Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015253.1 Kokia drynarioides strain JFW-HI SEQ_130298, 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: 611692
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 551 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:390844 original size:100 final size:100
Alignment explanation
Indices: 390740--390921 Score: 229
Period size: 100 Copynumber: 1.8 Consensus size: 100
390730 GTACACGGTC
* * * * *
390740 CGTCGTTGCGACTTAGACCTTTCCCTTTTGTCTCTTTGCAGTACTGGATCCGCCGTTGCGATCTT
1 CGTCGTTACGACTTAAACCTTTCCCTTCTGTCTCTTTGCAGTACTAGATCCGCCATTGCGATCTT
*
390805 AGATCTTTCCCTTCATGTTTCTGAGATACTGGATT
66 AGATCTTTCCCGTCATGTTTCTGAGATACTGGATT
* * * ** * * * *
390840 CGTCGTTACGGCTTAAATCTTTCCCTTCTGTGTCTTTGGGGTACTAGATCTGCCATTGTGGTGTT
1 CGTCGTTACGACTTAAACCTTTCCCTTCTGTCTCTTTGCAGTACTAGATCCGCCATTGCGATCTT
390905 AGATCTTTCCCGTCATG
66 AGATCTTTCCCGTCATG
390922 ATACAATTGG
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
100 67 1.00
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.40
Consensus pattern (100 bp):
CGTCGTTACGACTTAAACCTTTCCCTTCTGTCTCTTTGCAGTACTAGATCCGCCATTGCGATCTT
AGATCTTTCCCGTCATGTTTCTGAGATACTGGATT
Found at i:402510 original size:29 final size:29
Alignment explanation
Indices: 402478--402622 Score: 102
Period size: 29 Copynumber: 5.0 Consensus size: 29
402468 TGGATACCCG
*
402478 GAGGTAAAATGGTAATTTTGGGAAAATTC
1 GAGGTAAAATGGTAATTTTAGGAAAATTC
* *
402507 GAGGTCAAAAATAG-AATTTTTA-G-AAGTTC
1 GAGGT--AAAATGGTAA-TTTTAGGAAAATTC
*
402536 GAGGGTAAAATGATAATTTTAGGAAAA-TC
1 GA-GGTAAAATGGTAATTTTAGGAAAATTC
** *
402565 GAGGTCAAAAAT-GTAATTTTAGGAATTTTG
1 GAGGT--AAAATGGTAATTTTAGGAAAATTC
* * * *
402595 GGGGTAAAATGGTAGTTTTTGAAAAATT
1 GAGGTAAAATGGTAATTTTAGGAAAATT
402623 GGGGTCAAAA
Statistics
Matches: 89, Mismatches: 16, Indels: 22
0.70 0.13 0.17
Matches are distributed among these distances:
28 18 0.20
29 43 0.48
30 18 0.20
31 10 0.11
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.32
Consensus pattern (29 bp):
GAGGTAAAATGGTAATTTTAGGAAAATTC
Found at i:402600 original size:58 final size:57
Alignment explanation
Indices: 402480--402903 Score: 337
Period size: 58 Copynumber: 7.3 Consensus size: 57
402470 GATACCCGGA
* * * * * *
402480 GGTAAAATGGTAATTTTGGGAAAATTCGAGGTCAAAAATAGAATTTTTAGAAGTTCGAG
1 GGTAAAATGATAATTTT-TGAAAAATCGAGGTCAAAAATAGAA-TTTTGGAAGTTTGGG
* * *
402539 GGTAAAATGATAATTTTAGGAAAATCGAGGTCAAAAAT-GTAATTTTAGGAATTTTGGG
1 GGTAAAATGATAATTTTTGAAAAATCGAGGTCAAAAATAG-AATTTT-GGAAGTTTGGG
* * * *
402597 GGTAAAATGGTAGTTTTTGAAAAATTGGGGTCAAAAATAGAATTTTGGAAAGTTTGGG
1 GGTAAAATGATAATTTTTGAAAAATCGAGGTCAAAAATAGAATTTTGG-AAGTTTGGG
* * * *
402655 GGTAAAAT-AGTAATTTTTGAAAAAATCGTGAT-TAAAATAGAATTTTGGAAAGTTCGGG
1 GGTAAAATGA-TAATTTTTG-AAAAATCGAGGTCAAAAATAGAATTTTGG-AAGTTTGGG
* * * *
402713 GGTAAATTGGT-TTTTTTGAAAAAATCGAGGTTAAAAAT-GAAATTTTTGGAAGTTTGGG
1 GGTAAAATGATAATTTTTG-AAAAATCGAGGTCAAAAATAG-AA-TTTTGGAAGTTTGGG
* * *
402771 GGTAAAATTATAATTTTTGAAAAAAATC-AGGGT--AAAATGGAATTTTTGGAAGTTCGGG
1 GGTAAAATGATAATTTTTG--AAAAATCGA-GGTCAAAAATAGAA-TTTTGGAAGTTTGGG
* ** * * * *
402829 GGT-AAATGGTAATTTTTTGAAAAATTAAGTTTAAAAATGGAATTTTGGAAAGTTTAGG
1 GGTAAAATGATAA-TTTTTGAAAAATCGAGGTCAAAAATAGAATTTTGG-AAGTTTGGG
402887 GGTCAAAAT-ATAATTTT
1 GGT-AAAATGATAATTTT
402904 GGAGAAATTT
Statistics
Matches: 303, Mismatches: 41, Indels: 43
0.78 0.11 0.11
Matches are distributed among these distances:
56 8 0.03
57 39 0.13
58 198 0.65
59 43 0.14
60 15 0.05
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (57 bp):
GGTAAAATGATAATTTTTGAAAAATCGAGGTCAAAAATAGAATTTTGGAAGTTTGGG
Found at i:402624 original size:29 final size:29
Alignment explanation
Indices: 402592--402854 Score: 114
Period size: 29 Copynumber: 9.1 Consensus size: 29
402582 TTTAGGAATT
* *
402592 TTGGGGGTAAAATGGTAGTTTTTGAAAAA
1 TTGGGGGTAAAATAGTAATTTTTGAAAAA
* **
402621 TT-GGGGTCAAAAATAG-AATTTTGGAAAGT
1 TTGGGGGT--AAAATAGTAATTTTTGAAAAA
402650 TTGGGGGTAAAATAGTAATTTTTGAAAAAA
1 TTGGGGGTAAAATAGTAATTTTTG-AAAAA
* * ** * *
402680 TCGTGATTAAAATAG-AA-TTTTGGAAAG
1 TTGGGGGTAAAATAGTAATTTTTGAAAAA
* * *
402707 TTCGGGGGTAAATTGGT-TTTTTTGAAAAAA
1 TT-GGGGGTAAAATAGTAATTTTTG-AAAAA
* * * * * **
402737 TCGAGGTTAAAA-ATGAAATTTTTGGAAGT
1 TTGGGGGTAAAATA-GTAATTTTTGAAAAA
402766 TTGGGGGTAAAATTA-TAATTTTTGAAAAAA
1 TTGGGGGTAAAA-TAGTAATTTTTG-AAAAA
* ** * * *
402796 ATCAGGGTAAAAT-GGAATTTTTG-GAAG
1 TTGGGGGTAAAATAGTAATTTTTGAAAAA
*
402823 TTCGGGGGT-AAATGGTAATTTTTTGAAAAA
1 TT-GGGGGTAAAATAGTAA-TTTTTGAAAAA
402853 TT
1 TT
402855 AAGTTTAAAA
Statistics
Matches: 163, Mismatches: 52, Indels: 37
0.65 0.21 0.15
Matches are distributed among these distances:
27 11 0.07
28 32 0.20
29 69 0.42
30 50 0.31
31 1 0.01
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.35
Consensus pattern (29 bp):
TTGGGGGTAAAATAGTAATTTTTGAAAAA
Found at i:402771 original size:174 final size:173
Alignment explanation
Indices: 402559--402882 Score: 415
Period size: 174 Copynumber: 1.9 Consensus size: 173
402549 TAATTTTAGG
* * * * *
402559 AAAATCGAGGTCAAAAATGTAATTTTAGGAATTTTGGGGGTAAAATGGTAGTTTTTG-AAAAATT
1 AAAATCGAGGTCAAAAATGAAATTTTAGGAAGTTTGGGGGTAAAATGATAATTTTTGAAAAAATC
* * *
402623 GGGGTCAAAAATAGAA-TTTTGGAAAGTTTGGGGGTAAAATAGTAA-TTTTTGAAAAAAT-CGTG
66 AGGGT--AAAATAGAATTTTTGG-AAGTTCGGGGGT-AAATAGTAATTTTTTGAAAAAATAAGT-
402685 ATT-AAAATAGAATTTTGGAAAGTTCGGGGGTAAATTGGTTTTTTTGAA
126 -TTAAAAATAGAATTTTGGAAAGTTCGGGGGTAAATTGGTTTTTTTGAA
* * *
402733 AAAATCGAGGTTAAAAATGAAATTTTTGGAAGTTTGGGGGTAAAATTATAATTTTTGAAAAAAAT
1 AAAATCGAGGTCAAAAATGAAATTTTAGGAAGTTTGGGGGTAAAATGATAATTTTTG-AAAAAAT
* * *
402798 CAGGGTAAAATGGAATTTTTGGAAGTTCGGGGGTAAATGGTAATTTTTTGAAAAATTAAGTTTAA
65 CAGGGTAAAATAGAATTTTTGGAAGTTCGGGGGTAAATAGTAATTTTTTGAAAAAATAAGTTTAA
*
402863 AAATGGAATTTTGGAAAGTT
130 AAATAGAATTTTGGAAAGTT
402883 TAGGGGTCAA
Statistics
Matches: 129, Mismatches: 15, Indels: 12
0.83 0.10 0.08
Matches are distributed among these distances:
173 10 0.08
174 101 0.78
175 8 0.06
176 10 0.08
ACGTcount: A:0.39, C:0.02, G:0.24, T:0.35
Consensus pattern (173 bp):
AAAATCGAGGTCAAAAATGAAATTTTAGGAAGTTTGGGGGTAAAATGATAATTTTTGAAAAAATC
AGGGTAAAATAGAATTTTTGGAAGTTCGGGGGTAAATAGTAATTTTTTGAAAAAATAAGTTTAAA
AATAGAATTTTGGAAAGTTCGGGGGTAAATTGGTTTTTTTGAA
Found at i:402894 original size:29 final size:30
Alignment explanation
Indices: 402869--403006 Score: 174
Period size: 30 Copynumber: 4.7 Consensus size: 30
402859 TTAAAAATGG
402869 AATTTTGGA-AAGTTTAGGGGTCAAAATAT
1 AATTTTGGAGAAGTTTAGGGGTCAAAATAT
* * *
402898 AATTTTGGAGAAATTTAAGGGTTAAAATAT
1 AATTTTGGAGAAGTTTAGGGGTCAAAATAT
* * *
402928 AATTTTAGAGAGGTTTAGGGGT-AAAATGT
1 AATTTTGGAGAAGTTTAGGGGTCAAAATAT
*
402957 AATTTTGGATAAGTTTAGGGGTCAAAATAT
1 AATTTTGGAGAAGTTTAGGGGTCAAAATAT
*
402987 AATTTTTGGA-TAGTTTAGGG
1 AA-TTTTGGAGAAGTTTAGGG
403007 ACCTTCAAGG
Statistics
Matches: 93, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
29 34 0.37
30 52 0.56
31 7 0.08
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.37
Consensus pattern (30 bp):
AATTTTGGAGAAGTTTAGGGGTCAAAATAT
Found at i:402912 original size:58 final size:57
Alignment explanation
Indices: 402480--402965 Score: 274
Period size: 58 Copynumber: 8.3 Consensus size: 57
402470 GATACCCGGA
* * * * * * * *
402480 GGTAAAATGGTAATTTTGGGAAAATTCGAGGTCAAAAATAGAATTTT-TAGAAGTTCGAG
1 GGTAAAAT-ATAATTTTGGAAAAATT-AAGGTTAAAAATGGAATTTTGGA-AAGTTTGGG
** * * *
402539 GGTAAAATGATAATTTTAGG-AAAATCGAGGTCAAAAATGTAATTTTAGG-AATTTTGGG
1 GGTAAAAT-ATAATTTT-GGAAAAATTAAGGTTAAAAATGGAATTTT-GGAAAGTTTGGG
* * * ** * *
402597 GGTAAAATGGTAGTTTTTGAAAAATTGGGGTCAAAAATAGAATTTTGGAAAGTTTGGG
1 GGTAAAAT-ATAATTTTGGAAAAATTAAGGTTAAAAATGGAATTTTGGAAAGTTTGGG
* * * * *
402655 GGTAAAATAGTAATTTTTGAAAAAAT-CGTGATT-AAAATAGAATTTTGGAAAGTTCGGG
1 GGTAAAATA-TAATTTTGGAAAAATTAAG-G-TTAAAAATGGAATTTTGGAAAGTTTGGG
* * ** * ** *
402713 GGTAAATTGGTTTTTTTGAAAAAATCGAGGTTAAAAATGAAATTTTTGG-AAGTTTGGG
1 GGTAAAAT-ATAATTTTGGAAAAATTAAGGTTAAAAATGGAA-TTTTGGAAAGTTTGGG
* * * * *
402771 GGTAAAATTATAATTTTTGAAAAAAATCAGGGT-AAAATGGAATTTTTGG-AAGTTCGGG
1 GGTAAAA-TATAA-TTTTGGAAAAATTAAGGTTAAAAATGGAA-TTTTGGAAAGTTTGGG
* * * *
402829 GGT-AAATGGTAATTTTTTGAAAAATTAAGTTTAAAAATGGAATTTTGGAAAGTTTAGG
1 GGTAAAAT-ATAA-TTTTGGAAAAATTAAGGTTAAAAATGGAATTTTGGAAAGTTTGGG
* * * *
402887 GGTCAAAATATAATTTTGGAGAAATTTAAGGGTTAAAATAT--AATTTTAGAGAGGTTTAGG
1 GGT-AAAATATAATTTTGGA-AAAATTAA-GGTTAAAA-ATGGAATTTTGGA-AAGTTTGGG
*
402947 GGTAAAATGTAATTTTGGA
1 GGTAAAATATAATTTTGGA
402966 TAAGTTTAGG
Statistics
Matches: 344, Mismatches: 60, Indels: 46
0.76 0.13 0.10
Matches are distributed among these distances:
56 1 0.00
57 32 0.09
58 207 0.60
59 78 0.23
60 24 0.07
61 2 0.01
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (57 bp):
GGTAAAATATAATTTTGGAAAAATTAAGGTTAAAAATGGAATTTTGGAAAGTTTGGG
Found at i:402932 original size:59 final size:58
Alignment explanation
Indices: 402869--403006 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 58
402859 TTAAAAATGG
*
402869 AATTTTGGAAAGTTTAGGGGTCAAAATATAATTTTGGAGAAATTTAAGGGTTAAAATAT
1 AATTTTGGAAAGTTTAGGGGT-AAAATATAATTTTGGAGAAATTTAAGGGTCAAAATAT
* * * * * *
402928 AATTTTAGAGAGGTTTAGGGGTAAAATGTAATTTTGGATAAGTTTAGGGGTCAAAATAT
1 AATTTTGGA-AAGTTTAGGGGTAAAATATAATTTTGGAGAAATTTAAGGGTCAAAATAT
*
402987 AATTTTTGGATAGTTTAGGG
1 AA-TTTTGGAAAGTTTAGGG
403007 ACCTTCAAGG
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
59 50 0.75
60 17 0.25
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.37
Consensus pattern (58 bp):
AATTTTGGAAAGTTTAGGGGTAAAATATAATTTTGGAGAAATTTAAGGGTCAAAATAT
Found at i:402963 original size:116 final size:113
Alignment explanation
Indices: 402480--402963 Score: 399
Period size: 116 Copynumber: 4.2 Consensus size: 113
402470 GATACCCGGA
* * * * * *
402480 GGTAAAATGGTAATTTTGGGAAAATTCGAGGTCAAAAATAGAATTTT-TAGAAGTTCGAGGGTAA
1 GGTAAAATGGTAATTTT-GAAAAATT-GAGGTTAAAAATGGAATTTTGGA-AAGTTTGGGGGTAA
* * * * * *
402544 AATGATAATTTTAG-GAAAATCGAGGTCAAAA-ATGTAATTTTAGGAATTTTGGG
63 AAT-ATAATTTTTGAAAAAATAG-GGTTAAAATA-G-AATTTTAGGAAGTTCGGG
* * * *
402597 GGTAAAATGGTAGTTTTTGAAAAATTGGGGTCAAAAATAGAATTTTGGAAAGTTTGGGGGTAAAA
