCATCCC
Found at i:1256861 original size:85 final size:86
Alignment explanation
Indices: 1256692--1256864 Score: 289
Period size: 85 Copynumber: 2.0 Consensus size: 86
1256682 GGTACATTGC
1256692 TCGCTCCCTCGTTCATAGTAATTACCTTCCCCCCCCCCCCCCCAAGATTTTCTGTTTTGGCGATA
1 TCGCTCCCTCGTTCATAGTAATTACCTTCCCCCCCCCCCCCCCAAGA--TTCTGTTTTGGCGATA
1256757 TCCATACTCTTGGTTTTGAATTT
64 TCCATACTCTTGGTTTTGAATTT
1256780 TCGCTCCCTCGTTCATAGTAATTACCTTTCCCCCCCCCCCCCCCCAAGA-T-T-TTTTGGCGATA
1 TCGCTCCCTCGTTCATAGTAATTACC-TT-CCCCCCCCCCCCCCCAAGATTCTGTTTTGGCGATA
1256842 TCCATACTCTTGGTTTTGAATTT
64 TCCATACTCTTGGTTTTGAATTT
1256865 CGTAGGCGAA
Statistics
Matches: 83, Mismatches: 0, Indels: 7
0.92 0.00 0.08
Matches are distributed among these distances:
85 34 0.41
86 1 0.01
87 1 0.01
88 26 0.31
89 2 0.02
90 19 0.23
ACGTcount: A:0.16, C:0.35, G:0.12, T:0.37
Consensus pattern (86 bp):
TCGCTCCCTCGTTCATAGTAATTACCTTCCCCCCCCCCCCCCCAAGATTCTGTTTTGGCGATATC
CATACTCTTGGTTTTGAATTT
Found at i:1259809 original size:112 final size:112
Alignment explanation
Indices: 1259686--1259906 Score: 390
Period size: 112 Copynumber: 2.0 Consensus size: 112
1259676 CTCTCTCTTT
*
1259686 TATATATATATATTTGTTTCATATTAATAATTTTCTTGGAATATGATACGAGCGACATGCTTATT
1 TATATATATATATTTGATTCATATTAATAATTTTCTTGGAATATGATACGAGCGACATGCTTATT
*
1259751 TGTTT-GGTTTTTTGTGTCCTTAGGAGGAAGAGCGCGATACTAACTGA
66 TGTTTAGG-TTTTTGTGCCCTTAGGAGGAAGAGCGCGATACTAACTGA
* *
1259798 TATATATATATATTTGATTCATGTTAATAATTTTCTTGGAATATGATACGAGCGACATGTTTATT
1 TATATATATATATTTGATTCATATTAATAATTTTCTTGGAATATGATACGAGCGACATGCTTATT
1259863 TGTTTAGGTTTTTGTGCCCTTAGGAGGAAGAGCGCGATACTAAC
66 TGTTTAGGTTTTTGTGCCCTTAGGAGGAAGAGCGCGATACTAAC
1259907 AGTTGTATGT
Statistics
Matches: 104, Mismatches: 4, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
112 102 0.98
113 2 0.02
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (112 bp):
TATATATATATATTTGATTCATATTAATAATTTTCTTGGAATATGATACGAGCGACATGCTTATT
TGTTTAGGTTTTTGTGCCCTTAGGAGGAAGAGCGCGATACTAACTGA
Found at i:1272818 original size:42 final size:43
Alignment explanation
Indices: 1272723--1272820 Score: 112
Period size: 42 Copynumber: 2.3 Consensus size: 43
1272713 TTTTATAGTT
* * * *
1272723 TAAAAGATATTA-TTTAATTATTAAAAATATAATAAATTGTTA
1 TAAAATATATTATTTTAATTATTAAAAAGATAAGAAATTATTA
*
1272765 TAAAATATATTATTTTAA-TATTTTAAAAGATAAGAAATTATTA
1 TAAAATATATTATTTTAATTA-TTAAAAAGATAAGAAATTATTA
*
1272808 T-AAATGTATTATT
1 TAAAATATATTATT
1272821 ATAAAATATA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
42 24 0.50
43 24 0.50
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (43 bp):
TAAAATATATTATTTTAATTATTAAAAAGATAAGAAATTATTA
