Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold71
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: 5741892
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.33
Warning! 121862 characters in sequence are not A, C, G, or T
File 11 of 33
Found at i:1671970 original size:103 final size:104
Alignment explanation
Indices: 1671862--1672077 Score: 251
Period size: 104 Copynumber: 2.1 Consensus size: 104
1671852 GTACCCTCCG
* *
1671862 CATCTTTAAGTCCAATGTCACTAGCCTTGAATCAACAC-TTGGCACCTTTT-TCTTTC-TTAAGT
1 CATCTTTAAGTCCAATGTCACTAGCCTTGAATCAACACATTGGCA-CTTTTGT-TATCGTTAAGC
* * * *
1671924 CCTATATTGCTGGCCTTGAATTAGCATATT-GACATCTTTAT
64 CCAATATCGCTGGCCGTGAATTAGCATATTAG-CACCTTTAT
*** * *
1671965 CATCTTTAAGTCCAATGTGGTTGGCCTTGAATCAGCACATTGGCACTTTTGTTATCGTTAAGCCC
1 CATCTTTAAGTCCAATGTCACTAGCCTTGAATCAACACATTGGCACTTTTGTTATCGTTAAGCCC
* *
1672030 AATATCGTTTGCCGTGAATTAGCATATTAGCACCTTTAT
66 AATATCGCTGGCCGTGAATTAGCATATTAGCACCTTTAT
1672069 CATTCTTTA
1 CA-TCTTTA
1672078 CATCCTTAAG
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
103 41 0.43
104 47 0.49
105 7 0.07
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (104 bp):
CATCTTTAAGTCCAATGTCACTAGCCTTGAATCAACACATTGGCACTTTTGTTATCGTTAAGCCC
AATATCGCTGGCCGTGAATTAGCATATTAGCACCTTTAT
Found at i:1672850 original size:20 final size:20
Alignment explanation
Indices: 1672825--1672898 Score: 62
Period size: 20 Copynumber: 3.6 Consensus size: 20
1672815 TTGCCAAGGA
1672825 AATGTATCGATACATTACTC
1 AATGTATCGATACATTACTC
* *
1672845 AATGTACCAATACATATTTA-T-
1 AATGTATCGATAC--A-TTACTC
*
1672866 AATTGTATCGATACATTTCTC
1 AA-TGTATCGATACATTACTC
*
1672887 ATTGTATCGATA
1 AATGTATCGATA
1672899 TATTCTGAGT
Statistics
Matches: 42, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
19 2 0.05
20 23 0.55
21 3 0.07
22 11 0.26
23 3 0.07
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.39
Consensus pattern (20 bp):
AATGTATCGATACATTACTC
Found at i:1674663 original size:79 final size:79
Alignment explanation
Indices: 1674530--1674883 Score: 484
Period size: 79 Copynumber: 4.5 Consensus size: 79
1674520 ATAATAACGA
* *
1674530 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGATTT
**
1674595 AGAAATAAAA-TCAA
66 AGAAATAAAACT-GG
* * * * * * *
1674609 GTTTGGAGTATCCTCTCGGAAATAATGGGGTTGGAGTATCCCCGACTATTAAAAATTGATGTTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGATTT
1674674 AGAAATAAAACTGG
66 AGAAATAAAACTGG
* * *
1674688 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAAT-ATTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGA-TT
*
1674752 TAGAAATAAAGCTGG
65 TAGAAATAAAACTGG
* *
1674767 GGTTGGGGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCG---ATGAAAAATTGATGTTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGATTT
*
1674829 AGAAATAAAACCGG
66 AGAAATAAAACTGG
*
1674843 GGTTGGAGTGTCCCCTCGAAAATAACGGGGTTGGAGTATCC
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCC
1674884 TTGATAAAGA
Statistics
Matches: 243, Mismatches: 29, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
76 65 0.27
79 177 0.73
80 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.27, T:0.27
Consensus pattern (79 bp):
GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTATGAAAAATTGATGATTT
AGAAATAAAACTGG
Found at i:1674863 original size:76 final size:76
Alignment explanation
Indices: 1674530--1674931 Score: 482
Period size: 79 Copynumber: 5.2 Consensus size: 76
1674520 ATAATAACGA
* *
1674530 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCGATGATTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGA---TGAAAAATTGATGTTTT
* **
1674595 AGAAATAAAATCAA
63 AGAAATAAAACCGG
* * * * *
1674609 GTTTGGAGTATCCTCTCGGAAATAATGGGGTTGGAGTATCCCCGACTATTAAAAATTGATGTTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCG---ATGAAAAATTGATGTTTT
*
1674674 AGAAATAAAACTGG
63 AGAAATAAAACCGG
* * * *
1674688 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATTATGAGAAATTAATATTTT
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCG---ATGAAAAATTGATGTTTT
* *
1674753 AGAAATAAAGCTGG
63 AGAAATAAAACCGG
*
1674767 GGTTGGGGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGA
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGA
1674832 AATAAAACCGG
66 AATAAAACCGG
* ** *
1674843 GGTTGGAGTGTCCCCTCGAAAATAACGGGGTTGGAGTATCCTTGAT-AAAGAATTGATGTTTTGG
1 GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAA-AATTGATGTTTTAG
**
1674907 AAATGGAACCGG
65 AAATAAAACCGG
*
1674919 GATTGGAGTATCC
1 GGTTGGAGTATCC
1674932 TCGAGATGAA
Statistics
Matches: 283, Mismatches: 36, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
75 3 0.01
76 103 0.36
79 176 0.62
82 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (76 bp):
GGTTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCCCGATGAAAAATTGATGTTTTAGA
AATAAAACCGG
Found at i:1677246 original size:13 final size:13
Alignment explanation
Indices: 1677203--1677228 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1677193 ACCCAGAATA
1677203 TATCGATACAATG
1 TATCGATACAATG
1677216 TATCGATACAATG
1 TATCGATACAATG
1677229 AACAATGTAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TATCGATACAATG
Found at i:1681374 original size:2 final size:2
Alignment explanation
Indices: 1681367--1681402 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1681357 GGTACATGAA
*
1681367 AT AT AT AT GT 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
1681403 TATTGATACT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1681810 original size:27 final size:26
Alignment explanation
Indices: 1681780--1681843 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
1681770 AATATATATT
* **
1681780 TTTATTAAGTATTTATTATATTTAATA
1 TTTATTAAGTATTAAAAATATTTAA-A
1681807 TTTATTTAA-TATTAAAAATATTTAAA
1 TTTA-TTAAGTATTAAAAATATTTAAA
*
1681833 TTTTTTAAGTA
1 TTTATTAAGTA
1681844 AATAATTCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
25 4 0.13
26 6 0.19
27 17 0.55
28 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (26 bp):
TTTATTAAGTATTAAAAATATTTAAA
Found at i:1681821 original size:17 final size:16
Alignment explanation
Indices: 1681759--1681821 Score: 58
Period size: 17 Copynumber: 3.8 Consensus size: 16
1681749 AAAGATTATA
1681759 TTATTTA-ATTAAATAT
1 TTATTTATATT-AATAT
* *
1681775 ATATTTTTATTAAGTAT
1 TTATTTATATTAA-TAT
1681792 TTA-TTATATTTAATAT
1 TTATTTATA-TTAATAT
1681808 TTATTTAATATTAA
1 TTATTT-ATATTAA
1681822 AAATATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
16 17 0.45
17 18 0.47
18 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
TTATTTATATTAATAT
Found at i:1688182 original size:105 final size:103
Alignment explanation
Indices: 1687968--1688222 Score: 298
Period size: 105 Copynumber: 2.4 Consensus size: 103
1687958 CTAACCGCTC
* * * **
1687968 CTGATCGCCACTATGACATCATCATTATCAGTGACACTAAGTCAACCAAACTTTCATTGCCACCA
1 CTGATTGCCACCATGGCATCATCATTATCAGTGACACTAAGTC-ACCAAACTTTCATCACCACCA
** * *
1688033 TGACATCATCATTATCAGTGACACTAAGTCACCTACATT
65 CAACATCATCATTATCAGTGACACCAAGTCACCAACATT
* * * *
1688072 CTGATTGCCACCATGGCATCATCATTATCAGTGACACTAAGTCACTTGAATCTTTGATCACCATC
1 CTGATTGCCACCATGGCATCATCATTATCAGTGACACTAAGTCAC--CAAACTTTCATCACCACC
1688137 ACAACATCATCATTATCAGTGACACCAAGTCATCCGAAC-TT
64 ACAACATCATCATTATCAGTGACACCAAGTCA-CC-AACATT
** * *
1688178 -TGATTGCCACCACAGCATCATCATTATTAGTGACACCAAGTCACC
1 CTGATTGCCACCATGGCATCATCATTATCAGTGACACTAAGTCACC
1688223 CGAACTCTGA
Statistics
Matches: 129, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
103 2 0.02
104 40 0.31
105 81 0.63
106 4 0.03
107 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (103 bp):
CTGATTGCCACCATGGCATCATCATTATCAGTGACACTAAGTCACCAAACTTTCATCACCACCAC
AACATCATCATTATCAGTGACACCAAGTCACCAACATT
Found at i:1688262 original size:157 final size:157
Alignment explanation
Indices: 1687983--1688273 Score: 417
Period size: 157 Copynumber: 1.9 Consensus size: 157
1687973 CGCCACTATG
* *
1687983 ACATCATCATTATCAGTGACACTAAGTCAACCAAACTTTCATTGCCACCATGACATCATCATTAT
1 ACATCATCATTATCAGTGACACCAAGTCAACCAAACTTTCATTGCCACCAAGACATCATCATTAT
* * * * *
1688048 CAGTGACACTAAGTCACCTACATTCTGATTGCCACCATGGCATCATCATTATCAGTGACA-CTAA
66 CAGTGACACCAAGTCACCGACACTCTGATCGCCACCATGGCATCACCATTATCAGTGACATC-AA
1688112 GTCACTTGAATCTTTGATCACCATCACA
130 GTCACTTGAATCTTTGATCACCATCACA
* * *
1688140 ACATCATCATTATCAGTGACACCAAGTCATCCGAACTTTGATTGCCACCACAG-CATCATCATTA
1 ACATCATCATTATCAGTGACACCAAGTCAACCAAACTTTCATTGCCACCA-AGACATCATCATTA
* * *
1688204 TTAGTGACACCAAGTCACCCGA-ACTCTGATCGCCACCATGGCATCACCATTTTTAGTGACATCA
65 TCAGTGACACCAAGTCA-CCGACACTCTGATCGCCACCATGGCATCACCATTATCAGTGACATCA
1688268 AGTCAC
129 AGTCAC
1688274 CCTTATGAAC
Statistics
Matches: 118, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
157 113 0.96
158 5 0.04
ACGTcount: A:0.32, C:0.29, G:0.12, T:0.27
Consensus pattern (157 bp):
ACATCATCATTATCAGTGACACCAAGTCAACCAAACTTTCATTGCCACCAAGACATCATCATTAT
CAGTGACACCAAGTCACCGACACTCTGATCGCCACCATGGCATCACCATTATCAGTGACATCAAG
TCACTTGAATCTTTGATCACCATCACA
Found at i:1688273 original size:52 final size:52
Alignment explanation
Indices: 1687968--1688275 Score: 307
Period size: 52 Copynumber: 5.9 Consensus size: 52
1687958 CTAACCGCTC
* * *
1687968 CTGATCGCCACTATGACATCATCATTATCAGTGACACTAAGTCAACCAAACT
1 CTGATCGCCACCATGACATCATCATTATCAGTGACACTAAGTCACCCGAACT
* * * * *
1688020 TTCATTGCCACCATGACATCATCATTATCAGTGACACTAAGTCA-CCTACATT
1 CTGATCGCCACCATGACATCATCATTATCAGTGACACTAAGTCACCCGA-ACT
* * **
1688072 CTGATTGCCACCATGGCATCATCATTATCAGTGACACTAAGTCACTTGAATCT
1 CTGATCGCCACCATGACATCATCATTATCAGTGACACTAAGTCACCCGAA-CT
* * * ** * *
1688125 TTGATCACCATCACAACATCATCATTATCAGTGACACCAAGTCATCCGAACT
1 CTGATCGCCACCATGACATCATCATTATCAGTGACACTAAGTCACCCGAACT
* * * * *
1688177 TTGATTGCCACCA-CAGCATCATCATTATTAGTGACACCAAGTCACCCGAACT
1 CTGATCGCCACCATGA-CATCATCATTATCAGTGACACTAAGTCACCCGAACT
* * * *
1688229 CTGATCGCCACCATGGCATCACCATTTTTAGTGACA-TCAAGTCACCC
1 CTGATCGCCACCATGACATCATCATTATCAGTGACACT-AAGTCACCC
1688276 TTATGAACTC
Statistics
Matches: 213, Mismatches: 37, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
51 4 0.02
52 168 0.79
53 41 0.19
ACGTcount: A:0.31, C:0.30, G:0.12, T:0.27
Consensus pattern (52 bp):
CTGATCGCCACCATGACATCATCATTATCAGTGACACTAAGTCACCCGAACT
Found at i:1689179 original size:21 final size:21
Alignment explanation
Indices: 1689155--1689201 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
1689145 AGTTTTGATG
*
1689155 TCCTCCACATTTTTACCCGTC
1 TCCTCCACATTTTTACCCGCC
* *
1689176 TCCTTCACTTTTTTACCCGCC
1 TCCTCCACATTTTTACCCGCC
1689197 TCCTC
1 TCCTC
1689202 ATTAACTTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.11, C:0.45, G:0.04, T:0.40
Consensus pattern (21 bp):
TCCTCCACATTTTTACCCGCC
Found at i:1696140 original size:83 final size:82
Alignment explanation
Indices: 1696008--1696227 Score: 255
Period size: 83 Copynumber: 2.7 Consensus size: 82
1695998 TAAAAATCAT
* * * * * * * * *
1696008 GGTTGTAGTATCCCTTCGAAGATGGTGGGGTTGGAGTATCCCTTTAGATGGAAAAAATTTGATGT
1 GGTTGAAGTATCTCTTCGAAAATGATGGGATTGGAGTATCCCCTAAGATGAAAAAAAATTGATGT
1696073 TTGGGAAATAAAAATAGG
66 TTGGGAAATAAAAA-AGG
* *
1696091 GTTTGAAGTATCTCTTCGAAAATAATGGGATTGGAGTATCCCCTAAGATGAAAAAAAATTGATGT
1 GGTTGAAGTATCTCTTCGAAAATGATGGGATTGGAGTATCCCCTAAGATGAAAAAAAATTGATGT
*
1696156 TTGGGAAATAAAAACGG
66 TTGGGAAATAAAAAAGG
* * *
1696173 GGTTGGAGTAT-TCCTCTC-AGAAATGATGGGATTGAAGTATCCCCTAAGACGAAAA
1 GGTTGAAGTATCT-CT-TCGA-AAATGATGGGATTGGAGTATCCCCTAAGATGAAAA
1696228 TTTCGATGTT
Statistics
Matches: 117, Mismatches: 17, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
81 1 0.01
82 14 0.12
83 102 0.87
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (82 bp):
GGTTGAAGTATCTCTTCGAAAATGATGGGATTGGAGTATCCCCTAAGATGAAAAAAAATTGATGT
TTGGGAAATAAAAAAGG
Found at i:1696475 original size:78 final size:79
Alignment explanation
Indices: 1696270--1696515 Score: 322
Period size: 78 Copynumber: 3.2 Consensus size: 79
1696260 AGTATTCCCA
* * ** * *
1696270 AGATGAAAAATTTGATATTTGGGAAATAAAAACGGGGTTGGAAT-CCCATTAG-AAATGGTGGGG
1 AGATGAAAAATTTGATGTTTGGAAAATAAAAACGGGGTTGGAATACCCCCTCGAAAATGATGGGG
*
1696333 TTGGAGTATCCCCG
66 TTGGAGTATCCTCG
* * *
1696347 AGATGAAAAATTTGATGTTTGGAAAATAAAAACGGGGTTGGAGTATCCCCTCGAAAATAATGGGG