1 GGTAAAATGGTA-ATTTTGAAAAATTGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAA
* *
402662 TAGTAATTTTTGAAAAAATCGTGATTAAAATAGAATTTT-GGAAAGTTCGGG
65 TA-TAATTTTTGAAAAAATAG-GGTTAAAATAGAATTTTAGG-AAGTTCGGG
* ** * *
402713 GGTAAATTGGTTTTTTTGAAAAAATCGAGGTTAAAAATGAAATTTTTGG-AAGTTTGGGGGTAAA
1 GGTAAAATGGTAATTTTG-AAAAATTGAGGTTAAAAATGGAA-TTTTGGAAAGTTTGGGGGTAAA
* *
402777 ATTATAATTTTTGAAAAAAATCAGGG-TAAAATGGAATTTTTGGAAGTTCGGG
64 A-TATAATTTTTG-AAAAAAT-AGGGTTAAAATAGAATTTTAGGAAGTTCGGG
* * *
402829 GGT-AAATGGTAATTTTTTGAAAAATTAAGTTTAAAAATGGAATTTTGGAAAGTTTAGGGGTCAA
1 GGTAAAATGGTAA--TTTTGAAAAATTGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGT-AA
* ** * * **
402893 AATATAATTTTGGAGAAATTTAAGGGTTAAAATATAATTTTAGAGAGGTTTAGG
63 AATATAATTTTTGA-AAAAAT-AGGGTTAAAATAGAATTTTAG-GAAGTTCGGG
402947 GGTAAAAT-GTAATTTTG
1 GGTAAAATGGTAATTTTG
402964 GATAAGTTTA
Statistics
Matches: 306, Mismatches: 41, Indels: 41
0.79 0.11 0.11
Matches are distributed among these distances:
115 22 0.07
116 186 0.61
117 74 0.24
118 20 0.07
119 4 0.01
ACGTcount: A:0.39, C:0.02, G:0.25, T:0.34
Consensus pattern (113 bp):
GGTAAAATGGTAATTTTGAAAAATTGAGGTTAAAAATGGAATTTTGGAAAGTTTGGGGGTAAAAT
ATAATTTTTGAAAAAATAGGGTTAAAATAGAATTTTAGGAAGTTCGGG
Found at i:404018 original size:3 final size:3
Alignment explanation
Indices: 404006--404076 Score: 56
Period size: 3 Copynumber: 23.3 Consensus size: 3
403996 TATTTTTTAT
* * * * *
404006 TTA TTA -TA TTA TTTA TTA TTA TTA -AA TAA TTTA TTA TTG CTG TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
404051 TTA TTA TTA TTA TTA TTA TTAA TTA T
1 TTA TTA TTA TTA TTA TTA TT-A TTA T
404077 CATCAATGCC
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
2 3 0.05
3 46 0.81
4 8 0.14
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:404019 original size:12 final size:13
Alignment explanation
Indices: 404002--404076 Score: 66
Period size: 12 Copynumber: 5.8 Consensus size: 13
403992 TTTCTATTTT
404002 TTATTTATTA-TA
1 TTATTTATTATTA
404014 TTATTTATTATTA
1 TTATTTATTATTA
** *
404027 TTAAATAAT-TTA
1 TTATTTATTATTA
*
404039 TTATTGCTGTTATTA
1 TTATT--TATTATTA
404054 TTA-TTATTATTA
1 TTATTTATTATTA
*
404066 TTATTAATTAT
1 TTATTTATTAT
404077 CATCAATGCC
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
12 26 0.53
13 14 0.29
14 3 0.06
15 6 0.12
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:404684 original size:18 final size:17
Alignment explanation
Indices: 404663--404719 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 17
404653 TGTTTTGGAT
*
404663 TTTTAATTTAATATTAA
1 TTTTAATTCAATATTAA
* *
404680 GTTTTAAATCAATTTTAA
1 -TTTTAATTCAATATTAA
*
404698 TTTTAATTAAAT-TTAA
1 TTTTAATTCAATATTAA
*
404714 ATTTAA
1 TTTTAA
404720 AACAAATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
16 9 0.27
17 10 0.30
18 14 0.42
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (17 bp):
TTTTAATTCAATATTAA
Found at i:404703 original size:17 final size:17
Alignment explanation
Indices: 404682--404749 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 17
404672 AATATTAAGT
*
404682 TTTAAATC-AATTTTAA
1 TTTAAATCAAATTTAAA
* *
404698 TTTTAATTAAATTTAAA
1 TTTAAATCAAATTTAAA
*
404715 TTTAAAACAAATTTAAA
1 TTTAAATCAAATTTAAA
404732 TTTAAGAT-AAATTTAAA
1 TTTAA-ATCAAATTTAAA
404749 T
1 T
404750 CAATTTAAAC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
16 6 0.14
17 36 0.84
18 1 0.02
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (17 bp):
TTTAAATCAAATTTAAA
Found at i:406455 original size:81 final size:81
Alignment explanation
Indices: 406266--406707 Score: 521
Period size: 81 Copynumber: 5.5 Consensus size: 81
406256 CTCGGAGCTA
* ** * * *
406266 GCGGAGGATTAGAGTTATGAAGAGGATTTGGTATTCTCGGAGTTTCTCTCTTCACGATGACATT-
1 GCGGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCAGAGTTTCTCTCTTCACAATGACATTA
* *
406330 AAATCACTAGGTGTCT
66 AAACCACTAGGTGCCT
* *
406346 GCGGAGGATTAGAGTTATGAAGAGGATTTGATCCTCCCAGAGTTTCTCTCTTCACAATGACATTA
1 GCGGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCAGAGTTTCTCTCTTCACAATGACATTA
406411 AAACCACTAGGTGCCT
66 AAACCACTAGGTGCCT
* * * * *
406427 GCGGAGAATTAGAGTTATGAAGAGGATTTGGT-CTTCTAGGAGTTTCTCTCTTCACTATGACATT
1 GCGGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCA-GAGTTTCTCTCTTCACAATGACATT
***
406491 AAAATTGCTAGGTGCCT
65 AAAACCACTAGGTGCCT
** * * * ** *
406508 GCTAAGGATTAGAATTATAAAGAGGATTTGTTCCTCCCAGAGTTTCTCTCTTCACGATGATGTTT
1 GCGGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCAGAGTTTCTCTCTTCACAATGACATTA
*
406573 AAACCACTAAGTGCCT
66 AAACCACTAGGTGCCT
* * **
406589 GCGGTGGATTAGAATTATGAAGAGGATTTGGTCCTCCC-GAAGTTTCCCTCTTCACAATGATGTT
1 GCGGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCAG-AGTTTCTCTCTTCACAATGACATT
* *
406653 TAAACCACTAGGTGTCT
65 AAAACCACTAGGTGCCT
* * *
406670 GCAGAGGAATAGAATTATGAAGAGGATTTGGTCGTCCC
1 GCGGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCC
406708 GTAATTTCTG
Statistics
Matches: 313, Mismatches: 45, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
80 63 0.20
81 246 0.79
82 4 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.32
Consensus pattern (81 bp):
GCGGAGGATTAGAATTATGAAGAGGATTTGGTCCTCCCAGAGTTTCTCTCTTCACAATGACATTA
AAACCACTAGGTGCCT
Found at i:406579 original size:162 final size:160
Alignment explanation
Indices: 406266--406699 Score: 580
Period size: 162 Copynumber: 2.7 Consensus size: 160
406256 CTCGGAGCTA
* *
406266 GCGGAGGATTAGAGTTATGAAGAGGATTTGGTATTCTCGGAGTTTCTCTCTTCACGATGACATTA
1 GCGGAGGATTAGAGTTATGAAGAGGATTTGGTCTTCTCGGAGTTTCTCTCTTCACAATGACATTA
* *
406331 AATCACTAGGTGTCTGCGGAGGATTAGAGTTATGAAGAGGATTTGATCCTCCCAGAGTTTCTCTC
66 AATCACTAGGTGTCTGC-AAGGATTAGAATTATGAAGAGGATTTGATCCTCCCAGAGTTTCTCTC
*
406396 TTCACAATGACATTAAAACCACTAGGTGCCT
130 TTCACAATGACATTAAAACCACTAAGTGCCT
* * *
406427 GCGGAGAATTAGAGTTATGAAGAGGATTTGGTCTTCTAGGAGTTTCTCTCTTCACTATGACATTA
1 GCGGAGGATTAGAGTTATGAAGAGGATTTGGTCTTCTCGGAGTTTCTCTCTTCACAATGACATT-
** * * *
406492 AAATTGCTAGGTGCCTGCTAAGGATTAGAATTATAAAGAGGATTTGTTCCTCCCAGAGTTTCTCT
65 AAATCACTAGGTGTCTGC-AAGGATTAGAATTATGAAGAGGATTTGATCCTCCCAGAGTTTCTCT
* ** *
406557 CTTCACGATGATGTTTAAACCACTAAGTGCCT
129 CTTCACAATGACATTAAAACCACTAAGTGCCT
* * * * * * **
406589 GCGGTGGATTAGAATTATGAAGAGGATTTGGTCCTCCCGAAGTTTCCCTCTTCACAATGATGTTT
1 GCGGAGGATTAGAGTTATGAAGAGGATTTGGTCTTCTCGGAGTTTCTCTCTTCACAATGA-CATT
* *
406654 AAACCACTAGGTGTCTGCAGAGGAATAGAATTATGAAGAGGATTTG
65 AAATCACTAGGTGTCTGCA-AGGATTAGAATTATGAAGAGGATTTG
406700 GTCGTCCCGT
Statistics
Matches: 236, Mismatches: 34, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
161 61 0.26
162 173 0.73
163 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (160 bp):
GCGGAGGATTAGAGTTATGAAGAGGATTTGGTCTTCTCGGAGTTTCTCTCTTCACAATGACATTA
AATCACTAGGTGTCTGCAAGGATTAGAATTATGAAGAGGATTTGATCCTCCCAGAGTTTCTCTCT
TCACAATGACATTAAAACCACTAAGTGCCT
Found at i:407503 original size:7 final size:7
Alignment explanation
Indices: 407486--407518 Score: 57
Period size: 7 Copynumber: 4.6 Consensus size: 7
407476 ATCCTTAAAA
407486 TTTATATT
1 TTTA-ATT
407494 TTTAATT
1 TTTAATT
407501 TTTAATT
1 TTTAATT
407508 TTTAATT
1 TTTAATT
407515 TTTA
1 TTTA
407519 TCAATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.84
8 4 0.16
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
TTTAATT
Found at i:407510 original size:14 final size:15
Alignment explanation
Indices: 407486--407544 Score: 68
Period size: 15 Copynumber: 4.0 Consensus size: 15
407476 ATCCTTAAAA
407486 TTTATATTTTTAATT
1 TTTATATTTTTAATT
407501 TTTA-ATTTTTAATT
1 TTTATATTTTTAATT
* *
407515 TTTATCA-ATTTAATC
1 TTTAT-ATTTTTAATT
*
407530 TTTATTTTTTTAATT
1 TTTATATTTTTAATT
407545 CAACCTTACA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
14 14 0.39
15 21 0.58
16 1 0.03
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (15 bp):
TTTATATTTTTAATT
Found at i:408918 original size:21 final size:21
Alignment explanation
Indices: 408878--408919 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
408868 CCCTCTATTT
* *
408878 TATATAATATATTCTGAAATA
1 TATAAAATATATTCTAAAATA
*
408899 TATAAAATATATTTTAAAATA
1 TATAAAATATATTCTAAAATA
408920 AAAGTGATAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TATAAAATATATTCTAAAATA
Found at i:409248 original size:81 final size:81
Alignment explanation
Indices: 409153--409466 Score: 353
Period size: 81 Copynumber: 3.9 Consensus size: 81
409143 GTTAATGGAA
* * * * * *
409153 AATTAGAGTTATGAAGAAGATTTGGTTCTCCCGGAGTTTCTTTTTTCACGATAACATTAAAACCA
1 AATTAGAATTATGAAGAGGATCTGGTCCTCCCGGAGTTTCTTTCTTCACGATGACATTAAAACCA
*
409218 CTAGGTACCTGCGGAG
66 CTAGGTACCTGCAGAG
* * * *
409234 AATTAGAATTATGAAGAGGATTTGGTCCTCCCGAAATTT-TTCGCTTCACGATGACATTAAAACC
1 AATTAGAATTATGAAGAGGATCTGGTCCTCCCGGAGTTTCTT-TCTTCACGATGACATTAAAACC
* **
409298 ACTAGGTGCAAGCAGA-
65 ACTAGGTACCTGCAGAG
* * * ** *
409314 AGATTAGAATTATGAATAGGATCTGGTCCTCCCGGAGATTCTTTTTTCACGATGATGTTTAAACC
1 A-ATTAGAATTATGAAGAGGATCTGGTCCTCCCGGAGTTTCTTTCTTCACGATGACATTAAAACC
*
409379 ACTAAGTACCTGCAGAG
65 ACTAGGTACCTGCAGAG
* * * * * *
409396 AATTAGAATTATGAATAGGATCTAGTCCACCCGGAGTTTCTCTCTTCACAATGACATTAAAACTA
1 AATTAGAATTATGAAGAGGATCTGGTCCTCCCGGAGTTTCTTTCTTCACGATGACATTAAAACCA
409461 CTAGGT
66 CTAGGT
409467 GCCTCAATGA
Statistics
Matches: 192, Mismatches: 37, Indels: 8
0.81 0.16 0.03
Matches are distributed among these distances:
80 3 0.02
81 186 0.97
82 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (81 bp):
AATTAGAATTATGAAGAGGATCTGGTCCTCCCGGAGTTTCTTTCTTCACGATGACATTAAAACCA
CTAGGTACCTGCAGAG
Found at i:409452 original size:162 final size:162
Alignment explanation
Indices: 409154--409468 Score: 432
Period size: 162 Copynumber: 1.9 Consensus size: 162
409144 TTAATGGAAA
* * * *
409154 ATTAGAGTTATGAAGAAGATTTGGTTCTCCCGGAGTTTCTTTTTTCACGATAACATTAAAACCAC
1 ATTAGAATTATGAAGAAGATCTGGTCCTCCCGGAGATTCTTTTTTCACGATAACATTAAAACCAC
* * * * * * *
409219 TAGGTACCTGCGGAGAATTAGAATTATGAAGAGGATTTGGTCCTCCCGAAATTTTTCGCTTCACG
66 TAAGTACCTGCAGAGAATTAGAATTATGAAGAGGATCTAGTCCACCCGAAATTTCTCGCTTCACA
409284 ATGACATTAAAACCACTAGGTGCAAGCAGAAG
131 ATGACATTAAAACCACTAGGTGCAAGCAGAAG
