Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008656.1 Hibiscus syriacus cultivar Beakdansim tig00111650_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2456495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 12
Found at i:1444585 original size:2 final size:2
Alignment explanation
Indices: 1444574--1444655 Score: 92
Period size: 2 Copynumber: 45.0 Consensus size: 2
1444564 TTATGGTTTC
1444574 AT AT AT -T AT AT AT -T AT AT -T AT AT AT AT A- AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1444610 A- AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT CAT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
1444650 AT AT AT
1 AT AT AT
1444656 CTCGGTAGTT
Statistics
Matches: 70, Mismatches: 0, Indels: 20
0.78 0.00 0.22
Matches are distributed among these distances:
1 9 0.13
2 59 0.84
3 2 0.03
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1444610 original size:25 final size:22
Alignment explanation
Indices: 1444574--1444655 Score: 96
Period size: 25 Copynumber: 3.6 Consensus size: 22
1444564 TTATGGTTTC
1444574 ATATAT-TATATATTATATTAT
1 ATATATATATATATTATATTAT
*
1444595 ATATATAATAATTATAATATATTAT
1 ATATAT-AT-A-TATATTATATTAT
*
1444620 ATATATATATATATATATATCAT
1 ATATATATATATAT-TATATTAT
1444643 ATATAT-TATATAT
1 ATATATATATATAT
1444656 CTCGGTAGTT
Statistics
Matches: 53, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
21 6 0.11
22 11 0.21
23 15 0.28
24 3 0.06
25 18 0.34
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATATATATATATTATATTAT
Found at i:1444654 original size:39 final size:37
Alignment explanation
Indices: 1444574--1444655 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 37
1444564 TTATGGTTTC
1444574 ATATATTATATATTATATTATATATATAATAATTATA
1 ATATATTATATATTATATTATATATATAATAATTATA
*
1444611 ATATATTATATA-TATA-TATATATAT-AT-ATCAT-
1 ATATATTATATATTATATTATATATATAATAATTATA
1444643 ATATATTATATAT
1 ATATATTATATAT
1444656 CTCGGTAGTT
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
32 12 0.28
33 4 0.09
34 2 0.05
35 9 0.21
36 4 0.09
37 12 0.28
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (37 bp):
ATATATTATATATTATATTATATATATAATAATTATA
Found at i:1444846 original size:15 final size:15
Alignment explanation
Indices: 1444826--1444867 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
1444816 GATGGAGGCC
1444826 CAATCGAAAAGGGCA
1 CAATCGAAAAGGGCA
* *
1444841 CAATCGAAAAGAGCC
1 CAATCGAAAAGGGCA
1444856 CAATCGAAAAGG
1 CAATCGAAAAGG
1444868 AATTAGGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.48, C:0.21, G:0.24, T:0.07
Consensus pattern (15 bp):
CAATCGAAAAGGGCA
Found at i:1446302 original size:49 final size:49
Alignment explanation
Indices: 1446247--1446577 Score: 412
Period size: 49 Copynumber: 6.8 Consensus size: 49
1446237 TACACATAAA
* * * * *
1446247 TAGCACCACTGTCACAAAGCCATCAGGCATGCTAAATCATCATTAATAG
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* * *
1446296 TAGCACCAAC-GTCACAAAGACGTCAGATGTGCTAAGTCATCAATCATAG
1 TAGCACC-ACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* * * * * *
1446345 TAGCACCACTGTCACAAAGATGTCAAACGTGCTAGATCAACAATCATAT
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* **
1446394 TTGCACCACCATCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* *
1446443 TAGCACCATTGTCACAAAGACGTCAGACGTGCTAAATCATAATTCATAG
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* ** *
1446492 TAGCACTACCATCACAAAGACGTCAGATGTGCTAAATCATCATTCATAG
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* * *
1446541 TAGCACCACTGACACAAAGACGTCATATGTGCTAAAT
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAAT
1446578 GCTCCACCTA
Statistics
Matches: 240, Mismatches: 40, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
48 2 0.01
49 236 0.98
50 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (49 bp):
TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
Found at i:1449961 original size:15 final size:15
Alignment explanation
Indices: 1449941--1449969 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1449931 AACGATGGAG
1449941 GCCCAATCGAAAAGA
1 GCCCAATCGAAAAGA
1449956 GCCCAATCGAAAAG
1 GCCCAATCGAAAAG
1449970 GCATTAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.28, G:0.21, T:0.07
Consensus pattern (15 bp):
GCCCAATCGAAAAGA
Found at i:1451408 original size:49 final size:49
Alignment explanation
Indices: 1451353--1451683 Score: 430
Period size: 49 Copynumber: 6.8 Consensus size: 49
1451343 TACACATAAA
* * * *
1451353 TAGCACCACTGTCACAAAGACGTCAGGCATCCTAAATCATCATTAATAG
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* * *
1451402 TAGCACCAAC-GTCACAAAGACGTCAGATGTGCTAAGTCATCAATCATAG
1 TAGCACC-ACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* * * *
1451451 TAGCACCACTGTCACAAAGATGTCAAACGTGCTAGATCAACATTCATAG
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* **
1451500 TTGCACCACCATCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* * *
1451549 TAGCACCATTGTCACAAATACGTCAGACGTGCTAAATCATAATTCATAG
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* ** *
1451598 TAGCACTACCATCACAAAGACGTCAGATGTGCTAAATCATCATTCATAG
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* * *
1451647 TAGCACCACTGACACAAAGACGTCATATGTGCTAAAT
1 TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAAT
1451684 GCTCCACCTA
Statistics
Matches: 241, Mismatches: 39, Indels: 4
0.85 0.14 0.01
Matches are distributed among these distances:
48 2 0.01
49 237 0.98
50 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.15, T:0.23
Consensus pattern (49 bp):
TAGCACCACTGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
Found at i:1456911 original size:14 final size:14
Alignment explanation
Indices: 1456892--1456919 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1456882 TCGATAATTT
1456892 GTTCATTTATGTTC
1 GTTCATTTATGTTC
1456906 GTTCATTTATGTTC
1 GTTCATTTATGTTC
1456920 ATTTATGTTC
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:0.14, C:0.14, G:0.14, T:0.57
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:1456919 original size:10 final size:10
Alignment explanation
Indices: 1456906--1456933 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
1456896 ATTTATGTTC
1456906 GTTCATTTAT
1 GTTCATTTAT
1456916 GTTCATTTAT
1 GTTCATTTAT
1456926 GTTCATTT
1 GTTCATTT
1456934 GTTTATGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.18, C:0.11, G:0.11, T:0.61
Consensus pattern (10 bp):
GTTCATTTAT
Found at i:1456923 original size:24 final size:24
Alignment explanation
Indices: 1456857--1456966 Score: 98
Period size: 24 Copynumber: 4.7 Consensus size: 24
1456847 AGAGGGCTCA
* * * *
1456857 TTCGTTCATTTACGTTCGTTAACG
1 TTCGTTCATTTATGTTCATTTATG
* *
1456881 TTCGAT-AATT-TGTTCATTTATG
1 TTCGTTCATTTATGTTCATTTATG
1456903 TTCGTTCATTTATGTTCATTTATG
1 TTCGTTCATTTATGTTCATTTATG
* ** *
1456927 TTCATTTGTTTATGTTTATTTATG
1 TTCGTTCATTTATGTTCATTTATG
* *
1456951 TGCATTCATTTATGTT
1 TTCGTTCATTTATGTT
1456967 TAGCCCAATA
Statistics
Matches: 69, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
22 13 0.19
23 6 0.09
24 50 0.72
ACGTcount: A:0.18, C:0.12, G:0.14, T:0.56
Consensus pattern (24 bp):
TTCGTTCATTTATGTTCATTTATG
Found at i:1456968 original size:24 final size:24
Alignment explanation
Indices: 1456891--1456966 Score: 107
Period size: 24 Copynumber: 3.2 Consensus size: 24
1456881 TTCGATAATT
*
1456891 TGTTCATTTATGTTCGTTCATTTA
1 TGTTCATTTATGTTCATTCATTTA
**
1456915 TGTTCATTTATGTTCATTTGTTTA
1 TGTTCATTTATGTTCATTCATTTA
* *
1456939 TGTTTATTTATGTGCATTCATTTA
1 TGTTCATTTATGTTCATTCATTTA
1456963 TGTT
1 TGTT
1456967 TAGCCCAATA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.17, C:0.09, G:0.13, T:0.61
Consensus pattern (24 bp):
TGTTCATTTATGTTCATTCATTTA
Found at i:1457197 original size:24 final size:24
Alignment explanation
Indices: 1457132--1457267 Score: 127
Period size: 24 Copynumber: 5.8 Consensus size: 24
1457122 AAAGTCTATT
* *
1457132 TTCATTTATGTTCGTTTACGTTCA
1 TTCATTTGTGTTCGTTTACGTTCG
* **
1457156 TTTA-TTGTGTTCAATTACGTTCG
1 TTCATTTGTGTTCGTTTACGTTCG
*
1457179 TTCATTTTTGTTCGTTTACGTTCG
1 TTCATTTGTGTTCGTTTACGTTCG
* * *
1457203 TTTA-TTGTGTTCTTTTATGTTCG
1 TTCATTTGTGTTCGTTTACGTTCG
* *
1457226 TTTACA-TT-TGTTCGTTTATGTTTG
1 -TT-CATTTGTGTTCGTTTACGTTCG
1457250 TTCATTTGTGTTCGTTTA
1 TTCATTTGTGTTCGTTTA
1457268 TCATTTAAAT
Statistics
Matches: 91, Mismatches: 16, Indels: 10
0.78 0.14 0.09
Matches are distributed among these distances:
22 2 0.02
23 38 0.42
24 48 0.53
25 3 0.03
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.59
Consensus pattern (24 bp):
TTCATTTGTGTTCGTTTACGTTCG
Found at i:1457201 original size:47 final size:47
Alignment explanation
Indices: 1457132--1457243 Score: 152
Period size: 47 Copynumber: 2.4 Consensus size: 47
1457122 AAAGTCTATT
*
1457132 TTCATTTATGTTCGTTTACGTTCATTTATTGTGTTCAATTACGTTCG
1 TTCATTTTTGTTCGTTTACGTTCATTTATTGTGTTCAATTACGTTCG
* ** *
1457179 TTCATTTTTGTTCGTTTACGTTCGTTTATTGTGTTCTTTTATGTTCG
1 TTCATTTTTGTTCGTTTACGTTCATTTATTGTGTTCAATTACGTTCG
* **
1457226 TTTACATTTGTTCGTTTA
1 TTCATTTTTGTTCGTTTA
1457244 TGTTTGTTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 57 1.00
ACGTcount: A:0.13, C:0.13, G:0.15, T:0.58
Consensus pattern (47 bp):
TTCATTTTTGTTCGTTTACGTTCATTTATTGTGTTCAATTACGTTCG
Found at i:1464494 original size:23 final size:21
Alignment explanation
Indices: 1464442--1464503 Score: 81
Period size: 23 Copynumber: 2.9 Consensus size: 21
1464432 TTTTGGTGTA
*
1464442 GAGGGAATCGA-TCCCCCCTT
1 GAGGGAACCGATTCCCCCCTT
*
1464462 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCTT
1464483 GAAGGGGAACCGATTCCCCCC
1 G-A-GGGAACCGATTCCCCCC
1464504 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.28
21 9 0.25
22 1 0.03
23 16 0.44
ACGTcount: A:0.21, C:0.35, G:0.26, T:0.18
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCTT
Found at i:1467053 original size:22 final size:23
Alignment explanation