1 AGATGAAAAATTTGATGTTTGGAAAATAAAAACGGGGTTGGAATACCCCCTCGAAAATGATGGGG
1696412 TTGGAGTATCCTCG
66 TTGGAGTATCCTCG
*
1696426 AGATG-AAAATTCT-ATGTTTGGAAAATAAAAACGGGGTTAGAATACCCCCTCGAAAATGATGGG
1 AGATGAAAAATT-TGATGTTTGGAAAATAAAAACGGGGTTGGAATACCCCCTCGAAAATGATGGG
* *
1696489 GTTGGAATAT-CTCCA
65 GTTGGAGTATCCT-CG
1696504 AGATGAAAAATT
1 AGATGAAAAATT
1696516 CAGTGTTTTA
Statistics
Matches: 148, Mismatches: 16, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
77 43 0.29
78 71 0.48
79 34 0.23
ACGTcount: A:0.36, C:0.11, G:0.26, T:0.26
Consensus pattern (79 bp):
AGATGAAAAATTTGATGTTTGGAAAATAAAAACGGGGTTGGAATACCCCCTCGAAAATGATGGGG
TTGGAGTATCCTCG
Found at i:1698733 original size:59 final size:59
Alignment explanation
Indices: 1698641--1698762 Score: 244
Period size: 59 Copynumber: 2.1 Consensus size: 59
1698631 CTTTCATGCA
1698641 AGGTGGTTATCTGAAAGCCGAGGCTGTTTTCAATTTGAAAAGGCTGCTTGTCTTTTAGT
1 AGGTGGTTATCTGAAAGCCGAGGCTGTTTTCAATTTGAAAAGGCTGCTTGTCTTTTAGT
1698700 AGGTGGTTATCTGAAAGCCGAGGCTGTTTTCAATTTGAAAAGGCTGCTTGTCTTTTAGT
1 AGGTGGTTATCTGAAAGCCGAGGCTGTTTTCAATTTGAAAAGGCTGCTTGTCTTTTAGT
1698759 AGGT
1 AGGT
1698763 TATTAATTCT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (59 bp):
AGGTGGTTATCTGAAAGCCGAGGCTGTTTTCAATTTGAAAAGGCTGCTTGTCTTTTAGT
Found at i:1699015 original size:49 final size:50
Alignment explanation
Indices: 1698957--1699071 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 50
1698947 AATATTTTGC
* * * * *
1698957 ATGTATCGATACATTAAATAATGTATCAATACA-TGGGTCAAAACCT-AGA
1 ATGTATCGATACAATAAA-AATATATCAATAAATTGGGTCAAAAACTCAAA
* *
1699006 ATGTATCGATACAATAGAAATATATCGATAAATTTGGGTCAAAAACTCAAA
1 ATGTATCGATACAATAAAAATATATCAATAAA-TTGGGTCAAAAACTCAAA
1699057 ATGTATCGATACAAT
1 ATGTATCGATACAAT
1699072 GAAATGTATT
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 11 0.20
49 16 0.29
50 12 0.21
51 17 0.30
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (50 bp):
ATGTATCGATACAATAAAAATATATCAATAAATTGGGTCAAAAACTCAAA
Found at i:1699027 original size:51 final size:50
Alignment explanation
Indices: 1698957--1699087 Score: 135
Period size: 50 Copynumber: 2.6 Consensus size: 50
1698947 AATATTTTGC
* * *
1698957 ATGTATCGATAC-ATTAAATA-AT-GTATCAATACATGGGTCAAAACCT-AGA
1 ATGTATCGATACAATGAAATATATCG-AT-AA-ACATGGGTCAAAAACTCAAA
**
1699006 ATGTATCGATACAATAGAAATATATCGATAAATTTGGGTCAAAAACTCAAA
1 ATGTATCGATACAAT-GAAATATATCGATAAACATGGGTCAAAAACTCAAA
* *
1699057 ATGTATCGATACAATGAAATGTATTGATAAA
1 ATGTATCGATACAATGAAATATATCGATAAA
1699088 ATTTCCTTTC
Statistics
Matches: 70, Mismatches: 7, Indels: 9
0.81 0.08 0.10
Matches are distributed among these distances:
49 12 0.17
50 29 0.41
51 24 0.34
52 4 0.06
53 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.29
Consensus pattern (50 bp):
ATGTATCGATACAATGAAATATATCGATAAACATGGGTCAAAAACTCAAA
Found at i:1699091 original size:51 final size:50
Alignment explanation
Indices: 1698990--1699087 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
1698980 TATCAATACA
* *
1698990 TGGGTCAAAACCTAGAATGTATCGATACAATAGAAATATATCGATAAATT
1 TGGGTCAAAAACTAAAATGTATCGATACAATAGAAATATATCGATAAATT
* *
1699040 TGGGTCAAAAACTCAAAATGTATCGATACAAT-GAAATGTATTGATAAA
1 TGGGTCAAAAACT-AAAATGTATCGATACAATAGAAATATATCGATAAA
1699088 ATTTCCTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 26 0.60
51 17 0.40
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.28
Consensus pattern (50 bp):
TGGGTCAAAAACTAAAATGTATCGATACAATAGAAATATATCGATAAATT
Found at i:1699175 original size:20 final size:21
Alignment explanation
Indices: 1699150--1699200 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
1699140 TGTAGACATA
1699150 TATCGATACATTCACTCA-TG
1 TATCGATACATTCACTCATTG
* *
1699170 TATCGATACATTTACTTATTG
1 TATCGATACATTCACTCATTG
1699191 TATCGATACA
1 TATCGATACA
1699201 AATTGTAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (21 bp):
TATCGATACATTCACTCATTG
Found at i:1701967 original size:19 final size:20
Alignment explanation
Indices: 1701943--1701995 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
1701933 TAGTGATACA
1701943 TTGTATCGATACAACACT-T
1 TTGTATCGATACAACACTGT
**
1701962 TTGTATCG-TACAGTTACTGT
1 TTGTATCGATACA-ACACTGT
1701982 TTGTATCGATACAA
1 TTGTATCGATACAA
1701996 ATTGTTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 4 0.14
19 11 0.39
20 9 0.32
21 4 0.14
ACGTcount: A:0.28, C:0.17, G:0.15, T:0.40
Consensus pattern (20 bp):
TTGTATCGATACAACACTGT
Found at i:1702108 original size:12 final size:11
Alignment explanation
Indices: 1702082--1702110 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
1702072 AAAAATGTGG
1702082 TTTTTTCATCC
1 TTTTTTCATCC
1702093 TTTTTTCATCC
1 TTTTTTCATCC
1702104 TTTTTTC
1 TTTTTTC
1702111 CTTCCAGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.07, C:0.24, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTTCATCC
Found at i:1702911 original size:101 final size:97
Alignment explanation
Indices: 1702782--1703685 Score: 460
Period size: 101 Copynumber: 9.4 Consensus size: 97
1702772 GAAGAAGAAT
* * * * *
1702782 GCCAATGTGCTGAGA-CAAGGCCAACGACATTGGGCTTAGGAATGTTAAAAATGCCAATACGCTG
1 GCCAATATGCTGA-ATCAAGGCCAGCGACATTGGACTTA--AA-G-TAAAAGTGCCAATATGCTG
* *
1702846 ATTCAAGGCCAACGATATTGGACTTAAGGATAAAGGT
61 ATTCAAGGCCAACGATATTGGAATTAAGGATAAAGGC
* **
1702883 GCCAATGTGCTGAATCAAGGCCAGCGACATTGGTTTTAAAG-ACAAAGTGCCAATATGCTGATTC
1 GCCAATATGCTGAATCAAGGCCAGCGACATTGGACTTAAAGTA-AAAGTGCCAATATGCTGATTC
** *
1702947 AAGGCCAACGATATTGGTTTTAAAGATGACGAAGGC
65 AAGGCCAACGATATTGGAATTAAGGAT-A--AAGGC
* * * * * * *
1702983 ACCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTACTGATTC
1 GCCAATATGCTGAATCAAGGCCAGCGACATTGGACTTAAAG-TAAAAGTGCCAATATGCTGATTC
* * *
1703048 AAGGCCAGCGACATTGGAATTAAAGATGACAAAGGC
65 AAGGCCAACGATATTGGAATT-AAG--GATAAAGGC
* * * *
1703084 GCCAATATGCCGATTCAAGGCCAGCGATATTGGAC-T----T----GTGCCAATGTGCTGATTCA
1 GCCAATATGCTGAATCAAGGCCAGCGACATTGGACTTAAAGTAAAAGTGCCAATATGCTGATTCA
* * * ** * *
1703140 AGGCCAGCAACATTGGTCTTAAAAATGACAAAGGC
66 AGGCCAACGATATTGGAATT---AAGGATAAAGGC
* * * * * *
1703175 GCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTC
1 GCCAATATGCTGAATCAAGGCCAGCGACATTGGACTTAAAG-TAAAAGTGCCAATATGCTGATTC
* * * *
1703240 AAGGCCAGCGATATTGGACTTAAAGATGACGAAGGT
65 AAGGCCAACGATATTGGAATTAAGGAT-A--AAGGC
* * * * * *
1703276 ACCAATATGCTGATTCAAGGCTAGCGATATTGGGC-T----T----GTGCCAATGTGCTGATTCA
1 GCCAATATGCTGAATCAAGGCCAGCGACATTGGACTTAAAGTAAAAGTGCCAATATGCTGATTCA
* * * ** * * *
1703332 AAGCCAGCGACATTGGTTTTAAAGA-CAAGGT
66 AGGCCAACGATATTGGAATTAAGGATAAAGGC
* * ** * *
1703363 GCTAATGTGCTGGTTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACCAATATGCTGA
1 GCCAATATGCTGAATCAAGGCCAGCGACATTGGACTTAAAG-T-A--AAAGTGCCAATATGCTGA
* * **
1703428 TTCAAGGCTAGCGATATTGGGCTT----AT------
62 TTCAAGGCCAACGATATTGGAATTAAGGATAAAGGC
* * ** *
1703454 GCCAATGTGCTGATTCAAGGCCAGCGACATTGTTCTTAAAG-ACAAGGTGCCAATATGCTGATTC
1 GCCAATATGCTGAATCAAGGCCAGCGACATTGGACTTAAAGTA-AAAGTGCCAATATGCTGATTC
* * * * * * *
1703518 AAGGCCAGCAATATTGGACTCAAGAGGGTAAAAGT
65 AAGGCCAACGATATTGGAAT-TA-AGGATAAAGGC
* ** * *
1703553 GCCAATATGCTGATTCAATACCAGCGATATTGGACTTAAA-T----GTGCCAATGTGCTGATTCA
1 GCCAATATGCTGAATCAAGGCCAGCGACATTGGACTTAAAGTAAAAGTGCCAATATGCTGATTCA
* ** ** *
1703613 AGGCCAACGACATTGGTCTTAAATATAAAGGT
66 AGGCCAACGATATTGGAATTAAGGATAAAGGC
* * *
1703645 GCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 GCCAATATGCTGAATCAAGGCCAGCGACATTGGACTTAAAG
1703686 ACAAGGTGCC
Statistics
Matches: 657, Mismatches: 93, Indels: 114
0.76 0.11 0.13
Matches are distributed among these distances:
87 70 0.11
88 2 0.00
91 154 0.23
92 45 0.07
93 6 0.01
94 33 0.05
95 2 0.00
96 2 0.00
97 44 0.07
98 6 0.01
99 37 0.06
100 74 0.11
101 177 0.27
102 2 0.00
103 1 0.00
104 2 0.00
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (97 bp):
GCCAATATGCTGAATCAAGGCCAGCGACATTGGACTTAAAGTAAAAGTGCCAATATGCTGATTCA
AGGCCAACGATATTGGAATTAAGGATAAAGGC
Found at i:1703142 original size:192 final size:190
Alignment explanation
Indices: 1702929--1703447 Score: 736
Period size: 192 Copynumber: 2.7 Consensus size: 190
1702919 TAAAGACAAA
* * * *
1702929 GTGCCAATATGCTGATTCAAGGCCAACGATATTGGTTTTAAAGATGACGAAGGCACCAATATGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAA-ATGAC-AAGGCGCCAATATGCT
*
1702994 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTACTGATTCAAGGCCAGCGA
64 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
* *
1703059 CATTGGAATTAAAGATGACAAAGGCGCCAATATGCCGATTCAAGGCCAGCGATATTGGACTT
129 TATTGGAATTAAAGATGACAAAGGCACCAATATGCCGATTCAAGGCCAGCGATATTGGACTT
* *
1703121 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAAATGACAAAGGCGCCAATATGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGT-TTTAAAATGAC-AAGGCGCCAATATGCT
*
1703186 GATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
64 GATTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGA
* * * * * *
1703251 TATTGGACTTAAAGATGACGAAGGTACCAATATGCTGATTCAAGGCTAGCGATATTGGGCTT
129 TATTGGAATTAAAGATGACAAAGGCACCAATATGCCGATTCAAGGCCAGCGATATTGGACTT
* * * * *
1703313 GTGCCAATGTGCTGATTCAAAGCCAGCGACATTGGTTTT-AAA-GACAAGGTGCTAATGTGCTGG
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAATGACAAGGCGCCAATATGCTGA
* * * *
1703376 TTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACCAATATGCTGATTCAAGGCTAGCG
66 TTCAAGGCCAGCGATATTGGACTTAAAGAT---GAAGGTGCCAATGTGCTGATTCAAGGCCAGCG
1703441 ATATTGG
128 ATATTGG
1703448 GCTTATGCCA
Statistics
Matches: 294, Mismatches: 29, Indels: 9
0.89 0.09 0.03
Matches are distributed among these distances:
188 42 0.14
189 3 0.01
190 3 0.01
191 38 0.13
192 203 0.69
193 5 0.02
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (190 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTTTTAAAATGACAAGGCGCCAATATGCTGA
TTCAAGGCCAGCGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATA
TTGGAATTAAAGATGACAAAGGCACCAATATGCCGATTCAAGGCCAGCGATATTGGACTT
Found at i:1703190 original size:91 final size:91
Alignment explanation
Indices: 1703030--1703399 Score: 424
Period size: 91 Copynumber: 4.0 Consensus size: 91
1703020 AAAGATGAAG
* * * *
1703030 GTGCCAATGTACTGATTCAAGGCCAGCGACATTGGAATTAAAGATGACAAAGGCGCCAATATGCC
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGACAAAGGCGCCAATATGCT
1703095 GATTCAAGGCCAGCGATATTGGACTT
66 GATTCAAGGCCAGCGATATTGGACTT
* *
1703121 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAAATGACAAAGGCGCCAATATGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGACAAAGGCGCCAATATGCT
*
1703186 GATTCAAGGCCAACGATATTGGACTTAAAGAT
66 GATTCAAGGCCAGCGATATTGGAC-T-----T
* * * **
1703218 GAAGGTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAGGTACCAATA
1 ----GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGACAAAGGCGCCAATA
* *
1703283 TGCTGATTCAAGGCTAGCGATATTGGGCTT
62 TGCTGATTCAAGGCCAGCGATATTGGACTT
* ** * * *
1703313 GTGCCAATGTGCTGATTCAAAGCCAGCGACATTGG--TTTTAAA-GAC-AAGGTGCTAATGTGCT
1 GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGACAAAGGCGCCAATATGCT
* *
1703374 GGTTCAAGGCCAGCGACATTGGACTT
66 GATTCAAGGCCAGCGATATTGGACTT
1703400 AAAGATGACG
Statistics
Matches: 240, Mismatches: 29, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
87 35 0.15
88 3 0.01
89 4 0.02
91 115 0.48
92 1 0.00
95 1 0.00
97 1 0.00
100 1 0.00
101 79 0.33
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (91 bp):
GTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGACTTAAAAATGACAAAGGCGCCAATATGCT
GATTCAAGGCCAGCGATATTGGACTT
Found at i:1703207 original size:52 final size:51
Alignment explanation
Indices: 1703121--1703686 Score: 428
Period size: 52 Copynumber: 11.9 Consensus size: 51
1703111 TATTGGACTT
* * * * *
1703121 GTGCCAATGTGCTGATTCAAGGCCAGCAACATTGGTCTTAAAAATGACAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAC-AAG
* *
1703173 GCGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATG--AAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAG
*
1703222 GTGCCAATGTGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAC-AAG
* * *
1703274 GTACCAATATGCTGATTCAAGGCTAGCGATATTGGGC-T-----T------
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAG
* * * * *
