Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 178 of 226
Found at i:57047082 original size:85 final size:86
Alignment explanation
Indices: 57046988--57047146 Score: 221
Period size: 86 Copynumber: 1.8 Consensus size: 86
57046978 TAATGGCTTA
** * ** ***
57046988 ATTTTTTTTTTAAAGTTTGAGGTTCTTTTTT-ATGTATTTTGTCTGTTCAAGTACCCAATTGAGT
1 ATTTTTTTTGAAAAGTTTGAGG-GCTTTTTTAATACATTTTGAAAGTTCAAGTACCCAATTGAGT
57047052 GCAAAAAAAGGGGCTTAATTGC
65 GCAAAAAAAGGGGCTTAATTGC
*
57047074 ATTTTTTTTGAAAAGTTTGAGGGCTTTTTTAATACATTTTGAAAGTTCAAGTATCCAATTGAGTG
1 ATTTTTTTTGAAAAGTTTGAGGGCTTTTTTAATACATTTTGAAAGTTCAAGTACCCAATTGAGTG
57047139 CAAAAAAA
66 CAAAAAAA
57047147 AAAAGAATAC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
85 7 0.11
86 56 0.89
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (86 bp):
ATTTTTTTTGAAAAGTTTGAGGGCTTTTTTAATACATTTTGAAAGTTCAAGTACCCAATTGAGTG
CAAAAAAAGGGGCTTAATTGC
Found at i:57050102 original size:27 final size:28
Alignment explanation
Indices: 57050061--57050163 Score: 140
Period size: 27 Copynumber: 3.8 Consensus size: 28
57050051 TAACAATCAG
* *
57050061 TTTACCCTATGGGGGGTATTTCGGTAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
57050089 TTTA-CCTATCGGGGGTATTTCGATAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
***
57050116 TTTACCCT-TCTAAGGTATTTCGATAAT
1 TTTACCCTATCGGGGGTATTTCGATAAT
57050143 TTTACCC-ATCGGGGGTATTTC
1 TTTACCCTATCGGGGGTATTTC
57050164 AGTAATGTTA
Statistics
Matches: 65, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
27 58 0.89
28 7 0.11
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.41
Consensus pattern (28 bp):
TTTACCCTATCGGGGGTATTTCGATAAT
Found at i:57056585 original size:21 final size:22
Alignment explanation
Indices: 57056556--57056597 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
57056546 AGCTCAAAAG
57056556 TTAAGCAGAAGCTCGTAAGAGT
1 TTAAGCAGAAGCTCGTAAGAGT
57056578 TTAA-CAGAAGCTCGTAAGAG
1 TTAAGCAGAAGCTCGTAAGAG
57056598 CTGAACAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.38, C:0.14, G:0.26, T:0.21
Consensus pattern (22 bp):
TTAAGCAGAAGCTCGTAAGAGT
Found at i:57056604 original size:21 final size:21
Alignment explanation
Indices: 57056561--57056604 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
57056551 AAAAGTTAAG
* *
57056561 CAGAAGCTCGTAAGAGTTTAA
1 CAGAAGCTCGTAAGAGCTGAA
57056582 CAGAAGCTCGTAAGAGCTGAA
1 CAGAAGCTCGTAAGAGCTGAA
57056603 CA
1 CA
57056605 AAAAGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (21 bp):
CAGAAGCTCGTAAGAGCTGAA
Found at i:57058189 original size:15 final size:16
Alignment explanation
Indices: 57058154--57058193 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
57058144 GAATGATGAT
*
57058154 TGAGAGATGTGAAGAA
1 TGAGGGATGTGAAGAA
*
57058170 TGAGGGATGT-AAGGA
1 TGAGGGATGTGAAGAA
57058185 TGAGGGATG
1 TGAGGGATG
57058194 ATAAAAATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.35, C:0.00, G:0.45, T:0.20
Consensus pattern (16 bp):
TGAGGGATGTGAAGAA
Found at i:57058713 original size:5 final size:5
Alignment explanation
Indices: 57058674--57058802 Score: 189
Period size: 5 Copynumber: 26.6 Consensus size: 5
57058664 TTTTTATGTT
*
57058674 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATA TTA-A TTATA
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
57058722 TTA-A TTATA TTA-A TTATA TTATA TTATA TTATA TTATA TTATA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
57058770 TTATA TTATA TTATA TTATA TTATA TTATA TTA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTA
57058803 AATAAACTAA
Statistics
Matches: 114, Mismatches: 2, Indels: 16
0.86 0.02 0.12
Matches are distributed among these distances:
3 1 0.01
4 20 0.18
5 89 0.78
7 4 0.04
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:57059033 original size:22 final size:22
Alignment explanation
Indices: 57058994--57059041 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
57058984 AAACAAAAGA
*
57058994 AAAAGAAACAAAGGAAGA-ACAG
1 AAAAGAAACAAAGAAAGAGAC-G
* *
57059016 AAAAGAAATAGAGAAAGAGACG
1 AAAAGAAACAAAGAAAGAGACG
57059038 AAAA
1 AAAA
57059042 CAAGGGAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.69, C:0.06, G:0.23, T:0.02
Consensus pattern (22 bp):
AAAAGAAACAAAGAAAGAGACG
Found at i:57059433 original size:23 final size:23
Alignment explanation
Indices: 57059399--57059442 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
57059389 TATGGCAAGA
57059399 AATTAATTAGAAAAG-AAGTATG
1 AATTAATTAGAAAAGTAAGTATG
57059421 AATTAAGTTAGAAAAGTAAGTA
1 AATTAA-TTAGAAAAGTAAGTA
57059443 AGCTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 9 0.45
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (23 bp):
AATTAATTAGAAAAGTAAGTATG
Found at i:57059720 original size:24 final size:23
Alignment explanation
Indices: 57059679--57059725 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
57059669 TATTCATGGG
57059679 ACATTTAAAGTAAGGTAAGTAATA
1 ACATTTAAAGTAAGGTAAG-AATA
*
57059703 ACATTTGAAATTAA-GTAAGAATA
1 ACATTT-AAAGTAAGGTAAGAATA
57059726 TGTGTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (23 bp):
ACATTTAAAGTAAGGTAAGAATA
Found at i:57066086 original size:5 final size:5
Alignment explanation
Indices: 57066042--57066122 Score: 91
Period size: 5 Copynumber: 16.6 Consensus size: 5
57066032 ATTTTTATGT
*
57066042 TTATA -TATA TTAT- TT-TA TTATA TAATATA ATATA TTATA TTATA TTA-A
1 TTATA TTATA TTATA TTATA TTATA T--TATA TTATA TTATA TTATA TTATA
57066090 TTATA TTATA TTATA TTATA TTAT- TATATA TTA
1 TTATA TTATA TTATA TTATA TTATA T-TATA TTA
57066123 AATAAACTAA
Statistics
Matches: 66, Mismatches: 2, Indels: 16
0.79 0.02 0.19
Matches are distributed among these distances:
3 1 0.02
4 13 0.20
5 47 0.71
6 1 0.02
7 4 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (5 bp):
TTATA
Found at i:57066110 original size:34 final size:35
Alignment explanation
Indices: 57066042--57066123 Score: 100
Period size: 34 Copynumber: 2.4 Consensus size: 35
57066032 ATTTTTATGT
*
57066042 TTATA-TATATT-ATTTTATTATATAATATAATATA
1 TTATATTATATTAATTATATTATAT-ATATAATATA
*
57066076 TTATATTATATTAATTATATTATAT-TATATTATA
1 TTATATTATATTAATTATATTATATATATAATATA
57066110 TTAT-TATATATTAA
1 TTATAT-TATATTAA
57066124 ATAAACTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
33 1 0.02
34 25 0.58
35 6 0.14
36 11 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (35 bp):
TTATATTATATTAATTATATTATATATATAATATA
Found at i:57066738 original size:23 final size:23
Alignment explanation
Indices: 57066704--57066747 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
57066694 TATGGCAAGA
57066704 AATTAATTAGAAAAG-AAGTATG
1 AATTAATTAGAAAAGTAAGTATG
57066726 AATTAAGTTAGAAAAGTAAGTA
1 AATTAA-TTAGAAAAGTAAGTA
57066748 AGCTTAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 9 0.45
24 5 0.25
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (23 bp):
AATTAATTAGAAAAGTAAGTATG
Found at i:57067025 original size:24 final size:23
Alignment explanation
Indices: 57066984--57067030 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
57066974 TATTCATGGG
57066984 ACATTTAAAGTAAGGTAAGTAATA
1 ACATTTAAAGTAAGGTAAG-AATA
*
57067008 ACATTTGAAATTAA-GTAAGAATA
1 ACATTT-AAAGTAAGGTAAGAATA
57067031 TGCGTGAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 11 0.52
25 6 0.29
ACGTcount: A:0.51, C:0.04, G:0.15, T:0.30
Consensus pattern (23 bp):
ACATTTAAAGTAAGGTAAGAATA
Found at i:57072596 original size:22 final size:21
Alignment explanation
Indices: 57072567--57072608 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
57072557 TTGAACTAAA
57072567 ATGGTAATTTCGTAAATATTG
1 ATGGTAATTTCGTAAATATTG
* *
57072588 ATGGCTAATTTGGTTAATATT
1 ATGG-TAATTTCGTAAATATT
57072609 TTATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (21 bp):
ATGGTAATTTCGTAAATATTG
Found at i:57074896 original size:18 final size:19
Alignment explanation
Indices: 57074873--57074910 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
57074863 TTTTTTTACC
*
57074873 AAAATATTA-CAAAAAAAT
1 AAAATAATATCAAAAAAAT
*
57074891 AAAATAATATCAAAATAAT
1 AAAATAATATCAAAAAAAT
57074910 A
1 A
57074911 TAAACTTTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAATAATATCAAAAAAAT
Found at i:57075421 original size:153 final size:152
Alignment explanation
Indices: 57075148--57076711 Score: 2048
Period size: 153 Copynumber: 10.3 Consensus size: 152
57075138 GTTTTTATTG
* * * *
57075148 AAAGTAATAAAATCCGGTAAAAAAATACGAACAAAGGGCCAAAATAAGGTTTTTTTTAAATTTAT
1 AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGTTTTTTTAAAATTTAT
* * *
57075213 TTAAAAAA-ACACTAAATGAATACATTTCAAACATAATGTACTAAACTAATGTAAAATAATAAAA
66 TTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
*
57075277 TTCGAAAATATTATATTTTTTA
131 TTAGAAAATATTATATTTTTTA
* *
57075299 AAAGTAATAAAATCCGGAGAAAAAAATACGAACAAATGACCGAAATAATAG-TTTTTTAAAATTT
1 AAAGTAATAAAATCCGG-GAAAAAAATACGAACAAAGGGCCGAAATAA-AGTTTTTTTAAAATTT
*
57075363 ATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAA
64 ATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
* * *
57075428 AA-TACAAAAATAATATATTTTTATTG
129 AATTA-GAAAATATTATA-TTTT-TTA
* *
57075454 AAAGTAATAAAATCC-GGAAAAAAATACGAATAAAGGGCCGAAATAAGGATTATTTTTTAAAATT
1 AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAA--AGT-TTTTTTAAAATT
* * *
57075518 TATTT-AAAAACAAACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
63 TATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATA
*
57075582 AAATTAGAAAATAGTAT-TTTTTT-
128 AAATTAGAAAATATTATATTTTTTA
* * *
57075605 AAAGTAATAAAATTCAGGGAAAAAAATACGAACAAATGGCCGAAATAAGGATTTTTTT-AAATTT
1 AAAGTAATAAAA-TCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAG-TTTTTTTAAAATTT
* *
57075669 ATTTTAAAAACACAGTAAATTAATACATTTCAAAAATAATGTACTAAAATAATGTAAAATAATAA
64 ATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
57075734 AATTAGAAAATATTATATTTTTTA
129 AATTAGAAAATATTATATTTTTTA
* * *
57075758 AAAGTAATAAAATCCGGGGAAAAAATACGAATAAAGGGCCGAAATAAGAGTTATTTTTTAAATTT
1 AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAA-AGTT-TTTTTAAAATTT
*
57075823 ATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATATAAAATAATAA
64 ATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
* * *
57075888 AA-TACAAAAATAATATATTTTTATTG
129 AATTA-GAAAATATTATA-TTTT-TTA
* * * *
57075914 AAAGTAATAAAATCC-AG-AAAAAATATGAATAAAGGGCTGAAATAAAGATTTTTTT--AATTTA
1 AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAG-TTTTTTTAAAATTTA