Indices: 1467028--1467071 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
1467018 AATTAAGTTT
1467028 TAATCTTA-AAACAATTTCAAAA
1 TAATCTTACAAACAATTTCAAAA
* **
1467050 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
1467072 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.50, C:0.11, G:0.02, T:0.36
Consensus pattern (23 bp):
TAATCTTACAAACAATTTCAAAA
Found at i:1468104 original size:49 final size:49
Alignment explanation
Indices: 1468046--1468327 Score: 375
Period size: 49 Copynumber: 5.8 Consensus size: 49
1468036 TACAAATAAA
* *
1468046 TAGCACCACCGTCACAAAGACGTCAGACGTGCTAAATCATCGTTAATAG
1 TAGCACCACCGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* * * *
1468095 TAGCACCACCGTCACAAAGACATTAGATGTGCTAAATCATCGTTCATAG
1 TAGCACCACCGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* * * * *
1468144 TAGCACCACTGTCAAAAAGACGTTAGACGGGCTAGATCATCATTCATAG
1 TAGCACCACCGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* * * * *
1468193 TAGCACCACCATCACAAAGATGTCAGATGTGCTAAATCATAATTCATGG
1 TAGCACCACCGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* * *
1468242 TAGCACTACCGTCACAAAGATGTCAGACGTGCTAAATCATCATTTATAG
1 TAGCACCACCGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
* *
1468291 TAGCACCACCGTCACAAAGACGTCAAACGTGTTAAAT
1 TAGCACCACCGTCACAAAGACGTCAGACGTGCTAAAT
1468328 GCTCCACCTC
Statistics
Matches: 202, Mismatches: 31, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 202 1.00
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (49 bp):
TAGCACCACCGTCACAAAGACGTCAGACGTGCTAAATCATCATTCATAG
Found at i:1484494 original size:16 final size:17
Alignment explanation
Indices: 1484473--1484524 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 17
1484463 TTTTAAATTT
1484473 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
1484489 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
*
1484504 AATCACTCTAACTTTCA
1 AATTACTCTAACTTTCA
1484521 AATT
1 AATT
1484525 TTTTTCTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
14 4 0.14
15 9 0.31
16 7 0.24
17 6 0.21
18 3 0.10
ACGTcount: A:0.37, C:0.21, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:1487209 original size:59 final size:60
Alignment explanation
Indices: 1487146--1487304 Score: 191
Period size: 60 Copynumber: 2.7 Consensus size: 60
1487136 AAGGTACTAC
* *
1487146 TTTGTTGAGTCATCTAATTATTAAAAGTTACAAAATGATCC-CT-AACTATAGAATATTAT
1 TTTGTTGAGTCATCTAACTACTAAAAGTTACAAAATGATCCTCTGAA-TATAGAATATTAT
* * * *
1487205 TTTGTTGAGTC-CCTCGACTACAAAAAGTTACAAAATGATCCTTTGAATATAGAATATTAT
1 TTTGTTGAGTCATCT-AACTACTAAAAGTTACAAAATGATCCTCTGAATATAGAATATTAT
* *
1487265 ATTGTTGAGCCCATC-AACTACTAAAAGTTACAAAATGATC
1 TTTGTTGAG-TCATCTAACTACTAAAAGTTACAAAATGATC
1487305 ACCCATCTAT
Statistics
Matches: 84, Mismatches: 11, Indels: 9
0.81 0.11 0.09
Matches are distributed among these distances:
58 2 0.02
59 33 0.39
60 45 0.54
61 3 0.04
62 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (60 bp):
TTTGTTGAGTCATCTAACTACTAAAAGTTACAAAATGATCCTCTGAATATAGAATATTAT
Found at i:1487285 original size:60 final size:59
Alignment explanation
Indices: 1487168--1487304 Score: 197
Period size: 60 Copynumber: 2.3 Consensus size: 59
1487158 TCTAATTATT
* *
1487168 AAAAGTTACAAAATGATCCCTAACTATAGAATATTATTTTGTTGAGTCCCTCGACTACA
1 AAAAGTTACAAAATGATCCCTAACTATAGAATATTATATTGTTGAGTCCCTCAACTACA
* *
1487227 AAAAGTTACAAAATGATCCTTTGAA-TATAGAATATTATATTGTTGAG-CCCATCAACTACT
1 AAAAGTTACAAAATGATCC-CT-AACTATAGAATATTATATTGTTGAGTCCC-TCAACTACA
1487287 AAAAGTTACAAAATGATC
1 AAAAGTTACAAAATGATC
1487305 ACCCATCTAT
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
59 22 0.31
60 47 0.66
61 2 0.03
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (59 bp):
AAAAGTTACAAAATGATCCCTAACTATAGAATATTATATTGTTGAGTCCCTCAACTACA
Found at i:1487493 original size:28 final size:28
Alignment explanation
Indices: 1487453--1487509 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
1487443 TTCTTTTTTT
* *
1487453 ACATTATGTCGTC-AAGCTAATACTTGAA
1 ACATTATGACGTCGAA-CCAATACTTGAA
1487481 ACATTATGACGTCGAACCAATACTTGAA
1 ACATTATGACGTCGAACCAATACTTGAA
1487509 A
1 A
1487510 GTAACAATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 24 0.92
29 2 0.08
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (28 bp):
ACATTATGACGTCGAACCAATACTTGAA
Found at i:1490501 original size:23 final size:23
Alignment explanation
Indices: 1490444--1490501 Score: 57
Period size: 23 Copynumber: 2.5 Consensus size: 23
1490434 AAAGTTAGTG
1490444 ATATGATA-TATATTACATCAATA
1 ATAT-ATATTATATTACATCAATA
* **
1490467 AT-TAAATATATATTATGTCAATA
1 ATATATAT-TATATTACATCAATA
1490490 ATATATATTATA
1 ATATATATTATA
1490502 ATTCCTGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
21 2 0.07
22 1 0.04
23 21 0.75
24 4 0.14
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.43
Consensus pattern (23 bp):
ATATATATTATATTACATCAATA
Found at i:1491248 original size:3 final size:3
Alignment explanation
Indices: 1491242--1491333 Score: 175
Period size: 3 Copynumber: 30.3 Consensus size: 3
1491232 CTACTACTAC
1491242 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1491290 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT T
1491334 GGGTAGAATA
Statistics
Matches: 88, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 85 0.97
4 3 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1491383 original size:15 final size:16
Alignment explanation
Indices: 1491359--1491397 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
1491349 ATGTTATCCG
1491359 ATTA-TAAAATTA-TA
1 ATTATTAAAATTATTA
*
1491373 TTTATTAAAATTATTA
1 ATTATTAAAATTATTA
1491389 ATTATTAAA
1 ATTATTAAA
1491398 TGTTATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 3 0.14
15 8 0.38
16 10 0.48
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTATTAAAATTATTA
Found at i:1494721 original size:12 final size:12
Alignment explanation
Indices: 1494704--1494729 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1494694 ATTCAGTGAA
1494704 TGAAAAGTGGGT
1 TGAAAAGTGGGT
1494716 TGAAAAGTGGGT
1 TGAAAAGTGGGT
1494728 TG
1 TG
1494730 GTGTATATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.00, G:0.42, T:0.27
Consensus pattern (12 bp):
TGAAAAGTGGGT
Found at i:1495232 original size:17 final size:18
Alignment explanation
Indices: 1495197--1495232 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
1495187 ACTGTAGATT
*
1495197 AAATATTATTTAGAATAA
1 AAATAATATTTAGAATAA
1495215 AAATAATATTTA-AATAA
1 AAATAATATTTAGAATAA
1495232 A
1 A
1495233 TTTAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
AAATAATATTTAGAATAA
Found at i:1495963 original size:19 final size:19
Alignment explanation
Indices: 1495935--1495971 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1495925 AAATTATCAA
1495935 TAAAAAATATAAAAATATT
1 TAAAAAATATAAAAATATT
* *
1495954 TAAAATATATAATAATAT
1 TAAAAAATATAAAAATAT
1495972 ACTTTTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TAAAAAATATAAAAATATT
Found at i:1504396 original size:22 final size:21
Alignment explanation
Indices: 1504360--1504400 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
1504350 TTTCATAATA
1504360 ATAATTATAATTATTATTAAG
1 ATAATTATAATTATTATTAAG
*
1504381 ATAATATATCATTATTATTA
1 ATAAT-TATAATTATTATTA
1504401 TTTATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (21 bp):
ATAATTATAATTATTATTAAG
Found at i:1506254 original size:2 final size:2
Alignment explanation
Indices: 1506247--1506278 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
1506237 AAAAATAAAG
1506247 AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1506279 TTTCTTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1508519 original size:14 final size:14
Alignment explanation
Indices: 1508481--1508519 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
1508471 ATTTTAAATA
*
1508481 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
1508495 TTTTACATTTGCAT
1 ATTTACATTTGCAT
1508509 ATTTACATTTG
1 ATTTACATTTG
1508520 GAATCTTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.28, C:0.13, G:0.05, T:0.54
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:1508609 original size:12 final size:13
Alignment explanation
Indices: 1508592--1508620 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1508582 ACATTCACAT
1508592 ATTTACATTT-GC
1 ATTTACATTTAGC
1508604 ATTTACATTTAGC
1 ATTTACATTTAGC
1508617 ATTT
1 ATTT
1508621 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (13 bp):
ATTTACATTTAGC
Found at i:1510745 original size:90 final size:84
Alignment explanation
Indices: 1510633--1510791 Score: 201
Period size: 84 Copynumber: 1.8 Consensus size: 84
1510623 GATACCCATG
1510633 TTATATTAATATATACAATAAAGCTTGAGTTGTCCCACTAGAGCAAATGGTTAATCGCCCCGGCT
1 TTATATTAATATATACAATAAAGC-T-A----TCCCACTAGAGCAAATGGTTAATCGCCCCGGCT
1510698 TTATGGATAATATTCAGCCAACCCA
60 TTATGGATAATATTCAGCCAACCCA
* ** * * * *
1510723 TTATATTATTATATGTAATAAAGCTATCCCTCTAGAGCAATTGGTTAATGGCCCTGGCTTTATGG
1 TTATATTAATATATACAATAAAGCTATCCCACTAGAGCAAATGGTTAATCGCCCCGGCTTTATGG
1510788 ATAA
66 ATAA
1510792 GTTTCAGTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
84 39 0.63
88 1 0.02
89 1 0.02
90 21 0.34
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Consensus pattern (84 bp):
TTATATTAATATATACAATAAAGCTATCCCACTAGAGCAAATGGTTAATCGCCCCGGCTTTATGG
ATAATATTCAGCCAACCCA
Found at i:1515317 original size:22 final size:22
Alignment explanation
Indices: 1515291--1515367 Score: 145
Period size: 22 Copynumber: 3.5 Consensus size: 22
1515281 ATCTACACTC
1515291 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1515313 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
1515335 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
1515357 TTCAAAGATGA
1 TTCAAAGATGA
1515368 AAGCTTTATG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:1516148 original size:165 final size:166
Alignment explanation
Indices: 1515871--1516201 Score: 549
Period size: 165 Copynumber: 2.0 Consensus size: 166