Found at i:1272820 original size:14 final size:15
Alignment explanation
Indices: 1272801--1272835 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
1272791 AAGATAAGAA
*
1272801 ATTATTAT-AAATGT
1 ATTATTATAAAATAT
1272815 ATTATTATAAAATAT
1 ATTATTATAAAATAT
1272830 ATTATT
1 ATTATT
1272836 TTAATTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (15 bp):
ATTATTATAAAATAT
Found at i:1274033 original size:40 final size:42
Alignment explanation
Indices: 1273989--1274081 Score: 102
Period size: 40 Copynumber: 2.3 Consensus size: 42
1273979 AATTTTCTAA
* * *
1273989 TTTATATAAAAATTAAATATTTTATAATTA-AAAA-AAACAG
1 TTTATATAAAAATTAAATAATATATAATTATAAAATAAAAAG
* * *
1274029 TTTATA-ATTAATTTAAATAATATATAATTATAAAATAAAAAT
1 TTTATATA-AAAATTAAATAATATATAATTATAAAATAAAAAG
1274071 TTTATATAAAA
1 TTTATATAAAA
1274082 TTTTTAATTA
Statistics
Matches: 42, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
39 1 0.02
40 24 0.57
41 4 0.10
42 12 0.29
43 1 0.02
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (42 bp):
TTTATATAAAAATTAAATAATATATAATTATAAAATAAAAAG
Found at i:1274317 original size:20 final size:20
Alignment explanation
Indices: 1274294--1274367 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
1274284 TATAAAAGTT
1274294 AAATATTTTATAATTAAAAA
1 AAATATTTTATAATTAAAAA
* ***
1274314 AAATAGTTTATAATTAATTT
1 AAATATTTTATAATTAAAAA
* *
1274334 AAATAATATATAATTAAAAA
1 AAATATTTTATAATTAAAAA
*
1274354 TTAAAAATTTTATA
1 --AAATATTTTATA
1274368 TAAATTTTTT
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 31 0.77
22 9 0.22
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (20 bp):
AAATATTTTATAATTAAAAA
Found at i:1274325 original size:40 final size:41
Alignment explanation
Indices: 1274280--1274371 Score: 98
Period size: 40 Copynumber: 2.2 Consensus size: 41
1274270 AATTTTCTAA
* * *
1274280 TTTATATAAAAGTTAAATATTTTATAATTAAAAA-AAATAG
1 TTTATATAAAAGTTAAATAATATATAATTAAAAATAAAAAG
* * *
1274320 TTTATA-ATTAATTTAAATAATATATAATTAAAAATTAAAAAT
1 TTTATATA-AAAGTTAAATAATATATAATTAAAAA-TAAAAAG
1274362 TTTATATAAA
1 TTTATATAAA
1274372 TTTTTTAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
39 1 0.02
40 28 0.68
42 11 0.27
43 1 0.02
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (41 bp):
TTTATATAAAAGTTAAATAATATATAATTAAAAATAAAAAG
Found at i:1274349 original size:291 final size:289
Alignment explanation
Indices: 1273827--1274410 Score: 1053
Period size: 291 Copynumber: 2.0 Consensus size: 289
1273817 TGTTCATTCG
1273827 GTTAATTCAGTGGTCGAACCGACCGAACTACCATTAACCGATTTTTTTTTCTTTAATCGTTAACC
1 GTTAATTCAGTGGTCGAACCGACCGAACTACCATTAACCGATTTTTTTTTCTTTAATCGTTAACC
*
1273892 GAATCGAACTTTTTTCCGAAAATATTAACCGAACCGAATAAATTTCGGTTAATTCGGTTAATTTT
