Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D07
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: 58101237
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1550000 characters in sequence are not A, C, G, or T
File 133 of 199
Found at i:38682644 original size:16 final size:16
Alignment explanation
Indices: 38682599--38682649 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
38682589 AAAAGAGAAT
38682599 GAAAAAG-AAATA-AA
1 GAAAAAGAAAATATAA
*
38682613 GAAAAA-AAAAGAATAA
1 GAAAAAGAAAA-TATAA
38682629 GAAAAAGAAAATATAA
1 GAAAAAGAAAATATAA
38682645 -AAAAA
1 GAAAAA
38682650 TTAAGAAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
14 9 0.29
15 6 0.19
16 12 0.39
17 4 0.13
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (16 bp):
GAAAAAGAAAATATAA
Found at i:38682654 original size:25 final size:23
Alignment explanation
Indices: 38682610--38682665 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 23
38682600 AAAAAGAAAT
*
38682610 AAAGAAAA-AAAAAGAATAAGAA
1 AAAGAAAATAAAAAAAATAAGAA
38682632 AAAGAAAATATAAAAAAATTAAGAA
1 AAAGAAAATA-AAAAAAA-TAAGAA
38682657 ATAA-AAAAT
1 A-AAGAAAAT
38682666 GAATTTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
22 8 0.28
23 1 0.03
24 6 0.21
25 12 0.41
26 2 0.07
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (23 bp):
AAAGAAAATAAAAAAAATAAGAA
Found at i:38682656 original size:31 final size:31
Alignment explanation
Indices: 38682599--38682664 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
38682589 AAAAGAGAAT
38682599 GAAAAAGAAATAAAGAAAAAAAAAG-AATAA
1 GAAAAAGAAATAAAGAAAAAAAAAGAAATAA
**
38682629 GAAAAAGAAAATATAA-AAAAATTAAGAAATAA
1 GAAAAAG-AAATA-AAGAAAAAAAAAGAAATAA
38682661 -AAAA
1 GAAAA
38682665 TGAATTTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 7 0.23
31 17 0.55
32 7 0.23
ACGTcount: A:0.79, C:0.00, G:0.11, T:0.11
Consensus pattern (31 bp):
GAAAAAGAAATAAAGAAAAAAAAAGAAATAA
Found at i:38684798 original size:15 final size:16
Alignment explanation
Indices: 38684774--38684815 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
38684764 CAGCCATCTA
*
38684774 CTTCATCTCCA-GACT
1 CTTCACCTCCACGACT
38684789 CTTCACCTCCACGACT
1 CTTCACCTCCACGACT
* *
38684805 CATCCCCTCCA
1 CTTCACCTCCA
38684816 AATCTGCTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.19, C:0.50, G:0.05, T:0.26
Consensus pattern (16 bp):
CTTCACCTCCACGACT
Found at i:38692817 original size:6 final size:6
Alignment explanation
Indices: 38692806--38692847 Score: 56
Period size: 5 Copynumber: 7.7 Consensus size: 6
38692796 AAAATAAAGA
38692806 AAATAT AAATAT AAATAT -AATA- AAATA- AAATAT AAATA- AAAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AAAT
38692848 TGAGTTGCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
5 17 0.50
6 17 0.50
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAATAT
Found at i:38692828 original size:15 final size:14
Alignment explanation
Indices: 38692808--38692847 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 14
38692798 AATAAAGAAA
38692808 ATATAAATATAAAT
1 ATATAAATATAAAT
38692822 ATAATAAA-ATAAA-
1 AT-ATAAATATAAAT
38692835 ATATAAATA-AAAT
1 ATATAAATATAAAT
38692848 TGAGTTGCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
12 8 0.35
13 3 0.13
14 7 0.30
15 5 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
ATATAAATATAAAT
Found at i:38692836 original size:21 final size:21
Alignment explanation
Indices: 38692797--38692845 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 21
38692787 ACATGCAAGA
38692797 AAATAAAGAAAATATAAATAT
1 AAATAAAGAAAATATAAATAT
*
38692818 AAATATAATAAAATA-AAATAT
1 AAATA-AAGAAAATATAAATAT
38692839 AAATAAA
1 AAATAAA
38692846 ATTGAGTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.08
21 16 0.62
22 8 0.31
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (21 bp):
AAATAAAGAAAATATAAATAT
Found at i:38705487 original size:3 final size:3
Alignment explanation
Indices: 38705481--38705515 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
38705471 GTGTCTATTA
38705481 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
38705516 TTAGTTTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:38707483 original size:17 final size:19
Alignment explanation
Indices: 38707450--38707499 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
38707440 AATAGAATCC
*
38707450 TAATT-AAATTAAGTT-AA
1 TAATTAAAATTTAGTTAAA
38707467 TAATTAAAATTTA-TTAAAA
1 TAATTAAAATTTAGTT-AAA
38707486 TAATTAAAATTTAG
1 TAATTAAAATTTAG
38707500 AGTAGACTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 7 0.25
18 6 0.21
19 15 0.54
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.42
Consensus pattern (19 bp):
TAATTAAAATTTAGTTAAA
Found at i:38709426 original size:41 final size:43
Alignment explanation
Indices: 38709352--38709433 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 43
38709342 TACTTATAGA
* *
38709352 AAAAGTAGAAACTAGAGGAAGAAACAAAATGAAGATTTAAAAGG
1 AAAAGTAGAAAATAGAAGAAG-AACAAAATGAAGATTTAAAAGG
38709396 AAAAGTAGAAAATAGAAGAAG-A-AAAATGAAGATTTAAA
1 AAAAGTAGAAAATAGAAGAAGAACAAAATGAAGATTTAAA
38709434 GGTGAAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
41 16 0.44
42 1 0.03
44 19 0.53
ACGTcount: A:0.62, C:0.02, G:0.21, T:0.15
Consensus pattern (43 bp):
AAAAGTAGAAAATAGAAGAAGAACAAAATGAAGATTTAAAAGG
Found at i:38709444 original size:44 final size:44
Alignment explanation
Indices: 38709350--38709450 Score: 120
Period size: 44 Copynumber: 2.3 Consensus size: 44
38709340 CATACTTATA
* *
38709350 GAAAAAGTAGAAACTAGAGGAAGAAACAAAATGAAGATTTAAAAG
1 GAAAAAGTAGAAAATAGAAGAAG-AACAAAATGAAGATTTAAAAG
*
38709395 G-AAAAGTAGAAAATAGAAGAAG-A-AAAATGAAGATTTAAAGG
1 GAAAAAGTAGAAAATAGAAGAAGAACAAAATGAAGATTTAAAAG
38709436 TGAAAAAAG-AGAAAA
1 -G-AAAAAGTAGAAAA
38709451 ATGAGAGGTG
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
41 17 0.34
42 2 0.04
43 6 0.12
44 24 0.48
45 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.23, T:0.13
Consensus pattern (44 bp):
GAAAAAGTAGAAAATAGAAGAAGAACAAAATGAAGATTTAAAAG
Found at i:38710985 original size:20 final size:20
Alignment explanation
Indices: 38710942--38710985 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
