Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009086.1 Hibiscus syriacus cultivar Beakdansim tig00112530_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: 1596699
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 7
Found at i:1013228 original size:20 final size:21
Alignment explanation
Indices: 1013184--1013232 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
1013174 ATAGTCAGTA
*
1013184 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1013205 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1013225 TCGCATTG
1 TCGCATTG
1013233 TGAATTAGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.43
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1014034 original size:24 final size:24
Alignment explanation
Indices: 1014007--1014060 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1013997 GTATTCGAAA
*
1014007 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1014031 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1014055 TTTGAT
1 TTTGAT
1014061 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1014249 original size:12 final size:12
Alignment explanation
Indices: 1014232--1014268 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
1014222 ATATAATCCT
1014232 GAAGAAGAAAAA
1 GAAGAAGAAAAA
*
1014244 GAAGAAGGAAAA
1 GAAGAAGAAAAA
1014256 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1014268 G
1 G
1014269 TCCCCGAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1016608 original size:19 final size:19
Alignment explanation
Indices: 1016586--1016677 Score: 96
Period size: 19 Copynumber: 5.4 Consensus size: 19
1016576 GGAAATTACT
1016586 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1016605 ATCGCAA--CG--A-GATA
1 ATCGCAATGCGAAATGAAA
1016619 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1016638 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
1016652 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1016671 ATCGCAA
1 ATCGCAA
1016678 CGAGGGAATC
Statistics
Matches: 59, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 20 0.34
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 27 0.46
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1016623 original size:14 final size:14
Alignment explanation
Indices: 1016601--1016691 Score: 56
Period size: 14 Copynumber: 5.8 Consensus size: 14
1016591 AATGCGAAAT
1016601 GAAAATCGCAACGA
1 GAAAATCGCAACGA
*
1016615 GATAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
1016633 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
*
1016648 GAGAATCGCAATGCGAAA
1 GAAAATCGCAA--CG--A
1016666 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
**
1016681 GGGAATCGCAA
1 GAAAATCGCAA
1016692 AGCGAAATGA
Statistics
Matches: 61, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 29 0.48
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 20 0.33
ACGTcount: A:0.45, C:0.19, G:0.24, T:0.12
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:1016628 original size:33 final size:33
Alignment explanation
Indices: 1016586--1016712 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
1016576 GGAAATTACT
*
1016586 ATCGCAATGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1016619 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
1016652 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
1016685 ATCGCAAAGCGAAATGAAAATCACAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
1016713 CGAATTTAGT
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1016734 original size:19 final size:19
Alignment explanation
Indices: 1016712--1016772 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
1016702 AAATCACAAC
*
1016712 GCGAATTTAGTTTCGTGTT
1 GCGAATTTAGTTTCGCGTT
*
1016731 GCGATTTTAGTTTCGCGTT
1 GCGAATTTAGTTTCGCGTT
* *
1016750 GCGATTTTCA-TTTCGCATT
1 GCGAATTT-AGTTTCGCGTT
1016769 GCGA
1 GCGA
1016773 TTCTCTCGTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 37 0.97
20 1 0.03
ACGTcount: A:0.15, C:0.16, G:0.25, T:0.44
Consensus pattern (19 bp):
GCGAATTTAGTTTCGCGTT
Found at i:1016773 original size:19 final size:19
Alignment explanation
Indices: 1016729--1016839 Score: 109
Period size: 19 Copynumber: 6.4 Consensus size: 19
1016719 TAGTTTCGTG
*
1016729 TTGCGATTTT-AGTTTCGCG
1 TTGCGATTTTCA-TTTCGCA
1016748 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1016767 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1016781 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1016800 TTGCGA--TT-ATATCG--
1 TTGCGATTTTCATTTCGCA
1016814 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1016833 TTGCGAT
1 TTGCGAT
1016840 AGTAATTTTT
Statistics
Matches: 76, Mismatches: 5, Indels: 22
0.74 0.05 0.21
Matches are distributed among these distances:
14 12 0.16
16 14 0.18
17 14 0.18
19 35 0.46
20 1 0.01
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1016788 original size:33 final size:33
Alignment explanation
Indices: 1016746--1016839 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
1016736 TTTAGTTTCG
* *
1016746 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATAT
1016779 CGTTGCGATTTTCATTTCGCATTGCGATTATAT
1 CGTTGCGATTTTCATTTCGCATTGCGATTATAT
1016812 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
1016840 AGTAATTTTT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTATAT
Found at i:1018371 original size:21 final size:21
Alignment explanation
Indices: 1018305--1018371 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1018295 GTGAATCGGG
*
1018305 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1018325 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1018347 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1018368 CTCT
1 CTCT
1018372 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1018820 original size:91 final size:90
Alignment explanation
Indices: 1018645--1018826 Score: 294
Period size: 91 Copynumber: 2.0 Consensus size: 90
1018635 ATTTCAAACT
*
1018645 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
1018710 AGAATTGGCAGCAACCGAATAAATTTTC
63 AGAATTGGCAGCAACCGAATAAATTTTC
1018738 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
1018802 GTATTGGCAGCAACCGAATAAATTT
64 GAATTGGCAGCAACCGAATAAATTT
1018827 ACTAAGCAAT
Statistics
Matches: 85, Mismatches: 2, Indels: 6
0.91 0.02 0.06
Matches are distributed among these distances:
91 39 0.46
93 19 0.22
95 27 0.32
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTTC
Found at i:1020538 original size:20 final size:19
Alignment explanation
Indices: 1020511--1020651 Score: 95
Period size: 19 Copynumber: 7.8 Consensus size: 19
1020501 TATTTTGGTT
1020511 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1020530 GATAATGAAAATCGTAACGCG
1 GA-AATGAAAATCGCAACG-A
**
1020551 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
1020570 G--A-G--AATCGCAAAGT
1 GAAATGAAAATCGCAACGA
** *
1020584 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
1020603 GAAACGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
1020622 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
1020636 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1020652 TGCGATTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 20 0.22
16 4 0.04
17 4 0.04
19 35 0.38
20 28 0.30
21 2 0.02
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:1020685 original size:19 final size:19
Alignment explanation
Indices: 1020652--1020695 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
1020642 AAAATCGCAA
**
1020652 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
1020671 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
1020690 TGCGAT
1 TGCGAT
1020696 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.09, C:0.18, G:0.27, T:0.45
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:1021328 original size:20 final size:21
Alignment explanation
Indices: 1021284--1021335 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1021274 ATAGTCAGTA
*
1021284 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1021305 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1021325 TCGCATTGCGA
1 TCGCATTGCGA
1021336 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1021350 original size:41 final size:41
Alignment explanation
Indices: 1021242--1021350 Score: 96
Period size: 41 Copynumber: 2.7 Consensus size: 41
1021232 CGAATCGTAA
* * *
1021242 ATCGCAATGCGAATTAGGAAAATTGCATTGCGATAGTCAGT
1 ATCGCATTGCGAATTAGGAAAATCGCATTGCGATACTCAGT
* *** * *
1021283 ATCGCATTGCGATTTTCCAAATTCGCATTGCGATTTACTTA-T
1 ATCGCATTGCGAATTAGGAAAATCGCATTGCGA--TACTCAGT
*
1021325 -TCGCATTGCGAATTGGGAAAATCGCA
1 ATCGCATTGCGAATTAGGAAAATCGCA
1021351 ACGCGAAATT
Statistics
Matches: 52, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
41 47 0.90
42 1 0.02
43 4 0.08
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.31
Consensus pattern (41 bp):
ATCGCATTGCGAATTAGGAAAATCGCATTGCGATACTCAGT
Found at i:1021377 original size:21 final size:22
Alignment explanation
Indices: 1021325--1021377 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
1021315 ATTTACTTAT
1021325 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
1021346 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
1021367 TCGCATTGCGA
1 TCGCATTGCGA
1021378 TTGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:1021390 original size:20 final size:20