* * * ** *
409316 ATTAGAATTATGAATAGGATCTGGTCCTCCCGGAGATTCTTTTTTCACGATGATGTTTAAACCAC
1 ATTAGAATTATGAAGAAGATCTGGTCCTCCCGGAGATTCTTTTTTCACGATAACATTAAAACCAC
* * * *
409381 TAAGTACCTGCAGAGAATTAGAATTATGAATAGGATCTAGTCCACCCGGAGTTTCTCTCTTCACA
66 TAAGTACCTGCAGAGAATTAGAATTATGAAGAGGATCTAGTCCACCCGAAATTTCTCGCTTCACA
*
409446 ATGACATTAAAACTACTAGGTGC
131 ATGACATTAAAACCACTAGGTGC
409469 CTCAATGACA
Statistics
Matches: 131, Mismatches: 22, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
162 131 1.00
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.30
Consensus pattern (162 bp):
ATTAGAATTATGAAGAAGATCTGGTCCTCCCGGAGATTCTTTTTTCACGATAACATTAAAACCAC
TAAGTACCTGCAGAGAATTAGAATTATGAAGAGGATCTAGTCCACCCGAAATTTCTCGCTTCACA
ATGACATTAAAACCACTAGGTGCAAGCAGAAG
Found at i:409606 original size:81 final size:81
Alignment explanation
Indices: 409471--409642 Score: 258
Period size: 81 Copynumber: 2.1 Consensus size: 81
409461 CTAGGTGCCT
* * * *
409471 CAATGACATTAAAACCACTGGGTGTCTGTGGAAGATTAGAATTATGAAGAGGATTTGGTCCTCCC
1 CAATGACATTAAAACCACTAGATGTCTGTCGAAGACTAGAATTATGAAGAGGATTTGGTCCTCCC
409536 TG-AGTTTCTCTCTTCA
66 -GAAGTTTCTCTCTTCA
*
409552 CAATGACATTAAAACCACTAGATG-CTTGTCGAGGACTAGAATTATGAAGAGGATTTGGTCCTCC
1 CAATGACATTAAAACCACTAGATGTC-TGTCGAAGACTAGAATTATGAAGAGGATTTGGTCCTCC
409616 CGAAGTTTCTCTCTTCA
65 CGAAGTTTCTCTCTTCA
*
409633 CGATGACATT
1 CAATGACATT
409643 TTTAATGGCA
Statistics
Matches: 83, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
80 2 0.02
81 81 0.98
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (81 bp):
CAATGACATTAAAACCACTAGATGTCTGTCGAAGACTAGAATTATGAAGAGGATTTGGTCCTCCC
GAAGTTTCTCTCTTCA
Found at i:409625 original size:189 final size:189
Alignment explanation
Indices: 409284--409642 Score: 454
Period size: 189 Copynumber: 1.9 Consensus size: 189
409274 TCGCTTCACG
*
409284 ATGACATTAAAACCACTAGGTGCAAGCAGAAGATTAGAATTATGAATAGGATCTGGTCCTCCCGG
1 ATGACATTAAAACCACTAGGTGCAAGCAGAAGATTAGAATTATGAAGAGGATCTGGTCCTCCCGG
* * * ** * * *
409349 AGATTCTTTTTTCACGATGATGTTTAAACCACTAAGTACCTGCAGAGAATTAGAATTATGAATAG
66 AGATTCTCTCTTCACAATGACATTAAAACCACTAAGTACCTGCAGAGAACTAGAATTATGAAGAG
*
409414 GATCTAGTCCACCCGGAGTTTCTCTCTTCACAATGACATTAAAACTACTAGGTGCCTCA
131 GATCTAGTCCACCCGAAGTTTCTCTCTTCACAATGACATTAAAACTACTAGGTGCCTCA
* * ** * *
409473 ATGACATTAAAACCACTGGGTGTC-TGTGGAAGATTAGAATTATGAAGAGGATTTGGTCCTCCCT
1 ATGACATTAAAACCACTAGGTG-CAAGCAGAAGATTAGAATTATGAAGAGGATCTGGTCCTCCCG
* * * *
409537 GAGTTTCTCTCTTCACAATGACATTAAAACCACT-AGATGCTTGTC-GAGGACTAGAATTATGAA
65 GAGATTCTCTCTTCACAATGACATTAAAACCACTAAG-TACCTG-CAGAGAACTAGAATTATGAA
* * * *
409600 GAGGATTTGGTCCTCCCGAAGTTTCTCTCTTCACGATGACATT
128 GAGGATCTAGTCCACCCGAAGTTTCTCTCTTCACAATGACATT
409643 TTTAATGGCA
Statistics
Matches: 143, Mismatches: 24, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
188 2 0.01
189 139 0.97
190 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.30
Consensus pattern (189 bp):
ATGACATTAAAACCACTAGGTGCAAGCAGAAGATTAGAATTATGAAGAGGATCTGGTCCTCCCGG
AGATTCTCTCTTCACAATGACATTAAAACCACTAAGTACCTGCAGAGAACTAGAATTATGAAGAG
GATCTAGTCCACCCGAAGTTTCTCTCTTCACAATGACATTAAAACTACTAGGTGCCTCA
Found at i:410195 original size:18 final size:18
Alignment explanation
Indices: 410164--410198 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
410154 GCATTTGAAA
*
410164 ATTTTGGTTCAAAAAATT
1 ATTTTAGTTCAAAAAATT
*
410182 ATTTTAGTTGAAAAAAT
1 ATTTTAGTTCAAAAAAT
410199 AGCACATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (18 bp):
ATTTTAGTTCAAAAAATT
Found at i:411565 original size:81 final size:81
Alignment explanation
Indices: 411424--411747 Score: 436
Period size: 81 Copynumber: 4.0 Consensus size: 81
411414 AAAAAAGGAA
* * * * *
411424 AAACCACTACGTGCCTGCGGAGGATTAGAATTATGAAGAGGATTTGGTCCTCTCGAAGTTTCTCT
1 AAACCACTAGGTGCCTGCGGAAGATTAGAATTATGAAGAAGATTTGGTCCTCCCGGAGTTTCTCT
*
411489 CTTCACGATGATATTT
66 CTTCACAATGATATTT
* * * *
411505 ATACCACTAGGTGCCTGCGGAAGATTATAATTATGAAGAGGATTTGGTCCTCCCGGAGTTTCTTT
1 AAACCACTAGGTGCCTGCGGAAGATTAGAATTATGAAGAAGATTTGGTCCTCCCGGAGTTTCTCT
* *
411570 CTTCATAATGATGTTT
66 CTTCACAATGATATTT
*
411586 AAACCACTAGGTGCCTGCGG-AGTATTAGAATTATGTAGAAGATTTGGTCCTCCCGGAGTTTCTC
1 AAACCACTAGGTGCCTGCGGAAG-ATTAGAATTATGAAGAAGATTTGGTCCTCCCGGAGTTTCTC
*
411650 TCTTCACGATGATATTT
65 TCTTCACAATGATATTT
* * * * *
411667 AAACCACTAGGTGCCTGCAGAGGATTAGAATTAT-ATAAAAGATTTGGTCCTCCCAGAGTTTTTC
1 AAACCACTAGGTGCCTGCGGAAGATTAGAATTATGA-AGAAGATTTGGTCCTCCCGGAGTTTCTC
*
411731 TCTTCACAATGACATTT
65 TCTTCACAATGATATTT
411748 CTAATGGCAG
Statistics
Matches: 214, Mismatches: 26, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
80 2 0.01
81 211 0.99
82 1 0.00
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (81 bp):
AAACCACTAGGTGCCTGCGGAAGATTAGAATTATGAAGAAGATTTGGTCCTCCCGGAGTTTCTCT
CTTCACAATGATATTT
Found at i:411713 original size:162 final size:162
Alignment explanation
Indices: 411424--411742 Score: 480
Period size: 162 Copynumber: 2.0 Consensus size: 162
411414 AAAAAAGGAA
* *
411424 AAACCACTACGTGCCTGCGGAGGATTAGAATTATGAAGAGGATTTGGTCCTCTCGAAGTTTCTCT
1 AAACCACTACGTGCCTGCGGAGGATTAGAATTATGAAGAAGATTTGGTCCTCCCGAAGTTTCTCT
* * * * *
411489 CTTCACGATGATATTTATACCACTAGGTGCCTGCGGAAGATTATAATTATGAAGAGGATTTGGTC
66 CTTCACGATGATATTTAAACCACTAGGTGCCTGCAGAAGATTAGAATTATGAAAAAGATTTGGTC
* *
411554 CTCCCGGAGTTTCTT-TCTTCATAATGATGTTT
131 CTCCCAGAGTTT-TTCTCTTCACAATGATGTTT
* * * *
411586 AAACCACTAGGTGCCTGCGGAGTATTAGAATTATGTAGAAGATTTGGTCCTCCCGGAGTTTCTCT
1 AAACCACTACGTGCCTGCGGAGGATTAGAATTATGAAGAAGATTTGGTCCTCCCGAAGTTTCTCT
*
411651 CTTCACGATGATATTTAAACCACTAGGTGCCTGCAGAGGATTAGAATTAT-ATAAAAGATTTGGT
66 CTTCACGATGATATTTAAACCACTAGGTGCCTGCAGAAGATTAGAATTATGA-AAAAGATTTGGT
411715 CCTCCCAGAGTTTTTCTCTTCACAATGA
130 CCTCCCAGAGTTTTTCTCTTCACAATGA
411743 CATTTCTAAT
Statistics
Matches: 141, Mismatches: 14, Indels: 4
0.89 0.09 0.03
Matches are distributed among these distances:
161 3 0.02
162 138 0.98
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (162 bp):
AAACCACTACGTGCCTGCGGAGGATTAGAATTATGAAGAAGATTTGGTCCTCCCGAAGTTTCTCT
CTTCACGATGATATTTAAACCACTAGGTGCCTGCAGAAGATTAGAATTATGAAAAAGATTTGGTC
CTCCCAGAGTTTTTCTCTTCACAATGATGTTT
Found at i:419334 original size:31 final size:31
Alignment explanation
Indices: 419269--419334 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
419259 AAAGTTAGAG
* * **
419269 AAAAAAATTTTAAGCCTTTTAAAAGCTGGTA
1 AAAAAAATTTTAAGCCTCTTAAAAACTGAAA
419300 AAAAAAATTTT-AGCCCTCTTAAAAACTGAAA
1 AAAAAAATTTTAAG-CCTCTTAAAAACTGAAA
419331 AAAA
1 AAAA
419335 TTTGGACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (31 bp):
AAAAAAATTTTAAGCCTCTTAAAAACTGAAA
Found at i:427331 original size:221 final size:227
Alignment explanation
Indices: 427054--427666 Score: 807
Period size: 221 Copynumber: 2.7 Consensus size: 227
427044 AGGAGGGCCT
*
427054 TAGGGATCAAAACTAAAATTTAACCATAAAAATTTGAGGGATTAGAATTGAAATTTAGCAATTAT
1 TAGGGATCAAAACTAAAATTTAACCATAAAAATTAGAGGGATTAGAATTGAAATTTAGCAATTAT
* *
427119 CTTCTTGTGTAAAAAAGAAATTTAAGTGAAATATAAAGATCAGAATTGAAATTTAACCATAAAAA
66 CTTCTAGTGTAAAAAATAAATTTAAGTGAAATATAAAGATCAGAATTGAAATTTAACCATAAAAA
*
427184 TTAGAGGGATTAGAATT-AAAGTTTAGCCACTATC-T-T-G-T-CATTGGACATGTGTCATATAA
131 TTAGAGGGATTAGAATTGAAA-TTTAGCCACTATCTTGTCGTTACATTGAACATGTGTCATATAA
*
427243 GGAAGGCCTTAGAGCTAT-ATTTGAGTGAAATA
195 AGAAGGCCTTAGAGCTATAATTTGAGTGAAATA
*
427275 TAGGGATCAAAACTAAAATTTAACCATAAAAATTAGA-GGCTTGAGAATTGAAATTTAGCAATTA
1 TAGGGATCAAAACTAAAATTTAACCATAAAAATTAGAGGGATT-AGAATTGAAATTTAGCAATTA
* * * * *
427339 TCTTCTCA-TGTAAAAAAATAAATTTGAGTGAAATATAAGGATCAGAACTGAAAGTTAACCAT-T
65 TCTTCT-AGTGT-AAAAAATAAATTTAAGTGAAATATAAAGATCAGAATTGAAATTTAACCATAA
* *
427402 AAATTAGAGGGATTAGAATTGAAATTCAGCCATTATCTTGTCACGTTAAAAAAACATTGAACATG
128 AAATTAGAGGGATTAGAATTGAAATTTAGCCACTATCTTGT--CGTT------ACATTGAACATG
* *
427467 TGTCATGTAAAGAAGGCCTTAGGGCTATAAATTTGAGTGAAATA
185 TGTCATATAAAGAAGGCCTTAGAGCTAT-AATTTGAGTGAAATA
* * * * *
427511 CATGGATCAAAACTGAAATTTAACCATAAAAAATTAGAGGGATTAGAATTGAAATTTAGCCACTA
1 TAGGGATCAAAACTAAAATTTAACCAT-AAAAATTAGAGGGATTAGAATTGAAATTTAGCAATTA
* * *
427576 TTTTCTCAG-GTAAAAAATAAATTTAAGTGAAATATAAAAATCAAAATTGAAATTTAACCATAAA
65 TCTTCT-AGTGTAAAAAATAAATTTAAGTGAAATATAAAGATCAGAATTGAAATTTAACCATAAA
427640 AATTAGAGGGATTAGAATTGAAATTTA
129 AATTAGAGGGATTAGAATTGAAATTTA
427667 ACCATTATAT
Statistics
Matches: 339, Mismatches: 30, Indels: 30
0.85 0.08 0.08
Matches are distributed among these distances:
220 4 0.01
221 97 0.29
222 49 0.14
223 1 0.00
226 1 0.00
227 1 0.00
234 35 0.10
236 82 0.24
237 65 0.19
238 4 0.01
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.30
Consensus pattern (227 bp):
TAGGGATCAAAACTAAAATTTAACCATAAAAATTAGAGGGATTAGAATTGAAATTTAGCAATTAT
CTTCTAGTGTAAAAAATAAATTTAAGTGAAATATAAAGATCAGAATTGAAATTTAACCATAAAAA
TTAGAGGGATTAGAATTGAAATTTAGCCACTATCTTGTCGTTACATTGAACATGTGTCATATAAA
GAAGGCCTTAGAGCTATAATTTGAGTGAAATA
Found at i:427440 original size:98 final size:100
Alignment explanation
Indices: 427261--427455 Score: 270
Period size: 99 Copynumber: 2.0 Consensus size: 100
427251 TTAGAGCTAT
* * *
427261 ATTTGAGTGAAATATAGGGATCAAAACTAAAATTTAACCATAAAAATTAGAGGCTTGAGAATTGA
1 ATTTGAGTGAAATATAAGGATCAAAACTAAAAGTTAACCATAAAAATTAGAGGATTGAGAATTGA
* *
427326 AATTTAGCAATTATCTTCTCATG-TAAAAAAATAA
66 AATTCAGCAATTATCTTCTCACGTTAAAAAAATAA
* * *
427360 ATTTGAGTGAAATATAAGGATCAGAACTGAAAGTTAACCAT-TAAATTAGAGGGATT-AGAATTG
1 ATTTGAGTGAAATATAAGGATCAAAACTAAAAGTTAACCATAAAAATTAGA-GGATTGAGAATTG
* *
427423 AAATTCAGCCATTATCTTGTCACGTTAAAAAAA
65 AAATTCAGCAATTATCTTCTCACGTTAAAAAAA
427456 CATTGAACAT
Statistics
Matches: 84, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
98 35 0.42
99 49 0.58
ACGTcount: A:0.45, C:0.10, G:0.16, T:0.30
Consensus pattern (100 bp):
ATTTGAGTGAAATATAAGGATCAAAACTAAAAGTTAACCATAAAAATTAGAGGATTGAGAATTGA
AATTCAGCAATTATCTTCTCACGTTAAAAAAATAA
Found at i:438894 original size:6 final size:6
Alignment explanation
Indices: 438885--438921 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
438875 AATGTTTTTG
438885 TTTATA TTTATA TTTATA TTTATA TTTATA TTT-TA TT
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TT