* * *
57075975 TTTAAAAATACAC--TAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATTAGAA
65 TTTAAAAA-ACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
57076038 AATTAGAAAATA--ATATTTTTT-
129 AATTAGAAAATATTATATTTTTTA
* **
57076059 AAAGTAATAAAATCCATGG-AAAAAATACGAACAAAGGGCCGAAATGAGGGTTTTTTTAAAATTT
1 AAAGTAATAAAATCC-GGGAAAAAAATACGAACAAAGGGCCGAAAT-AAAGTTTTTTTAAAATTT
* **
57076123 ATTTTAAAAACACAGTAAATTAATACATTTCAAACATAACATACTAAAATAATGTAAAATAATAA
64 ATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
*
57076188 AATTATAAAATATTATATTTTTTA
129 AATTAGAAAATATTATATTTTTTA
* *
57076212 AAAGTAATAAAATTCGGGAAAAAAATACGAACAAATGGCCGAAATAATAGTTTTTTTAAAATTTA
1 AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAA-AGTTTTTTTAAAATTTA
* ** * *
57076277 TTTAAAAAACACAGTAAATTAATACATTTAAAACATAACATACTAAAATAATGTAAAATTAGAAA
65 TTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
* *
57076342 ATTAGAAAATAGTATATTTTTTT
130 ATTAGAAAATATTATATTTTTTA
* * * * *
57076365 AAAGTATTAAACTCTGGGGAAAAAAATACGAACAAAGGGCCAAAATAAGGGTTTTTTT-AAATTT
1 AAAGTAATAAAATC-CGGGAAAAAAATACGAACAAAGGGCCGAAATAA-AGTTTTTTTAAAATTT
* *
57076429 ATTTAAAAAACAC--TAAATTAATACATTTCAAACTTGATGTACTAAAATAATGTAAAATAATAA
64 ATTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAA
* *
57076492 AATTAGAAAATAATATATTTTTATTG
129 AATTAGAAAATATTATA-TTTT-TTA
*
57076518 AAAGTAATAAAATCCGGGAAAAAAATATGAACAAAGGGCCGAAATAAAGATTTTTTT--AATTTA
1 AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAG-TTTTTTTAAAATTTA
* * * * * * *
57076581 TTT-AACAACATACTAAATTAATACATTTAAAAGATAATGTATTAAAATAATATAAAATAA-AAA
65 TTTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAA
57076644 ATTAGAAAATATTATATTTTTTA
130 ATTAGAAAATATTATATTTTTTA
* *
57076667 AAAGTAATAAAATCC-GGAAAAAAATACGAACAGAGGGCCAAAATA
1 AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATA
57076712 CGAACAATTA
Statistics
Matches: 1255, Mismatches: 115, Indels: 89
0.86 0.08 0.06
Matches are distributed among these distances:
145 15 0.01
146 2 0.00
147 35 0.03
148 36 0.03
149 30 0.02
150 130 0.10
151 209 0.17
152 191 0.15
153 330 0.26
154 152 0.12
155 89 0.07
156 36 0.03
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (152 bp):
AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGTTTTTTTAAAATTTAT
TTAAAAAACACAGTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAA
TTAGAAAATATTATATTTTTTA
Found at i:57075426 original size:13 final size:13
Alignment explanation
Indices: 57075393--57075444 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
57075383 TAATACATTT
* *
57075393 CAAACATAATGTA
1 CAAAAATAATATA
*
57075406 CTAAAATAATATA
1 CAAAAATAATATA
*
57075419 -AAATAATAAAATA
1 CAAA-AATAATATA
57075432 CAAAAATAATATA
1 CAAAAATAATATA
57075445 TTTTTATTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
12 2 0.06
13 26 0.84
14 3 0.10
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (13 bp):
CAAAAATAATATA
Found at i:57075886 original size:13 final size:13
Alignment explanation
Indices: 57075853--57075904 Score: 52
Period size: 13 Copynumber: 4.0 Consensus size: 13
57075843 TAATACATTT
* *
57075853 CAAACATAATGTA
1 CAAAAATAATATA
*
57075866 CTAAAATAATATA
1 CAAAAATAATATA
*
57075879 -AAATAATAAAATA
1 CAAA-AATAATATA
57075892 CAAAAATAATATA
1 CAAAAATAATATA
57075905 TTTTTATTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
12 2 0.06
13 26 0.84
14 3 0.10
ACGTcount: A:0.65, C:0.08, G:0.02, T:0.25
Consensus pattern (13 bp):
CAAAAATAATATA
Found at i:57076216 original size:454 final size:453
Alignment explanation
Indices: 57075139--57076711 Score: 2313
Period size: 454 Copynumber: 3.5 Consensus size: 453
57075129 ATTTAGTGTG
* * * *
57075139 TTTTTATTGAAAGTAATAAAATCCGGTAAAAAAATACGAACAAAGGGCCAAAATAAGGTTTTTTT
1 TTTTT-TT-AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGATTTTTT
* * *
57075204 TAAATTTATTTAAAAAAACACTAAATGAATACATTTCAAACATAATGTACTAAACTAATGTAAAA
64 TAAATTTATTTAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
*
57075269 TAATAAAATTCGAAAATATTATATTTTTTAAAAGTAATAAAATCCGGAGAAAAAAATACGAACAA
129 TAATAAAATTAGAAAATATTATATTTTTTAAAAGTAATAAAATCCGG-GAAAAAAATACGAACAA
* *
57075334 ATGACCGAAATAATAG-TTTTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAAC
193 AGGGCCGAAATAATAGTTTTTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAAC
57075398 ATAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATA
258 ATAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATA
57075463 AAATCCGGAAAAAAATACGAATAAAGGGCCGAAATAAGGATTATTTTTTAAAATTTATTTAAAAA
323 AAATCCGGAAAAAAATACGAATAAAGGGCCGAAATAAGGA-T-TTTTTT-AAATTTATTTAAAAA
*
57075528 CAAACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAA
385 -ACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAA
*
57075593 TAGTA
449 TAATA
* * *
57075598 TTTTTTTAAAGTAATAAAATTCAGGGAAAAAAATACGAACAAATGGCCGAAATAAGGATTTTTTT
1 TTTTTTTAAAGTAATAAAA-TCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGATTTTTTT
* *
57075663 AAATTTATTTTAAAAACACAGTAAATTAATACATTTCAAAAATAATGTACTAAAATAATGTAAAA
65 AAATTTA-TTTAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
* *
57075728 TAATAAAATTAGAAAATATTATATTTTTTAAAAGTAATAAAATCCGGGGAAAAAATACGAATAAA
129 TAATAAAATTAGAAAATATTATATTTTTTAAAAGTAATAAAATCCGGGAAAAAAATACGAACAAA
* *
57075793 GGGCCGAAATAAGAGTTATTTTTTAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAAC
194 GGGCCGAAATAATAGTT-TTTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAAC
57075858 ATAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATA
258 ATAATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATA
* * * *
57075923 AAATCCAG-AAAAAATATGAATAAAGGGCTGAAATAAAGATTTTTTT-AATTTATTTAAAAATAC
323 AAATCCGGAAAAAAATACGAATAAAGGGCCGAAATAAGGATTTTTTTAAATTTATTTAAAAA-AC
* *
57075986 ACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATTAGAAAATTAGAAAATAA
387 ACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAA
57076051 TA
452 TA
* * * *
57076053 -TTTTTTAAAGTAATAAAATCCATGG-AAAAAATACGAACAAAGGGCCGAAATGAGGGTTTTTTT
1 TTTTTTTAAAGTAATAAAATCC-GGGAAAAAAATACGAACAAAGGGCCGAAATAAAGATTTTTTT
* **
57076116 AAAATTTATTTTAAAAACACAGTAAATTAATACATTTCAAACATAACATACTAAAATAATGTAAA
65 -AAATTTA-TTTAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAA
* *
57076181 ATAATAAAATTATAAAATATTATATTTTTTAAAAGTAATAAAATTCGGGAAAAAAATACGAACAA
128 ATAATAAAATTAGAAAATATTATATTTTTTAAAAGTAATAAAATCCGGGAAAAAAATACGAACAA
* *
57076246 ATGGCCGAAATAATAGTTTTTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTAAAAC
193 AGGGCCGAAATAATAGTTTTTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAAC
** * * * * * *
57076311 ATAACATACTAAAATAATGTAAAATTAGAAAATTA-GAAAATAGTATATTTTT-TT-AAAGTATT
258 ATAATGTACTAAAATAATATAAAATAATAAAA-TACAAAAATAATATATTTTTATTGAAAGTAAT
* * * * *
57076373 AAACTCTGGGGAAAAAAATACGAACAAAGGGCCAAAATAAGGGTTTTTTTAAATTTATTTAAAAA
322 AAAATC--CGGAAAAAAATACGAATAAAGGGCCGAAATAAGGATTTTTTTAAATTTATTTAAAAA
* * *
57076438 ACACTAAATTAATACATTTCAAACTTGATGTACTAAAATAATGTAAAATAATAAAATTAGAAAAT
385 ACACTAAATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAAT
57076503 AATATA
450 -A-ATA
*
57076509 TTTTTATTGAAAGTAATAAAATCCGGGAAAAAAATATGAACAAAGGGCCGAAATAAAGATTTTTT
1 TTTTT-TT-AAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGATTTTTT
* * * * * *
57076574 T-AATTTATTTAACAACATACTAAATTAATACATTTAAAAGATAATGTATTAAAATAATATAAAA
64 TAAATTTATTTAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAA
*
57076638 TAA-AAAATTAGAAAATATTATATTTTTTAAAAGTAATAAAATCC-GGAAAAAAATACGAACAGA
129 TAATAAAATTAGAAAATATTATATTTTTTAAAAGTAATAAAATCCGGGAAAAAAATACGAACAAA
*
57076701 GGGCCAAAATA
194 GGGCCGAAATA
57076712 CGAACAATTA
Statistics
Matches: 1014, Mismatches: 83, Indels: 39
0.89 0.07 0.03
Matches are distributed among these distances:
451 12 0.01
452 2 0.00
453 125 0.12
454 279 0.28
455 133 0.13
456 54 0.05
457 28 0.03
458 82 0.08
459 181 0.18
460 118 0.12
ACGTcount: A:0.52, C:0.08, G:0.09, T:0.31
Consensus pattern (453 bp):
TTTTTTTAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGGGCCGAAATAAAGATTTTTTTA
AATTTATTTAAAAACACACTAAATTAATACATTTCAAACATAATGTACTAAAATAATGTAAAATA
ATAAAATTAGAAAATATTATATTTTTTAAAAGTAATAAAATCCGGGAAAAAAATACGAACAAAGG
GCCGAAATAATAGTTTTTTTAAAATTTATTTAAAAAACACAGTAAATTAATACATTTCAAACATA
ATGTACTAAAATAATATAAAATAATAAAATACAAAAATAATATATTTTTATTGAAAGTAATAAAA
TCCGGAAAAAAATACGAATAAAGGGCCGAAATAAGGATTTTTTTAAATTTATTTAAAAAACACTA
AATGAATACATTTCAAACATAATGTACTAAAATAATGTAAAATAATAAAATTAGAAAATAATA
Found at i:57076750 original size:22 final size:22
Alignment explanation
Indices: 57076722--57076785 Score: 119
Period size: 22 Copynumber: 2.9 Consensus size: 22
57076712 CGAACAATTA
*
57076722 GTGCCGCCTCTACCACAGGCGG
1 GTGCCGCCTCTGCCACAGGCGG
57076744 GTGCCGCCTCTGCCACAGGCGG
1 GTGCCGCCTCTGCCACAGGCGG
57076766 GTGCCGCCTCTGCCACAGGC
1 GTGCCGCCTCTGCCACAGGC
57076786 ACCAAAGGTG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.11, C:0.42, G:0.33, T:0.14
Consensus pattern (22 bp):
GTGCCGCCTCTGCCACAGGCGG
Found at i:57076914 original size:11 final size:11
Alignment explanation
Indices: 57076870--57076912 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
57076860 AAATAAAAAA
57076870 ATTTT-ATATT
1 ATTTTAATATT
57076880 ATTTTAATATT
1 ATTTTAATATT
57076891 ATTTTAAT-TT
1 ATTTTAATATT
*
57076901 TTTTGTAATATT
1 ATTT-TAATATT
57076913 TTAGTAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 10 0.34
11 17 0.59
12 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
ATTTTAATATT
Found at i:57078377 original size:21 final size:22
Alignment explanation
Indices: 57078351--57078392 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
57078341 GGAGTTTTTG
57078351 GAAAGGAAAA-GAGAAAGGAAA
1 GAAAGGAAAATGAGAAAGGAAA
*
57078372 GAAAGGAAAATGAGAAGGGAA
1 GAAAGGAAAATGAGAAAGGAA
57078393 GGGACTTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.36, T:0.02
Consensus pattern (22 bp):
GAAAGGAAAATGAGAAAGGAAA
Found at i:57080030 original size:18 final size:20
Alignment explanation
Indices: 57079996--57080033 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
57079986 TATACTATAT
57079996 ACTACTACATAATATAATAA
1 ACTACTACATAATATAATAA
57080016 ACTA-TACAT-ATATAATAA
1 ACTACTACATAATATAATAA
57080034 TCAATATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
19 5 0.28
20 4 0.22
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (20 bp):
ACTACTACATAATATAATAA
Found at i:57080871 original size:5 final size:5
Alignment explanation