1703313 GTGCCAATGTGCTGATTCAAAGCCAGCGACATTGG-TTTTAA-A-GACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAG
* * * *
1703361 GTGCTAATGTGCTGGTTCAAGGCCAGCGACATTGGACTTAAAGATGACGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGAC-AAG
* * *
1703413 GTACCAATATGCTGATTCAAGGCTAGCGATATTGGGC-T-----T----A-
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAG
* * **
1703453 -TGCCAATGTGCTGATTCAAGGCCAGCGACATTGTTCTT-AA-A-GACAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAG
* * * *
1703500 GTGCCAATATGCTGATTCAAGGCCAGCAATATTGGAC-TCAAGAGGGTA-AAA
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA-TG-ACAAG
**
1703551 GTGCCAATATGCTGATTCAATACCAGCGATATTGGACTT-AA-AT------
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAG
* * * * *
1703594 GTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAATAT-A-AAG
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAG
*
1703643 GTGCTAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
1 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGA
1703687 CAAGGTGCCA
Statistics
Matches: 414, Mismatches: 60, Indels: 83
0.74 0.11 0.15
Matches are distributed among these distances:
39 61 0.15
40 1 0.00
41 1 0.00
43 33 0.08
44 2 0.00
45 2 0.00
46 3 0.01
47 1 0.00
48 65 0.16
49 89 0.21
50 2 0.00
51 44 0.11
52 110 0.27
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (51 bp):
GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGACAAG
Found at i:1703426 original size:139 final size:140
Alignment explanation
Indices: 1703175--1703686 Score: 697
Period size: 139 Copynumber: 3.6 Consensus size: 140
1703165 TGACAAAGGC
* * * * *
1703175 GCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATTC
1703240 AAGGCCAGCGATATTGGACTTAAAGATGACGAAGGTACCAATATGCTGATTCAAGGCTAGCGATA
66 AAGGCCAGCGATATTGGACTTAAAGATGACGAAGGTACCAATATGCTGATTCAAGGCTAGCGATA
1703305 TTGGGCTTGT
131 TTGGGCTTGT
* * * * * *
1703315 GCCAATGTGCTGATTCAAAGCCAGCGACATTGGTTTTAAAGA-CAAGGTGCTAATGTGCTGGTTC
1 GCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATTC
*
1703379 AAGGCCAGCGACATTGGACTTAAAGATGACGAAGGTACCAATATGCTGATTCAAGGCTAGCGATA
66 AAGGCCAGCGATATTGGACTTAAAGATGACGAAGGTACCAATATGCTGATTCAAGGCTAGCGATA
*
1703444 TTGGGCTTAT
131 TTGGGCTTGT
* *
1703454 GCCAATGTGCTGATTCAAGGCCAGCGACATTGTTCTTAAAGA-CAAGGTGCCAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATTC
* * * *** * * ** *
1703518 AAGGCCAGCAATATTGGAC-TCAAGAGGGTAAAAGTGCCAATATGCTGATTCAATACCAGCGATA
66 AAGGCCAGCGATATTGGACTTAAAGATGACGAAGGTACCAATATGCTGATTCAAGGCTAGCGATA
*
1703582 TTGGACTTAAATGT
131 TTGGGC-T---TGT
* * *
1703596 GCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAATATAAAGGTGCTAATATGCTGATTC
1 GCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATTC
1703661 AAGGCCAGCGATATTGGACTTAAAGA
66 AAGGCCAGCGATATTGGACTTAAAGA
1703687 CAAGGTGCCA
Statistics
Matches: 328, Mismatches: 38, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
138 40 0.12
139 168 0.51
140 36 0.11
142 41 0.12
143 38 0.12
144 5 0.02
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (140 bp):
GCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAAGATCAAGGTGCCAATATGCTGATTC
AAGGCCAGCGATATTGGACTTAAAGATGACGAAGGTACCAATATGCTGATTCAAGGCTAGCGATA
TTGGGCTTGT
Found at i:1703560 original size:51 final size:46
Alignment explanation
Indices: 1703453--1703680 Score: 210
Period size: 51 Copynumber: 4.8 Consensus size: 46
1703443 ATTGGGCTTA
* * ** * *
1703453 TGCCAATGTGCTGATTCAAGGCCAGCGACATTGTTCTTAAAGACAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-TAAATA-AAAG
*
1703501 TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTCAAGAGGGTAAAAG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT-AA-A---TAAAAG
** *
1703552 TGCCAATATGCTGATTCAATACCAGCGATATTGGACT---TAAATG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTAAATAAAAG
* * * *
1703595 TGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCTTAAATATAAAGG
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-TAAATA-AAA-G
*
1703644 TGCTAATATGCTGATTCAAGGCCAGCGATATTGGACT
1 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
1703681 TAAAGACAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
43 35 0.24
44 1 0.01
47 3 0.02
48 36 0.25
49 33 0.23
51 37 0.25
52 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (46 bp):
TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTAAATAAAAG
Found at i:1703599 original size:43 final size:43
Alignment explanation
Indices: 1703546--1703684 Score: 152
Period size: 43 Copynumber: 3.1 Consensus size: 43
1703536 CTCAAGAGGG
* **
1703546 TAAAAGTGCCAATATGCTGATTCAATACCAGCGATATTGGACT
1 TAAATGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
* * * *
1703589 TAAATGTGCCAATGTGCTGATTCAAGGCCAACGACATTGGTCT
1 TAAATGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
*
1703632 TAAATATAAAGGTGCTAATATGCTGATTCAAGGCCAGCGATATTGGACT
1 T-AA-AT----GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
1703681 TAAA
1 TAAA
1703685 GACAAGGTGC
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
43 37 0.47
44 2 0.03
45 2 0.03
47 1 0.01
48 2 0.03
49 34 0.44
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (43 bp):
TAAATGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
Found at i:1703755 original size:27 final size:27
Alignment explanation
Indices: 1703723--1704013 Score: 249
Period size: 27 Copynumber: 10.0 Consensus size: 27
1703713 AAAAGAAAAA
* *
1703723 GTGCCACGGAGTTCTGGGCTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
1703750 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
1703777 GTGCCACGGAGTTGTGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
1703804 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAG
1 GTGCCACGGAGTTGTGGACTTAAAA-G-----G
* * * *
1703837 AGTACCACGAAGTTATGGGCTTAAAAGG
1 -GTGCCACGGAGTTGTGGACTTAAAAGG
1703865 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAG
1 GTGCCACGGAGTTGTGGACTTAAAA-G-----G
* * *
1703898 AGTGCCATGGAGTTGTGGGCTTGAAAGG
1 -GTGCCACGGAGTTGTGGACTTAAAAGG
* *
1703926 ATGCCACAGAGTTGTGGACTTAAAAGGAACAAG
1 GTGCCACGGAGTTGTGGACTTAAAA-G-----G
* *
1703959 AGTGCCACAGAGTTGTGGGCTTAAAAGG
1 -GTGCCACGGAGTTGTGGACTTAAAAGG
* * *
1703987 GTGTCACAGAGTTATGGACTTAAAAGG
1 GTGCCACGGAGTTGTGGACTTAAAAGG
1704014 AACAAGAGTG
Statistics
Matches: 220, Mismatches: 23, Indels: 42
0.77 0.08 0.15
Matches are distributed among these distances:
27 142 0.65
28 6 0.03
33 6 0.03
34 66 0.30
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (27 bp):
GTGCCACGGAGTTGTGGACTTAAAAGG
Found at i:1703845 original size:34 final size:34
Alignment explanation
Indices: 1703798--1704109 Score: 261
Period size: 34 Copynumber: 9.8 Consensus size: 34
1703788 TTGTGGACTT
*
1703798 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * * *
1703832 AAAAGAGTACCACGAAGTTATGGGCTTAAAA-G-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
1703864 ----G-GTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
1703893 AAAAGAGTGCCATGGAGTTGTGGGCTT-----G-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* *
1703921 AAAGGA-TGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
1703954 ACAAGAGTGCCACAGAGTTGTGGGCTTAAAA-G-
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
1703986 ----G-GTGTCACAGAGTTATGGACTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
1704015 ACAAGAGTGCCACAGAGTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
1704049 AAAAGAGCGCCACGAAGTTGTGGGCTTAAAAGGA
1 AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
* * *
1704083 AAAAGAATGCCACGAAATTGTGGACTT
1 AAAAGAGTGCCACGGAGTTGTGGACTT
1704110 TGAAAAGAGA
Statistics
Matches: 225, Mismatches: 32, Indels: 42
0.75 0.11 0.14
Matches are distributed among these distances:
27 60 0.27
28 9 0.04
29 1 0.00
32 1 0.00
33 8 0.04
34 146 0.65
ACGTcount: A:0.36, C:0.13, G:0.32, T:0.20
Consensus pattern (34 bp):
AAAAGAGTGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:1703866 original size:61 final size:61
Alignment explanation
Indices: 1703771--1704105 Score: 388
Period size: 61 Copynumber: 5.4 Consensus size: 61
1703761 TTGTGGACTT
* * * *
1703771 AAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * *
1703832 AAAAGAGTACCACGAAGTTATGGGCTTAAAAGGGTGCCACGGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * * *
1703893 AAAAGAGTGCCATGGAGTTGTGGGCTTGAAAGGATGCCACAGAGTTGTGGACTTAAAAGGA
1 AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * *
1703954 ACAAGAGTGCCAC-AGAGTTGTGGGCTTAAAAGGGTGTCACAGAGTTATGGACTTAAAAGGA
1 AAAAGAGTGCCACGA-AGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
* * *
1704015 ACAAGAGTGCCAC-AGAGTTGTGGGCTTAAAAGGAAAAAGAGCGC-CACGAAGTTGTGGGCTTAA
1 AAAAGAGTGCCACGA-AGTTGTGGGCTTAAAAGG-----GTGC-CACA-G-AGTTGTGGACTTAA
1704078 AAGGA
57 AAGGA
* *
1704083 AAAAGAATGCCACGAAATTGTGG
1 AAAAGAGTGCCACGAAGTTGTGG
1704106 ACTTTGAAAA
Statistics
Matches: 238, Mismatches: 26, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
61 196 0.82
66 4 0.02
67 2 0.01
68 35 0.15
69 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (61 bp):
AAAAGAGTGCCACGAAGTTGTGGGCTTAAAAGGGTGCCACAGAGTTGTGGACTTAAAAGGA
Found at i:1703946 original size:122 final size:120
Alignment explanation
Indices: 1703688--1704098 Score: 464
Period size: 122 Copynumber: 3.4 Consensus size: 120
1703678 ACTTAAAGAC
* * * *
1703688 AAGG-TGCCACGAAGTTGTGGCCTTAAAAAG-AAAA-AGTGCCACGGAGTTCTGGGCTTAAAAGG
1 AAGGATGCCACG-AGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGAAGTTATGGGCTTAAAAGG
*
1703750 GTGCCACGGAGTTGTGGACTTAAAA-G----G-GTGCCACGGAGTTGTGGACTTAA
65 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAA
* *
1703800 AAGGGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTACCACGAAGTTATGGGCTTAAAAGG
1 AAGGATGCCAC-GAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGAAGTTATGGGCTTAAAAGG
* *
1703865 GTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTGA
65 GTGCCACGGAGTTGTGGACTTAAAAGG-AAAAGAGTGCCACGGAGTTGTGGGCTTAA
* *
1703922 AAGGATGCCACAGAGTTGTGGACTTAAAAGGAACAAGAGTGCCAC-AGAGTTGTGGGCTTAAAAG
1 AAGGATGCCAC-GAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGA-AGTTATGGGCTTAAAAG
* * * *
1703986 GGTGTCACAGAGTTATGGACTTAAAAGGAACAAGAGTGCCACAGAGTTGTGGGCTTAA
64 GGTGCCACGGAGTTGTGGACTTAAAAGGAA-AAGAGTGCCACGGAGTTGTGGGCTTAA
* * *
1704044 AAGGAAAAAGAGCGCCACGAAGTTGTGGGCTTAAAAGGAAAAAGAATGCCACGAA
1 AA-G-----GA-TGCCACG-AGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGAA
1704099 ATTGTGGACT
Statistics
Matches: 254, Mismatches: 23, Indels: 27
0.84 0.08 0.09
Matches are distributed among these distances:
112 4 0.02
113 22 0.09
114 5 0.02
115 50 0.20
116 1 0.00
121 4 0.02
122 128 0.50
123 1 0.00
128 3 0.01
129 35 0.14
130 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.32, T:0.19
Consensus pattern (120 bp):
AAGGATGCCACGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGAAGTTATGGGCTTAAAAGGG
TGCCACGGAGTTGTGGACTTAAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTAA
Found at i:1703948 original size:88 final size:85
Alignment explanation
Indices: 1703690--1703952 Score: 268
Period size: 88 Copynumber: 3.0 Consensus size: 85
1703680 TTAAAGACAA
* * * * *
1703690 GGTGCCACGAAGTTGTGGCCTTAAAAAGAAAA-AGTGCCACGGAGTTCTGGGCTTAAAAGGGTGC
1 GGTGCCACGGAGTTGTGGACTT-AAAAGAAAAGAGTGCCACGGAGTTGTGGGCTTGAAAGGATGC
1703754 CACGGAGTTGTGGACTTAAAAG
65 CAC-GAGTTGTGGACTTAAAAG
* *
1703776 GGTGCCACGGAGTTGTGGACTTAAAAG----G-GTGCCACGGAGTTGTGGACTTAAAAGGAAAAA
1 GGTGCCACGGAGTTGTGGACTTAAAAGAAAAGAGTGCCACGGAGTTGTGGGCTT-----G-AAAG
* * *
1703836 GAGTACCACGAAGTTATGGGCTTAAAAG
60 GA-TGCCACG-AGTTGTGGACTTAAAAG
*
1703864 GGTGCCACGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTGAAAGGATG
1 GGTGCCACGGAGTTGTGGACTTAAAA-G-AAAAGAGTGCCACGGAGTTGTGGGCTTGAAAGGATG
1703929 CCACAGAGTTGTGGACTTAAAAG
64 CCAC-GAGTTGTGGACTTAAAAG
1703952 G
1 G
1703953 AACAAGAGTG
Statistics
Matches: 144, Mismatches: 16, Indels: 32
0.75 0.08 0.17
Matches are distributed among these distances:
81 19 0.13
85 5 0.03
86 20 0.14
87 5 0.03
88 67 0.47
89 7 0.05
90 1 0.01
94 1 0.01
95 19 0.13
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.21
Consensus pattern (85 bp):
GGTGCCACGGAGTTGTGGACTTAAAAGAAAAGAGTGCCACGGAGTTGTGGGCTTGAAAGGATGCC
ACGAGTTGTGGACTTAAAAG
Found at i:1704141 original size:31 final size:30