438922 AATTAATGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (6 bp):
TTTATA
Found at i:438908 original size:18 final size:17
Alignment explanation
Indices: 438880--438921 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
438870 AGAATAATGT
*
438880 TTTTGTTTATATTTATA
1 TTTTATTTATATTTATA
438897 TTTATATTTATATTTATA
1 TTT-TATTTATATTTATA
438915 TTTTATT
1 TTTTATT
438922 AATTAATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTTTATTTATATTTATA
Found at i:440606 original size:2 final size:2
Alignment explanation
Indices: 440599--440631 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
440589 TAATTGAAGA
440599 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 A
440632 ATTTAATTAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:441505 original size:17 final size:16
Alignment explanation
Indices: 441483--441540 Score: 64
Period size: 15 Copynumber: 3.6 Consensus size: 16
441473 TTTTTACTCT
441483 TTTAAAATTGATAAAAA
1 TTTAAAATT-ATAAAAA
441500 TTTAAAAATTATAAAAA
1 TTT-AAAATTATAAAAA
* * *
441517 TAT-AAACTATTAAAA
1 TTTAAAATTATAAAAA
441532 TTTAAAATT
1 TTTAAAATT
441541 TAATTTCAGC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
15 12 0.35
16 4 0.12
17 12 0.35
18 6 0.18
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (16 bp):
TTTAAAATTATAAAAA
Found at i:444734 original size:25 final size:25
Alignment explanation
Indices: 444702--444761 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
444692 TACCATCCAT
* *
444702 ATAA-ATTTCTAAGTTGTTTGA-AAA
1 ATAATATTTATAAGTT-TTTCATAAA
*
444726 ATAATATTTATATGTTTTTCATAAA
1 ATAATATTTATAAGTTTTTCATAAA
444751 ATAAATATTTA
1 AT-AATATTTA
444762 AAATATTAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 8 0.27
25 14 0.47
26 8 0.27
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (25 bp):
ATAATATTTATAAGTTTTTCATAAA
Found at i:462605 original size:15 final size:15
Alignment explanation
Indices: 462539--462608 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 15
462529 TCATGTGACA
*
462539 ATTAAAATA-AAAAT
1 ATTAAAATATTAAAT
462553 ATT-AAAT-TTAAAT
1 ATTAAAATATTAAAT
* *
462566 -TTAAAA-AATAGAAA
1 ATTAAAATATTA-AAT
* *
462580 ACTATAATATTAAAT
1 ATTAAAATATTAAAT
462595 ATTAAAATATTAAA
1 ATTAAAATATTAAA
462609 AAAAACTTTT
Statistics
Matches: 41, Mismatches: 9, Indels: 11
0.67 0.15 0.18
Matches are distributed among these distances:
12 2 0.05
13 13 0.32
14 5 0.12
15 18 0.44
16 3 0.07
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (15 bp):
ATTAAAATATTAAAT
Found at i:469285 original size:19 final size:19
Alignment explanation
Indices: 469258--469295 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
469248 TTTAAATTTT
*
469258 AATTATATTTAGTAAATTA
1 AATTATATTGAGTAAATTA
*
469277 AATTTTATTGAGTAAATTA
1 AATTATATTGAGTAAATTA
469296 CACTCGTAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (19 bp):
AATTATATTGAGTAAATTA
Found at i:470271 original size:21 final size:20
Alignment explanation
Indices: 470206--470272 Score: 54
Period size: 21 Copynumber: 3.5 Consensus size: 20
470196 TTATACAAAT
470206 TCAGGCTTTGTGCCGGTGTTA
1 TCAGGCTTTGTG-CGGTGTTA
* *
470227 TCGGGCTTTGTGC----CTA
1 TCAGGCTTTGTGCGGTGTTA
470243 GT-AGGCTTTGTGCTGGTGTTA
1 -TCAGGCTTTGTGC-GGTGTTA
470264 TCAGGCTTT
1 TCAGGCTTT
470273 ATGCCAGTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
16 12 0.34
17 1 0.03
20 2 0.06
21 20 0.57
ACGTcount: A:0.09, C:0.18, G:0.33, T:0.40
Consensus pattern (20 bp):
TCAGGCTTTGTGCGGTGTTA
Found at i:473439 original size:6 final size:6
Alignment explanation
Indices: 473428--473459 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
473418 TTCCATCTCT
473428 GGGAAA GGGAAA --GAAA GGGAAA GGGAAA GGGA
1 GGGAAA GGGAAA GGGAAA GGGAAA GGGAAA GGGA
473460 GGCAGATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
4 4 0.17
6 20 0.83
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (6 bp):
GGGAAA
Found at i:485200 original size:20 final size:20
Alignment explanation
Indices: 485177--485238 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 20
485167 GTAATTCTAA
485177 AAGATATTCAATAATTTTAT
1 AAGATATTCAATAATTTTAT
* * * ** *
485197 AAGAGATTTAGTAAAATTGT
1 AAGATATTCAATAATTTTAT
* *
485217 AACATCTTCAATAATTTTAT
1 AAGATATTCAATAATTTTAT
485237 AA
1 AA
485239 AAAAATTAGT
Statistics
Matches: 28, Mismatches: 14, Indels: 0
0.67 0.33 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.45, C:0.06, G:0.08, T:0.40
Consensus pattern (20 bp):
AAGATATTCAATAATTTTAT
Found at i:485362 original size:25 final size:25
Alignment explanation
Indices: 485329--485378 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
485319 GATTAGATAA
485329 TTTAGTAATTTAAAAA-TTATTATT
1 TTTAGTAATTTAAAAAGTTATTATT
485353 TTTAGATAATTTAAAAAGTTATTATT
1 TTTAG-TAATTTAAAAAGTTATTATT
485379 CATGAGCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 5 0.21
25 11 0.46
26 8 0.33
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (25 bp):
TTTAGTAATTTAAAAAGTTATTATT
Found at i:487047 original size:3 final size:3
Alignment explanation
Indices: 487041--487081 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
487031 CAAACAACAT
*
487041 ATA ATA ATA ATA ATA ATA ATA TTA ATAA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA A
487082 CCCATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:497228 original size:24 final size:26
Alignment explanation
Indices: 497201--497249 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 26
497191 ATTCAAATTC
497201 AAGAC-TTAAATTATCTTA-GAAAAT
1 AAGACTTTAAATTATCTTAGGAAAAT
*
497225 AAGACTTTAATTTATCTTAGGAAAA
1 AAGACTTTAAATTATCTTAGGAAAA
497250 AAAAAACTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 5 0.23
25 12 0.55
26 5 0.23
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.35
Consensus pattern (26 bp):
AAGACTTTAAATTATCTTAGGAAAAT
Found at i:516076 original size:93 final size:93
Alignment explanation
Indices: 515906--516077 Score: 276
Period size: 92 Copynumber: 1.8 Consensus size: 93
515896 ACATGAATCA
* * * *
515906 TTGTATAAAAAGCCTTGTTTTACATAATCTTTGTTGAGTAATACAAGCTATAGCATTCTTTTACA
1 TTGTATAAAAAGCCTTGTTGTACATAAGCTTTGTCGAGTAATACAAGCTATAGCATTCTCTTACA
515971 CTCACTTTCCTTGAGTCTTGCATTTGGT
66 CTCACTTTCCTTGAGTCTTGCATTTGGT
515999 TTGTAT-AAAAGCCTTGTTGTACATAAGCTTTGTCGAGTAATACAAGCTAATAGCA-TCGTCTTA
1 TTGTATAAAAAGCCTTGTTGTACATAAGCTTTGTCGAGTAATACAAGCT-ATAGCATTC-TCTTA
516062 CACTCACTTTCCTTGA
64 CACTCACTTTCCTTGA
516078 ATATTAGCTC
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
92 41 0.56
93 32 0.44
ACGTcount: A:0.27, C:0.19, G:0.15, T:0.40
Consensus pattern (93 bp):
TTGTATAAAAAGCCTTGTTGTACATAAGCTTTGTCGAGTAATACAAGCTATAGCATTCTCTTACA
CTCACTTTCCTTGAGTCTTGCATTTGGT
Found at i:518848 original size:32 final size:30
Alignment explanation
Indices: 518788--518850 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
518778 TTAGACAAAA
**
518788 AAAAAAATTAAAAATTCAAATCTTAATATG
1 AAAAAAATTAAAAATTCAAATCAAAATATG
*
518818 AAAAAAATTATCAAATTCAAACTCAAAATATG
1 AAAAAAATTA-AAAATTCAAA-TCAAAATATG
518850 A
1 A
518851 TTTATAACCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 10 0.36
31 9 0.32
32 9 0.32
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.27
Consensus pattern (30 bp):
AAAAAAATTAAAAATTCAAATCAAAATATG
Found at i:519585 original size:4 final size:4
Alignment explanation
Indices: 519569--519607 Score: 69
Period size: 4 Copynumber: 9.8 Consensus size: 4
519559 ATAAGATAAA
*
519569 ATGT ATAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATG
519608 AAATAGTCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.49
Consensus pattern (4 bp):
ATGT
Found at i:520244 original size:6 final size:6
Alignment explanation
Indices: 520191--520242 Score: 86
Period size: 6 Copynumber: 8.7 Consensus size: 6
520181 AAGAAAGAAT
* *
520191 CATACA CATACA CATACA CATACA CATACA CATACA CATATA CATATA
1 CATACA CATACA CATACA CATACA CATACA CATACA CATACA CATACA
520239 CATA
1 CATA
520243 TATGCCATAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (6 bp):
CATACA
Found at i:522063 original size:30 final size:31
Alignment explanation
Indices: 521985--522063 Score: 74
Period size: 30 Copynumber: 2.6 Consensus size: 31
521975 TAATAAGTAA
* *
521985 AATTAAATTGATAAAA-TGTCTAAAGTTGAG
1 AATTAAATTGATAAAATTTTCTAAAATTGAG
* ** *
522015 AATTAGA-TGTATTGAATTTTTTAAAATT-AG
1 AATTAAATTG-ATAAAATTTTCTAAAATTGAG
522045 AATTAAATTGATAAAATTT
1 AATTAAATTGATAAAATTT
522064 GTAAACATTG
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
29 2 0.05
30 25 0.68
31 10 0.27
ACGTcount: A:0.46, C:0.01, G:0.13, T:0.41
Consensus pattern (31 bp):
AATTAAATTGATAAAATTTTCTAAAATTGAG
Found at i:527817 original size:20 final size:21
Alignment explanation
Indices: 527792--527831 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
527782 ATCTGAAGCA
* *
527792 AGTTTTCA-AAAAATTACTCG
1 AGTTTTAACAAAAACTACTCG
527812 AGTTTTAACAAAAACTACTC
1 AGTTTTAACAAAAACTACTC
527832 TTTAAGGTTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (21 bp):
AGTTTTAACAAAAACTACTCG
Found at i:528075 original size:14 final size:14
Alignment explanation
Indices: 528056--528082 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
528046 TCTAATTAAT
528056 TAAATCAATAAAAA
1 TAAATCAATAAAAA
528070 TAAATCAATAAAA
1 TAAATCAATAAAA
528083 GATGGATTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAATCAATAAAAA
Found at i:528721 original size:3 final size:3
Alignment explanation
Indices: 528715--528752 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
528705 AGAGGAGGAA
*
528715 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAG GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
528753 AGAAGAAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:531422 original size:43 final size:43
Alignment explanation
Indices: 531331--531422 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
531321 TAGCTCTCTC
* *
531331 TTATAATTGCCATTAGTGTACCTTAATTGGACATTTAGCATCG
1 TTATAATTACCATTAGTGTACCTTAATTGGACATTTAACATCG
* ** * *
531374 ATATAATTACCATTAGTGTTGCTTAATTGGACATTTAACGTTG