Indices: 57080861--57080892 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
57080851 ATTTGAATAC
57080861 TTATT TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TTATT TT
57080893 TGCTTTTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:57082075 original size:27 final size:27
Alignment explanation
Indices: 57082045--57082110 Score: 89
Period size: 27 Copynumber: 2.4 Consensus size: 27
57082035 CTAGACTAAT
57082045 GTAAAATGACTGTTATG-CCCTCACGTG
1 GTAAAATGACTGTTATGCCCCT-ACGTG
* *
57082072 GTAAAATGATTGTTATGCCCCTACGTT
1 GTAAAATGACTGTTATGCCCCTACGTG
*
57082099 ATAAAATGACTG
1 GTAAAATGACTG
57082111 CATGCTCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 30 0.88
28 4 0.12
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (27 bp):
GTAAAATGACTGTTATGCCCCTACGTG
Found at i:57085689 original size:2 final size:2
Alignment explanation
Indices: 57085682--57085712 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57085672 CAATAATAAA
57085682 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
57085713 TATATAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:57094532 original size:13 final size:13
Alignment explanation
Indices: 57094514--57094540 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
57094504 GAAATATGCC
57094514 AAAATTGCTGGAA
1 AAAATTGCTGGAA
57094527 AAAATTGCTGGAA
1 AAAATTGCTGGAA
57094540 A
1 A
57094541 TTGCTAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.07, G:0.22, T:0.22
Consensus pattern (13 bp):
AAAATTGCTGGAA
Found at i:57100112 original size:47 final size:46
Alignment explanation
Indices: 57100043--57100158 Score: 135
Period size: 47 Copynumber: 2.5 Consensus size: 46
57100033 AACACACAAT
* * **
57100043 TTGTGGACAAGCTACCACATAAATGT-TGAAAACAGTCACATAGCACA
1 TTGT-GACAAGCCACCACATAAAT-TCCGAAAACAACCACATAGCACA
*
57100090 TTGTGAACAAGCCATCACATAAATTCCGAAAACAACCACATAGCACA
1 TTGTG-ACAAGCCACCACATAAATTCCGAAAACAACCACATAGCACA
*
57100137 ATGTTGACAAGCCACCACATAA
1 TTG-TGACAAGCCACCACATAA
57100159 TTATCTATAA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
46 2 0.03
47 55 0.93
48 2 0.03
ACGTcount: A:0.42, C:0.25, G:0.14, T:0.19
Consensus pattern (46 bp):
TTGTGACAAGCCACCACATAAATTCCGAAAACAACCACATAGCACA
Found at i:57104379 original size:27 final size:27
Alignment explanation
Indices: 57104349--57104409 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
57104339 AGCTAAATCC
57104349 AAATGTAAAAACCTTATGGCTTCATTA
1 AAATGTAAAAACCTTATGGCTTCATTA
*
57104376 AAATGTAAAAACCTTATGGTTTCATTA
1 AAATGTAAAAACCTTATGGCTTCATTA
57104403 AAATGTA
1 AAATGTA
57104410 TCACCTACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (27 bp):
AAATGTAAAAACCTTATGGCTTCATTA
Found at i:57105092 original size:2 final size:2
Alignment explanation
Indices: 57105085--57105110 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
57105075 TCATTTATTA
57105085 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
57105111 TTGTAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57105903 original size:14 final size:15
Alignment explanation
Indices: 57105884--57105913 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
57105874 TTTTTAAAGA
57105884 AAACATATAT-ATAT
1 AAACATATATAATAT
57105898 AAACATATATAATAT
1 AAACATATATAATAT
57105913 A
1 A
57105914 GAAAAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (15 bp):
AAACATATATAATAT
Found at i:57105927 original size:89 final size:91
Alignment explanation
Indices: 57105787--57105961 Score: 284
Period size: 89 Copynumber: 1.9 Consensus size: 91
57105777 ATTTAATCAA
57105787 TAAAAAAACAGATATATATACATACATATATAAATATAGAAAAATATTCGTTAGAAAAAAAATAA
1 TAAAAAAACAGATATATATACATACATATATAAATATAGAAAAATATTCGTTAGAAAAAAAATAA
*
57105852 ATATACATACATGTACATATAATTTT
66 ATATACATACATCTACATATAATTTT
* *
57105878 TAAAGAAAACATATATATATA-A-ACATATAT-AATATAGAAAAATATTCGTTAGAAGAAAAATA
1 TAAA-AAAACAGATATATATACATACATATATAAATATAGAAAAATATTCGTTAGAAAAAAAATA
*
57105940 AATATACATACATCTACGTATA
65 AATATACATACATCTACATATA
57105962 TAAATAAATA
Statistics
Matches: 79, Mismatches: 4, Indels: 4
0.91 0.05 0.05
Matches are distributed among these distances:
89 51 0.65
90 8 0.10
91 5 0.06
92 15 0.19
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.30
Consensus pattern (91 bp):
TAAAAAAACAGATATATATACATACATATATAAATATAGAAAAATATTCGTTAGAAAAAAAATAA
ATATACATACATCTACATATAATTTT
Found at i:57106040 original size:18 final size:18
Alignment explanation
Indices: 57106019--57106065 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
57106009 AAATATGTGT
**
57106019 ATATATATATGGAAATAA
1 ATATATATATAAAAATAA
*
57106037 ATATATACATAAAAATAA
1 ATATATATATAAAAATAA
*
57106055 ATATACATATA
1 ATATATATATA
57106066 TATAGAAAGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (18 bp):
ATATATATATAAAAATAA
Found at i:57107773 original size:44 final size:44
Alignment explanation
Indices: 57107719--57108352 Score: 315
Period size: 44 Copynumber: 14.7 Consensus size: 44
57107709 CCATTTTGAG
* * *
57107719 TCTGCCCCACTGCAACTTTAGGGGGATAAGACCTGCTTATTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCTTATTCAA
*
57107763 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTAG---A-TGAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCT-GCTTATTCA-A
* * * ** * *
57107804 TCTGCT-CTCTGTAACTTCAGAGAGATAAGATTTG-TGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCTTA-TTCAA
* * * **
57107847 TCCGCTCCACTGCAACTTCAGTGAGATAGGATTATAGGCTTA---AA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CCT--GCTTATTCAA
* * ** ***
57107891 TCTGCTCCACTGCAACTTCAGAGAGATAAGATTCACCATT-TTGGG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CCTGC-TTATTCAA
* *
57107936 TCTGCCCCACTGCAACTTCAGGG-GATAAGACCTGCTTATTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCTTATTCAA
* *
57107979 TCTGCTCCACTGCAACTTCAGGGGGATAAGACCTGCTTATTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCTTATTCAA
*
57108023 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CTAG---A-TGAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCT-GCTTATTCA-A
* * * * * * *
57108064 TATGCT-CTCTGTAACTTCAGAGAGATAAGATCTG-TGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCTTA-TTCAA
* ** * * **
57108107 TCCGCTCCACTAAAACTTCAAGGAGATAGGATTATAGGCTTA---AA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CCT--GCTTATTCAA
* ** ***
57108151 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACCATT-TTGGG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-CCTGC-TTATTCAA
* *
57108196 TCTG-TCCCACTGCAACTTCA-GGAGGATAAGACTTGCTTACTT-AG
1 TCTGCT-CCACTGCAACTTCAGGGA-GATAAGACCTGCTTA-TTCAA
* * * *
57108240 TCTGCTCCACTGCAACTTCAGGAAGATAAGA-CT--ATATGCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCTTATTCAA
* * * * * *
57108281 TCTGCT-CTCTGCAACTTCTGAGAGATAAGATCTG-TGATTTTAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCTTA-TTCAA
57108324 T-TCGCTCCACTGCAACTTCAGGGAGATAA
1 TCT-GCTCCACTGCAACTTCAGGGAGATAA
57108353 AATTATTGGC
Statistics
Matches: 461, Mismatches: 83, Indels: 92
0.72 0.13 0.14
Matches are distributed among these distances:
40 69 0.15
41 27 0.06
42 8 0.02
43 55 0.12
44 241 0.52
45 55 0.12
47 2 0.00
48 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.29
Consensus pattern (44 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGCTTATTCAA
Found at i:57107896 original size:128 final size:127
Alignment explanation
Indices: 57107761--57108181 Score: 485
Period size: 128 Copynumber: 3.3 Consensus size: 127
57107751 CTGCTTATTC
57107761 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGAGATCTGCTCTCTGTAACTTCAGAG
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGAGATCTGCTCTCTGTAACTTCAGAG
*
57107826 AGATAAGATTTGTGATTTTAATCCGCTCCACTGCAACTTCAGTGAGATAGGATTATAGGCTTA
66 AGATAAGATCTGTGATTTTAATCCGCTCCACTGCAACTTCAG-GAGATAGGATTATAGGCTTA
* * * * * * *
57107889 AATCTGCTCCACTGCAACTTCAGAGAGATAAGATTCACCATTTTG-GGTCTGCCCCACTGCAACT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACT-A-GA---TGAGATCTG-CTCTCTGTAACT
* * * * * * * * **
57107953 TCAG-GGGATAAGACCTGCTTA-TTCAGTCTGCTCCACTGCAACTTCAGGGGGATAAGA-CCT--
60 TCAGAGAGATAAGATCTG-TGATTTTAATCCGCTCCACTGCAACTTCA-GGAGATAGGATTATAG
57108013 GCTTA
123 GCTTA
* *
57108018 TTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGAGATATGCTCTCTGTAACTTCA
1 ---AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGAGATCTGCTCTCTGTAACTTCA
**
57108083 GAGAGATAAGATCTGTGATTTTAATCCGCTCCACTAAAACTTCAAGGAGATAGGATTATAGGCTT
63 GAGAGATAAGATCTGTGATTTTAATCCGCTCCACTGCAACTTC-AGGAGATAGGATTATAGGCTT
57108148 A
127 A
57108149 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
57108182 TTCACCATTT
Statistics
Matches: 235, Mismatches: 40, Indels: 36
0.76 0.13 0.12
Matches are distributed among these distances:
127 17 0.07
128 107 0.46
129 8 0.03
130 2 0.01
131 7 0.03
132 76 0.32
133 18 0.08
ACGTcount: A:0.29, C:0.22, G:0.21, T:0.28
Consensus pattern (127 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGAGATCTGCTCTCTGTAACTTCAGAG
AGATAAGATCTGTGATTTTAATCCGCTCCACTGCAACTTCAGGAGATAGGATTATAGGCTTA
Found at i:57108011 original size:260 final size:261
Alignment explanation
Indices: 57107717--57108271 Score: 963
Period size: 260 Copynumber: 2.1 Consensus size: 261
57107707 CGCCATTTTG
* *
57107717 AGTCTGCCCCACTGCAACTTTAGGGGGATAAGACCTGCTTATTCAATCTGCTCCACTGCAACTTC
1 AGTCTGCTCCACTGCAACTTCAGGGGGATAAGACCTGCTTATTCAATCTGCTCCACTGCAACTTC
* *
57107782 AGGGAGATAAGACTAGATGAGATCTGCTCTCTGTAACTTCAGAGAGATAAGATTTGTGATTTTAA
66 AGGGAGATAAGACTAGATGAGATATGCTCTCTGTAACTTCAGAGAGATAAGATCTGTGATTTTAA
**
57107847 TCCGCTCCACTGCAACTTC-AGTGAGATAGGATTATAGGCTTAAATCTGCTCCACTGCAACTTCA
131 TCCGCTCCACTAAAACTTCAAG-GAGATAGGATTATAGGCTTAAATCTGCTCCACTGCAACTTCA
57107911 GAGAGATAAGATTCACCATTTTGGGTCTGCCCCACTGCAACTTCAGG-GGATAAGACCTGCTTA-
195 GAGAGATAAGATTCACCATTTTGGGTCTGCCCCACTGCAACTTCAGGAGGATAAGACCTGCTTAC
57107974 TT
260 TT
*
57107976 CAGTCTGCTCCACTGCAACTTCAGGGGGATAAGACCTGCTTATTCAGTCTGCTCCACTGCAACTT
1 -AGTCTGCTCCACTGCAACTTCAGGGGGATAAGACCTGCTTATTCAATCTGCTCCACTGCAACTT
57108041 CAGGGAGATAAGACTAGATGAGATATGCTCTCTGTAACTTCAGAGAGATAAGATCTGTGATTTTA
65 CAGGGAGATAAGACTAGATGAGATATGCTCTCTGTAACTTCAGAGAGATAAGATCTGTGATTTTA
57108106 ATCCGCTCCACTAAAACTTCAAGGAGATAGGATTATAGGCTTAAATCTGCTCCACTGCAACTTCA
130 ATCCGCTCCACTAAAACTTCAAGGAGATAGGATTATAGGCTTAAATCTGCTCCACTGCAACTTCA
* * *
57108171 GGGAGATAAGATTCACCATTTTGGGTCTGTCCCACTGCAACTTCAGGAGGATAAGACTTGCTTAC
195 GAGAGATAAGATTCACCATTTTGGGTCTGCCCCACTGCAACTTCAGGAGGATAAGACCTGCTTAC