66 GAACCGAACTTTTTTCCGAAAATATTAACCGAACCGAATAAATTTCGGTTAATTCGGTTAATTTT
1273957 CGAATTAACCGAACTTTTTTAAAATTTTCTAATTTATATAAAAATTAAATATTTTATAATTAAAA
131 CGAATTAACCGAACTTTTTTAAAATTTTCTAATTTATATAAAAATTAAATATTTTATAATTAAAA
1274022 AAAACAGTTTATAATTAATTTAAATAATATATAATTATAAAA-TAAAAATTTTATATAAAATTTT
196 AAAACAGTTTATAATTAATTTAAATAATATATAATTA-AAAATTAAAAATTTTATATAAAATTTT
1274086 TAATTAATTAATATTGATTTAGGTTTAAAA
260 TAATTAATTAATATTGATTTAGGTTTAAAA
*
1274116 GTTAATTCGGTGGTCGAACCGACCGAACTACCATTAACCGAATTTTTTTTTTCTTTAATCGTTAA
1 GTTAATTCAGTGGTCGAACCGACCGAACTACCATTAACCG-A-TTTTTTTTTCTTTAATCGTTAA
* *
1274181 CCGAACCGAACTTTTTTCCGAAAATATTAATCGAACCGAATAAATTTTGGTTAATTCGGTTAATT
64 CCGAACCGAACTTTTTTCCGAAAATATTAACCGAACCGAATAAATTTCGGTTAATTCGGTTAATT
* *
1274246 TTCGAATTAACCGAATTTTTTTAAAATTTTCTAATTTATATAAAAGTTAAATATTTTATAATTAA
129 TTCGAATTAACCGAACTTTTTTAAAATTTTCTAATTTATATAAAAATTAAATATTTTATAATTAA
* *
1274311 AAAAAATAGTTTATAATTAATTTAAATAATATATAATTAAAAATTAAAAATTTTATATAAATTTT
194 AAAAAACAGTTTATAATTAATTTAAATAATATATAATTAAAAATTAAAAATTTTATATAAAATTT
*
1274376 TTAATTAATTAATTTTGATTTAGGTTTAAAA
259 TTAATTAATTAATATTGATTTAGGTTTAAAA
1274407 GTTA
1 GTTA
1274411 TTGGATCTTA
Statistics
Matches: 283, Mismatches: 9, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
289 39 0.14
290 5 0.02
291 239 0.84
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (289 bp):
GTTAATTCAGTGGTCGAACCGACCGAACTACCATTAACCGATTTTTTTTTCTTTAATCGTTAACC
GAACCGAACTTTTTTCCGAAAATATTAACCGAACCGAATAAATTTCGGTTAATTCGGTTAATTTT
CGAATTAACCGAACTTTTTTAAAATTTTCTAATTTATATAAAAATTAAATATTTTATAATTAAAA
AAAACAGTTTATAATTAATTTAAATAATATATAATTAAAAATTAAAAATTTTATATAAAATTTTT
AATTAATTAATATTGATTTAGGTTTAAAA
Found at i:1275215 original size:16 final size:16
Alignment explanation
Indices: 1275194--1275230 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
1275184 TTTTGATTTT
1275194 GGATGATGTTATTTCA
1 GGATGATGTTATTTCA
1275210 GGATGATGTTATTTCA
1 GGATGATGTTATTTCA
1275226 GGATG
1 GGATG
1275231 CAAAGAAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.24, C:0.05, G:0.30, T:0.41
Consensus pattern (16 bp):
GGATGATGTTATTTCA
Found at i:1280277 original size:35 final size:35
Alignment explanation
Indices: 1280231--1280301 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
1280221 GCAATTGAGT
1280231 GTCTACCGTGATTTGGTTATGTAGATGGATACATA
1 GTCTACCGTGATTTGGTTATGTAGATGGATACATA
* *
1280266 GTCTACCGTGATTTGGTTCTGTTGATGGATACATA
1 GTCTACCGTGATTTGGTTATGTAGATGGATACATA
1280301 G
1 G
1280302 CTTTCTTTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.23, C:0.13, G:0.27, T:0.38
Consensus pattern (35 bp):
GTCTACCGTGATTTGGTTATGTAGATGGATACATA
Done.