Alignment explanation
Indices: 1704102--1704364 Score: 310
Period size: 31 Copynumber: 8.6 Consensus size: 30
1704092 CCACGAAATT
1704102 GTGGACTTTGAAAAGAGATTGCCACTGAGTC
1 GTGGACTTTGAAAAGAGA-TGCCACTGAGTC
* **
1704133 GTGTACTTTGGGAAGAGATGCCACTGAGTC
1 GTGGACTTTGAAAAGAGATGCCACTGAGTC
* * *
1704163 GTGGATTTTGGAAAGAGATGCTACTGAGTC
1 GTGGACTTTGAAAAGAGATGCCACTGAGTC
* *
1704193 GTGGACTTTGAAGAAAAGATGCCACTGAGTT
1 GTGGACTTTGAA-AAGAGATGCCACTGAGTC
* *
1704224 GTGGACTTTGAAGAAAAGATGCCACTCAGTC
1 GTGGACTTTGAA-AAGAGATGCCACTGAGTC
* * *
1704255 GTGGACTTTGAGAAGAGATGCTACTAAGTC
1 GTGGACTTTGAAAAGAGATGCCACTGAGTC
* * *
1704285 GTGAACTTTGAAGAAAAGATGCCACTGAGTT
1 GTGGACTTTGAA-AAGAGATGCCACTGAGTC
* *
1704316 GTGGACTTTGAAGAAAAAATGCCACTGAGTC
1 GTGGACTTTGAA-AAGAGATGCCACTGAGTC
*
1704347 GTGGACTTTGAGAAGAGA
1 GTGGACTTTGAAAAGAGA
1704365 GATTTGAAGA
Statistics
Matches: 200, Mismatches: 30, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
30 77 0.38
31 123 0.62
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (30 bp):
GTGGACTTTGAAAAGAGATGCCACTGAGTC
Found at i:1704156 original size:61 final size:61
Alignment explanation
Indices: 1704102--1704357 Score: 329
Period size: 61 Copynumber: 4.2 Consensus size: 61
1704092 CCACGAAATT
* * *
1704102 GTGGACTTTGAA-AAGAGATTGCCACTGAGTCGTGTACTTTGGGAAGAGATGCCACTGAGTC
1 GTGGACTTTGAAGAAAAGA-TGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTGAGTC
* * * *
1704163 GTGGATTTTG--GAAAGAGATGCTACTGAGTCGTGGACTTTGAAGAAAAGATGCCACTGAGTT
1 GTGGACTTTGAAGAAA-AGATGCCACTGAGTCGTGGACTTTG-AGAAGAGATGCCACTGAGTC
* * *
1704224 GTGGACTTTGAAGAAAAGATGCCACTCAGTCGTGGACTTTGAGAAGAGATGCTACTAAGTC
1 GTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTGAGTC
* * * *
1704285 GTGAACTTTGAAGAAAAGATGCCACTGAGTTGTGGACTTTGAAGAAAAAATGCCACTGAGTC
1 GTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTG-AGAAGAGATGCCACTGAGTC
1704347 GTGGACTTTGA
1 GTGGACTTTGA
1704358 GAAGAGAGAT
Statistics
Matches: 167, Mismatches: 22, Indels: 11
0.83 0.11 0.05
Matches are distributed among these distances:
60 22 0.13
61 92 0.55
62 49 0.29
63 4 0.02
ACGTcount: A:0.30, C:0.14, G:0.29, T:0.26
Consensus pattern (61 bp):
GTGGACTTTGAAGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAGAGATGCCACTGAGTC
Found at i:1704276 original size:92 final size:92
Alignment explanation
Indices: 1704102--1704364 Score: 397
Period size: 92 Copynumber: 2.9 Consensus size: 92
1704092 CCACGAAATT
* * * * *
1704102 GTGGACTTTGAA-AAGAGATTGCCACTGAGTCGTGTACTTTG-GGAAGAGATGCCACTGAGTCGT
1 GTGGACTTTGAAGAAAAGA-TGCCACTGAGTTGTGGACTTTGAAGAAAAGATGCCACTGAGTCGT
* *
1704165 GGATTTTG-GAAAGAGATGCTACTGAGTC
65 GGACTTTGAG-AAGAGATGCTACTAAGTC
*
1704193 GTGGACTTTGAAGAAAAGATGCCACTGAGTTGTGGACTTTGAAGAAAAGATGCCACTCAGTCGTG
1 GTGGACTTTGAAGAAAAGATGCCACTGAGTTGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTG
1704258 GACTTTGAGAAGAGATGCTACTAAGTC
66 GACTTTGAGAAGAGATGCTACTAAGTC
* *
1704285 GTGAACTTTGAAGAAAAGATGCCACTGAGTTGTGGACTTTGAAGAAAAAATGCCACTGAGTCGTG
1 GTGGACTTTGAAGAAAAGATGCCACTGAGTTGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTG
1704350 GACTTTGAGAAGAGA
66 GACTTTGAGAAGAGA
1704365 GATTTGAAGA
Statistics
Matches: 158, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
91 32 0.20
92 125 0.79
93 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.30, T:0.25
Consensus pattern (92 bp):
GTGGACTTTGAAGAAAAGATGCCACTGAGTTGTGGACTTTGAAGAAAAGATGCCACTGAGTCGTG
GACTTTGAGAAGAGATGCTACTAAGTC
Found at i:1705595 original size:15 final size:15
Alignment explanation
Indices: 1705575--1705605 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1705565 CACTTTTTTG
1705575 TGTTTTTTTTTGTGT
1 TGTTTTTTTTTGTGT
1705590 TGTTTTTTTTTGTGT
1 TGTTTTTTTTTGTGT
1705605 T
1 T
1705606 TGTACTTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.00, G:0.19, T:0.81
Consensus pattern (15 bp):
TGTTTTTTTTTGTGT
Found at i:1705606 original size:12 final size:13
Alignment explanation
Indices: 1705568--1705598 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
1705558 GCCTTTGCAC
1705568 TTTTTTGTGTT-T
1 TTTTTTGTGTTGT
1705580 TTTTTTGTGTTGT
1 TTTTTTGTGTTGT
1705593 TTTTTT
1 TTTTTT
1705599 TTGTGTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (13 bp):
TTTTTTGTGTTGT
Found at i:1712110 original size:19 final size:19
Alignment explanation
Indices: 1712086--1712148 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
1712076 AGCGATACAT
1712086 TGTATCGATACAACACTTA
1 TGTATCGATACAACACTTA
1712105 TGTATCGAT---ACA--T-
1 TGTATCGATACAACACTTA
*
1712118 TGTATCCATACAACACTTA
1 TGTATCGATACAACACTTA
*
1712137 TATATCGATACA
1 TGTATCGATACA
1712149 GTTACTGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 8 0.23
14 1 0.03
16 6 0.17
18 1 0.03
19 19 0.54
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.33
Consensus pattern (19 bp):
TGTATCGATACAACACTTA
Found at i:1712119 original size:32 final size:32
Alignment explanation
Indices: 1712073--1712148 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
1712063 CTAGTAGCTT
* *
1712073 TGTAGCGATACATTGTATCGATACAACACTTA
1 TGTATCGATACATTGTATCCATACAACACTTA
1712105 TGTATCGATACATTGTATCCATACAACACTTA
1 TGTATCGATACATTGTATCCATACAACACTTA
*
1712137 TATATCGATACA
1 TGTATCGATACA
1712149 GTTACTGTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATTGTATCCATACAACACTTA
Found at i:1712802 original size:13 final size:13
Alignment explanation
Indices: 1712772--1712796 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1712762 ATTGTAATTT
1712772 AATTAATTTAAAA
1 AATTAATTTAAAA
1712785 AATTAATTTAAA
1 AATTAATTTAAA
1712797 TTATTATTTA
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AATTAATTTAAAA
Found at i:1712897 original size:18 final size:18
Alignment explanation
Indices: 1712874--1712936 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
1712864 AATGCAAATA
1712874 ATATTTTTATAATTAATT
1 ATATTTTTATAATTAATT
* *
1712892 ATATTTTAAAAATTAATT
1 ATATTTTTATAATTAATT
*
1712910 -TA-ATTTATAATATAAATT
1 ATATTTTTATAAT-T-AATT
1712928 ATTATTTTT
1 A-TATTTTT
1712937 TATTTGTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
16 6 0.18
17 3 0.09
18 20 0.59
20 2 0.06
21 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTTTTATAATTAATT
Found at i:1713760 original size:77 final size:77
Alignment explanation
Indices: 1713633--1713790 Score: 246
Period size: 77 Copynumber: 2.1 Consensus size: 77
1713623 CTATCCATTA
*
1713633 ATATCGACTCTAAGCTTAATCATCATTCACAAGTATAATTTTCACAATTTAAAG-ATAGGTCTTA
1 ATATCGACTCTAAGCTTAATCATCATTCACAAGTATAATTTTCACAATTT-AAGTATAGGTCCTA
*
1713697 TATACACACATAT
65 TACACACACATAT
* *
1713710 ATATCGACTTTAAGCTTAATCATCATTTACAAGTATAATTTTCACAATTTAAGTATAGGTCCTAT
1 ATATCGACTCTAAGCTTAATCATCATTCACAAGTATAATTTTCACAATTTAAGTATAGGTCCTAT
* *
1713775 ACACATATATAT
66 ACACACACATAT
1713787 ATAT
1 ATAT
1713791 ATATATATGA
Statistics
Matches: 74, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
76 3 0.04
77 71 0.96
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (77 bp):
ATATCGACTCTAAGCTTAATCATCATTCACAAGTATAATTTTCACAATTTAAGTATAGGTCCTAT
ACACACACATAT
Found at i:1717554 original size:50 final size:50
Alignment explanation
Indices: 1717490--1717741 Score: 434
Period size: 50 Copynumber: 5.0 Consensus size: 50
1717480 ACTTAGAGTT
* *
1717490 AACAATTATAGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATCGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
1717540 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
*
1717590 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAAAATCGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
*
1717640 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAAAATCGTC
1 AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
* *
1717690 AACAATTATGGCCACCT-CTCTCTATTGTCAAAGGTTGGTGAAGGATAGTC
1 AACAATTATGGCCACCTCCT-TCTATTGTCAAAGGTTGGTGAAGAATCGTC
1717740 AA
1 AA
1717742 AAATGGCAAC
Statistics
Matches: 195, Mismatches: 6, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
49 2 0.01
50 193 0.99
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (50 bp):
AACAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATCGTC
Found at i:1722199 original size:50 final size:50
Alignment explanation
Indices: 1722139--1722347 Score: 319
Period size: 50 Copynumber: 4.2 Consensus size: 50
1722129 TTTACTTAGA
* *
1722139 GTCAACAATTATAGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATT
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* *
1722189 GTCAATAATTATGGCCACCTCCTTCTATTGTCAAAGGTTGGTGAAGAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * * *
1722239 GTCAATAATTATGGTCACCTCCTTCTATTGTCAAAGGTTGGTGAAAAATC
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
* * *
1722289 GTCAACAATTATGGCCACCTCTCTCTATTGTCAAAGGTTGGTGAAGGATA
1 GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
1722339 GTCAACAAT
1 GTCAACAAT
1722348 GACAACAACT
Statistics
Matches: 146, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 146 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (50 bp):
GTCAACAATTATGGCCACCTCCCTCTATTGTCAAAGGTTGGTGAAGAATC
Found at i:1728036 original size:26 final size:27
Alignment explanation
Indices: 1728007--1728066 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
1727997 TAAAAGATTT
1728007 TTAATATTTATA-AATATTT-AATTAAA
1 TTAATATTTATATAA-ATTTAAATTAAA
1728033 TTAAT-TGTTATATAAATTTAAATTAAA
1 TTAATAT-TTATATAAATTTAAATTAAA
1728060 TT-ATATT
1 TTAATATT
1728067 AAATAATTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
25 1 0.03
26 17 0.57
27 12 0.40
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (27 bp):
TTAATATTTATATAAATTTAAATTAAA
Found at i:1728197 original size:11 final size:10
Alignment explanation
Indices: 1728181--1728244 Score: 53
Period size: 11 Copynumber: 6.4 Consensus size: 10
1728171 ATTAAGATAC
1728181 AATATAAATAT
1 AATATAAA-AT
1728192 AATATAAAAAT
1 AATAT-AAAAT
1728203 AAT-TAAAAT
1 AATATAAAAT
* **
1728212 AAAATACGAT
1 AATATAAAAT
1728222 -ATA-AAAAT
1 AATATAAAAT
1728230 AATATAAACAT
1 AATATAAA-AT
1728241 AATA
1 AATA
1728245 CAGATACATA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
8 3 0.07
9 12 0.29
10 8 0.19
11 16 0.38
12 3 0.07
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.28
Consensus pattern (10 bp):
AATATAAAAT
Found at i:1728244 original size:27 final size:27
Alignment explanation
Indices: 1728184--1728250 Score: 77
Period size: 27 Copynumber: 2.5 Consensus size: 27
1728174 AAGATACAAT
*
1728184 ATAAATATA-ATATAAAAATAATTAAA
1 ATAAATACAGATATAAAAATAATTAAA
1728210 ATAAAATAC-GATATAAAAATAATATAAA
1 AT-AAATACAGATATAAAAATAAT-TAAA
1728238 CAT-AATACAGATA
1 -ATAAATACAGATA
1728251 CATAATATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
26 2 0.06
27 23 0.66
28 8 0.23
29 2 0.06
ACGTcount: A:0.66, C:0.04, G:0.03, T:0.27
Consensus pattern (27 bp):
ATAAATACAGATATAAAAATAATTAAA
Found at i:1728806 original size:32 final size:32
Alignment explanation
Indices: 1728770--1728857 Score: 122
Period size: 32 Copynumber: 2.8 Consensus size: 32
1728760 AACCCGAATA
* *
1728770 ATCCGAACCCGAAATGATCTAAACCTAAAATG
1 ATCCGAACCCGAAATGACCCAAACCTAAAATG
* * *
1728802 ATCCGAACCCGAAATAACCCGAATCTAAAATG
1 ATCCGAACCCGAAATGACCCAAACCTAAAATG
*
1728834 ATCCAAACCCGAAATGACCCAAAC
1 ATCCGAACCCGAAATGACCCAAAC
1728858 AATTAACCCA
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.44, C:0.30, G:0.11, T:0.15
Consensus pattern (32 bp):
ATCCGAACCCGAAATGACCCAAACCTAAAATG
Found at i:1728855 original size:16 final size:16
Alignment explanation
Indices: 1728759--1728857 Score: 74
Period size: 16 Copynumber: 6.2 Consensus size: 16
1728749 AGCCGACCTA
*
1728759 AAACCCG-AATAATCC
1 AAACCCGAAATGATCC
* *
1728774 GAACCCGAAATGATCT
1 AAACCCGAAATGATCC
**
1728790 AAACCTAAAATGATCC
1 AAACCCGAAATGATCC
* * *
1728806 GAACCCGAAATAACCC
1 AAACCCGAAATGATCC
* * **
1728822 GAATCTAAAATGATCC
1 AAACCCGAAATGATCC
*
1728838 AAACCCGAAATGACCC
1 AAACCCGAAATGATCC
1728854 AAAC
1 AAAC
1728858 AATTAACCCA
Statistics
Matches: 61, Mismatches: 22, Indels: 1
0.73 0.26 0.01
Matches are distributed among these distances:
15 6 0.10
16 55 0.90
ACGTcount: A:0.45, C:0.29, G:0.11, T:0.14
Consensus pattern (16 bp):
AAACCCGAAATGATCC