38710932 AAGTTTATTC
*
38710942 AATTTAGTCTAAATTATTTC
1 AATTTAGTCTAAATTATTTA
*
38710962 AATTTAGTCCTTAA-TATTTA
1 AATTTAGT-CTAAATTATTTA
38710982 AATT
1 AATT
38710986 AATTATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (20 bp):
AATTTAGTCTAAATTATTTA
Found at i:38714107 original size:50 final size:50
Alignment explanation
Indices: 38713983--38714162 Score: 184
Period size: 50 Copynumber: 3.6 Consensus size: 50
38713973 AATAATAACA
* * * *
38713983 TGCCAAAGCCATGTCCCAAACATGGTCTTACAGGGGATGTT-TCCTAT-AT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-GTTCTCATATCAG
* * * * * *
38714032 TGCAAATGTCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGAGTTCTCATATCAG
* * ** *
38714082 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGAGTTCTCATATCAG
* *
38714132 TACCAACGCCATGTCCCAGACATGGTCTTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC
38714163 GTGGGACCTC
Statistics
Matches: 105, Mismatches: 24, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
48 3 0.03
49 34 0.32
50 68 0.65
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGAGTTCTCATATCAG
Found at i:38714163 original size:50 final size:50
Alignment explanation
Indices: 38714071--38714177 Score: 169
Period size: 50 Copynumber: 2.1 Consensus size: 50
38714061 ACATGAGAGT
* * *
38714071 TCTCATATCAGTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACC
1 TCTCATATCAGTACCAACGCCATGTCCCAGACATGGTCTTACGGGGGACC
* *
38714121 TCTCATCTCAGTACCAACGCCATGTCCCAGACATGGTCTTACGTGGGACC
1 TCTCATATCAGTACCAACGCCATGTCCCAGACATGGTCTTACGGGGGACC
38714171 TCTCATA
1 TCTCATA
38714178 ACCTCAATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.21, C:0.33, G:0.21, T:0.25
Consensus pattern (50 bp):
TCTCATATCAGTACCAACGCCATGTCCCAGACATGGTCTTACGGGGGACC
Found at i:38715953 original size:21 final size:19
Alignment explanation
Indices: 38715917--38715957 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
38715907 TCATTGTAAC
*
38715917 TATATTACAACCTGACCCA
1 TATATTACAACATGACCCA
38715936 TATACTTACGAACATGACCCA
1 TATA-TTAC-AACATGACCCA
38715957 T
1 T
38715958 TTAACATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 4 0.21
20 4 0.21
21 11 0.58
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (19 bp):
TATATTACAACATGACCCA
Found at i:38725645 original size:22 final size:22
Alignment explanation
Indices: 38725613--38725727 Score: 99
Period size: 22 Copynumber: 5.1 Consensus size: 22
38725603 TGCACTAATG
* *
38725613 AACAGAAAGCACTAAAGTGCTA
1 AACAGAGAGCACTAACGTGCTA
* *
38725635 TACAGAGAGCA-TAGATGTGCTA
1 AACAGAGAGCACTA-ACGTGCTA
*
38725657 AACAGAGAGCACTGACGTGCTAA
1 AACAGAGAGCACTAACGTGCT-A
* *
38725680 TAATCAGAGAGTAC-AGATGTGCTA
1 -AA-CAGAGAGCACTA-ACGTGCTA
*
38725704 AATAGAGAGCACTAACGTGCTA
1 AACAGAGAGCACTAACGTGCTA
38725726 AA
1 AA
38725728 TATTAGAGAG
Statistics
Matches: 74, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
21 2 0.03
22 49 0.66
23 5 0.07
24 3 0.04
25 15 0.20
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (22 bp):
AACAGAGAGCACTAACGTGCTA
Found at i:38725690 original size:25 final size:24
Alignment explanation
Indices: 38725637--38725738 Score: 88
Period size: 22 Copynumber: 4.3 Consensus size: 24
38725627 AAGTGCTATA
*
38725637 CAGAGAGCA-TAGATGTGCT-AAA-
1 CAGAGAGCACT-GACGTGCTAAAAT
38725659 CAGAGAGCACTGACGTGCTAATAAT
1 CAGAGAGCACTGACGTGCTAA-AAT
* * *
38725684 CAGAGAGTACAGATGTGCT-AAAT
1 CAGAGAGCACTGACGTGCTAAAAT
*
38725707 -AGAGAGCACTAACGTGCTAAATAT
1 CAGAGAGCACTGACGTGCTAAA-AT
*
38725731 TAGAGAGC
1 CAGAGAGC
38725739 GCGCTAGAGT
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
22 30 0.46
23 7 0.11
24 5 0.08
25 23 0.35
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (24 bp):
CAGAGAGCACTGACGTGCTAAAAT
Found at i:38725737 original size:47 final size:47
Alignment explanation
Indices: 38725613--38725726 Score: 153
Period size: 47 Copynumber: 2.5 Consensus size: 47
38725603 TGCACTAATG
* * *
38725613 AACAGAAAGCACTAAAGTGCT-AT-A-CAGAGAGCATAGATGTGCTA
1 AACAGAGAGCACTAACGTGCTAATAATCAGAGAGCACAGATGTGCTA
* *
38725657 AACAGAGAGCACTGACGTGCTAATAATCAGAGAGTACAGATGTGCTA
1 AACAGAGAGCACTAACGTGCTAATAATCAGAGAGCACAGATGTGCTA
*
38725704 AATAGAGAGCACTAACGTGCTAA
1 AACAGAGAGCACTAACGTGCTAA
38725727 ATATTAGAGA
Statistics
Matches: 60, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
44 18 0.30
45 2 0.03
46 1 0.02
47 39 0.65
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (47 bp):
AACAGAGAGCACTAACGTGCTAATAATCAGAGAGCACAGATGTGCTA
Found at i:38726829 original size:5 final size:5
Alignment explanation
Indices: 38726819--38726911 Score: 77
Period size: 5 Copynumber: 18.6 Consensus size: 5
38726809 TATATATATA
* * * * *
38726819 ATAAT ATAAT ATTAT ATAAT ATTAT AAAAAT ATAAT GTAAT A-ACAT ACTTAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT ATA-AT A-TAAT
38726871 -TAAT -TAAGT A-AAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
1 ATAAT ATAA-T ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA
38726912 TATTTTAAAT
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
4 9 0.13
5 57 0.80
6 5 0.07
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (5 bp):
ATAAT
Found at i:38726837 original size:15 final size:15
Alignment explanation
Indices: 38726808--38726915 Score: 55
Period size: 15 Copynumber: 7.1 Consensus size: 15
38726798 TTCTGTTGTT
38726808 TTATATATATAATAATA
1 TTATATA-AT-ATAATA
* *
38726825 TAATATTATATAATA
1 TTATATAATATAATA
*
38726840 TTATAAAAATATAAT-
1 TTAT-ATAATATAATA
* * *
38726855 GTA-ATAACATACTTA
1 TTATATAATATA-ATA
38726870 TTA-ATTAAGTA-AATA
1 TTATA-TAA-TATAATA
*
38726885 TAATATAATATAATA
1 TTATATAATATAATA
*
38726900 TAATATAATAT-ATA
1 TTATATAATATAATA
38726914 TT
1 TT
38726916 TTAAATTAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 17
0.69 0.14 0.17
Matches are distributed among these distances:
13 6 0.09
14 7 0.10
15 36 0.51
16 15 0.21
17 6 0.09
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (15 bp):
TTATATAATATAATA
Found at i:38730731 original size:9 final size:9
Alignment explanation
Indices: 38730717--38730745 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
38730707 CATCCCCAAG
38730717 ATTCCACTA
1 ATTCCACTA
38730726 ATTCCACTA
1 ATTCCACTA