1515861 TAATCCACAA
*
1515871 AACAACCTTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAATGAG
1 AACAACCTTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAACGAG
* **
1515936 AAAACAATTTCCATAGTTTTTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAAC
66 AAAACAATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAAC
*
1516001 GATTTCCTTAG-TTTTTTACTTAGTAAACTATTTCC
131 GATTTCCTTAGTTTTTTTACTTAATAAACTATTTCC
* * **
1516036 AACAGCCTTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-TGAAAAATAACGAG
1 AACAACCTTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAACGAG
*
1516100 AAAACGATTTCCATAGTTTCTCATTCAATCTTTTCTAGAAATGAAATTGTTGAAAAGTAAGAAAA
66 AAAACAATTTCCATAGTTTCTCATTCAATCTTTTCTA-AAATGAAATTGTTGAAAAGTAAGAAAA
1516165 CGATTTCCTTAGTTTTTTTACTTAATAAACTATTTCC
130 CGATTTCCTTAGTTTTTTTACTTAATAAACTATTTCC
1516202 CACATCTGTA
Statistics
Matches: 154, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
164 44 0.29
165 87 0.56
166 23 0.15
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (166 bp):
AACAACCTTATCTTAAGATTGGGGCATGTTACCCAATCAACATGTTATTTCAAAAAAATAACGAG
AAAACAATTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAAC
GATTTCCTTAGTTTTTTTACTTAATAAACTATTTCC
Found at i:1516346 original size:76 final size:76
Alignment explanation
Indices: 1516204--1517387 Score: 2075
Period size: 76 Copynumber: 15.6 Consensus size: 76
1516194 CTATTTCCCA
* *
1516204 CATCTGTAAGTCCTGCAGTGCATGATGTTTTC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1516268 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
1516279 CATCTGTAAGTCCTATAGTGCATGATGTTTTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1516344 AGCCTTAAGGT
66 AGCCTTAGGGT
* *
1516355 CATCTGTAATTCCTACAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1516420 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1516431 CATCTGTAAGTCCTACAGTGCAAGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1516496 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1516507 CATCTGTAAGTCCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1516572 AGCCTTAGGGT
66 AGCCTTAGGGT
1516583 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1516648 AGCCTTAGGGT
66 AGCCTTAGGGT
1516659 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1516724 AGCCTTAGGGT
66 AGCCTTAGGGT
1516735 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1516800 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1516811 CATTTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* *
1516876 AGTCTCAGGGT
66 AGCCTTAGGGT
* * * * *
1516887 CATCTCTAAGTCCTACAGGGCATGATGTTTCCAAAAAGCCTTCTGGAGTTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1516952 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
1516963 CATCTGTAAGTCCTACAGTTCCTGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1517028 AGCCTTAGGGT
66 AGCCTTAGGGT
1517039 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1517104 AGCCTTAGGAT
66 AGCCTTAGGGT
*
1517115 CATCTGTAAGTCCTAAAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1517180 AGCCTTAGGGT
66 AGCCTTAGGGT
*
1517191 CATCTGTAAGTCCTATAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1517256 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
1517267 CATCTATAAGTCCTACAGTGCATGATGTTTCCAAAAACCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
1517332 AGTCTTAGGGT
66 AGCCTTAGGGT
* *
1517343 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAA-CCTTCGGG
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGG
1517388 TCATCTGTAA
Statistics
Matches: 1059, Mismatches: 49, Indels: 2
0.95 0.04 0.00
Matches are distributed among these distances:
75 38 0.04
76 1021 0.96
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:1517397 original size:46 final size:46
Alignment explanation
Indices: 1517320--1517422 Score: 156
Period size: 46 Copynumber: 2.3 Consensus size: 46
1517310 GGGAGCTTTT
** *
1517320 TGATGTTTTC-AAAGTCTTAGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCA
*
1517365 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCA
1517411 TGAT-TTTTCAAA
1 TGATGTTTTCAAA
1517423 CATTTCCATC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
45 18 0.34
46 35 0.66
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (46 bp):
TGATGTTTTCAAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1517553 original size:3 final size:3
Alignment explanation
Indices: 1517547--1517597 Score: 57
Period size: 3 Copynumber: 16.3 Consensus size: 3
1517537 TTTAATAATA
* * *
1517547 ATT ATT ATA ATT ATT ATT AAT ATA ATAT ATT ATT ATT ATT ATTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT A-TT ATT
1517594 ATT A
1 ATT A
1517598 AATATATATA
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
3 35 0.88
4 5 0.12
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1517567 original size:25 final size:25
Alignment explanation
Indices: 1517531--1517633 Score: 79
Period size: 25 Copynumber: 3.9 Consensus size: 25
1517521 CTGTAGACAT
1517531 TAATT-TT-TTAATAATAAT-TATTA
1 TAATTATTATTAAT-ATAATATATTA
1517554 TAATTATTATTAATATAATATATTA
1 TAATTATTATTAATATAATATATTA
* *
1517579 TTATTATTATTTATTATTAA-ATATATA
1 TAATTATTA-TTAATA-TAATATAT-TA
1517606 TATATATATATATTATATATATATATAT
1 TA-AT-TAT-TATTA-ATATA-ATATAT
1517634 ATATTACAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
23 5 0.08
24 7 0.11
25 18 0.28
26 9 0.14
27 6 0.09
28 2 0.03
29 8 0.12
30 5 0.08
31 4 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
TAATTATTATTAATATAATATATTA
Found at i:1517578 original size:19 final size:20
Alignment explanation
Indices: 1517552--1517639 Score: 84
Period size: 23 Copynumber: 4.6 Consensus size: 20
1517542 TAATAATTAT
1517552 TATA-ATTATTATTAATATA
1 TATATATTATTATTAATATA
1517571 -ATATATTATTATT-AT-TA
1 TATATATTATTATTAATATA
1517588 T-T-TATTATTA--AATATA
1 TATATATTATTATTAATATA
1517604 TATATATATATATATTATATATA
1 TATATAT-TAT-TATTA-ATATA
1517627 TATATATATATTA
1 TATATAT-TATTA
1517640 CAAATTACAT
Statistics
Matches: 58, Mismatches: 0, Indels: 19
0.75 0.00 0.25
Matches are distributed among these distances:
15 2 0.03
16 11 0.19
17 4 0.07
18 8 0.14
19 12 0.21
20 2 0.03
22 3 0.05
23 16 0.28
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATATATTATTATTAATATA
Found at i:1517606 original size:2 final size:2
Alignment explanation
Indices: 1517599--1517637 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
1517589 TTATTATTAA
1517599 AT AT AT AT AT AT AT AT AT AT -T 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
1517638 TACAAATTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1520406 original size:15 final size:16
Alignment explanation
Indices: 1520373--1520410 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1520363 CTCAATTATC
*
1520373 AAAATAAAATAAATTA
1 AAAATAAAATAAATAA
*
1520389 AAAATATAAT-AATAA
1 AAAATAAAATAAATAA
1520404 AAAATAA
1 AAAATAA
1520411 TTTTTTAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 10 0.53
16 9 0.47
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAAAATAAATAA
Found at i:1520791 original size:17 final size:17
Alignment explanation
Indices: 1520769--1520814 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
1520759 AATATGTGTC
* *
1520769 ATCCCCTTAAGCAGCGT
1 ATCCCCTTAAACAACGT
1520786 ATCCCCTTAAACAACGT
1 ATCCCCTTAAACAACGT
1520803 ATCCCCTTAAAC
1 ATCCCCTTAAAC
1520815 CAACAATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.30, C:0.37, G:0.09, T:0.24
Consensus pattern (17 bp):
ATCCCCTTAAACAACGT
Found at i:1523874 original size:13 final size:13
Alignment explanation
Indices: 1523846--1523884 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
1523836 TTGGCGAGGT
*
1523846 TTTGAAAA-ACTA
1 TTTGAAAATAATA
1523858 TTTGAAAATAATA
1 TTTGAAAATAATA
*
1523871 TTTGTAAATAATA
1 TTTGAAAATAATA
1523884 T
1 T
1523885 GTATAGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 8 0.33
13 16 0.67
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (13 bp):
TTTGAAAATAATA
Found at i:1533954 original size:22 final size:21
Alignment explanation
Indices: 1533912--1533951 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1533902 GAGTTTATTT
*
1533912 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
1533933 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
1533952 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:1536020 original size:45 final size:46
Alignment explanation
Indices: 1535932--1536022 Score: 139
Period size: 45 Copynumber: 2.0 Consensus size: 46
1535922 TTGAAAAAGC
* *
1535932 CTGAGTGCATCGATGCATAGTCTTGTGCATCGATGCATCAAATGCA
1 CTGAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
* *
1535978 CTGAGTGTATCGATGCATGGT-ATGTGCATCGATGCATAAAATGCA
1 CTGAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
1536023 TTCGATGTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 22 0.54
46 19 0.46
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (46 bp):
CTGAGTGCATCGATGCATAGTCATGTGCATCGATGCATAAAATGCA
Found at i:1536401 original size:2 final size:2
Alignment explanation
Indices: 1536312--1536385 Score: 125
Period size: 2 Copynumber: 38.0 Consensus size: 2
1536302 GTTTTTCAAC
1536312 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AT A- 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
*
1536352 AT AT AT AT CT 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
1536386 TATCTCAACG
Statistics
Matches: 68, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
1 2 0.03
2 66 0.97
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1536699 original size:21 final size:22
Alignment explanation
Indices: 1536673--1536720 Score: 89
Period size: 21 Copynumber: 2.2 Consensus size: 22
1536663 CAGAAGGCAG
1536673 TAAATAAAAATGATTGGCTAA-
1 TAAATAAAAATGATTGGCTAAT
1536694 TAAATAAAAATGATTGGCTAAT
1 TAAATAAAAATGATTGGCTAAT
1536716 TAAAT
1 TAAAT
1536721 TTTATCTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 21 0.81
22 5 0.19