57108236 TT
260 TT
**
57108238 AGTCTGCTCCACTGCAACTTCAGGAAGATAAGAC
1 AGTCTGCTCCACTGCAACTTCAGGGGGATAAGAC
57108272 TATATGCGAT
Statistics
Matches: 280, Mismatches: 12, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
260 229 0.82
261 49 0.17
262 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (261 bp):
AGTCTGCTCCACTGCAACTTCAGGGGGATAAGACCTGCTTATTCAATCTGCTCCACTGCAACTTC
AGGGAGATAAGACTAGATGAGATATGCTCTCTGTAACTTCAGAGAGATAAGATCTGTGATTTTAA
TCCGCTCCACTAAAACTTCAAGGAGATAGGATTATAGGCTTAAATCTGCTCCACTGCAACTTCAG
AGAGATAAGATTCACCATTTTGGGTCTGCCCCACTGCAACTTCAGGAGGATAAGACCTGCTTACT
T
Found at i:57108244 original size:217 final size:217
Alignment explanation
Indices: 57107985--57108400 Score: 645
Period size: 217 Copynumber: 1.9 Consensus size: 217
57107975 TCAGTCTGCT
* *
57107985 CCACTGCAACTTCAGGGGGATAAGACCTGCTTATTCAGTCTGCTCCACTGCAACTTCAGGGAGAT
1 CCACTGCAACTTCAGGAGGATAAGACCTGCTTATTCAGTCTGCTCCACTGCAACTTCAGGAAGAT
*
57108050 AAGACTAGATGAGATATGCTCTCTGTAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCC
66 AAGACTAGATGAGATATGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCC
** *
57108115 ACTAAAACTTCAAGGAGATAGGATTATAGGCTTAAATCTGCTCCACTGCAACTTCAGGGAGATAA
131 ACTAAAACTTCAAGGAGATAAAATTATAGGCTTAAATCTGCTCCACTACAACTTCAGGGAGATAA
57108180 GATTCACCATTTTGGGTCTGTC
196 GATTCACCATTTTGGGTCTGTC
*
57108202 CCACTGCAACTTCAGGAGGATAAGACTTGCTTACTT-AGTCTGCTCCACTGCAACTTCAGGAAGA
1 CCACTGCAACTTCAGGAGGATAAGACCTGCTTA-TTCAGTCTGCTCCACTGCAACTTCAGGAAGA
* * * * *
57108266 TAAGACTATATGCGATCTGCTCTCTGCAACTTCTGAGAGATAAGATCTGTGATTTTAATTCGCTC
65 TAAGACTAGATGAGATATGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTC
** * * * * *
57108331 CACTGCAACTTCAGGGAGATAAAATTATTGGCTTTAGTCTGCTCCACTACAACTTCAGGGAGATT
130 CACTAAAACTTCAAGGAGATAAAATTATAGGCTTAAATCTGCTCCACTACAACTTCAGGGAGATA
57108396 AGATT
195 AGATT
57108401 TGCCATCTTC
Statistics
Matches: 179, Mismatches: 19, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
217 177 0.99
218 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (217 bp):
CCACTGCAACTTCAGGAGGATAAGACCTGCTTATTCAGTCTGCTCCACTGCAACTTCAGGAAGAT
AAGACTAGATGAGATATGCTCTCTGCAACTTCAGAGAGATAAGATCTGTGATTTTAATCCGCTCC
ACTAAAACTTCAAGGAGATAAAATTATAGGCTTAAATCTGCTCCACTACAACTTCAGGGAGATAA
GATTCACCATTTTGGGTCTGTC
Found at i:57108714 original size:44 final size:44
Alignment explanation
Indices: 57108651--57108741 Score: 164
Period size: 44 Copynumber: 2.1 Consensus size: 44
57108641 GTCAGGAAAG
*
57108651 TAGGATTCACAATCTTCAACCTATTCCACTGCCGACCAAGGAGA
1 TAGGACTCACAATCTTCAACCTATTCCACTGCCGACCAAGGAGA
*
57108695 TAGGACTCACAATCTTCAACCTATTCCACTGCTGACCAAGGAGA
1 TAGGACTCACAATCTTCAACCTATTCCACTGCCGACCAAGGAGA
57108739 TAG
1 TAG
57108742 AATTATATCT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.23
Consensus pattern (44 bp):
TAGGACTCACAATCTTCAACCTATTCCACTGCCGACCAAGGAGA
Found at i:57108849 original size:43 final size:43
Alignment explanation
Indices: 57108792--57108928 Score: 139
Period size: 43 Copynumber: 3.1 Consensus size: 43
57108782 CAAGATCTGC
57108792 TATCTTCAACCTGCTCCACTATAACCCAGGGAGGCAAGGCTGG
1 TATCTTCAACCTGCTCCACTATAACCCAGGGAGGCAAGGCTGG
* * * * * * *** * * *
57108835 TATCTTCGATCTGCTTCGCTGTCGATGTAGGAAGGCAAGATCTGC
1 TATCTTCAACCTGCTCCACTAT-AACCCAGGGAGGCAAG-GCTGG
*
57108880 TATCTTCAACCTGCTCCACTACAACCCAGGGAGGCAAGGCTGG
1 TATCTTCAACCTGCTCCACTATAACCCAGGGAGGCAAGGCTGG
57108923 TATCTT
1 TATCTT
57108929 GGATCTGCTT
Statistics
Matches: 67, Mismatches: 25, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
43 26 0.39
44 22 0.33
45 19 0.28
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (43 bp):
TATCTTCAACCTGCTCCACTATAACCCAGGGAGGCAAGGCTGG
Found at i:57108854 original size:88 final size:88
Alignment explanation
Indices: 57108747--57109010 Score: 431
Period size: 88 Copynumber: 3.0 Consensus size: 88
57108737 GATAGAATTA
57108747 TATCTTCGATCTGCTTCGCTGTCGATTG-AGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
1 TATCTTCGATCTGCTTCGCTGTCGA-TGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCAC
*
57108811 TATAACCCAGGGAGGCAAGGCTGG
65 TACAACCCAGGGAGGCAAGGCTGG
*
57108835 TATCTTCGATCTGCTTCGCTGTCGATGTAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
1 TATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
57108900 ACAACCCAGGGAGGCAAGGCTGG
66 ACAACCCAGGGAGGCAAGGCTGG
* * * * *
57108923 TATCTTGGATCTGCTTCGCTGTCGATGCAGGAAGGTAAGATCTGTTATCTTCAACCTACTCTACT
1 TATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
* *
57108988 ACAACTCAGGGAGGCAAGACTGG
66 ACAACCCAGGGAGGCAAGGCTGG
57109011 GAATTTCACC
Statistics
Matches: 166, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
87 2 0.01
88 164 0.99
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.27
Consensus pattern (88 bp):
TATCTTCGATCTGCTTCGCTGTCGATGCAGGAAGGCAAGATCTGCTATCTTCAACCTGCTCCACT
ACAACCCAGGGAGGCAAGGCTGG
Found at i:57108871 original size:44 final size:45
Alignment explanation
Indices: 57108747--57108974 Score: 167
Period size: 44 Copynumber: 5.2 Consensus size: 45
57108737 GATAGAATTA
** *
57108747 TATCTTCGATCTGCTTCGCTGTCGATTGAGGAAGGCAAGATCTGC
1 TATCTTCGATCTGCTTCGCTGTCGATCCAGGAAGGCAAGAGCTGC
* * * * * * * * *
57108792 TATCTTCAACCTGCTCCACTAT-AACCCAGGGAGGCAAG-GCTGG
1 TATCTTCGATCTGCTTCGCTGTCGATCCAGGAAGGCAAGAGCTGC
** *
57108835 TATCTTCGATCTGCTTCGCTGTCGATGTAGGAAGGCAAGATCTGC
1 TATCTTCGATCTGCTTCGCTGTCGATCCAGGAAGGCAAGAGCTGC
* * * * * * * * *
57108880 TATCTTCAACCTGCTCCACT-ACAACCCAGGGAGGCAAG-GCTGG
1 TATCTTCGATCTGCTTCGCTGTCGATCCAGGAAGGCAAGAGCTGC
* * * * *
57108923 TATCTTGGATCTGCTTCGCTGTCGATGCAGGAAGGTAAGATCTGT
1 TATCTTCGATCTGCTTCGCTGTCGATCCAGGAAGGCAAGAGCTGC
57108968 TATCTTC
1 TATCTTC
57108975 AACCTACTCT
Statistics
Matches: 129, Mismatches: 50, Indels: 8
0.69 0.27 0.04
Matches are distributed among these distances:
43 38 0.29
44 46 0.36
45 45 0.35
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (45 bp):
TATCTTCGATCTGCTTCGCTGTCGATCCAGGAAGGCAAGAGCTGC
Found at i:57118281 original size:15 final size:16
Alignment explanation
Indices: 57118247--57118284 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
57118237 AAAAAAAAAT
*
57118247 ATAAATAGACATGAAA
1 ATAAATAAACATGAAA
*
57118263 ATAAATAAAGATG-AA
1 ATAAATAAACATGAAA
57118278 ATAAATA
1 ATAAATA
57118285 TAAATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.66, C:0.03, G:0.11, T:0.21
Consensus pattern (16 bp):
ATAAATAAACATGAAA
Found at i:57122940 original size:2 final size:2
Alignment explanation
Indices: 57122933--57122968 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
57122923 AAAATATGTT
57122933 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57122969 CAACATAACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57124997 original size:24 final size:24
Alignment explanation
Indices: 57124970--57125025 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
57124960 TATATGTATT
57124970 TGAAAAAAATTTCAAAGCAAAATA
1 TGAAAAAAATTTCAAAGCAAAATA
57124994 TGAAAAAAATTTCAAAGCAAAATA
1 TGAAAAAAATTTCAAAGCAAAATA
*
57125018 AGAAAAAA
1 TGAAAAAA
57125026 TACTTTAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.66, C:0.07, G:0.09, T:0.18
Consensus pattern (24 bp):
TGAAAAAAATTTCAAAGCAAAATA
Found at i:57134349 original size:2 final size:2
Alignment explanation
Indices: 57134342--57134371 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
57134332 GCATGATAAG
57134342 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
57134372 ACAACTGTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:57135491 original size:2 final size:2
Alignment explanation
Indices: 57135480--57135524 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
57135470 GACTATTGAA
* *
57135480 AG AG -G AG AG AG AG AG AG AG GG AG AG AG AG AG AG AG AG AG AA
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
57135521 AG AG
1 AG AG
57135525 GATCCCCCGA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
AG
Found at i:57137273 original size:35 final size:35
Alignment explanation
Indices: 57137234--57137303 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
57137224 TGTTGAAGAG
57137234 TTAATGTTGGGATATGGTTGAAGTTTGAAGTAGGT
1 TTAATGTTGGGATATGGTTGAAGTTTGAAGTAGGT
57137269 TTAATGTTGGGATATGGTTGAAGTTTGAAGTAGGT
1 TTAATGTTGGGATATGGTTGAAGTTTGAAGTAGGT
57137304 GATACCACTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.34, T:0.40
Consensus pattern (35 bp):
TTAATGTTGGGATATGGTTGAAGTTTGAAGTAGGT
Found at i:57140039 original size:23 final size:23
Alignment explanation
Indices: 57139996--57140039 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
57139986 CGAAATAAAT
**
57139996 TGTAATTTTTACTATAGTAAAAA
1 TGTAATTTTTAAAATAGTAAAAA
*
57140019 TGTAATTTTTAAAATATTAAA
1 TGTAATTTTTAAAATAGTAAA
57140040 TCAAAATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (23 bp):
TGTAATTTTTAAAATAGTAAAAA
Found at i:57141856 original size:14 final size:14
Alignment explanation
Indices: 57141826--57141871 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 14
57141816 GATTCTAAAA
57141826 ATTATAGATTATTATT
1 ATTATA-ATT-TTATT
57141842 ATTATAATTTTATT
1 ATTATAATTTTATT
* *
57141856 ATTAAAATTTTTTT
1 ATTATAATTTTATT
57141870 AT
1 AT
57141872 ACCTATGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 19 0.68
15 3 0.11
16 6 0.21
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
ATTATAATTTTATT
Found at i:57147958 original size:62 final size:61
Alignment explanation
Indices: 57147848--57148047 Score: 190
Period size: 62 Copynumber: 3.2 Consensus size: 61
57147838 TCAATTTAAC
* * * *
57147848 ATTAAATTAATATAATATTTAT-T-AAGATAAATATTAGATTAAATTTAATATTAAATATT
1 ATTAAAATAATAAAATATTTATCTAAAGATAAACATTAAATTAAATTTAATATTAAATATT
**
57147907 ATTAAAATAATAAAATATTTATCTACAAGATAAACATTAAATTAAATTTAATATTAAGATAACC
1 ATTAAAATAATAAAATATTTATCTA-AAGATAAACATTAAATTAAATTTAATATTAA-AT-ATT
* * * ** **
57147971 ATTTAAATATTAAATTAATAAAATACTATTAAGATATGCATTAAATTAAATTTAATATTAAA-AT
1 ATTAAAATAATAAAAT-AT-TTAT-CTA--AAGATAAACATTAAATTAAATTTAATATTAAATAT
57148035 T
61 T
57148036 ATTAAAATAATA
1 ATTAAAATAATA
57148048 TTATTTTTGG
Statistics
Matches: 114, Mismatches: 18, Indels: 12
0.79 0.12 0.08
Matches are distributed among these distances:
59 20 0.18
60 1 0.01
62 29 0.25
63 2 0.02
64 14 0.12
65 13 0.11
66 2 0.02
67 4 0.04
68 29 0.25
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.40
Consensus pattern (61 bp):
ATTAAAATAATAAAATATTTATCTAAAGATAAACATTAAATTAAATTTAATATTAAATATT