1 TTATAATTACCATTAGTGTACCTTAATTGGACATTTAACATCG
531417 TTATAA
1 TTATAA
531423 CTATCATCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (43 bp):
TTATAATTACCATTAGTGTACCTTAATTGGACATTTAACATCG
Found at i:533667 original size:26 final size:26
Alignment explanation
Indices: 533638--533689 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
533628 TTGAGTTTAT
533638 ACAAAACATTATGAAATTTGTAACAA
1 ACAAAACATTATGAAATTTGTAACAA
533664 ACAAAACATTATGAAATTTGTAACAA
1 ACAAAACATTATGAAATTTGTAACAA
533690 TTTGTCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.54, C:0.12, G:0.08, T:0.27
Consensus pattern (26 bp):
ACAAAACATTATGAAATTTGTAACAA
Found at i:534706 original size:44 final size:44
Alignment explanation
Indices: 534649--534736 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
534639 TATGTTGCCA
534649 ATGTGTTTGGTCATAAGTGAGTAAAGCTTTAAATCGATCAATGG
1 ATGTGTTTGGTCATAAGTGAGTAAAGCTTTAAATCGATCAATGG
534693 ATGTGTTTGGTCATAAGTGAGTAAAGCTTTAAATCGATCAATGG
1 ATGTGTTTGGTCATAAGTGAGTAAAGCTTTAAATCGATCAATGG
534737 CAAAGGAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.34
Consensus pattern (44 bp):
ATGTGTTTGGTCATAAGTGAGTAAAGCTTTAAATCGATCAATGG
Found at i:540843 original size:153 final size:152
Alignment explanation
Indices: 540626--541019 Score: 535
Period size: 153 Copynumber: 2.6 Consensus size: 152
540616 AAAGGAATGG
* * *
540626 TGATGAAATTCTTACCACTAAGATCAAGACGTATCAAAGAGGATAGACCTGAAATTTCACTATGA
1 TGATGAAATTGTTACCACTAAGATCAAGACGTATCAAAGAGGATAGACCAGAAATATCACTATGA
*
540691 ATATCTGCTTCACCAAGAGTGCACATGTTGCAATTTGACAAGTA-AAGAAAC-TGAAGCTTGGAG
66 ATATCT-CTTCACCAAGAGTGCACATGTTGCAATTTGACAA-TATAAG-AACTTCAAGCTTGGAG
*
540754 AGTCGAGTAAGAGATGCAGGTATGC
128 AGTCGAGTAAGAGATGCAGGCATGC
**
540779 TGATGAAATTGTTACCACTAAGATCAAGACACCA-CAAAGAGGATAGACCAGAAATATCACTATG
1 TGATGAAATTGTTACCACTAAGATCAAGAC-GTATCAAAGAGGATAGACCAGAAATATCACTATG
* * *
540843 AGTATCCTCTTCACCAAGAGTGCACATTTTGCAATTTGACAATATAAGATCTTCAAGCTTGGAGA
65 AATAT-CTCTTCACCAAGAGTGCACATGTTGCAATTTGACAATATAAGAACTTCAAGCTTGGAGA
*
540908 GTCGAGTAAGAGATGCGGGCATGC
129 GTCGAGTAAGAGATGCAGGCATGC
* * * * *
540932 TGATGAAATTGTTACCACTAAGTTCGAGACGTATCAAAGAGGGTCGACCAGAAATATCACGT-GG
1 TGATGAAATTGTTACCACTAAGATCAAGACGTATCAAAGAGGATAGACCAGAAATATCAC-TATG
* *
540996 AATATCTCCTTCACAAAGATTGCA
65 AATATCT-CTTCACCAAGAGTGCA
541020 GTCCCTTAGT
Statistics
Matches: 213, Mismatches: 21, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
152 7 0.03
153 202 0.95
154 4 0.02
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (152 bp):
TGATGAAATTGTTACCACTAAGATCAAGACGTATCAAAGAGGATAGACCAGAAATATCACTATGA
ATATCTCTTCACCAAGAGTGCACATGTTGCAATTTGACAATATAAGAACTTCAAGCTTGGAGAGT
CGAGTAAGAGATGCAGGCATGC
Found at i:547316 original size:102 final size:102
Alignment explanation
Indices: 547140--547346 Score: 405
Period size: 102 Copynumber: 2.0 Consensus size: 102
547130 TGTCTTATGA
547140 CATACAATGCCTATGGGCTTAGCACTTCGGTGCTCAGGTGTGTATTGGAGTTATGGCTGTGTTTT
1 CATACAATGCCTATGGGCTTAGCACTTCGGTGCTCAGGTGTGTATTGGAGTTATGGCTGTGTTTT
547205 GTAGTTACTCGCGTATCCGTATTTGTTTGTTATAGTT
66 GTAGTTACTCGCGTATCCGTATTTGTTTGTTATAGTT
*
547242 CATACAATGCCTATGGGCTTAGCACTTCGGTGCTCAGGTGTGTATTGGAGTTATGGTTGTGTTTT
1 CATACAATGCCTATGGGCTTAGCACTTCGGTGCTCAGGTGTGTATTGGAGTTATGGCTGTGTTTT
547307 GTAGTTACTCGCGTATCCGTATTTGTTTGTTATAGTT
66 GTAGTTACTCGCGTATCCGTATTTGTTTGTTATAGTT
547344 CAT
1 CAT
547347 CAAGTTAAAT
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
102 104 1.00
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.42
Consensus pattern (102 bp):
CATACAATGCCTATGGGCTTAGCACTTCGGTGCTCAGGTGTGTATTGGAGTTATGGCTGTGTTTT
GTAGTTACTCGCGTATCCGTATTTGTTTGTTATAGTT
Found at i:550838 original size:17 final size:16
Alignment explanation
Indices: 550818--550907 Score: 73
Period size: 17 Copynumber: 5.6 Consensus size: 16
550808 TAAATTTATA
*
550818 TTAAGTTTAAATTGGTT
1 TTAAATTTAAATT-GTT
550835 TTAAATTT--A-T-TT
1 TTAAATTTAAATTGTT
550847 TTAAATTTAAATTTGTT
1 TTAAATTTAAA-TTGTT
550864 TTAAATTTAAATT-TAAT
1 TTAAATTTAAATTGT--T
*
550881 TTAAATTTGAAATGGTT
1 TTAAATTT-AAATTGTT
*
550898 TTAAACTTAA
1 TTAAATTTAA
550908 TTTTAAAATT
Statistics
Matches: 61, Mismatches: 3, Indels: 19
0.73 0.04 0.23
Matches are distributed among these distances:
12 10 0.16
14 2 0.03
15 2 0.03
16 5 0.08
17 37 0.61
18 4 0.07
19 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.53
Consensus pattern (16 bp):
TTAAATTTAAATTGTT
Found at i:550843 original size:6 final size:6
Alignment explanation
Indices: 550834--550893 Score: 61
Period size: 6 Copynumber: 10.2 Consensus size: 6
550824 TTAAATTGGT
** **
550834 TTTAAA TTTATT TTTAAA TTTAAA TTT-GT TTTAAA TTTAAA TTT-AA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
550880 TTTAAA TTTGAAA T
1 TTTAAA TTT-AAA T
550894 GGTTTTAAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
5 8 0.19
6 31 0.72
7 4 0.09
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (6 bp):
TTTAAA
Found at i:550881 original size:11 final size:12
Alignment explanation
Indices: 550834--550893 Score: 61
Period size: 11 Copynumber: 5.1 Consensus size: 12
550824 TTAAATTGGT
**
550834 TTTAAATTTATT
1 TTTAAATTTAAA
550846 TTTAAATTTAAA
1 TTTAAATTTAAA
**
550858 TTT-GTTTTAAA
1 TTTAAATTTAAA
550869 TTTAAATTT-AA
1 TTTAAATTTAAA
550880 TTTAAATTTGAAA
1 TTTAAATTT-AAA
550893 T
1 T
550894 GGTTTTAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
11 20 0.51
12 16 0.41
13 3 0.08
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (12 bp):
TTTAAATTTAAA
Found at i:552548 original size:30 final size:29
Alignment explanation
Indices: 552505--552724 Score: 78
Period size: 30 Copynumber: 7.5 Consensus size: 29
552495 TAAACTATCT
* *
552505 AAAAATCATATTTTGACCCCCGAACTTTAC
1 AAAAATTACATTTTGACCCCCGAACTTT-C
*
552535 AAAAATTACATTTTGGA-CCTCGAACTTTC
1 AAAAATTACATTTT-GACCCCCGAACTTTC
* * * * * **
552564 CAAAATTCCAATTTCAACCCTAAACTTTCC
1 AAAAATTACATTTTGACCCCCGAACTTT-C
* *
552594 AAAAATTACCATTTT-A-ACCCGAAAC-ATC
1 AAAAATTA-CATTTTGACCCCCG-AACTTTC
* * *
552622 CAAAATTACCATTTT-ACCCTC-ATA-TGTCC
1 AAAAATTA-CATTTTGACCCCCGA-ACT-TTC
* * **
552651 AAAAATTACATTTTTAACCCTAAACTTTCC
1 AAAAATTACATTTTGACCCCCGAACTTT-C
* * * *
552681 AAAAATTACCA-TTTCACCCTCGAACATCC
1 AAAAATTA-CATTTTGACCCCCGAACTTTC
552710 AAAAATTACCATTTT
1 AAAAATTA-CATTTT
552725 ACTCTTGGAT
Statistics
Matches: 141, Mismatches: 34, Indels: 30
0.69 0.17 0.15
Matches are distributed among these distances:
27 1 0.01
28 24 0.17
29 50 0.35
30 57 0.40
31 9 0.06
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (29 bp):
AAAAATTACATTTTGACCCCCGAACTTTC
Found at i:552589 original size:29 final size:30
Alignment explanation
Indices: 552557--552723 Score: 154
Period size: 29 Copynumber: 5.7 Consensus size: 30
552547 TTGGACCTCG
552557 AACTTTCC-AAAATT-CCAATTTCAACCCTA
1 AACTTTCCAAAAATTACC-ATTTCAACCCTA
* *
552586 AACTTTCCAAAAATTACCATTTTAACCCGA
1 AACTTTCCAAAAATTACCATTTCAACCCTA
* *
552616 AAC-ATCC-AAAATTACCATTT-TACCCTCA
1 AACTTTCCAAAAATTACCATTTCAACCCT-A
* * *
552644 TA-TGTCCAAAAATTA-CATTTTTAACCCTA
1 AACTTTCCAAAAATTACCA-TTTCAACCCTA
*
552673 AACTTTCCAAAAATTACCATTTC-ACCCTCG
1 AACTTTCCAAAAATTACCATTTCAACCCT-A
*
552703 AAC-ATCCAAAAATTACCATTT
1 AACTTTCCAAAAATTACCATTT
552724 TACTCTTGGA
Statistics
Matches: 115, Mismatches: 13, Indels: 20
0.78 0.09 0.14
Matches are distributed among these distances:
27 4 0.03
28 20 0.17
29 45 0.39
30 42 0.37
31 4 0.03
ACGTcount: A:0.39, C:0.28, G:0.02, T:0.31
Consensus pattern (30 bp):
AACTTTCCAAAAATTACCATTTCAACCCTA
Found at i:552670 original size:87 final size:87
Alignment explanation
Indices: 552565--552929 Score: 414
Period size: 87 Copynumber: 4.2 Consensus size: 87
552555 CGAACTTTCC
* * *
552565 AAAATTCCAATTTCAACCCTAAACTTTCCAAAAATTACCATTTTAACCCGAAACATCC-AAAATT
1 AAAATTACATTTTTAACCCTAAACTTTCCAAAAATTACCATTTTAACCCG-AACATCCAAAAATT
**
552629 ACCATTTTACCCTCATATGTCCA
65 ACCATTTTACCCTCGGATGTCCA
* *
552652 AAAATTACATTTTTAACCCTAAACTTTCCAAAAATTACCATTTCACCCTCGAACATCCAAAAATT
1 AAAATTACATTTTTAACCCTAAACTTTCCAAAAATTACCATTTTAACC-CGAACATCCAAAAATT
* *
552717 ACCATTTTACTCTTGGATGTCCA
65 ACCATTTTACCCTCGGATGTCCA
* * * * **
552740 AAATTTACATTTTTTACTCC-AAACTTTTCAAAAATTACCATTTTACCCCTTACATCCAAAAATT
1 AAAATTACATTTTTAAC-CCTAAACTTTCCAAAAATTACCATTTTAACCCGAACATCCAAAAATT
*
552804 ACCATTTTACCCCCGGATGTCCA
65 ACCATTTTACCCTCGGATGTCCA
* * * ***
552827 AAAATTACATTTTTTACCTTAAACTTTTCAAAAATTACCATTTT-ACCCATGAGTGTCCAAAAAT
1 AAAATTACATTTTTAACCCTAAACTTTCCAAAAATTACCATTTTAACCC--GAACATCCAAAAAT
* * *
552891 TACCGTTTTACCC-CTGAACGTCCA
64 TACCATTTTACCCTC-GGATGTCCA
552915 AAAATTACCATTTTT
1 AAAATTA-CATTTTT
552930 CCCCTTAATA
Statistics
Matches: 241, Mismatches: 29, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
86 4 0.02
87 125 0.52
88 103 0.43
89 9 0.04
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (87 bp):
AAAATTACATTTTTAACCCTAAACTTTCCAAAAATTACCATTTTAACCCGAACATCCAAAAATTA
CCATTTTACCCTCGGATGTCCA
Found at i:552739 original size:29 final size:29
Alignment explanation
Indices: 552591--552990 Score: 231
Period size: 29 Copynumber: 13.8 Consensus size: 29
552581 CCCTAAACTT
**
552591 TCCAAAAATTACCATTTTAACCC--GAAACA
1 TCCAAAAATTACCATTTT-ACCCTTG-AATG
*
552620 TCC-AAAATTACCATTTTACCC-TCATATG
1 TCCAAAAATTACCATTTTACCCTTGA-ATG
* *
552648 TCCAAAAATTA-CATTTTTAACCC-TAAACTT
1 TCCAAAAATTACCA-TTTT-ACCCTTGAA-TG
* * **
552678 TCCAAAAATTACCATTTCACCCTCGAACA
1 TCCAAAAATTACCATTTTACCCTTGAATG
* *
552707 TCCAAAAATTACCATTTTACTCTTGGATG
1 TCCAAAAATTACCATTTTACCCTTGAATG
* * *
552736 TCCAAAATTTA-CATTTTTTACTCC--AAACTT
1 TCCAAAAATTACCA--TTTTAC-CCTTGAA-TG
*
552766 TTCAAAAATTACCATTTTACCCCTT-ACA--
1 TCCAAAAATTACCATTTTA-CCCTTGA-ATG
** *
552794 TCCAAAAATTACCATTTTACCCCCGGATG
1 TCCAAAAATTACCATTTTACCCTTGAATG
* *
552823 TCCAAAAATTA-CATTTTTTA-CCTTAAACTT
1 TCCAAAAATTACCA--TTTTACCCTTGAA-TG
* * *
552853 TTCAAAAATTACCATTTTACCCATGAGTG
1 TCCAAAAATTACCATTTTACCCTTGAATG
* * *
552882 TCCAAAAATTACCGTTTTACCCCTGAACG
1 TCCAAAAATTACCATTTTACCCTTGAATG
* *
552911 TCCAAAAATTACCATTTTTCCCCTT-AATA
1 TCCAAAAATTACCA-TTTTACCCTTGAATG
* * * *
552940 TCTAAATATTACCGTTTTACCC-TCAATTG