38730735 ATTCCACTA
1 ATTCCACTA
38730744 AT
1 AT
38730746 GCTGCAGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (9 bp):
ATTCCACTA
Found at i:38738656 original size:15 final size:15
Alignment explanation
Indices: 38738632--38738681 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
38738622 ATAACTTAAA
38738632 TTCAACACTTAATTT
1 TTCAACACTTAATTT
*
38738647 TTCAATACTTAATTT
1 TTCAACACTTAATTT
*
38738662 TTCAACA-TAAACTTT
1 TTCAACACTTAA-TTT
38738677 TTCAA
1 TTCAA
38738682 TAGTTAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
14 3 0.10
15 28 0.90
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (15 bp):
TTCAACACTTAATTT
Found at i:38743690 original size:27 final size:27
Alignment explanation
Indices: 38743658--38743719 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
38743648 AAATATATAT
38743658 AAAATATACATATTTGATTAAAAATAA
1 AAAATATACATATTTGATTAAAAATAA
*
38743685 AAAATATAGATATTTGATTAAAAATAA
1 AAAATATACATATTTGATTAAAAATAA
38743712 AAAATATA
1 AAAATATA
38743720 TTTAATATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.61, C:0.02, G:0.05, T:0.32
Consensus pattern (27 bp):
AAAATATACATATTTGATTAAAAATAA
Found at i:38743954 original size:37 final size:37
Alignment explanation
Indices: 38743904--38743977 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
38743894 ACCTCTATCA
38743904 TGTACTCATAAAAACTTCACAAAAACAAAATTAATTC
1 TGTACTCATAAAAACTTCACAAAAACAAAATTAATTC
38743941 TGTACTCATAAAAACTTCACAAAAACAAAATTAATTC
1 TGTACTCATAAAAACTTCACAAAAACAAAATTAATTC
38743978 GGTTGGGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.51, C:0.19, G:0.03, T:0.27
Consensus pattern (37 bp):
TGTACTCATAAAAACTTCACAAAAACAAAATTAATTC
Found at i:38746774 original size:50 final size:50
Alignment explanation
Indices: 38746584--38746773 Score: 290
Period size: 50 Copynumber: 3.8 Consensus size: 50
38746574 TCCTGTACTA
* * ** *
38746584 CCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
* * **
38746634 CCCATGCCATGTCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
*
38746684 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTTATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
38746734 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
38746774 TTACCCAAAT
Statistics
Matches: 126, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 126 1.00
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTG
Found at i:38752891 original size:40 final size:40
Alignment explanation
Indices: 38752847--38753234 Score: 677
Period size: 40 Copynumber: 9.7 Consensus size: 40
38752837 GCAAACACAT
* * *
38752847 TTGCCTTCGGGTCTTAACCCGGACATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
38752887 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
* *
38752927 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
38752967 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
38753007 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
38753047 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCGTAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
38753087 TTGCCTTCGGGTCTTAGCCCGGATATATCATCTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
*
38753127 TTGCCTTCGGGTCATAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
38753167 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
1 TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
38753207 TTGCCTTCGGGTCTTAGCCCGGATATAT
1 TTGCCTTCGGGTCTTAGCCCGGATATAT
38753235 TCCAATGCTC
Statistics
Matches: 331, Mismatches: 17, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 331 1.00
ACGTcount: A:0.22, C:0.27, G:0.21, T:0.30
Consensus pattern (40 bp):
TTGCCTTCGGGTCTTAGCCCGGATATATCAACTCGCATAA
Found at i:38759554 original size:56 final size:56
Alignment explanation
Indices: 38759463--38759585 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
38759453 GAGATTGGCG
* * *
38759463 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
38759520 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
38759575 CTGAGTGTGCG
1 CTAAGTGTGCG
38759586 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:38759572 original size:27 final size:28
Alignment explanation
Indices: 38759463--38759585 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
38759453 GAGATTGGCG
* * * *
38759463 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
38759492 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
38759520 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
38759548 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
38759575 CTGAGTGTGCG
1 CTAAGTGTGCG
38759586 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:38759596 original size:27 final size:27
Alignment explanation
Indices: 38759488--38759598 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
38759478 TAAATTGTAC
* * *
38759488 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
38759516 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
38759544 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
38759571 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
38759598 A
1 A
38759599 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:38762250 original size:41 final size:41
Alignment explanation
Indices: 38762106--38762252 Score: 190
Period size: 41 Copynumber: 3.6 Consensus size: 41
38762096 TTTAACATAT
* *
38762106 TCACCGACACTTAACCTGCTA-AGCTTATAGCCTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGA-CTTATAGCCTGATTCAGA
** * *
38762147 TCACCGGCACTTAGCCTGCTAGGTTTATAACTTGATTCAGA
1 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTCAGA
*
38762188 TCACCGACACTTAGCCTGCTAGACTTATAGCCT-ATTTCAGA
1 TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGA-TTCAGA
*
38762229 TCATCGGCACTTAGCCTGCTAGAC
1 TCACCGGCACTTAGCCTGCTAGAC
38762253 GTAAAGTCTG
Statistics
Matches: 91, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
40 1 0.01
41 90 0.99
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.29
Consensus pattern (41 bp):
TCACCGGCACTTAGCCTGCTAGACTTATAGCCTGATTCAGA
Found at i:38762902 original size:114 final size:114
Alignment explanation
Indices: 38762739--38763073 Score: 618
Period size: 114 Copynumber: 2.9 Consensus size: 114