Alignment explanation
Indices: 1021266--1021397 Score: 65
Period size: 21 Copynumber: 6.5 Consensus size: 20
1021256 TAGGAAAATT
*
1021266 GCATTGCGATAGTCAGT-ATC
1 GCATTGCGATTGTCA-TAATC
*
1021286 GCATTGCGATTTTCCA-AATTC
1 GCATTGCGATTGT-CATAA-TC
* *
1021307 GCATTGCGATT-TACTTATTC
1 GCATTGCGATTGT-CATAATC
** *
1021327 GCATTGCGAATTGGGAAAATC
1 GCATTGCG-ATTGTCATAATC
** * *
1021348 GCAACGCGAAATTG-GAAAATC
1 GCATTGCG--ATTGTCATAATC
1021369 GCATTGCGATTGTCATAATC
1 GCATTGCGATTGTCATAATC
*
1021389 GCGTTGCGA
1 GCATTGCGA
1021398 ATCTGGAAAC
Statistics
Matches: 87, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
19 4 0.05
20 37 0.43
21 41 0.47
22 5 0.06
ACGTcount: A:0.27, C:0.20, G:0.23, T:0.30
Consensus pattern (20 bp):
GCATTGCGATTGTCATAATC
Found at i:1023206 original size:2 final size:2
Alignment explanation
Indices: 1023201--1023231 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1023191 TGGGGGTGTG
1023201 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1023232 GTATCATTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1023722 original size:14 final size:14
Alignment explanation
Indices: 1023705--1023738 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1023695 TGTTTCACTG
1023705 AAAATGTTTTTCGA
1 AAAATGTTTTTCGA
* *
1023719 AAAATATTTTTCGT
1 AAAATGTTTTTCGA
1023733 AAAATG
1 AAAATG
1023739 AATTACATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (14 bp):
AAAATGTTTTTCGA
Found at i:1024014 original size:32 final size:30
Alignment explanation
Indices: 1023945--1024015 Score: 72
Period size: 32 Copynumber: 2.2 Consensus size: 30
1023935 AAAATATTTT
* *
1023945 TTATAATTTTATTAATAAAAATATTAATAT
1 TTATATTTTTATTAATAAAAATATTAATAA
1023975 TGATATATTTTTATTGAAATAAAAATATT-ATAAA
1 T--TATATTTTTATT--AATAAAAATATTAAT-AA
1024009 TTATATT
1 TTATATT
1024016 AATTATTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
30 1 0.03
32 17 0.50
33 2 0.06
34 14 0.41
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (30 bp):
TTATATTTTTATTAATAAAAATATTAATAA
Found at i:1024035 original size:37 final size:33
Alignment explanation
Indices: 1023946--1024035 Score: 94
Period size: 34 Copynumber: 2.6 Consensus size: 33
1023936 AAATATTTTT
* *
1023946 TATAATTTTATT-AATAAAAATATTAATATTGA
1 TATATTTTTATTAAATAAAAATATTAAAATTGA
1023978 TATATTTTTATTGAAATAAAAATATTATAAATT-A
1 TATATTTTTATT-AAATAAAAATATTA-AAATTGA
1024012 TATTAATTATTTATTAAAGTAAAA
1 TA-T-ATT-TTTATTAAA-TAAAA
1024036 GTGTTGTATT
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
32 11 0.22
34 16 0.33
35 5 0.10
36 6 0.12
37 11 0.22
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (33 bp):
TATATTTTTATTAAATAAAAATATTAAAATTGA
Found at i:1024075 original size:23 final size:23
Alignment explanation
Indices: 1024045--1024089 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1024035 AGTGTTGTAT
1024045 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAAAATATTAATTAG
* *
1024068 TATATTTTAAATATATTTATTA
1 TATATTTTAAAAATATTAATTA
1024090 AAATATTATT
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:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
TATATTTTAAAAATATTAATTAG
Found at i:1024093 original size:35 final size:34
Alignment explanation
Indices: 1024045--1024142 Score: 89
Period size: 34 Copynumber: 2.9 Consensus size: 34
1024035 AGTGTTGTAT
*
1024045 TATATTTTAAAAATATTAATTAGTA-T-ATTTTAAA
1 TATATTTTAAAAATATT-ATTA-TATTAATATTAAA
*
1024079 TATATTTATTAAAATATTATTATATTAATATTAAA
1 TATATTT-TAAAAATATTATTATATTAATATTAAA
1024114 TATA---TAAATAATATTATTCATTATTAATA
1 TATATTTTAAA-AATATTATT-A-TATTAATA
1024143 ATTTAATAAT
Statistics
Matches: 55, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
31 3 0.05
32 9 0.16
33 3 0.05
34 20 0.36
35 20 0.36
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (34 bp):
TATATTTTAAAAATATTATTATATTAATATTAAA
Found at i:1024095 original size:23 final size:23
Alignment explanation
Indices: 1024046--1024096 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1024036 GTGTTGTATT
**
1024046 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* *
1024069 ATATTTTAAATATATTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
1024092 ATATT
1 ATATT
1024097 ATTATATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:1024142 original size:27 final size:26
Alignment explanation
Indices: 1024107--1024181 Score: 73
Period size: 27 Copynumber: 2.7 Consensus size: 26
1024097 ATTATATTAA
1024107 TATTAAATATATAAATAATATTATTCAT
1 TATT-AATA-ATAAATAATATTATTCAT
*
1024135 TATTAATAATTTAATAATATTATT--T
1 TATTAATAA-TAAATAATATTATTCAT
1024160 CTATTAAATTAATAAATAATAT
1 -TATT-AA-TAATAAATAATAT
1024182 AAATTTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
25 1 0.02
26 5 0.12
27 28 0.68
28 7 0.17
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (26 bp):
TATTAATAATAAATAATATTATTCAT
Found at i:1024209 original size:54 final size:53
Alignment explanation
Indices: 1024107--1024212 Score: 126
Period size: 54 Copynumber: 2.0 Consensus size: 53
1024097 ATTATATTAA
* *
1024107 TATTAAATATATAAATAATATTATTCATTATTAATAATTTAATAATATTATTTC
1 TATTAAATATATAAATAATATAATT-ATTATTAATAATGTAATAATATTATTTC
* *
1024161 TATTAAAT-TAATAAATAATATAAATT-TTATTATTAATGTATTATATATTATT
1 TATTAAATAT-ATAAATAATAT-AATTATTATTAATAATGTAATA-ATATTATT
1024213 AAAATAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
53 15 0.33
54 27 0.60
55 3 0.07
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (53 bp):
TATTAAATATATAAATAATATAATTATTATTAATAATGTAATAATATTATTTC
Found at i:1024239 original size:44 final size:45
Alignment explanation
Indices: 1024170--1024257 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 45
1024160 CTATTAAATT
* *
1024170 AATAAATAATATAAATTTTATTATTAATGTATTATATATT-ATTAA
1 AATAAATAATATAAATCTTATTATTAATATATTATA-ATTGATTAA
*
1024215 AATAAA-AATATAATATCTTA-TATTATTATATTATAATTGATTA
1 AATAAATAATATAA-ATCTTATTATTAATATATTATAATTGATTA
1024258 TTTTATTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
43 3 0.08
44 24 0.63
45 11 0.29
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.48
Consensus pattern (45 bp):
AATAAATAATATAAATCTTATTATTAATATATTATAATTGATTAA
Found at i:1024289 original size:22 final size:23
Alignment explanation
Indices: 1024261--1024307 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1024251 TTGATTATTT
1024261 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
1024283 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
1024306 TA
1 TA
1024308 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:1024312 original size:22 final size:22
Alignment explanation
Indices: 1024269--1024312 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1024259 TTTATTATAA
*
1024269 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
1024291 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
1024313 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:1027081 original size:27 final size:27
Alignment explanation
Indices: 1027051--1027107 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
1027041 CAGCAATACT
1027051 CGAGTTCGACTTGGCTCATTTAACAAA
1 CGAGTTCGACTTGGCTCATTTAACAAA
*
1027078 CGAGTTTGACTTGGCTCATTTAACAAA
1 CGAGTTCGACTTGGCTCATTTAACAAA
1027105 CGA
1 CGA
1027108 CGTTGTTTGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (27 bp):
CGAGTTCGACTTGGCTCATTTAACAAA
Found at i:1031948 original size:21 final size:21
Alignment explanation
Indices: 1031922--1031961 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1031912 CAGAACCCCA
*
1031922 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1031943 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1031962 TCAAAGGGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1038424 original size:31 final size:31
Alignment explanation
Indices: 1038389--1038497 Score: 146
Period size: 31 Copynumber: 3.5 Consensus size: 31
1038379 TTCAATGTCC
* * * * *
1038389 AAGTGACCAAAACTTTATGAAACTATAACGT
1 AAGTAACCAAAACTTAATAAAACGATAATGT
* *
1038420 AAGTGATCAAAACTTAATAAAACGATAATGT
1 AAGTAACCAAAACTTAATAAAACGATAATGT
1038451 AAGTAACCAAAACTTAATAAAACGATAATGT
1 AAGTAACCAAAACTTAATAAAACGATAATGT
*
1038482 AAGTAATCAAAACTTA
1 AAGTAACCAAAACTTA
1038498 TGTTTTTTAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 70 1.00
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (31 bp):
AAGTAACCAAAACTTAATAAAACGATAATGT
Found at i:1038914 original size:3 final size:3
Alignment explanation
Indices: 1038906--1038987 Score: 155
Period size: 3 Copynumber: 27.0 Consensus size: 3
1038896 ATGGTTATAC
1038906 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1038954 AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1038988 TTAACTTCAA
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
3 75 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1042585 original size:13 final size:13
Alignment explanation
Indices: 1042567--1042592 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1042557 AGTCTTTATA
1042567 ATTTTAAAATTTT
1 ATTTTAAAATTTT
1042580 ATTTTAAAATTTT
1 ATTTTAAAATTTT
1042593 TTAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
ATTTTAAAATTTT
Found at i:1049342 original size:17 final size:17
Alignment explanation
Indices: 1049316--1049353 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1049306 ATCACTACGT
*
