Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009624.1 Hibiscus syriacus cultivar Beakdansim tig00117016_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: 8249038
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 38
Found at i:624878 original size:22 final size:23
Alignment explanation
Indices: 624838--624881 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
624828 TGCAGACCTA
624838 AATTTGTTGTTTTAATTAAAATT
1 AATTTGTTGTTTTAATTAAAATT
* *
624861 AATTT-TTTTTTTATTTAAAAT
1 AATTTGTTGTTTTAATTAAAAT
624882 GGCAAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (23 bp):
AATTTGTTGTTTTAATTAAAATT
Found at i:625839 original size:47 final size:46
Alignment explanation
Indices: 625769--625889 Score: 179
Period size: 47 Copynumber: 2.6 Consensus size: 46
625759 GAATAAATGT
625769 ATGCGAACTAGAAATCATGCGGTTAGGTATATTTTCTCGAACAAAGC
1 ATGCGAACTAGAAATCATGCGGTTAGGTATATTTTCTCGAAC-AAGC
* * *
625816 ATGCGAACTAGAAATCATACGGTTATGTTTATTTTCTCGAACAAGC
1 ATGCGAACTAGAAATCATGCGGTTAGGTATATTTTCTCGAACAAGC
* * *
625862 ATGCGAATTAGATATCATGCGATTAGGT
1 ATGCGAACTAGAAATCATGCGGTTAGGT
625890 TTTCTTTTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
46 27 0.41
47 39 0.59
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (46 bp):
ATGCGAACTAGAAATCATGCGGTTAGGTATATTTTCTCGAACAAGC
Found at i:630528 original size:125 final size:125
Alignment explanation
Indices: 630302--630530 Score: 309
Period size: 125 Copynumber: 1.8 Consensus size: 125
630292 TAGGATATGT
* *
630302 TGGGGCACGACTGAACCCCTATCATGTTGAGATGACAAAACCCAGACCAAAGAGGCATGAAGAAC
1 TGGGGCACGACTGAACCCATATCATGTTGAGATGACAAAACCAAGACCAAAGAGGCATGAAGAAC
630367 GAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCCTGCACCAGTATGAGATGATGA
66 GAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCCTGCACCAGTATGAGATGATGA
* ** * **
630427 TGGGGTACGACTGAACCCATATCATGTTGAGATGATGAGATTAAGACC-AAGAAGGCATTG-AGA
1 TGGGGCACGACTGAACCCATATCATGTTGAGATGACAAAACCAAGACCAAAG-AGGCA-TGAAGA
* * * * *
630490 ATGAGCCTTACAATTTGAGGTGTTGGGGCATTTTGAAGGCC
64 ACGAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCC
630531 CATATCAGTA
Statistics
Matches: 89, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
124 3 0.03
125 84 0.94
126 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (125 bp):
TGGGGCACGACTGAACCCATATCATGTTGAGATGACAAAACCAAGACCAAAGAGGCATGAAGAAC
GAGCCTTACAAATAGAGGTGATGGGGCATTTCGAAGGCCTGCACCAGTATGAGATGATGA
Found at i:631770 original size:36 final size:36
Alignment explanation
Indices: 631728--631849 Score: 111
Period size: 36 Copynumber: 3.4 Consensus size: 36
631718 AGCAAAGTCA
631728 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
* * * * * *
631764 GTCTTAAGCATGCACCAAAGAATAATGAAGCAAACC
1 ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
** * * *
631800 ATCTTGTGTCTTCA-TCAAAGAGTCGTGAAGGAAATCC
1 ATCTTAAGCCTTCACT-AAAGAGTAGTGAAGCAAA-CC
*
631837 ATTTTAAGCCTTC
1 ATCTTAAGCCTTC
631850 TCATAAGAGT
Statistics
Matches: 63, Mismatches: 21, Indels: 3
0.72 0.24 0.03
Matches are distributed among these distances:
36 52 0.83
37 11 0.17
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (36 bp):
ATCTTAAGCCTTCACTAAAGAGTAGTGAAGCAAACC
Found at i:632361 original size:54 final size:54
Alignment explanation
Indices: 632219--632910 Score: 909
Period size: 54 Copynumber: 12.9 Consensus size: 54
632209 AGTGAAGCAA
* * *
632219 AAGAAGATTTTCGAGTTCCATACTCCCTAGAGAAAAAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * *
632273 AAG-A-TTGTTCGAGTTTCATACTCCCT-GAAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAG-AGAAAGAGGGAGCGAACCCGTTTG
* * ** * * *
632325 AAGAAGAGGTACGAGTTTTATACTCCTTAAAGAAAGAGGGAGCGAACCAGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * *
632379 AAGAAGATGTCCTAGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACTCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
632433 AAGAAAATATCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
632487 AAGAAGATGTACGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
*
632541 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
632595 AAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGAAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* *
632649 AAGAAGATTTCCGAGTTCCATACTTCCTAGAGAAAGAGGGAGCGAACCCG--TG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * * *
632701 TA-AAGATATCCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
**
632754 AAG-AGATGTTTGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
* * * *
632807 AAGAAGATTTTCGAGTTCCATACTTCCTAGAGAAAGAGGGAGTGAACCCCG--T-
1 AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAA-CCCGTTTG
* * * * *
632859 AAGAAGATTATTCGAGTTCTATACTGCCTGAAAGAAAGAGGGAGCGAACCCG
1 AAGAAGA-TGTCCGAGTTCCATACTCCCT-AGAGAAAGAGGGAGCGAACCCG
632911 ATTGTTGAAG
Statistics
Matches: 569, Mismatches: 58, Indels: 23
0.88 0.09 0.04
Matches are distributed among these distances:
51 43 0.08
52 55 0.10
53 75 0.13
54 392 0.69
55 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (54 bp):
AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTTG
Found at i:633030 original size:55 final size:55
Alignment explanation
Indices: 632861--633132 Score: 338
Period size: 55 Copynumber: 4.9 Consensus size: 55
632851 AACCCCGTAA
* * * *
632861 GAAGATTATTCGAGT-TCTATACTGC-CTGAAAGAAAGAGGGAGC-GAACCCGATTGTT
1 GAAGATTGTTCGAGTCT-TATACT-CTCTG-AAGAAATAGGGAGCAG-ACACGATCGTT
*
632917 GAAGATTGTTCGAGTCTTATACTCTCTCTGAAGAAATAGGGAGTAGACACGA-CTGTT
1 GAAGATTGTTCGAGTCTTATA--CTCTCTGAAGAAATAGGGAGCAGACACGATC-GTT
632974 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
* * *
633029 GAAGATTGTTCGAGTCTTATACTCTTTGAAGGAATAGGGAGCAGACACGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
* * *
633084 GAAGATTGTTTGAGTCTTATACTCTCTGAA-AGAATAGAGAGCGGACACG
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGA-AATAGGGAGCAGACACG
633133 TTTTCCGAAG
Statistics
Matches: 194, Mismatches: 14, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
55 126 0.65
56 19 0.10
57 43 0.22
58 6 0.03
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACGATCGTT
Found at i:635381 original size:21 final size:23
Alignment explanation
Indices: 635342--635384 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 23
635332 TGCAGACCTA
635342 AATTTGTTGTTTTAATTAAAATT
1 AATTTGTTGTTTTAATTAAAATT
*
635365 AATTT-TT-TTTTATTTAAAAT
1 AATTTGTTGTTTTAATTAAAAT
635385 GGCAAAACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 2 0.11
23 5 0.26
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (23 bp):
AATTTGTTGTTTTAATTAAAATT
Found at i:639697 original size:75 final size:77
Alignment explanation
Indices: 639521--639738 Score: 325
Period size: 75 Copynumber: 2.8 Consensus size: 77
639511 TAATTACAAA
*
639521 AAAATAATCGTGATTTATCTTTTATTTTTTTAATAATTTTTGTTTAAAATTTTTAAATTATTTTT
1 AAAATAATCGTGATTTATCTTTTA-TTTTTTAATAATTTTAGTTTAAAATTTTTAAATTATTTTT
*
639586 ATATTCTTGATTT
65 ATATTCTCGATTT
* * *
639599 -AAATAATCATGATTTTTTCTTTTATTTTTTAATAATTTCAGTTTAAAA-TTTTAAATT-TTTTT
1 AAAATAATCGTGA-TTTATCTTTTATTTTTTAATAATTTTAGTTTAAAATTTTTAAATTATTTTT
639661 ATATTCTCGATTT
65 ATATTCTCGATTT
* *
639674 AAAATAATTGTGATTTATCTTTTATTTTTTAATAATTTTGGTTTAAAATTTTTAAATTATATTTT
1 AAAATAATCGTGATTTATCTTTTATTTTTTAATAATTTTAGTTTAAAATTTTTAAATTAT-TTTT
639739 TTATAATCAA
Statistics
Matches: 125, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
75 49 0.39
76 28 0.22
77 34 0.27
78 14 0.11
ACGTcount: A:0.32, C:0.04, G:0.05, T:0.59
Consensus pattern (77 bp):
AAAATAATCGTGATTTATCTTTTATTTTTTAATAATTTTAGTTTAAAATTTTTAAATTATTTTTA
TATTCTCGATTT
Found at i:639987 original size:14 final size:14
Alignment explanation
Indices: 639970--639996 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
639960 AATATTTAAT
639970 TAAATAAATAAAAA
1 TAAATAAATAAAAA
639984 TAAATAAATAAAA
1 TAAATAAATAAAA
639997 TCCACCAATC
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:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAATAAATAAAAA
Found at i:639995 original size:22 final size:22
Alignment explanation
Indices: 639954--639995 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
639944 CTTCTGATTG
** *
639954 AATAAAAATATTTAATTAAATA
1 AATAAAAATAAATAAATAAATA
639976 AATAAAAATAAATAAATAAA
1 AATAAAAATAAATAAATAAA
639996 ATCCACCAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (22 bp):
AATAAAAATAAATAAATAAATA
Found at i:640057 original size:16 final size:16
Alignment explanation
Indices: 640014--640057 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
640004 ATCATATATT
*
640014 GACACGTGTCACTAAC
1 GACACGTGTCATTAAC
*
640030 GACAAGTGTCATTAAC
1 GACACGTGTCATTAAC
640046 GACACGTGTCAT
1 GACACGTGTCAT
640058 AATCTTATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (16 bp):
GACACGTGTCATTAAC
Found at i:643683 original size:14 final size:14
Alignment explanation
Indices: 643660--643694 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
643650 ACATTGATTA
*
643660 ATTTAATTCGAATT
1 ATTTATTTCGAATT
643674 ATTTATTTCGAATT
1 ATTTATTTCGAATT
643688 ATTTATT
1 ATTTATT
643695 AGGGAAAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (14 bp):
ATTTATTTCGAATT
Found at i:645317 original size:21 final size:21
Alignment explanation
Indices: 645283--645325 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
645273 CTCTTTTTTA
* *
645283 CTCTCCCTCGCTCTGATCTTC
1 CTCTCACTCGCTCTAATCTTC
*
645304 CTCTCACTCTCTCTAATCTTC
1 CTCTCACTCGCTCTAATCTTC
645325 C
1 C
645326 ACCTCCCCGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.47, G:0.05, T:0.40
Consensus pattern (21 bp):
CTCTCACTCGCTCTAATCTTC
Found at i:646506 original size:137 final size:138
Alignment explanation
Indices: 646109--646521 Score: 519
Period size: 138 Copynumber: 3.0 Consensus size: 138
646099 TAGGTAAATT
* * * * * *
646109 TGGAGATAGCATGGTTCCTACGCGATGAGGAAGTCTTGCTATCTAAGGTTGACGCGACTCCTACG
1 TGGAGATAACACGATTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACGCGACTCCTACG
* * *
646174 TGATGAGGAGATCTGGTCGGTGGATGACACAATTCCTATGTGAT-A-AAAATGTATGGCCATCTT
66 TGATGAGGAGATCTGGTCGGTGGATGACACAATTCCTACGTGATGAGAACATCT-TGGCCATCTT
646237 TAGGGATAAA
130 TAGGGAT-AA
* * * * * * * *
646247 TGGATATAACACGGTTCCTACGTGATGAGGAAGTCTGGCTATCTACGGGCGATGTGGCTCCTATG
1 TGGAGATAACACGATTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACGCGACTCCTACG
* * * **
646312 TGATAAGGAGATCTGGTCGATGGATGACACGATTCCTACGTGATGAGAACGGC-TGGCCATCTTT
66 TGATGAGGAGATCTGGTCGGTGGATGACACAATTCCTACGTGATGAGAACATCTTGGCCATCTTT
646376 AGGGATAA
131 AGGGATAA
* * * *
646384 TGGAGATAACACGATTTCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGGCGCAACTTCT-CG
1 TGGAGATAACACGATTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACGCGACTCCTACG
* * *
646448 TTATGAGGAGATCTGGTCGGTGGATGACACTATTCCTACGTGATGAGGACATCTTGGCCATCTTT
66 TGATGAGGAGATCTGGTCGGTGGATGACACAATTCCTACGTGATGAGAACATCTTGGCCATCTTT
646513 AGGGATAA
131 AGGGATAA
646521 T
1 T
646522 TTATTTCAAT
Statistics
Matches: 233, Mismatches: 39, Indels: 7
0.84 0.14 0.03
Matches are distributed among these distances:
136 47 0.20
137 73 0.31
138 110 0.47
139 1 0.00
140 2 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (138 bp):
TGGAGATAACACGATTCCTACGTGATGAGGAAGTCTGGCTATCTAAGGGTGACGCGACTCCTACG
TGATGAGGAGATCTGGTCGGTGGATGACACAATTCCTACGTGATGAGAACATCTTGGCCATCTTT
AGGGATAA
Found at i:647017 original size:37 final size:37
Alignment explanation
Indices: 646966--647118 Score: 193
Period size: 37 Copynumber: 4.1 Consensus size: 37
646956 CACCTCAATG
* *
646966 GAAAAATGTCTCAAGCGAGACGAAATTT-TTTTTAGA
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* *
647002 GAGATATTGTCTCAAGAGAGACAAAATTTGTTTTTAGA
1 GA-AAATTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
647040 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTA-A
1 GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
* * **
647076 GAAAAATTGTCTCTAGCGAGACAACACTTTGTTTCGAGA
1 G-AAAATTGTCTCAAGCGAGACAA-AATTTGTTTTTAGA
647115 GAAA
1 GAAA
647119 TAATCTCGAA
Statistics
Matches: 102, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
36 4 0.04
37 74 0.73
38 22 0.22
39 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.31
Consensus pattern (37 bp):
GAAAATTGTCTCAAGCGAGACAAAATTTGTTTTTAGA
Found at i:649545 original size:9 final size:8
Alignment explanation
Indices: 649530--649585 Score: 51
Period size: 8 Copynumber: 6.8 Consensus size: 8