Found at i:1729699 original size:16 final size:16
Alignment explanation
Indices: 1729680--1729753 Score: 85
Period size: 16 Copynumber: 4.6 Consensus size: 16
1729670 GACCTGAATC
1729680 CGAAATGACCCAAACT
1 CGAAATGACCCAAACT
* * *
1729696 CGAAATGACTCGAACC
1 CGAAATGACCCAAACT
* *
1729712 CGAAATGATCCGAACT
1 CGAAATGACCCAAACT
*
1729728 CGAAATAACCCAAACT
1 CGAAATGACCCAAACT
1729744 CGAAAATGAC
1 CG-AAATGAC
1729754 TCGAAAATTT
Statistics
Matches: 47, Mismatches: 10, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
16 41 0.87
17 6 0.13
ACGTcount: A:0.43, C:0.28, G:0.15, T:0.14
Consensus pattern (16 bp):
CGAAATGACCCAAACT
Found at i:1729788 original size:15 final size:15
Alignment explanation
Indices: 1729770--1729801 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1729760 ATTTTAAAAT
1729770 CCGAAATGACCCAAC
1 CCGAAATGACCCAAC
*
1729785 CCGAAATGATCCAAC
1 CCGAAATGACCCAAC
1729800 CC
1 CC
1729802 AAAACCAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.38, C:0.41, G:0.12, T:0.09
Consensus pattern (15 bp):
CCGAAATGACCCAAC
Found at i:1730091 original size:23 final size:22
Alignment explanation
Indices: 1730042--1730088 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 22
1730032 ACACAACATA
1730042 AATA-AAAAAATAATTAAAACG
1 AATACAAAAAATAATTAAAACG
1730063 CAATACAAAAAATAATATAAACACG
1 -AATACAAAAAATAAT-TAAA-ACG
1730088 A
1 A
1730089 TACGAATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 4 0.18
23 10 0.45
24 5 0.23
25 3 0.14
ACGTcount: A:0.68, C:0.11, G:0.04, T:0.17
Consensus pattern (22 bp):
AATACAAAAAATAATTAAAACG
Found at i:1730326 original size:13 final size:13
Alignment explanation
Indices: 1730294--1730345 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
1730284 TCATATTTTA
1730294 AATAATAAAAAAT
1 AATAATAAAAAAT
*
1730307 -ATGAATAATAAAT
1 AAT-AATAAAAAAT
*
1730320 AATAATAAAATAT
1 AATAATAAAAAAT
1730333 -A-AATAAAAAAT
1 AATAATAAAAAAT
1730344 AA
1 AA
1730346 ATATGTGAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
11 9 0.28
12 4 0.12
13 17 0.53
14 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (13 bp):
AATAATAAAAAAT
Found at i:1730337 original size:24 final size:23
Alignment explanation
Indices: 1730292--1730345 Score: 81
Period size: 24 Copynumber: 2.3 Consensus size: 23
1730282 TATCATATTT
*
1730292 TAAATAATAAAAAATATGAATAA
1 TAAATAATAAAAAATATAAATAA
1730315 TAAATAATAATAAAATATAAATAA
1 TAAATAATAA-AAAATATAAATAA
*
1730339 AAAATAA
1 TAAATAA
1730346 ATATGTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
23 10 0.36
24 18 0.64
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (23 bp):
TAAATAATAAAAAATATAAATAA
Found at i:1731328 original size:27 final size:28
Alignment explanation
Indices: 1731298--1731420 Score: 106
Period size: 27 Copynumber: 4.3 Consensus size: 28
1731288 ACTAATAAAA
*
1731298 ATAAATTTTTTAATT-AATTTTTTATAT
1 ATAAATTTTTTAATTAAATTTTTTACAT
* * * * *
1731325 ATAAAATTTTTAATT-GATATTCTATAT
1 ATAAATTTTTTAATTAAATTTTTTACAT
* * *
1731352 ATAAAATTTTTAATTAAACTTTTGACAT
1 ATAAATTTTTTAATTAAATTTTTTACAT
1731380 ATTAAATTAATTTTTAATTAAATTTTTTACAT
1 A-TAAA-T--TTTTTAATTAAATTTTTTACAT
1731412 ATTAAATTT
1 A-TAAATTT
1731421 ACAGATGATA
Statistics
Matches: 78, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
27 38 0.49
28 7 0.09
29 6 0.08
31 1 0.01
32 26 0.33
ACGTcount: A:0.41, C:0.03, G:0.02, T:0.54
Consensus pattern (28 bp):
ATAAATTTTTTAATTAAATTTTTTACAT
Found at i:1731397 original size:32 final size:32
Alignment explanation
Indices: 1731356--1731419 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
1731346 CTATATATAA
1731356 AATTTTTAATTAAACTTTTGACATATTAAATT
1 AATTTTTAATTAAACTTTTGACATATTAAATT
* *
1731388 AATTTTTAATTAAATTTTTTACATATTAAATT
1 AATTTTTAATTAAACTTTTGACATATTAAATT
1731420 TACAGATGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (32 bp):
AATTTTTAATTAAACTTTTGACATATTAAATT
Found at i:1731415 original size:16 final size:16
Alignment explanation
Indices: 1731364--1731420 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
1731354 AAAATTTTTA
* *
1731364 ATTAAACTTTTGACAT
1 ATTAAATTTTTTACAT
*
1731380 ATTAAATTAATTTT-TA-
1 ATTAAATT--TTTTACAT
1731396 ATTAAATTTTTTACAT
1 ATTAAATTTTTTACAT
1731412 ATTAAATTT
1 ATTAAATTT
1731421 ACAGATGATA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
14 4 0.12
15 1 0.03
16 24 0.73
17 1 0.03
18 3 0.09
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (16 bp):
ATTAAATTTTTTACAT
Found at i:1734333 original size:36 final size:36
Alignment explanation
Indices: 1734286--1734354 Score: 138
Period size: 36 Copynumber: 1.9 Consensus size: 36
1734276 TATCTAAAGG
1734286 TAGAGGATGTGGGAAATAAATAAAAAGAATAGAAGA
1 TAGAGGATGTGGGAAATAAATAAAAAGAATAGAAGA
1734322 TAGAGGATGTGGGAAATAAATAAAAAGAATAGA
1 TAGAGGATGTGGGAAATAAATAAAAAGAATAGA
1734355 GAGAAAGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (36 bp):
TAGAGGATGTGGGAAATAAATAAAAAGAATAGAAGA
Found at i:1734404 original size:13 final size:14
Alignment explanation
Indices: 1734382--1734416 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1734372 GAAAAAAATC
*
1734382 AAATTGAATTGATT
1 AAATTAAATTGATT
1734396 -AATTAAATTGATT
1 AAATTAAATTGATT
1734409 AAATTAAA
1 AAATTAAA
1734417 AATTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (14 bp):
AAATTAAATTGATT
Found at i:1740509 original size:20 final size:19
Alignment explanation
Indices: 1740459--1740509 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
1740449 CCCTTAAAAA
*
1740459 TATCGATACACAATTCAAAG
1 TATCGATACA-TATTCAAAG
*
1740479 TATCGATACATATTGCAATG
1 TATCGATACATATT-CAAAG
1740499 TATCGATACAT
1 TATCGATACAT
1740510 GAAAAAGATG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (19 bp):
TATCGATACATATTCAAAG
Found at i:1740587 original size:13 final size:13
Alignment explanation
Indices: 1740569--1740594 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1740559 TACAGCAAGT
1740569 ATGTATCGATACA
1 ATGTATCGATACA
1740582 ATGTATCGATACA
1 ATGTATCGATACA
1740595 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1742845 original size:21 final size:21
Alignment explanation
Indices: 1742812--1742856 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1742802 TTGCAAGTTG
*
1742812 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1742834 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1742854 AAA
1 AAA
1742857 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1744679 original size:15 final size:15
Alignment explanation
Indices: 1744659--1744689 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1744649 TAAAAATGTC
*
1744659 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1744674 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1744689 C
1 C
1744690 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1746539 original size:8 final size:8
Alignment explanation
Indices: 1746528--1746553 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1746518 ATGTTTTATT
1746528 TGATTTTG
1 TGATTTTG
1746536 TGATTTTG
1 TGATTTTG
1746544 TGATTTTG
1 TGATTTTG
1746552 TG
1 TG
1746554 TTGAATGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.27, T:0.62
Consensus pattern (8 bp):
TGATTTTG
Found at i:1746769 original size:20 final size:20
Alignment explanation
Indices: 1746690--1746769 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1746680 AATGTCCAAA
*
1746690 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1746710 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1746735 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1746755 TTGTATCGATACATT
1 ATGTATCGATACATT
1746770 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1746773 original size:13 final size:13
Alignment explanation
Indices: 1746755--1746793 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1746745 ACATTTTTCT
1746755 TTGTATCGATACA
1 TTGTATCGATACA
1746768 TTGTATCGATACA
1 TTGTATCGATACA
*
1746781 CTGTATCGATACA
1 TTGTATCGATACA
1746794 GGGTGATTAT
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:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1746938 original size:21 final size:21
Alignment explanation
Indices: 1746914--1746960 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1746904 AAATCTTTTG
1746914 CAAAAT-ACTT-GTTTTTCACTT
1 CAAAATAACTTCGTTTTTCA--T
1746935 C-AAATAACTTCGTTTTTCAT
1 CAAAATAACTTCGTTTTTCAT
1746955 CAAAAT
1 CAAAAT
1746961 CAGCATCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
20 6 0.26
21 9 0.39
22 8 0.35
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (21 bp):
CAAAATAACTTCGTTTTTCAT
Found at i:1746957 original size:20 final size:19
Alignment explanation
Indices: 1746916--1746958 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
1746906 ATCTTTTGCA
1746916 AAATACTTGTTTTTCACTTC
1 AAATACTTGTTTTTCAC-TC
1746936 AAATAACTTCGTTTTTCA-TC
1 AAAT-ACTT-GTTTTTCACTC
1746956 AAA
1 AAA
1746959 ATCAGCATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.43
21 4 0.19
22 8 0.38
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (19 bp):
AAATACTTGTTTTTCACTC
Found at i:1749273 original size:20 final size:19
Alignment explanation
Indices: 1749219--1749273 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1749209 AAAACCCTTA
*
1749219 AAAGTATCGATACACAATTC
1 AAAGTATCGATACA-TATTC
1749239 AAAGTATCGATACATATTGC
1 AAAGTATCGATACATATT-C
*
1749259 AATGTATCGATACAT
1 AAAGTATCGATACAT
1749274 GAAAAAGATG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.09
20 29 0.91
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
AAAGTATCGATACATATTC
Found at i:1749351 original size:13 final size:13
Alignment explanation
Indices: 1749333--1749358 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1749323 TACAGCAAGT
1749333 ATGTATCGATACA
1 ATGTATCGATACA
1749346 ATGTATCGATACA
1 ATGTATCGATACA
1749359 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1750466 original size:155 final size:155
Alignment explanation
Indices: 1750113--1750469 Score: 362
Period size: 155 Copynumber: 2.3 Consensus size: 155
1750103 GCTTTCAGAA
* * * * * * *
1750113 ATACCTTCGATGTAGAAA-TACTCGATACCCTTAAAGGACTTAAAAAGGATTATACATGGGGTGA
1 ATACCTTCAACGTA-AAAGTACACGATACCCCTAAAGGACTTAAAAAGGATTAGACATAGGATGA
* * *
1750177 ACCTATCCTAAATACCACCTTCAACATGAAAGCAAATCTAGTGATAACCCAGGGCTTGGTTCTAA
65 ACCTATCCTAAATACCACCTTCAACATAAAAGCAAATCTAGTGACAACCCAGGGCTTAGTTCTAA
* * **
1750242 AAAAATTATGAAAATGCTCTTAGGAG
130 AAAAATTATGAAAATACTCCTAAAAG
* * * ** *
1750268 ATACCTTCAATGTAAAAGTACCCGATACCTCTAAAAAACTTAAAAAGGATTAGAGATAGGATGAA
1 ATACCTTCAACGTAAAAGTACACGATACCCCTAAAGGACTTAAAAAGGATTAGACATAGGATGAA
* ** *
1750333 CCTATCCTAAATACCCACCTTCGACATAAAAGCGGA-CTCAGTGACAACCTAGGAG-TTAGTTCT
66 CCTATCCTAAATA-CCACCTTCAACATAAAAGCAAATCT-AGTGACAACCCAGG-GCTTAGTTCT
* **
1750396 -AGATTATTATGAAAATACTCCTAAAAG
128 AAAAAAATTATGAAAATACTCCTAAAAG
* * * * *
1750423 ATACTTTTAACGTAAAAGTATATGATACCCCTAAAGGATTTAAAAAG
1 ATACCTTCAACGTAAAAGTACACGATACCCCTAAAGGACTTAAAAAG
1750470 ATTGGTAAAG
Statistics
Matches: 164, Mismatches: 34, Indels: 8
0.80 0.17 0.04
Matches are distributed among these distances:
154 3 0.02
155 123 0.75
156 37 0.23
157 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.16, T:0.26
Consensus pattern (155 bp):
ATACCTTCAACGTAAAAGTACACGATACCCCTAAAGGACTTAAAAAGGATTAGACATAGGATGAA
CCTATCCTAAATACCACCTTCAACATAAAAGCAAATCTAGTGACAACCCAGGGCTTAGTTCTAAA
AAAATTATGAAAATACTCCTAAAAG
Found at i:1751862 original size:11 final size:10
Alignment explanation
Indices: 1751843--1751878 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
1751833 CCAAATATTT
1751843 TTTTTGTTTC
1 TTTTTGTTTC
1751853 TTTTTCGTTTC
1 TTTTT-GTTTC
1751864 TTTTTGTTCTC
1 TTTTTGTT-TC
1751875 TTTT
1 TTTT
1751879 CCTTCTTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.78
Consensus pattern (10 bp):
TTTTTGTTTC
Found at i:1751884 original size:20 final size:21
Alignment explanation
Indices: 1751843--1751885 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1751833 CCAAATATTT
*
1751843 TTTTTGTTTCTTTTTCGTTTC
1 TTTTTGTTTCTTTTTCGCTTC
1751864 TTTTTG-TTCTCTTTTC-CTTC
1 TTTTTGTTTCT-TTTTCGCTTC
1751884 TT
1 TT
1751886 CATCTCGTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.00, C:0.19, G:0.07, T:0.74