38762729 TCATATATAC
* * *
38762739 ATATTCGAACTTCATTTATG-ATATATATAACATTCATCCTTAACTAATTTCAATTTATATACTT
1 ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTCATATATTT
*
38762803 TCAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
66 TTAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
38762852 ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTCATATATTT
1 ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTCATATATTT
38762917 TTAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
66 TTAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
38762966 ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTCATATATTT
1 ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTCATATATTT
*
38763031 TTAATTATAGCTCATCAAATATAAAATAGATATACATATATAT
66 TTAATTATAGCTCATCAAATATACAATAGATATACATATATAT
38763074 ATATGCTGAT
Statistics
Matches: 216, Mismatches: 5, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
113 20 0.09
114 196 0.91
ACGTcount: A:0.41, C:0.14, G:0.04, T:0.42
Consensus pattern (114 bp):
ATATTCGAACTTCATTTATGCATATATATAACATTCATACTTAACTAATTTCAATTCATATATTT
TTAATTATAGCTCATCAAATATACAATAGATATACATATATATTTACAT
Found at i:38764063 original size:13 final size:13
Alignment explanation
Indices: 38764045--38764069 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38764035 CAATCAAATG
38764045 CACACAAAATAAA
1 CACACAAAATAAA
38764058 CACACAAAATAA
1 CACACAAAATAA
38764070 TATTAAAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.24, G:0.00, T:0.08
Consensus pattern (13 bp):
CACACAAAATAAA
Found at i:38764492 original size:5 final size:6
Alignment explanation
Indices: 38764463--38764496 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
38764453 TCGCTCGCAC
**
38764463 TCTTTT TCTTTT TCACTT TCTTTT TCTTTT TCTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTTTT TCTT
38764497 ATTTTTCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (6 bp):
TCTTTT
Found at i:38767504 original size:24 final size:24
Alignment explanation
Indices: 38767476--38767527 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
38767466 TTTTTAGAAG
* **
38767476 ATTTAGTATTTATTAGTATAATAT
1 ATTTAGCATTTATTAACATAATAT
38767500 ATTTAGCATTTATTAACATAATAT
1 ATTTAGCATTTATTAACATAATAT
38767524 ATTT
1 ATTT
38767528 GACTGTGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAACATAATAT
Found at i:38777740 original size:29 final size:29
Alignment explanation
Indices: 38777629--38777736 Score: 72
Period size: 29 Copynumber: 3.7 Consensus size: 29
38777619 ATCATTAGGG
* **
38777629 TTTATCAGGCACTATGCGCCAGTGATTATA
1 TTTATCAAGCACTATGTACCAGTG-TTATA
* * * *
38777659 TTTATCAAGTACTTTGGACCAGTGTTACA
1 TTTATCAAGCACTATGTACCAGTGTTATA
* * * * **
38777688 GTTATCAAACACTCTGTGCTGGTGTTATA
1 TTTATCAAGCACTATGTACCAGTGTTATA
* *
38777717 TTTATCAGGTACTATGTACC
1 TTTATCAAGCACTATGTACC
38777737 GGTGGTGGAT
Statistics
Matches: 56, Mismatches: 22, Indels: 1
0.71 0.28 0.01
Matches are distributed among these distances:
29 37 0.66
30 19 0.34
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.37
Consensus pattern (29 bp):
TTTATCAAGCACTATGTACCAGTGTTATA
Found at i:38780233 original size:39 final size:40
Alignment explanation
Indices: 38780190--38780357 Score: 139
Period size: 40 Copynumber: 4.2 Consensus size: 40
38780180 CTCGTTCAAG
* * * *
38780190 TGCCTTCGGGACATAGCCCGG-TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGATTATA-AAACTCACACGAA
* *
38780229 TGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
* * *
38780269 TGCCTTCGGGACTTAACCCGGAATTAGT--ATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTA-TAAAACTCACACGAA
* * * * *
38780309 GGCCTTCGGGACTTAACCTGGAATTA-ATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGG-ATTATAAAACTCACACGAA
38780349 TGCCTTCGG
1 TGCCTTCGG
38780358 ATCTTAGTCC
Statistics
Matches: 110, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
39 26 0.24
40 80 0.73
41 3 0.03
42 1 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGATTATAAAACTCACACGAA
Found at i:38780279 original size:40 final size:39
Alignment explanation
Indices: 38780227--38780357 Score: 181
Period size: 40 Copynumber: 3.3 Consensus size: 39
38780217 TAACTCATAC
* *
38780227 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-ATTAAAACTCGCACA
* *
38780267 AATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTA-AAACTCGCACA
* *
38780307 AAGGCCTTCGGGACTTAACCTGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTAA-AACTCGCACA
38780347 AATGCCTTCGG
1 AATGCCTTCGG
38780358 ATCTTAGTCC
Statistics
Matches: 80, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
39 3 0.04
40 77 0.96
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGAATTAAAACTCGCACA
Found at i:38780341 original size:80 final size:80
Alignment explanation
Indices: 38780225--38780410 Score: 220
Period size: 80 Copynumber: 2.3 Consensus size: 80
38780215 AGTAACTCAT
* * *
38780225 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTC-GGATCTTAACCCG
*
38780289 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
* **
38780304 ACAAAGGCCTTCGGGACTTAACCTGGA-ATTAATAACTCGCACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATGCCTTCGGATCTTAACCC
38780368 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
38780385 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
38780411 CAGCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 11
0.82 0.08 0.10
Matches are distributed among these distances:
79 11 0.12
80 70 0.76
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:38788253 original size:80 final size:80
Alignment explanation
Indices: 38788137--38788322 Score: 220
Period size: 80 Copynumber: 2.3 Consensus size: 80
38788127 AGTAACTCAT
* * * *
38788137 ACAATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCACACAAATGCCTTC-GGATCTTAACCCG
*
38788201 GA-ATTAGT-A-TCTCGC
65 GATA-TAGTCACT-TAGC
**
38788216 ACAAAGGCCTTCGGGACTTAACCCGGA-ATTAATAACTCACACAAATGCCTTCGGATCTTAGTCC
1 ACAAA-GCCTTCGGGACTTAACCCGGATATTAA-AACTCACACAAATGCCTTCGGATCTTAACCC
38788280 GGATATAGTCACTTAGC
64 GGATATAGTCACTTAGC
*
38788297 ACAAAGCCTTCGGGACTTAGCCCGGA
1 ACAAAGCCTTCGGGACTTAACCCGGA
38788323 CAGCATTCAA
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