Found at i:57148048 original size:68 final size:69
Alignment explanation
Indices: 57147894--57148050 Score: 158
Period size: 68 Copynumber: 2.2 Consensus size: 69
57147884 GATTAAATTT
* *
57147894 AATATTAAATATTATTAAAATAATAAAATATTTATCTACAAGATAAACATTAAATTAAATTTAAT
1 AATATTAAATAATATTAAAATAATAAAATATCTATCTA-AAGATAAACATTAAATTAAATTTAAT
57147959 ATTAA
65 ATTAA
* ** ** * **
57147964 GATAACCATTTAAATATTAAATTAATAAAATA-CTAT-T-AAGATATGCATTAAATTAAATTTAA
1 AAT-ATTAAAT-AATATTAAAATAATAAAATATCTATCTAAAGATAAACATTAAATTAAATTTAA
57148026 TATTAA
64 TATTAA
57148032 AATTATTAAAATAATATTA
1 AA-TATT-AAATAATATTA
57148051 TTTTTGGAAT
Statistics
Matches: 68, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
68 38 0.56
69 3 0.04
70 3 0.04
71 6 0.09
72 18 0.26
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (69 bp):
AATATTAAATAATATTAAAATAATAAAATATCTATCTAAAGATAAACATTAAATTAAATTTAATA
TTAA
Found at i:57149900 original size:42 final size:43
Alignment explanation
Indices: 57149774--57149925 Score: 121
Period size: 43 Copynumber: 3.5 Consensus size: 43
57149764 ATAGGCTTCT
* ** * *
57149774 GATATGTGATTTCGTGTAAGACCACGTTTGGGAC-GTTGGCATC
1 GATATATGATTTCGTGTAAGACCATATCTGGGACAG-TGGCACC
* * * *
57149817 GATTTGA-GATTTACGTGTAAGACCATGTCTGGGGCATTGGCACC
1 GATAT-ATGATTT-CGTGTAAGACCATATCTGGGACAGTGGCACC
* * *
57149861 G-TATATGATTTCGTGTAAGACCCTATCTGGGATAGTGGCATC
1 GATATATGATTTCGTGTAAGACCATATCTGGGACAGTGGCACC
* * *
57149903 GATATTTGATTACATGTAAGACC
1 GATATATGATTTCGTGTAAGACC
57149926 TCGTCTGGGA
Statistics
Matches: 87, Mismatches: 17, Indels: 10
0.76 0.15 0.09
Matches are distributed among these distances:
42 27 0.31
43 34 0.39
44 26 0.30
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (43 bp):
GATATATGATTTCGTGTAAGACCATATCTGGGACAGTGGCACC
Found at i:57158037 original size:23 final size:23
Alignment explanation
Indices: 57157994--57158042 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
57157984 GAGACGTGGC
* *
57157994 ATCGCGTCGTCGAGACAAGGGGT
1 ATCGCGTCATCGAGACAAGGGCT
**
57158017 ATCGCGTCATCGAGATGAGGGCT
1 ATCGCGTCATCGAGACAAGGGCT
57158040 ATC
1 ATC
57158043 TTCTCGTCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.22, G:0.35, T:0.20
Consensus pattern (23 bp):
ATCGCGTCATCGAGACAAGGGCT
Found at i:57158493 original size:19 final size:19
Alignment explanation
Indices: 57158465--57158504 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
57158455 ATATATTAAA
*
57158465 AAATATTTTTATAATTTTT
1 AAATAATTTTATAATTTTT
*
57158484 AAATAATTTTATGATTTTT
1 AAATAATTTTATAATTTTT
57158503 AA
1 AA
57158505 TTTTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
AAATAATTTTATAATTTTT
Found at i:57158517 original size:38 final size:40
Alignment explanation
Indices: 57158475--57158553 Score: 108
Period size: 38 Copynumber: 2.0 Consensus size: 40
57158465 AAATATTTTT
*
57158475 ATAATTTTTAAATAATTTTATG-ATTTTT-AATTTTTAAA
1 ATAATTTTTAAATAATTTTATGAATTTTTAAATTTTCAAA
** *
57158513 ATAATTTTTTTATAATTTTTTGAATTTTTAAATTTTCAAA
1 ATAATTTTTAAATAATTTTATGAATTTTTAAATTTTCAAA
57158553 A
1 A
57158554 ATTAATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 19 0.54
39 6 0.17
40 10 0.29
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (40 bp):
ATAATTTTTAAATAATTTTATGAATTTTTAAATTTTCAAA
Found at i:57161134 original size:20 final size:20
Alignment explanation
Indices: 57161102--57161154 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
57161092 ACCAATTTAT
*
57161102 AGACAAGCCACCAG-ATTCAC
1 AGACAAGCTACCAGAATT-AC
* *
57161122 AGATAAGCTACCAGAATTGC
1 AGACAAGCTACCAGAATTAC
57161142 AGACAAGCTACCA
1 AGACAAGCTACCA
57161155 TAAATGTGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.42, C:0.28, G:0.17, T:0.13
Consensus pattern (20 bp):
AGACAAGCTACCAGAATTAC
Found at i:57169705 original size:25 final size:25
Alignment explanation
Indices: 57169629--57169731 Score: 109
Period size: 25 Copynumber: 4.2 Consensus size: 25
57169619 GTTATAAACA
* *
57169629 GTAAGCTCATCCGAGCTGAACAACG
1 GTAAGCTCATCCGAGCTGAATAATG
* *
57169654 GTAAGCTCCTCCGAGATGAATAATG
1 GTAAGCTCATCCGAGCTGAATAATG
* * *
57169679 GTAAGCTCATGCGAGCTGAGTATTG
1 GTAAGCTCATCCGAGCTGAATAATG
* * *
57169704 GTAAGCTCATACAAGCTGAA-ATTG
1 GTAAGCTCATCCGAGCTGAATAATG
57169728 GTAA
1 GTAA
57169732 CCCTAATGAC
Statistics
Matches: 66, Mismatches: 12, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
24 8 0.12
25 58 0.88
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.23
Consensus pattern (25 bp):
GTAAGCTCATCCGAGCTGAATAATG
Found at i:57171436 original size:21 final size:21
Alignment explanation
Indices: 57171386--57171436 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
57171376 TAGATAGTTC
*
57171386 TTTTATTTTTGTATATTGTTG
1 TTTTATTTTTGTAAATTGTTG
*
57171407 TTTTCTTTTTGTGAAATT-TT-
1 TTTTATTTTTGT-AAATTGTTG
57171427 TATTTATTTT
1 T-TTTATTTT
57171437 CCTTGTTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
20 1 0.04
21 20 0.80
22 4 0.16
ACGTcount: A:0.16, C:0.02, G:0.10, T:0.73
Consensus pattern (21 bp):
TTTTATTTTTGTAAATTGTTG
Found at i:57174667 original size:22 final size:21
Alignment explanation
Indices: 57174602--57174667 Score: 55
Period size: 22 Copynumber: 3.1 Consensus size: 21
57174592 TACTTTCCAA
*
57174602 TTTTAGTT-T-TATTTTTATGC
1 TTTTAGTTATGTATTTCT-TGC
* * *
57174622 TTTTAGTTATGTTTTTGTTTC
1 TTTTAGTTATGTATTTCTTGC
*
57174643 TTTTCGTTCATGTATTTCTTGC
1 TTTTAGTT-ATGTATTTCTTGC
57174665 TTT
1 TTT
57174668 GTTTTGTAGG
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
20 8 0.22
21 10 0.28
22 18 0.50
ACGTcount: A:0.11, C:0.09, G:0.12, T:0.68
Consensus pattern (21 bp):
TTTTAGTTATGTATTTCTTGC
Found at i:57176215 original size:7 final size:7
Alignment explanation
Indices: 57176198--57176226 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
57176188 AAGGGTAGTG
57176198 ATAAT-A
1 ATAATCA
57176204 ATAATCA
1 ATAATCA
57176211 ATAATCA
1 ATAATCA
57176218 ATAATCA
1 ATAATCA
57176225 AT
1 AT
57176227 TTATTGTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 5 0.23
7 17 0.77
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (7 bp):
ATAATCA
Found at i:57176888 original size:19 final size:20
Alignment explanation
Indices: 57176849--57176889 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
57176839 GATGGATAGG
*
57176849 ATCGTTTTCCTAAAATATGC
1 ATCGTTTTACTAAAATATGC
*
57176869 ATCGTTTTAC-AAATTATGC
1 ATCGTTTTACTAAAATATGC
57176888 AT
1 AT
57176890 TGACATATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.32, C:0.17, G:0.10, T:0.41
Consensus pattern (20 bp):
ATCGTTTTACTAAAATATGC
Found at i:57179083 original size:43 final size:44
Alignment explanation
Indices: 57178923--57179084 Score: 116
Period size: 43 Copynumber: 3.8 Consensus size: 44
57178913 CGATATGTAA
* * * * * * *
57178923 TTACATGTAAGAACACGTCTGGGACGTTGGCGTCGATTGGTGAT
1 TTACATGTAAGACCATGTCTGGGACATTGGCATCGATAGTTGAG
* * * **
57178967 TTACGTGTAAGACCATGTCTAGGATATCAGCATCG-TA-TATGAG
1 TTACATGTAAGACCATGTCTGGGACATTGGCATCGATAGT-TGAG
* * * * *
57179010 TT-CGTGTAAGACCCTTTCGGGGACAATGGCATCGATAGTTGA-
1 TTACATGTAAGACCATGTCTGGGACATTGGCATCGATAGTTGAG
* *
57179052 TTACATGTAAGACCATGCCTGGGACGTTGGCAT
1 TTACATGTAAGACCATGTCTGGGACATTGGCAT
57179085 TGTACGAGCT
Statistics
Matches: 87, Mismatches: 27, Indels: 9
0.71 0.22 0.07
Matches are distributed among these distances:
42 26 0.30
43 34 0.39
44 27 0.31
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (44 bp):
TTACATGTAAGACCATGTCTGGGACATTGGCATCGATAGTTGAG
Found at i:57183828 original size:20 final size:20
Alignment explanation
Indices: 57183715--57183841 Score: 69
Period size: 20 Copynumber: 6.3 Consensus size: 20
57183705 GGATCATAGA
* *
57183715 TGCATAACAGAGGCACCAAAG
1 TGCA-AACAAAGGCACCGAAG
57183736 TG-AAAGCAAAGGCA-CGAATG
1 TGCAAA-CAAAGGCACCGAA-G
** * * *
57183756 TGCAAGTAGAGGCACAGTAG
1 TGCAAACAAAGGCACCGAAG
** * *
57183776 TGTGAACAAAGACACTGAAG
1 TGCAAACAAAGGCACCGAAG
* * *
57183796 TGTATAGAAAGGCACCGAAG
1 TGCAAACAAAGGCACCGAAG
* *
57183816 TGCAAACAGAGGCACTGAAG
1 TGCAAACAAAGGCACCGAAG
57183836 TGCAAA
1 TGCAAA
57183842 TCCCGTACAA
Statistics
Matches: 77, Mismatches: 25, Indels: 9
0.69 0.23 0.08
Matches are distributed among these distances:
19 5 0.06
20 66 0.86
21 6 0.08
ACGTcount: A:0.42, C:0.17, G:0.28, T:0.13
Consensus pattern (20 bp):
TGCAAACAAAGGCACCGAAG
Found at i:57197339 original size:35 final size:35
Alignment explanation
Indices: 57197293--57197360 Score: 136
Period size: 35 Copynumber: 1.9 Consensus size: 35
57197283 CATAGTGATG
57197293 CCATTCTTTTTAGGCACACATTGTATTAAACTTAC
1 CCATTCTTTTTAGGCACACATTGTATTAAACTTAC
57197328 CCATTCTTTTTAGGCACACATTGTATTAAACTT
1 CCATTCTTTTTAGGCACACATTGTATTAAACTT
57197361 CCTTTATCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.28, C:0.22, G:0.09, T:0.41
Consensus pattern (35 bp):
CCATTCTTTTTAGGCACACATTGTATTAAACTTAC
Found at i:57203234 original size:9 final size:9
Alignment explanation
Indices: 57203220--57203244 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
57203210 ATCATAGTTG
57203220 AACTCTCTA
1 AACTCTCTA
57203229 AACTCTCTA
1 AACTCTCTA
57203238 AACTCTC
1 AACTCTC
57203245 CCCATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.36, G:0.00, T:0.32
Consensus pattern (9 bp):
AACTCTCTA
Found at i:57206462 original size:18 final size:18
Alignment explanation
Indices: 57206436--57206480 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
57206426 AATTAAAGAA
57206436 AATGTTTTG-AAATTGAAT
1 AATGTTTTGTAAA-TGAAT
*
57206454 AATGATTTGTAAATGAAT
1 AATGTTTTGTAAATGAAT
57206472 AATGTTTTG
1 AATGTTTTG
57206481 GAAACGAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.18, T:0.44
Consensus pattern (18 bp):
AATGTTTTGTAAATGAAT
Found at i:57211588 original size:4 final size:4
Alignment explanation
Indices: 57211579--57211612 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
57211569 TCACATTTCC
57211579 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT AT
57211613 CATTCTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
ATTT
Found at i:57217758 original size:18 final size:18
Alignment explanation
Indices: 57217731--57217765 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
57217721 AAATGGGGTT
57217731 TAAAATTTAAAACTAAAAC
1 TAAAATTTAAAAC-AAAAC
57217750 TAAAA-TTAAAACAAAA
1 TAAAATTTAAAACAAAA
57217766 TAAGAAGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 7 0.44
19 5 0.31
ACGTcount: A:0.69, C:0.09, G:0.00, T:0.23