Consensus pattern (21 bp):
TTTTTGTTTCTTTTTCGCTTC
Found at i:1752097 original size:13 final size:13
Alignment explanation
Indices: 1752079--1752103 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1752069 ACTTTTTCTC
1752079 TTTTCTTCCTCTT
1 TTTTCTTCCTCTT
1752092 TTTTCTTCCTCT
1 TTTTCTTCCTCT
1752104 CGTCATGCTT
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTCTTCCTCTT
Found at i:1752305 original size:180 final size:181
Alignment explanation
Indices: 1752119--1752464 Score: 493
Period size: 180 Copynumber: 1.9 Consensus size: 181
1752109 TGCTTCTTTT
* * ** *
1752119 CTGATTTGGGGAGCTTTCTTTGCTGATTTCCAACACCAGAA-CTGAAACTAGTAGCTGTTGTTGC
1 CTGATTTGGGGAACTTTCTTTGCTGATTTCCAACACCAAAATC-GAAACTAGTAGCTGCCGCTGC
* *
1752183 TGGAGTT-CTAAA-CAACAGCTAAAGCTGCCGAACATTGCTTCTTTTCCAT-CATTTCCCCTTTT
65 TGGAGTTCCAAAACCAACAGCTAAAGCTGCCGAACATT-ATTCTTTTCCATCCATTTCCCC-TTT
* *
1752245 TTTTTCTTTTCTTTCTCCGTTCTCTTTTCTTCTTCTTCTACCCATGCTTAGTTA
128 TTTTCCTCTTCTTTCTCCGTTCTCTTTTCTTCTTCTTCTACCCATGCTTAGTTA
*
1752299 CTGATTTGGGGAACTTTCTTTGCTGATTTCCAGCACCAAAATCGAAACTAGTAGCTGCCGCTGCT
1 CTGATTTGGGGAACTTTCTTTGCTGATTTCCAACACCAAAATCGAAACTAGTAGCTGCCGCTGCT
* * * *
1752364 GGAGTTCCAAAACCAGCAGCTGAAGCTGCCGAACATTATTTTTTTCTATCCATTTCCCCTTTTTT
66 GGAGTTCCAAAACCAACAGCTAAAGCTGCCGAACATTATTCTTTTCCATCCATTTCCCCTTTTTT
* *
1752429 TCCTCTTCTTTCTTCTTTCTCTTTTCTTCTTCTTCT
131 TCCTCTTCTTTCTCCGTTCTCTTTTCTTCTTCTTCT
1752465 CCTTATGCTC
Statistics
Matches: 146, Mismatches: 16, Indels: 7
0.86 0.09 0.04
Matches are distributed among these distances:
180 63 0.43
181 52 0.36
182 31 0.21
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.42
Consensus pattern (181 bp):
CTGATTTGGGGAACTTTCTTTGCTGATTTCCAACACCAAAATCGAAACTAGTAGCTGCCGCTGCT
GGAGTTCCAAAACCAACAGCTAAAGCTGCCGAACATTATTCTTTTCCATCCATTTCCCCTTTTTT
TCCTCTTCTTTCTCCGTTCTCTTTTCTTCTTCTTCTACCCATGCTTAGTTA
Found at i:1752649 original size:22 final size:22
Alignment explanation
Indices: 1752611--1752662 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
1752601 TTTTCGTTGT
*
1752611 TTGCTT-CTTTAGCTGCTACCA
1 TTGCTTGCTTCAGCTGCTACCA
* *
1752632 TTGCTTGCTTCAGCTGCTGCCT
1 TTGCTTGCTTCAGCTGCTACCA
1752654 TTGC-TGCTT
1 TTGCTTGCTT
1752663 GTTTCGCTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 11 0.41
22 16 0.59
ACGTcount: A:0.08, C:0.29, G:0.19, T:0.44
Consensus pattern (22 bp):
TTGCTTGCTTCAGCTGCTACCA
Found at i:1752792 original size:14 final size:14
Alignment explanation
Indices: 1752768--1752801 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1752758 TTTTTTCATC
*
1752768 CTTTTTCTTTTTTT
1 CTTTTTGTTTTTTT
1752782 -TTTTTGTTTTTTT
1 CTTTTTGTTTTTTT
1752795 CTTTTTG
1 CTTTTTG
1752802 ATTTGATTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.00, C:0.09, G:0.06, T:0.85
Consensus pattern (14 bp):
CTTTTTGTTTTTTT
Found at i:1752944 original size:14 final size:13
Alignment explanation
Indices: 1752912--1752960 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
1752902 TAATTATATC
1752912 ATAAAAATT-AAT
1 ATAAAAATTAAAT
1752924 A-AAAAATTAAATT
1 ATAAAAATTAAA-T
*
1752937 ATAAAAATTAAAA
1 ATAAAAATTAAAT
*
1752950 ATTAAAATTAA
1 ATAAAAATTAA
1752961 GATAAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 7 0.22
12 3 0.09
13 12 0.38
14 10 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
ATAAAAATTAAAT
Found at i:1752951 original size:16 final size:17
Alignment explanation
Indices: 1752913--1752953 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
1752903 AATTATATCA
1752913 TAAAAATTAATAAAAAAT
1 TAAAAATT-ATAAAAAAT
1752931 T--AAATTAT-AAAAAT
1 TAAAAATTATAAAAAAT
1752945 TAAAAATTA
1 TAAAAATTA
1752954 AAATTAAGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 6
0.78 0.00 0.22
Matches are distributed among these distances:
14 7 0.33
15 2 0.10
16 11 0.52
18 1 0.05
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
TAAAAATTATAAAAAAT
Found at i:1752965 original size:25 final size:25
Alignment explanation
Indices: 1752903--1752967 Score: 62
Period size: 25 Copynumber: 2.6 Consensus size: 25
1752893 TAATTTGTAT
* * *
1752903 AATTATATCATAAAAATTAATAAAA
1 AATTAAATGATAAAAATTAAAAAAA
*
1752928 AATTAAATTATAAAAATTAAAAATTAA
1 AATTAAATGATAAAAATTAAAAA--AA
1752955 AATT-AA-GATAAAA
1 AATTAAATGATAAAA
1752968 TTTATATAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 26 0.76
26 2 0.06
27 6 0.18
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (25 bp):
AATTAAATGATAAAAATTAAAAAAA
Found at i:1753445 original size:20 final size:22
Alignment explanation
Indices: 1753403--1753446 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 22
1753393 TCCGTATTTC
*
1753403 AAAAATAGAAAAATTTCAAGAA
1 AAAAATAGAAAAATCTCAAGAA
*
1753425 AAAAATA-AAAAA-CTCATGAA
1 AAAAATAGAAAAATCTCAAGAA
1753445 AA
1 AA
1753447 TGAATGAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 5 0.25
22 7 0.35
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.16
Consensus pattern (22 bp):
AAAAATAGAAAAATCTCAAGAA
Found at i:1753506 original size:162 final size:162
Alignment explanation
Indices: 1753169--1753774 Score: 701
Period size: 163 Copynumber: 3.7 Consensus size: 162
1753159 ACAGTATTAT
* * * * * * *
1753169 ATAAGTTTTAAAAAATTATAAACCAAGAAAAATCCCTCGAAAAAATTCACGGAGAAGAAAA-TTC
1 ATAAATTTTAAAAAA-TAAAAATCAAG-AAAATCTCTC-AAAAAATT-ACGAAGTAGAAAACTCC
* * * *** * * * **
1753233 G-ATTTCTCAAAAAAAGTAGAATTTCAAAGAAAAAAATCTGAAACTCATGAAAGTAAATTAA-AA
62 GTA-TT-TCAAAAATAGAAAAATTTC-AAGAAAAAAATAAAAAACTCATGAAAATGAATGAATCT
* **
1753296 TTTCAAACTGAA-TTAATAT-AAATTAAATAAAAATATTTG
124 TTTAAAACT-AATTTAATATGAAA-TAAATAATGATATTTG
* *
1753335 ATGAATTTTAAAAAGTAAAAA-CTAAGAAAGATCTC-CAAAAAATTACGAAGTAGAAAACTCCGT
1 ATAAATTTTAAAAAATAAAAATC-AAGAAA-ATCTCTCAAAAAATTACGAAGTAGAAAACTCCGT
1753398 ATTTCAAAAATAGAAAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATCTTTTAA
64 ATTTCAAAAATAGAAAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATCTTTTAA
1753463 AACTAATTTAATATGAAATAAATAATGATATTTG
129 AACTAATTTAATATGAAATAAATAATGATATTTG
* *
1753497 ATAAATTTTAAAAAATAAAAATCAAGCAAATTCTCTCAAAAAATTACGAAGTAGAAAACTCTGTA
1 ATAAATTTTAAAAAATAAAAATCAAG-AAAATCTCTCAAAAAATTACGAAGTAGAAAACTCCGTA
*
1753562 TTTCAAAAATAGAAAAATTTCAAGAAAAAAATAAAAGACTCATGAAAATGAATGAATCTTTTAAA
65 TTTCAAAAATAGAAAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATCTTTTAAA
*
1753627 ACTGATTTAATATGAAATAAATAATGATATTTG
130 ACTAATTTAATATGAAATAAATAATGATATTTG
* * * **
1753660 ATAAATTTTAAAAAATAAAAATCAAGAAAATTCCCTCAAAAAATTACAAAGAAGAAAACAACGTA
1 ATAAATTTTAAAAAATAAAAATCAAGAAAA-TCTCTCAAAAAATTACGAAGTAGAAAACTCCGTA
* *
1753725 TTTCCAAAAA-A-AGAAATTTTAAGGAAAAAAAT-AAAAACTCATGAAAATGA
65 TTT-CAAAAATAGAAAAATTTCAA-GAAAAAAATAAAAAACTCATGAAAATGA
1753775 TTGAGTTTTT
Statistics
Matches: 389, Mismatches: 38, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
161 31 0.08
162 111 0.29
163 211 0.54
164 12 0.03
165 12 0.03
166 12 0.03
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.26
Consensus pattern (162 bp):
ATAAATTTTAAAAAATAAAAATCAAGAAAATCTCTCAAAAAATTACGAAGTAGAAAACTCCGTAT
TTCAAAAATAGAAAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATCTTTTAAAA
CTAATTTAATATGAAATAAATAATGATATTTG
Found at i:1753864 original size:162 final size:159
Alignment explanation
Indices: 1753169--1753881 Score: 643
Period size: 163 Copynumber: 4.4 Consensus size: 159
1753159 ACAGTATTAT
* * * * ** **
1753169 ATAAGTTTTAAAAAATTATAAACCAAGAAAAATCCCTCGAAAAAATTCACGGAGAAGAAAATTCG
1 ATAAATTTTAAAAAA-TAAAAATCAAGAAAATTCCC-C-AAAAAATT-ACAAAGAAGAAAACACG
* * * ** * * * **
1753234 -ATTTCTCAAAAAAAGTAGAATTTCAAAGAAAAAAATCTGAAACTCATGAAAGTAAATTAA-AAT
62 TA-TT-TCAAAAATAGAAAAATTTC-AAGAAAAAAAT-AAAAACTCATGAAAATGAATGAATCTT
* * **
1753297 TTCAAACTGAATTAATAT-AAATTAAATAAAAATATTTG
123 TTAAAACT-ATTTAATATGAAA-TAAATAATGATATTTG
* * * * * *
1753335 ATGAATTTTAAAAAGTAAAAA-CTAAGAAAGA-TCTCCAAAAAATTACGAAGTAGAAAACTCCGT
1 ATAAATTTTAAAAAATAAAAATC-AAGAAA-ATTCCCCAAAAAATTACAAAGAAGAAAAC-ACGT
1753398 ATTTCAAAAATAGAAAAATTTCAAGAAAAAAATAAAAAACTCATGAAAATGAATGAATCTTTTAA
63 ATTTCAAAAATAGAAAAATTTCAAGAAAAAAAT-AAAAACTCATGAAAATGAATGAATCTTTTAA
1753463 AACTAATTTAATATGAAATAAATAATGATATTTG
127 AACT-ATTTAATATGAAATAAATAATGATATTTG
* * * * *
1753497 ATAAATTTTAAAAAATAAAAATCAAGCAAATTCTCTCAAAAAATTACGAAGTAGAAAACTCTGTA
1 ATAAATTTTAAAAAATAAAAATCAAGAAAATTC-CCCAAAAAATTACAAAGAAGAAAACAC-GTA
1753562 TTTCAAAAATAGAAAAATTTCAAGAAAAAAATAAAAGACTCATGAAAATGAATGAATCTTTTAAA
64 TTTCAAAAATAGAAAAATTTCAAGAAAAAAATAAAA-ACTCATGAAAATGAATGAATCTTTTAAA
1753627 ACTGATTTAATATGAAATAAATAATGATATTTG
128 ACT-ATTTAATATGAAATAAATAATGATATTTG
1753660 ATAAATTTTAAAAAATAAAAATCAAGAAAATTCCCTCAAAAAATTACAAAGAAGAAAACAACGTA
1 ATAAATTTTAAAAAATAAAAATCAAGAAAATTCCC-CAAAAAATTACAAAGAAGAAAAC-ACGTA
* * * * *
1753725 TTTCCAAAAA-A-AGAAATTTTAAGGAAAAAAATAAAAACTCATGAAAATGATTGAGT-TTTTGC
64 TTT-CAAAAATAGAAAAATTTCAA-GAAAAAAATAAAAACTCATGAAAATGAATGAATCTTTT-A
* * * * *
1753787 AAACTACTTTAAT-TGTGATTAAACAATAATATTTA
126 AAACTA-TTTAATATG-AAATAAATAATGATATTTG
** * ** * * *
1753822 AGGAATTTTAATATTTGAAATTCAAGAAAATTCCACCAAAAAATATACAAATAAAGAAAA
1 ATAAATTTTAAAAAATAAAAATCAAGAAAATTCC-CCAAAAAAT-TACAAA-GAAGAAAA
1753882 ACTTGTGTTT
Statistics
Matches: 471, Mismatches: 55, Indels: 44
0.83 0.10 0.08
Matches are distributed among these distances:
161 37 0.08
162 176 0.37
163 214 0.45
164 17 0.04
165 14 0.03
166 13 0.03
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.27
Consensus pattern (159 bp):
ATAAATTTTAAAAAATAAAAATCAAGAAAATTCCCCAAAAAATTACAAAGAAGAAAACACGTATT
TCAAAAATAGAAAAATTTCAAGAAAAAAATAAAAACTCATGAAAATGAATGAATCTTTTAAAACT
ATTTAATATGAAATAAATAATGATATTTG
Found at i:1755354 original size:13 final size:13
Alignment explanation
Indices: 1755336--1755392 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1755326 CATAAAGTGT
1755336 TGTATCGATACAA
1 TGTATCGATACAA
1755349 TGTATCGATACATAA
1 TGTATCGATAC--AA
1755364 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1755381 TGTATCGATACA
1 TGTATCGATACA
1755393 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1755371 original size:32 final size:32
Alignment explanation
Indices: 1755316--1755416 Score: 175
Period size: 32 Copynumber: 3.1 Consensus size: 32
1755306 TTCAACGATT
1755316 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACAT-AAGTGTTGTATCGATACAA
1755349 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
* *
1755381 TGTATCGATACATAAGTTTTGTATCAATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1755413 TGTA
1 TGTA
1755417 AGCTACTGCC
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 53 0.80
33 13 0.20
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1755373 original size:19 final size:18
Alignment explanation
Indices: 1755314--1755411 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
1755304 ATTTCAACGA
1755314 TTTGTATCGATACATAAAG
1 TTTGTATCGATACAT-AAG
1755333 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1755349 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1755365 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1755381 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
*
1755397 TTTTGTATCAATACA
1 -TTTGTATCGATACA
1755412 ATGTAAGCTA
Statistics
Matches: 65, Mismatches: 1, Indels: 26
0.71 0.01 0.28
Matches are distributed among these distances:
13 22 0.34
15 4 0.06
17 4 0.06
19 23 0.35
20 12 0.18
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1755472 original size:13 final size:13
Alignment explanation
Indices: 1755454--1755478 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1755444 ATTACTCAAA
1755454 TGTATCGATACAT
1 TGTATCGATACAT
1755467 TGTATCGATACA
1 TGTATCGATACA
1755479 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:1755531 original size:52 final size:52
Alignment explanation
Indices: 1755487--1755615 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1755477 CACTAATCTT
*
1755487 TGTATCGATACATGCAGGTAAATTTGCCCAGATGTATCGATACACTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1755539 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1755591 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1755616 TCATATTTTA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 75 1.00