1049316 GGCGCTAACTCAGAGAA
1 GGCGCCAACTCAGAGAA
*
1049333 GGCGCCAACTTAGAGAA
1 GGCGCCAACTCAGAGAA
1049350 GGCG
1 GGCG
1049354 TAGATGACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.24, G:0.34, T:0.11
Consensus pattern (17 bp):
GGCGCCAACTCAGAGAA
Found at i:1049932 original size:21 final size:21
Alignment explanation
Indices: 1049907--1049947 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1049897 AAAAAATTAC
1049907 CTAAAACATT-ATTATTTTTAT
1 CTAAAACATTAATT-TTTTTAT
*
1049928 CTAAAACGTTAATTTTTTTA
1 CTAAAACATTAATTTTTTTA
1049948 ACATTTCCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.37, C:0.10, G:0.02, T:0.51
Consensus pattern (21 bp):
CTAAAACATTAATTTTTTTAT
Found at i:1050909 original size:18 final size:19
Alignment explanation
Indices: 1050875--1050910 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1050865 TTAAATAAAA
1050875 TAAAATAATATTCTATAAT
1 TAAAATAATATTCTATAAT
*
1050894 TAAAAT-ATATTTTATAA
1 TAAAATAATATTCTATAA
1050911 CTTTTAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAATAATATTCTATAAT
Found at i:1051893 original size:37 final size:36
Alignment explanation
Indices: 1051848--1051921 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 36
1051838 GTTGGAAAAT
*
1051848 ATTTATAT-ATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATAATTTT-TTTAAAAAATTTAAAAT-ATAAA
*
1051885 ATTTATATAATTTTTTTACAAAATTTAAAATATAAA
1 ATTTATATAATTTTTTTAAAAAATTTAAAATATAAA
1051921 A
1 A
1051922 AAGTTTAATG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 6 0.18
37 23 0.68
38 5 0.15
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (36 bp):
ATTTATATAATTTTTTTAAAAAATTTAAAATATAAA
Found at i:1052287 original size:31 final size:31
Alignment explanation
Indices: 1052251--1052344 Score: 179
Period size: 31 Copynumber: 3.0 Consensus size: 31
1052241 TATGGATTCT
1052251 ATTCCCATGAGAATCTCACATTCCCCAAACC
1 ATTCCCATGAGAATCTCACATTCCCCAAACC
*
1052282 ATTCCCATGGGAATCTCACATTCCCCAAACC
1 ATTCCCATGAGAATCTCACATTCCCCAAACC
1052313 ATTCCCATGAGAATCTCACATTCCCCAAACC
1 ATTCCCATGAGAATCTCACATTCCCCAAACC
1052344 A
1 A
1052345 AACACTAATA
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.32, C:0.38, G:0.07, T:0.22
Consensus pattern (31 bp):
ATTCCCATGAGAATCTCACATTCCCCAAACC
Found at i:1053175 original size:27 final size:27
Alignment explanation
Indices: 1053144--1053202 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
1053134 AATTATTGGA
* *
1053144 GCTTATAAATCTTGAACTAGGAAGTTT
1 GCTTATAAAACTTAAACTAGGAAGTTT
1053171 GCTTATAAAACTTAAACTAGGAAGTTT
1 GCTTATAAAACTTAAACTAGGAAGTTT
*
1053198 ACTTA
1 GCTTA
1053203 CGAGCTTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.36
Consensus pattern (27 bp):
GCTTATAAAACTTAAACTAGGAAGTTT
Found at i:1063929 original size:2 final size:2
Alignment explanation
Indices: 1063922--1063963 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
1063912 AAAATAAGAC
1063922 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1063964 GCATTGTCAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1065071 original size:11 final size:11
Alignment explanation
Indices: 1065051--1065083 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
1065041 TGTGCTCTAT
*
1065051 CAACTGAGCAC
1 CAACTAAGCAC
1065062 CAACTAAGCAC
1 CAACTAAGCAC
1065073 CAACTAAGCAC
1 CAACTAAGCAC
1065084 GATAGTCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.42, C:0.36, G:0.12, T:0.09
Consensus pattern (11 bp):
CAACTAAGCAC
Found at i:1070405 original size:24 final size:23
Alignment explanation
Indices: 1070359--1070415 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 23
1070349 TTTGAACTTG
1070359 AATCGAGCTCAGAATCGAGCTTC
1 AATCGAGCTCAGAATCGAGCTTC
** *
1070382 AATCGAGCTCGAGTCTCGATCTTC
1 AATCGAGCTC-AGAATCGAGCTTC
1070406 AATCGAGCTC
1 AATCGAGCTC
1070416 CTGAATTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 10 0.33
24 20 0.67
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (23 bp):
AATCGAGCTCAGAATCGAGCTTC
Found at i:1079930 original size:22 final size:22
Alignment explanation
Indices: 1079905--1079950 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
1079895 ATGAGGCATC
1079905 CAGAAGGCTTCATAGAAGCAGA
1 CAGAAGGCTTCATAGAAGCAGA
1079927 CAGAAGGCTTCATAGAAGCAGA
1 CAGAAGGCTTCATAGAAGCAGA
1079949 CA
1 CA
1079951 AGAAAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.26, T:0.13
Consensus pattern (22 bp):
CAGAAGGCTTCATAGAAGCAGA
Found at i:1081301 original size:30 final size:30
Alignment explanation
Indices: 1081265--1081332 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 30
1081255 TTAGTCCTTA
1081265 AGCTTCAACTATAAATACCCTTACCCATTT
1 AGCTTCAACTATAAATACCCTTACCCATTT
*
1081295 AGCTTCAACTATAAATACTCTTACCCATTT
1 AGCTTCAACTATAAATACCCTTACCCATTT
1081325 AGCTTCAA
1 AGCTTCAA
1081333 AATCATCCCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (30 bp):
AGCTTCAACTATAAATACCCTTACCCATTT
Found at i:1082834 original size:33 final size:33
Alignment explanation
Indices: 1082792--1082870 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
1082782 ACTTCCCGAC
1082792 TGAAAGAAAAGAAAAACAAGAAGAACATTATCA
1 TGAAAGAAAAGAAAAACAAGAAGAACATTATCA
* *
1082825 TGAAAGAAAAGAAAAACGAGAAGATCATTATCA
1 TGAAAGAAAAGAAAAACAAGAAGAACATTATCA
**
1082858 TGAATTAAAAGAA
1 TGAAAGAAAAGAA
1082871 CTTGGAAAGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.15
Consensus pattern (33 bp):
TGAAAGAAAAGAAAAACAAGAAGAACATTATCA
Found at i:1088373 original size:29 final size:29
Alignment explanation
Indices: 1088328--1088386 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
1088318 ATTTTCACCT
*
1088328 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATATAAGCAATGACATCAA
1088357 AACTAAATTGATATAAGCAATGACATCAA
1 AACTAAATTGATATAAGCAATGACATCAA
1088386 A
1 A
1088387 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATATAAGCAATGACATCAA
Found at i:1092846 original size:29 final size:29
Alignment explanation
Indices: 1092804--1092862 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
1092794 ATTTTCACCT
1092804 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1092833 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
1092862 A
1 A
1092863 TTAATTTAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:1096473 original size:25 final size:25
Alignment explanation
Indices: 1096406--1096477 Score: 74
Period size: 24 Copynumber: 2.9 Consensus size: 25
1096396 TAACAATGTT
* * **
1096406 TGTCTAAATTAATTCGAGCAAAGTA
1 TGTCTAAATCAATTCGAGCTAACAA
* * *
1096431 TGTCTTAGTCGA-TCGAGCTAACAA
1 TGTCTAAATCAATTCGAGCTAACAA
1096455 TGTCTAAATCAATTCGAGCTAAC
1 TGTCTAAATCAATTCGAGCTAAC
1096478 TAAGTTTGAA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
24 18 0.50
25 18 0.50
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (25 bp):
TGTCTAAATCAATTCGAGCTAACAA
Found at i:1098059 original size:13 final size:14
Alignment explanation
Indices: 1098019--1098062 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 14
1098009 ATTAATTTTA
1098019 AAAATAATTAAATT
1 AAAATAATTAAATT
1098033 AGAAATAATTAAATT
1 A-AAATAATTAAATT
*
1098048 AAAAT-TTTAAATT
1 AAAATAATTAAATT
1098061 AA
1 AA
1098063 CTAACCTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 9 0.32
14 5 0.18
15 14 0.50
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (14 bp):
AAAATAATTAAATT
Found at i:1104380 original size:18 final size:18
Alignment explanation
Indices: 1104357--1104401 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
1104347 AGAATTGTAT
1104357 TGAATCAATTTCTTTTAA
1 TGAATCAATTTCTTTTAA
1104375 TGAATCAATTTCTTTTAA
1 TGAATCAATTTCTTTTAA
1104393 TGAATCAAT
1 TGAATCAAT
1104402 CCAATCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (18 bp):
TGAATCAATTTCTTTTAA
Found at i:1104493 original size:2 final size:2
Alignment explanation
Indices: 1104488--1104514 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1104478 TGTGTGTGTT
1104488 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1104515 TACCTTTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1106267 original size:30 final size:29
Alignment explanation
Indices: 1106207--1106274 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 29
1106197 GTTAAATTGA
* *
1106207 TATTTTATATAAAGTTAAGATTAAATTAG
1 TATTTTATATAAAGTTAAGATCAAAATAG
* *
1106236 TATTTTATGTAAAGTTTAAGGTCAAAATAG
1 TATTTTATATAAAG-TTAAGATCAAAATAG
*
1106266 TATTATATA
1 TATTTTATA
1106275 AAAAATTCAA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.41
30 19 0.59
ACGTcount: A:0.43, C:0.01, G:0.12, T:0.44
Consensus pattern (29 bp):
TATTTTATATAAAGTTAAGATCAAAATAG
Found at i:1107643 original size:2 final size:2
Alignment explanation
Indices: 1107636--1107680 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
1107626 TAAATCCACA
1107636 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1107677 AT AT
1 AT AT
1107681 TTGTAAATGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 41 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1113769 original size:21 final size:20
Alignment explanation
Indices: 1113683--1113840 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1113673 AAATGACCAA
**
1113683 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1113702 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1113722 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1113742 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