649520 GTTTCTTGTC
649530 TTCTTTTT
1 TTCTTTTT
649538 TCTCTTTTT
1 T-TCTTTTT
649547 TTC-TTTT
1 TTCTTTTT
* *
649554 TGCTTATT
1 TTCTTTTT
649562 TTCTTTTT
1 TTCTTTTT
*
649570 GCTTCTTTAT
1 --TTCTTTTT
649580 TTCTTT
1 TTCTTT
649586 GCTTTTTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
7 6 0.15
8 18 0.46
9 8 0.21
10 7 0.18
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.77
Consensus pattern (8 bp):
TTCTTTTT
Found at i:649597 original size:32 final size:31
Alignment explanation
Indices: 649530--649594 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
649520 GTTTCTTGTC
* *
649530 TTCTTTTTTCTCTTTTTTTCTTTTTGCTTATT
1 TTCTTTTTGCTCTTTATTTC-TTTTGCTTATT
*
649562 TTCTTTTTGCTTCTTTATTTC-TTTGCTTTTT
1 TTCTTTTTGC-TCTTTATTTCTTTTGCTTATT
649593 TT
1 TT
649595 TCTCTTTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 11 0.38
32 9 0.31
33 9 0.31
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (31 bp):
TTCTTTTTGCTCTTTATTTCTTTTGCTTATT
Found at i:649600 original size:16 final size:16
Alignment explanation
Indices: 649542--649606 Score: 62
Period size: 15 Copynumber: 4.1 Consensus size: 16
649532 CTTTTTTCTC
*
649542 TTTTTTTCTTTTTGC-
1 TTTTTTTCTCTTTGCT
* *
649557 TTATTTTCTTTTTGCT
1 TTTTTTTCTCTTTGCT
*
649573 TCTTTATT-TCTTTGCT
1 T-TTTTTTCTCTTTGCT
*
649589 TTTTTTTCTCTTTACT
1 TTTTTTTCTCTTTGCT
649605 TT
1 TT
649607 GATTTGATAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
15 19 0.46
16 18 0.44
17 4 0.10
ACGTcount: A:0.05, C:0.15, G:0.05, T:0.75
Consensus pattern (16 bp):
TTTTTTTCTCTTTGCT
Found at i:652881 original size:2 final size:2
Alignment explanation
Indices: 652874--652898 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
652864 AAAACCATTA
652874 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
652899 CACGTAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:654201 original size:55 final size:56
Alignment explanation
Indices: 654142--655615 Score: 1198
Period size: 55 Copynumber: 26.8 Consensus size: 56
654132 AAAGCGTGTC
* * * * *
654142 CGCTCCCTATT-CTTTCAGAGAGTATAAG-ACTCGAAAAATATTCGGTAAACAGGTT
1 CGCTCCCTATTGC-TTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * * * * * *
654197 CGCTCCCT-TTTCTTTCAGGGAATAT-AGCACTTGAATAATCTTCGGAAAA-AGGGT
1 CGCTCCCTATTGC-TTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * * * * * * * *
654251 C-CACTACTTTTTCTTTCAAGGAATAT-AGGACTCGAATAATCTTC--AACAA-ACGTGT
1 CGCTC-CCTATTGC-TTCAGGGAGTATAAGAACTCGAACAATCTTCTGAA-AACAGGT-T
* *
654306 CTGCTCCCTATT-CTTTCAGGTAGTATAAG-ACTCGAACAATCTTC-AACAAAC-GTGTAT
1 C-GCTCCCTATTGC-TTCAGGGAGTATAAGAACTCGAACAATCTTCTGA-AAACAG-GT-T
* * * *
654363 -ACTCCCTATT-CTTTTAGGGAGTATAAG-ACTTGAACAATCTTCTGAAAATAGGTT
1 CGCTCCCTATTGC-TTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* *
654417 CGCTCCCTATT-CTTTCAGGGAGTAT-AGAATTCGAAAAATCTTCTGAAAAC-GAGTT
1 CGCTCCCTATTGC-TTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAG-GTT
** * *
654472 TTCTCCCTATTGCTTCAGGGAGTAT-AGAACTCGAACAATCTTCTAAAAACGGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * *
654527 CGCTCCCTATTGCTTCAGGGAGTAT-ATAACTTGAAAAATCTTCTGAAAACAGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
*
654582 CGCTCCATATTGCTTCAGGGAGTAT-AGAACTCGAACAATCTTCT-AAAA-ATGGATT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACA-GG-TT
* ** * * *
654637 CGCTCCTTATTGCTTCAATGAGTATAA-AACTCGATCAATCTTCT-ACCAACGGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGA-AAACAGGTT
* * **
654692 CGCTCCCTATTGCTTCAGGGAGTAT-AGAACTCAAACAATCTTCTAAAAATGGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* *
654747 CGCTCCCTATTACTTCAGGGAGTAT-AGAACTCGAACAATCTTCTGAAAACGGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * * * * * *
654802 TGCTCCTTATTGATTAAGGGAGTAT-ATAACTCGAATAATCTTCTGAAAACGGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * * **
654857 CGCTCCCTATTGCTTCAGGGAGTAT-AGAACTCGGACAATTTTCTGCAAATGGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* *
654912 CGCTCCCTATTGCTTCAGAGG-GTATAA-AACTCGAGA-AATCTTTTGAAAACGGGTT
1 CGCTCCCTATTGCTTCAG-GGAGTATAAGAACTCGA-ACAATCTTCTGAAAACAGGTT
* * * * *
654967 TGCTCCCTATTACTTCAGGGAGTAT-AGAATTCGAACAATCTTTTG-CAACAGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * ***
655021 CGCTCCCTATTGCTTCAGTGAGTAT-AGAACTCAAACAATCTTCTTCCAAC-GAGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAG-GTT
* * * ** *
655076 CGATCCCTATTGCTTTAGGGAGTAT-AGAACTCGAACAATCTTTTGCCAACGGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * * * * *
655131 CACTCGCTATTACTTCAGGGAGTAT-GGAACTCGAACAATCTTCTGCAAACGGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * * * ** *
655186 CGCTCCCTATTGCTTTAGGGAGTAT-AGAACTCAAATAATCTTCCGCCAACGGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * * *
655241 CTCTCCATATTGCTTTAGGGAGTAT-AGAACTCGAACAATCTTC-GACTAAC-GTGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGA-AAACAG-GTT
* * ** *
655296 CGCTCCCTGTTGCTTCAGGGAGTAT-AGAACTCGAACAATCTTTTGCCAACGGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * * * * * * **
655351 TGCTCCCTCTTGTTTTAGGGAGTATGA-AACTCGAATAATCTTTTGCTAACAGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * * * * *
655406 TGATCCCTATTGCTTCAAGGAGTAT-GGAACTCGAACAATCTTCT-ACAAACGGGTC
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGA-AAACAGGTT
* * * * * * *
655461 CACTCCCTATTGTTTC-GAGGAGTAT-GGAACTCGAATAATCTTTTGCAAACGGGTT
1 CGCTCCCTATTGCTTCAG-GGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * **
655516 CGCTCCCTATTGCTTCAGGGAGTAT-AGAACTCGAACAATCTTGTGGAAATGGGTT
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
* * *
655571 CGCTCCCTATTACTTCAGGGAGTAT-ATAACTTGAACAATCTTCTG
1 CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTG
655616 CAATGATTCT
Statistics
Matches: 1196, Mismatches: 177, Indels: 92
0.82 0.12 0.06
Matches are distributed among these distances:
53 5 0.00
54 78 0.07
55 1079 0.90
56 28 0.02
57 6 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (56 bp):
CGCTCCCTATTGCTTCAGGGAGTATAAGAACTCGAACAATCTTCTGAAAACAGGTT
Found at i:655618 original size:110 final size:110
Alignment explanation
Indices: 654142--655615 Score: 1472
Period size: 110 Copynumber: 13.4 Consensus size: 110
654132 AAAGCGTGTC
* * * * * *
654142 CGCTCCCTATT-CTTTCAGAGAGTATA-AGACTCGAAAAATATTCGGTAAACAGGTTCGCTCCCT
1 CGCTCCCTATTGC-TTCAGGGAGTATAGA-ACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCT
* * * * * * * * *
654205 -TTTCTTTCAGGGAATATAGCACTTGAATAATCTTCGGAAAAAGGGTC
64 ATTGC-TTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
* * * * * * * * * *
654252 CACT-ACTTTTTCTTTCAAGGAATATAGGACTCGAATAATCTTC-AACAAACGTG-TCTGCTCCC
1 CGCTCCCTATTGC-TTCAGGGAGTATAGAACTCGAACAATCTTCTGA-AAACGGGTTC-GCTCCC
* ** *
654314 TATT-CTTTCAGGTAGTATA-AGACTCGAACAATCTTCAACAAACGTGTAT
63 TATTGC-TTCAGGGAGTATAGA-ACTCGAACAATCTTCTGCAAACGGGT-T
* * * **
654363 -ACTCCCTATT-CTTTTAGGGAGTATA-AGACTTGAACAATCTTCTGAAAATAGGTTCGCTCCCT
1 CGCTCCCTATTGC-TTCAGGGAGTATAGA-ACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCT
* * * *
654425 ATT-CTTTCAGGGAGTATAGAATTCGAAAAATCTTCTGAAAACGAGTT
64 ATTGC-TTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
** *
654472 TTCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTAAAAACGGGTTCGCTCCCTAT
1 CGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTAT
* * * * *
654537 TGCTTCAGGGAGTATATAACTTGAAAAATCTTCTGAAAACAGGTT
66 TGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
* * * * *
654582 CGCTCCATATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTAAAAATGGATTCGCTCCTTAT
1 CGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTAT
** * * * *
654647 TGCTTCAATGAGTATAAAACTCGATCAATCTTCTACCAACGGGTT
66 TGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
* * *
654692 CGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAACAATCTTCTAAAAATGGGTTCGCTCCCTAT
1 CGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTAT
* *
654757 TACTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTT
66 TGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
* * * * * *
654802 TGCTCCTTATTGATTAAGGGAGTATATAACTCGAATAATCTTCTGAAAACGGGTTCGCTCCCTAT
1 CGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTAT
* * *
654867 TGCTTCAGGGAGTATAGAACTCGGACAATTTTCTGCAAATGGGTT
66 TGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
* * *
654912 CGCTCCCTATTGCTTCAGAGG-GTATAAAACTCGAGA-AATCTTTTGAAAACGGGTTTGCTCCCT
1 CGCTCCCTATTGCTTCAG-GGAGTATAGAACTCGA-ACAATCTTCTGAAAACGGGTTCGCTCCCT
* * * *
654975 ATTACTTCAGGGAGTATAGAATTCGAACAATCTTTTGC-AACAGGTT
64 ATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
* * *** * *
655021 CGCTCCCTATTGCTTCAGTGAGTATAGAACTCAAACAATCTTCTTCCAACGAGTTCGATCCCTAT
1 CGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTAT
* * *
655086 TGCTTTAGGGAGTATAGAACTCGAACAATCTTTTGCCAACGGGTT
66 TGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
* * * * *
655131 CACTCGCTATTACTTCAGGGAGTATGGAACTCGAACAATCTTCTGCAAACGGGTTCGCTCCCTAT
1 CGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTAT
* * * * *
655196 TGCTTTAGGGAGTATAGAACTCAAATAATCTTCCGCCAACGGGTT
66 TGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
* * * * * *
655241 CTCTCCATATTGCTTTAGGGAGTATAGAACTCGAACAATCTTC-GACTAACGTGTTCGCTCCCTG
1 CGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGA-AAACGGGTTCGCTCCCTA
* *
655305 TTGCTTCAGGGAGTATAGAACTCGAACAATCTTTTGCCAACGGGTT
65 TTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
* * * * * * ** * * *
655351 TGCTCCCTCTTGTTTTAGGGAGTAT-GAAACTCGAATAATCTTTTGCTAACAGGTTTGATCCCTA
1 CGCTCCCTATTGCTTCAGGGAGTATAG-AACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTA
* * * *
655415 TTGCTTCAAGGAGTATGGAACTCGAACAATCTTCTACAAACGGGTC
65 TTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
* * * * * *
655461 CACTCCCTATTGTTTC-GAGGAGTATGGAACTCGAATAATCTTTTGCAAACGGGTTCGCTCCCTA
1 CGCTCCCTATTGCTTCAG-GGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTA
* * *
655525 TTGCTTCAGGGAGTATAGAACTCGAACAATCTTGTGGAAATGGGTT
65 TTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
* * *
655571 CGCTCCCTATTACTTCAGGGAGTATATAACTTGAACAATCTTCTG
1 CGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTG
655616 CAATGATTCT
Statistics
Matches: 1142, Mismatches: 195, Indels: 54
0.82 0.14 0.04
Matches are distributed among these distances:
108 2 0.00
109 100 0.09
110 1021 0.89
111 19 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (110 bp):
CGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTCGCTCCCTAT
TGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCAAACGGGTT
Found at i:660656 original size:6 final size:6
Alignment explanation
Indices: 660645--660676 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
660635 AAATAAATAC
660645 ATGCAA ATGCAA ATGCTAA ATGCAA ATGCAA A
1 ATGCAA ATGCAA ATGC-AA ATGCAA ATGCAA A
660677 AGGTGTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (6 bp):
ATGCAA
Found at i:660667 original size:13 final size:12
Alignment explanation
Indices: 660645--660676 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
660635 AAATAAATAC
660645 ATGCAAATGCAA
1 ATGCAAATGCAA
660657 ATGCTAAATGCAA
1 ATGC-AAATGCAA
660670 ATGCAAA
1 ATGCAAA
660677 AGGTGTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.19
Consensus pattern (12 bp):
ATGCAAATGCAA
Found at i:664277 original size:26 final size:26
Alignment explanation
Indices: 664248--664297 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
664238 ATGATGAATG
664248 CTAATCCCTTTATTTTTTTTCTTCAC
1 CTAATCCCTTTATTTTTTTTCTTCAC
*
664274 CTAATCCCTTTGTTTTTTTTCTTC
1 CTAATCCCTTTATTTTTTTTCTTC
664298 TTTGCTTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.12, C:0.26, G:0.02, T:0.60
Consensus pattern (26 bp):
CTAATCCCTTTATTTTTTTTCTTCAC
Found at i:667641 original size:3 final size:3
Alignment explanation
Indices: 667623--667694 Score: 101
Period size: 3 Copynumber: 24.3 Consensus size: 3
667613 GCAAAAAATG
* * * *
667623 TAA TAA TAT TAA -AA TAA TAC TAA TAA TAA TAA TAA TAA GAA GAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
667670 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
667695 TTTAATTTGA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
2 2 0.03
3 60 0.97
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:668909 original size:94 final size:92
Alignment explanation
Indices: 668715--669021 Score: 404