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.31
Consensus pattern (22 bp):
TAAATAAAAATGATTGGCTAAT
Found at i:1537249 original size:29 final size:30
Alignment explanation
Indices: 1537197--1537259 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
1537187 CGTGTTCGTT
*
1537197 TTTATATTTGAAAGTGTTCATATT-GTTTA
1 TTTATATTTGAAAGTGTTCATATTCATTTA
* * **
1537226 TTTATTTTTGAAGGTGTTTGTATTCATTTA
1 TTTATATTTGAAAGTGTTCATATTCATTTA
1537256 TTTA
1 TTTA
1537260 CTGTTCACAG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.24, C:0.03, G:0.14, T:0.59
Consensus pattern (30 bp):
TTTATATTTGAAAGTGTTCATATTCATTTA
Found at i:1538012 original size:37 final size:37
Alignment explanation
Indices: 1537939--1538013 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 37
1537929 GTTGGAAAAT
* *
1537939 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
*
1537976 ATTTATATAATTGTT-TTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATT-TTCTTTAAAAAATTGAAAATCATAAA
1538013 A
1 A
1538014 AGGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 14 0.42
38 17 0.52
39 2 0.06
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:1538372 original size:42 final size:42
Alignment explanation
Indices: 1538313--1538402 Score: 180
Period size: 42 Copynumber: 2.1 Consensus size: 42
1538303 AACCAAATGG
1538313 GAGAATGTGGATTCCATTCCTATTGGAATCTCACATTCCCAT
1 GAGAATGTGGATTCCATTCCTATTGGAATCTCACATTCCCAT
1538355 GAGAATGTGGATTCCATTCCTATTGGAATCTCACATTCCCAT
1 GAGAATGTGGATTCCATTCCTATTGGAATCTCACATTCCCAT
1538397 GAGAAT
1 GAGAAT
1538403 CTCACATTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.32
Consensus pattern (42 bp):
GAGAATGTGGATTCCATTCCTATTGGAATCTCACATTCCCAT
Found at i:1538417 original size:21 final size:19
Alignment explanation
Indices: 1538338--1538411 Score: 69
Period size: 19 Copynumber: 3.7 Consensus size: 19
1538328 ATTCCTATTG
1538338 GAATCTCACATTCCCATGA
1 GAATCTCACATTCCCATGA
* * *
1538357 GAATGTGGATTCCATTCCTATTG-
1 GAATCT-CA---CATTCCCA-TGA
1538380 GAATCTCACATTCCCATGA
1 GAATCTCACATTCCCATGA
1538399 GAATCTCACATTC
1 GAATCTCACATTC
1538412 TCCCATCCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
18 2 0.05
19 25 0.58
20 1 0.02
22 1 0.02
23 12 0.28
24 2 0.05
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (19 bp):
GAATCTCACATTCCCATGA
Found at i:1542521 original size:21 final size:18
Alignment explanation
Indices: 1542492--1542547 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
1542482 AAATCATATG
1542492 TGTGA-TATCGATACTAA
1 TGTGAGTATCGATACTAA
* *
1542509 TGTAATTAGTATCGATACTTA
1 TG---TGAGTATCGATACTAA
1542530 TGTGAGTATCGATACTAA
1 TGTGAGTATCGATACTAA
1542548 GAGAAAGGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
17 2 0.06
18 14 0.45
20 2 0.06
21 13 0.42
ACGTcount: A:0.34, C:0.11, G:0.18, T:0.38
Consensus pattern (18 bp):
TGTGAGTATCGATACTAA
Found at i:1543142 original size:63 final size:63
Alignment explanation
Indices: 1543045--1543446 Score: 714
Period size: 63 Copynumber: 6.4 Consensus size: 63
1543035 TTTTAAAATG
*
1543045 AAAGAATAAATGCCTAACTGTGCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTG
1 AAAGAATAAATGCCTAACTGTGCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTA
* *
1543108 AAAGAATAAATGTCTATCTGTGCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTA
1 AAAGAATAAATGCCTAACTGTGCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTA
1543171 AAAGAATAAATGCCTAACTGTGCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTA
1 AAAGAATAAATGCCTAACTGTGCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTA
* * *
1543234 AAAGAATAAATACCTAATTGTGCAATCATGCAAGTTAGATGAAAGGATAAATGCCTTTGAGTA
1 AAAGAATAAATGCCTAACTGTGCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTA
*
1543297 AAAGAATAAATGCCTAACTGTGCAATCATGCAAGTTAGATGAAAGGCTAAATACCTTTGAGTA
1 AAAGAATAAATGCCTAACTGTGCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTA
*
1543360 AAAGAATAAATGCCTAACTGTGCAATAATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTA
1 AAAGAATAAATGCCTAACTGTGCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTA
* *
1543423 AAAGATTAAATGCCTAACTATGCA
1 AAAGAATAAATGCCTAACTGTGCA
1543447 TTTGGAAGAA
Statistics
Matches: 323, Mismatches: 16, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
63 323 1.00
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (63 bp):
AAAGAATAAATGCCTAACTGTGCAATCATGCAAGTTAGATGAAAGGCTAAATGCCTTTGAGTA
Found at i:1549257 original size:21 final size:18
Alignment explanation
Indices: 1549231--1549282 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
1549221 CAGATATGCG
*
1549231 GTATCGATACTAATGTAATTA
1 GTATCGATACTAATG---TGA
*
1549252 GTATCGATACTGATGTGA
1 GTATCGATACTAATGTGA
1549270 GTATCGATACTAA
1 GTATCGATACTAA
1549283 GAGAAAGGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 14 0.50
21 14 0.50
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.35
Consensus pattern (18 bp):
GTATCGATACTAATGTGA
Found at i:1550322 original size:62 final size:62
Alignment explanation
Indices: 1550225--1550350 Score: 243
Period size: 62 Copynumber: 2.0 Consensus size: 62
1550215 TGCTTAATAC
*
1550225 TATGTCCAAGTGTGCATTGAGTGTTGGGGTCAATTGTATGAATTTATTTCGTTGGAATAAAA
1 TATGTCCAAGTGTCCATTGAGTGTTGGGGTCAATTGTATGAATTTATTTCGTTGGAATAAAA
1550287 TATGTCCAAGTGTCCATTGAGTGTTGGGGTCAATTGTATGAATTTATTTCGTTGGAATAAAA
1 TATGTCCAAGTGTCCATTGAGTGTTGGGGTCAATTGTATGAATTTATTTCGTTGGAATAAAA
1550349 TA
1 TA
1550351 GGGGATAGTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.28, C:0.09, G:0.25, T:0.39
Consensus pattern (62 bp):
TATGTCCAAGTGTCCATTGAGTGTTGGGGTCAATTGTATGAATTTATTTCGTTGGAATAAAA
Found at i:1550369 original size:3 final size:3
Alignment explanation
Indices: 1550361--1550401 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1550351 GGGGATAGTT
1550361 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1550402 GGATGAGGCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1551134 original size:2 final size:2
Alignment explanation
Indices: 1551127--1551207 Score: 162
Period size: 2 Copynumber: 40.5 Consensus size: 2
1551117 TATAAAAATA
1551127 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1551169 AT AT AT AT 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 AT AT AT AT A
1551208 AATTAACAAA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 79 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1553887 original size:23 final size:23
Alignment explanation
Indices: 1553867--1553931 Score: 82
Period size: 21 Copynumber: 3.0 Consensus size: 23
1553857 AGTAGTTAAT
1553867 GGTTAGCTGTTAGAAAAGTTAGC
1 GGTTAGCTGTTAGAAAAGTTAGC
**
1553890 GGTTAGCACTTAG-AAA-TTAGC
1 GGTTAGCTGTTAGAAAAGTTAGC
*
1553911 GGTTAG-TGTTAGAAATGTTAG
1 GGTTAGCTGTTAGAAAAGTTAG
1553932 TAGAGTCTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
20 4 0.11
21 13 0.37
22 7 0.20
23 11 0.31
ACGTcount: A:0.31, C:0.08, G:0.29, T:0.32
Consensus pattern (23 bp):
GGTTAGCTGTTAGAAAAGTTAGC
Found at i:1555034 original size:11 final size:11
Alignment explanation
Indices: 1555020--1555045 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1555010 TTATTTTTTA
1555020 ATAATAATAAT
1 ATAATAATAAT
1555031 ATAATAATAAT
1 ATAATAATAAT
1555042 ATAA
1 ATAA
1555046 AAAATGGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATAATAAT
Found at i:1559052 original size:21 final size:21
Alignment explanation
Indices: 1559026--1559067 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1559016 ATGCAGTCTG
1559026 ATGCAAGAATTTTAGTGGTTT
1 ATGCAAGAATTTTAGTGGTTT
1559047 ATGCAAGAATTTTAGTGGTTT
1 ATGCAAGAATTTTAGTGGTTT
1559068 CAATGTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.29, C:0.05, G:0.24, T:0.43
Consensus pattern (21 bp):
ATGCAAGAATTTTAGTGGTTT
Found at i:1565377 original size:15 final size:15
Alignment explanation
Indices: 1565359--1565388 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1565349 CCTACTTGAA
1565359 ATTCTATATCATTTG
1 ATTCTATATCATTTG
1565374 ATTCTATATCATTTG
1 ATTCTATATCATTTG
1565389 GTATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTCTATATCATTTG
Found at i:1568031 original size:30 final size:30
Alignment explanation
Indices: 1567984--1568088 Score: 124
Period size: 30 Copynumber: 3.5 Consensus size: 30
1567974 TTTACATTGG
*
1567984 GCTACAAAATG-AAAAAGTGAATAGTATAA
1 GCTATAAAATGAAAAAAGTGAATAGTATAA
*
1568013 GCTATAAAATGAAAAAAGTGAATAGTACAA
1 GCTATAAAATGAAAAAAGTGAATAGTATAA
*
1568043 GCTATGAAAA-GAAAAAAAAGTGAAGAGTATAA
1 GCTAT-AAAATG--AAAAAAGTGAATAGTATAA
* *
1568075 CCTATAAGATGAAA
1 GCTATAAAATGAAA
1568089 GTGAATGATA
Statistics
Matches: 65, Mismatches: 6, Indels: 9
0.81 0.08 0.11
Matches are distributed among these distances:
29 10 0.15
30 26 0.40
31 7 0.11
32 22 0.34
ACGTcount: A:0.56, C:0.07, G:0.18, T:0.19
Consensus pattern (30 bp):
GCTATAAAATGAAAAAAGTGAATAGTATAA
Found at i:1568142 original size:30 final size:30
Alignment explanation
Indices: 1568108--1568168 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
1568098 ACAGATTACA
*
1568108 AAATAAATTAAATGAA-CGATACATGCTATG
1 AAATAAATGAAATGAATCGA-ACATGCTATG
* *
1568138 AAATAAATGAAATTAATGGAACATGCTATG
1 AAATAAATGAAATGAATCGAACATGCTATG
1568168 A
1 A
1568169 TGTTGCTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 25 0.93
31 2 0.07
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (30 bp):
AAATAAATGAAATGAATCGAACATGCTATG
Found at i:1572631 original size:2 final size:2
Alignment explanation
Indices: 1572624--1572660 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1572614 TATTAAAGAA
1572624 AT AT AT 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 AT AT AT A
1572661 GTAAAATATA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1572723 original size:15 final size:17
Alignment explanation
Indices: 1572624--1572716 Score: 54
Period size: 17 Copynumber: 5.6 Consensus size: 17
1572614 TATTAAAGAA
*
1572624 ATAT-ATATATATATAT
1 ATATAATATATATATAC
*
1572640 ATATATATATATATATAT