79 11 0.12
80 71 0.76
81 10 0.11
82 1 0.01
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.24
Consensus pattern (80 bp):
ACAAAGCCTTCGGGACTTAACCCGGATATTAAAACTCACACAAATGCCTTCGGATCTTAACCCGG
ATATAGTCACTTAGC
Found at i:38788282 original size:40 final size:40
Alignment explanation
Indices: 38788102--38788322 Score: 195
Period size: 40 Copynumber: 5.5 Consensus size: 40
38788092 CTCCTTCAAG
* * *
38788102 TGCCTTCGGGACATAGCCCGG--TTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGGAATTA-A-TAACTCACACAAA
* * *
38788141 TGCCTTCGGGACTTAACCCGGATTTTAA-AACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGA-ATTAATAACTCACACAAA
* * *
38788181 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGGAATTAATAACTCACACAAA
*
38788221 GGCCTTCGGGACTTAACCCGGAATTAATAACTCACACAAA
1 TGCCTTCGGGACTTAACCCGGAATTAATAACTCACACAAA
** * * *
38788261 TGCCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA
1 TGCCTTCGGGA-CTTAACCCGGAAT-TAATAACTCA-CACAAA
*
38788302 -GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGACTTAACCCGGA
38788323 CAGCATTCAA
Statistics
Matches: 153, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
39 34 0.22
40 106 0.69
41 10 0.07
42 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
TGCCTTCGGGACTTAACCCGGAATTAATAACTCACACAAA
Found at i:38795842 original size:40 final size:40
Alignment explanation
Indices: 38795765--38795936 Score: 215
Period size: 40 Copynumber: 4.2 Consensus size: 40
38795755 GGACTAAGAT
38795765 CCGAAGGCATTTGTGCTAGTGA-TATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
38795804 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
38795844 CCGAAGGCATTTGTGCTAGTGACTATGTCAAATGTCCGGGCTAAGTC
1 CCGAAGGCATTTGTGCTAGTGACTA--T---A--TCCGGGCTAAGTC
* * * *
38795891 CCGAAGGCATTCGTGCGAGTTG-CTATATCC-GGCTAAATT
1 CCGAAGGCATTTGTGCTAG-TGACTATATCCGGGCTAAGTC
38795930 CCGAAGG
1 CCGAAGG
38795937 TACTTGGGTT
Statistics
Matches: 120, Mismatches: 4, Indels: 18
0.85 0.03 0.13
Matches are distributed among these distances:
39 36 0.30
40 45 0.38
42 2 0.02
45 2 0.02
47 33 0.28
48 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGTC
Found at i:38814165 original size:76 final size:78
Alignment explanation
Indices: 38814076--38814241 Score: 300
Period size: 78 Copynumber: 2.2 Consensus size: 78
38814066 TGATGATTTA
*
38814076 AATATGTGTTATATATACATCTGTATGATGAGATCCATGAATT-A-ATGAAAATATATTAAAGCA
1 AATATGTGATATATATACATCTGTATGATGAGATCCATGAATTAATATGAAAATATATTAAAGCA
38814139 TGCTAAAGTGAAT
66 TGCTAAAGTGAAT
*
38814152 AATATGTGATATATATACATCTGTATGATGAGATCCATGATTTAATATGAAAATATATTAAAGCA
1 AATATGTGATATATATACATCTGTATGATGAGATCCATGAATTAATATGAAAATATATTAAAGCA
38814217 TGCTAAAGTGAAT
66 TGCTAAAGTGAAT
38814230 AATATGTGATAT
1 AATATGTGATAT
38814242 GTGATATATG
Statistics
Matches: 86, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
76 41 0.48
77 1 0.01
78 44 0.51
ACGTcount: A:0.42, C:0.07, G:0.16, T:0.35
Consensus pattern (78 bp):
AATATGTGATATATATACATCTGTATGATGAGATCCATGAATTAATATGAAAATATATTAAAGCA
TGCTAAAGTGAAT
Found at i:38819688 original size:17 final size:17
Alignment explanation
Indices: 38819666--38819721 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
38819656 AAATTGGGTC
38819666 GTGTGGGCCACACAGGT
1 GTGTGGGCCACACAGGT
*
38819683 GTGTGGGCCCCACA--T
1 GTGTGGGCCACACAGGT
* **
38819698 GGGTGAACCACACAGGT
1 GTGTGGGCCACACAGGT
38819715 GTGTGGG
1 GTGTGGG
38819722 AATATTAGGC
Statistics
Matches: 29, Mismatches: 8, Indels: 4
0.71 0.20 0.10
Matches are distributed among these distances:
15 11 0.38
17 18 0.62
ACGTcount: A:0.18, C:0.23, G:0.41, T:0.18
Consensus pattern (17 bp):
GTGTGGGCCACACAGGT
Found at i:38819702 original size:19 final size:19
Alignment explanation
Indices: 38819660--38819702 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 19
38819650 CAGGCCAAAT
38819660 TGGGTCGTGTGGGCCACACA
1 TGGGT-GTGTGGGCCACACA
*
38819680 --GGTGTGTGGGCCCCACA
1 TGGGTGTGTGGGCCACACA
38819697 TGGGTG
1 TGGGTG
38819703 AACCACACAG
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
17 13 0.65
18 3 0.15
19 4 0.20
ACGTcount: A:0.12, C:0.23, G:0.44, T:0.21
Consensus pattern (19 bp):
TGGGTGTGTGGGCCACACA
Found at i:38833393 original size:20 final size:20
Alignment explanation
Indices: 38833368--38833408 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
38833358 ATTTCTAAGC
* *
38833368 TTCAAAATCTACCATTAACA
1 TTCAAAAACTACAATTAACA
*
38833388 TTCAAAAACTTCAATTAACA
1 TTCAAAAACTACAATTAACA
38833408 T
1 T
38833409 CAATGGAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (20 bp):
TTCAAAAACTACAATTAACA
Found at i:38837493 original size:20 final size:21
Alignment explanation
Indices: 38837441--38837484 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
38837431 ACCCTTTCAA
*
38837441 ATTTTATTA-TTTCCATTTGC
1 ATTTCATTACTTTCCATTTGC
38837461 ATTTCATTACTTTCCA-TTGC
1 ATTTCATTACTTTCCATTTGC
38837481 ATTT
1 ATTT
38837485 ACTTTCTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.20, C:0.18, G:0.05, T:0.57
Consensus pattern (21 bp):
ATTTCATTACTTTCCATTTGC
Found at i:38847287 original size:40 final size:39
Alignment explanation
Indices: 38847189--38847411 Score: 207
Period size: 40 Copynumber: 5.6 Consensus size: 39
38847179 TCCTCGTTCA
* * * * *
38847189 AATGCCTTCGGGACATAGCCCGGTTTTAGTAATTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
38847228 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
38847267 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
38847307 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
38847347 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
38847388 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
38847412 CAGCATTCAA
Statistics
Matches: 156, Mismatches: 22, Indels: 11
0.83 0.12 0.06
Matches are distributed among these distances:
39 39 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:38847371 original size:80 final size:81
Alignment explanation
Indices: 38847187--38847411 Score: 237
Period size: 80 Copynumber: 2.8 Consensus size: 81
38847177 GCTCCTCGTT
* * * * *
38847187 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAAT-TCACACAATGCCTTCGGGACATAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATCTCGCACAAAGCCTTCGGGACTTAACCCGG