Period size: 94 Copynumber: 3.4 Consensus size: 92
668705 TTCTTTAACC
** *
668715 GTTAATCGAACTGAAATTTATTTGAAAATTATTAACCGAACCAAATTAACCGATTTTTTCTTTAA
1 GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACTGATTTTTTCTTTAA
* *
668780 CATTAATTGAACCTAAATTATTTGACT
66 CATTAATCGAACCAAAATTATTTGACT
*
668807 GTTAATCGAACCAAAATTTATTTGAAACTTATTAACCGAACCAAATTAACTGAAATTTTTTCTTT
1 GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACTG--ATTTTTTCTTT
* *
668872 AACATTAATCCAACCGAAATTATTTGACT
64 AACATTAATCGAACCAAAATTATTTGACT
*
668901 GTTAATCGAACCAAAATTTATTTGAAAATTTTTAACCG------A-T---T--TTTTTTCTTTAA
1 GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACTGATTTTTTCTTTAA
668954 CCATTAATCGAACCAAAATTATTTGACT
66 -CATTAATCGAACCAAAATTATTTGACT
* *
668982 GTTAATCGAACCCAAATTTATTTGAAAATTATTAGCCGAA
1 GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAA
669022 TTAACTGAAT
Statistics
Matches: 196, Mismatches: 14, Indels: 19
0.86 0.06 0.08
Matches are distributed among these distances:
80 12 0.06
81 60 0.31
84 1 0.01
87 1 0.01
88 1 0.01
92 48 0.24
94 73 0.37
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (92 bp):
GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATTAACTGATTTTTTCTTTAA
CATTAATCGAACCAAAATTATTTGACT
Found at i:668980 original size:81 final size:80
Alignment explanation
Indices: 668862--669188 Score: 270
Period size: 81 Copynumber: 4.0 Consensus size: 80
668852 TTAACTGAAA
*
668862 TTTTTTCTTTAACATTAATCCAACCGAAATTATTTGACTGTTAATCGAACCAAAATTTATTTGAA
1 TTTTTTCTTTAACATTAATCCAACCAAAATTATTTGACTGTTAATCGAACCAAAATTTATTTGAA
*
668927 AATTTTTAACCGATT
66 AATTATTAACCGATT
* *
668942 TTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACTGTTAATCGAACCCAAATTTATTTGA
1 TTTTTTCTTTAA-CATTAATCCAACCAAAATTATTTGACTGTTAATCGAACCAAAATTTATTTGA
*
669007 AAATTATTAGCCGA--
65 AAATTATTAACCGATT
* ** * * * * ** *** * * *
669021 -ATTAAC-TGAATA-AAAT-AAATTATTTTTCTTTAACCGTTAATCGAACCAAAATTTATTTGAA
1 TTTTTTCTTTAACATTAATCCAACCAAAATTATTTGACTGTTAATCGAACCAAAATTTATTTGAA
669082 AATTATTAACCGAACCAAATCAACCGT
66 AATTATTAACCG------AT------T
* * *
669109 TTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTGACTGTTAATCGAATCAAAATTTATTTG
1 TTTTTT-CTTTAA-CATTAATCCAACCAAAATTATTTGACTGTTAATCGAACCAAAATTTATTTG
669174 AAAATTATTAACCGA
64 AAAATTATTAACCGA
669189 ATAAAATAAA
Statistics
Matches: 187, Mismatches: 39, Indels: 34
0.72 0.15 0.13
Matches are distributed among these distances:
74 46 0.25
75 3 0.02
76 1 0.01
77 3 0.02
78 3 0.02
80 13 0.07
81 61 0.33
88 1 0.01
89 2 0.01
90 1 0.01
91 3 0.02
92 1 0.01
93 3 0.02
94 46 0.25
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.39
Consensus pattern (80 bp):
TTTTTTCTTTAACATTAATCCAACCAAAATTATTTGACTGTTAATCGAACCAAAATTTATTTGAA
AATTATTAACCGATT
Found at i:669173 original size:94 final size:93
Alignment explanation
Indices: 669056--669240 Score: 275
Period size: 94 Copynumber: 2.0 Consensus size: 93
669046 TTCTTTAACC
* * *
669056 GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACCAAATCAACCGTT-TTTTTTCTTT
1 GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACAAAAT-AA--ATTATTTTTTCCTT
669120 AACCATTAATCGAACCGAAA-TTATTTGACT
63 AACCATTAATCGAACCGAAATTTATTTGACT
* *
669150 GTTAATCGAATCAAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCCTTAAC
1 GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACAAAATAAATTATTTTTTCCTTAAC
*
669215 CGTTAATCGAACCGAAATTTATTTGA
66 CATTAATCGAACCGAAATTTATTTGA
669241 AAATTATTAA
Statistics
Matches: 83, Mismatches: 6, Indels: 5
0.88 0.06 0.05
Matches are distributed among these distances:
91 2 0.02
92 28 0.34
93 10 0.12
94 43 0.52
ACGTcount: A:0.39, C:0.15, G:0.09, T:0.37
Consensus pattern (93 bp):
GTTAATCGAACCAAAATTTATTTGAAAATTATTAACCGAACAAAATAAATTATTTTTTCCTTAAC
CATTAATCGAACCGAAATTTATTTGACT
Found at i:669297 original size:69 final size:66
Alignment explanation
Indices: 669163--669308 Score: 179
Period size: 66 Copynumber: 2.2 Consensus size: 66
669153 AATCGAATCA
* * * *
669163 AAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTCCTTAACCGTTAATCGAACC
1 AAATTTATTTGAAAATTATTAACCAAATAAAATAAAATATTTTTTCCTTAACCATTAATAGAACC
669228 G
66 G
* * *
669229 AAATTTATTTGAAAATTATTAACCAAATCGAATTAACCGAAT-TTTTTTCTTTAACCATTAATAG
1 AAATTTATTTGAAAATTATTAACCAAAT-AAAATAA---AATATTTTTTCCTTAACCATTAATAG
669293 AACCG
62 AACCG
669298 AAA-TTATTTGA
1 AAATTTATTTGA
669309 CAGTTAATTG
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
66 27 0.39
67 5 0.07
68 8 0.12
69 27 0.39
70 2 0.03
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (66 bp):
AAATTTATTTGAAAATTATTAACCAAATAAAATAAAATATTTTTTCCTTAACCATTAATAGAACC
G
Found at i:675208 original size:38 final size:39
Alignment explanation
Indices: 675145--675235 Score: 105
Period size: 38 Copynumber: 2.3 Consensus size: 39
675135 TTGGACAATG
*
675145 AAAATATATGAGAAAGTTCTGAAATATATTC-AAAAGAAA
1 AAAAAATATGA-AAAGTTCTGAAATATATTCTAAAAGAAA
* * *
675184 AATAAAATATGAAAA-TTCTTAAATATATTCTAAATGGAA
1 AA-AAAATATGAAAAGTTCTGAAATATATTCTAAAAGAAA
*
675223 AAAGAATATGAAA
1 AAAAAATATGAAA
675236 TGATTATTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
38 24 0.53
39 13 0.29
40 8 0.18
ACGTcount: A:0.57, C:0.04, G:0.11, T:0.27
Consensus pattern (39 bp):
AAAAAATATGAAAAGTTCTGAAATATATTCTAAAAGAAA
Found at i:676792 original size:44 final size:44
Alignment explanation
Indices: 676742--676878 Score: 202
Period size: 44 Copynumber: 3.0 Consensus size: 44
676732 CCTTGTTACA
*
676742 AGAAAAAAAGGGTAAACCACGCCAGTGATTACTAATGTAACATT
1 AGAAAAAAAGGGTAAACTACGCCAGTGATTACTAATGTAACATT
* * *
676786 AGAAAAAAAGGGTAAACTACGCTAGTAATCACTAATGTAACATT
1 AGAAAAAAAGGGTAAACTACGCCAGTGATTACTAATGTAACATT
*
676830 AAAAAAAAGAGAAGGTAAACTACGCCAGTGATTACTAATGTAACATT
1 AGAAAAAA-AG--GGTAAACTACGCCAGTGATTACTAATGTAACATT
676877 AG
1 AG
676879 TGTTTACCGC
Statistics
Matches: 81, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
44 47 0.58
45 2 0.02
47 32 0.40
ACGTcount: A:0.47, C:0.14, G:0.18, T:0.21
Consensus pattern (44 bp):
AGAAAAAAAGGGTAAACTACGCCAGTGATTACTAATGTAACATT
Found at i:677923 original size:2 final size:2
Alignment explanation
Indices: 677918--677950 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
677908 ACACACACAC
677918 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
677951 CAAACCTTTC
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:684917 original size:37 final size:37
Alignment explanation
Indices: 684875--684951 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
684865 TTACATATTT
684875 ATATGA-ATAC-AAGAAAATGTGACATGACATATATGTG
1 ATATGAGATACTAAGAAAATGTGACATG--ATATATGTG
* * *
684912 ATATGAGATTCTAAGAGAATGTTACATGATATATGTG
1 ATATGAGATACTAAGAAAATGTGACATGATATATGTG
684949 ATA
1 ATA
684952 CAAAAGTATG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 18 0.51
38 3 0.09
39 14 0.40
ACGTcount: A:0.43, C:0.06, G:0.19, T:0.31
Consensus pattern (37 bp):
ATATGAGATACTAAGAAAATGTGACATGATATATGTG
Found at i:686820 original size:54 final size:53
Alignment explanation
Indices: 686704--686825 Score: 145
Period size: 54 Copynumber: 2.3 Consensus size: 53
686694 TACCACCCCC
* * * *
686704 TTCAAGGGTATCGATACCTCCACATGTACCGATACCAAAATTACATTCGATGT
1 TTCAAGGGTATCGATACCTCCACAGGTACCAATACCAAAATTAAATCCGATGT
* * * *
686757 TTCAAGGGTATCGATACCTCCTCAAGGTACTAATATCGAAATTAAATCCGATGT
1 TTCAAGGGTATCGATACCTCCAC-AGGTACCAATACCAAAATTAAATCCGATGT
* *
686811 TTTAAGGGTAACGAT
1 TTCAAGGGTATCGAT
686826 GCCATCCTTC
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
53 22 0.38
54 36 0.62
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (53 bp):
TTCAAGGGTATCGATACCTCCACAGGTACCAATACCAAAATTAAATCCGATGT
Found at i:691078 original size:23 final size:23
Alignment explanation
Indices: 691052--691096 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
691042 CACCACAGTT
*
691052 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
691075 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
691097 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:692722 original size:21 final size:21
Alignment explanation
Indices: 692692--692736 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
692682 TTTTGTTCGT
692692 TTGAAGGGGTA-TCGATTCCCC
1 TTGAAGGGGTACT-GATTCCCC
*
692713 TTGAATGGGTACTGATTCCCC
1 TTGAAGGGGTACTGATTCCCC
692734 TTG
1 TTG
692737 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 21 0.95
22 1 0.05
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACTGATTCCCC
Found at i:696048 original size:23 final size:23
Alignment explanation
Indices: 696022--696066 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
696012 CACCACAGCT
*
696022 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
696045 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
696067 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:697685 original size:21 final size:21
Alignment explanation
Indices: 697661--697705 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
697651 TTTTGTTCGT
* *
697661 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
697682 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
697703 TTG
1 TTG
697706 CCCAAAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:701498 original size:20 final size:23
Alignment explanation
Indices: 701475--701530 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 23
701465 TATACTTAGA
*
701475 GGTATCGATAGCA-C-CTT-AAG
1 GGTATCGATACCACCTCTTCAAG
701495 GGTATCGATACCACCCTCTTCAAG
1 GGTATCGATACCA-CCTCTTCAAG
701519 GGTATCGATACC
1 GGTATCGATACC
701531 TCCACATGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 12 0.39
22 1 0.03
23 3 0.10
24 15 0.48
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (23 bp):
GGTATCGATACCACCTCTTCAAG
Found at i:701760 original size:22 final size:22
Alignment explanation
Indices: 701732--701787 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
701722 CAACCCATGA
*
701732 GGTATCGATACTTGTTCATAAG
1 GGTATCGATACCTGTTCATAAG
*
701754 GGTATCGGTACCTGTTCATAAG
1 GGTATCGATACCTGTTCATAAG
701776 GGTATCGATACC
1 GGTATCGATACC
701788 CTAAGCCCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (22 bp):
GGTATCGATACCTGTTCATAAG
Found at i:705879 original size:2 final size:2
Alignment explanation
Indices: 705874--705935 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
705864 AAATAGTAGT
705874 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
705916 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
705936 ATTAGCATCT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:710370 original size:258 final size:258
Alignment explanation
Indices: 709913--710430 Score: 982
Period size: 258 Copynumber: 2.0 Consensus size: 258
709903 AAATAGTGTG
*
709913 AGAAATAAGATATTGGTCAGCAAGTAGAGAAGATTGAAAAACTCGGACAAAATCATTTAATTAGT
1 AGAAATAAGATATTGATCAGCAAGTAGAGAAGATTGAAAAACTCGGACAAAATCATTTAATTAGT
*
709978 TGGGTGGCTTGATAGTCCTAGTGGACCTTCTAACAAGATTAGATTCAACAAGCTGGATGGTAATA
66 TGGGTGACTTGATAGTCCTAGTGGACCTTCTAACAAGATTAGATTCAACAAGCTGGATGGTAATA
* *
710043 GGTGCAGGACAGAATGGCTTGATAGTCGTTGTATGAGAATGAGTAAGAGTGGGTTCAGCAGAACT
131 GGTGCAGGACAGAATGGCTTGATAGTCGTAGTATGAGAATGAGTAAGAGAGGGTTCAGCAGAACT
710108 GACAATAGGTGATTCTGTTGAGGCACTAGATTGCAATAAAGGCGAAACAAATGACTACTCCAT
196 GACAATAGGTGATTCTGTTGAGGCACTAGATTGCAATAAAGGCGAAACAAATGACTACTCCAT
710171 AGAAATAAGATATTGATCAGCAAGTAGAGAAGATTGAAAAACTCGGACAAAATCATTTAATTAGT
1 AGAAATAAGATATTGATCAGCAAGTAGAGAAGATTGAAAAACTCGGACAAAATCATTTAATTAGT
710236 TGGGTGACTTGATAGTCCTAGTGGACCTTCTAACAAGATTAGATTCAACAAGCTGGATGGTAATA
66 TGGGTGACTTGATAGTCCTAGTGGACCTTCTAACAAGATTAGATTCAACAAGCTGGATGGTAATA
*
710301 GGTGCAGGACAGAATGGCTTGATAGTCGTAGTATGAGAATGATTAAGAGAGGGTTCAGCAGAACT
131 GGTGCAGGACAGAATGGCTTGATAGTCGTAGTATGAGAATGAGTAAGAGAGGGTTCAGCAGAACT
*
710366 GACAATAGGTGATTCTGTTGAGGCACTAGATTGCAATAAAGGCGAAACAAATGACTACTCTAT
196 GACAATAGGTGATTCTGTTGAGGCACTAGATTGCAATAAAGGCGAAACAAATGACTACTCCAT
710429 AG
1 AG
710431 GAATTGAAGT
Statistics
Matches: 254, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
258 254 1.00
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.25
Consensus pattern (258 bp):
AGAAATAAGATATTGATCAGCAAGTAGAGAAGATTGAAAAACTCGGACAAAATCATTTAATTAGT
TGGGTGACTTGATAGTCCTAGTGGACCTTCTAACAAGATTAGATTCAACAAGCTGGATGGTAATA
GGTGCAGGACAGAATGGCTTGATAGTCGTAGTATGAGAATGAGTAAGAGAGGGTTCAGCAGAACT
GACAATAGGTGATTCTGTTGAGGCACTAGATTGCAATAAAGGCGAAACAAATGACTACTCCAT