1113763 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1113784 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
1113804 CCATAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
1113825 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1113841 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 40 0.39
21 46 0.45
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1113833 original size:20 final size:20
Alignment explanation
Indices: 1113808--1114001 Score: 78
Period size: 20 Copynumber: 9.7 Consensus size: 20
1113798 GATTTTCCAT
* *
1113808 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
1113828 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
1113848 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1113868 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1113888 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1113908 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
1113928 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
1113948 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
1113969 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
1113989 AATCGCAACGCGA
1 AATCGCAACGCGA
1114002 TATTTAAAGC
Statistics
Matches: 147, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.02
20 128 0.87
21 15 0.10
22 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:1113855 original size:40 final size:39
Alignment explanation
Indices: 1113804--1114001 Score: 209
Period size: 40 Copynumber: 5.0 Consensus size: 39
1113794 TTGCGATTTT
* ** *
1113804 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
1113842 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * * *
1113883 CCGTATATCGCAACGCGTATCCGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
1113923 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
1113962 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1114002 TATTTAAAGC
Statistics
Matches: 136, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 98 0.72
41 33 0.24
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:1113893 original size:60 final size:60
Alignment explanation
Indices: 1113808--1114000 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
1113798 GATTTTCCAT
* ** *
1113808 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
* * * * *
1113868 AATCGCAACGTGTATCCGTATATCGCAACGCGTATC-CGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACATAAATCGCAACGCGTATCCGTA
* ** *
1113928 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT-AAATCGCAACGCGTATCCGTA
1113989 AATCGCAACGCG
1 AATCGCAACGCG
1114001 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.01
60 77 0.69
61 33 0.30
ACGTcount: A:0.35, C:0.27, G:0.19, T:0.20
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
Found at i:1114421 original size:33 final size:33
Alignment explanation
Indices: 1114382--1114452 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1114372 TTCACTTAGA
*
1114382 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
1114415 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1114448 TTTCA
1 TTTCA
1114453 AGTTAGTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1114558 original size:21 final size:20
Alignment explanation
Indices: 1114532--1114623 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
1114522 TGCAGAAGAG
1114532 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
1114553 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
1114573 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* *
1114594 TTGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
1114613 TCGCAACGAGA
1 TCGCAACGAGA
1114624 GAATCGCAAC
Statistics
Matches: 57, Mismatches: 12, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
19 17 0.30
20 16 0.28
21 24 0.42
ACGTcount: A:0.46, C:0.17, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:1114589 original size:41 final size:40
Alignment explanation
Indices: 1114530--1114626 Score: 131
Period size: 41 Copynumber: 2.4 Consensus size: 40
1114520 TTTGCAGAAG
* *
1114530 AGTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGAC
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGA-AATGAA
* * *
1114571 TGTCGCAACGAGAGAAATGAAAATTGCAACGCGAAATGAA
1 AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGAA
*
1114611 AATCGCAACGAGAGAA
1 AGTCGCAACGAGAGAA
1114627 TCGCAACGCG
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
40 19 0.39
41 30 0.61
ACGTcount: A:0.46, C:0.16, G:0.25, T:0.12
Consensus pattern (40 bp):
AGTCGCAACGAGAGAAATGAAAATCGCAACGAGAAATGAA
Found at i:1114608 original size:19 final size:19
Alignment explanation
Indices: 1114544--1114620 Score: 73
Period size: 19 Copynumber: 3.9 Consensus size: 19
1114534 GCAACGAGAT
*
1114544 AAATGAAAATCGCAACGAG
1 AAATGAAAATCGCAACGCG
*** *
1114563 AGAATGACTGTCGCAACGAGAG
1 A-AATGAAAATCGCAAC--GCG
*
1114585 AAATGAAAATTGCAACGCG
1 AAATGAAAATCGCAACGCG
1114604 AAATGAAAATCGCAACG
1 AAATGAAAATCGCAACG
1114621 AGAGAATCGC
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
19 19 0.41
20 12 0.26
21 11 0.24
22 4 0.09
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (19 bp):
AAATGAAAATCGCAACGCG
Found at i:1114668 original size:19 final size:19
Alignment explanation
Indices: 1114646--1114759 Score: 94
Period size: 19 Copynumber: 6.1 Consensus size: 19
1114636 GAAACCAAAA
*
1114646 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1114665 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
1114679 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
1114698 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
1114718 CTCTCGTTGCGACAATCATT
1 -TCGCGTTGCGATTTTCATT
*
1114738 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
1114758 TC
1 TC
1114760 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
14 10 0.12
16 3 0.04
17 3 0.04
19 29 0.36
20 21 0.26
21 14 0.17
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1114755 original size:41 final size:40
Alignment explanation
Indices: 1114676--1114759 Score: 132
Period size: 41 Copynumber: 2.1 Consensus size: 40
1114666 CGCGTTGCGA
***
1114676 TTCTCTCGTTGCGATTTTCATTTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAATCATTTCTCGTTGCGATTTTCAT
1114716 TTCTCTCGTTGCGACAATCATTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAATCATT-TCTCGTTGCGATTTTCAT
1114757 TTC
1 TTC
1114760 AACCAAAAGA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
40 19 0.47
41 21 0.52
ACGTcount: A:0.12, C:0.25, G:0.14, T:0.49
Consensus pattern (40 bp):
TTCTCTCGTTGCGACAATCATTTCTCGTTGCGATTTTCAT
Found at i:1114756 original size:20 final size:20
Alignment explanation
Indices: 1114675--1114757 Score: 123
Period size: 20 Copynumber: 4.2 Consensus size: 20
1114665 TCGCGTTGCG
1114675 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1114695 ATT-TCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
1114714 ATTTCTCTCGTTGCGACAATC
1 A-TTCTCTCGTTGCGATTTTC
1114735 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
1114755 ATT
1 ATT
1114758 TCAACCAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
19 17 0.31
20 24 0.44
21 14 0.25
ACGTcount: A:0.13, C:0.24, G:0.14, T:0.48
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1116619 original size:93 final size:93
Alignment explanation
Indices: 1116458--1116930 Score: 921
Period size: 93 Copynumber: 5.1 Consensus size: 93
1116448 TAGATTGCTT
*
1116458 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1116523 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1116551 AATAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1116616 TTTGTCTTTGTTTTGTC-TTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1116643 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1116708 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1116736 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1116801 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1116829 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1116894 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1116922 AGTAAATTT
1 AGTAAATTT
1116931 ATCCATTCAA
Statistics
Matches: 376, Mismatches: 3, Indels: 2
0.99 0.01 0.01
Matches are distributed among these distances:
92 91 0.24
93 285 0.76
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1116688 original size:185 final size:186
Alignment explanation
Indices: 1116458--1116930 Score: 921
Period size: 185 Copynumber: 2.5 Consensus size: 186
1116448 TAGATTGCTT
*
1116458 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1116523 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAATAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1116588 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTC-TTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1116643 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1116708 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
1116773 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
1116829 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1116894 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
1116931 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
185 173 0.61
186 112 0.39
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1117014 original size:19 final size:19