1 ATATA-ATATATATATAC
1572658 ATAGTAA-A-ATATAGTA-
1 ATA-TAATATATATA-TAC
* * *
1572674 A-AAAATAAATGAAATA-
1 ATATAATATAT-ATATAC
*
1572690 ATTTAATATATATATAC
1 ATATAATATATATATAC
1572707 ATATAATATA
1 ATATAATATA
1572717 ATAACATGAA
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
14 2 0.03
15 2 0.03
16 19 0.31
17 20 0.33
18 16 0.26
19 2 0.03
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (17 bp):
ATATAATATATATATAC
Found at i:1573183 original size:37 final size:36
Alignment explanation
Indices: 1573140--1573240 Score: 163
Period size: 37 Copynumber: 2.9 Consensus size: 36
1573130 ATAGTATAAC
1573140 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
1573177 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
1573211 TCTATCCTA-TTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1573241 TAGGACGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
33 19 0.32
34 13 0.22
37 28 0.47
ACGTcount: A:0.28, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1574075 original size:105 final size:105
Alignment explanation
Indices: 1573774--1574433 Score: 895
Period size: 105 Copynumber: 6.3 Consensus size: 105
1573764 CATTGTTCCA
* * * * *
1573774 AGTCTAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACTGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * * *
1573838 CCAGTC-GTCCCTTCGTTGTGAAGTTGAATTTGTGTTGTCTCG
64 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
1573880 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1573940 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1573980 AATCCAATATCCTTCGTTGTGAAATTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* * *
1574045 AGCGGTCCCTTCGTTGTGAAGTTGAACTTGCATTGTATGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
1574085 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
1574150 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * ** *
1574190 AGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTGTTGACAAGT
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1574255 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
1574295 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
* * * * *
1574360 AATC-GTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCG
66 -AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
1574400 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
1574434 CGCAGATGGC
Statistics
Matches: 502, Mismatches: 41, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
99 1 0.00
100 81 0.16
101 1 0.00
102 7 0.01
104 6 0.01
105 345 0.69
106 39 0.08
108 22 0.04
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:1575323 original size:209 final size:209
Alignment explanation
Indices: 1574963--1575410 Score: 869
Period size: 209 Copynumber: 2.1 Consensus size: 209
1574953 GTAACGGTTC
1574963 AGATGATGCTTCAAGAGAAATTGTCTCAAAAGAGACAGAACTCGTTTCAAGGGAAACGATCTCAA
1 AGATGATGCTTCAAGAGAAATTGTCTCAAAAGAGACAGAACTCGTTTCAAGGGAAACGATCTCAA
1575028 AGATATTTGTTGTTTCAAGGGAAACGGTCTTAAGGGAGACAAAATTTTGTTTTAAGAAAAACTGT
66 AGATATTTGTTGTTTCAAGGGAAACGGTCTTAAGGGAGACAAAATTTTGTTTTAAGAAAAACTGT
1575093 CTCAAGAGAGACTAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGAAATTAGTTCCAAG
131 CTCAAGAGAGACTAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGAAATTAGTTCCAAG
*
1575158 GAAAATATATTCAA
196 GAAAACATATTCAA
1575172 AGATGATGCTTCAAGAGAAATTGTCTCAAAAGAGACAGAACTCGTTTCAAGGGAAACGATCTCAA
1 AGATGATGCTTCAAGAGAAATTGTCTCAAAAGAGACAGAACTCGTTTCAAGGGAAACGATCTCAA
1575237 AGATATTTGTTGTTTCAAGGGAAACGGTCTTAAGGGAGACAAAATTTTGTTTTAAGAAAAACTGT
66 AGATATTTGTTGTTTCAAGGGAAACGGTCTTAAGGGAGACAAAATTTTGTTTTAAGAAAAACTGT
1575302 CTCAAGAGAGACTAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGAAATTAGTTCCAAG
131 CTCAAGAGAGACTAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGAAATTAGTTCCAAG
1575367 GAAAACATATTCAA
196 GAAAACATATTCAA
*
1575381 AGATGATGCTTCAAGAGAAAACTGTCTCAA
1 AGATGATGCTTCAAGAG-AAATTGTCTCAA
1575411 GGGAGACAAA
Statistics
Matches: 236, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
209 225 0.95
210 11 0.05
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (209 bp):
AGATGATGCTTCAAGAGAAATTGTCTCAAAAGAGACAGAACTCGTTTCAAGGGAAACGATCTCAA
AGATATTTGTTGTTTCAAGGGAAACGGTCTTAAGGGAGACAAAATTTTGTTTTAAGAAAAACTGT
CTCAAGAGAGACTAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGAAATTAGTTCCAAG
GAAAACATATTCAA
Found at i:1575405 original size:104 final size:103
Alignment explanation
Indices: 1575081--1575446 Score: 300
Period size: 104 Copynumber: 3.5 Consensus size: 103
1575071 ATTTTGTTTT
1575081 AAGAAAAACTGTCTCAAGAGAGACTAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGAA
1 AAGAAAAACTGTCTCAAGAGAGACTAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGAA
*
1575146 ATTAGTTCCAAGGAAAATATATTCAAAGATGATGCTTC
66 ATTAGTTCCAAGGAAAACATATTCAAAGATGATGCTTC
* * * * * ** * *
1575184 AAGAGAAATTGTCTCAAAAGAGAC-AGAAC-TCGTTTCAAGGGAAA-CGATCTCA----AAGAT-
1 AAGAAAAACTGTCTCAAGAGAGACTA-AACTTAGTTCCAAAAGAAATTG-TCTCACGGGGAGATG
** * * * * * ** * *
1575241 ATTTGTTGTTTCAAGGGAAACGGTCTT-AAGGGAGACAAAATTTTGTTTT
64 AAAT-TAGTTCCAAGGAAAAC-ATATTCAA---AG-----ATGATGCTTC
1575290 AAGAAAAACTGTCTCAAGAGAGACTAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGAA
1 AAGAAAAACTGTCTCAAGAGAGACTAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGAA
1575355 ATTAGTTCCAAGGAAAACATATTCAAAGATGATGCTTC
66 ATTAGTTCCAAGGAAAACATATTCAAAGATGATGCTTC
* * * * * * *
1575393 AAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCA
1 AAGA-AAAACTGTCTCAAGAGAGACTAAACTTAGTTCCAAAAGAAATTGTCTCA
1575447 AGAGAGACGA
Statistics
Matches: 193, Mismatches: 48, Indels: 43
0.68 0.17 0.15
Matches are distributed among these distances:
97 2 0.01
98 18 0.09
99 3 0.02
101 3 0.02
102 17 0.09
103 34 0.18
104 42 0.22
106 30 0.16
107 17 0.09
108 3 0.02
110 3 0.02
111 19 0.10
112 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.25
Consensus pattern (103 bp):
AAGAAAAACTGTCTCAAGAGAGACTAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGAA
ATTAGTTCCAAGGAAAACATATTCAAAGATGATGCTTC
Found at i:1575529 original size:65 final size:65
Alignment explanation
Indices: 1575425--1575590 Score: 296
Period size: 65 Copynumber: 2.6 Consensus size: 65
1575415 GACAAAATTT
*
1575425 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATTTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
1575490 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
1575555 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
1575591 TTGTTTCGAG
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 96 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:1575596 original size:102 final size:102
Alignment explanation
Indices: 1575490--1575845 Score: 640
Period size: 102 Copynumber: 3.5 Consensus size: 102
1575480 TCAATGTTTA
* *
1575490 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1575555 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
1575592 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1575657 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
1575694 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1575759 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * **
1575796 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
1575846 CTGTCTCAAG
Statistics
Matches: 245, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 245 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:1575606 original size:37 final size:37
Alignment explanation
Indices: 1575555--1575863 Score: 266
Period size: 37 Copynumber: 8.9 Consensus size: 37
1575545 TCAATGTTTA
* *
1575555 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
1575592 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * *
1575628 CATTTCAAGGGAAA-TGTTTTC-A-A-TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATTT
* *
1575656 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
1575694 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
** * **
1575730 CATTTCAAGGGAAA-TGTTTC--------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
* *
1575758 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
*
1575796 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
1575832 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1575864 TAGTGAGCAC
Statistics
Matches: 213, Mismatches: 34, Indels: 50
0.72 0.11 0.17
Matches are distributed among these distances:
27 3 0.01
28 4 0.02
29 25 0.12
30 8 0.04
32 1 0.00
33 1 0.00
34 1 0.00
35 6 0.03
36 65 0.31
37 90 0.42
38 9 0.04
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:1575680 original size:167 final size:169
Alignment explanation
Indices: 1575390--1575707 Score: 532
Period size: 167 Copynumber: 1.9 Consensus size: 169
1575380 AAGATGATGC
*
1575390 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
* *
1575455 GAAATTCATTTCAAGGGAAATTTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
1575520 GAAA-TTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
131 AAAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
* *
1575558 TTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTTTGTTTCGAGGGAAACTATCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
* *
1575622 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
**
1575687 AAAATTTTGTTTCAAGGGAAA
131 AAAATTTCATTTCAAGGGAAA
1575708 CTATCTCAAG
Statistics
Matches: 139, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
167 117 0.84
168 22 0.16
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (169 bp):
TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
Found at i:1576748 original size:22 final size:22
Alignment explanation
Indices: 1576723--1576773 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
1576713 TTGTGTTTGG
1576723 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
1576745 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
1576767 TCAAAGG
1 TCAAAGG
1576774 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:1581234 original size:2 final size:2