Found at i:721082 original size:17 final size:17
Alignment explanation
Indices: 721054--721136 Score: 112
Period size: 17 Copynumber: 4.7 Consensus size: 17
721044 TATTTTGAAA
721054 CATCGAATGCACTTGATG
1 CATCG-ATGCACTTGATG
721072 CATCGATGCACTTGATG
1 CATCGATGCACTTGATG
*
721089 CATCGATGTACTTGATG
1 CATCGATGCACTTGATG
*
721106 CATCGATGCACTCTTAGTG
1 CATCGATGCACT-TGA-TG
*
721125 CACCGATGCACT
1 CATCGATGCACT
721137 AAGGATCCAA
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
17 39 0.66
18 7 0.12
19 13 0.22
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (17 bp):
CATCGATGCACTTGATG
Found at i:721204 original size:21 final size:21
Alignment explanation
Indices: 721174--721229 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
721164 TTTTACACTG
*
721174 ATGCACCGATGCACCATGGGT
1 ATGCATCGATGCACCATGGGT
721195 ATGCATCGATGCACCATGGGT
1 ATGCATCGATGCACCATGGGT
721216 ATGCATCGATGCAC
1 ATGCATCGATGCAC
721230 TGACGCTCCC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.27, G:0.27, T:0.21
Consensus pattern (21 bp):
ATGCATCGATGCACCATGGGT
Found at i:721947 original size:20 final size:20
Alignment explanation
Indices: 721905--721949 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
721895 AGTCAGTCAA
**
721905 TATCGATACCAAGAGGTGGG
1 TATCGATACCAAGAGGTAAG
721925 TATCGATACTCAAG-GGTAAG
1 TATCGATAC-CAAGAGGTAAG
721945 TATCG
1 TATCG
721950 GTATTGAAGG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (20 bp):
TATCGATACCAAGAGGTAAG
Found at i:734344 original size:22 final size:23
Alignment explanation
Indices: 734319--734370 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 23
734309 TACCAAGAGG
734319 AAGGT-ATCTGACTTTGTCATTC
1 AAGGTCATCTGACTTTGTCATTC
734341 AAGGAGTGCATCTGACTTTGTCATTC
1 AA-G-GT-CATCTGACTTTGTCATTC
734367 AAGG
1 AAGG
734371 ATCGCCTCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
22 2 0.08
23 1 0.04
24 3 0.12
25 1 0.04
26 19 0.73
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (23 bp):
AAGGTCATCTGACTTTGTCATTC
Found at i:736497 original size:144 final size:143
Alignment explanation
Indices: 736235--736524 Score: 352
Period size: 144 Copynumber: 2.0 Consensus size: 143
736225 ATATATTTCG
* * * *
736235 AGGGTAGTTGGGAGGACAACCTACCACTAGTTAAATTTGCGTACAATAACTATTTTCAGTCGAGC
1 AGGGTAGTTGGGAGGACAACCTACAACTAGTGAAATTTACG-ACAACAACTATTTTCAGTCGAGC
* * * *
736300 ATCTAGATGGATCCGTCTTAGGCACTGCATGGGCATAAGTGTAGAACTCTACTATGTTGGATAAA
65 ATCCAGATGGATCCGTCTGAGGCACTGCATGAGCATAAGTGTAGAACTCTACTATGTTGGACAAA
736365 GCTTAGTGAAGGTA
130 GCTTAGTGAAGGTA
*
736379 AGGGTAGTTGGGAGGACCACCTACAACTAGTGAAATTCATAC-ACAACAAC-AGTTTTCAGTCGA
1 AGGGTAGTTGGGAGGACAACCTACAACTAGTGAAATT--TACGACAACAACTA-TTTTCAGTCGA
** * * ** *
736442 GCATCCAGATGTCTTCGTAC-GAGGCATTTTATGAGCATAAGTGTAGAACTTTACTATGTTGGAC
63 GCATCCAGATGGATCCGT-CTGAGGCACTGCATGAGCATAAGTGTAGAACTCTACTATGTTGGAC
* *
736506 ATAGCTTAGTGAAGTTA
127 AAAGCTTAGTGAAGGTA
736523 AG
1 AG
736525 ATAGTAAGGT
Statistics
Matches: 124, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
143 1 0.01
144 120 0.97
145 1 0.01
146 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (143 bp):
AGGGTAGTTGGGAGGACAACCTACAACTAGTGAAATTTACGACAACAACTATTTTCAGTCGAGCA
TCCAGATGGATCCGTCTGAGGCACTGCATGAGCATAAGTGTAGAACTCTACTATGTTGGACAAAG
CTTAGTGAAGGTA
Found at i:738725 original size:144 final size:144
Alignment explanation
Indices: 738465--738754 Score: 350
Period size: 144 Copynumber: 2.0 Consensus size: 144
738455 ATATATTTCG
* * ** * *
738465 AGGGTAGTTGGGAGAACAACCTACCACTAGTTGAATTTGCGTACAACAACTATTTTCAGTCGAGC
1 AGGGTAGTTGGGAGAACAACCTACAACTAGTGGAATTCACATACAACAACTACTTTCAGTCGAGC
* * * * *
738530 ATCCAGATGGATCCGTGTTAGGCACTGCTTGGGCATAAGTGTAGTACTCTACTATGTTGGATAAA
66 ATCCAGATGGATCCGTATGAGGCACTGCTTGAGCATAAGTGTAGAACTCTACTATGTTGGACAAA
*
738595 TCTTAGTGAAGGTA
131 GCTTAGTGAAGGTA
* * *
738609 AGGGTAGTTGGGAGGACCACCTACAACTAGTGGAATTCATATACAACAAC-AGCTTTCAGTCGAG
1 AGGGTAGTTGGGAGAACAACCTACAACTAGTGGAATTCACATACAACAACTA-CTTTCAGTCGAG
* * * **
738673 CATCTAGATGGCTTCGTATGAGGCA-TTTTATGAGCATAAGTGTAGAACTCTACTATGTTGGACA
65 CATCCAGATGGATCCGTATGAGGCACTGCT-TGAGCATAAGTGTAGAACTCTACTATGTTGGACA
* *
738737 TAGCTTAGTGAAGTTA
129 AAGCTTAGTGAAGGTA
738753 AG
1 AG
738755 ATAGTGAGAT
Statistics
Matches: 122, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
143 3 0.02
144 119 0.98
ACGTcount: A:0.30, C:0.17, G:0.25, T:0.29
Consensus pattern (144 bp):
AGGGTAGTTGGGAGAACAACCTACAACTAGTGGAATTCACATACAACAACTACTTTCAGTCGAGC
ATCCAGATGGATCCGTATGAGGCACTGCTTGAGCATAAGTGTAGAACTCTACTATGTTGGACAAA
GCTTAGTGAAGGTA
Found at i:745194 original size:18 final size:19
Alignment explanation
Indices: 745171--745208 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
745161 TATTTAAGTG
*
745171 ATAAAAGCGA-TTAAATAA
1 ATAAAAGCAATTTAAATAA
745189 ATAAAAGCAATTTAAATAA
1 ATAAAAGCAATTTAAATAA
745208 A
1 A
745209 AATAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (19 bp):
ATAAAAGCAATTTAAATAA
Found at i:750523 original size:10 final size:10
Alignment explanation
Indices: 750508--750664 Score: 53
Period size: 10 Copynumber: 14.1 Consensus size: 10
750498 CATTTAAATG
750508 ATAAACGAAC
1 ATAAACGAAC
750518 ATAAACGAAC
1 ATAAACGAAC
* **
750528 ACAAATAAAC
1 ATAAACGAAC
750538 ATAATAAACGAAC
1 ---ATAAACGAAC
* *
750551 AAAAAAGAAC
1 ATAAACGAAC
750561 ATAAAACGAAC
1 AT-AAACGAAC
* **
750572 ACAAATAAAC
1 ATAAACGAAC
750582 ATAATAAACGAAC
1 ---ATAAACGAAC
* *
750595 AAAAATGAAC
1 ATAAACGAAC
*
750605 ATAATAAATGAAC
1 ---ATAAACGAAC
*
750618 ATAAACGGACAAA
1 ATAAAC-G--AAC
*
750631 ATAAATGAAC
1 ATAAACGAAC
750641 ATAAACGGACAC
1 ATAAAC-GA-AC
750653 AATAAACGAAC
1 -ATAAACGAAC
750664 A
1 A
750665 ACACACACAA
Statistics
Matches: 107, Mismatches: 24, Indels: 32
0.66 0.15 0.20
Matches are distributed among these distances:
10 53 0.50
11 13 0.12
12 5 0.05
13 36 0.34
ACGTcount: A:0.64, C:0.16, G:0.09, T:0.11
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:750547 original size:23 final size:23
Alignment explanation
Indices: 750518--750618 Score: 136
Period size: 23 Copynumber: 4.5 Consensus size: 23
750508 ATAAACGAAC
750518 ATAAACGAACACAAATAAACATA
1 ATAAACGAACACAAATAAACATA
*
750541 ATAAACGAACA-AAAAAGAACAT-
1 ATAAACGAACACAAATA-AACATA
750563 A-AAACGAACACAAATAAACATA
1 ATAAACGAACACAAATAAACATA
* *
750585 ATAAACGAACAAAAATGAACATA
1 ATAAACGAACACAAATAAACATA
*
750608 ATAAATGAACA
1 ATAAACGAACA
750619 TAAACGGACA
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
21 14 0.20
22 10 0.14
23 45 0.65
ACGTcount: A:0.66, C:0.15, G:0.07, T:0.12
Consensus pattern (23 bp):
ATAAACGAACACAAATAAACATA
Found at i:750576 original size:44 final size:44
Alignment explanation
Indices: 750514--750608 Score: 174
Period size: 44 Copynumber: 2.2 Consensus size: 44
750504 AATGATAAAC
750514 GAACAT-AAACGAACACAAATAAACATAATAAACGAACAAAAAA
1 GAACATAAAACGAACACAAATAAACATAATAAACGAACAAAAAA
*
750557 GAACATAAAACGAACACAAATAAACATAATAAACGAACAAAAAT
1 GAACATAAAACGAACACAAATAAACATAATAAACGAACAAAAAA
750601 GAACATAA
1 GAACATAA
750609 TAAATGAACA
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
43 6 0.12
44 44 0.88
ACGTcount: A:0.66, C:0.16, G:0.07, T:0.11
Consensus pattern (44 bp):
GAACATAAAACGAACACAAATAAACATAATAAACGAACAAAAAA
Found at i:750613 original size:13 final size:13
Alignment explanation
Indices: 750574--750621 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
750564 AAACGAACAC
*
750574 AAATAAACATAAT
1 AAATGAACATAAT
*
750587 AAACGAAC--AA-
1 AAATGAACATAAT
750597 AAATGAACATAAT
1 AAATGAACATAAT
750610 AAATGAACATAA
1 AAATGAACATAA
750622 ACGGACAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
10 7 0.24
11 2 0.07
12 2 0.07
13 18 0.62
ACGTcount: A:0.67, C:0.10, G:0.06, T:0.17
Consensus pattern (13 bp):
AAATGAACATAAT
Found at i:750633 original size:23 final size:23
Alignment explanation
Indices: 750584--750664 Score: 99
Period size: 23 Copynumber: 3.5 Consensus size: 23
750574 AAATAAACAT
* * * *
750584 AATAAACGAACAAAAATGAACAT
1 AATAAACGAACATAAACGGACAA
*
750607 AATAAATGAACATAAACGGACAA
1 AATAAACGAACATAAACGGACAA
* *
750630 AATAAATGAACATAAACGGACAC
1 AATAAACGAACATAAACGGACAA
750653 AATAAACGAACA
1 AATAAACGAACA
750665 ACACACACAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.62, C:0.15, G:0.11, T:0.12
Consensus pattern (23 bp):
AATAAACGAACATAAACGGACAA
Found at i:750641 original size:46 final size:46
Alignment explanation
Indices: 750518--750664 Score: 154
Period size: 46 Copynumber: 3.2 Consensus size: 46
750508 ATAAACGAAC
* *
750518 ATAAACGAACACAAATAAACATAATAAACGAACAAAAAAGAACAT-
1 ATAAACGAACACAAACAAACAAAATAAACGAACAAAAAAGAACATA
* * *
750563 A-AAACGAACACAAATAAACATAATAAACGAACAAAAATGAACATA
1 ATAAACGAACACAAACAAACAAAATAAACGAACAAAAAAGAACATA
* * ** * * * * *
750608 ATAAATGAACATAAACGGACAAAATAAATGAACATAAACGGACACA
1 ATAAACGAACACAAACAAACAAAATAAACGAACAAAAAAGAACATA
750654 ATAAACGAACA
1 ATAAACGAACA
750665 ACACACACAA
Statistics
Matches: 87, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
44 42 0.48
45 2 0.02
46 43 0.49
ACGTcount: A:0.64, C:0.16, G:0.09, T:0.12
Consensus pattern (46 bp):
ATAAACGAACACAAACAAACAAAATAAACGAACAAAAAAGAACATA
Found at i:753919 original size:44 final size:45
Alignment explanation
Indices: 753837--753923 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 45
753827 TCATACTTAT
* *
753837 AATGCACCATTATGCATTTTCATTTATGTCATTCTTTCATGCCAA
1 AATGCACCATTATGCATTTTCATTGATGGCATTCTTTCATGCCAA
* *
753882 AATGTACCCTTATGCA-TTTCATTGATGGC-TTCTTTTCATGCC
1 AATGCACCATTATGCATTTTCATTGATGGCATTC-TTTCATGCC
753924 TTTTATACAC
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
43 3 0.08
44 20 0.54
45 14 0.38
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (45 bp):
AATGCACCATTATGCATTTTCATTGATGGCATTCTTTCATGCCAA
Found at i:753949 original size:45 final size:45
Alignment explanation
Indices: 753891--754019 Score: 186
Period size: 45 Copynumber: 2.9 Consensus size: 45
753881 AAATGTACCC
* * * *
753891 TTATGCATTTCATTGATGGCTTCTTTTCATGCCTTTTATACACTA
1 TTATACATTTCATTTATGACATCTTTTCATGCCTTTTATACACTA
* *
753936 TTATACATTTCATTTATGACATCCTTTCATGCTTTTTATACACTA
1 TTATACATTTCATTTATGACATCTTTTCATGCCTTTTATACACTA
* *
753981 TTATACATTACATTTATGACATCTTTTCATGACTTTTAT
1 TTATACATTTCATTTATGACATCTTTTCATGCCTTTTAT
754020 GTACTATTTA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 74 1.00
ACGTcount: A:0.25, C:0.19, G:0.07, T:0.50
Consensus pattern (45 bp):
TTATACATTTCATTTATGACATCTTTTCATGCCTTTTATACACTA
Found at i:754019 original size:22 final size:22
Alignment explanation
Indices: 753948--754020 Score: 62
Period size: 22 Copynumber: 3.3 Consensus size: 22
753938 ATACATTTCA
*
753948 TTTATGACATCCTTTCATG-CTT
1 TTTATGACATCTTTTCATGAC-T
* *
753970 TTTAT-ACA-CTATTATACATTACA
1 TTTATGACATCT-TT-T-CATGACT
753993 TTTATGACATCTTTTCATGACT
1 TTTATGACATCTTTTCATGACT
754015 TTTATG
1 TTTATG
754021 TACTATTTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
20 1 0.03
21 5 0.12
22 17 0.43
23 9 0.22
24 6 0.15
25 2 0.05
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (22 bp):
TTTATGACATCTTTTCATGACT
Found at i:754214 original size:81 final size:81
Alignment explanation
Indices: 754122--754656 Score: 734
Period size: 81 Copynumber: 6.6 Consensus size: 81
754112 CAAAGACGTA
* * * * * *
754122 TAACCTTTCATCTAACTTGCATGATTGACACTTTTTTGCCAAATGCATA-ATAAGGCCATTTATC
1 TAACCATTCATCTAACTGGCATAATTGACACCTTTTTGCCAAATGCACAGCT-AGGCCATTTATC
*
754186 CTTTACTCAACGGTCTT
65 TTTTACTCAACGGTCTT
* * *
754203 TAACCATTCATCTAACTGGCACAATTGACACCTTTTTGCCAAATGCATAGTTAGGCCATTTATCT
1 TAACCATTCATCTAACTGGCATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCATTTATCT
754268 TTTACTCAACGGTCTT
66 TTTACTCAACGGTCTT
* * *
754284 TAACCGTTCATCTAACTAGCATAATTGACACCTTTATGCCAAATGCACAGCTAGGCCATTTATCT
1 TAACCATTCATCTAACTGGCATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCATTTATCT
754349 TTTACTCAACGGTCTT
66 TTTACTCAACGGTCTT
* * * * * **
754365 TAA-CAGTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATTCATATCTAGGCCATATAAA
1 TAACCA-TTCATCTAACTGGCATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCATTTATC
*
754429 TTTTACTCAATGGTCTT
65 TTTTACTCAACGGTCTT
** * * * *
754446 TAACTGTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGCACAGCTAGACCATTTATCT
1 TAACCATTCATCTAACTGGCATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCATTTATCT
*
754511 TTTACTCAACGATCTT
66 TTTACTCAACGGTCTT
* *