38847251 -ATTTAATAACTCGCA
66 AATTTAATAACTCGCA
* * *
38847266 CGAATGCCTTCGGGACTTAACCCGGATTTAGT-ATCTCGCACAAAGGCCTTCGGGGCTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATCTCGCACAAA-GCCTTCGGGACTTAACCCG
* *
38847330 GAATTT-GTATCTCGCA
65 GAATTTAATAACTCGCA
* * * * * *
38847346 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCA-CTTAGCACAAAGCCTTCGGGACTTAGCCC
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAATC-TCGCACAAAGCCTTCGGGACTTAACCC
38847409 GGA
64 GGA
38847412 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 2 0.02
79 38 0.31
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAATCTCGCACAAAGCCTTCGGGACTTAACCCGG
AATTTAATAACTCGCA
Found at i:38847420 original size:41 final size:41
Alignment explanation
Indices: 38847343--38847420 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
38847333 TTTGTATCTC
* * *
38847343 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
38847384 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
38847421 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:38854111 original size:40 final size:40
Alignment explanation
Indices: 38854074--38854205 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 40
38854064 GCTACTCGTT
* *
38854074 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATT-TAATAACTCGCA
*
38854114 CAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
* * * * * * * *
38854154 CCAATGCCTTCGAG-CTTAGCCCGAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
38854193 CAAATGCCTTCGG
1 CAAATGCCTTCGG
38854206 ATCTTAGTCC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
39 31 0.39
40 46 0.58
41 2 0.03
ACGTcount: A:0.27, C:0.29, G:0.20, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
Found at i:38854199 original size:39 final size:40
Alignment explanation
Indices: 38854102--38854204 Score: 136
Period size: 39 Copynumber: 2.6 Consensus size: 40
38854092 AGCCCGGTTA
* * *
38854102 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATT
1 TAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGAAAT
* * *
38854142 TAATAACTCGCACCAATGCCTTCGAG-CTTAGCCCGAAAT
1 TAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGAAAT
*
38854181 TAGTATCTCGCACAAATGCCTTCG
1 TAGTAACTCGCACAAATGCCTTCG
38854205 GATCTTAGTC
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
39 31 0.57
40 23 0.43
ACGTcount: A:0.28, C:0.29, G:0.17, T:0.25
Consensus pattern (40 bp):
TAGTAACTCGCACAAATGCCTTCGAGACTTAACCCGAAAT
Found at i:38854242 original size:79 final size:80
Alignment explanation
Indices: 38854102--38854256 Score: 181
Period size: 79 Copynumber: 1.9 Consensus size: 80
38854092 AGCCCGGTTA
* * *
38854102 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACCAATGCCTTCGA
1 TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTAGCACCAAAGCCTTCGA
38854167 G-CTTAGCCCGAAAT
66 GACTTAGCCCGAAAT
* ** ** *
38854181 TAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA-CAAAGCCTTC
1 TAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAAC-TAGCACCAAAGCCTTC
*
38854244 GGGACTTAGCCCG
64 GAGACTTAGCCCG
38854257 GACATCATTC
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
78 3 0.05
79 47 0.75
80 13 0.21
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (80 bp):
TAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTAGCACCAAAGCCTTCGA
GACTTAGCCCGAAAT
Found at i:38855452 original size:56 final size:56
Alignment explanation
Indices: 38855385--38855504 Score: 240
Period size: 56 Copynumber: 2.1 Consensus size: 56
38855375 TATTAGTTTA
38855385 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
38855441 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
38855497 TTGCCCAT
1 TTGCCCAT
38855505 CATCCCTTGT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 64 1.00
ACGTcount: A:0.23, C:0.24, G:0.09, T:0.44
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:38862619 original size:42 final size:42
Alignment explanation
Indices: 38862572--38862655 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
38862562 GACACGATAC
38862572 TTAATCAGTGCATGTTTAATCATCTAAGGTAGTTGGGGGTTA
1 TTAATCAGTGCATGTTTAATCATCTAAGGTAGTTGGGGGTTA
38862614 TTAATCAGTGCATGTTTAATCATCTAAGGTAGTTGGGGGTTA
1 TTAATCAGTGCATGTTTAATCATCTAAGGTAGTTGGGGGTTA
38862656 AATTAGCAAC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (42 bp):
TTAATCAGTGCATGTTTAATCATCTAAGGTAGTTGGGGGTTA
Found at i:38874088 original size:27 final size:27
Alignment explanation
Indices: 38874058--38874235 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
38874048 ATATTGAGCC
* *
38874058 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
38874085 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
38874112 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
38874140 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
38874167 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
38874194 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
38874221 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38874236 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:38874170 original size:55 final size:54
Alignment explanation
Indices: 38874058--38874235 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
38874048 ATATTGAGCC
* * * * *
38874058 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
38874112 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
38874167 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
38874221 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38874236 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:38882078 original size:27 final size:27
Alignment explanation
Indices: 38882048--38882225 Score: 137
Period size: 27 Copynumber: 6.6 Consensus size: 27
38882038 ATATTGAGCC
* *
38882048 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* * * *
38882075 CGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
* *
38882102 CGCACACTTAGTGCTACATAGTCAAACC
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
38882130 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
38882157 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