Alignment explanation
Indices: 1581223--1581254 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1581213 AAAAGGAAAA
*
1581223 AT AT AA 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
1581255 CAAAGTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1581742 original size:41 final size:43
Alignment explanation
Indices: 1581675--1581754 Score: 105
Period size: 41 Copynumber: 1.9 Consensus size: 43
1581665 ATATATATAT
1581675 ATATATATAGTAAAATATAAAAAATAA-ATGAA-AATAATTTA
1 ATATATATAGTAAAATATAAAAAATAACATGAATAATAATTTA
*
1581716 ATATATATA-T-ACATATAATAATAATAACATGAATAATAA
1 ATATATATAGTAAAATATAA-AA-AATAACATGAATAATAA
1581755 AAATAAATGA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
39 7 0.21
40 3 0.09
41 14 0.41
42 5 0.15
43 5 0.15
ACGTcount: A:0.61, C:0.03, G:0.04, T:0.33
Consensus pattern (43 bp):
ATATATATAGTAAAATATAAAAAATAACATGAATAATAATTTA
Found at i:1581753 original size:18 final size:17
Alignment explanation
Indices: 1581730--1581772 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
1581720 ATATATACAT
1581730 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
1581748 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
1581765 ATAA-AATA
1 ATAATAATA
1581773 TCCATATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:1582207 original size:37 final size:36
Alignment explanation
Indices: 1582164--1582265 Score: 172
Period size: 34 Copynumber: 2.9 Consensus size: 36
1582154 ATAGTATAAC
1582164 TCTATCCTATTTTTAGGAGTTTGAATCCTAGCAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG-AAAAT
*
1582201 TTTATCCTATTTTTAGGAGTTTGAATCCT--AAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
1582235 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1 TCTATCCTATTTTTAGGAGTTTGAATCCTAG
1582266 TAGGACGAAA
Statistics
Matches: 61, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
34 33 0.54
37 28 0.46
ACGTcount: A:0.27, C:0.15, G:0.14, T:0.44
Consensus pattern (36 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAGAAAAT
Found at i:1586001 original size:19 final size:20
Alignment explanation
Indices: 1585972--1586011 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1585962 TTTGGGTTCG
1585972 TTTACTTTTTTTTAAATTTT
1 TTTACTTTTTTTTAAATTTT
*
1585992 TTTA-TTTTTTTTATATTTT
1 TTTACTTTTTTTTAAATTTT
1586011 T
1 T
1586012 GAATAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTACTTTTTTTTAAATTTT
Found at i:1598610 original size:16 final size:18
Alignment explanation
Indices: 1598574--1598613 Score: 66
Period size: 16 Copynumber: 2.3 Consensus size: 18
1598564 ACTAATTTCA
1598574 TCAAAAACACATTATTTT
1 TCAAAAACACATTATTTT
1598592 TCAAAAACA-ATTA-TTT
1 TCAAAAACACATTATTTT
1598608 TCAAAA
1 TCAAAA
1598614 TAAAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 9 0.41
17 4 0.18
18 9 0.41
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (18 bp):
TCAAAAACACATTATTTT
Found at i:1600778 original size:20 final size:20
Alignment explanation
Indices: 1600753--1600790 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1600743 ATTTACAAAG
*
1600753 AGATGTGCCGATACACTCTT
1 AGATGTACCGATACACTCTT
*
1600773 AGATGTATCGATACACTC
1 AGATGTACCGATACACTC
1600791 CAACATCGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (20 bp):
AGATGTACCGATACACTCTT
Found at i:1604111 original size:2 final size:2
Alignment explanation
Indices: 1604104--1604132 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1604094 AGATTAGACT
1604104 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 T
1604133 GTATGTACAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1607044 original size:3 final size:3
Alignment explanation
Indices: 1607029--1607067 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1607019 AAATATGTAT
* *
1607029 TAA TAA TAG TAA TAA TAA TAA TAA TAA CATA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TA
1607068 TTATATATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.94
4 2 0.06
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1607896 original size:134 final size:135
Alignment explanation
Indices: 1607311--1607896 Score: 529
Period size: 133 Copynumber: 4.4 Consensus size: 135
1607301 GTGACACGAA
* * * * * * *
1607311 TCCTACGTGATGAGGAGATATGATCGGTGTATGACTCGGCTCATACGTGATGAAGAGTTCTGGTC
1 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
* * * * * * *
1607376 ATCTTTAGGGAGGATGATAACACGGTTCCTACACAATAAGGACGG-CTGGTTATCTAGGGGTGAC
66 ATCTTTAGGGAGGGTGATAACACAGTTCCTACACGATGAGGACGGACAGGTTATCTAGGGTTGAT
*
1607440 ACCGC
131 ACGGC
** * * * * * * *
1607445 TCCTATATGATAAAGTGGTCTGGTCGGGGGATGACATGACTCATAC-AGATGAAGAGTTCTGGTT
1 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
* * * * ** * *
1607509 ATCTTTAGGAAGGGAGATAACACAGTTTCTACACGATGAGGATGGTTA-GTTATCTAAGG-CGAT
66 ATCTTTAGGGAGGGTGATAACACAGTTCCTACACGATGAGGACGGACAGGTTATCTAGGGTTGAT
* *
1607572 ATGAC
131 ACGGC
* * * * * * *** **
1607577 TCTTACGTGATGAGGAGGTCTGGTCGGAGGATGGCACGGTTCCTACGCGATGAGGACAGCAAGTC
1 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
* * * * *
1607642 ATCTTTA-GGATGGCGATAACACGGTTCCTACATGATGAGGAC-GACAGGTTATCTAGTGTTGAT
66 ATCTTTAGGGAGGGTGATAACACAGTTCCTACACGATGAGGACGGACAGGTTATCTAGGGTTGAT
*
1607705 GCGGC
131 ACGGC
* * * * * *
1607710 TCCTAGGTGATGAGGAGGTCTGGTCAGGGGATTACACGACTCATACGTGATGAAGAGTTCTGGCC
1 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
* * * *
1607775 ATCTTTAGGGAGGGTGATAACACAATTTCTACATGATGAGGACAG-CAGGTTATCTAGGGTTGAT
66 ATCTTTAGGGAGGGTGATAACACAGTTCCTACACGATGAGGACGGACAGGTTATCTAGGGTTGAT
*
1607839 GCGGC
131 ACGGC
* * * *
1607844 TCCTACGTGATGAGGAGGTATGGTCGGGGGATGGCACGGTTCCTACGCGATGA
1 TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGCTCATACGCGATGA
1607897 TGACAGCTGG
Statistics
Matches: 348, Mismatches: 98, Indels: 12
0.76 0.21 0.03
Matches are distributed among these distances:
131 2 0.01
132 75 0.22
133 140 0.40
134 130 0.37
135 1 0.00
ACGTcount: A:0.25, C:0.17, G:0.32, T:0.26
Consensus pattern (135 bp):
TCCTACGTGATGAGGAGGTCTGGTCGGGGGATGACACGGCTCATACGCGATGAAGAGTTCTGGTC
ATCTTTAGGGAGGGTGATAACACAGTTCCTACACGATGAGGACGGACAGGTTATCTAGGGTTGAT
ACGGC
Found at i:1607949 original size:42 final size:42
Alignment explanation
Indices: 1607822--1607949 Score: 102
Period size: 42 Copynumber: 3.1 Consensus size: 42
1607812 GAGGACAGCA
* ** * *
1607822 GGTTATCTAGGGTTGATGCGGCTCCTACGTGATGAGGAGGTAT
1 GGTTATC-AGGGGTGACACGGCTCCTACGTGATGAAGAGGTCT
* * * * * *
1607865 GG---TCGGGGGATGGCACGGTTCCTACGCGATGATGACAG-CT
1 GGTTATCAGGGG-TGACACGGCTCCTACGTGATGAAGA-GGTCT
1607905 GGTTATCAGGGGTGACACGGCTCCTACGTGATGAAGAGGTCT
1 GGTTATCAGGGGTGACACGGCTCCTACGTGATGAAGAGGTCT
1607947 GGT
1 GGT
1607950 CGAGGGATGA
Statistics
Matches: 63, Mismatches: 16, Indels: 13
0.68 0.17 0.14
Matches are distributed among these distances:
39 3 0.05
40 24 0.38
41 2 0.03
42 26 0.41
43 8 0.13
ACGTcount: A:0.19, C:0.18, G:0.38, T:0.25
Consensus pattern (42 bp):
GGTTATCAGGGGTGACACGGCTCCTACGTGATGAAGAGGTCT
Found at i:1607978 original size:82 final size:83
Alignment explanation
Indices: 1607808--1607978 Score: 191
Period size: 82 Copynumber: 2.1 Consensus size: 83
1607798 AATTTCTACA
* ** * *
1607808 TGATGAGGACAGCAGGTTATCTAGGGTTGATGCGGCTCCTACGTGATGAGGAGGTATGGTCGGGG
1 TGATGAGGACAGCAGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGGTATGGTCGAGG
* *** *
1607873 GATGGCACGGTTCCTACG
66 GATGACACAACTCATACG
* * * *
1607891 CGATGATGACAGCTGGTTATC-AGGGGTGACACGGCTCCTACGTGATGAAGAGGTCTGGTCGAGG
1 TGATGAGGACAGCAGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGGTATGGTCGAGG
* *
1607955 GATGACATAACTCATATG
66 GATGACACAACTCATACG
1607973 TGATGA
1 TGATGA
1607979 ATAGTTCTGG
Statistics
Matches: 71, Mismatches: 17, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
82 53 0.75
83 18 0.25
ACGTcount: A:0.23, C:0.17, G:0.36, T:0.24
Consensus pattern (83 bp):
TGATGAGGACAGCAGGTTATCTAGGGGTGACACGGCTCCTACGTGATGAAGAGGTATGGTCGAGG
GATGACACAACTCATACG
Found at i:1608080 original size:29 final size:31
Alignment explanation
Indices: 1608015--1608081 Score: 75
Period size: 33 Copynumber: 2.2 Consensus size: 31
1608005 TGGTTTCAAA
* * *
1608015 AGAAACCGACTCAAAGATGATTTTTGTTTCATG
1 AGAAACAGACTCAAAGAT-ATTTGTGTTTCA-C
1608048 AGAAACAGACTCAAAGAT-TTTGTGTTTC-C
1 AGAAACAGACTCAAAGATATTTGTGTTTCAC
1608077 AGAAA
1 AGAAA
1608082 AACTGTCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 5 0.16
31 9 0.29
33 17 0.55
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (31 bp):
AGAAACAGACTCAAAGATATTTGTGTTTCAC
Found at i:1608397 original size:33 final size:33
Alignment explanation
Indices: 1608340--1608405 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1608330 ATTGAATCCC
* * *
1608340 CAAATATGCCCCAACGTTCGATGTTGATTGCTT
1 CAAAGATGCCCCAACATTCAATGTTGATTGCTT
*
1608373 CAAAGATGCCCCAATATTCAATGTTGATTGCTT
1 CAAAGATGCCCCAACATTCAATGTTGATTGCTT
1608406 TTGCACTGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (33 bp):
CAAAGATGCCCCAACATTCAATGTTGATTGCTT
Found at i:1609458 original size:10 final size:10
Alignment explanation
Indices: 1609445--1609533 Score: 60
Period size: 10 Copynumber: 8.5 Consensus size: 10
1609435 TTGTCCAATC
1609445 TTTTTCTTTG
1 TTTTTCTTTG
1609455 TTTTTCTTTTG
1 TTTTTC-TTTG
1609466 TTTTTTTTCTTTG
1 ---TTTTTCTTTG
1609479 -TTTTCTTTGCG
1 TTTTTCTTT--G
1609490 TTTTTCTCTT-
1 TTTTTCT-TTG
1609500 TTTTTCTTCT-
1 TTTTTCTT-TG
*
1609510 TTTCTCTTTG
1 TTTTTCTTTG
*
1609520 TTTTT-TTTC
1 TTTTTCTTTG
1609529 TTTTT
1 TTTTT
1609534 GTTCTTTATA
Statistics
Matches: 66, Mismatches: 3, Indels: 21
0.73 0.03 0.23
Matches are distributed among these distances:
9 18 0.27
10 25 0.38
11 5 0.08
12 6 0.09
13 6 0.09
14 6 0.09
ACGTcount: A:0.00, C:0.13, G:0.07, T:0.80
Consensus pattern (10 bp):
TTTTTCTTTG
Found at i:1609472 original size:24 final size:25
Alignment explanation
Indices: 1609445--1609549 Score: 74
Period size: 24 Copynumber: 4.1 Consensus size: 25
1609435 TTGTCCAATC