1 TCCAAAAATTACCATTTTACCCTTGAA-TG
*
552969 TCC-CAAATTACCATTTTACCCT
1 TCCAAAAATTACCATTTTACCCT
552991 CTGGCATCTA
Statistics
Matches: 286, Mismatches: 56, Indels: 58
0.71 0.14 0.14
Matches are distributed among these distances:
27 10 0.03
28 66 0.23
29 133 0.47
30 69 0.24
31 8 0.03
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCTTGAATG
Found at i:552826 original size:175 final size:176
Alignment explanation
Indices: 552585--552929 Score: 471
Period size: 175 Copynumber: 2.0 Consensus size: 176
552575 TTTCAACCCT
* * *
552585 AAACTTTCCAAAAATTACCATTTTAACCCGAAACATCCAAAATTACCATTTTACCCTCATATGTC
1 AAACTTTCCAAAAATTACCATTTTAACCCCAAACATCCAAAATTACCATTTTACCCCCAGATGTC
552650 CAAAAATTACATTTTTAACCCTAAACTTTCCAAAAATTACCATTTCACCC-TCGAACATCCAAAA
66 CAAAAATTACATTTTTAACCCTAAACTTTCCAAAAATTACCATTTCACCCAT-GAACATCCAAAA
* * * * *
552714 ATTACCATTTTACTCTTGGATGTCCAAAATTTA-CATTTTTTACTCC
130 ATTACCATTTTACCCCTGAACGTCCAAAAATTACCATTTTTTACTCC
* ** *
552760 AAACTTTTCAAAAATTACCATTTT-ACCCCTTACATCCAAAAATTACCATTTTACCCCCGGATGT
1 AAACTTTCCAAAAATTACCATTTTAACCCCAAACATCC-AAAATTACCATTTTACCCCCAGATGT
* * * * ***
552824 CCAAAAATTACATTTTTTACCTTAAACTTTTCAAAAATTACCATTTTACCCATGAGTGTCCAAAA
65 CCAAAAATTACATTTTTAACCCTAAACTTTCCAAAAATTACCATTTCACCCATGAACATCCAAAA
*
552889 ATTACCGTTTTACCCCTGAACGTCCAAAAATTACCATTTTT
130 ATTACCATTTTACCCCTGAACGTCCAAAAATTACCATTTTT
552930 CCCCTTAATA
Statistics
Matches: 147, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
174 10 0.07
175 129 0.88
176 8 0.05
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (176 bp):
AAACTTTCCAAAAATTACCATTTTAACCCCAAACATCCAAAATTACCATTTTACCCCCAGATGTC
CAAAAATTACATTTTTAACCCTAAACTTTCCAAAAATTACCATTTCACCCATGAACATCCAAAAA
TTACCATTTTACCCCTGAACGTCCAAAAATTACCATTTTTTACTCC
Found at i:552859 original size:59 final size:59
Alignment explanation
Indices: 552534--552933 Score: 200
Period size: 59 Copynumber: 6.9 Consensus size: 59
552524 CCGAACTTTA
** ** * * * *
552534 CAAAAATTACATTTTGGACCTCGAACTTTCC-AAAATT-CCAATTTCAACCCTAAACTTTC
1 CAAAAATTACATTTTTTACCTTAAACTTTCCAAAAATTACC-ATTTTACCCCCAAA-TGTC
* ** * * *
552593 CAAAAATTACCA-TTTTAACCCGAAAC-ATCC-AAAATTACCATTTTACCCTCATATGTC
1 CAAAAATTA-CATTTTTTACCTTAAACTTTCCAAAAATTACCATTTTACCCCCAAATGTC
* * * * * **
552650 CAAAAATTACATTTTTAACCCTAAACTTTCCAAAAATTACCATTTCACCCTCGAACATC
1 CAAAAATTACATTTTTTACCTTAAACTTTCCAAAAATTACCATTTTACCCCCAAATGTC
** * * * * *
552709 CAAAAATTACCA--TTTTACTCTTGGA-TGTCCAAAATTTA-CATTTTTTA-CTCCAAACTTTT
1 CAAAAATTA-CATTTTTTAC-CTTAAACTTTCCAAAAATTACCA--TTTTACCCCCAAA-TGTC
*** * **
552768 CAAAAATTACCATTTTACCCCTT--AC-ATCCAAAAATTACCATTTTACCCCCGGATGTC
1 CAAAAATTA-CATTTTTTACCTTAAACTTTCCAAAAATTACCATTTTACCCCCAAATGTC
* *** *
552825 CAAAAATTACATTTTTTACCTTAAACTTTTCAAAAATTACCATTTTACCCATGAGTGTC
1 CAAAAATTACATTTTTTACCTTAAACTTTCCAAAAATTACCATTTTACCCCCAAATGTC
** * * * *
552884 CAAAAATTAC-CGTTTTACCCCTGAAC-GTCCAAAAATTACCATTTTTCCCC
1 CAAAAATTACATTTTTTA-CCTTAAACTTTCCAAAAATTACCATTTTACCCC
552934 TTAATATCTA
Statistics
Matches: 263, Mismatches: 59, Indels: 39
0.73 0.16 0.11
Matches are distributed among these distances:
56 12 0.05
57 43 0.16
58 83 0.32
59 115 0.44
60 7 0.03
61 3 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (59 bp):
CAAAAATTACATTTTTTACCTTAAACTTTCCAAAAATTACCATTTTACCCCCAAATGTC
Found at i:557361 original size:12 final size:11
Alignment explanation
Indices: 557344--557407 Score: 58
Period size: 11 Copynumber: 5.7 Consensus size: 11
557334 ATAAANGAAT
*
557344 AAAAAGGAAAA
1 AAAAAAGAAAA
*
557355 AAAAAAGAAAG
1 AAAAAAGAAAA
* *
557366 TAAAAA-TAAA
1 AAAAAAGAAAA
*
557376 AAAATAGAAAA
1 AAAAAAGAAAA
557387 AAAAAGAGAAAA
1 AAAAA-AGAAAA
557399 AGAAAAAGA
1 A-AAAAAGA
557408 GAGGTCGAGG
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
10 6 0.15
11 21 0.51
12 10 0.24
13 4 0.10
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:557375 original size:45 final size:43
Alignment explanation
Indices: 557310--557407 Score: 105
Period size: 45 Copynumber: 2.2 Consensus size: 43
557300 AAAAATAAAT
*
557310 AAAAAAAAG-AGAAAGAATAAAAGAATA-AANGAATAAAAAG-GAA
1 AAAAAAAAGAAGAAAGAATAAAAAAATAGAA--AA-AAAAAGAGAA
557353 AAAAAAAAGAAAGTAAA-AATAAAAAAATAGAAAAAAAAAGAGAA
1 AAAAAAAAG-AAG-AAAGAATAAAAAAATAGAAAAAAAAAGAGAA
557397 AAAGAAAAAGA
1 AAA-AAAAAGA
557408 GAGGTCGAGG
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
43 15 0.31
44 9 0.19
45 19 0.40
46 5 0.10
ACGTcount: A:0.79, C:0.00, G:0.14, T:0.06
Consensus pattern (43 bp):
AAAAAAAAGAAGAAAGAATAAAAAAATAGAAAAAAAAAGAGAA
Found at i:557386 original size:10 final size:10
Alignment explanation
Indices: 557297--557399 Score: 57
Period size: 10 Copynumber: 9.9 Consensus size: 10
557287 GGATTCAATG
*
557297 AAGAAAAATA
1 AAGAAAAAAA
*
557307 AATAAAAAAA
1 AAGAAAAAAA
557317 AGAGAAAGAATAA
1 A-AGAAA-AA-AA
*
557330 AAG--AATAA
1 AAGAAAAAAA
* *
557338 ANGAATAAAA
1 AAGAAAAAAA
*
557348 AGGAAAAAAAA
1 AAG-AAAAAAA
*
557359 AAGAAAGTAAA
1 AAGAAA-AAAA
*
557370 AATAAAAAAA
1 AAGAAAAAAA
*
557380 TAGAAAAAAA
1 AAGAAAAAAA
557390 AAGAGAAAAA
1 AAGA-AAAAA
557400 GAAAAAGAGA
Statistics
Matches: 69, Mismatches: 16, Indels: 15
0.69 0.16 0.15
Matches are distributed among these distances:
8 4 0.06
9 1 0.01
10 32 0.46
11 25 0.36
12 4 0.06
13 3 0.04
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:557391 original size:21 final size:21
Alignment explanation
Indices: 557300--557391 Score: 53
Period size: 21 Copynumber: 4.4 Consensus size: 21
557290 TTCAATGAAG
*
557300 AAAAATAAATAAAAAAAAGAGA
1 AAAAAAAAATAAAAAAAA-AGA
* * * * *
557322 AAGAATAAA-AGAATAAANGA
1 AAAAAAAAATAAAAAAAAAGA
**
557342 ATAAAAAGGA-AAAAAAAAAGA
1 A-AAAAAAAATAAAAAAAAAGA
** *
557363 AAGTAAAAATAAAAAAATAGA
1 AAAAAAAAATAAAAAAAAAGA
557384 AAAAAAAA
1 AAAAAAAA
557392 GAGAAAAAGA
Statistics
Matches: 50, Mismatches: 18, Indels: 5
0.68 0.25 0.07
Matches are distributed among these distances:
20 7 0.14
21 35 0.70
22 8 0.16
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.09
Consensus pattern (21 bp):
AAAAAAAAATAAAAAAAAAGA
Found at i:558450 original size:50 final size:50
Alignment explanation
Indices: 558330--558680 Score: 228
Period size: 50 Copynumber: 7.1 Consensus size: 50
558320 TGAAGGGAGG
** * * * *
558330 GATTGAGGCCG-AGACAACGAATCCGATATCTTAGAAGATGTGACGGGAAA
1 GATTGAGGCCGCA-ACGGCGAATCCGGTACCTTAGAAGATATGATGGGAAA
* * * * * *
558380 GGTTGAGGTCGCGACAGCGAATCCAGTACCTTAGAAGATGTGATGGGAAA
1 GATTGAGGCCGCAACGGCGAATCCGGTACCTTAGAAGATATGATGGGAAA
* * * *
558430 GATTGAGACCGCAACGGCGAATTCAGTACCAT-G-AGATATGA-GGAGAAA
1 GATTGAGGCCGCAACGGCGAATCCGGTACCTTAGAAGATATGATGG-GAAA
** * * * * * * *
558478 GATTGAGATCACAATGGCGAACCCGATACCTCAGAAGATGTGATAGGAAA
1 GATTGAGGCCGCAACGGCGAATCCGGTACCTTAGAAGATATGATGGGAAA
* * ** *
558528 GATTGAGGTCGTAACGTTGAATCCGGTACCAT-GAA-ATATGATGGGAAA
1 GATTGAGGCCGCAACGGCGAATCCGGTACCTTAGAAGATATGATGGGAAA
* * ** * *
558576 GGTTGAGGCCACAACAGGAAAACCCGGTACCTTAGAAGATATGAAGGGAAA
1 GATTGAGGCCGCAAC-GGCGAATCCGGTACCTTAGAAGATATGATGGGAAA
* * * * * * * * *
558627 GGTTGAGGCTGCAACGGCAAACCCGGTAACTTAGAAAACAAGATGGAAAA
1 GATTGAGGCCGCAACGGCGAATCCGGTACCTTAGAAGATATGATGGGAAA
558677 GATT
1 GATT
558681 AAATCCGCAA
Statistics
Matches: 234, Mismatches: 59, Indels: 16
0.76 0.19 0.05
Matches are distributed among these distances:
47 2 0.01
48 56 0.24
49 17 0.07
50 133 0.57
51 26 0.11
ACGTcount: A:0.36, C:0.16, G:0.29, T:0.18
Consensus pattern (50 bp):
GATTGAGGCCGCAACGGCGAATCCGGTACCTTAGAAGATATGATGGGAAA
Found at i:558508 original size:98 final size:99
Alignment explanation
Indices: 558406--558644 Score: 266
Period size: 98 Copynumber: 2.4 Consensus size: 99
558396 GCGAATCCAG
* * *
558406 TACCTTAGAAGATGTGATGGGAAAGATTGAGACCGCAACGGCGAATTCAGTACCATGAGATATGA
1 TACCTTAGAAGATGTGATGGGAAAGATTGAGGCCGCAACGGCGAATCCAGTACCATGAAATATGA
* * **
558471 -GGAGAAAGATTGAGATCACAA-TGGCGAACCCGA
66 TGG-GAAAGATTGAGACCACAACAGGAAAACCCGA
* * * * ** *
558504 TACCTCAGAAGATGTGATAGGAAAGATTGAGGTCGTAACGTTGAATCCGGTACCATGAAATATGA
1 TACCTTAGAAGATGTGATGGGAAAGATTGAGGCCGCAACGGCGAATCCAGTACCATGAAATATGA
* * *
558569 TGGGAAAGGTTGAGGCCACAACAGGAAAACCCGG
66 TGGGAAAGATTGAGACCACAACAGGAAAACCCGA
* * * *
558603 TACCTTAGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGGC
1 TACCTTAGAAGATGTGATGGGAAAGATTGAGGCCGCAACGGC
558645 AAACCCGGTA
Statistics
Matches: 112, Mismatches: 27, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
98 70 0.62
99 42 0.38
ACGTcount: A:0.36, C:0.16, G:0.30, T:0.19
Consensus pattern (99 bp):
TACCTTAGAAGATGTGATGGGAAAGATTGAGGCCGCAACGGCGAATCCAGTACCATGAAATATGA
TGGGAAAGATTGAGACCACAACAGGAAAACCCGA
Found at i:558625 original size:51 final size:49
Alignment explanation
Indices: 558550--558663 Score: 149
Period size: 51 Copynumber: 2.3 Consensus size: 49
558540 AACGTTGAAT
* *
558550 CCGGTACCAT-GAAATATGATGGGAAAGGTTGAGGCCACAACAGGAAAAC
1 CCGGTACCTTAGAAATATGAAGGGAAAGGTTGAGGCCACAAC-GGAAAAC
** *
558599 CCGGTACCTTAGAAGATATGAAGGGAAAGGTTGAGGCTGCAACGGCAAAC
1 CCGGTACCTTAGAA-ATATGAAGGGAAAGGTTGAGGCCACAACGGAAAAC
*
558649 CCGGTAACTTAGAAA
1 CCGGTACCTTAGAAA
558664 ACAAGATGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
49 10 0.18
50 22 0.39
51 25 0.44
ACGTcount: A:0.37, C:0.18, G:0.29, T:0.16
Consensus pattern (49 bp):
CCGGTACCTTAGAAATATGAAGGGAAAGGTTGAGGCCACAACGGAAAAC
Found at i:559009 original size:37 final size:37
Alignment explanation
Indices: 558962--559086 Score: 133
Period size: 37 Copynumber: 3.3 Consensus size: 37
558952 AAAGATTTTG
*
558962 ATCTCATACCCCGACATGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGACATGGGCAGATCACCATCAGCCA
* ** * ** *
558999 ATCTCTTACCCCGAGCCTCGGGCAGATTGCCACCATTCG
1 ATCTCTTACCCCGA-CAT-GGGCAGATCACCATCAGCCA
** *
559038 ATCTCTTACCCTAACATAGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGACATGGGCAGATCACCATCAGCCA
559075 ATCTCTTACCCC
1 ATCTCTTACCCC
559087 ATGCCTGGGG
Statistics
Matches: 67, Mismatches: 19, Indels: 4
0.74 0.21 0.04
Matches are distributed among these distances:
37 37 0.55
38 4 0.06
39 26 0.39
ACGTcount: A:0.26, C:0.38, G:0.14, T:0.22
Consensus pattern (37 bp):
ATCTCTTACCCCGACATGGGCAGATCACCATCAGCCA
Found at i:559219 original size:78 final size:78