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1760047 original size:52 final size:51
Alignment explanation
Indices: 1759968--1760221 Score: 328
Period size: 52 Copynumber: 4.9 Consensus size: 51
1759958 CTAGCCATTC
* * *
1759968 CTGATCGCCACCATGACATCATCATTATTAGTGACACCAAGTCACCCAAACT
1 CTGATCACCACCAT-ACATCATCATTATCAGTGACACCAAGTCACCCGAACT
* * *
1760020 TTGATCACCACCATGACATCATCATTATCAGTGACACTAAGTCACCTGAACT
1 CTGATCACCACCAT-ACATCATCATTATCAGTGACACCAAGTCACCCGAACT
* *
1760072 CTGATCACCACCACAACATCATCATTATCAGTGACACTAAGTCACCCGAACT
1 CTGATCACCACCA-TACATCATCATTATCAGTGACACCAAGTCACCCGAACT
** *
1760124 CTGATTGCAACCATAGCATCATCATTATCAGTGACACCAAGTCACCCGAACT
1 CTGATCACCACCATA-CATCATCATTATCAGTGACACCAAGTCACCCGAACT
* ** *
1760176 CTAATTTCCACCATAGCATCACCATTATCAGTGACACCAAGTCACC
1 CTGATCACCACCATA-CATCATCATTATCAGTGACACCAAGTCACC
1760222 TTTATGAACT
Statistics
Matches: 182, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
51 1 0.01
52 181 0.99
ACGTcount: A:0.33, C:0.32, G:0.11, T:0.24
Consensus pattern (51 bp):
CTGATCACCACCATACATCATCATTATCAGTGACACCAAGTCACCCGAACT
Found at i:1761128 original size:21 final size:21
Alignment explanation
Indices: 1761083--1761130 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
1761073 AGTTTTGGCA
**
1761083 TCCTCCACCTTTTTACCTGCC
1 TCCTCCACCTTTTTACCCACC
* *
1761104 TCCTCCACTTTTTTACCCACT
1 TCCTCCACCTTTTTACCCACC
1761125 TCCTCC
1 TCCTCC
1761131 TTAACTTGAC
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:0.10, C:0.48, G:0.02, T:0.40
Consensus pattern (21 bp):
TCCTCCACCTTTTTACCCACC
Found at i:1762870 original size:122 final size:122
Alignment explanation
Indices: 1762648--1762881 Score: 310
Period size: 122 Copynumber: 1.9 Consensus size: 122
1762638 GAAATAAAAA
* * * *
1762648 TCGGGGTTGGAGTATCCCCTCGAAAATAACAGGATTGGAGTATCCCTGATTATAGAAACTCGGTA
1 TCGGGGTTGGAGTATCCCCTAGAAAATAACAGGATTAGAGTATCCCCGATTATAGAAAATCGGTA
* * * *
1762713 TTTTGAAAATAAAATCAAAGTTTGAGTAACCCCGATTGTGGAAAATTGGTAATAAAG
66 TTTTGAAAATAAAACCAAAGTTGGAATAACCCCGATTATGGAAAATTGGTAATAAAG
* * *
1762770 TCGGGGTTGGAGTATCCCCTTAG-AAATAACGGGGTTAGAGTATCCCCGATTAT-GATAAATTGG
1 TCGGGGTTGGAGTATCCCC-TAGAAAATAACAGGATTAGAGTATCCCCGATTATAGA-AAATCGG
* * *
1762833 TGTTTTGAAAATAAAACCAAAGTTGGAATATCTCCGATTATGGAAAATT
64 TATTTTGAAAATAAAACCAAAGTTGGAATAACCCCGATTATGGAAAATT
1762882 CGTATTTTAG
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
121 2 0.02
122 92 0.96
123 2 0.02
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.29
Consensus pattern (122 bp):
TCGGGGTTGGAGTATCCCCTAGAAAATAACAGGATTAGAGTATCCCCGATTATAGAAAATCGGTA
TTTTGAAAATAAAACCAAAGTTGGAATAACCCCGATTATGGAAAATTGGTAATAAAG
Found at i:1766327 original size:28 final size:28
Alignment explanation
Indices: 1766263--1766339 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 28
1766253 GGAATAAAAT
***
1766263 CGGGGTTGGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
* * * *
1766291 TGAGATTGGAGTATCCCCGATGACATAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
1766319 CGGGGTTGGAGTA-CCTCCGAT
1 CGGGGTTGGAGTATCC-CCGAT
1766340 TATGAAAAAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 2 0.05
28 36 0.95
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1768744 original size:20 final size:19
Alignment explanation
Indices: 1768719--1768833 Score: 131
Period size: 20 Copynumber: 5.8 Consensus size: 19
1768709 AAAATGCCTG
* *
1768719 AATGTATTGATACATTGTAA
1 AATGTATCGATACAATG-AA
*
1768739 AATGTATCGATACAATGAGC
1 AATGTATCGATACAATGA-A
1768759 AATGTATCGATACAATGCAA
1 AATGTATCGATACAATG-AA
* * *
1768779 AATATATTGATAGAATGCAA
1 AATGTATCGATACAATG-AA
1768799 AATGTATCGATACAATGAA
1 AATGTATCGATACAATGAA
1768818 CAATGTATCGATACAA
1 -AATGTATCGATACAA
1768834 ATTGTGAAAA
Statistics
Matches: 82, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.04
20 78 0.95
21 1 0.01
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (19 bp):
AATGTATCGATACAATGAA
Found at i:1770830 original size:20 final size:22
Alignment explanation
Indices: 1770792--1770835 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
1770782 AGAAAATGAA
1770792 AAAAAACTGAAGAACGATACCC
1 AAAAAACTGAAGAACGATACCC
*
1770814 AAAAAACT-AA-AATGATACCC
1 AAAAAACTGAAGAACGATACCC
1770834 AA
1 AA
1770836 CCGTTACGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 11 0.52
21 2 0.10
22 8 0.38
ACGTcount: A:0.59, C:0.20, G:0.09, T:0.11
Consensus pattern (22 bp):
AAAAAACTGAAGAACGATACCC
Found at i:1773987 original size:21 final size:21
Alignment explanation
Indices: 1773945--1773984 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
1773935 ATTAGACATG
1773945 TTAAAATGCATGGAACATGGC
1 TTAAAATGCATGGAACATGGC
1773966 TTAAAATGCAT-GAACATGG
1 TTAAAATGCATGGAACATGG
1773985 GCTGTTTAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (21 bp):
TTAAAATGCATGGAACATGGC
Found at i:1774943 original size:52 final size:51
Alignment explanation
Indices: 1774886--1775056 Score: 193
Period size: 52 Copynumber: 3.4 Consensus size: 51
1774876 GGATATATTG
* * *
1774886 ATACAATAAAAAATGTATCGATACATTTGGTTCAAAAACCCAAAATGTATCG
1 ATACAATGAAAAATGTATCGATACATTTGG-TCAAAAACCCAGAATGTATCA
* * * *
1774938 ATACAATGAAGAATTTATCGATGCATTCGGGTCAAAAACCCAGAATGTATCA
1 ATACAATGAAAAATGTATCGATACATT-TGGTCAAAAACCCAGAATGTATCA
* * * * * *
1774990 ACACAATGAAAAATGTATCGATATATTTAGAC-CAAACCTAGAATGTATCA
1 ATACAATGAAAAATGTATCGATACATTTGGTCAAAAACCCAGAATGTATCA
1775040 ATACAAT-AAAAATGTAT
1 ATACAATGAAAAATGTAT
1775057 TGACACATCC
Statistics
Matches: 100, Mismatches: 18, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
49 10 0.10
50 22 0.22
51 2 0.02
52 64 0.64
53 2 0.02
ACGTcount: A:0.46, C:0.15, G:0.13, T:0.26
Consensus pattern (51 bp):
ATACAATGAAAAATGTATCGATACATTTGGTCAAAAACCCAGAATGTATCA
Found at i:1777050 original size:23 final size:23
Alignment explanation
Indices: 1777014--1777059 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1777004 TATTGATGTC
* *
1777014 CATTGGTGATGATGTAGAGATCT
1 CATTGGCGACGATGTAGAGATCT
1777037 CATTGGCGACGATGTAGAGATCT
1 CATTGGCGACGATGTAGAGATCT
1777060 TATTAGCTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.30
Consensus pattern (23 bp):
CATTGGCGACGATGTAGAGATCT
Found at i:1778527 original size:166 final size:163
Alignment explanation
Indices: 1778099--1778694 Score: 570
Period size: 166 Copynumber: 3.7 Consensus size: 163
1778089 TCGAGAGGAT
* * * * * * *
1778099 TTTTCCTAATTTTTAATTTTTAAAATTCATCAAATATTATTATTTATTTTC-TATTAAATCGGTT
1 TTTT-CTAGTTTTCAATTTTTAAAATTCATCAAACATCATCATTTA-TTTCATATTAATTCAGTT
* * ** * * *
1778163 TGT-AAAAATTAATTCATTTTCATAAGTCCTTG-A-TTTTTTCCTTGAAATTTTCCTTTTTCTGA
64 T-TCAAAAATTCATTCA-TTTCATGAGTTTTTGAATTTTTTTCTTTGAAATTCT-CTTTTTCCGA
* *
1778225 AATACGGTATTTACTACTCCGTAATTTTTTTTGAGGGGA
126 AATACAGTATTTTCTACTCCGTAATTTTTTTT-AGGGGA
* * * * *
1778264 TTTTTCTAGGTTTTCAATTTTTAAAATTCATCAAATATTATCATATATTTCATATTAATTTAGTG
1 -TTTTCTA-GTTTTCAATTTTTAAAATTCATCAAACATCATCATTTATTTCATATTAATTCAGTT
*
1778329 TTCAAAAATTCATTCATTTTCATGAGTTTTTGAATTTTTTTCTTTGAAATTCTCTTTTTCCAAAA
64 TTCAAAAATTCATTCA-TTTCATGAGTTTTTGAATTTTTTTCTTTGAAATTCTCTTTTTCCGAAA
*
1778394 TACAGTTTTTTCTACTCCGTAATTTTTTTTAGGGGA
128 TACAGTATTTTCTACTCCGTAATTTTTTTTAGGGGA
* *
1778430 CTTTTCCTAGTTTTCAATTTTCAAAATTCATCAAACATCATCATTTGA-TTCATATTAATTCATT
1 -TTTT-CTAGTTTTCAATTTTTAAAATTCATCAAACATCATCATTT-ATTTCATATTAATTCAGT
* * * *
1778494 TTTCAAATATTCATTCATTGTCATGATTTTTTG-ATTTTTTTC-TTGTAACTTCCCTTCTTT-CG
63 TTTCAAAAATTCATTCATT-TCATGAGTTTTTGAATTTTTTTCTTTG-AAATTCTCTT-TTTCCG
* * * *
1778556 AAATA-TGATATTTTCTACTTCGTAA-ATTTTTCA----A
125 AAATACAG-TATTTTCTACTCCGTAATTTTTTTTAGGGGA
* *
1778590 ------GGTTTTCAATTTTTAAAATTCATCAAACATCATTATTTATTTCATATTAATTCAGTTTT
1 TTTTCTAGTTTTCAATTTTTAAAATTCATCAAACATCATCATTTATTTCATATTAATTCAGTTTT
1778649 CAAAAATTCATTCATCTTCATGAGTTTTTGAA--TTTTTCTTTGAAAT
66 CAAAAATTCATTCAT-TTCATGAGTTTTTGAATTTTTTTCTTTGAAAT
1778695 CCCCATTTTC
Statistics
Matches: 371, Mismatches: 44, Indels: 45
0.81 0.10 0.10
Matches are distributed among these distances:
151 10 0.03
152 82 0.22
153 2 0.01
160 1 0.00
164 10 0.03
165 48 0.13
166 160 0.43
167 42 0.11
168 16 0.04
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (163 bp):
TTTTCTAGTTTTCAATTTTTAAAATTCATCAAACATCATCATTTATTTCATATTAATTCAGTTTT
CAAAAATTCATTCATTTCATGAGTTTTTGAATTTTTTTCTTTGAAATTCTCTTTTTCCGAAATAC
AGTATTTTCTACTCCGTAATTTTTTTTAGGGGA
Found at i:1778724 original size:152 final size:152
Alignment explanation
Indices: 1778439--1778712 Score: 387
Period size: 152 Copynumber: 1.8 Consensus size: 152
1778429 ACTTTTCCTA
* *
1778439 GTTTTCAATTTTCAAAATTCATCAAACATCATCATTTGATTCATATTAATTCATTTTTCAAATAT
1 GTTTTCAATTTTCAAAATTCATCAAACATCATCATTTGATTCATATTAATTCAGTTTTCAAAAAT
* * * * *
1778504 TCATTCATTGTCATGATTTTTTGATTTTTTTCTTGTAACTTCCCTTCTTTCGAAATATGATATTT
66 TCATTCATTGTCATGAGTTTTTGATTTTTCTCTTGTAAATCCCCTTCTTTCGAAAAATGATATTT
1778569 TCTACTTCGTAAATTTTTCAAG
131 TCTACTTCGTAAATTTTTCAAG
* *
1778591 GTTTTCAATTTTTAAAATTCATCAAACATCATTATTT-ATTTCATATTAATTCAGTTTTCAAAAA
1 GTTTTCAATTTTCAAAATTCATCAAACATCATCATTTGA-TTCATATTAATTCAGTTTTCAAAAA
1778655 TTCATTCATCT-TCATGAGTTTTTGAATTTTTCT-TTG-AAATCCCCATT-TTCTCGAAAAA
65 TTCATTCAT-TGTCATGAGTTTTTG-ATTTTTCTCTTGTAAATCCCC-TTCTT-TCGAAAAA
1778713 CTGAGTTTTC
Statistics
Matches: 108, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
151 9 0.08
152 91 0.84
153 8 0.07
ACGTcount: A:0.30, C:0.16, G:0.06, T:0.49
Consensus pattern (152 bp):
GTTTTCAATTTTCAAAATTCATCAAACATCATCATTTGATTCATATTAATTCAGTTTTCAAAAAT
TCATTCATTGTCATGAGTTTTTGATTTTTCTCTTGTAAATCCCCTTCTTTCGAAAAATGATATTT
TCTACTTCGTAAATTTTTCAAG
Found at i:1778851 original size:318 final size:317
Alignment explanation
Indices: 1778263--1778852 Score: 663
Period size: 318 Copynumber: 1.9 Consensus size: 317
1778253 TTTTGAGGGG
* * * *
1778263 ATTTTTCTAGGTTTTCAATTTTTAAAATTCATCAAATATTATCATATATTTCATATTAATTTAGT
1 ATTTTTCAAGGTTTTCAATTTTTAAAATTCATCAAACATCATCATATATTTCATATTAATTCAGT
* * *
1778328 GTTCAAAAATTCATTCATTTTCATGAGTTTTTGAATTTTTTTCTTTGAAATTCTCTTTTTCCAAA
66 GTTCAAAAATTCATTCATCTTCATGAGTTTTTGAA-TTTTTTCTTTGAAATCCCCTTTTTCCAAA
** * * ** * **
1778393 ATACAGTTTTTTCTACTCCGTAATTTTTTTTAGGGGACTTTTCCTAGTTTTCAATTTTCAAAATT
130 ATACAGAGTTTTCTACTCCATAATATTTTCGAGGGGACTTTTCCTAGTCTAAAATTTTCAAAATT
* * * * * * *
1778458 CATCAAACATCATCATTTGATTCATATTAATTCATTTTTCAAATATTCATTCATTGTCATGATTT
195 CATCAAACATCATCATTTGACTCACATTAATTCAGTTTTAAAAAATTAATTCATTGTCATGATCT
1778523 TTTGATTTTTTTCTTGTAACTTCCCTTCTTTCGAAATATGATATTTTCTACTTCGTAA
260 TTTGATTTTTTTCTTGTAACTTCCCTTCTTTCGAAATATGATATTTTCTACTTCGTAA
* *
1778581 ATTTTTCAAGGTTTTCAATTTTTAAAATTCATCAAACATCATTATTTATTTCATATTAATTCAGT
1 ATTTTTCAAGGTTTTCAATTTTTAAAATTCATCAAACATCATCATATATTTCATATTAATTCAGT
* *
1778646 TTTCAAAAATTCATTCATCTTCATGAGTTTTTGAA-TTTTTCTTTGAAATCCCCATTTTCTCGAA
66 GTTCAAAAATTCATTCATCTTCATGAGTTTTTGAATTTTTTCTTTGAAATCCCC-TTTT-TCCAA
* * * * * * *
1778710 AA-ACTGAGTTTTCTATTCTATAAATATTTTCGGGGGGA-TTTTCTTTGATCTAAAATTTTTAAA
129 AATACAGAGTTTTCTACTCCAT-AATATTTTCGAGGGGACTTTTCCTAG-TCTAAAATTTTCAAA
* * ** * * * *
1778773 ATGT-ATCTAATATTGTCA-TTGAACTCCCATTAGTTTAGTTTTAAAAAATTTAATTTATT-TCA
192 AT-TCATCAAACATCATCATTTG-ACTCACATTAATTCAGTTTTAAAAAA-TTAATTCATTGTCA
*
1778835 TTA-CTTTTGAATTTTTTT
254 TGATCTTTTG-ATTTTTTT
1778853 GTATATATTG
Statistics
Matches: 221, Mismatches: 43, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
316 16 0.07
317 32 0.14
318 164 0.74
319 9 0.04
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.50
Consensus pattern (317 bp):
ATTTTTCAAGGTTTTCAATTTTTAAAATTCATCAAACATCATCATATATTTCATATTAATTCAGT
GTTCAAAAATTCATTCATCTTCATGAGTTTTTGAATTTTTTCTTTGAAATCCCCTTTTTCCAAAA
TACAGAGTTTTCTACTCCATAATATTTTCGAGGGGACTTTTCCTAGTCTAAAATTTTCAAAATTC
ATCAAACATCATCATTTGACTCACATTAATTCAGTTTTAAAAAATTAATTCATTGTCATGATCTT
TTGATTTTTTTCTTGTAACTTCCCTTCTTTCGAAATATGATATTTTCTACTTCGTAA
Found at i:1780899 original size:154 final size:156
Alignment explanation
Indices: 1780670--1781322 Score: 555
Period size: 154 Copynumber: 4.2 Consensus size: 156
1780660 CTTTCACATT
* * * * **
1780670 GAAAGTAT-CCCTATAGGGGTATTTTCGTAATTTTATAAAATCGAGTCCTAGGTTGCCATC-AGG
1 GAAAGTATCCCCTA-A-GGGCATTTTCGTAATTTTA-AGAATCAACTCCTAGGTTATCATCGAGG
* * * * *
1780733 TCCGCTTCTATGCTGAAGGTAGGTATTTAGGAT-GGTTTCAT-CTTTTTAAAGTCCTTTTTAAGT