Alignment explanation
Indices: 1116974--1117102 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1116964 TAGTTTACTT
* *
1116974 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
1116994 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
1117013 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
1117032 TCGCAA--CG--A-CATAA
1 TCGCAACGCGAAACCAAAA
1117046 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
1117065 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
1117079 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
1117098 TCGCA
1 TCGCA
1117103 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:1117053 original size:33 final size:32
Alignment explanation
Indices: 1117010--1117102 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
1117000 CGCGAAACCA
**
1117010 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
1117042 ATAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
1117075 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
1117103 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.17, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:1117100 original size:52 final size:52
Alignment explanation
Indices: 1116974--1117102 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
1116964 TAGTTTACTT
**
1116974 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
1117026 T-G-AAAATCGCAACGACATAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
1117079 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
1117103 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:1117120 original size:19 final size:19
Alignment explanation
Indices: 1117098--1117232 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1117088 GAAACCAAAA
*
1117098 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
1117117 TCGCGTTGCGA--TT-ATT
1 TCGCGTTGCGATTTTCATT
1117133 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
1117150 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
1117166 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
1117183 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
1117202 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
1117222 TCGTGTTGCGA
1 TCGCGTTGCGA
1117233 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:1117139 original size:14 final size:14
Alignment explanation
Indices: 1117120--1117176 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
1117110 TTTCATTTCG
1117120 CGTTGCGATTATTT
1 CGTTGCGATTATTT
1117134 CGTTGCGATTTTCATTT
1 CGTTGCGA--TT-ATTT
* *
1117151 CGCATTGCGATTCTGT
1 CG--TTGCGATTATTT
1117167 CGTTGCGATT
1 CGTTGCGATT
1117177 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 6 0.17
17 8 0.22
19 6 0.17
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTATTT
Found at i:1117145 original size:33 final size:33
Alignment explanation
Indices: 1117103--1117195 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
1117093 CAAAATCGCA
*
1117103 TTGCGATTTTCATTTCGCGTTGCGATTATTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
* *
1117136 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
1117169 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
1117196 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
Found at i:1119150 original size:57 final size:54
Alignment explanation
Indices: 1119042--1119157 Score: 180
Period size: 57 Copynumber: 2.1 Consensus size: 54
1119032 GTATGGCTGC
*
1119042 AAAAGTTGATTCAATAGTTTAATTGATTGTTTTTTGATTGTTTAATTGATTTGT
1 AAAAGTTGAATCAATAGTTTAATTGATTGTTTTTTGATTGTTTAATTGATTTGT
1119096 AAAAGTTGAATCAATAGTTTAATT-ATTGCTTATTTTTTGATTGTTTAATTGATTTGT
1 AAAAGTTGAATCAATAGTTTAATTGATTG----TTTTTTGATTGTTTAATTGATTTGT
1119153 AAAAG
1 AAAAG
1119158 ATGATTTGTA
Statistics
Matches: 57, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
53 4 0.07
54 23 0.40
57 30 0.53
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.51
Consensus pattern (54 bp):
AAAAGTTGAATCAATAGTTTAATTGATTGTTTTTTGATTGTTTAATTGATTTGT
Found at i:1119164 original size:14 final size:14
Alignment explanation
Indices: 1119145--1119180 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1119135 ATTGTTTAAT
1119145 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1119159 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1119173 TGATTTGT
1 TGATTTGT
1119181 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:1119311 original size:19 final size:19
Alignment explanation
Indices: 1119287--1119384 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
1119277 AAAATTGACT
1119287 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
1119306 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
1119325 ATCCCAA--C---ATGAAA
1 ATCGCAATGCGAAATGAAA
*
1119339 ATCGCAATGCGGAATGAAA
1 ATCGCAATGCGAAATGAAA
1119358 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
1119378 ATCGCAA
1 ATCGCAA
1119385 CGGGAGAATC
Statistics
Matches: 70, Mismatches: 3, Indels: 11
0.83 0.04 0.13
Matches are distributed among these distances:
14 12 0.17
16 1 0.01
17 1 0.01
19 41 0.59
20 15 0.21
ACGTcount: A:0.46, C:0.18, G:0.20, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:1119365 original size:52 final size:53
Alignment explanation
Indices: 1119287--1119403 Score: 182
Period size: 53 Copynumber: 2.2 Consensus size: 53
1119277 AAAATTGACT
*
1119287 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCCCAACATGAAA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCCCAACAGGAAA
* * * *
1119339 ATCGCAATGCGGAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCCCAACAGGAAA
1119392 ATCGCAATGCGA
1 ATCGCAATGCGA
1119404 TTTTAATTTC
Statistics
Matches: 58, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
52 28 0.48
53 30 0.52
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCCCAACAGGAAA
Found at i:1119421 original size:19 final size:19
Alignment explanation
Indices: 1119393--1119771 Score: 351
Period size: 19 Copynumber: 21.7 Consensus size: 19
1119383 AACGGGAGAA
* *
1119393 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
1119412 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1119428 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1119445 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
**
1119464 TCGCATTGCGA--TTC-CC
1 TCGCATTGCGATTTTCATT
1119480 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1119497 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
**
1119516 TCGCATTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
1119535 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
* *
1119549 TCCCATTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
1119568 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1119586 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1119602 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
1119621 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
1119637 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1119654 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
**
1119673 TCGCATTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
1119692 TCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATT
* *
1119706 TCCCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
1119725 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
1119743 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
1119759 TCGCATTGCGATT
1 TCGCATTGCGATT
1119772 CTCTCGTTGC
Statistics
Matches: 295, Mismatches: 28, Indels: 74
0.74 0.07 0.19
Matches are distributed among these distances:
14 59 0.20
16 29 0.10
17 25 0.08
18 2 0.01
19 152 0.52
20 28 0.09
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:1119456 original size:52 final size:52
Alignment explanation
Indices: 1119393--1119771 Score: 431
Period size: 52 Copynumber: 7.2 Consensus size: 52
1119383 AACGGGAGAA
* *
1119393 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1119445 TCGCATTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1119497 TCGCATTGCGATTTTCATTTCGCATTGCGATAGTCATTTCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT--TC-TCTCG--TTGCGATTTTCATT
* * * *
1119549 TCCCATTGCGATTTTTATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATT
1119602 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
1119654 TCGCATTGCGATTTTCATTTCGCATTGCGATAGTCATTTCGCATTGCGA--TTC---
1 TCGCATTGCGATTTTCATTTCGCATTGCGAT--TC-TCTCG--TTGCGATTTTCATT
* * * *
1119706 TCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATT
1 TCGCATTGCGATTTTCATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATT
1119759 TCGCATTGCGATT
1 TCGCATTGCGATT
1119772 CTCTCGTTGC
Statistics
Matches: 280, Mismatches: 22, Indels: 49
0.80 0.06 0.14
Matches are distributed among these distances:
48 10 0.04
50 10 0.04
51 5 0.02
52 175 0.62
53 51 0.18
54 4 0.01
55 13 0.05
57 12 0.04
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:1119596 original size:157 final size:157
Alignment explanation
Indices: 1119399--1119771 Score: 669
Period size: 157 Copynumber: 2.4 Consensus size: 157
1119389 AGAATCGCAA
* *
1119399 TGCGATTTTAATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATTTTCA
1 TGCGATTTTAATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATTTTCA
1119462 TTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