754527 TAACCTTTCATCTAACTGGCATAATTGACACTTTTTTGCCAAATGCACAGCTAGGCCATTTATCT
1 TAACCATTCATCTAACTGGCATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCATTTATCT
* *
754592 TTTACTCAACGATCTC
66 TTTACTCAACGGTCTT
*
754608 TAACCATTCATCTAACTGGCATAATTGACACCTTTTTGTC-AATGCACAG
1 TAACCATTCATCTAACTGGCATAATTGACACCTTTTTGCCAAATGCACAG
754657 TTAGCCTCAA
Statistics
Matches: 405, Mismatches: 46, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
80 10 0.02
81 394 0.97
82 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (81 bp):
TAACCATTCATCTAACTGGCATAATTGACACCTTTTTGCCAAATGCACAGCTAGGCCATTTATCT
TTTACTCAACGGTCTT
Found at i:754772 original size:67 final size:66
Alignment explanation
Indices: 754614--754921 Score: 413
Period size: 67 Copynumber: 4.8 Consensus size: 66
754604 TCTCTAACCA
* *
754614 TTCATCTAACTGGCATAATTGACACCTTTTTGTCAATGCACAGTTA-GCCTCAAAGGTACTTAGC
1 TTCATCTAACTGGCATAATTGACACC-TTTCGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
754678 CT
65 CT
** * *
754680 TTTGTCTAACTGGCATAATTGACACCTTTCGATCGATGCACAGTTAGGCCTCAAAGACACTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTCG-TCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
754745 CT
65 CT
* *
754747 TTCATCTAACTGGCATAATTAACACCTTTCTGTCAATGCACAGTTAGGCCTAAAAGGCACTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTC-GTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
754812 CT
65 CT
754814 TTCATCTAACTGGCATAATTGACACCTTTCTGT---T--A-A--T-GGCCTCAAAGGCACTTAGC
1 TTCATCTAACTGGCATAATTGACACCTTTC-GTCAATGCACAGTTAGGCCTCAAAGGCACTTAGC
754870 CT
65 CT
*
754872 TT-ATCTAACTGGCATAATTGACACCTTTCTGTCAATGCACAGTTAAGCCT
1 TTCATCTAACTGGCATAATTGACACCTTTC-GTCAATGCACAGTTAGGCCT
754922 TATAATCTTT
Statistics
Matches: 215, Mismatches: 15, Indels: 24
0.85 0.06 0.09
Matches are distributed among these distances:
57 30 0.14
58 22 0.10
59 1 0.00
60 1 0.00
61 1 0.00
62 2 0.01
63 1 0.00
64 1 0.00
65 5 0.02
66 41 0.19
67 109 0.51
68 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.32
Consensus pattern (66 bp):
TTCATCTAACTGGCATAATTGACACCTTTCGTCAATGCACAGTTAGGCCTCAAAGGCACTTAGCC
T
Found at i:754895 original size:57 final size:58
Alignment explanation
Indices: 754793--754908 Score: 207
Period size: 57 Copynumber: 2.0 Consensus size: 58
754783 TGCACAGTTA
*
754793 GGCCTAAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTTAAT
1 GGCCTAAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
*
754851 GGCCTCAAAGGCACTTAGCCTTT-ATCTAACTGGCATAATTGACACCTTTCTGTCAAT
1 GGCCTAAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
754908 G
1 G
754909 CACAGTTAAG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 34 0.61
58 22 0.39
ACGTcount: A:0.27, C:0.25, G:0.16, T:0.32
Consensus pattern (58 bp):
GGCCTAAAAGGCACTTAGCCTTTCATCTAACTGGCATAATTGACACCTTTCTGTCAAT
Found at i:755569 original size:19 final size:20
Alignment explanation
Indices: 755511--755569 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 20
755501 ATCGAGACCC
*
755511 CTACCATGGTATCAATACTA
1 CTACTATGGTATCAATACTA
* **
755531 CTATACTATGATATTGATACT-
1 C--TACTATGGTATCAATACTA
755552 CTACTATGGTATCAATAC
1 CTACTATGGTATCAATAC
755570 CATTTTTGCA
Statistics
Matches: 30, Mismatches: 7, Indels: 5
0.71 0.17 0.12
Matches are distributed among these distances:
19 14 0.47
20 1 0.03
21 1 0.03
22 14 0.47
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.36
Consensus pattern (20 bp):
CTACTATGGTATCAATACTA
Found at i:757636 original size:21 final size:23
Alignment explanation
Indices: 757612--757666 Score: 71
Period size: 21 Copynumber: 2.5 Consensus size: 23
757602 AATTTCCCTT
*
757612 AGTATAGATACTC-CTATATGA-
1 AGTATCGATACTCTCTATATGAG
*
757633 AGTATCGAAAC-CTCTATATGAG
1 AGTATCGATACTCTCTATATGAG
757655 AGTATCGATACT
1 AGTATCGATACT
757667 AAAAATAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
22 10 0.36
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.31
Consensus pattern (23 bp):
AGTATCGATACTCTCTATATGAG
Found at i:771831 original size:139 final size:141
Alignment explanation
Indices: 771641--771974 Score: 422
Period size: 140 Copynumber: 2.4 Consensus size: 141
771631 ATTCTAATCA
* * * * ** *
771641 ATTTTAATCAATTATTAAATTAAATATTCAAAATGGAACGTCGAGCATTAAGGTGAGGACCAACT
1 ATTTTAATCAATTATTAAATTGAATAATCAAAATGGAACCTCGAGCATTAAGGCGAGGAAAAAAT
* * * * *
771706 -AAAAAATCCACCTAAATTAAGGGACTAAAAGTGAAATTAGTCTTAAGTGGAGG-TTCTAATTAT
66 AAAAAAATCCACCTAAATTAACGAACTAAAAATGAAATTAGTATAAAGTGGAGGCTT-TAATTAT
*
771769 CAATCCTAATTG
130 CAACCCTAATTG
* * * *
771781 ATTTTAATCAATT-TTAAATTGAATAATCGAAATAGAACCTCGTGTATTAAGGCGAGGAAAAAAT
1 ATTTTAATCAATTATTAAATTGAATAATCAAAATGGAACCTCGAGCATTAAGGCGAGGAAAAAAT
* * * *
771845 AAAAAAATCCACCTAAGTTAACGAACTAAAAATGAAATTATTATAAATTGGAGGCTTTAATTATT
66 AAAAAAATCCACCTAAATTAACGAACTAAAAATGAAATTAGTATAAAGTGGAGGCTTTAATTATC
771910 AACCCTAATTG
131 AACCCTAATTG
* * *
771921 ATTTTAATCAATTATTGAATCGAATAATCAAAATGGAACCTTGAGCATTAAGGC
1 ATTTTAATCAATTATTAAATTGAATAATCAAAATGGAACCTCGAGCATTAAGGC
771975 AATGACCAAG
Statistics
Matches: 163, Mismatches: 28, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
139 40 0.25
140 88 0.54
141 35 0.21
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (141 bp):
ATTTTAATCAATTATTAAATTGAATAATCAAAATGGAACCTCGAGCATTAAGGCGAGGAAAAAAT
AAAAAAATCCACCTAAATTAACGAACTAAAAATGAAATTAGTATAAAGTGGAGGCTTTAATTATC
AACCCTAATTG
Found at i:774162 original size:22 final size:22
Alignment explanation
Indices: 774136--774185 Score: 100
Period size: 22 Copynumber: 2.3 Consensus size: 22
774126 TCATTATGAA
774136 CTTCTCCTTCATCTGAGAAGTT
1 CTTCTCCTTCATCTGAGAAGTT
774158 CTTCTCCTTCATCTGAGAAGTT
1 CTTCTCCTTCATCTGAGAAGTT
774180 CTTCTC
1 CTTCTC
774186 ATTATTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.30, G:0.12, T:0.42
Consensus pattern (22 bp):
CTTCTCCTTCATCTGAGAAGTT
Found at i:781585 original size:140 final size:140
Alignment explanation
Indices: 781361--781728 Score: 514
Period size: 139 Copynumber: 2.6 Consensus size: 140
781351 AAATGAGTTG
* * * * * *
781361 AGGTTGAAGAAGTTCTTCTCATTATGAATTTCTTCT-CCTTTATCAGATGAGTTCTTCTAATTAT
1 AGGTTGAACAAGTTATTCTCATTATGAATTTCTTCTCCCTCTATCGGATGAGTTCTTCTTATTGT
**
781425 GAACTCTCCACTTGAAATGTTGA-TCTCTCGAGTAAGGTGTTGCTGATTCAACTCC-ATATGTGA
66 GAACTCTCCACTTGAAATGTTGATTC-CTCGAGTAAGGTGTTGCTGATTCAAC-CCTATATACGA
*
781488 TGAATCTAGCAA
129 TAAATCTAGCAA
* *
781500 AGGTTGAACAAGTTATTCTCATTATGAATTTCTTCTCCCTCTACCGGATGAGTTATTCTTATTGT
1 AGGTTGAACAAGTTATTCTCATTATGAATTTCTTCTCCCTCTATCGGATGAGTTCTTCTTATTGT
* *
781565 GAACTCTCCAC-TGAAAATGTTGATTCCTTGAGTGAGGTGTTGCTGATTCAACCCTATATACGAT
66 GAACTCTCCACTTG-AAATGTTGATTCCTCGAGTAAGGTGTTGCTGATTCAACCCTATATACGAT
781629 AAATCTAGCAA
130 AAATCTAGCAA
* *
781640 A-GTTGAATAAGTTATTCTCATTATGAATTTCTTCTCCCTCTATCGAATGAGTTCTTCTTATTGT
1 AGGTTGAACAAGTTATTCTCATTATGAATTTCTTCTCCCTCTATCGGATGAGTTCTTCTTATTGT
*
781704 GAACTCTCCA-TTAGAAATATTGATT
66 GAACTCTCCACTT-GAAATGTTGATT
781729 GGTTTATCCT
Statistics
Matches: 205, Mismatches: 18, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
139 118 0.58
140 85 0.41
141 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (140 bp):
AGGTTGAACAAGTTATTCTCATTATGAATTTCTTCTCCCTCTATCGGATGAGTTCTTCTTATTGT
GAACTCTCCACTTGAAATGTTGATTCCTCGAGTAAGGTGTTGCTGATTCAACCCTATATACGATA
AATCTAGCAA
Found at i:782120 original size:69 final size:69
Alignment explanation
Indices: 782037--782171 Score: 216
Period size: 69 Copynumber: 2.0 Consensus size: 69
782027 AACAATTGTG
*
782037 AAATCTGTGTTCCAAGGGGAACTATCTCAAACAAAATTGATTTTAAGAAAAAACATCTCAACTGA
1 AAATCTATGTTCCAAGGGGAACTATCTCAAACAAAATTGATTTTAAGAAAAAACATCTCAACTGA
782102 TTCC
66 TTCC
* ** * *
782106 AAATCTATGTTCCAAGGGGAACTATTTCAAGTAAAATTGATTTTAAGAAAAATCATCTCAAGTGA
1 AAATCTATGTTCCAAGGGGAACTATCTCAAACAAAATTGATTTTAAGAAAAAACATCTCAACTGA
782171 T
66 T
782172 AAATTTTTGT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 60 1.00
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.30
Consensus pattern (69 bp):
AAATCTATGTTCCAAGGGGAACTATCTCAAACAAAATTGATTTTAAGAAAAAACATCTCAACTGA
TTCC
Found at i:782265 original size:95 final size:95
Alignment explanation
Indices: 782102--782496 Score: 520
Period size: 95 Copynumber: 4.1 Consensus size: 95
782092 TCTCAACTGA
* * *
782102 TTCCAAATCTATGTTCCAAGGGGAACTATTTCAAGTAAAATTGATTTTAAGAAAAATCATCTCAA
1 TTCCAAATCTATGTTCCAAGGGAAACTATTTCAAGAAAAATTGATTTTAAGAAAAACCATCTCAA
782167 GTGATAAATTTTTGTTTCAAGTGAAACAAT
66 GTGATAAATTTTTGTTTCAAGTGAAACAAT
* * *
782197 TTCCAAATCTGTGTTCCAAGGGAAACTATTTCAAGAAAAATTGATTTTAGGAAAAACCGTCTCAA
1 TTCCAAATCTATGTTCCAAGGGAAACTATTTCAAGAAAAATTGATTTTAAGAAAAACCATCTCAA
*
782262 GTGATAAAATTTTGTTTCAAGTGAAACAAT
66 GTGATAAATTTTTGTTTCAAGTGAAACAAT
* * * *
782292 TTCCAAATTTATGTTCCAAGGGGAACTATTTCAAGCAAAATTGATTATAAGAAAAACCATCTCAA
1 TTCCAAATCTATGTTCCAAGGGAAACTATTTCAAGAAAAATTGATTTTAAGAAAAACCATCTCAA
* *
782357 GTAATAAATTTTTGTTTCAAGTGAAAAAAT
66 GTGATAAATTTTTGTTTCAAGTGAAACAAT
* * * * ** * *
782387 TTCAAAATTTATGTTTCAAGGGAATCTACCTTAAAAAGACGAAATTGATTTTAAGAGAAACCATC
1 TTCCAAATCTATGTTCCAAGGGAAACTA--TT-TCAAGA-AAAATTGATTTTAAGAAAAACCATC
*
782452 TCAAGTGAGATAAATTTTTTATTTCAAGTGAAACAAT
62 TCAAGT--GATAAA-TTTTTGTTTCAAGTGAAACAAT
*
782489 TTCAAAAT
1 TTCCAAAT
782497 TTAATTCAAG
Statistics
Matches: 263, Mismatches: 30, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
95 197 0.75
97 2 0.01
98 3 0.01
99 28 0.11
101 5 0.02
102 28 0.11
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.33
Consensus pattern (95 bp):
TTCCAAATCTATGTTCCAAGGGAAACTATTTCAAGAAAAATTGATTTTAAGAAAAACCATCTCAA
GTGATAAATTTTTGTTTCAAGTGAAACAAT
Found at i:782322 original size:29 final size:28
Alignment explanation
Indices: 782268--782323 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
782258 TCAAGTGATA
* *
782268 AAATTTTGTTTCAAGTGAAACAATTTCC
1 AAATTTTGTTCCAAGGGAAACAATTTCC
* *
782296 AAATTTATGTTCCAAGGGGAACTATTTC
1 AAATTT-TGTTCCAAGGGAAACAATTTC
782324 AAGCAAAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (28 bp):
AAATTTTGTTCCAAGGGAAACAATTTCC
Found at i:788526 original size:55 final size:54
Alignment explanation
Indices: 788451--788854 Score: 493
Period size: 55 Copynumber: 7.4 Consensus size: 54
788441 TTTTTTGAGG
* *
788451 TGCACACGTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATT-TATGGTTT
* * * * * *
788506 TGCACAATTAATGTTGATACGATCTTTCATAAAAATATTATGAATTTCATGGTTT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTT-ATGGTTT
* * * * *
788561 TGCATACTTAGTGTCGATATGATCGTTCATAAATATATTATGAATTTCGTGGTTT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTT-ATGGTTT
* * *
788616 TGCCCACTTAGTGTCGATACGGTCGTTCAAAAACAAATTATGAATTATATGGTTT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATT-TATGGTTT
* * * *
788671 TGCACACTTAATGCCGATATGGTCGTTCAGAAACATATTATGAATTTCATGGTTT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTT-ATGGTTT
* * * * * *
788726 TGCACATTTAGCGACGATATGGTCGTTCATAAACATATTATGAATTCTGTTGTTT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATT-TATGGTTT
* *
788781 TGCACACTTAGTGTAGATACGATCGTTCATAAACATATTATGAATTTTATGGTTT
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAA-TTTATGGTTT
788836 TGCACACTTAGTGTCGATA
1 TGCACACTTAGTGTCGATA
788855 GTACACATAG
Statistics
Matches: 298, Mismatches: 46, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
54 2 0.01
55 292 0.98
56 4 0.01
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (54 bp):
TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTTATGGTTT
Found at i:788746 original size:165 final size:165
Alignment explanation
Indices: 788451--788854 Score: 576
Period size: 165 Copynumber: 2.4 Consensus size: 165
788441 TTTTTTGAGG
* * *
788451 TGCACACGTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTATGTGGTTTTGCACAATTA
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTATATGGTTTTGCACACTTA
* * * * * *
788516 ATGTTGATACGATCTTTCATAAAAATATTATGAATTTCATGGTTTTGCATACTTAGTGTCGATAT
66 ATGTCGATACGATCGTTCAGAAAAATATTATGAATTTCATGGTTTTGCACACTTAGCGACGATAT
*
788581 GATCGTTCATAAATATATTATGAATT-TCGTGGTTT
131 GATCGTTCATAAACATATTATGAATTCT-GTGGTTT
* * *
788616 TGCCCACTTAGTGTCGATACGGTCGTTCAAAAACAAATTATGAATTATATGGTTTTGCACACTTA
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTATATGGTTTTGCACACTTA
* * * * *
788681 ATGCCGATATGGTCGTTCAGAAACATATTATGAATTTCATGGTTTTGCACATTTAGCGACGATAT
66 ATGTCGATACGATCGTTCAGAAAAATATTATGAATTTCATGGTTTTGCACACTTAGCGACGATAT
* *