1609445 TTTTTCTTTGTTTTTCTTT-TGTTT
1 TTTTTCTTTGTTTTTCTTTATGTTT
**
1609469 TTTTTCTTTG-TTTTCTTTGCGTTTT
1 TTTTTCTTTGTTTTTCTTTATG-TTT
* *
1609494 TCTCTTTTTTTCTTCTTTTCTCTT-TGTTT
1 T-T-TTTCTTT-GT-TTTTCT-TTATGTTT
* *
1609523 TTTTTCTTT-TTGTTCTTTATATTT
1 TTTTTCTTTGTTTTTCTTTATGTTT
1609547 TTT
1 TTT
1609550 CCTTGGCTTC
Statistics
Matches: 65, Mismatches: 7, Indels: 18
0.72 0.08 0.20
Matches are distributed among these distances:
23 10 0.15
24 23 0.35
25 5 0.08
26 1 0.02
27 12 0.18
28 1 0.02
29 4 0.06
30 7 0.11
31 2 0.03
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (25 bp):
TTTTTCTTTGTTTTTCTTTATGTTT
Found at i:1609482 original size:23 final size:24
Alignment explanation
Indices: 1609445--1609507 Score: 78
Period size: 23 Copynumber: 2.7 Consensus size: 24
1609435 TTGTCCAATC
*
1609445 TTTTTCTTTGTTTTTCTTTTG-TTT
1 TTTTTCTTTG-TTTTCTTTTGCGTT
1609469 TTTTTCTTTGTTTTC-TTTGCGTT
1 TTTTTCTTTGTTTTCTTTTGCGTT
*
1609492 TTTCTCTTT-TTTTCTT
1 TTTTTCTTTGTTTTCTT
1609508 CTTTTCTCTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 9 0.26
23 16 0.46
24 10 0.29
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (24 bp):
TTTTTCTTTGTTTTCTTTTGCGTT
Found at i:1609518 original size:32 final size:30
Alignment explanation
Indices: 1609467--1609540 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
1609457 TTTCTTTTGT
1609467 TTTTTTTCTTTGTTTTCTTTGCGTTTTTCTC
1 TTTTTTTCTTTGTTTTCTTTG-GTTTTTCTC
* *
1609498 TTTTTTTCTTCT-TTTCTCTTTGTTTTTTTTC
1 TTTTTTTCTT-TGTTT-TCTTTGGTTTTTCTC
1609529 TTTTTGTTCTTT
1 TTTTT-TTCTTT
1609541 ATATTTTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
31 26 0.68
32 12 0.32
ACGTcount: A:0.00, C:0.15, G:0.07, T:0.78
Consensus pattern (30 bp):
TTTTTTTCTTTGTTTTCTTTGGTTTTTCTC
Found at i:1609528 original size:23 final size:23
Alignment explanation
Indices: 1609498--1609574 Score: 75
Period size: 23 Copynumber: 3.1 Consensus size: 23
1609488 CGTTTTTCTC
1609498 TTTTTTTCTTCTTTTCTCTTTGT
1 TTTTTTTCTTCTTTTCTCTTTGT
* *
1609521 TTTTTTTCTTTTTGTTCT-TTATAT
1 TTTTTTTCTTCTT-TTCTCTT-TGT
1609545 TTTTTCCTTGGCTTCTTTTCTCTTTGT
1 TTTTT--TT--CTTCTTTTCTCTTTGT
1609572 TTT
1 TTT
1609575 GATTTGATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
23 14 0.33
24 11 0.26
26 2 0.05
27 9 0.21
28 7 0.16
ACGTcount: A:0.03, C:0.16, G:0.06, T:0.75
Consensus pattern (23 bp):
TTTTTTTCTTCTTTTCTCTTTGT
Found at i:1609528 original size:45 final size:45
Alignment explanation
Indices: 1609445--1609531 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
1609435 TTGTCCAATC
* *
1609445 TTTTTCTTTGTTTTTCTTTTGTTTTTTTTCTTTGTTTTCTTTGCG
1 TTTTTCTTTGTTTTTCTTTTGTTCTCTTTCTTTGTTTTCTTTGCG
* *
1609490 TTTTTCTCTT-TTTTTCTTCTT-TTCTCTTTGTTTTTTTTCTTT
1 TTTTTCT-TTGTTTTTCTT-TTGTTCTCTTTCTTTGTTTTCTTT
1609532 TTGTTCTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 32 0.89
46 4 0.11
ACGTcount: A:0.00, C:0.14, G:0.07, T:0.79
Consensus pattern (45 bp):
TTTTTCTTTGTTTTTCTTTTGTTCTCTTTCTTTGTTTTCTTTGCG
Found at i:1609548 original size:54 final size:51
Alignment explanation
Indices: 1609456--1609574 Score: 134
Period size: 54 Copynumber: 2.3 Consensus size: 51
1609446 TTTTCTTTGT
* * * **
1609456 TTTTCT-TTTGTTTTTTTTCTTTGTTTTCTTTGCGTTTTTCTCTTTTTTTCTTC
1 TTTTCTCTTTGTTTTTTTTCTTTGTTTTCTTTACATTTTT-TC--CTTGGCTTC
*
1609509 TTTTCTCTTTGTTTTTTTTCTTT-TTGTTCTTTATATTTTTTCCTTGGCTTC
1 TTTTCTCTTTGTTTTTTTTCTTTGTT-TTCTTTACATTTTTTCCTTGGCTTC
1609560 TTTTCTCTTTGTTTT
1 TTTTCTCTTTGTTTT
1609575 GATTTGATCT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
51 21 0.36
53 10 0.17
54 27 0.47
ACGTcount: A:0.02, C:0.15, G:0.08, T:0.76
Consensus pattern (51 bp):
TTTTCTCTTTGTTTTTTTTCTTTGTTTTCTTTACATTTTTTCCTTGGCTTC
Found at i:1611604 original size:15 final size:15
Alignment explanation
Indices: 1611584--1611614 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
1611574 CGAACATGCT
1611584 TTCAATAGATAGCAA
1 TTCAATAGATAGCAA
1611599 TTCAATAGATAGCAA
1 TTCAATAGATAGCAA
1611614 T
1 T
1611615 CCTATTCGGA
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:0.45, C:0.13, G:0.13, T:0.29
Consensus pattern (15 bp):
TTCAATAGATAGCAA
Found at i:1619910 original size:131 final size:130
Alignment explanation
Indices: 1619724--1620125 Score: 456
Period size: 131 Copynumber: 3.1 Consensus size: 130
1619714 TATTACATAT
* * * *
1619724 TAACCACTAACTTTTATTTTTATTGCAATCTAACCATTTTATTTATTTATTTATTTATTGTTTAT
1 TAACTACTAATTTTTA-TTTTATTGC-ATTTAACCA--TTATTTAATTATTTATTTATTGTTTAT
* * *
1619789 ATTATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACTTTATTATGGTTCAGATT
62 ATTATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCGGACT
1619854 CTGC
127 CTGC
* *
1619858 TAACTACTGATTTTTATTTTATTGCACTTTAACCATTATTTAATTATTTATTTATTGTTTCTATT
1 TAACTACTAATTTTTATTTTATTGCA-TTTAACCATTATTTAATTATTTATTTATTGTTTATATT
* * *
1619923 ATTTGATTCGACCTTGTGGTGACCAGATCCAGGGTATGATTCACATTATTATGGTTCGGACTCTG
65 ATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCGGACTCTG
1619988 C
130 C
* * * ** * * *
1619989 TAACTACTAATTTTT-TATATATT-TATTTTA-TTTTATTTTA-T-TTTGTTCATTTGTTTGA-A
1 TAACTACTAATTTTTAT-TTTATTGCATTTAACCATTATTTAATTATTTATTTA-TTGTTT-ATA
* * * * *
1620048 TTATTCGATTCGACCTTATGGTGAGCAGATCCGAGATATGATCAACATTATTATGGTTCGGACTC
63 TTATTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCGGACTC
1620113 TGC
128 TGC
*
1620116 TAACTGCTAA
1 TAACTACTAA
1620126 CCTTTCTAAC
Statistics
Matches: 233, Mismatches: 31, Indels: 15
0.84 0.11 0.05
Matches are distributed among these distances:
126 6 0.03
127 77 0.33
128 7 0.03
129 4 0.02
130 2 0.01
131 107 0.46
132 1 0.00
133 16 0.07
134 13 0.06
ACGTcount: A:0.25, C:0.15, G:0.14, T:0.47
Consensus pattern (130 bp):
TAACTACTAATTTTTATTTTATTGCATTTAACCATTATTTAATTATTTATTTATTGTTTATATTA
TTCGATTCGACCTTGTGGTGACCAGATCCGGGGTATGATCCACATTATTATGGTTCGGACTCTGC
Found at i:1620212 original size:15 final size:16
Alignment explanation
Indices: 1620188--1620222 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1620178 ATTTAAGCTA
1620188 TTTAACTTTATGCACT
1 TTTAACTTTATGCACT
*
1620204 TTTAA-TTTATGCATT
1 TTTAACTTTATGCACT
1620219 TTTA
1 TTTA
1620223 TTATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (16 bp):
TTTAACTTTATGCACT
Found at i:1620827 original size:16 final size:17
Alignment explanation
Indices: 1620790--1620827 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1620780 CGCAGACTAA
1620790 TTTTTGTCTTAAAAATG
1 TTTTTGTCTTAAAAATG
* *
1620807 ATTTT-TCTTAAAATTG
1 TTTTTGTCTTAAAAATG
1620823 TTTTT
1 TTTTT
1620828 AAAAGACATT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.26, C:0.05, G:0.08, T:0.61
Consensus pattern (17 bp):
TTTTTGTCTTAAAAATG
Found at i:1624487 original size:2 final size:2
Alignment explanation
Indices: 1624480--1624524 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
1624470 TATACCCATA
*
1624480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1624522 AT A
1 AT A
1624525 CAATAAATCT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1626032 original size:37 final size:36
Alignment explanation
Indices: 1625978--1626049 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 36
1625968 ACAAAGTGTC
* *
1625978 GTCTCGTTAGAGGCAATTTTTCTTAAAAACAAATTTT
1 GTCTCGTTAGAGACAATTTCTC-TAAAAACAAATTTT
*
1626015 GTCTCGCTT-GAGACAATTTCTCTCAAAACAAATTT
1 GTCTCG-TTAGAGACAATTTCTCTAAAAACAAATTT
1626050 CATCTCAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 12 0.39
37 17 0.55
38 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (36 bp):
GTCTCGTTAGAGACAATTTCTCTAAAAACAAATTTT
Found at i:1626062 original size:36 final size:35
Alignment explanation
Indices: 1625957--1626070 Score: 111
Period size: 36 Copynumber: 3.1 Consensus size: 35
1625947 TTTGAGATTG
* * *
1625957 TTTCTCTCGAAACAAAGTGTCGTCTCGTTAGAGGCAA
1 TTTCTCTCAAAACAAA-TTTCGTCTCGTT-GAGACAA
* * *
1625994 TTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAA
1 TTTCTC-TCAAAACAAATTTCGTCTCG-TTGAGACAA
* *
1626031 TTTCTCTCAAAACAAATTTCATCTCAGTTGAGAAAA
1 TTTCTCTCAAAACAAATTTCGTCTC-GTTGAGACAA
1626067 TTTC
1 TTTC
1626071 CCCATGAGAT
Statistics
Matches: 63, Mismatches: 11, Indels: 7
0.78 0.14 0.09
Matches are distributed among these distances:
36 28 0.44
37 25 0.40
38 10 0.16
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (35 bp):
TTTCTCTCAAAACAAATTTCGTCTCGTTGAGACAA
Found at i:1626496 original size:32 final size:32
Alignment explanation
Indices: 1626434--1626512 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
1626424 TCTTGAGACA
* *
1626434 GTTTCTCTGGAAACATAAAAACCTTCGAGATT
1 GTTTCTCTTGAAACATAAAAACATTCGAGATT
1626466 GTTTCTCTTGAAACATAAAAACAATT-GAGATT
1 GTTTCTCTTGAAACATAAAAAC-ATTCGAGATT
* * *
1626498 ATTTCCCTTGTAACA
1 GTTTCTCTTGAAACA
1626513 AGTTTTGTCT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
32 39 0.95
33 2 0.05
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (32 bp):
GTTTCTCTTGAAACATAAAAACATTCGAGATT
Found at i:1626554 original size:36 final size:36
Alignment explanation
Indices: 1626499--1626584 Score: 120
Period size: 36 Copynumber: 2.4 Consensus size: 36
1626489 ATTGAGATTA
1626499 TTTCCCTTGT-AACAAGTTTTGTCTCCCTTAAGACAG
1 TTTCCCTT-TAAACAAGTTTTGTCTCCCTTAAGACAG
* * *
1626535 TTTCCCTTTAAACAGGTTTTGTCTCTCTTGAGACAG
1 TTTCCCTTTAAACAAGTTTTGTCTCCCTTAAGACAG
*
1626571 TTTCCCTTGAAACA
1 TTTCCCTTTAAACA
1626585 CAATTATTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
35 1 0.02
36 44 0.98
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.40
Consensus pattern (36 bp):
TTTCCCTTTAAACAAGTTTTGTCTCCCTTAAGACAG
Found at i:1626900 original size:134 final size:133
Alignment explanation
Indices: 1626676--1627050 Score: 455
Period size: 134 Copynumber: 2.8 Consensus size: 133
1626666 TGGCCAGTCG
* * * * *
1626676 TCCTCATCATGTGGGAACCATGTCATCGACCTG-CCAGATCTCCTCATCACGTAGGAGCTGCATC
1 TCCTCATCATGTAGGAACCGTGTCATCCACC-GACCAGATCTCCTCATCACATAGGAGC-GCGTC
** * *
1626740 AACCTTAGATAATTAGCTGTCCTCATCACGTAGGAACCATGTTATCATCATCCCTAAAGATAGCC