65 TTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
1119527 TAGTCATTTCGCATTGCGATTCTCCCAT
130 TAGTCATTTCGCATTGCGATTCTCCCAT
*
1119555 TGCGATTTTTATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATTTTCAT
*
1119620 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
66 TTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
*
1119685 AGTCATTTCGCATTGCGATTCTCCCGT
131 AGTCATTTCGCATTGCGATTCTCCCAT
*
1119712 TGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATT
1 TGCGATTTTAATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATT
1119772 CTCTCGTTGC
Statistics
Matches: 209, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
156 13 0.06
157 195 0.93
158 1 0.00
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (157 bp):
TGCGATTTTAATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGATTTTCAT
TTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
AGTCATTTCGCATTGCGATTCTCCCAT
Found at i:1119780 original size:67 final size:70
Alignment explanation
Indices: 1119399--1119804 Score: 344
Period size: 71 Copynumber: 5.8 Consensus size: 70
1119389 AGAATCGCAA
*
1119399 TGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCA-
1119463 TTCGCAT
65 TTCG-AT
* * * * * * **
1119470 TGCGATTCCCTCGTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTCATTT-CGCATTGCGATAGT
1 TGCGATT--TTCATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTT
1119531 CATTTCGCAT
63 CA-TTCG-AT
* * *** *
1119541 TGCGATTCTCCCATTGCG-ATTTTTATT-TC-CGCATTGCGATTTTCA--T--G--TTGGGATTT
1 TGCGATT-T-TCATTTCGCATTGCGATTCTCTCG--TTGCGATTTTCATTTCCGCATTGCGATTT
1119597 TCATTTCGCAT
62 TCA-TTCG-AT
1119608 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCA-
1119672 TTCGCAT
65 TTCG-AT
** *
1119679 TGCGATAGTCATTTCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCA-
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
1119743 T-G-T
66 TCGAT
* * * **
1119746 TGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTGTAATTTCCGTGTTGCGAT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGAT
1119805 AGTCAAATGC
Statistics
Matches: 285, Mismatches: 34, Indels: 36
0.80 0.10 0.10
Matches are distributed among these distances:
65 6 0.02
66 19 0.07
67 78 0.27
68 3 0.01
69 3 0.01
70 7 0.02
71 129 0.45
72 32 0.11
73 8 0.03
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.45
Consensus pattern (70 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCAT
TCGAT
Found at i:1119793 original size:33 final size:33
Alignment explanation
Indices: 1119399--1119785 Score: 252
Period size: 33 Copynumber: 11.2 Consensus size: 33
1119389 AGAATCGCAA
*
1119399 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1119432 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * * *
1119470 TGCGATTCCCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT--TTCATTTCGCA-TTGCGATTCTCTCGT
*
1119503 TGCGATTTTCATTTCGCATTGCGATAGTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGAT--TC-TCTCG--T
* * ***
1119541 TGCGATTCTCCCATTGCG-ATTTTTATT-TC-CGCAT
1 TGCGATT-T-TCATTTCGCATTGCGATTCTCTCG--T
* * * * *
1119575 TGCGATTTTCATGTTGGGATTTTC-ATT-TCGCAT
1 TGCGATTTTCAT-TTCGCA-TTGCGATTCTCTCGT
1119608 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1119641 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
** *
1119679 TGCGATAGTCATTTCGCATTGCGATTCTCCCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
1119712 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
1119746 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1119779 TGCGATT
1 TGCGATT
1119786 GTAATTTCCG
Statistics
Matches: 278, Mismatches: 44, Indels: 64
0.72 0.11 0.17
Matches are distributed among these distances:
31 12 0.04
32 14 0.05
33 110 0.40
34 48 0.17
35 16 0.06
36 13 0.05
37 3 0.01
38 39 0.14
39 8 0.03
40 15 0.05
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:1122302 original size:24 final size:24
Alignment explanation
Indices: 1122268--1122314 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1122258 CTGAAACATC
1122268 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
1122292 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
1122315 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:1123025 original size:20 final size:20
Alignment explanation
Indices: 1122997--1123265 Score: 279
Period size: 20 Copynumber: 13.4 Consensus size: 20
1122987 AAATTTCAGT
* * *
1122997 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1123017 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1123037 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1123057 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* **
1123077 GTTGCGATTTACAGATTATC
1 GTTGCGATTTACGGATTCGC
**
1123097 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1123117 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1123137 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1123157 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* * *
1123177 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
1123197 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
1123217 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1123237 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1123257 GTTGCGATT
1 GTTGCGATT
1123266 ATGGAAAATC
Statistics
Matches: 221, Mismatches: 26, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
20 220 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1131276 original size:225 final size:225
Alignment explanation
Indices: 1130885--1131333 Score: 799
Period size: 225 Copynumber: 2.0 Consensus size: 225
1130875 AACATGGGGG
1130885 AATTGTAGGGGCATTTTTATAAATATGGAAGAAAATTGAAACTCAGCTGTGCATTGTCAATTGTT
1 AATTGTAGGGGCATTTTTATAAATATGGAAGAAAATTGAAACTCAGCTGTGCATTGTCAATTGTT
* * *
1130950 AAGATAGATTCTGAATAGATACTAGCTAGTAATCATGACAAGCTAATGGGTTAATAAATTTGTAA
66 AAGATAGATTCTGAAGAGATACTAGCTAGTAATCACGACAAACTAATGGGTTAATAAATTTGTAA
1131015 GAAAGAAGAGTCCCTTTTTATCGTGCTTCGGATATCAATTTTGTATAGGTTATTCACCCTATACA
131 GAAAGAAGAGTCCCTTTTTATCGTGCTTCGGATATCAATTTTGTATAGGTTATTCACCCTATACA
1131080 GTTACTAATGGAAATGAATTGCTGAATAAA
196 GTTACTAATGGAAATGAATTGCTGAATAAA
* * *
1131110 AATTGTAGGGGCATTTTTATAAATATGGATGAAAATTGAGACTCAGTTGTGCATTGTCAATTGTT
1 AATTGTAGGGGCATTTTTATAAATATGGAAGAAAATTGAAACTCAGCTGTGCATTGTCAATTGTT
* *
1131175 AAGATAGATTCTGAAGAGATACTAGCTTGTAATCACGACAAACTATTGGGTTAATAAATTTGTAA
66 AAGATAGATTCTGAAGAGATACTAGCTAGTAATCACGACAAACTAATGGGTTAATAAATTTGTAA
* *
1131240 GAAAGATGAGTCTCTTTTTATCGTGCTTCGGATATCAATTTTGTATAGGTTATTCACCCTATACA
131 GAAAGAAGAGTCCCTTTTTATCGTGCTTCGGATATCAATTTTGTATAGGTTATTCACCCTATACA
*
1131305 GTTATTAATGGAAATGAATTGCTGAATAA
196 GTTACTAATGGAAATGAATTGCTGAATAA
1131334 GCAAGTTTTC
Statistics
Matches: 213, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
225 213 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (225 bp):
AATTGTAGGGGCATTTTTATAAATATGGAAGAAAATTGAAACTCAGCTGTGCATTGTCAATTGTT
AAGATAGATTCTGAAGAGATACTAGCTAGTAATCACGACAAACTAATGGGTTAATAAATTTGTAA
GAAAGAAGAGTCCCTTTTTATCGTGCTTCGGATATCAATTTTGTATAGGTTATTCACCCTATACA
GTTACTAATGGAAATGAATTGCTGAATAAA
Found at i:1137628 original size:2 final size:2
Alignment explanation
Indices: 1137623--1137687 Score: 78
Period size: 2 Copynumber: 32.0 Consensus size: 2
1137613 ACACACACAC
*
1137623 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T TT GAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* *
1137665 AGG AC AT AT AT AT AT AT AT AT AT
1 A-T AT AT AT AT AT AT AT AT AT AT
1137688 TTGGCACTGA
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
1 1 0.02
2 53 0.95
3 2 0.04
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1145303 original size:55 final size:55
Alignment explanation
Indices: 1145237--1145345 Score: 191
Period size: 55 Copynumber: 2.0 Consensus size: 55
1145227 CCGACTCGTA
* *
1145237 AAGTTTCGAATCAATCCGATATCTTTATCATGTCGATCGAGAACCGGAGTTTTTC
1 AAGTTCCGAATCAACCCGATATCTTTATCATGTCGATCGAGAACCGGAGTTTTTC
*
1145292 AAGTTCCGAATCAACCCGATATCTTTATCATGTTGATCGAGAACCGGAGTTTTT
1 AAGTTCCGAATCAACCCGATATCTTTATCATGTCGATCGAGAACCGGAGTTTTT
1145346 TTTTCATAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.34
Consensus pattern (55 bp):
AAGTTCCGAATCAACCCGATATCTTTATCATGTCGATCGAGAACCGGAGTTTTTC
Found at i:1150160 original size:60 final size:60
Alignment explanation
Indices: 1150076--1150188 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
1150066 GTCCATAAAT
* * * * *
1150076 TATAAGATGTTGTTTTGTTGAGTCTTCT-AATTATCAAAAGTTATAAAATGGTCTTTTAAC
1 TATAAGATGTTATTTTATTCAGTCTCCTGAA-TATCAAAAGTTACAAAATGGTCTTTTAAC
* *
1150136 TATATGATGTTATTTTATTCAGTCTCCTGAATATTAAAAGTTACAAAATGGTC
1 TATAAGATGTTATTTTATTCAGTCTCCTGAATATCAAAAGTTACAAAATGGTC
1150189 ACTAGACCAT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 43 0.96
61 2 0.04
ACGTcount: A:0.33, C:0.10, G:0.14, T:0.43
Consensus pattern (60 bp):
TATAAGATGTTATTTTATTCAGTCTCCTGAATATCAAAAGTTACAAAATGGTCTTTTAAC
Found at i:1150944 original size:31 final size:31
Alignment explanation
Indices: 1150899--1150976 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
1150889 CTTTTAAAAC
** * * *
1150899 TTGCAATACAGTCCCCCGATATTTAGTCTGT
1 TTGCAATATGGTCCCCCAACATTTAGTCTAT
*
1150930 TTGCAATATGGTCCCCTAACATTTAGTCTAT
1 TTGCAATATGGTCCCCCAACATTTAGTCTAT
*
1150961 TTGTAATATGGTCCCC
1 TTGCAATATGGTCCCC