63 TCCGCTTTTATGCCGAAGATGGGTATTTAGGATAGG-TTCATCCTTTTTATAGTCCTTTTTAAGT
* *
1780796 CCTTTAGGGGTACCAAGATACTTTCAACTC
127 CTTTTAGGGGTACCGAGATACTTTCAACTC
* *
1780826 GAAAGAATCCCCTAAGGGCATTTTCGTAACTTTAAGAATCAACTCCTAGGTTATCATCGA-GTCC
1 GAAAGTATCCCCTAAGGGCATTTTCGTAATTTTAAGAATCAACTCCTAGGTTATCATCGAGGTCC
* * * * * *
1780890 GATTTTATGCTGAAGATGGGCATTTATGATAGGTTCATCCGTTTTATGAGT-CTTTTTAAGTTTT
66 GCTTTTATGCCGAAGATGGGTATTTAGGATAGGTTCATCCTTTTTAT-AGTCCTTTTTAAGTCTT
* **
1780954 TTAGGGTTACCGAGATA-TTTTTACGTC
130 TTAGGGGTACCGAGATACTTTCAAC-TC
* * * * * *
1780981 GAAGGTAT-ACCTATAGAGACATTTTCGTAATTTTCAA-AACCAACTCCTATGTCATCATCGA-G
1 GAAAGTATCCCCTA-AG-GGCATTTTCGTAATTTT-AAGAATCAACTCCTAGGTTATCATCGAGG
* * * *
1781043 TTCGCTTTTATGCCGAAGGTGGGTATTTAGGATAGGTTCATCCCTTTTATAGTCTTTTTTAAGTC
63 TCCGCTTTTATGCCGAAGATGGGTATTTAGGATAGGTTCATCCTTTTTATAGTCCTTTTTAAGTC
* **
1781108 TTTTA--GGTACCGGGATACTTTCATGTC
128 TTTTAGGGGTACCGAGATACTTTCAACTC
* * * * * * * * * *
1781135 GAAAGTATCCTCTAGGGGTATTTTGGTAATTTTTTAGAATCCAGTCCTAGGCTATTA-CCAGGTC
1 GAAAGTATCCCCTAAGGGCATTTTCGTAA-TTTTAAGAATCAACTCCTAGGTTATCATCGAGGTC
* * *
1781199 TGCTTTTATGCCGAAAATGGGTATTTAGGATAGGTTCAT-CTCTTTTATAGTCCTTTTGAAGTCT
65 CGCTTTTATGCCGAAGATGGGTATTTAGGATAGGTTCATCCT-TTTTATAGTCCTTTTTAAGTCT
* * * **
1781263 TTTAGAGGTATCG-GGTAC-TTCTATGTC
129 TTTAGGGGTACCGAGATACTTTC-AACTC
* * * *
1781290 GAAGGTATCTCCTAAGGGAATTTTCATAATTTT
1 GAAAGTATCCCCTAAGGGCATTTTCGTAATTTT
1781323 TCTTGAACTT
Statistics
Matches: 401, Mismatches: 77, Indels: 40
0.77 0.15 0.08
Matches are distributed among these distances:
153 14 0.03
154 167 0.42
155 102 0.25
156 111 0.28
157 7 0.02
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (156 bp):
GAAAGTATCCCCTAAGGGCATTTTCGTAATTTTAAGAATCAACTCCTAGGTTATCATCGAGGTCC
GCTTTTATGCCGAAGATGGGTATTTAGGATAGGTTCATCCTTTTTATAGTCCTTTTTAAGTCTTT
TAGGGGTACCGAGATACTTTCAACTC
Found at i:1783848 original size:82 final size:82
Alignment explanation
Indices: 1783762--1783942 Score: 240
Period size: 82 Copynumber: 2.2 Consensus size: 82
1783752 GCAGTTAGAA
* * * *
1783762 TATCCCTTGAGATGGAAAAAATTTGATGTTTGGGAAATAAAAACAG-GGTTAGAGTA-TCTCCTC
1 TATCCCCTAAGATGAAAAAAATTTCATGTTTGGGAAA-AAAAAC-GTGGTTAGAGTATTCTCCTC
* *
1783825 AAAAATAATGGGATTGGAG
64 AAAAATAATGGAATTGAAG
* *
1783844 TATCCCCTAAGATGAAAAAAATTTCATGTTTGGGAAAAAAAACGTGGTTGGAGTATTCTTCTCAA
1 TATCCCCTAAGATGAAAAAAATTTCATGTTTGGGAAAAAAAACGTGGTTAGAGTATTCTCCTCAA
*
1783909 AAATGATGGAATTGAAG
66 AAATAATGGAATTGAAG
*
1783926 TATCCCCTAAAATGAAA
1 TATCCCCTAAGATGAAA
1783943 TTTTTTATGT
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
80 1 0.01
81 15 0.17
82 71 0.82
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (82 bp):
TATCCCCTAAGATGAAAAAAATTTCATGTTTGGGAAAAAAAACGTGGTTAGAGTATTCTCCTCAA
AAATAATGGAATTGAAG
Found at i:1784227 original size:78 final size:77
Alignment explanation
Indices: 1783970--1784237 Score: 274
Period size: 79 Copynumber: 3.5 Consensus size: 77
1783960 ATAAAATCGA
* * * * *
1783970 GGTTAGAGTATCCTCAAGATGAAAA-TTTGATGTTTTGAAAATAAAAACAGGGTTGGAATCCCCT
1 GGTTAGAGTATCCCCAAGATGAAAATTTTGATGTTTGGAAAATAAAAACAGAGTTGGAGTCTCCT
*
1784034 TGAAAATGGT-G
66 TGAAAATGATGG
* * * * * * *
1784045 GGTTGGAGTATCCCCGAGATGAAAAATTCGGTGTTTGGGAAATAAAAAC-GAGGTTGGAGTATTT
1 GGTTAGAGTATCCCCAAGATGAAAATTTTGATGTTTGGAAAATAAAAACAGA-GTTGGAG--TCT
*
1784109 CCTT-AGAAATAATGG
63 CCTTGA-AAATGATGG
* * * *
1784124 GGTTGGAGTATCCTCGAGATGAAAATTTTGATATTTGGAAAATAAAAACAGAGTTGGAGTCTCCT
1 GGTTAGAGTATCCCCAAGATGAAAATTTTGATGTTTGGAAAATAAAAACAGAGTTGGAGTCTCCT
1784189 TCGAAAATGATGG
66 T-GAAAATGATGG
* * *
1784202 GGTTAGAGCATCCCCAAGAAGAAAATTTTGGTGTTT
1 GGTTAGAGTATCCCCAAGATGAAAATTTTGATGTTT
1784238 TAGAAGTGAA
Statistics
Matches: 156, Mismatches: 28, Indels: 15
0.78 0.14 0.08
Matches are distributed among these distances:
75 23 0.15
76 25 0.16
77 7 0.04
78 47 0.30
79 52 0.33
80 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (77 bp):
GGTTAGAGTATCCCCAAGATGAAAATTTTGATGTTTGGAAAATAAAAACAGAGTTGGAGTCTCCT
TGAAAATGATGG
Found at i:1786654 original size:31 final size:31
Alignment explanation
Indices: 1786616--1786693 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
1786606 AATACATTAA
* *
1786616 AGAATGTATTGATACATTTAGGT-CAAAACCT
1 AGAATGTATCGATACATTT-GGTCCAAAACCC
*
1786647 AGAATGTATCGATAAATTTGGTCCAAAACCC
1 AGAATGTATCGATACATTTGGTCCAAAACCC
*
1786678 AAAATGTATCGATACA
1 AGAATGTATCGATACA
1786694 ATCAAGTATC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
30 3 0.07
31 38 0.93
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (31 bp):
AGAATGTATCGATACATTTGGTCCAAAACCC
Found at i:1787418 original size:18 final size:18
Alignment explanation
Indices: 1787395--1787457 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
1787385 AATGCAAATA
1787395 ATATTTTTATAATTAATT
1 ATATTTTTATAATTAATT
* *
1787413 ATATTTTAAAAATTAATT
1 ATATTTTTATAATTAATT
*
1787431 -TA-ATTTATAATATAAATT
1 ATATTTTTATAAT-T-AATT
1787449 ATTATTTTT
1 A-TATTTTT
1787458 TATTTGTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
16 6 0.18
17 3 0.09
18 20 0.59
20 2 0.06
21 3 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTTTTATAATTAATT
Found at i:1788315 original size:79 final size:79
Alignment explanation
Indices: 1788171--1788319 Score: 217
Period size: 79 Copynumber: 1.9 Consensus size: 79
1788161 ATATTGACTT
* *
1788171 TAAGATTAATCATCATTCACAAGTATAATTTTTACAATTTAAGGATAGGTCCTATACACACATAT
1 TAAGATTAATCATCATTCACAAGTATAATTTTCACAATTTAAGGATAAGTCCTATACACACATAT
1788236 ATATTTATCGATTC
66 ATATTTATCGATTC
* * * * * * *
1788250 TAAGCTTAATCATCATTCAGAGGTATAATTTTCACAATTTAAGGATAATTCGTATATACATATAT
1 TAAGATTAATCATCATTCACAAGTATAATTTTCACAATTTAAGGATAAGTCCTATACACACATAT
1788315 ATATT
66 ATATT
1788320 AATGATAATG
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
79 61 1.00
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.39
Consensus pattern (79 bp):
TAAGATTAATCATCATTCACAAGTATAATTTTCACAATTTAAGGATAAGTCCTATACACACATAT
ATATTTATCGATTC
Found at i:1788800 original size:2 final size:2
Alignment explanation
Indices: 1788788--1788839 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
1788778 TCACTTTTCC
*
1788788 AT AT GT 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
*
1788830 AA AT AT AT AT
1 AT AT AT AT AT
1788840 CAAGATGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1791602 original size:5 final size:5
Alignment explanation
Indices: 1791571--1791601 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1791561 ACCCTTATGG
*
1791571 TTTTA TTTTA TTTTA TTTTA TTTTA TATTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
1791602 AAAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:1792540 original size:31 final size:32
Alignment explanation
Indices: 1792463--1792541 Score: 83
Period size: 31 Copynumber: 2.5 Consensus size: 32
1792453 AAGCTTTTAG
*
1792463 ATAAAAATA-ATTTTAATAAATTTTTATTATTT
1 ATAAAAATATATTTT-ATAAATTTTAATTATTT
* * *
1792495 -TAAATATATAATTTT-TATATTTTAATTCTTT
1 ATAAAAATAT-ATTTTATAAATTTTAATTATTT
1792526 ATAAAAATATATTTTA
1 ATAAAAATATATTTTA
1792542 ATGTCAAATA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
31 25 0.66
32 8 0.21
33 5 0.13
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (32 bp):
ATAAAAATATATTTTATAAATTTTAATTATTT
Found at i:1792580 original size:15 final size:14
Alignment explanation
Indices: 1792560--1792595 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
1792550 TACTTAAAAA
1792560 TTTTTAAATTATAT
1 TTTTTAAATTATAT
*
1792574 TTTTT-TATTATAT
1 TTTTTAAATTATAT
1792587 TTTTTAAAT
1 TTTTTAAAT
1792596 ACGTACTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTTAAATTATAT
Found at i:1793893 original size:2 final size:2
Alignment explanation
Indices: 1793857--1793883 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1793847 GTGTGTGTAG
1793857 AT 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 AT A
1793884 AGAAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1798712 original size:15 final size:15
Alignment explanation
Indices: 1798692--1798783 Score: 54
Period size: 15 Copynumber: 6.5 Consensus size: 15
1798682 TTTAACTGAT
1798692 TTTTTATATATAAAA
1 TTTTTATATATAAAA
* *
1798707 TTTTTA-AT-TGATA
1 TTTTTATATATAAAA
*
1798720 -TTCTATATATAAAA
1 TTTTTATATATAAAA
*
1798734 TTTTTA-AT-TATAA
1 TTTTTATATATAAAA
*
1798747 -TTTTACATATTAAAA
1 TTTTTATATA-TAAAA
* *
1798762 -TTTTACAAATAAAA
1 TTTTTATATATAAAA
1798776 TTGTTTAT
1 TT-TTTAT
1798784 TAAATTTTTT
Statistics
Matches: 59, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
12 9 0.15
13 11 0.19
14 12 0.20
15 23 0.39
16 4 0.07
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTTTATATATAAAA
Found at i:1798766 original size:27 final size:27
Alignment explanation
Indices: 1798680--1798765 Score: 111
Period size: 27 Copynumber: 3.1 Consensus size: 27
1798670 AAAATAAACT
* *
1798680 TTTTTAACTGATTTTTTATATATAAAA
1 TTTTTAATTGATATTTTATATATAAAA
*
1798707 TTTTTAATTGATATTCTATATATAAAA
1 TTTTTAATTGATATTTTATATATAAAA
*
1798734 TTTTTAATT-ATAATTTTACATATTAAAA
1 TTTTTAATTGAT-ATTTTATATA-TAAAA
1798762 TTTT
1 TTTT
1798766 ACAAATAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 2 0.04
27 41 0.79
28 9 0.17
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.56
Consensus pattern (27 bp):
TTTTTAATTGATATTTTATATATAAAA
Found at i:1798830 original size:32 final size:32
Alignment explanation
Indices: 1798774--1798835 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
1798764 TTACAAATAA
* *
1798774 AATTGTTTATTAAATTTTTTACATATTAAACT
1 AATTGTTTATTAAAATTTTCACATATTAAACT
1798806 AATT-TTTATTTAAAATTTTCACATATTAAA
1 AATTGTTTA-TTAAAATTTTCACATATTAAA
1798836 TTCGCAGATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (32 bp):
AATTGTTTATTAAAATTTTCACATATTAAACT
Found at i:1801620 original size:2 final size:2
Alignment explanation
Indices: 1801613--1801640 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1801603 GGTACGTGGA
1801613 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
1801641 TATTGGTACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1801803 original size:9 final size:9
Alignment explanation
Indices: 1801782--1801822 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
1801772 AAAAATACCT
1801782 AATTGAATT-
1 AATT-AATTA
1801791 AATTAATTA
1 AATTAATTA
1801800 AATTAATTA
1 AATTAATTA
1801809 AATTAA--A
1 AATTAATTA
1801816 AATTAAT
1 AATTAAT
1801823 AGTAATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
7 7 0.23
8 4 0.13
9 19 0.63
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (9 bp):
AATTAATTA
Found at i:1801803 original size:13 final size:13
Alignment explanation
Indices: 1801781--1801815 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1801771 AAAAAATACC
*
1801781 TAATTGAATTAAT
1 TAATTAAATTAAT
1801794 TAATTAAATTAAT
1 TAATTAAATTAAT
1801807 TAAATTAAA
1 T-AATTAAA
1801816 AATTAATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (13 bp):
TAATTAAATTAAT
Found at i:1802032 original size:17 final size:17
Alignment explanation
Indices: 1801997--1802099 Score: 72
Period size: 16 Copynumber: 6.1 Consensus size: 17
1801987 AAATTATATC
**
1801997 ATTTA-ATTAAATACAT
1 ATTTATATTAAATATTT
*
1802013 ATTTTTATTAAATATTT
1 ATTTATATTAAATATTT
*
1802030 A-TTATATTTAATATTT
1 ATTTATATTAAATATTT
1802046 ATTTAATATTAAAAATATTT
1 ATTT-ATATT--AAATATTT
* *
1802066 AATTAATATT-TATATTT
1 -ATTTATATTAAATATTT
1802083 -TTTA-ATTAAATAATTT
1 ATTTATATTAAAT-ATTT
1802099 A
1 A
1802100 ATTCAATTTA
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
14 3 0.04
15 5 0.07
16 22 0.32
17 18 0.26
18 5 0.07
20 12 0.18
21 3 0.04
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTATATTAAATATTT
Found at i:1802048 original size:11 final size:11
Alignment explanation
Indices: 1802029--1802078 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
1802019 ATTAAATATT
1802029 TATTATATTTAA
1 TATT-TATTTAA
1802041 TATTTATTTAA
1 TATTTATTTAA
**
1802052 TA-TTA-AAAA
1 TATTTATTTAA
*
1802061 TATTTAATTAA
1 TATTTATTTAA
1802072 TATTTAT
1 TATTTAT
1802079 ATTTTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
9 4 0.13
10 6 0.19
11 17 0.55
12 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTATTTAA
Done.