Alignment explanation
Indices: 558961--559230 Score: 309
Period size: 78 Copynumber: 3.5 Consensus size: 78
558951 TAAAGATTTT
* * *
558961 GATCTCATACCCCGA-CATGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTCGGGCAGA
1 GATCTCTTACCCCGAGCATAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
559025 TTGCCA-CCATTC
66 TTGCCAGCCATTC
* *
559037 GATCTCTTA-CCCTAACATAGGCAGATCACCATCAGCCAATCTCTTACCCC-ATGCCTGGGGCAG
1 GATCTCTTACCCCGAGCATAGGCAGATCACCATCAGCCAATCTCTTACCCCGA-GCCTGGGGCAG
* *
559100 ATTGTC-GCCATTT
65 ATTGCCAGCCATTC
* * * ** * * * *
559113 GATCTTTTACCTCGAGCCTAGAATAGATCACTATTAGCCAATCTTTTACCCCGAGCCTGGGGAAG
1 GATCTCTTACCCCGAGCATAG-GCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAG
*
559178 ATTG-CAGTCATTC
65 ATTGCCAGCCATTC
*
559191 GATCTCTTACCCCGAGCATGGTGCAGATCACCATCAGCCA
1 GATCTCTTACCCCGAGCATAG-GCAGATCACCATCAGCCA
559231 CCCGATCTCT
Statistics
Matches: 159, Mismatches: 28, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
75 5 0.03
76 70 0.44
77 8 0.05
78 75 0.47
79 1 0.01
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (78 bp):
GATCTCTTACCCCGAGCATAGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGGGGCAGA
TTGCCAGCCATTC
Found at i:559675 original size:209 final size:208
Alignment explanation
Indices: 559315--559946 Score: 788
Period size: 209 Copynumber: 3.0 Consensus size: 208
559305 TATCCAAAGC
* * * * *
559315 AATAAAGAGGTTACCTTCCTAATGAGATACAGAGAAGTGAACCAGATTCGTCTTCCTGATGAGAG
1 AATAAAGCGGTTACCTTCTTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGAC
** * * * * * * *
559380 ACAGAGAAACGGATTGAAACAAGTGATAC-TGCCATCTTCTTGATGAGATATTGAAAAGTGGGCC
66 ACAGAG-AACGGATCAAAACAAGTGATGCGT-TCATCTTCCTGATGAGATACTGAGAAGTAGACC
* *
559444 AAATTAATGAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCTCAGCTTCCTAATGAGATACTGA
129 AAATCAATGAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCTCAGCTTCCTGATGAGATACTGA
*
559509 GAAGCAGGTCGAAGT
194 GAAGCAGGTCGAAGA
* *
559524 AATAAAGCGGTTACCTTCTTGATGAGATACAGAGAAGTGAATCAGATCCGTCTTCTTGATGAGAC
1 AATAAAGCGGTTACCTTCTTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGAC
* * *
559589 ATAGAGAAGTGGATCAAAACAAGAGATGCGTTCATCTTCCTGATGAGATACTGAGAAGTAGACCA
66 ACAGAGAA-CGGATCAAAACAAGTGATGCGTTCATCTTCCTGATGAGATACTGAGAAGTAGACCA
* *
559654 AGTCAATGAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGATACTGAG
130 AATCAATGAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCTCAGCTTCCTGATGAGATACTGAG
*
559719 AAACAGGTCGAA-A
195 AAGCAGGTCGAAGA
* * * * * *
559732 CAATAAAACAGTTACCTT-TCTGATGAGATATAGAAAAGTGAACCAGATCTGTCTTCCTGGTGAG
1 -AATAAAGCGGTTACCTTCT-TGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAG
* * * *
559796 ACACAGA-AACGAATCAAAATAAGTGATGCGGTCATCTTCCTGATGAGATACTAAGAAGTAGACC
64 ACACAGAGAACGGATCAAAACAAGTGATGCGTTCATCTTCCTGATGAGATACTGAGAAGTAGACC
* * * * * * *
559860 AAATCAATGAAACCAAAGCTCGATGTGAGCGAAA-CGTCTAACCTCAGCTTCCTGATGAGGTACG
129 AAATCAATGAAACC-AGGCTCAAAGTGAGC-AAATCTTCGAACCTCAGCTTCCTGATGAGATACT
559924 GAGAAGCAGGTCGAAGA
192 GAGAAGCAGGTCGAAGA
559941 AATAAA
1 AATAAA
559947 ATGGTCATCT
Statistics
Matches: 366, Mismatches: 50, Indels: 15
0.85 0.12 0.03
Matches are distributed among these distances:
207 62 0.17
208 62 0.17
209 241 0.66
210 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (208 bp):
AATAAAGCGGTTACCTTCTTGATGAGATACAGAGAAGTGAACCAGATCCGTCTTCCTGATGAGAC
ACAGAGAACGGATCAAAACAAGTGATGCGTTCATCTTCCTGATGAGATACTGAGAAGTAGACCAA
ATCAATGAAACCAGGCTCAAAGTGAGCAAATCTTCGAACCTCAGCTTCCTGATGAGATACTGAGA
AGCAGGTCGAAGA
Found at i:560418 original size:18 final size:18
Alignment explanation
Indices: 560395--560438 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
560385 TTTAAATTGG
* *
560395 TTTTAAATTTATTTTTAA
1 TTTTAAATTTAGTTTAAA
560413 TTTTAAATTTAGTTTAAA
1 TTTTAAATTTAGTTTAAA
*
560431 TTTGAAAT
1 TTTTAAAT
560439 GGTTTTAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTTAAATTTAGTTTAAA
Found at i:560442 original size:46 final size:46
Alignment explanation
Indices: 560361--560458 Score: 128
Period size: 46 Copynumber: 2.1 Consensus size: 46
560351 TGGATCAAAC
* * * *
560361 TTTTGATTTTAAATTTATATTAAGTTTAAATTGGTTTTAAATTTAT
1 TTTTAATTTTAAATTTATATTAAATTTAAATTGGTTTTAAACTTAA
560407 TTTTAATTTTAAATTTAGT-TTAAATTTGAAA-TGGTTTTAAACTTAA
1 TTTTAATTTTAAATTTA-TATTAAATTT-AAATTGGTTTTAAACTTAA
560453 TTTTAA
1 TTTTAA
560459 AATTTAATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
46 42 0.91
47 4 0.09
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.56
Consensus pattern (46 bp):
TTTTAATTTTAAATTTATATTAAATTTAAATTGGTTTTAAACTTAA
Found at i:562110 original size:30 final size:29
Alignment explanation
Indices: 562067--562139 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 29
562057 TAAACTAAAC
* *
562067 AAAAATCATATTTTAAACCCCAAAATTTAT
1 AAAAATTACATTTTAAACCCC-AAATTTAT
* * * *
562097 AAAAATTACATTTTAGACCTCAATTTTTT
1 AAAAATTACATTTTAAACCCCAAATTTAT
*
562126 CAAAATTACATTTT
1 AAAAATTACATTTT
562140 TGCCCCAAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 19 0.53
30 17 0.47
ACGTcount: A:0.44, C:0.15, G:0.01, T:0.40
Consensus pattern (29 bp):
AAAAATTACATTTTAAACCCCAAATTTAT
Found at i:562183 original size:28 final size:28
Alignment explanation
Indices: 562098--562185 Score: 70
Period size: 29 Copynumber: 3.1 Consensus size: 28
562088 AAAATTTATA
* ** * *
562098 AAAATTACATTTTAGACCTCAATTTTTTC
1 AAAATTACATTTTA-ACCCCAAACTATCC
** *
562127 AAAATTACATTTTTGCCCCAAACTTTCC
1 AAAATTACATTTTAACCCCAAACTATCC
*
562155 AAAATTACCATTTTAACCCCTAAC-ATCC
1 AAAATTA-CATTTTAACCCCAAACTATCC
562183 AAA
1 AAA
562186 TTTTACCCTC
Statistics
Matches: 48, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
28 22 0.46
29 26 0.54
ACGTcount: A:0.38, C:0.25, G:0.02, T:0.35
Consensus pattern (28 bp):
AAAATTACATTTTAACCCCAAACTATCC
Found at i:562237 original size:30 final size:29
Alignment explanation
Indices: 562185--562455 Score: 136
Period size: 29 Copynumber: 9.3 Consensus size: 29
562175 TAACATCCAA
* *
562185 ATTTTACCCTCAAATA-TCCAAAAATT-CT
1 ATTTTA-CCTCGAATATTCCAAAAATTACC
562213 ATTTTTGACCTCGAACT-TTCCAAAAATTACC
1 A-TTTT-ACCTCGAA-TATTCCAAAAATTACC
562244 ATTTTACCTCGAATATT-CAAAAATTACC
1 ATTTTACCTCGAATATTCCAAAAATTACC
* *
562272 ATTTTACTCTCGGAT-GTCCAAAAATTA-C
1 ATTTTAC-CTCGAATATTCCAAAAATTACC
***
562300 ATTTTTTAGCC-C-AA-ACTTTTTAAAATTACC
1 A--TTTTA-CCTCGAATA-TTCCAAAAATTACC
* * * * *
562330 ATTTTACCCCCAAAACATCTAAAAATTACC
1 ATTTTACCTCGAATA-TTCCAAAAATTACC
* *
562360 ATTTTACCCTCGGAT-GTCCAAAAATTA-C
1 ATTTTA-CCTCGAATATTCCAAAAATTACC
* *
562388 ATTTTTTACCTCGAACT-TTTCAAAAATTAGC
1 A--TTTTACCTCGAA-TATTCCAAAAATTACC
* * * *
562419 ATTTTACCCTCGAGT-GTCTAAAAATTATC
1 ATTTTA-CCTCGAATATTCCAAAAATTACC
562448 ATTTTACC
1 ATTTTACC
562456 CCCGGACGTC
Statistics
Matches: 194, Mismatches: 26, Indels: 46
0.73 0.10 0.17
Matches are distributed among these distances:
27 2 0.01
28 34 0.18
29 84 0.43
30 65 0.34
31 9 0.05
ACGTcount: A:0.35, C:0.23, G:0.06, T:0.37
Consensus pattern (29 bp):
ATTTTACCTCGAATATTCCAAAAATTACC
Found at i:562391 original size:58 final size:58
Alignment explanation
Indices: 562321--562624 Score: 251
Period size: 58 Copynumber: 5.2 Consensus size: 58
562311 CAAACTTTTT
* *
562321 AAAATTACCATTTTACCCCCAAAACATCTAAAAATTACCATTTTACCCTCGGATGTCCA
1 AAAATTACCATTTTACCCCC-GAACATCCAAAAATTACCATTTTACCCTCGGATGTCCA
* * * * *
562380 AAAATTA-CATTTTTTA-CCTCGAACTTTTCAAAAATTAGCATTTTACCCTC-GAGTGTCTA
1 AAAATTACCA--TTTTACCCCCGAAC-ATCCAAAAATTACCATTTTACCCTCGGA-TGTCCA
* * * * * *
562439 AAAATTATCATTTTACCCCCGGACGTCCAAAAATTACAATTTTGCCCTCGGGTGTCCA
1 AAAATTACCATTTTACCCCCGAACATCCAAAAATTACCATTTTACCCTCGGATGTCCA
* * * * * * * *
562497 AAGATTACCATTTTACCCCCGATCATCCCAAAATTACCATTTTTCCCACGGGTATCTA
1 AAAATTACCATTTTACCCCCGAACATCCAAAAATTACCATTTTACCCTCGGATGTCCA
* ** * * * * *
562555 AAAATT-GCATTTTTGCTCCGAACTTCCAAAAATTACCCTTTTGCCCTCGGGCT-TCCA
1 AAAATTACCATTTTACCCCCGAACATCCAAAAATTACCATTTTACCCTC-GGATGTCCA
562612 AAAATTA-CATTTT
1 AAAATTACCATTTT
562625 TTACTCCGTT
Statistics
Matches: 196, Mismatches: 40, Indels: 20
0.77 0.16 0.08
Matches are distributed among these distances:
57 47 0.24
58 92 0.47
59 50 0.26
60 7 0.04
ACGTcount: A:0.31, C:0.27, G:0.09, T:0.33
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACATCCAAAAATTACCATTTTACCCTCGGATGTCCA
Found at i:562488 original size:88 final size:88
Alignment explanation
Indices: 562185--562603 Score: 381
Period size: 88 Copynumber: 4.8 Consensus size: 88
562175 TAACATCCAA
** * *
562185 ATTTTACCCTCAAATATCCAAAAATT-CTATTTTTGACCTCGAACTTTCCAAAAATTACCATTTT
1 ATTTTACCCTCGGATGTCCAAAAATTAC-ATTTTTGACCTCGAACTTTTCAAAAATTACCATTTT
562249 A-CCTCGAATAT-TCAAAAATTACC
65 ACCCTCGAATATCT-AAAAATTACC
* * * *
562272 ATTTTACTCTCGGATGTCCAAAAATTACATTTTTTAGCC-CAAACTTTT-TAAAATTACCATTTT
1 ATTTTACCCTCGGATGTCCAAAAATTACATTTTTGA-CCTCGAACTTTTCAAAAATTACCATTTT
* * *
562335 ACCCCCAAAACATCTAAAAATTACC
65 ACCCTC-GAATATCTAAAAATTACC
* *
562360 ATTTTACCCTCGGATGTCCAAAAATTACATTTTTTACCTCGAACTTTTCAAAAATTAGCATTTTA
1 ATTTTACCCTCGGATGTCCAAAAATTACATTTTTGACCTCGAACTTTTCAAAAATTACCATTTTA
* * *
562425 CCCTCGAGTGTCTAAAAATTATC
66 CCCTCGAATATCTAAAAATTACC
* * * * ** * * *
562448 ATTTTACCCCCGGACGTCCAAAAATTACAATTTTGCCCTCG-GGTGTCCAAAGATTACCATTTTA
1 ATTTTACCCTCGGATGTCCAAAAATTACATTTTTGACCTCGAACTTTTCAAAAATTACCATTTTA
* **
562512 CCCCCG-ATCATCCCAAAATTACC
66 CCCTCGAAT-ATCTAAAAATTACC
* * * * * * * *
562535 ATTTTTCCCACGGGTATCTAAAAATTGCATTTTTG--CTCCGAAC-TTCCAAAAATTACCCTTTT
1 ATTTTACCCTCGGATGTCCAAAAATTACATTTTTGACCT-CGAACTTTTCAAAAATTACCATTTT
*
562597 GCCCTCG
65 ACCCTCG
562604 GGCTTCCAAA
Statistics
Matches: 269, Mismatches: 53, Indels: 21
0.78 0.15 0.06
Matches are distributed among these distances:
85 2 0.01
86 39 0.14
87 100 0.37
88 109 0.41
89 19 0.07
ACGTcount: A:0.32, C:0.26, G:0.08, T:0.34
Consensus pattern (88 bp):
ATTTTACCCTCGGATGTCCAAAAATTACATTTTTGACCTCGAACTTTTCAAAAATTACCATTTTA
CCCTCGAATATCTAAAAATTACC
Found at i:562532 original size:29 final size:29
Alignment explanation
Indices: 562231--562539 Score: 145
Period size: 29 Copynumber: 10.6 Consensus size: 29
562221 CCTCGAACTT
* *