Consensus pattern (18 bp):
TAAAATTTAAAACAAAAC
Found at i:57218635 original size:9 final size:9
Alignment explanation
Indices: 57218621--57218651 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
57218611 GTTAAACGAA
57218621 TCGAGTTAT
1 TCGAGTTAT
*
57218630 TCGAGTTAA
1 TCGAGTTAT
57218639 TCGAGTTAT
1 TCGAGTTAT
57218648 TCGA
1 TCGA
57218652 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:57218722 original size:9 final size:9
Alignment explanation
Indices: 57218705--57218741 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
57218695 TGAGTTTTCG
57218705 AATTCGAAT
1 AATTCGAAT
*
57218714 AACTCGAAT
1 AATTCGAAT
57218723 AATTCGAAT
1 AATTCGAAT
57218732 AATTCGAAT
1 AATTCGAAT
57218741 A
1 A
57218742 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:57220500 original size:5 final size:5
Alignment explanation
Indices: 57220490--57220515 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
57220480 CTCGAAAATT
57220490 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
57220516 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:57221318 original size:16 final size:16
Alignment explanation
Indices: 57221292--57221331 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 16
57221282 TTAATCATGC
57221292 AATAAATTATTA--AT
1 AATAAATTATTATTAT
*
57221306 -ATAAATTATTATTTT
1 AATAAATTATTATTAT
57221321 AATAAATTATT
1 AATAAATTATT
57221332 TAATATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
13 11 0.50
15 1 0.05
16 10 0.45
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATAAATTATTATTAT
Found at i:57221325 original size:29 final size:30
Alignment explanation
Indices: 57221292--57221356 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 30
57221282 TTAATCATGC
57221292 AATAAATTA-TTAATA-TAAATTATTATTTT
1 AATAAATTATTTAATATTAAATT-TTATTTT
*
57221321 AATAAATTATTTAATATTTTAATTTTATTTT
1 AATAAATTATTTAATA-TTAAATTTTATTTT
57221352 AATAA
1 AATAA
57221357 TAAATTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 9 0.28
30 6 0.19
31 12 0.38
32 5 0.16
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (30 bp):
AATAAATTATTTAATATTAAATTTTATTTT
Found at i:57221375 original size:14 final size:14
Alignment explanation
Indices: 57221347--57221386 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
57221337 TTTTAATTTT
*
57221347 ATTTTAATAAT-AA
1 ATTTTAAAAATAAA
57221360 ATTTTAAAAATAAA
1 ATTTTAAAAATAAA
57221374 ATTTTAAATAATA
1 ATTTTAAA-AATA
57221387 TTCTTCAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 10 0.42
14 10 0.42
15 4 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
ATTTTAAAAATAAA
Found at i:57222875 original size:2 final size:2
Alignment explanation
Indices: 57222868--57222900 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
57222858 AGGAAGTCGT
57222868 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
57222901 GTTAAAATCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:57225866 original size:9 final size:9
Alignment explanation
Indices: 57225852--57225900 Score: 64
Period size: 9 Copynumber: 5.4 Consensus size: 9
57225842 TTTGGTTAAA
57225852 AATTAACCG
1 AATTAACCG
*
57225861 AATTAATCG
1 AATTAACCG
*
57225870 AATTACCCG
1 AATTAACCG
57225879 AATT-ACTCG
1 AATTAAC-CG
57225888 AATTAACCG
1 AATTAACCG
57225897 AATT
1 AATT
57225901 GAATCACTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
8 1 0.03
9 31 0.91
10 2 0.06
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (9 bp):
AATTAACCG
Found at i:57225879 original size:18 final size:18
Alignment explanation
Indices: 57225852--57225905 Score: 81
Period size: 18 Copynumber: 2.9 Consensus size: 18
57225842 TTTGGTTAAA
57225852 AATTAACCGAATTAATCG
1 AATTAACCGAATTAATCG
* *
57225870 AATTACCCGAATTACTCG
1 AATTAACCGAATTAATCG
57225888 AATTAACCGAATTGAATC
1 AATTAACCGAATT-AATC
57225906 ACTACATAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 28 0.90
19 3 0.10
ACGTcount: A:0.41, C:0.20, G:0.11, T:0.28
Consensus pattern (18 bp):
AATTAACCGAATTAATCG
Found at i:57225999 original size:19 final size:20
Alignment explanation
Indices: 57225975--57226012 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
57225965 TTGTTTAGAC
57225975 TTTTAG-ATTTTAGTTTTAG
1 TTTTAGAATTTTAGTTTTAG
*
57225994 TTTTAGAATTTTATTTTTA
1 TTTTAGAATTTTAGTTTTA
57226013 TTTATTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.24, C:0.00, G:0.11, T:0.66
Consensus pattern (20 bp):
TTTTAGAATTTTAGTTTTAG
Found at i:57226023 original size:20 final size:19
Alignment explanation
Indices: 57225939--57226023 Score: 55
Period size: 20 Copynumber: 4.2 Consensus size: 19
57225929 TAAGTCTTTG
*
57225939 AATTTTGTTTTTATTTATTA
1 AATTTTATTTTTATTT-TTA
* *
57225959 AATTATT-TGTTTAGACTTTTA
1 AATT-TTAT-TTT-TATTTTTA
* * *
57225980 GATTTTAGTTTTAGTTTTA
1 AATTTTATTTTTATTTTTA
57225999 GAATTTTATTTTTATTTATTA
1 -AATTTTATTTTTATTT-TTA
57226020 AATT
1 AATT
57226024 ATTTGTAATT
Statistics
Matches: 50, Mismatches: 9, Indels: 12
0.70 0.13 0.17
Matches are distributed among these distances:
19 6 0.12
20 27 0.54
21 14 0.28
22 3 0.06
ACGTcount: A:0.27, C:0.01, G:0.08, T:0.64
Consensus pattern (19 bp):
AATTTTATTTTTATTTTTA
Found at i:57228542 original size:28 final size:28
Alignment explanation
Indices: 57228510--57228607 Score: 151
Period size: 28 Copynumber: 3.5 Consensus size: 28
57228500 TAATGAGATT
57228510 AGCACTAAGTGTGCGAGTTTAATTGTAA
1 AGCACTAAGTGTGCGAGTTTAATTGTAA
*
57228538 AGCACTAAGTGTGCGAGTTTAATGGTAA
1 AGCACTAAGTGTGCGAGTTTAATTGTAA
* * * *
57228566 AGCACTAAGTGTGTGAGTTTGATTATTA
1 AGCACTAAGTGTGCGAGTTTAATTGTAA
57228594 AGCACTAAGTGTGC
1 AGCACTAAGTGTGC
57228608 AAACTTATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 63 1.00
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.32
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTTTAATTGTAA
Found at i:57237547 original size:20 final size:21
Alignment explanation
Indices: 57237504--57237547 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
57237494 TCATGATATA
* *
57237504 TTATAAAAAATAATATACTTAT
1 TTATAAAAAAAAATATAC-AAT
57237526 TTATAAAAAAAAATATA-AAT
1 TTATAAAAAAAAATATACAAT
57237546 TT
1 TT
57237548 TTTCATAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
22 16 0.80
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TTATAAAAAAAAATATACAAT
Found at i:57239149 original size:15 final size:15
Alignment explanation
Indices: 57239111--57239152 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
57239101 GAAAGTTTTG
*
57239111 AAAATTTTCAAAAAA
1 AAAATATTCAAAAAA
57239126 AAAA-ATTCAAAAAA
1 AAAATATTCAAAAAA
*
57239140 AAAATCTTCAAAA
1 AAAATATTCAAAA
57239153 TTTAAAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (15 bp):
AAAATATTCAAAAAA
Found at i:57249673 original size:21 final size:21
Alignment explanation
Indices: 57249649--57249702 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 21
57249639 CATTTTCTAA
57249649 AACCATTTGACTTTTGGAATT
1 AACCATTTGACTTTTGGAATT
*
57249670 AACCACTTG---TTTGGAATT
1 AACCATTTGACTTTTGGAATT
*
57249688 AACCACTTTAACTTT
1 AACCA-TTTGACTTT
57249703 ATTATACGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 7
0.72 0.08 0.19
Matches are distributed among these distances:
18 14 0.54
19 2 0.08
21 8 0.31
22 2 0.08
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (21 bp):
AACCATTTGACTTTTGGAATT
Found at i:57249684 original size:18 final size:18
Alignment explanation
Indices: 57249661--57249695 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
57249651 CCATTTGACT
57249661 TTTGGAATTAACCACTTG
1 TTTGGAATTAACCACTTG
57249679 TTTGGAATTAACCACTT
1 TTTGGAATTAACCACTT
57249696 TAACTTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (18 bp):
TTTGGAATTAACCACTTG
Found at i:57255994 original size:14 final size:14
Alignment explanation
Indices: 57255975--57256002 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
57255965 GTTTAAAGAT
57255975 GGTTAAAAACTAAG
1 GGTTAAAAACTAAG
57255989 GGTTAAAAACTAAG
1 GGTTAAAAACTAAG
57256003 TAAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.07, G:0.21, T:0.21
Consensus pattern (14 bp):
GGTTAAAAACTAAG
Found at i:57258485 original size:15 final size:16
Alignment explanation
Indices: 57258462--57258491 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
57258452 AAAAATTAAT
57258462 ATATAAATTATAAATA
1 ATATAAATTATAAATA
57258478 ATAT-AATTATAAAT
1 ATATAAATTATAAAT
57258492 TAAAGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATATAAATTATAAATA
Found at i:57258489 original size:22 final size:21
Alignment explanation
Indices: 57258450--57258493 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
57258440 AGCTAAGTTG
57258450 ATAAAAATTAATATATAAATT
1 ATAAAAATTAATATATAAATT
57258471 ATAAATAATATAAT-TATAAATT
1 ATAAA-AAT-TAATATATAAATT
57258493 A
1 A
57258494 AAGTTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.24
22 12 0.57
23 4 0.19
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
ATAAAAATTAATATATAAATT
Found at i:57266188 original size:19 final size:20
Alignment explanation
Indices: 57266144--57266188 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
57266134 ATCATGTTCA
57266144 TATTTTTAACATAGTTTAAT
1 TATTTTTAACATAGTTTAAT
57266164 TA-TTTTATA-ATA-TTTAAT
1 TATTTTTA-ACATAGTTTAAT
57266182 TATTTTT
1 TATTTTT
57266189 CGACAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.35
19 12 0.52
20 3 0.13
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (20 bp):
TATTTTTAACATAGTTTAAT
Found at i:57272066 original size:29 final size:29
Alignment explanation
Indices: 57272004--57272209 Score: 114
Period size: 29 Copynumber: 7.0 Consensus size: 29
57271994 AGTGGGATCA
* * *
57272004 CGATGGTCGTCACCGTCCCTTTTCATAGT
1 CGATAGTCGTCACCATCCCTTTTCATAAT
*
57272033 TGATAGTCGTCACCATCCCTTTTCATAAT
1 CGATAGTCGTCACCATCCCTTTTCATAAT
* * * * *
57272062 CGATAG-C-TGAAGCTATTCATTTTCATAGTT
1 CGATAGTCGT-CA-CCATCCCTTTTCATA-AT
* * * * *
57272092 TGATGGTTGTCACCATCCTTTTTCAATATT
1 CGATAGTCGTCACCATCCCTTTTC-ATAAT
* * * *
57272122 CGATAGCCG-AAGCTATACCTTTTCATAATT
1 CGATAGTCGTCA-CCATCCCTTTTCATAA-T
* *
57272152 CAATGGTCGTCACCATCCCTTTTCATAAT
1 CGATAGTCGTCACCATCCCTTTTCATAAT
* * *
57272181 CGATAGCCG-AAGCTATCCCTTTTCATAAT
1 CGATAGTCGTCA-CCATCCCTTTTCATAAT
57272210 TCGGTGATCA
Statistics
Matches: 130, Mismatches: 37, Indels: 20
0.70 0.20 0.11
Matches are distributed among these distances:
27 1 0.01
28 3 0.02
29 69 0.53
30 51 0.39
31 5 0.04