38882184 CGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTACATAA-TCA-ACT
38882211 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38882226 GTACAATTTA
Statistics
Matches: 121, Mismatches: 25, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
26 2 0.02
27 96 0.79
28 23 0.19
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:38882160 original size:55 final size:54
Alignment explanation
Indices: 38882048--38882225 Score: 164
Period size: 54 Copynumber: 3.3 Consensus size: 54
38882038 ATATTGAGCC
* * * * *
38882048 CGCACACTCAGTGCTATATAATCAACTCGCACATTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
* * ** *
38882102 CGCACACTTAGTGCTACATAGTCAAACCCGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATC-AACCCGCACACTTAGTGCCACATAATCAAAT
* *** *
38882157 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACA-AAGT-AGAAT
1 CGCACACTTAGTGCTA-CATAATCAACCCGCACACTTAGTGCCACATAA-TCA-AAT
38882211 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38882226 GTACAATTTA
Statistics
Matches: 100, Mismatches: 19, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
53 1 0.01
54 55 0.55
55 44 0.44
ACGTcount: A:0.30, C:0.28, G:0.16, T:0.26
Consensus pattern (54 bp):
CGCACACTTAGTGCTACATAATCAACCCGCACACTTAGTGCCACATAATCAAAT
Found at i:38885137 original size:8 final size:8
Alignment explanation
Indices: 38885124--38885153 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
38885114 GTGAATTGGC
38885124 AAAAGCTG
1 AAAAGCTG
*
38885132 AAAAGCCG
1 AAAAGCTG
38885140 AAAAGCTG
1 AAAAGCTG
38885148 AAAAGC
1 AAAAGC
38885154 CGTATCTCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.53, C:0.17, G:0.23, T:0.07
Consensus pattern (8 bp):
AAAAGCTG
Found at i:38885145 original size:16 final size:16
Alignment explanation
Indices: 38885124--38885155 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
38885114 GTGAATTGGC
38885124 AAAAGCTGAAAAGCCG
1 AAAAGCTGAAAAGCCG
38885140 AAAAGCTGAAAAGCCG
1 AAAAGCTGAAAAGCCG
38885156 TATCTCTCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.25, T:0.06
Consensus pattern (16 bp):
AAAAGCTGAAAAGCCG
Found at i:38886347 original size:27 final size:27
Alignment explanation
Indices: 38886308--38886567 Score: 305
Period size: 27 Copynumber: 9.7 Consensus size: 27
38886298 GGAAATTTTA
* *
38886308 TAAAATGACCGTAATACCCCTGTAGGA
1 TAAAATGATCGTAATACCCCTGTAGGG
* *
38886335 TAAAATGATCGTAATGCCCTTGTAGGG
1 TAAAATGATCGTAATACCCCTGTAGGG
38886362 TAAAATGA-CTGTAATACCCCTGTAGGG
1 TAAAATGATC-GTAATACCCCTGTAGGG
* *
38886389 TAAAATGATCGTAATGCCCCTGTAAGG
1 TAAAATGATCGTAATACCCCTGTAGGG
* * * *
38886416 TAAAATGA-CTATAATTCCTCTATAGGG
1 TAAAATGATC-GTAATACCCCTGTAGGG
38886443 TAAAATGA-CTGTAATACCCCTGTAGGG
1 TAAAATGATC-GTAATACCCCTGTAGGG
* * *
38886470 TAAAATGATCGTAATGCCCTTTTAGGG
1 TAAAATGATCGTAATACCCCTGTAGGG
*
38886497 TAAAATGATCGT-ATA-CCCTTTAGGG
1 TAAAATGATCGTAATACCCCTGTAGGG
* * *
38886522 TAAAATGACCGTAATGCCCCTGTAAGG
1 TAAAATGATCGTAATACCCCTGTAGGG
38886549 TAAAATGATCGTAATACCC
1 TAAAATGATCGTAATACCC
38886568 TCGAGGTCAA
Statistics
Matches: 199, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
25 20 0.10
26 6 0.03
27 171 0.86
28 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (27 bp):
TAAAATGATCGTAATACCCCTGTAGGG
Found at i:38886647 original size:24 final size:24
Alignment explanation
Indices: 38886600--38886656 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
38886590 TCTGTGGTTA
* * *
38886600 AATGACTTATTTGTTTATGTTTTG
1 AATGACTGATTTGTCTATGATTTG
* *
38886624 TATGACTGATTTGTCTGTGATTTG
1 AATGACTGATTTGTCTATGATTTG
38886648 AATGACTGA
1 AATGACTGA
38886657 CTCTGAGCAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.23, C:0.07, G:0.21, T:0.49
Consensus pattern (24 bp):
AATGACTGATTTGTCTATGATTTG
Found at i:38886770 original size:27 final size:27
Alignment explanation
Indices: 38886727--38886780 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
38886717 GGAAGTACTG
38886727 TACTGGTGGCTCTGCCACA-ATCACTAT
1 TACTGGTGGCTCTGCCACATAT-ACTAT
38886754 TACTGGTGGCT-TGGCCACATATACTAT
1 TACTGGTGGCTCT-GCCACATATACTAT
38886781 ACTAGCAGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 1 0.04
27 22 0.88
28 2 0.08
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.31
Consensus pattern (27 bp):
TACTGGTGGCTCTGCCACATATACTAT
Found at i:38886862 original size:32 final size:32
Alignment explanation
Indices: 38886826--38886886 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
38886816 TTTGGTGCGT
*
38886826 TGCTACTAATGACTGTGTGCCGATCATATCAC
1 TGCTACTAATGACTGTGTGCCAATCATATCAC
* *
38886858 TGCTACTAATGGCTTTGTGCCAATCATAT
1 TGCTACTAATGACTGTGTGCCAATCATAT
38886887 TACTATACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.18, T:0.34
Consensus pattern (32 bp):
TGCTACTAATGACTGTGTGCCAATCATATCAC
Found at i:38887904 original size:27 final size:27
Alignment explanation
Indices: 38887873--38887928 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
38887863 AGTAAACCAA
*
38887873 TACTATAGAGAGTATTGACCTAAAACT
1 TACTATAGAGAGTATTGACCCAAAACT
*
38887900 TACTATAGAGAGTATTGACCCGAAACT
1 TACTATAGAGAGTATTGACCCAAAACT
38887927 TA
1 TA
38887929 TAAGTCACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (27 bp):
TACTATAGAGAGTATTGACCCAAAACT
Found at i:38888943 original size:28 final size:28
Alignment explanation
Indices: 38888890--38888943 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
38888880 CATTAAAATG
*
38888890 ATGTAATATACTAAGACAAATCAATGAT
1 ATGTAATATACTAAGACAAATAAATGAT
* *
38888918 ATGTACTA-ACTAAGACATATTAAATG
1 ATGTAATATACTAAGACA-AATAAATG
38888944 CATGCATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 9 0.41
28 13 0.59
ACGTcount: A:0.48, C:0.11, G:0.11, T:0.30
Consensus pattern (28 bp):
ATGTAATATACTAAGACAAATAAATGAT
Found at i:38893986 original size:25 final size:26
Alignment explanation
Indices: 38893944--38893997 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 26
38893934 TTCTCCTGAA
*
38893944 TTTCAATTTTATTTAATTATTTAAT-T
1 TTTCAATTTTATTGAATTA-TTAATAT
38893970 TTTCAA-TTTATTGAATTATTAATAT
1 TTTCAATTTTATTGAATTATTAATAT
38893995 TTT
1 TTT
38893998 ATACTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
24 5 0.19
25 15 0.58
26 6 0.23