64 AACCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCATCATCCCTAAAGATAGCC
1626805 AACCA
129 AACCA
* * * * *
1626810 TCCTCATCATGTAGGAATCGTGTTATCCACCGACCAGATCTCCTTATCATATAGAAGTCGCGTCA
1 TCCTCATCATGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCACATAGGAG-CGCGTCA
* *
1626875 ACCTTAGATAACCAGCCGTCCTCATCACGTAGGATCCGTGTTATCATCATCCCTAAAGATGGCCA
65 ACCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCATCATCCCTAAAGATAGCCA
****
1626940 GTTG
130 ACCA
* ** *
1626944 TTCTCATCATGTAGGAACCGTGTCATCCATTGACCAGATCTCCTCATCACATAGGAGCCGTGTCA
1 TCCTCATCATGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCACATAGGAG-CGCGTCA
* * * *
1627009 CCCTTAGATAGCCAGACTTCCTCATCACGTAGGAACCGTGTT
65 ACCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTT
1627051 GTCTCCAAAT
Statistics
Matches: 204, Mismatches: 35, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
133 1 0.00
134 202 0.99
135 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (133 bp):
TCCTCATCATGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCATCACATAGGAGCGCGTCAA
CCTTAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCATCATCCCTAAAGATAGCCAA
CCA
Found at i:1628399 original size:29 final size:29
Alignment explanation
Indices: 1628360--1628420 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
1628350 TGCTATATTA
* *
1628360 TTTATTGCATATTAACCACTAAATTTTAT
1 TTTATTACATATGAACCACTAAATTTTAT
* *
1628389 TTTATTACATATGAACGACTAACTTTTAT
1 TTTATTACATATGAACCACTAAATTTTAT
1628418 TTT
1 TTT
1628421 TATTGCACTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.05, T:0.49
Consensus pattern (29 bp):
TTTATTACATATGAACCACTAAATTTTAT
Found at i:1629118 original size:23 final size:22
Alignment explanation
Indices: 1629054--1629119 Score: 55
Period size: 23 Copynumber: 2.9 Consensus size: 22
1629044 TCTTAACAAT
*
1629054 CATATCATT-CATTTAACATTTAA
1 CATAT-ATTACATTT-ACATATAA
*
1629077 TATATATTCGACA-TTACATATAA
1 CATATATT--ACATTTACATATAA
1629100 CATATATTACATTTCACATA
1 CATATATTACATTT-ACATA
1629120 GCAAAGCAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
21 3 0.09
22 5 0.14
23 23 0.66
24 2 0.06
25 2 0.06
ACGTcount: A:0.41, C:0.17, G:0.02, T:0.41
Consensus pattern (22 bp):
CATATATTACATTTACATATAA
Found at i:1629618 original size:2 final size:2
Alignment explanation
Indices: 1629611--1629664 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1629601 ATACCAAATC
*
1629611 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1629653 AT AT AT AT AT AT
1 AT AT AT AT AT AT
1629665 CTTATGCAAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1634616 original size:20 final size:20
Alignment explanation
Indices: 1634579--1634616 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1634569 CTTAAACTTC
*
1634579 TTAACAATCATATCATTCAT
1 TTAACAATAATATCATTCAT
1634599 TTAACAATTAATAT-ATTC
1 TTAACAA-TAATATCATTC
1634617 GACATTACAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAACAATAATATCATTCAT
Found at i:1634795 original size:23 final size:23
Alignment explanation
Indices: 1634769--1634837 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
1634759 CACCACAGCT
*
1634769 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
1634792 CGTAGAATTGCACCGTAA-TGCCG
1 CGTAGAAATGCACCG-AAGTGCCA
*
1634815 CTTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
1634838 TATAATATGT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
22 2 0.05
23 34 0.89
24 2 0.05
ACGTcount: A:0.32, C:0.26, G:0.23, T:0.19
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:1635198 original size:2 final size:2
Alignment explanation
Indices: 1635191--1635226 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1635181 AATCATATGA
1635191 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
1635227 CTTATGCAAT
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):
AT
Found at i:1636550 original size:50 final size:50
Alignment explanation
Indices: 1636449--1636550 Score: 168
Period size: 50 Copynumber: 2.0 Consensus size: 50
1636439 AAGAATCCTC
* * *
1636449 GAAAATATTCATTTGGATCAAGCAACCAACTCTCTTTTCATATCTACCAT
1 GAAAATATTCATTTGGATCAAGCAACAAACTCTCTTTTCATATCCAACAT
*
1636499 GAAAATATTCCTTTGGATCAAGCAACAAACTCTCTTTTCATATCCAACAT
1 GAAAATATTCATTTGGATCAAGCAACAAACTCTCTTTTCATATCCAACAT
1636549 GA
1 GA
1636551 TTGGGATCTT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (50 bp):
GAAAATATTCATTTGGATCAAGCAACAAACTCTCTTTTCATATCCAACAT
Found at i:1637671 original size:16 final size:17
Alignment explanation
Indices: 1637637--1637671 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1637627 CCATCTATTT
1637637 TTATTTTTATATTTTAAA
1 TTATTTTTATA-TTTAAA
1637655 TTATTTTTATA-TTAAA
1 TTATTTTTATATTTAAA
1637671 T
1 T
1637672 GACAATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
18 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTTTTATATTTAAA
Found at i:1641019 original size:2 final size:2
Alignment explanation
Indices: 1641012--1641050 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1641002 ATAATTGATA
1641012 AT AT AT AT 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 AT AT AT AT A
1641051 AATTTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1641726 original size:2 final size:2
Alignment explanation
Indices: 1641721--1641757 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1641711 ATATAGAAGG
1641721 AT AT AT 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 AT AT AT A
1641758 GTGACACATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1642990 original size:4 final size:4
Alignment explanation
Indices: 1642968--1643148 Score: 61
Period size: 4 Copynumber: 43.0 Consensus size: 4
1642958 TACATAATTA
* * *
1642968 TATT CATT T-TT TCATT TATT TATTT TATA TATT T-TT T-GT TATT TATT
1 TATT TATT TATT T-ATT TATT TA-TT TATT TATT TATT TATT TATT TATT
* * *
1643015 TA-T TATT TATTT TATT CTATT ATATA TATT T-TA TATCAT TATT ATATA
1 TATT TATT TA-TT TATT -TATT -TATT TATT TATT TAT--T TATT -TATT
* * * * * *
1643063 TATA TATAT TATT TTTAT TATT TGTTT TCTT TATA TATA TATT TATT TATCT
1 TATT TAT-T TATT TAT-T TATT T-ATT TATT TATT TATT TATT TATT TAT-T
1643115 ATATT T-TCT TATT GCT-TT TATT TATT TATT TATT
1 -TATT TAT-T TATT --TATT TATT TATT TATT TATT
1643149 ATGTACATAT
Statistics
Matches: 136, Mismatches: 20, Indels: 42
0.69 0.10 0.21
Matches are distributed among these distances:
3 15 0.11
4 79 0.58
5 35 0.26
6 7 0.05
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (4 bp):
TATT
Found at i:1642995 original size:27 final size:26
Alignment explanation
Indices: 1642965--1643054 Score: 71
Period size: 27 Copynumber: 3.4 Consensus size: 26
1642955 TTATACATAA
1642965 TTATATTCATTTTTTCATTTATTTATT
1 TTATA-TCATTTTTTCATTTATTTATT
*
1642992 TTATAT-ATTTTTTGTTATTTATTTATT
1 TTATATCA-TTTTT-TCATTTATTTATT
* *
1643019 ATT-TAT--TTTATTCTATTATATATATT
1 -TTATATCATTTTTTC-ATT-TATTTATT
1643045 TTATATCATT
1 TTATATCATT
1643055 ATTATATATA
Statistics
Matches: 51, Mismatches: 4, Indels: 15
0.73 0.06 0.21
Matches are distributed among these distances:
24 1 0.02
25 10 0.20
26 16 0.31
27 20 0.39
28 4 0.08
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.69
Consensus pattern (26 bp):
TTATATCATTTTTTCATTTATTTATT
Found at i:1643002 original size:23 final size:22
Alignment explanation
Indices: 1642976--1643065 Score: 71
Period size: 22 Copynumber: 4.0 Consensus size: 22
1642966 TATATTCATT
1642976 TTTTCATTTATTTATTTTATATA
1 TTTT-ATTTATTTATTTTATATA
*
1642999 TTTTTTGTTATTTA-TTTAT-TA
1 TTTTAT-TTATTTATTTTATATA
*
1643020 -TTTATTTTATTCTATTATATATA
1 TTTTA-TTTATT-TATTTTATATA
* *
1643043 TTTTATATCA-TTATTATATATA
1 TTTTAT-TTATTTATTTTATATA
1643065 T
1 T
1643066 ATATATTATT
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
20 8 0.14
21 5 0.09
22 22 0.39
23 15 0.27
24 6 0.11
ACGTcount: A:0.28, C:0.03, G:0.01, T:0.68
Consensus pattern (22 bp):
TTTTATTTATTTATTTTATATA
Found at i:1643080 original size:24 final size:24
Alignment explanation
Indices: 1642993--1643083 Score: 73
Period size: 26 Copynumber: 3.8 Consensus size: 24
1642983 TTATTTATTT
* *
1642993 TATATATTTTTTGTTATT-TATTTA
1 TATATATTATTT-TTATTATATATA
*
1643017 T-TAT-TTA-TTTTATTCTATTATA
1 TATATATTATTTTTATTATA-TATA
* *
1643039 TATATTTTATATCATTATTATATATA
1 TATATATTAT-T-TTTATTATATATA
1643065 TATATATTATTTTTATTAT
1 TATATATTATTTTTATTAT
1643084 TTGTTTTCTT
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
20 5 0.09
21 4 0.07
22 6 0.11
23 6 0.11
24 11 0.20
25 1 0.02
26 14 0.26
27 7 0.13
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (24 bp):
TATATATTATTTTTATTATATATA
Found at i:1643122 original size:31 final size:32
Alignment explanation
Indices: 1643007--1643124 Score: 88
Period size: 33 Copynumber: 3.8 Consensus size: 32
1642997 TATTTTTTGT
*
1643007 TATT-TATTTATTATTTATTTTATTCTAT-TATA
1 TATTATATTTATTA-TTATTTTCTT-TATATATA
* * *
1643039 TA-TAT-TTTA-TATCATTATTATATATATATA
1 TATTATATTTATTATTATT-TTCTTTATATATA
* *
1643069 TATTATTTTTATTATTTGTTTTCTTTATATATA
1 TATTATATTTATTA-TTATTTTCTTTATATATA
1643102 TATT-TATTTATCTA-TATTTTCTT
1 TATTATATTTAT-TATTATTTTCTT
1643125 ATTGCTTTTA
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
29 7 0.10
30 12 0.17
31 16 0.23
32 13 0.19
33 19 0.27
34 3 0.04
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (32 bp):
TATTATATTTATTATTATTTTCTTTATATATA
Found at i:1643139 original size:43 final size:40
Alignment explanation
Indices: 1643053--1643140 Score: 97
Period size: 43 Copynumber: 2.1 Consensus size: 40
1643043 TTTTATATCA
* *
1643053 TTATTATATATATATATATTATTTTTATTATTTGTTTTCT
1 TTATTATATATTTATATATTATTTTTATTATTTGTTTTAT
* *
1643093 TTATATATATATTTATTTATCTATATTTTCTTA-TTGCTTTTAT
1 TTAT-TATATATTTATATAT-TAT-TTTTATTATTTG-TTTTAT
1643136 TTATT
1 TTATT
1643141 TATTTATTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
40 4 0.10
41 13 0.32
42 7 0.17
43 16 0.40
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (40 bp):
TTATTATATATTTATATATTATTTTTATTATTTGTTTTAT
Done.