1150977 AATGTGACTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.23, C:0.24, G:0.15, T:0.37
Consensus pattern (31 bp):
TTGCAATATGGTCCCCCAACATTTAGTCTAT
Found at i:1151842 original size:21 final size:20
Alignment explanation
Indices: 1151816--1151966 Score: 79
Period size: 21 Copynumber: 7.9 Consensus size: 20
1151806 CAACTCGATT
1151816 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
** *
1151837 TTGCGATTTTCCAA-AT---
1 TTGCGATAGTCCAAGTTCCG
* * *
1151853 TTACGTTAGTCCAAATT-CG
1 TTGCGATAGTCCAAGTTCCG
1151872 TTGCGATAGTCCAAGTTCACG
1 TTGCGATAGTCCAAGTTC-CG
* *
1151893 TTGCAATAGTCGAAGTTCGCG
1 TTGCGATAGTCCAAGTTC-CG
** *
1151914 TTGCGATTTTCCAA-AT---
1 TTGCGATAGTCCAAGTTCCG
* * *
1151930 TTACGTTAGTCCAAATT-CG
1 TTGCGATAGTCCAAGTTCCG
1151949 TTGCGATAGTCCAAGTTC
1 TTGCGATAGTCCAAGTTC
1151967 TCTTCCACGA
Statistics
Matches: 94, Mismatches: 27, Indels: 19
0.67 0.19 0.14
Matches are distributed among these distances:
16 20 0.21
17 2 0.02
19 28 0.30
20 2 0.02
21 42 0.45
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (20 bp):
TTGCGATAGTCCAAGTTCCG
Found at i:1151877 original size:35 final size:35
Alignment explanation
Indices: 1151835--1151955 Score: 125
Period size: 35 Copynumber: 3.3 Consensus size: 35
1151825 TCCAAGTTCG
1151835 CGTTGCGATTTTCCAAATTTACGTTAGTCCAAATT
1 CGTTGCGATTTTCCAAATTTACGTTAGTCCAAATT
** * * * *
1151870 CGTTGCGATAGTCCAAGTTCACGTTGCAATAGTCGAAGTT
1 CGTTGCGATTTTCCAAATTTACG-T----TAGTCCAAATT
1151910 CGCGTTGCGATTTTCCAAATTTACGTTAGTCCAAATT
1 --CGTTGCGATTTTCCAAATTTACGTTAGTCCAAATT
1151947 CGTTGCGAT
1 CGTTGCGAT
1151956 AGTCCAAGTT
Statistics
Matches: 67, Mismatches: 12, Indels: 14
0.72 0.13 0.15
Matches are distributed among these distances:
35 28 0.42
36 1 0.01
37 9 0.13
40 9 0.13
41 1 0.01
42 19 0.28
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.36
Consensus pattern (35 bp):
CGTTGCGATTTTCCAAATTTACGTTAGTCCAAATT
Found at i:1151948 original size:77 final size:77
Alignment explanation
Indices: 1151816--1151966 Score: 284
Period size: 77 Copynumber: 2.0 Consensus size: 77
1151806 CAACTCGATT
*
1151816 TTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTTACGTTAGTCCAAATTCGTTGCGATAG
1 TTGCAATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTTACGTTAGTCCAAATTCGTTGCGATAG
1151881 TCCAAGTTCACG
66 TCCAAGTTCACG
*
1151893 TTGCAATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTTACGTTAGTCCAAATTCGTTGCGATAG
1 TTGCAATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTTACGTTAGTCCAAATTCGTTGCGATAG
1151958 TCCAAGTTC
66 TCCAAGTTC
1151967 TCTTCCACGA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
77 72 1.00
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (77 bp):
TTGCAATAGTCCAAGTTCGCGTTGCGATTTTCCAAATTTACGTTAGTCCAAATTCGTTGCGATAG
TCCAAGTTCACG
Found at i:1152310 original size:19 final size:20
Alignment explanation
Indices: 1152285--1152375 Score: 87
Period size: 19 Copynumber: 4.4 Consensus size: 20
1152275 CTTATTTTGG
1152285 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
1152305 -TTTTTCACTATCGTAACAACAC
1 ATTTTTCACTATCG---CAACAC
* * *
1152327 GTTTTTCAAATTCTCGCAACAC
1 ATTTTTC--ACTATCGCAACAC
*
1152349 A-TTTTAACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
1152368 ATTTTTCA
1 ATTTTTCA
1152376 AAATCGCGTT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
19 25 0.44
20 5 0.09
21 4 0.07
22 12 0.21
23 6 0.11
25 5 0.09
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.37
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:1152347 original size:44 final size:41
Alignment explanation
Indices: 1152296--1152377 Score: 110
Period size: 44 Copynumber: 1.9 Consensus size: 41
1152286 TTTTTCACTA
* * *
1152296 TCGCAACACTTTTTCACTATCGTAACAACACGTTTTTCAAATTC
1 TCGCAACACATTTTAACTATCG---CAACACATTTTTCAAATTC
1152340 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1 TCGCAACACATTTTAACTATCGCAACACATTTTTCAAA
1152378 ATCGCGTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
41 15 0.43
44 20 0.57
ACGTcount: A:0.33, C:0.27, G:0.06, T:0.34
Consensus pattern (41 bp):
TCGCAACACATTTTAACTATCGCAACACATTTTTCAAATTC
Found at i:1152428 original size:21 final size:21
Alignment explanation
Indices: 1152377--1152437 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
1152367 CATTTTTCAA
*
1152377 AATCGCGTTGCGAATCT-TAC
1 AATCGCGTTGCGAATCTGGAC
* *
1152397 AATCACGTTGCGAATCTGGAT
1 AATCGCGTTGCGAATCTGGAC
* *
1152418 ATTCGCGTTGCGAATTTGGA
1 AATCGCGTTGCGAATCTGGA
1152438 AACTGAGTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (21 bp):
AATCGCGTTGCGAATCTGGAC
Found at i:1152705 original size:23 final size:24
Alignment explanation
Indices: 1152666--1152711 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
1152656 CAATGAATTA
*
1152666 TTATTATTGTATATATTT-TTATG
1 TTATTATTGAATATATTTATTATG
1152689 TTATTATT-AATAGTATTTATTAT
1 TTATTATTGAATA-TATTTATTAT
1152712 TCTATCACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 3 0.15
23 13 0.65
24 4 0.20
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (24 bp):
TTATTATTGAATATATTTATTATG
Found at i:1152964 original size:14 final size:14
Alignment explanation
Indices: 1152945--1152984 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
1152935 AATGTGAAGT
1152945 AATCCCTGCA-AATA
1 AATCCCTGCATAA-A
1152959 AATCCCTGCATAAA
1 AATCCCTGCATAAA
*
1152973 AATCTCTGCATA
1 AATCCCTGCATA
1152985 TAGACAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 22 0.92
15 2 0.08
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (14 bp):
AATCCCTGCATAAA
Found at i:1155186 original size:2 final size:2
Alignment explanation
Indices: 1155179--1155205 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1155169 TTAAACTATT
1155179 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1155206 GAACCAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1155429 original size:2 final size:2
Alignment explanation
Indices: 1155422--1155448 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1155412 CACAGCCACA
1155422 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1155449 TGAAAGGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1157019 original size:2 final size:2
Alignment explanation
Indices: 1156977--1157002 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1156967 GTTTAAAATA
1156977 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1157003 TAAACAGCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1157222 original size:19 final size:20
Alignment explanation
Indices: 1157184--1157222 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
1157174 AATTATATAT
1157184 ATATATATATATAAACAATC
1 ATATATATATATAAACAATC
1157204 ATAT-TATATGATAAA-AATC
1 ATATATATAT-ATAAACAATC
1157223 TGTTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.36
Consensus pattern (20 bp):
ATATATATATATAAACAATC
Found at i:1163275 original size:24 final size:24
Alignment explanation
Indices: 1163248--1163295 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1163238 TGTGTTTTAA
1163248 TGTAGAGTTTTAATGGATATATAT
1 TGTAGAGTTTTAATGGATATATAT
1163272 TGTAGAGTTTTAATGGATATATAT
1 TGTAGAGTTTTAATGGATATATAT
1163296 GTATGTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (24 bp):
TGTAGAGTTTTAATGGATATATAT
Found at i:1165373 original size:98 final size:98
Alignment explanation
Indices: 1165204--1165411 Score: 355
Period size: 98 Copynumber: 2.1 Consensus size: 98
1165194 CTAGTGTCTG
* *
1165204 TTATGGATGATTTGAGCCTACTTTTTAATTGCTTTTACTCCGCTGATTATGACTGAAATAGTGAA
1 TTATGGATGATTTGAGCCTACTTTGTAATTGCTTTTACTCCGCTGATGATGACTGAAATAGTGAA
* *
1165269 ATGCTTCCCTTTGAGAGGTTGAATGTTAAATAT
66 ATGCTTCCCTATGAGAGGTCGAATGTTAAATAT
* *
1165302 TTATGGATGATTTGAGGCTACTTTGTAATTGCTTTTTCTCCGCTGATGATGACTGAAATAGTGAA
1 TTATGGATGATTTGAGCCTACTTTGTAATTGCTTTTACTCCGCTGATGATGACTGAAATAGTGAA
1165367 ATGCTTCCCTATGAGAGGTCGAATGTTAAATAT
66 ATGCTTCCCTATGAGAGGTCGAATGTTAAATAT
1165400 TTATGGAT-ATTT
1 TTATGGATGATTT
1165412 CGGTATTATA
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
97 4 0.04
98 100 0.96
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (98 bp):
TTATGGATGATTTGAGCCTACTTTGTAATTGCTTTTACTCCGCTGATGATGACTGAAATAGTGAA
ATGCTTCCCTATGAGAGGTCGAATGTTAAATAT
Found at i:1166437 original size:32 final size:32
Alignment explanation
Indices: 1166396--1166461 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
1166386 CTGGTAGATG
1166396 TTGGTCTATAAATAATAATTATAATCTTAAAT
1 TTGGTCTATAAATAATAATTATAATCTTAAAT
*
1166428 TTGGTCTATAAATAGTAATTATAATCTTAAAT
1 TTGGTCTATAAATAATAATTATAATCTTAAAT
1166460 TT
1 TT
1166462 AACGCTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.41, C:0.06, G:0.08, T:0.45
Consensus pattern (32 bp):
TTGGTCTATAAATAATAATTATAATCTTAAAT
Found at i:1169002 original size:2 final size:2
Alignment explanation
Indices: 1168995--1169020 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1168985 AAAGTTATTA
1168995 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
1169021 CTTCAATCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1174934 original size:23 final size:23
Alignment explanation
Indices: 1174908--1174953 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1174898 CACCACAGCT
*
1174908 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
1174931 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