788746 GGTCGTTCATAAACATATTATGAATTCTGTTGTTT
131 GATCGTTCATAAACATATTATGAATTCTGTGGTTT
* * *
788781 TGCACACTTAGTGTAGATACGATCGTTCATAAACATATTATGAATTTTATGGTTTTGCACACTTA
1 TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTATATGGTTTTGCACACTTA
*
788846 GTGTCGATA
66 ATGTCGATA
788855 GTACACATAG
Statistics
Matches: 210, Mismatches: 28, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
165 209 1.00
166 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (165 bp):
TGCACACTTAGTGTCGATACGGTCGTTCATAAACATATTATGAATTATATGGTTTTGCACACTTA
ATGTCGATACGATCGTTCAGAAAAATATTATGAATTTCATGGTTTTGCACACTTAGCGACGATAT
GATCGTTCATAAACATATTATGAATTCTGTGGTTT
Found at i:795407 original size:55 final size:54
Alignment explanation
Indices: 795346--795686 Score: 359
Period size: 55 Copynumber: 6.2 Consensus size: 54
795336 TTCTTTGAGG
* *
795346 TGCACACGTAGTGTCAATACGGTTGTTCATAAACATATTATGAATTATGTGGTTT
1 TGCACACTTAGTGTCAATACGGTCGTTCATAAACATATTATGAATT-TGTGGTTT
* * ** * *
795401 TGCACACTTAATTTTGATACGGTCGTTCATAAAAATATTATGAATTTCTTGGTTT
1 TGCACACTTAGTGTCAATACGGTCGTTCATAAACATATTATGAATTT-GTGGTTT
* * * *
795456 TGCACGCTTAGTG-CTTATACAGTCATTCATAAACATATTATGAATTATGTGGTTT
1 TGCACACTTAGTGTC-AATACGGTCGTTCATAAACATATTATGAATT-TGTGGTTT
* * *
795511 TGCACACTTAGTGTCGATAAGGTCGTTCA-AAACATATTATGAATTTCATGGTTT
1 TGCACACTTAGTGTCAATACGGTCGTTCATAAACATATTATGAATTT-GTGGTTT
* ** * *
795565 TGCACACTTAG-GGCAGATA-TATCGTTCATAAACATATTTTGAATTCCGTGGTTT
1 TGCACACTTAGTGTCA-ATACGGTCGTTCATAAACATATTATGAATT-TGTGGTTT
* * *
795619 TGCACACTTAGTGT-AGATTCGGTCATTCATAAACATATTATGAATTCTATGGTTT
1 TGCACACTTAGTGTCA-ATACGGTCGTTCATAAACATATTATGAATT-TGTGGTTT
795674 TGCACACTTAGTG
1 TGCACACTTAGTG
795687 CCGATAGTAC
Statistics
Matches: 238, Mismatches: 38, Indels: 20
0.80 0.13 0.07
Matches are distributed among these distances:
53 10 0.04
54 73 0.31
55 153 0.64
56 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (54 bp):
TGCACACTTAGTGTCAATACGGTCGTTCATAAACATATTATGAATTTGTGGTTT
Found at i:795646 original size:163 final size:165
Alignment explanation
Indices: 795346--795692 Score: 441
Period size: 163 Copynumber: 2.1 Consensus size: 165
795336 TTCTTTGAGG
* * * * *
795346 TGCACACGTAGTGTCAATACGGTTGTTCATAAACATATTATGAATTATGTGGTTTTGCACACTTA
1 TGCACACTTAGTGTCGATAAGGTCGTTCATAAACATATTATGAATTATATGGTTTTGCACACTTA
**** * * * * *
795411 ATTTTGATACGGTCGTTCATAAAAATATTATGAATTTCTTGGTTTTGCACGCTTAGTGCTTATAC
66 AGGCAGATACGATCGTTCATAAAAATATTATGAATTCCGTGGTTTTGCACACTTAGTGCTGATAC
*
795476 AGTCATTCATAAACATATTATGAATTATGTGGTTT
131 AGTCATTCATAAACATATTATGAATTATATGGTTT
795511 TGCACACTTAGTGTCGATAAGGTCGTTCA-AAACATATTATGAATT-TCATGGTTTTGCACACTT
1 TGCACACTTAGTGTCGATAAGGTCGTTCATAAACATATTATGAATTAT-ATGGTTTTGCACACTT
* * * *
795574 AGGGCAGATA-TATCGTTCATAAACATATTTTGAATTCCGTGGTTTTGCACACTTAGTG-TAGAT
65 AAGGCAGATACGATCGTTCATAAAAATATTATGAATTCCGTGGTTTTGCACACTTAGTGCT-GAT
* * *
795637 TCGGTCATTCATAAACATATTATGAATTCTATGGTTT
129 ACAGTCATTCATAAACATATTATGAATTATATGGTTT
*
795674 TGCACACTTAGTGCCGATA
1 TGCACACTTAGTGTCGATA
795693 GTACACATAA
Statistics
Matches: 157, Mismatches: 23, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
162 1 0.01
163 95 0.61
164 36 0.23
165 25 0.16
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.39
Consensus pattern (165 bp):
TGCACACTTAGTGTCGATAAGGTCGTTCATAAACATATTATGAATTATATGGTTTTGCACACTTA
AGGCAGATACGATCGTTCATAAAAATATTATGAATTCCGTGGTTTTGCACACTTAGTGCTGATAC
AGTCATTCATAAACATATTATGAATTATATGGTTT
Found at i:797347 original size:12 final size:12
Alignment explanation
Indices: 797330--797383 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
797320 TTTTTAATAC
*
797330 TAATAATATTTA
1 TAATAATATTAA
797342 TAATAATATTAA
1 TAATAATATTAA
* *
797354 TAACAAAATGGTAA
1 TAATAATAT--TAA
797368 TAATAATA-TAA
1 TAATAATATTAA
797379 TAATA
1 TAATA
797384 TAAGGTATTA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 8 0.23
12 18 0.51
14 9 0.26
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (12 bp):
TAATAATATTAA
Found at i:801245 original size:17 final size:16
Alignment explanation
Indices: 801198--801246 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
801188 CAAAATTTGT
801198 TTAATGAATGTAAATAA
1 TTAATGAATGTAAA-AA
* *
801215 TGAA-GAATGAAAAAA
1 TTAATGAATGTAAAAA
801230 TATAATGAATGTAAAAA
1 T-TAATGAATGTAAAAA
801247 ATGATTGGCA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 10 0.38
17 13 0.50
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.27
Consensus pattern (16 bp):
TTAATGAATGTAAAAA
Found at i:804528 original size:62 final size:62
Alignment explanation
Indices: 804451--804576 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 62
804441 ATGTGACGTT
804451 ATAGTGGAGTTAACATAATGGTTTGGATGTCAAGTATGAACGATTACAGTTGATAATATAGC
1 ATAGTGGAGTTAACATAATGGTTTGGATGTCAAGTATGAACGATTACAGTTGATAATATAGC
* * * * *
804513 ATAGTGGTGTTAACATAATGGTTTGGATGTCAAGTGTGAATGATTCCAGTTGATAATGTAGC
1 ATAGTGGAGTTAACATAATGGTTTGGATGTCAAGTATGAACGATTACAGTTGATAATATAGC
804575 AT
1 AT
804577 CAATATAAGC
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.34
Consensus pattern (62 bp):
ATAGTGGAGTTAACATAATGGTTTGGATGTCAAGTATGAACGATTACAGTTGATAATATAGC
Found at i:806691 original size:20 final size:20
Alignment explanation
Indices: 806666--806704 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
806656 ATTTTTAGTA
*
806666 GAAGTATCCATATTTCTAGG
1 GAAGTATCAATATTTCTAGG
806686 GAAGTATCAATATTTCTAG
1 GAAGTATCAATATTTCTAG
806705 AAACAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (20 bp):
GAAGTATCAATATTTCTAGG
Found at i:810559 original size:28 final size:29
Alignment explanation
Indices: 810505--810567 Score: 101
Period size: 28 Copynumber: 2.2 Consensus size: 29
810495 AAAATAGATT
810505 AAAAGCTATATGTCATGATCAGATATATC
1 AAAAGCTATATGTCATGATCAGATATATC
* *
810534 AAAAGCTATTTGT-ATGGTCAGATATATC
1 AAAAGCTATATGTCATGATCAGATATATC
810562 AAAAGC
1 AAAAGC
810568 GAATGATGCG
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 20 0.62
29 12 0.38
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.30
Consensus pattern (29 bp):
AAAAGCTATATGTCATGATCAGATATATC
Found at i:832055 original size:31 final size:31
Alignment explanation
Indices: 832019--832077 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
832009 AACTTAAAAG
* *
832019 AGTTTTGCAATACTGAAATTTAAATAATTTT
1 AGTTTTACAATACTAAAATTTAAATAATTTT
*
832050 AGTTTTATAATACTAAAATTTAAATAAT
1 AGTTTTACAATACTAAAATTTAAATAAT
832078 CCATAAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (31 bp):
AGTTTTACAATACTAAAATTTAAATAATTTT
Found at i:832126 original size:22 final size:22
Alignment explanation
Indices: 832101--832705 Score: 673
Period size: 22 Copynumber: 27.5 Consensus size: 22
832091 ACAATAAATT
832101 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
832123 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
832145 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
* *
832167 TATTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
* *** *
832189 TTTTAAAATAATTTTTTTTATA
1 TTTTAAAATAAATCAATTCATA
832211 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
**
832233 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATTCATA
*
832255 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
832277 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
832299 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
832321 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
**
832343 TTTTAAAATAAAT-TTTTCTATA
1 TTTTAAAATAAATCAATTC-ATA
*
832365 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
832387 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCA-ATT-CATA
* *
832409 TTTTAAAATAAAGCAATCCATA
1 TTTTAAAATAAATCAATTCATA
832431 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATA
*
832453 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
*
832475 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCA-ATT-CATA
*
832497 TTTTAAAATAAA--ATTTTCCATA
1 TTTTAAAATAAATCA-ATT-CATA
832519 TTTTAAAATAAATCAA-TCAATA
1 TTTTAAAATAAATCAATTC-ATA
** *
832541 TTTTAAAATAAATTTATCCATA
1 TTTTAAAATAAATCAATTCATA
832563 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
**
832585 TTTTAAAATAAAAT-TTTTCATA
1 TTTTAAAAT-AAATCAATTCATA
* *
832607 TTTTAAAATAAATTAATCCATA
1 TTTTAAAATAAATCAATTCATA
* **
832629 TTTTAAAATTAAT-TTTTCATA
1 TTTTAAAATAAATCAATTCATA
*
832650 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATA
832672 TTTTAAAATAAATCAA-TCTATA
1 TTTTAAAATAAATCAATTC-ATA
832694 TTTTAAAATAAA
1 TTTTAAAATAAA
832706 ATTTTAAAAT
Statistics
Matches: 502, Mismatches: 57, Indels: 48
0.83 0.09 0.08
Matches are distributed among these distances:
20 2 0.00
21 34 0.07
22 447 0.89
23 17 0.03
24 2 0.00
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (22 bp):
TTTTAAAATAAATCAATTCATA
Found at i:832150 original size:44 final size:44
Alignment explanation
Indices: 832101--832705 Score: 751
Period size: 44 Copynumber: 13.8 Consensus size: 44
832091 ACAATAAATT
832101 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
*
832145 TTTTAAAATAAATCAA-TCTATATATTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTC-ATATTTTAAAATAAATCAATCCATA
* *** * *
832189 TTTTAAAATAATTTTTTTTATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
**
832233 TTTTAAAATAAAAT-TTTTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAAT-AAATCAATTCATATTTTAAAATAAATCAATCCATA
*
832277 TTTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
* *** *
832321 TTTTAAAATAAATCAATCCATATTTTAAAATAAATTTTTCTATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
* **
832365 TTTTAAAATAAATCAATCCATATTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAAT-AAATCAATCCATA
* * *
832409 TTTTAAAATAAAGCAATCCATATTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
* **
832453 TTTTAAAATAAATCAATCCATATTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAAT-AAATCAATCCATA
* *
832497 TTTTAAAATAAA--ATTTTCCATATTTTAAAATAAATCAATCAATA
1 TTTTAAAATAAATCA-ATT-CATATTTTAAAATAAATCAATCCATA
** * *
832541 TTTTAAAATAAATTTATCCATATTTTAAAATAAATCAATCTATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
** *
832585 TTTTAAAATAAAAT-TTTTCATATTTTAAAATAAATTAATCCATA
1 TTTTAAAAT-AAATCAATTCATATTTTAAAATAAATCAATCCATA
* **
832629 TTTTAAAATTAAT-TTTTCATATTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
832672 TTTTAAAATAAATCAA-TCTATATTTTAAAATAAA
1 TTTTAAAATAAATCAATTC-ATATTTTAAAATAAA
832706 ATTTTAAAAT
Statistics
Matches: 501, Mismatches: 45, Indels: 30
0.87 0.08 0.05
Matches are distributed among these distances:
42 1 0.00
43 61 0.12
44 422 0.84
45 17 0.03
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.42
Consensus pattern (44 bp):
TTTTAAAATAAATCAATTCATATTTTAAAATAAATCAATCCATA
Found at i:835473 original size:140 final size:139
Alignment explanation
Indices: 835096--835480 Score: 445
Period size: 140 Copynumber: 2.8 Consensus size: 139
835086 AATATATAGA
* * ** *
835096 CTTTAA-TATTAATCTTAATTGATTTTAATAAATTATTGAATTGAATAATTGAAATGGAACCTCG
1 CTTTAATTATTAATCCTAATTGATTTTAATCAATTATTGAATTGAATAATCAAAATAGAACCTCG
*
835160 AGCATTAAGGCAAGGACCAA-CTAAAAATCCACCTAAATTAAGGGACTAAAACTAAAATTAATCT
66 AGCATTAAGGCGAGGACCAATC-AAAAATCCACCTAAATTAAGGGACTAAAACTAAAATTAATCT
* *
835224 AAAGTGGAGG
130 AAAATGGAGC
* * * *
835234 CTCTAATTATTAATACTAATTGATTTTAATCAATAACTT-AATTGAATAATCAAAATTGAACCTC
1 CTTTAATTATTAATCCTAATTGATTTTAATCAATTA-TTGAATTGAATAATCAAAATAGAACCTC
* * * * * * * *
835298 GAGCATTAAGACGATGATCAAATAAAAAATCCACCTAAGTTAAGGGGCTAAAAGTGAAATTAATC
65 GAGCATTAAGGCGAGGA-CCAATCAAAAATCCACCTAAATTAAGGGACTAAAACTAAAATTAATC
835363 TAAAATGGAGC
129 TAAAATGGAGC
* **
835374 CTTTAATTATTAATCCTAATTTATTTTAATCAATTATTGAATCAAATAATCAAAATAGAACCTC-
1 CTTTAATTATTAATCCTAATTGATTTTAATCAATTATTGAATTGAATAATCAAAATAGAACCTCG
* * * * *
835438 AGGTAGTAAGGCGAGGACCGAATCAAATATTCACCTAATTTAA
66 A-GCATTAAGGCGAGGACC-AATCAAAAATCCACCTAAATTAA
835481 AAGGTTTAGG
Statistics
Matches: 205, Mismatches: 35, Indels: 12
0.81 0.14 0.05
Matches are distributed among these distances:
138 5 0.02
139 65 0.32
140 135 0.66
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.31
Consensus pattern (139 bp):
CTTTAATTATTAATCCTAATTGATTTTAATCAATTATTGAATTGAATAATCAAAATAGAACCTCG
AGCATTAAGGCGAGGACCAATCAAAAATCCACCTAAATTAAGGGACTAAAACTAAAATTAATCTA
AAATGGAGC
Found at i:835709 original size:22 final size:23
Alignment explanation
Indices: 835684--835726 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