32 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.14, T:0.37
Consensus pattern (29 bp):
CGATAGTCGTCACCATCCCTTTTCATAAT
Found at i:57272145 original size:30 final size:29
Alignment explanation
Indices: 57272047--57272212 Score: 102
Period size: 30 Copynumber: 5.6 Consensus size: 29
57272037 AGTCGTCACC
* *
57272047 ATCCCTTTTCATAATCGATAGCTGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
* * * * ** * *
57272076 ATTCATTTTCATAGTTTGATGGTTGTCA-CC
1 ATCCCTTTTCATA-TTCGATAGCCG-AAGCT
*
57272106 ATCCTTTTTCAATATTCGATAGCCGAAGCT
1 ATCCCTTTTC-ATATTCGATAGCCGAAGCT
* * * * * *
57272136 ATACCTTTTCATAATTCAATGGTCGTCA-CC
1 ATCCCTTTTCAT-ATTCGATAGCCG-AAGCT
*
57272166 ATCCCTTTTCATAATCGATAGCCGAAGCT
1 ATCCCTTTTCATATTCGATAGCCGAAGCT
57272195 ATCCCTTTTCATAATTCG
1 ATCCCTTTTCAT-ATTCG
57272213 GTGATCATCG
Statistics
Matches: 98, Mismatches: 31, Indels: 15
0.68 0.22 0.10
Matches are distributed among these distances:
28 1 0.01
29 35 0.36
30 57 0.58
31 5 0.05
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (29 bp):
ATCCCTTTTCATATTCGATAGCCGAAGCT
Found at i:57272208 original size:59 final size:59
Alignment explanation
Indices: 57272019--57272212 Score: 264
Period size: 59 Copynumber: 3.3 Consensus size: 59
57272009 GTCGTCACCG
* * *
57272019 TCCCTTTTCATAGTT-GATAGTCGTCACCATCCCTTTTCATAATCGATAGCTGAAGCTA
1 TCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTA
* * * * * * *
57272077 TTCATTTTCATAGTTTGATGGTTGTCACCATCCTTTTTCAATATTCGATAGCCGAAGCTA
1 TCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTC-ATAATCGATAGCCGAAGCTA
* *
57272137 TACCTTTTCATAATTCAATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTA
1 TCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTA
57272196 TCCCTTTTCATAATTCG
1 TCCCTTTTCATAATTCG
57272213 GTGATCATCG
Statistics
Matches: 117, Mismatches: 17, Indels: 3
0.85 0.12 0.02
Matches are distributed among these distances:
58 13 0.11
59 54 0.46
60 50 0.43
ACGTcount: A:0.24, C:0.25, G:0.13, T:0.38
Consensus pattern (59 bp):
TCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAATCGATAGCCGAAGCTA
Found at i:57298008 original size:40 final size:40
Alignment explanation
Indices: 57297953--57298130 Score: 205
Period size: 40 Copynumber: 4.5 Consensus size: 40
57297943 GTATAAATAG
* **
57297953 GGGCACGTAAGTGCATTCCGGGGTACCGAAGTACAAACAA
1 GGGCACGTATGTGCATTCAAGGGTACCGAAGTACAAACAA
*
57297993 GGGCACGTATGTGCATTCAAGGGTACTGAAGTACAAACAA
1 GGGCACGTATGTGCATTCAAGGGTACCGAAGTACAAACAA
* * * ** *
57298033 GGTCACATATGTGCATTCAGGGGTACAAAAGTACAATCAA
1 GGGCACGTATGTGCATTCAAGGGTACCGAAGTACAAACAA
* * * *
57298073 GGGCACATATGTGCATT-TAGGGTACCGAAGTACAAATAG
1 GGGCACGTATGTGCATTCAAGGGTACCGAAGTACAAACAA
* *
57298112 GGGCATGTATGTGTATTCA
1 GGGCACGTATGTGCATTCA
57298131 TTCAATAATT
Statistics
Matches: 115, Mismatches: 22, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
39 29 0.25
40 86 0.75
ACGTcount: A:0.33, C:0.17, G:0.28, T:0.22
Consensus pattern (40 bp):
GGGCACGTATGTGCATTCAAGGGTACCGAAGTACAAACAA
Found at i:57298033 original size:20 final size:19
Alignment explanation
Indices: 57297973--57298034 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
57297963 GTGCATTCCG
57297973 GGGTACCGAAGTACAAACAA
1 GGGTA-CGAAGTACAAACAA
* * * **
57297993 GGGCACGTATGTGCATTCAA
1 GGGTACG-AAGTACAAACAA
57298013 GGGTACTGAAGTACAAACAA
1 GGGTAC-GAAGTACAAACAA
57298033 GG
1 GG
57298035 TCACATATGT
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 2 0.07
20 27 0.90
21 1 0.03
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (19 bp):
GGGTACGAAGTACAAACAA
Found at i:57299636 original size:82 final size:82
Alignment explanation
Indices: 57299512--57299667 Score: 294
Period size: 82 Copynumber: 1.9 Consensus size: 82
57299502 AATCTATACT
*
57299512 GTCTTAGCATTGAAACGTGGAACACGTTATGAATTTTCTCAAGTTCAAGAGGTAAAGCTAATTTG
1 GTCTTAGCATTGAAACATGGAACACGTTATGAATTTTCTCAAGTTCAAGAGGTAAAGCTAATTTG
57299577 TAAGCTATAGCACTGAA
66 TAAGCTATAGCACTGAA
57299594 GTCTTAGCATTGAAACATGGAACACGTTATGAATTTTCTCAAGTTCAAGAGGTAAAGCTAATTTG
1 GTCTTAGCATTGAAACATGGAACACGTTATGAATTTTCTCAAGTTCAAGAGGTAAAGCTAATTTG
*
57299659 TAAGGTATA
66 TAAGCTATA
57299668 TACTGATTCT
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 72 1.00
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (82 bp):
GTCTTAGCATTGAAACATGGAACACGTTATGAATTTTCTCAAGTTCAAGAGGTAAAGCTAATTTG
TAAGCTATAGCACTGAA
Found at i:57319944 original size:23 final size:24
Alignment explanation
Indices: 57319888--57319947 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
57319878 TTATTAACAT
*
57319888 TGTTCGTGAATATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTATA
* *
57319912 TGTTCATGAACATGTTCATTTA-A
1 TGTTCGTGAACATGTTCAATTATA
57319935 TGTTCGTGAACAT
1 TGTTCGTGAACAT
57319948 TAAACAAACG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 13 0.41
24 19 0.59
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCAATTATA
Found at i:57324572 original size:2 final size:2
Alignment explanation
Indices: 57324565--57324595 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57324555 ACCCTATCTC
57324565 AT AT 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 AT AT A
57324596 CATTATTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:57328304 original size:16 final size:16
Alignment explanation
Indices: 57328281--57328330 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
57328271 TAAAAAGTAA
57328281 TTAGAATATATAATAT
1 TTAGAATATATAATAT
* *
57328297 TTCA-AATA-AAAATAA
1 TT-AGAATATATAATAT
57328312 TTAGAATATATAATAT
1 TTAGAATATATAATAT
57328328 TTA
1 TTA
57328331 AAAATAAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
14 1 0.04
15 11 0.41
16 14 0.52
17 1 0.04
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (16 bp):
TTAGAATATATAATAT
Found at i:57328316 original size:31 final size:32
Alignment explanation
Indices: 57328266--57328338 Score: 121
Period size: 31 Copynumber: 2.3 Consensus size: 32
57328256 AGATACTAAC
57328266 TCAAATAAAAAGTAATTAGAATATATAATATT
1 TCAAATAAAAAGTAATTAGAATATATAATATT
57328298 TCAAATAAAAA-TAATTAGAATATATAATATT
1 TCAAATAAAAAGTAATTAGAATATATAATATT
*
57328329 TAAAAATAAA
1 T-CAAATAAA
57328339 TTTTAAATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
31 21 0.54
32 18 0.46
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (32 bp):
TCAAATAAAAAGTAATTAGAATATATAATATT
Found at i:57328319 original size:15 final size:15
Alignment explanation
Indices: 57328269--57328319 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
57328259 TACTAACTCA
57328269 AATAAAAAGTAATTAG
1 AATAAAAA-TAATTAG
* *
57328285 AATATATAATATTTCA-
1 AATA-AAAATAATT-AG
57328301 AATAAAAATAATTAG
1 AATAAAAATAATTAG
57328316 AATA
1 AATA
57328320 TATAATATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 7
0.72 0.10 0.18
Matches are distributed among these distances:
14 1 0.04
15 11 0.39
16 12 0.43
17 4 0.14
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (15 bp):
AATAAAAATAATTAG
Found at i:57328495 original size:17 final size:17
Alignment explanation
Indices: 57328454--57328495 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
57328444 TTTCATTGCT
*
57328454 ATTATTTTGATTGTCAA
1 ATTATTTGGATTGTCAA
57328471 ATTAATTTGGA-TGTCTAA
1 ATT-ATTTGGATTGTC-AA
57328489 ATTATTT
1 ATTATTT
57328496 AAACAATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.31, C:0.05, G:0.12, T:0.52
Consensus pattern (17 bp):
ATTATTTGGATTGTCAA
Found at i:57329766 original size:27 final size:27
Alignment explanation
Indices: 57329682--57329767 Score: 86
Period size: 27 Copynumber: 3.2 Consensus size: 27
57329672 TCGCGAGGTG
*
57329682 GGGTTCGCCAGTTGGTTTGGC-AAGCTA
1 GGGTTTGCCAGTTGGTTTGGCGAA-CTA
* * * *
57329709 AGGTTTGCTAGTTGGTTTGGTG-AGTA
1 GGGTTTGCCAGTTGGTTTGGCGAACTA
*
57329735 GGGGTTTGCCAGTTCGTTTGGCGAACTA
1 -GGGTTTGCCAGTTGGTTTGGCGAACTA
57329763 GGGTT
1 GGGTT
57329768 GGCCGGTATA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
26 2 0.04
27 41 0.89
28 3 0.07
ACGTcount: A:0.14, C:0.13, G:0.38, T:0.35
Consensus pattern (27 bp):
GGGTTTGCCAGTTGGTTTGGCGAACTA
Found at i:57332244 original size:33 final size:33
Alignment explanation
Indices: 57332200--57332360 Score: 157
Period size: 33 Copynumber: 4.9 Consensus size: 33
57332190 CATGGCATCC
* * * *
57332200 ATAGAGGTAGTCCGCTGAGACAGTAAACACAGA
1 ATAGAGATAGTCCACTGAGACAATAAACACAAA
* *
57332233 ATAGAGATAGTCCGCTGGGACAATAAACACAAA
1 ATAGAGATAGTCCACTGAGACAATAAACACAAA
* * * * *
57332266 ATAGAGATAGTCCACTGGGATAGTAAACATAGA
1 ATAGAGATAGTCCACTGAGACAATAAACACAAA
* * *
57332299 ATAAAGATAGTCCATTGAGACAATAAACATAAA
1 ATAGAGATAGTCCACTGAGACAATAAACACAAA
*
57332332 AT--AGATAGTCCA-TTAGGACAATAAACACA
1 ATAGAGATAGTCCACTGA-GACAATAAACACA
57332361 GAACAAATAA
Statistics
Matches: 110, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
30 2 0.02
31 22 0.20
33 86 0.78
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.19
Consensus pattern (33 bp):
ATAGAGATAGTCCACTGAGACAATAAACACAAA
Found at i:57332307 original size:66 final size:66
Alignment explanation
Indices: 57332200--57332363 Score: 190
Period size: 66 Copynumber: 2.5 Consensus size: 66
57332190 CATGGCATCC
* * * * *
57332200 ATAGAGGTAGTCCGCTGAGACAGTAAACACAGAATAGAGATAGTCCGCTGGGACAATAAACACAA
1 ATAGAGATAGTCCACTGAGACAGTAAACACAGAATAAAGATAGTCCACTGAGACAATAAACACAA
57332265 A
66 A
* * * * *
57332266 ATAGAGATAGTCCACTGGGATAGTAAACATAGAATAAAGATAGTCCATTGAGACAATAAACATAA
1 ATAGAGATAGTCCACTGAGACAGTAAACACAGAATAAAGATAGTCCACTGAGACAATAAACACAA
57332331 A
66 A
* *
57332332 AT--AGATAGTCCA-TTAGGACAATAAACACAGAA
1 ATAGAGATAGTCCACTGA-GACAGTAAACACAGAA
57332364 CAAATAAAGT
Statistics
Matches: 82, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
63 1 0.01
64 23 0.28
66 58 0.71
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.18
Consensus pattern (66 bp):
ATAGAGATAGTCCACTGAGACAGTAAACACAGAATAAAGATAGTCCACTGAGACAATAAACACAA
A
Found at i:57332384 original size:64 final size:65
Alignment explanation
Indices: 57332251--57332392 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 65
57332241 AGTCCGCTGG
* * * * * * *
57332251 GACAATAAACACAAAATAGAGATAGTCCACTGGGATAGTAAACATAGAATAAAGATAGTCCATTG
1 GACAATAAACACAAAATA-AGATAGTCCACTAGGACAATAAACACAGAACAAAGAAAGTCCATTA
57332316 A
65 A
* * * **
57332317 GACAATAAACATAAAAT-AGATAGTCCATTAGGACAATAAACACAGAACAAATAAAGTCTGTTAA
1 GACAATAAACACAAAATAAGATAGTCCACTAGGACAATAAACACAGAACAAAGAAAGTCCATTAA
*
57332381 GACAGTAAACAC
1 GACAATAAACAC
57332393 GAGGTAAGCC