1174954 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:1175477 original size:151 final size:149
Alignment explanation
Indices: 1174931--1175532 Score: 1136
Period size: 149 Copynumber: 4.0 Consensus size: 149
1174921 CGAAGTGCCA
1174931 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1174996 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAG-A-ATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1175059 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1175078 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1175143 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
*
1175208 TATATATCACGAAGGACCG
131 TATATATCCCGAAGGACCG
1175227 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1175292 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAG-A-ATA
1175357 TATATATATCCCGAAGGACCG
129 TATATATATCCCGAAGGACCG
** *
1175378 CGTCTAATGGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1175443 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1175508 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1175527 CGTAGA
1 CGTAGA
1175533 CCCTCTACCC
Statistics
Matches: 444, Mismatches: 7, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
147 124 0.28
148 1 0.00
149 173 0.39
150 2 0.00
151 144 0.32
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:1175496 original size:300 final size:296
Alignment explanation
Indices: 1174931--1175532 Score: 1132
Period size: 300 Copynumber: 2.0 Consensus size: 296
1174921 CGAAGTGCCA
1174931 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1174996 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
*
1175061 TATATCCCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACA
131 TATATCCCGAAGGACCGCGTAGAATGGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACA
1175126 TATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACAC
196 TATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACAC
1175191 ATGTTCCACAGAATATATATATATCACGAAGGACCG
261 ATGTTCCACAGAATATATATATATCACGAAGGACCG
1175227 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1175292 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAG---A-A
**
1175357 TATATATATCCCGAAGGACCGCGTCTAATGGCACCGTAGTGCCATATAATAATGTCCATAAGGAC
127 TATATATATCCCGAAGGACCGCGTAGAATGGCACCGTAGTGCCATATAATAATGTCCATAAGGAC
1175422 CACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTC
192 CACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTC
*
1175487 ACACATGTTCCACAGAATATATATATATCCCGAAGGACCG
257 ACACATGTTCCACAGAATATATATATATCACGAAGGACCG
1175527 CGTAGA
1 CGTAGA
1175533 CCCTCTACCC
Statistics
Matches: 298, Mismatches: 4, Indels: 4
0.97 0.01 0.01
Matches are distributed among these distances:
296 124 0.42
299 1 0.00
300 173 0.58
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (296 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATCCCGAAGGACCGCGTAGAATGGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACA
TATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACAC
ATGTTCCACAGAATATATATATATCACGAAGGACCG
Found at i:1176117 original size:63 final size:63
Alignment explanation
Indices: 1175988--1176127 Score: 192
Period size: 63 Copynumber: 2.2 Consensus size: 63
1175978 TAATGGAGGC
* * *
1175988 ATGCATCGATGCACTCCTGATGCATCGATGCACTGAGGGCATTCGATGTTCATTTTATTAGAA
1 ATGCATCGATGCACTCCTGATGCATCGATGCACTGACGACATTCGATGTTCATTTTATAAGAA
* ** **
1176051 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTA-AATTA
1 ATGCATCGATGCACTCCTGATGCATCGATGCACTGACGACATTCGATGTTCAT-TTTATAAGAA
1176114 ATGCATCGATGCAC
1 ATGCATCGATGCAC
1176128 CTTCAACAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
63 64 0.94
64 4 0.06
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTGATGCATCGATGCACTGACGACATTCGATGTTCATTTTATAAGAA
Found at i:1182488 original size:149 final size:149
Alignment explanation
Indices: 1182249--1182701 Score: 888
Period size: 149 Copynumber: 3.0 Consensus size: 149
1182239 CGAAGTGCCA
* *
1182249 CGTAGAATTGCACTGTAGTGCTATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1182314 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1182379 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1182398 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1182463 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1182528 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1182547 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
1182612 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1182677 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1182696 CGTAGA
1 CGTAGA
1182702 CCCTCTACCC
Statistics
Matches: 302, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 302 1.00
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATCATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:1183263 original size:63 final size:63
Alignment explanation
Indices: 1183157--1183315 Score: 212
Period size: 63 Copynumber: 2.5 Consensus size: 63
1183147 TAATGGAGGC
* * * *
1183157 ATGCATCGATGCACTCCTGATGCATCGATGCACTGAGGGCATTCGATGTTCAT-TTTATTAGAA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTA-AAGAA
** **
1183220 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTTGTATTTAAATTA
1 ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
* *
1183283 ATGCATCGATGCACTTCATATGCATCGATGCAC
1 ATGCATCGATGCACTCCTTATGCATCGATGCAC
1183316 CTTCAACAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
63 81 0.95
64 4 0.05
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.32
Consensus pattern (63 bp):
ATGCATCGATGCACTCCTTATGCATCGATGCACTGACGACATTCGATGTTCATATTTAAAGAA
Found at i:1183307 original size:19 final size:20
Alignment explanation
Indices: 1183283--1183320 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
1183273 ATTTAAATTA
1183283 ATGCATCGATGCA-CTTCAT
1 ATGCATCGATGCACCTTCAT
1183302 ATGCATCGATGCACCTTCA
1 ATGCATCGATGCACCTTCA
1183321 ACAAATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGCATCGATGCACCTTCAT
Found at i:1184622 original size:2 final size:2
Alignment explanation
Indices: 1184615--1184675 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
1184605 AGGAAAGACG
1184615 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1184657 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1184676 GGATGAATTA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1184740 original size:2 final size:2
Alignment explanation
Indices: 1184733--1184762 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1184723 GAACATGTGA
1184733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1184763 GATAAGACAT
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):
AT
Found at i:1185188 original size:23 final size:23
Alignment explanation
Indices: 1185155--1185222 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
1185145 AACCTTATAT
*
1185155 GGCACTTCGGTGTATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
1185178 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
1185201 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
1185223 AGCTGTGGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.18, C:0.25, G:0.26, T:0.31
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:1188638 original size:27 final size:27
Alignment explanation
Indices: 1188584--1188637 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
1188574 TCAGGATGAT
*
1188584 ATAAATTATATGATATATAAAAATAAA
1 ATAAAATATATGATATATAAAAATAAA
* *
1188611 ATAAAATATAT-ATTTATAAAATTAAA
1 ATAAAATATATGATATATAAAAATAAA
1188637 A
1 A
1188638 AATCAGTGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
ATAAAATATATGATATATAAAAATAAA
Found at i:1190472 original size:25 final size:24
Alignment explanation
Indices: 1190425--1190472 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1190415 TAATTGAAAC
*
1190425 AAAAATTAAAGTTTAGTGTTATAA
1 AAAAATTAAAGTTTAGTGGTATAA
1190449 AAAAATTTAAAGCTTT-GTGGTATA
1 AAAAA-TTAAAG-TTTAGTGGTATA
1190473 GACAATACAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 13 0.62
26 3 0.14
ACGTcount: A:0.46, C:0.02, G:0.15, T:0.38
Consensus pattern (24 bp):
AAAAATTAAAGTTTAGTGGTATAA
Found at i:1205299 original size:12 final size:10
Alignment explanation
Indices: 1205267--1205297 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
1205257 TTCATCACAC
1205267 CAAATTCTCT
1 CAAATTCTCT
1205277 CAAATTCTCT
1 CAAATTCTCT
*
1205287 CAAATACTCT
1 CAAATTCTCT
1205297 C
1 C
1205298 TCGTTTAAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1207418 original size:3 final size:3
Alignment explanation
Indices: 1207410--1207446 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1207400 GCTCAGGACA
* *
1207410 ACG ACG ACG ACA ACG ACG ACG ATG ACG ACG ACG ACG A
1 ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG ACG A
1207447 TGATGATGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.38, C:0.30, G:0.30, T:0.03
Consensus pattern (3 bp):
ACG
Found at i:1207423 original size:12 final size:12
Alignment explanation
Indices: 1207406--1207444 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
1207396 ATCTGCTCAG
1207406 GACAACGACGAC
1 GACAACGACGAC
1207418 GACAACGACGAC
1 GACAACGACGAC
**
1207430 GATGACGACGAC
1 GACAACGACGAC
1207442 GAC
1 GAC
1207445 GATGATGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.38, C:0.31, G:0.28, T:0.03
Consensus pattern (12 bp):
GACAACGACGAC
Done.