835674 ATTAGAGGAC
*
835684 TAAATTACA-AAATTCAAAAAAT
1 TAAATGACATAAATTCAAAAAAT
*
835706 TAAATGACATAAATTTAAAAA
1 TAAATGACATAAATTCAAAAA
835727 CATGAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.63, C:0.07, G:0.02, T:0.28
Consensus pattern (23 bp):
TAAATGACATAAATTCAAAAAAT
Found at i:838330 original size:30 final size:30
Alignment explanation
Indices: 838225--838377 Score: 135
Period size: 30 Copynumber: 5.0 Consensus size: 30
838215 ATCGGATTAG
* *
838225 CACTGTAGTGTGTAAAGACACTTAGTGTAA
1 CACTGTAGTGTGTAAGGACACTTAGTGCAA
* * * *
838255 CAATATGGTGTGTAAGGACACTTAGTTCATA
1 CACTGTAGTGTGTAAGGACACTTAGTGCA-A
* * *
838286 TGGTACTATAGTGTGTAAGGACACTTAGTACAA
1 ---CACTGTAGTGTGTAAGGACACTTAGTGCAA
* * *
838319 CATTGTAGTGTGTAAGGATACTTAGTGCAG
1 CACTGTAGTGTGTAAGGACACTTAGTGCAA
* * *
838349 CACTGTGGTATGTAAGGACACTCAGTGCA
1 CACTGTAGTGTGTAAGGACACTTAGTGCA
838378 TATGGTAAGC
Statistics
Matches: 98, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
30 71 0.72
31 1 0.01
33 1 0.01
34 25 0.26
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (30 bp):
CACTGTAGTGTGTAAGGACACTTAGTGCAA
Found at i:842124 original size:15 final size:15
Alignment explanation
Indices: 842104--842133 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
842094 ATACCTCCCT
842104 TATGGTATCGATACC
1 TATGGTATCGATACC
842119 TATGGTATCGATACC
1 TATGGTATCGATACC
842134 ACATTCCCAG
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:0.20, G:0.20, T:0.33
Consensus pattern (15 bp):
TATGGTATCGATACC
Found at i:848190 original size:142 final size:142
Alignment explanation
Indices: 847934--848220 Score: 538
Period size: 142 Copynumber: 2.0 Consensus size: 142
847924 AAACTCTCAA
*
847934 ATTTTCATAATTTGATCATAAAATTACAAAAACTTCCATTTTAGTCACTAACCTTGTTTTTGGGA
1 ATTTTCATAATTTGATCACAAAATTACAAAAACTTCCATTTTAGTCACTAACCTTGTTTTTGGGA
847999 TGTTACAATCGAAAGTTCATAAAGAACTTTTCGATGATTGTCTTCCCTCTAACCAAGCTATTGAG
66 TGTTACAATCGAAAGTTCATAAAGAACTTTTCGATGATTGTCTTCCCTCTAACCAAGCTATTGAG
*
848064 AAAAGACACACT
131 AAAAGACACAAT
*
848076 ATTTTCATAATTTGATCACAAAATTTCAAAAACTTCCATTTTAGTCACTAACCTTGTTTTTGGGA
1 ATTTTCATAATTTGATCACAAAATTACAAAAACTTCCATTTTAGTCACTAACCTTGTTTTTGGGA
*
848141 TGTTACAATCGAAAGTTCATAAAGAACTTTTCTATGATTGTCTTCCCTCTAACCAAGCTATTGAG
66 TGTTACAATCGAAAGTTCATAAAGAACTTTTCGATGATTGTCTTCCCTCTAACCAAGCTATTGAG
848206 AAAAGACACAAT
131 AAAAGACACAAT
848218 ATT
1 ATT
848221 CATTTGGGCT
Statistics
Matches: 141, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 141 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.36
Consensus pattern (142 bp):
ATTTTCATAATTTGATCACAAAATTACAAAAACTTCCATTTTAGTCACTAACCTTGTTTTTGGGA
TGTTACAATCGAAAGTTCATAAAGAACTTTTCGATGATTGTCTTCCCTCTAACCAAGCTATTGAG
AAAAGACACAAT
Found at i:849421 original size:22 final size:21
Alignment explanation
Indices: 849404--849443 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
849394 ATAAAATTTG
849404 AAAATTTAGTGG-CCAAAATAT
1 AAAATTTAG-GGACCAAAATAT
*
849425 AAAGTTTAGGGACCAAAAT
1 AAAATTTAGGGACCAAAAT
849444 GGTAATGATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.25
Consensus pattern (21 bp):
AAAATTTAGGGACCAAAATAT
Found at i:849473 original size:15 final size:15
Alignment explanation
Indices: 849425--849475 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
849415 GCCAAAATAT
849425 AAAGTTTAGGGACCA
1 AAAGTTTAGGGACCA
* **
849440 AAA-TGGTAATGATCCA
1 AAAGT-TTAGGGA-CCA
849456 AAAGTTTAGGGACCA
1 AAAGTTTAGGGACCA
849471 AAAGT
1 AAAGT
849476 GTAATTTCCA
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 1 0.04
15 15 0.56
16 10 0.37
17 1 0.04
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.22
Consensus pattern (15 bp):
AAAGTTTAGGGACCA
Found at i:849480 original size:31 final size:30
Alignment explanation
Indices: 849425--849488 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
849415 GCCAAAATAT
849425 AAAGTTTAGGGACCAAAATGGTAATGATCCA
1 AAAGTTTAGGGACCAAAATGGTAAT-ATCCA
*
849456 AAAGTTTAGGGACCAAAA-GTGTAATTTCCA
1 AAAGTTTAGGGACCAAAATG-GTAATATCCA
849486 AAA
1 AAA
849489 ATTATATATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 8 0.26
31 23 0.74
ACGTcount: A:0.44, C:0.12, G:0.20, T:0.23
Consensus pattern (30 bp):
AAAGTTTAGGGACCAAAATGGTAATATCCA
Found at i:851873 original size:22 final size:22
Alignment explanation
Indices: 851845--851887 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
851835 ATTAATCGTT
*
851845 ATATATGATGTTTATCATGAAC
1 ATATATGATATTTATCATGAAC
851867 ATATATGATATTTATCATGAA
1 ATATATGATATTTATCATGAA
851888 TGATATTTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.07, G:0.12, T:0.42
Consensus pattern (22 bp):
ATATATGATATTTATCATGAAC
Found at i:852147 original size:30 final size:30
Alignment explanation
Indices: 852042--852154 Score: 109
Period size: 30 Copynumber: 3.6 Consensus size: 30
852032 ACCGGATTAG
* * *
852042 CACTATAATGTGTAAGGACACTTAGTGCAA
1 CACTATAGTGTGTAAGGACACTTAGTACAT
* * * *
852072 CAGTATGGTGTGTAAGAACACTTAGTTTATAT
1 CACTATAGTGTGTAAGGACACTTAG--TACAT
*
852104 GGTACTATAGTGTGTAAGGACACTTAGTACAT
1 --CACTATAGTGTGTAAGGACACTTAGTACAT
*
852136 CACTGTAGTGTGTAAGGAC
1 CACTATAGTGTGTAAGGAC
852155 GCTCACTATA
Statistics
Matches: 65, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
30 38 0.58
32 6 0.09
34 21 0.32
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (30 bp):
CACTATAGTGTGTAAGGACACTTAGTACAT
Found at i:852170 original size:30 final size:30
Alignment explanation
Indices: 852111--852189 Score: 95
Period size: 30 Copynumber: 2.6 Consensus size: 30
852101 TATGGTACTA
* * *
852111 TAGTGTGTAAGGACACTTAGTACATCACTG
1 TAGTGTGTAAGGACACTCACTACAGCACTG
* *
852141 TAGTGTGTAAGGACGCTCACTATAGCACTG
1 TAGTGTGTAAGGACACTCACTACAGCACTG
* *
852171 TGGTATGTAAGGACACTCA
1 TAGTGTGTAAGGACACTCA
852190 GTGCATATGG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (30 bp):
TAGTGTGTAAGGACACTCACTACAGCACTG
Found at i:852701 original size:155 final size:155
Alignment explanation
Indices: 852427--852736 Score: 566
Period size: 155 Copynumber: 2.0 Consensus size: 155
852417 ATATTATTAT
852427 TGTTTACATTTATGTGTTGCATTGCCTTGAATATATTTCTATTGATTGTCTCACTAAGTGTATAC
1 TGTTTACATTTATGTGTTGCATTGCCTTGAATATATTTCTATTGATTGTCTCACTAAGTGTATAC
* * *
852492 TTAGCGTGTGATGATTTTCACGCGTAGGTAAATTAAAACGGAAGGAGTATGGAGCTTAGCTTGGC
66 TTAGAGTGTGATGATTTTCACGCGTAGGTAAATTAAAACAGAAGGAGTAGGGAGCTTAGCTTGGC
852557 ATCAATCACTAAGGAATATTTACAG
131 ATCAATCACTAAGGAATATTTACAG
852582 TGTTTACATTTATGTGTTGCATTGCCTTGAATATATTTCTATTGATTGTCTCACTAAGTGTATAC
1 TGTTTACATTTATGTGTTGCATTGCCTTGAATATATTTCTATTGATTGTCTCACTAAGTGTATAC
* * *
852647 TTAGAGTGTGATTATTTTCACGCTTAGGTAAATTAAAGCAGAAGGAGTAGGGAGCTTAGCTTGGC
66 TTAGAGTGTGATGATTTTCACGCGTAGGTAAATTAAAACAGAAGGAGTAGGGAGCTTAGCTTGGC
852712 ATCAATCACTAAGGAATATTTACAG
131 ATCAATCACTAAGGAATATTTACAG
852737 GTAGCAGAAA
Statistics
Matches: 149, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
155 149 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (155 bp):
TGTTTACATTTATGTGTTGCATTGCCTTGAATATATTTCTATTGATTGTCTCACTAAGTGTATAC
TTAGAGTGTGATGATTTTCACGCGTAGGTAAATTAAAACAGAAGGAGTAGGGAGCTTAGCTTGGC
ATCAATCACTAAGGAATATTTACAG
Found at i:854527 original size:24 final size:24
Alignment explanation
Indices: 854471--854530 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
854461 TTCGTGAACG
**
854471 TTCAGTTATGTTCGTTTATATTTG
1 TTCAGTTATGTTCGTTTATATTCA
* *
854495 TTCGGTTATGTTCGTTTATGTTCA
1 TTCAGTTATGTTCGTTTATATTCA
*
854519 TTCATTTATGTT
1 TTCAGTTATGTT
854531 TAAGCCAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.15, C:0.10, G:0.17, T:0.58
Consensus pattern (24 bp):
TTCAGTTATGTTCGTTTATATTCA
Found at i:855200 original size:10 final size:10
Alignment explanation
Indices: 855185--855258 Score: 50
Period size: 10 Copynumber: 7.6 Consensus size: 10
855175 GGTCTCCAAT
855185 GTTTATGTTC
1 GTTTATGTTC
855195 GTTTATGTTC
1 GTTTATGTTC
855205 G----TGTTC
1 GTTTATGTTC
*
855211 ATTTATGTTC
1 GTTTATGTTC
* *
855221 GTGTT-CGTTTAT
1 GT-TTATG-TT-C
*
855233 GTTTGTGTTC
1 GTTTATGTTC
855243 GTTTATGTTC
1 GTTTATGTTC
855253 GTTTAT
1 GTTTAT
855259 TTATTAAATG
Statistics
Matches: 49, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 33 0.67
11 8 0.16
12 3 0.06
ACGTcount: A:0.09, C:0.09, G:0.22, T:0.59
Consensus pattern (10 bp):
GTTTATGTTC
Found at i:855209 original size:16 final size:16
Alignment explanation
Indices: 855190--855254 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
855180 CCAATGTTTA
855190 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
855206 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
855222 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
855238 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
855254 T
1 T
855255 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:855345 original size:16 final size:16
Alignment explanation
Indices: 855324--855356 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
855314 AAAAACATTT
855324 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
855340 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
855356 T
1 T
855357 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:856981 original size:32 final size:32
Alignment explanation
Indices: 856930--857000 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 32
856920 GAAAGGGTTT
* *
856930 CAATTCCTTCAACATATATCAAGTAACTTCTC
1 CAATACCTTAAACATATATCAAGTAACTTCTC
856962 CAATACCTTAAACATATATCAAGTAACTTCTC
1 CAATACCTTAAACATATATCAAGTAACTTCTC
856994 CAATACC
1 CAATACC
857001 CAATAACTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.38, C:0.28, G:0.03, T:0.31
Consensus pattern (32 bp):
CAATACCTTAAACATATATCAAGTAACTTCTC
Found at i:857163 original size:30 final size:30
Alignment explanation
Indices: 857127--857205 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
857117 GTCCTAATTA
857127 TGGAAATTTAGAGACTTATTAGAAGACAAT
1 TGGAAATTTAGAGACTTATTAGAAGACAAT
*
857157 TGGAAATTTAGAGACTTATTAGAAGTCAAT
1 TGGAAATTTAGAGACTTATTAGAAGACAAT
* *
857187 TGAAAATGTTAGATACTTA
1 TGGAAAT-TTAGAGACTTA
857206 AACATAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
30 35 0.78
31 10 0.22
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (30 bp):
TGGAAATTTAGAGACTTATTAGAAGACAAT
Found at i:862319 original size:14 final size:14
Alignment explanation
Indices: 862300--862326 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
862290 TTTATTAGTT
862300 AAATTTTTATTTTA
1 AAATTTTTATTTTA
862314 AAATTTTTATTTT
1 AAATTTTTATTTT
862327 TCTAATCGTT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
AAATTTTTATTTTA
Found at i:863469 original size:26 final size:28
Alignment explanation
Indices: 863439--863490 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
863429 CTTCTATTGC
* *
863439 CACAT-TTAT-TCTTTTGTTTTTATTCT
1 CACATGTTATCTCTTCTGCTTTTATTCT
863465 CACATGTTATCTCTTCTGCTTTTATT
1 CACATGTTATCTCTTCTGCTTTTATT
863491 TCCCTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 4 0.18
28 13 0.59
ACGTcount: A:0.15, C:0.19, G:0.06, T:0.60
Consensus pattern (28 bp):
CACATGTTATCTCTTCTGCTTTTATTCT
Found at i:867439 original size:35 final size:34
Alignment explanation
Indices: 867355--867440 Score: 95
Period size: 35 Copynumber: 2.5 Consensus size: 34
867345 AAATAATTTC
*
867355 AAATACAACAAACTTACAATAAGTATTAAATGGT
1 AAATACAACAAAATTACAATAAGTATTAAATGGT
* *
867389 AAATGATAACCAAATTACAATAACTGATATTAAATGGT
1 AAAT-ACAACAAAATTACAATAA--G-TATTAAATGGT
867427 -AATA-AACAAAATTA
1 AAATACAACAAAATTA
867441 ACTGAAATAC
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
34 4 0.09
35 24 0.55
36 1 0.02
37 4 0.09
38 11 0.25
ACGTcount: A:0.55, C:0.10, G:0.08, T:0.27
Consensus pattern (34 bp):
AAATACAACAAAATTACAATAAGTATTAAATGGT
Found at i:867695 original size:12 final size:12
Alignment explanation
Indices: 867680--867705 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
867670 ACCATCATCA
867680 TCGTCGTTGTCG
1 TCGTCGTTGTCG
867692 TCGTCGTTGTCG
1 TCGTCGTTGTCG
867704 TC
1 TC
867706 CTGAGTAAGT
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:0.00, C:0.27, G:0.31, T:0.42
Consensus pattern (12 bp):
TCGTCGTTGTCG
Found at i:874005 original size:25 final size:25
Alignment explanation
Indices: 873977--874040 Score: 101
Period size: 25 Copynumber: 2.6 Consensus size: 25
873967 AATGAATAAT
873977 TTTTTAAAAATGTTTGATAAAACAA
1 TTTTTAAAAATGTTTGATAAAACAA
* *