562231 TCCAAAAATTACCATTTTA-CCTCGAAT-A
1 TCCAAAAATTACCATTTTACCCCCG-ATCG
* * *
562259 TTCAAAAATTACCATTTTACTCTCGGAT-G
1 TCCAAAAATTACCATTTTAC-CCCCGATCG
* * * *
562288 TCCAAAAATTA-CATTTTTTA-GCCCAAACT
1 TCCAAAAATTACCA--TTTTACCCCCGATCG
*** * * *
562317 TTTTAAAATTACCATTTTACCCCCAAAACA
1 TCCAAAAATTACCATTTTACCCCC-GATCG
* *
562347 TCTAAAAATTACCATTTTACCCTCGGAT-G
1 TCCAAAAATTACCATTTTACCC-CCGATCG
* * *
562376 TCCAAAAATTA-CATTTTTTA-CCTCGAACTT
1 TCCAAAAATTACCA--TTTTACCCCCGATC-G
* * *
562406 TTCAAAAATTAGCATTTTACCCTCGAGT-G
1 TCCAAAAATTACCATTTTACCCCCGA-TCG
* *
562435 TCTAAAAATTATCATTTTACCCCCGGA-CG
1 TCCAAAAATTACCATTTTACCCCC-GATCG
* * * *
562464 TCCAAAAATTACAATTTTGCCCTCGGGT-G
1 TCCAAAAATTACCATTTTACCC-CCGATCG
* *
562493 TCCAAAGATTACCATTTTACCCCCGATCA
1 TCCAAAAATTACCATTTTACCCCCGATCG
*
562522 TCCCAAAATTACCATTTT
1 TCCAAAAATTACCATTTT
562540 TCCCACGGGT
Statistics
Matches: 211, Mismatches: 49, Indels: 41
0.70 0.16 0.14
Matches are distributed among these distances:
28 34 0.16
29 116 0.55
30 58 0.27
31 3 0.01
ACGTcount: A:0.33, C:0.25, G:0.07, T:0.34
Consensus pattern (29 bp):
TCCAAAAATTACCATTTTACCCCCGATCG
Found at i:562596 original size:29 final size:29
Alignment explanation
Indices: 562215--562619 Score: 83
Period size: 29 Copynumber: 13.9 Consensus size: 29
562205 AAAATTCTAT
* *
562215 TTTTGACCTCGAACTTTCCAAAAATTACCA
1 TTTTGCCCTCGAAC-TTCCAAAAATTACCC
* * *
562245 TTTT-ACCTCGAA-TATTCAAAAATTACCA
1 TTTTGCCCTCGAACT-TCCAAAAATTACCC
* * * **
562273 TTTTACTCTCGGA-TGTCCAAAAATTACATT
1 TTTTGCCCTCGAACT-TCCAAAAATTAC-CC
* *** *
562303 TTTTAG-CC-CAAACTTTTTAAAATTACCA
1 TTTT-GCCCTCGAACTTCCAAAAATTACCC
* * * * * *
562331 TTTTACCCCCAAAACATCTAAAAATTACCA
1 TTTTGCCCTC-GAACTTCCAAAAATTACCC
* * **
562361 TTTTACCCTCGGA-TGTCCAAAAATTACAT
1 TTTTGCCCTCGAACT-TCCAAAAATTACCC
** * * *
562390 TTTTTACCTCGAACTTTTCAAAAATTAGCA
1 TTTTGCCCTCGAAC-TTCCAAAAATTACCC
* * * * *
562420 TTTTACCCTCG-AGTGTCTAAAAATTATCA
1 TTTTGCCCTCGAACT-TCCAAAAATTACCC
* * * * **
562449 TTTTACCCCCGGACGTCCAAAAATTACAA
1 TTTTGCCCTCGAACTTCCAAAAATTACCC
** * *
562478 TTTTGCCCTCG-GGTGTCCAAAGATTACCA
1 TTTTGCCCTCGAACT-TCCAAAAATTACCC
* * * * * *
562507 TTTTACCCCCGATCATCCCAAAATTACCA
1 TTTTGCCCTCGAACTTCCAAAAATTACCC
* * ** * * **
562536 TTTTTCCCACG-GGTATCTAAAAATTGCAT
1 TTTTGCCCTCGAACT-TCCAAAAATTACCC
*
562565 TTTTGCTC-CGAACTTCCAAAAATTACCC
1 TTTTGCCCTCGAACTTCCAAAAATTACCC
**
562593 TTTTGCCCTCGGGCTTCCAAAAATTAC
1 TTTTGCCCTCGAACTTCCAAAAATTAC
562620 ATTTTTTACT
Statistics
Matches: 275, Mismatches: 82, Indels: 37
0.70 0.21 0.09
Matches are distributed among these distances:
27 1 0.00
28 43 0.16
29 175 0.64
30 55 0.20
31 1 0.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.34
Consensus pattern (29 bp):
TTTTGCCCTCGAACTTCCAAAAATTACCC
Found at i:562625 original size:29 final size:29
Alignment explanation
Indices: 562350--562624 Score: 154
Period size: 29 Copynumber: 9.5 Consensus size: 29
562340 CAAAACATCT
*
562350 AAAAATTACCATTTTACCCTC-GGATGTCC
1 AAAAATTACCATTTTACCCTCGGGCT-TCC
** *
562379 AAAAATTA-CATTTTTTA-CCTCGAACTTTTC
1 AAAAATTACCA--TTTTACCCTCGGGC-TTCC
* * *
562409 AAAAATTAGCATTTTACCCTCGAG-TGTCT
1 AAAAATTACCATTTTACCCTCGGGCT-TCC
* * * *
562438 AAAAATTATCATTTTACCCCCGGACGTCC
1 AAAAATTACCATTTTACCCTCGGGCTTCC
* *
562467 AAAAATTACAATTTTGCCCTCGGG-TGTCC
1 AAAAATTACCATTTTACCCTCGGGCT-TCC
* * ** *
562496 AAAGATTACCATTTTACCCCCGATCATCC
1 AAAAATTACCATTTTACCCTCGGGCTTCC
* * * *
562525 CAAAATTACCATTTTTCCCACGGG-TATCT
1 AAAAATTACCATTTTACCCTCGGGCT-TCC
* ** **
562554 AAAAATT-GCATTTT-TGCTCCGAACTTCC
1 AAAAATTACCATTTTACCCT-CGGGCTTCC
* *
562582 AAAAATTACCCTTTTGCCCTCGGGCTTCC
1 AAAAATTACCATTTTACCCTCGGGCTTCC
562611 AAAAATTA-CATTTT
1 AAAAATTACCATTTT
562625 TTACTCCGTT
Statistics
Matches: 182, Mismatches: 49, Indels: 31
0.69 0.19 0.12
Matches are distributed among these distances:
27 1 0.01
28 25 0.14
29 130 0.71
30 23 0.13
31 3 0.02
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.33
Consensus pattern (29 bp):
AAAAATTACCATTTTACCCTCGGGCTTCC
Found at i:567913 original size:24 final size:23
Alignment explanation
Indices: 567875--567924 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
567865 TTAATATATG
* *
567875 AAATATTAATTTTAAATATTTTT
1 AAATATTAATATTAAATATTTAT
*
567898 AAATAATTAATATTAATTATTTAT
1 AAAT-ATTAATATTAAATATTTAT
567922 AAA
1 AAA
567925 ATCTAATTAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATATTAATATTAAATATTTAT
Found at i:569342 original size:55 final size:53
Alignment explanation
Indices: 569223--569360 Score: 143
Period size: 55 Copynumber: 2.5 Consensus size: 53
569213 AGGTGATGTT
* *
569223 GACCAATAGGTGTCAAAAACCCAAAAAAAAATTTAATCTATGTTTTTTGGTGCC
1 GACCAATAGGTGTCAAAAACCCAAAAAAAAATTT-ATCTATGTTTTTTGGTACA
* * *
569277 GGCCAATAGGTATCAAAAACCCAAAAAAAATATTT-TTTAATGTGTTTTTGGTACA
1 GACCAATAGGTGTCAAAAACCCAAAAAAAA-ATTTATCT-ATGT-TTTTTGGTACA
* * * * *
569332 GACTATTAGGTGGCAAACACTCAAAAAAA
1 GACCAATAGGTGTCAAAAACCCAAAAAAA
569361 TTTCAAAATT
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
53 2 0.03
54 32 0.46
55 35 0.51
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (53 bp):
GACCAATAGGTGTCAAAAACCCAAAAAAAAATTTATCTATGTTTTTTGGTACA
Found at i:578423 original size:17 final size:17
Alignment explanation
Indices: 578397--578434 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
578387 CTTTTGACCA
*
578397 TTAACTTTCCATATTTT
1 TTAACCTTCCATATTTT
*
578414 TTAACCTTCCATCTTTT
1 TTAACCTTCCATATTTT
578431 TTAA
1 TTAA
578435 ATTTTCATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (17 bp):
TTAACCTTCCATATTTT
Found at i:583242 original size:17 final size:17
Alignment explanation
Indices: 583222--583261 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
583212 TCCTTGACCA
*
583222 TTAACCTTCCATCTTCT
1 TTAACCTTCCATATTCT
*
583239 TTAACCTTTCATATTCT
1 TTAACCTTCCATATTCT
583256 TGTAAC
1 T-TAAC
583262 TACTTTTTCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.23, C:0.28, G:0.03, T:0.47
Consensus pattern (17 bp):
TTAACCTTCCATATTCT
Found at i:584369 original size:34 final size:34
Alignment explanation
Indices: 584331--584408 Score: 156
Period size: 34 Copynumber: 2.3 Consensus size: 34
584321 TTATATATAA
584331 TTAAATTTAAATAACAAAAATTATTTTTTAATAT
1 TTAAATTTAAATAACAAAAATTATTTTTTAATAT
584365 TTAAATTTAAATAACAAAAATTATTTTTTAATAT
1 TTAAATTTAAATAACAAAAATTATTTTTTAATAT
584399 TTAAATTTAA
1 TTAAATTTAA
584409 TTCGACTTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (34 bp):
TTAAATTTAAATAACAAAAATTATTTTTTAATAT
Found at i:589562 original size:18 final size:19
Alignment explanation
Indices: 589529--589564 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
589519 TTATTTTGTC
589529 AAATTTAGTAGTGAAATTA
1 AAATTTAGTAGTGAAATTA
*
589548 AAATTTA-TGGTGAAATT
1 AAATTTAGTAGTGAAATT
589565 TGTTTGGATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.39
Consensus pattern (19 bp):
AAATTTAGTAGTGAAATTA
Found at i:592069 original size:25 final size:25
Alignment explanation
Indices: 592035--592083 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
592025 TAGACAATCA
592035 AAGTTCCTCTAGTTGTTTATTATTT
1 AAGTTCCTCTAGTTGTTTATTATTT
592060 AAGTTCCTCTAGTTGTTTATTATT
1 AAGTTCCTCTAGTTGTTTATTATT
592084 CCTTTTTAGC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.20, C:0.12, G:0.12, T:0.55
Consensus pattern (25 bp):
AAGTTCCTCTAGTTGTTTATTATTT
Found at i:596036 original size:18 final size:18
Alignment explanation
Indices: 596013--596053 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
596003 AAGAAAGAGA
596013 AAGACGAGGATTTAGAAT
1 AAGACGAGGATTTAGAAT
596031 AAGACGAGGATTTAGAAT
1 AAGACGAGGATTTAGAAT
596049 AAGAC
1 AAGAC
596054 TCGCTGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.27, T:0.20
Consensus pattern (18 bp):
AAGACGAGGATTTAGAAT
Found at i:598359 original size:28 final size:29
Alignment explanation
Indices: 598321--598382 Score: 108
Period size: 28 Copynumber: 2.2 Consensus size: 29
598311 CGTATGTTGT
598321 AAATAAGTGTACATTTGGAATCTAAAATA
1 AAATAAGTGTACATTTGGAATCTAAAATA
*
598350 AAATAA-TGTACATTTGGAATGTAAAATA
1 AAATAAGTGTACATTTGGAATCTAAAATA
598378 AAATA
1 AAATA
598383 TACAATTTGA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
28 26 0.81
29 6 0.19
ACGTcount: A:0.52, C:0.05, G:0.13, T:0.31
Consensus pattern (29 bp):
AAATAAGTGTACATTTGGAATCTAAAATA
Found at i:605100 original size:19 final size:21
Alignment explanation
Indices: 605078--605119 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
605068 TATTTTGCAT
605078 AAATAATATT-A-TATATTTA
1 AAATAATATTGATTATATTTA
**
605097 AAATTTTATTGATTATATTTA
1 AAATAATATTGATTATATTTA
605118 AA
1 AA
605120 TATTTAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 8 0.42
20 1 0.05
21 10 0.53
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATAATATTGATTATATTTA
Found at i:605246 original size:24 final size:25
Alignment explanation
Indices: 605190--605246 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
605180 TAAAAATGTT
*
605190 TAAAAATTATTTTTTTTATATTTTA
1 TAAAAATTATTTTTTATATATTTTA
605215 TAATAAATTATTTTTTATAT-TTTTA
1 TAA-AAATTATTTTTTATATATTTTA
*
605240 TTAAAAT
1 TAAAAAT
605247 ATCGTAACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 4 0.14
25 10 0.34
26 15 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TAAAAATTATTTTTTATATATTTTA
Found at i:607587 original size:21 final size:21
Alignment explanation
Indices: 607561--607601 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
607551 ACAAAAAAAT
607561 TGCAAGAAAAAAATAACACAC
1 TGCAAGAAAAAAATAACACAC
*
607582 TGCAAGAAAAGAATAACACA
1 TGCAAGAAAAAAATAACACA
607602 GTGTTTGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.61, C:0.17, G:0.12, T:0.10
Consensus pattern (21 bp):
TGCAAGAAAAAAATAACACAC
Found at i:611626 original size:15 final size:16
Alignment explanation
Indices: 611602--611634 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
611592 TATTTTAAGT
611602 TTATAATA-TTTTATA
1 TTATAATATTTTTATA
*
611617 TTATATTATTTTTATA
1 TTATAATATTTTTATA
611633 TT
1 TT
611635 TTATGCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTATAATATTTTTATA
Done.