Statistics
Matches: 62, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
64 46 0.74
66 16 0.26
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.19
Consensus pattern (65 bp):
GACAATAAACACAAAATAAGATAGTCCACTAGGACAATAAACACAGAACAAAGAAAGTCCATTAA
Found at i:57353984 original size:45 final size:45
Alignment explanation
Indices: 57353935--57354127 Score: 219
Period size: 45 Copynumber: 4.3 Consensus size: 45
57353925 TATCATAAAT
*
57353935 GAGTAAGACCATGACTAAAAGACGTTATGACATCATGATTCTATC
1 GAGTAAGACCATGACTAAAAGACGTTATGACATCACGATTCTATC
* * * *
57353980 GAGTAAGACCATGAATGAAAGACGTTATGGCATCACGACTCTATC
1 GAGTAAGACCATGACTAAAAGACGTTATGACATCACGATTCTATC
* * *
57354025 GAGTAAGACCATGAC-AGAAAGACGTTATGGCATCACAATTCTATA
1 GAGTAAGACCATGACTA-AAAGACGTTATGACATCACGATTCTATC
* * * * * *
57354070 TAGTAAGACCAT-AGCTAAAAGATGCTATGACATCACGAATCAAAC
1 GAGTAAGACCATGA-CTAAAAGACGTTATGACATCACGATTCTATC
*
57354115 GAATAAGACCATG
1 GAGTAAGACCATG
57354128 GTTGAAAGAC
Statistics
Matches: 123, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
44 1 0.01
45 121 0.98
46 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.22
Consensus pattern (45 bp):
GAGTAAGACCATGACTAAAAGACGTTATGACATCACGATTCTATC
Found at i:57354009 original size:90 final size:90
Alignment explanation
Indices: 57353905--57354081 Score: 209
Period size: 90 Copynumber: 2.0 Consensus size: 90
57353895 AGACCATAGT
*
57353905 TGAAAGACACTATGGCACCA-TA-TCATAAAT-GAGTAAGACCATGACTA-AAAGACGTTATGAC
1 TGAAAGACACTATGGCACCACGACTC-T--ATCGAGTAAGACCATGAC-AGAAAGACGTTATGAC
** *
57353966 ATCATGATTCTATCGAGTAAGACCATGAA
62 ATCACAATTCTATAGAGTAAGACCATGAA
** * *
57353995 TGAAAGACGTTATGGCATCACGACTCTATCGAGTAAGACCATGACAGAAAGACGTTATGGCATCA
1 TGAAAGACACTATGGCACCACGACTCTATCGAGTAAGACCATGACAGAAAGACGTTATGACATCA
*
57354060 CAATTCTATATAGTAAGACCAT
66 CAATTCTATAGAGTAAGACCAT
57354082 AGCTAAAAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
89 3 0.04
90 67 0.91
91 2 0.03
92 2 0.03
ACGTcount: A:0.39, C:0.19, G:0.19, T:0.24
Consensus pattern (90 bp):
TGAAAGACACTATGGCACCACGACTCTATCGAGTAAGACCATGACAGAAAGACGTTATGACATCA
CAATTCTATAGAGTAAGACCATGAA
Found at i:57354135 original size:90 final size:90
Alignment explanation
Indices: 57353938--57354149 Score: 228
Period size: 90 Copynumber: 2.4 Consensus size: 90
57353928 CATAAATGAG
* * ** * *
57353938 TAAGACCATGACTAAAAGACGTTATGACATCATGATTCTATCGAGTAAGACCATGAATGAAAGAC
1 TAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATAGAGTAAGACCATGAATAAAAGAC
* * * * * *
57354003 GTTATGGCATCACGACTCTATCGAG
66 GCTATGACATCACGAATCAAACGAA
* * *
57354028 TAAGACCATGACAGAAAGACGTTATGGCATCACAATTCTATATAGTAAGACCAT-AGCTAAAAGA
1 TAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATAGAGTAAGACCATGA-ATAAAAGA
*
57354092 TGCTATGACATCACGAATCAAACGAA
65 CGCTATGACATCACGAATCAAACGAA
** **
57354118 TAAGACCATGGTTGAAAGACACTATGGCATCA
1 TAAGACCATGACTGAAAGACGTTATGGCATCA
57354150 AGATGAGAAT
Statistics
Matches: 100, Mismatches: 21, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
89 1 0.01
90 99 0.99
ACGTcount: A:0.40, C:0.19, G:0.19, T:0.23
Consensus pattern (90 bp):
TAAGACCATGACTGAAAGACGTTATGGCATCACAATTCTATAGAGTAAGACCATGAATAAAAGAC
GCTATGACATCACGAATCAAACGAA
Found at i:57354136 original size:45 final size:45
Alignment explanation
Indices: 57354094--57354184 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
57354084 CTAAAAGATG
* *
57354094 CTATGACATCACGAATCA-AACGAATAAGACCATGGTTGAAAGACA
1 CTATGACATCAAG-ATCAGAACAAATAAGACCATGGTTGAAAGACA
* * *
57354139 CTATGGCATCAAGATGAGAATAAATAAGACCATGGTTGAAAGACA
1 CTATGACATCAAGATCAGAACAAATAAGACCATGGTTGAAAGACA
57354184 C
1 C
57354185 CATGGCACAC
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 3 0.08
45 37 0.93
ACGTcount: A:0.44, C:0.18, G:0.20, T:0.19
Consensus pattern (45 bp):
CTATGACATCAAGATCAGAACAAATAAGACCATGGTTGAAAGACA
Found at i:57354180 original size:135 final size:136
Alignment explanation
Indices: 57353847--57354192 Score: 323
Period size: 135 Copynumber: 2.6 Consensus size: 136
57353837 GGAACATGAT
* * * *
57353847 TAAGACCATAGTTGAAA-AGCACTATGGCA-CTATACTGGAGAATAAATAAGACCATAGTTGAAA
1 TAAGACCATGGTTGAAAGA-CACTATGGCATCAAGACT-GAGAATAAATAAGACCATGGTTGAAA
* * *
57353910 GACACTATGGCACCATATCATAAATGAGTAAGACCATGACTAAAAGACGTTATGACATCATGATT
64 GACACTATGGCACCATATCATAAATGAGTAAGACCATGACTAAAAGACGCTATGACATCACGAAT
* * *
57353975 CTATCGAG
129 CAAACGAA
** ** * ** * * ***
57353983 TAAGACCATGAATGAAAGACGTTATGGCATCACGACT--CTATCGAGTAAGACCATGACAGAAAG
1 TAAGACCATGGTTGAAAGACACTATGGCATCAAGACTGAGAAT-AAATAAGACCATGGTTGAAAG
** * *
57354046 ACGTTATGGCATCACA-ATTC-TATAT-AGTAAGACCAT-AGCTAAAAGATGCTATGACATCACG
65 ACACTATGGCA-C-CATA-TCATAAATGAGTAAGACCATGA-CTAAAAGACGCTATGACATCACG
57354107 AATCAAACGAA
126 AATCAAACGAA
57354118 TAAGACCATGGTTGAAAGACACTATGGCATCAAGA-TGAGAATAAATAAGACCATGGTTGAAAGA
1 TAAGACCATGGTTGAAAGACACTATGGCATCAAGACTGAGAATAAATAAGACCATGGTTGAAAGA
*
57354182 CACCATGGCAC
66 CACTATGGCAC
57354193 ACTCCGATCA
Statistics
Matches: 160, Mismatches: 41, Indels: 20
0.72 0.19 0.09
Matches are distributed among these distances:
134 5 0.03
135 116 0.73
136 30 0.19
137 9 0.06
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (136 bp):
TAAGACCATGGTTGAAAGACACTATGGCATCAAGACTGAGAATAAATAAGACCATGGTTGAAAGA
CACTATGGCACCATATCATAAATGAGTAAGACCATGACTAAAAGACGCTATGACATCACGAATCA
AACGAA
Found at i:57355080 original size:20 final size:20
Alignment explanation
Indices: 57355055--57355108 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
57355045 TATTTAAGCT
*
57355055 AAAGTAAGTAAATGCACTGA
1 AAAGTAAGTAAATGCAATGA
*
57355075 AAAGTAAGTAAATGCAATGG
1 AAAGTAAGTAAATGCAATGA
57355095 AAAGTAAGTAAATG
1 AAAGTAAGTAAATG
57355109 GAAGGGTTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.52, C:0.06, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAGTAAGTAAATGCAATGA
Found at i:57356625 original size:13 final size:13
Alignment explanation
Indices: 57356607--57356649 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
57356597 TAGATTTTTC
57356607 CTAAATATTATCA
1 CTAAATATTATCA
57356620 CTAAATA--ATC-
1 CTAAATATTATCA
*
57356630 CTAAATGTTATCA
1 CTAAATATTATCA
57356643 CTAAATA
1 CTAAATA
57356650 ATTCAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 6 0.24
11 3 0.12
12 3 0.12
13 13 0.52
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:57356632 original size:23 final size:23
Alignment explanation
Indices: 57356605--57356651 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
57356595 GCTAGATTTT
57356605 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
57356628 TCCTAAATGTTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
57356651 T
1 T
57356652 TCAAAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:57356658 original size:23 final size:23
Alignment explanation
Indices: 57356609--57356658 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
57356599 GATTTTTCCT
*
57356609 AAATATTATCACTAAATAATCCT
1 AAATATTATCACTAAATAATCCA
* *
57356632 AAATGTTATCACTAAATAATTCA
1 AAATATTATCACTAAATAATCCA
57356655 AAAT
1 AAAT
57356659 TTAAAAATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.34
Consensus pattern (23 bp):
AAATATTATCACTAAATAATCCA
Found at i:57357628 original size:4 final size:4
Alignment explanation
Indices: 57357619--57357643 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
57357609 CTATTAGCAA
57357619 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
57357644 AACGAGTACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:57361116 original size:5 final size:5
Alignment explanation
Indices: 57361106--57361132 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
57361096 TATGAAGTGT
57361106 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
57361133 ACAAATTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:57362049 original size:13 final size:13
Alignment explanation
Indices: 57362031--57362096 Score: 81
Period size: 13 Copynumber: 5.5 Consensus size: 13
57362021 TAGATTTTTC
57362031 CTAAATATTATCA
1 CTAAATATTATCA
57362044 CTAAATA--ATC-
1 CTAAATATTATCA
57362054 CTAAATATTATCA
1 CTAAATATTATCA
*
57362067 CTAAATA--AT-T
1 CTAAATATTATCA
57362077 CTAAATATTATCA
1 CTAAATATTATCA
57362090 CTAAATA
1 CTAAATA
57362097 ATACAAAATT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
10 14 0.31
11 5 0.11
12 5 0.11
13 21 0.47
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.36
Consensus pattern (13 bp):
CTAAATATTATCA
Found at i:57362059 original size:23 final size:23
Alignment explanation
Indices: 57362029--57362098 Score: 131
Period size: 23 Copynumber: 3.0 Consensus size: 23
57362019 GCTAGATTTT
57362029 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
57362052 TCCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
*
57362075 TTCTAAATATTATCACTAAATAA
1 TCCTAAATATTATCACTAAATAA
57362098 T
1 T
57362099 ACAAAATTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (23 bp):
TCCTAAATATTATCACTAAATAA
Found at i:57372786 original size:50 final size:50
Alignment explanation
Indices: 57372657--57372788 Score: 147
Period size: 50 Copynumber: 2.6 Consensus size: 50
57372647 GGGAATGAGA
* * * **
57372657 TCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
** ** *
57372707 TCCCCCGTAAGACCATGTCTTAGACATGGCATGGGCACCGATATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
* * *
57372757 TCTCATGTAAGACCATATCTGGGATATGGCAT
1 TCCCATGTAAGACCATGTCTGGGACATGGCAT
57372789 TGACAGTATA
Statistics
Matches: 65, Mismatches: 17, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 65 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGATGAGAAC
Found at i:57372819 original size:13 final size:13
Alignment explanation
Indices: 57372801--57372828 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
57372791 ACAGTATAAG
57372801 AAACATCCCATGT
1 AAACATCCCATGT
57372814 AAACATCCCATGT
1 AAACATCCCATGT
57372827 AA
1 AA
57372829 GACCATGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.29, G:0.07, T:0.21
Consensus pattern (13 bp):
AAACATCCCATGT
Found at i:57384473 original size:15 final size:16
Alignment explanation
Indices: 57384453--57384482 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
57384443 TTTTGTGCAT
57384453 CCAATAAA-GATAAGA
1 CCAATAAAGGATAAGA
57384468 CCAATAAAGGATAAG
1 CCAATAAAGGATAAG
57384483 TAGATATTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.13, G:0.17, T:0.13
Consensus pattern (16 bp):
CCAATAAAGGATAAGA
Done.