874002 TTTTTGAAAATGTTTGATAAAAGAA
1 TTTTTAAAAATGTTTGATAAAACAA
*
874027 TTTTGAAAAATGTT
1 TTTTTAAAAATGTT
874041 ACCTTTTACT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.42
Consensus pattern (25 bp):
TTTTTAAAAATGTTTGATAAAACAA
Found at i:876685 original size:22 final size:22
Alignment explanation
Indices: 876645--876687 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
876635 CAAAAAATAA
**
876645 ATGTTGATCCCAATTATGAATC
1 ATGTTGATCCCAACGATGAATC
*
876667 ATGTTGATCCTAACGATGAAT
1 ATGTTGATCCCAACGATGAAT
876688 ATCATAGGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (22 bp):
ATGTTGATCCCAACGATGAATC
Found at i:878074 original size:37 final size:37
Alignment explanation
Indices: 878016--878088 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
878006 ACATAATCTC
* *
878016 TATCATATATACATTTCTTAACTTATCTCATAGTTATG
1 TATCATATATACATATCTTAACTTATATCATA-TTATG
878054 TATCATAT-TACATAAT-TTAACTTATATCATATTAT
1 TATCATATATACAT-ATCTTAACTTATATCATATTAT
878089 CATGTGTGCA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
36 4 0.12
37 19 0.59
38 9 0.28
ACGTcount: A:0.36, C:0.14, G:0.03, T:0.48
Consensus pattern (37 bp):
TATCATATATACATATCTTAACTTATATCATATTATG
Found at i:878515 original size:20 final size:22
Alignment explanation
Indices: 878490--878547 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 22
878480 TTCCCCTTGA
878490 AGTGCATCGATGCATTC-T-AC
1 AGTGCATCGATGCATTCTTAAC
878510 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC-TTAAC
878533 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
878548 CTACCCATGC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
20 17 0.50
22 1 0.03
23 3 0.09
24 13 0.38
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.31
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTAAC
Found at i:878678 original size:65 final size:65
Alignment explanation
Indices: 878536--878672 Score: 165
Period size: 65 Copynumber: 2.1 Consensus size: 65
878526 CTTTAACATG
** * *
878536 TGCATCGATGCACT-ACCCATGCATCGATACACAAATTACCTTCGATGTTTTCATTTTTAAAGGG
1 TGCATCGATGCACTCA-TTATGCATCGATACACAAATTACATTCGATGTTTTCATTTTTAAAGAG
878600 A
65 A
* * *
878601 TGCATCGATGCACTCATTATGCATCGATGCACCAATTGCATTCGATG-TTTC-TTCTTTAAAGAG
1 TGCATCGATGCACTCATTATGCATCGATACACAAATTACATTCGATGTTTTCATT-TTTAAAGAG
878664 -
65 A
878664 TGCATCGAT
1 TGCATCGAT
878673 ATGCACATTG
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
63 11 0.17
64 12 0.19
65 39 0.62
66 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.34
Consensus pattern (65 bp):
TGCATCGATGCACTCATTATGCATCGATACACAAATTACATTCGATGTTTTCATTTTTAAAGAGA
Found at i:881985 original size:26 final size:26
Alignment explanation
Indices: 881956--882016 Score: 122
Period size: 26 Copynumber: 2.3 Consensus size: 26
881946 GGAGCGGATG
881956 GATTTGATTTGATTTTTACTAGTTTT
1 GATTTGATTTGATTTTTACTAGTTTT
881982 GATTTGATTTGATTTTTACTAGTTTT
1 GATTTGATTTGATTTTTACTAGTTTT
882008 GATTTGATT
1 GATTTGATT
882017 CGGTTGATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.20, C:0.03, G:0.16, T:0.61
Consensus pattern (26 bp):
GATTTGATTTGATTTTTACTAGTTTT
Found at i:882308 original size:2 final size:2
Alignment explanation
Indices: 882301--882330 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
882291 AATTGGTTGC
882301 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
882331 CATGTTTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:887221 original size:3 final size:3
Alignment explanation
Indices: 887215--887244 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
887205 TAGTAGTATA
887215 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
887245 GTTTTTAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:891416 original size:15 final size:15
Alignment explanation
Indices: 891396--891452 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
891386 CCAGATGTTA
891396 CGGGTACCCGGTAAT
1 CGGGTACCCGGTAAT
* **
891411 CGGGTACCTGGATTTT
1 CGGGTACCCGG-TAAT
891427 GCGGGTACCCGGTAAT
1 -CGGGTACCCGGTAAT
891443 CGGGTACCCG
1 CGGGTACCCG
891453 ATACCCGGTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 20 0.59
16 4 0.12
17 10 0.29
ACGTcount: A:0.16, C:0.26, G:0.35, T:0.23
Consensus pattern (15 bp):
CGGGTACCCGGTAAT
Found at i:891693 original size:100 final size:100
Alignment explanation
Indices: 891582--891791 Score: 379
Period size: 101 Copynumber: 2.1 Consensus size: 100
891572 CGAAATACAA
891582 AATAAATAATCCATAATAAAATAATTCATTATA-TTTATATAATTATATATAAAAAA-AAAAAAT
1 AATAAATAATCCATAAT-AAATAATTCATTATATTTTATATAATTATATATAAAAAATAAAAAAT
891645 AATAAAAACTAACCGGGATTGGTGGGTGTCGAATCC
65 AATAAAAACTAACCGGGATTGGTGGGTGTCGAATCC
891681 AATATAATAATCCATAATAAATAATTCATTATATTTTATATAATTATATATAAAAAATAAAAAAT
1 AATA-AATAATCCATAATAAATAATTCATTATATTTTATATAATTATATATAAAAAATAAAAAAT
891746 AATAAAAACTAACCGGGATTGGTGGGTGTCGAATCC
65 AATAAAAACTAACCGGGATTGGTGGGTGTCGAATCC
*
891782 AACAAATAAT
1 AATAAATAAT
891792 AATACTTGCT
Statistics
Matches: 107, Mismatches: 1, Indels: 5
0.95 0.01 0.04
Matches are distributed among these distances:
99 19 0.18
100 42 0.39
101 46 0.43
ACGTcount: A:0.50, C:0.09, G:0.10, T:0.31
Consensus pattern (100 bp):
AATAAATAATCCATAATAAATAATTCATTATATTTTATATAATTATATATAAAAAATAAAAAATA
ATAAAAACTAACCGGGATTGGTGGGTGTCGAATCC
Found at i:893496 original size:3 final size:3
Alignment explanation
Indices: 893488--894270 Score: 445
Period size: 3 Copynumber: 262.3 Consensus size: 3
893478 AGTGCCAAGA
* * * * *
893488 TTC TTC TTC TTC TTC TTC TTG TCC TTC TTC -TC ATTC TTG TCC TTG
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC
* * * * *
893533 TTC TTA TTC TT- GTC ATTC TTC TTC TTC TTA TTC TAC TTC TTC TTT
1 TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * *
893578 TTC TTC TTC TTC TTC TTC TTC TCC TTA TTC -TC TTTC TTG TCC CTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC
* * *
893623 TTC -TC ATTC TCC TTC TTC TTC TTC TCC TTC TAC TTC TTC TTC TTC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * *
893668 TTC TTC TCC TCC TCC TCC TTC TTC TTC TTC TTC TTC TTC TCC TTC TCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * *
893716 TTC -TC TTTC TCC TTC TTC TTC -TC CTC ATTC TTC TTC -TC TTTC TCC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC -TTC TTC
* *
893761 TTC -TC ATTC TTC TTC TCC TTC TTC TTC TTC TTC TTC TTC TCC TTC
1 TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * * *
893806 TTC -TC CTC ATTC -TC ATCC TTC TCC TTG TTC TCC TCC TCC TCC TCC
1 TTC TTC TTC -TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * *
893851 TCC TCC TCC TCC TCC TCCC TTC TTC TTC TTC TTC TTC TTC TTC TT-
1 TTC TTC TTC TTC TTC T-TC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * *
893896 TTC TTC TCC TTC TTC TTC -TC CTC CTC CTC CTC ATCC TCC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC
* * * * * * * *
893941 TCC TTC TCC TCC TTC -TC CTC ATTC TCC TTC TTC TCC TTC TCC TCC
1 TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * * *
893986 TTC TCC TTA TTC TCC TTC TTC TTC TCC TCC TTC TCC TCC TCC TTC TAC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
** *
894034 TTC TTC TTC TTC TTC TTC TTC TTC TTC CCC TTC TCC TTC TTC TTC -TC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * * * *
894081 ATTC TCC TCC TT- TTC CTC ATCC TCC TTC TCC TCC TCC TCC TTC TCC
1 -TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TTC TTC
* * * * * * * * * * * *
894127 TCC TCC TCC TCC TCC TAC TTC TAC -TC ATTA TCC TCC TCC TTC TCC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC TTC
894172 TTC TTC TTC TTC TT- TTC TTC TTC TT- TT- TTC TTC TTC -TC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
894216 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
894264 TTC TTC T
1 TTC TTC T
894271 CGAGTACAAT
Statistics
Matches: 632, Mismatches: 113, Indels: 70
0.78 0.14 0.09
Matches are distributed among these distances:
2 38 0.06
3 565 0.89
4 29 0.05
ACGTcount: A:0.03, C:0.41, G:0.01, T:0.55
Consensus pattern (3 bp):
TTC
Found at i:894419 original size:80 final size:80
Alignment explanation
Indices: 894281--894440 Score: 275
Period size: 80 Copynumber: 2.0 Consensus size: 80
894271 CGAGTACAAT
* *
894281 CCATTGGGAACCTCTACAGTAAGAGCTAGTCAATGTTATGAACTTTTCCTGCCCAGCTACATGAT
1 CCATTGGGAACCTCTACAGTAAGAGCTAGACAATGTTATGAACCTTTCCTGCCCAGCTACATGAT
894346 GTGTTATGGTTCCAC
66 GTGTTATGGTTCCAC
* * *
894361 CCATTGGGCACCTCTACAGTAAGAGCTTGACAATGTTATGAACCTTTCCTGCCTAGCTACATGAT
1 CCATTGGGAACCTCTACAGTAAGAGCTAGACAATGTTATGAACCTTTCCTGCCCAGCTACATGAT
894426 GTGTTATGGTTCCAC
66 GTGTTATGGTTCCAC
894441 AAATCAATCA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 75 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (80 bp):
CCATTGGGAACCTCTACAGTAAGAGCTAGACAATGTTATGAACCTTTCCTGCCCAGCTACATGAT
GTGTTATGGTTCCAC
Found at i:895544 original size:49 final size:49
Alignment explanation
Indices: 895458--895560 Score: 125
Period size: 49 Copynumber: 2.1 Consensus size: 49
895448 ACCCCATCTC
* *
895458 CAACTTCATCTCCAGCGCCAACTTTCCCATCAACCATCGCCATTTCTGA
1 CAACTCCATCTCCAGCGCCAACTTTCCCATCAACCATCGCCATCTCTGA
* * * *** *
895507 TAACTCCATCTCCAGTGCCAACTTTTCCATTGGCCATCTCCATCTCTGA
1 CAACTCCATCTCCAGCGCCAACTTTCCCATCAACCATCGCCATCTCTGA
895556 CAACT
1 CAACT
895561 GTTTAATCTC
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.23, C:0.39, G:0.09, T:0.29
Consensus pattern (49 bp):
CAACTCCATCTCCAGCGCCAACTTTCCCATCAACCATCGCCATCTCTGA
Found at i:901637 original size:45 final size:45
Alignment explanation
Indices: 901570--901692 Score: 160
Period size: 45 Copynumber: 2.8 Consensus size: 45
901560 ACCAATTTGT
* *
901570 ATAAATG-AATGAAT-ATAGAGTATAAAAGGCATAAAAGGATGCC
1 ATAAATGAAATGTATAATAGAGTATAAAAGGCATAAAAGAATGCC
* * * *
901613 ATAAATGAAATGTATAATAGAGTATAAAAGGCGTGACATAATGCC
1 ATAAATGAAATGTATAATAGAGTATAAAAGGCATAAAAGAATGCC
*
901658 ATAAATGAAATGTATAATAGTGTATAAAAAGGCAT
1 ATAAATGAAATGTATAATAGAGTAT-AAAAGGCAT
901693 GACGGTTACC
Statistics
Matches: 69, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
43 7 0.10
44 6 0.09
45 48 0.70
46 8 0.12
ACGTcount: A:0.50, C:0.07, G:0.20, T:0.24
Consensus pattern (45 bp):
ATAAATGAAATGTATAATAGAGTATAAAAGGCATAAAAGAATGCC
Found at i:901721 original size:46 final size:44
Alignment explanation
Indices: 901570--901721 Score: 148
Period size: 45 Copynumber: 3.4 Consensus size: 44
901560 ACCAATTTGT
* * * * *
901570 ATAAATG-AATGAAT-ATAGAGTATAAAAGGCATAAAAGGATGCC
1 ATAAATGAAATGTATAATAGAGTATAAAAGGCATGACA-TATACC
* *
901613 ATAAATGAAATGTATAATAGAGTATAAAAGGCGTGACATAATGCC
1 ATAAATGAAATGTATAATAGAGTATAAAAGGCATGACAT-ATACC
* *
901658 ATAAATGAAATGTATAATAGTGTATAAAAAGGCATGACGGT-TACC
1 ATAAATGAAATGTATAATAGAGTAT-AAAAGGCATGAC-ATATACC
*
901703 ATAAATGAAAATGCATAAT
1 ATAAATG-AAATGTATAAT
901722 GGTGCATTAT
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
43 7 0.08
44 6 0.06
45 58 0.62
46 21 0.23
47 1 0.01
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.24
Consensus pattern (44 bp):
ATAAATGAAATGTATAATAGAGTATAAAAGGCATGACATATACC
Found at i:905485 original size:45 final size:44
Alignment explanation
Indices: 905418--905569 Score: 164
Period size: 45 Copynumber: 3.4 Consensus size: 44
905408 ACCAATTTTT
*
905418 ATAAATG-AATGAAT-ATAGAGTATAAAAGGCATAAAAGGATGCC
1 ATAAATGAAATGCATAATAGAGTATAAAAGGCAT-AAAGGATGCC
* * *
905461 ATAAATGAAATGCATAATAGAGTATAAAAGGAATGACAGGATGTC
1 ATAAATGAAATGCATAATAGAGTATAAAAGGCAT-AAAGGATGCC
* * * * *
905506 ATAAATGAAATGTATAATAGCGTATAAAAAGGCATGATGGTTGCC
1 ATAAATGAAATGCATAATAGAGTAT-AAAAGGCATAAAGGATGCC
*
905551 ATAAATGAAAATACATAAT
1 ATAAATG-AAATGCATAAT
905570 GGTGCATTAT
Statistics
Matches: 90, Mismatches: 15, Indels: 5
0.82 0.14 0.05
Matches are distributed among these distances:
43 7 0.08
44 6 0.07
45 60 0.67
46 17 0.19
ACGTcount: A:0.49, C:0.07, G:0.20, T:0.24
Consensus pattern (44 bp):
ATAAATGAAATGCATAATAGAGTATAAAAGGCATAAAGGATGCC
Found at i:914772 original size:19 final size:18
Alignment explanation
Indices: 914735--914784 Score: 59
Period size: 19 Copynumber: 2.8 Consensus size: 18
914725 TTTAATTTTC
*
914735 ATTATTTATTTATATATAT
1 ATTATTAATTTA-ATATAT
914754 ATTATTAATTTAATCATAT
1 ATTATTAATTTAAT-ATAT
914773 -TT-TTAATTTAAT
1 ATTATTAATTTAAT
914785 TTTATAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 10 0.34
18 4 0.14
19 15 0.52
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTATTAATTTAATATAT
Done.