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (26 bp):
TTTCAATTTTATTGAATTATTAATAT
Found at i:38899967 original size:18 final size:18
Alignment explanation
Indices: 38899908--38899967 Score: 50
Period size: 18 Copynumber: 3.1 Consensus size: 18
38899898 ACATAAAAAA
*
38899908 TTAATAATGTTAATAGCATAA
1 TTAATAAT-TTAATA--ATAT
*
38899929 TTAATTAA-TTAATTAAAAT
1 TTAA-TAATTTAA-TAATAT
38899948 TTAATAATTTAATAATAT
1 TTAATAATTTAATAATAT
38899966 TT
1 TT
38899968 TTTACCATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
18 10 0.30
19 10 0.30
20 4 0.12
21 6 0.18
22 3 0.09
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (18 bp):
TTAATAATTTAATAATAT
Found at i:38900118 original size:21 final size:21
Alignment explanation
Indices: 38900094--38900134 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38900084 AACATTTGAA
38900094 ACGAAATTATCGAGAGAATTG
1 ACGAAATTATCGAGAGAATTG
* *
38900115 ACGAATTTATTGAGAGAATT
1 ACGAAATTATCGAGAGAATT
38900135 TAGAATTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (21 bp):
ACGAAATTATCGAGAGAATTG
Found at i:38904537 original size:21 final size:22
Alignment explanation
Indices: 38904498--38904538 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
38904488 TCCGCCTCGC
*
38904498 ATGGTCTCGTTTCGAGTCATGG
1 ATGGTCTCGTTTCCAGTCATGG
*
38904520 ATGG-CTCGTTTCCTGTCAT
1 ATGGTCTCGTTTCCAGTCAT
38904539 AATCATGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.12, C:0.22, G:0.27, T:0.39
Consensus pattern (22 bp):
ATGGTCTCGTTTCCAGTCATGG
Found at i:38906173 original size:57 final size:58
Alignment explanation
Indices: 38906105--38906225 Score: 163
Period size: 57 Copynumber: 2.1 Consensus size: 58
38906095 TCATTTTCAT
* * ** *
38906105 TTTTAATTTTCATTTTGGAGAAAACTACATTCATTTCCAAAT-TATTCTATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAACCACAACCATTTCCAAATGTATTCCATTTCTCCA
* *
38906162 TTTTCATTTTCATTTTGGAGAAAACCATAACCATTTCCAAATGTTTTCCATTTCTCCA
1 TTTTCATTTTCATTTTGGAGAAAACCACAACCATTTCCAAATGTATTCCATTTCTCCA
*
38906220 CTTTCA
1 TTTTCA
38906226 CCATTTTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 37 0.67
58 18 0.33
ACGTcount: A:0.28, C:0.21, G:0.06, T:0.45
Consensus pattern (58 bp):
TTTTCATTTTCATTTTGGAGAAAACCACAACCATTTCCAAATGTATTCCATTTCTCCA
Found at i:38918743 original size:14 final size:13
Alignment explanation
Indices: 38918715--38918757 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 13
38918705 GTACACTTTG
38918715 ACAAGAAAAATAAA
1 ACAA-AAAAATAAA
*
38918729 AGAAAAAACATAAA
1 ACAAAAAA-ATAAA
38918743 ACAAAATAAATAAA
1 ACAAAA-AAATAAA
38918757 A
1 A
38918758 TTCCCTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 4 0.16
14 19 0.76
15 2 0.08
ACGTcount: A:0.79, C:0.07, G:0.05, T:0.09
Consensus pattern (13 bp):
ACAAAAAAATAAA
Found at i:38923590 original size:66 final size:66
Alignment explanation
Indices: 38923478--38923610 Score: 178
Period size: 66 Copynumber: 2.0 Consensus size: 66
38923468 ATGATAATGG
** * *
38923478 TTCCCTTAGTCTTGTAATTATGGGTTTGAATTGAATTTCAAGGCAAGAATATACCTCATCTTATT
1 TTCCCTTAGTCTTGTAATTACCGGTTTGAATTGAATTTCAAAGCAAGAATATACCTCATCTCATT
38923543 T
66 T
* * * *
38923544 TTCCCTTGGTCTTGTAATTACCTGTTTTAATTGAATTGT-AAAGCAAGAATATACTTCATCTCAT
1 TTCCCTTAGTCTTGTAATTACCGGTTTGAATTGAATT-TCAAAGCAAGAATATACCTCATCTCAT
38923608 TT
65 TT
38923610 T
1 T
38923611 AAGCTCATCA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
66 57 0.98
67 1 0.02
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.44
Consensus pattern (66 bp):
TTCCCTTAGTCTTGTAATTACCGGTTTGAATTGAATTTCAAAGCAAGAATATACCTCATCTCATT
T
Found at i:38932393 original size:9 final size:9
Alignment explanation
Indices: 38932368--38932400 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
38932358 AAAAATTAAC
38932368 CGAATTAAC-
1 CGAATT-ACT
38932377 CGAATTACT
1 CGAATTACT
38932386 CGAATTACT
1 CGAATTACT
38932395 CGAATT
1 CGAATT
38932401 GAATCACTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 2 0.09
9 21 0.91
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.30
Consensus pattern (9 bp):
CGAATTACT
Found at i:38932676 original size:39 final size:40
Alignment explanation
Indices: 38932593--38932705 Score: 178
Period size: 39 Copynumber: 2.9 Consensus size: 40
38932583 ACTTAAGAGT
*
38932593 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAA-TTAGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTTAGG
*
38932631 TGGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTTA-G
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTTAGG
*
38932670 TAGACTTTAGTTTTAGTTTTATTGGGTTGAGTAATT
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATT
38932706 AACCGAATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
38 26 0.38
39 40 0.58
40 3 0.04
ACGTcount: A:0.20, C:0.03, G:0.25, T:0.52
Consensus pattern (40 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTTAGG
Found at i:38933080 original size:14 final size:14
Alignment explanation
Indices: 38933061--38933090 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
38933051 ATGTGCAATA
38933061 CTTTGTACTTGTCT
1 CTTTGTACTTGTCT
38933075 CTTTGTACTTGTCT
1 CTTTGTACTTGTCT
38933089 CT
1 CT
38933091 ATCACTATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.07, C:0.23, G:0.13, T:0.57
Consensus pattern (14 bp):
CTTTGTACTTGTCT
Found at i:38952392 original size:37 final size:37
Alignment explanation
Indices: 38952337--38952419 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 37
38952327 TTGAGTATTA
* * *
38952337 CTCAACTGAGCATCACCTACTGATATACTGACTAAAG
1 CTCAACTGAGCATCACCTACTGATAAACCGAATAAAG
*
38952374 CTCAACTGAGCGAT-ACCTACTGGTAAACCGAATAAAG
1 CTCAACTGAGC-ATCACCTACTGATAAACCGAATAAAG
*
38952411 CTTAACTGA
1 CTCAACTGA
38952420 ACATTATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
37 38 0.95
38 2 0.05
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (37 bp):
CTCAACTGAGCATCACCTACTGATAAACCGAATAAAG
Found at i:38954642 original size:33 final size:30
Alignment explanation
Indices: 38954605--38954684 Score: 72
Period size: 29 Copynumber: 2.6 Consensus size: 30
38954595 GACAGCTGCG
*
38954605 AAGGCATCCTTGCACAATATATAGATAGCCACA
1 AAGGCATCC-TACAC-ATAT-TAGATAGCCACA
* *
38954638 AAGGCA-CCTACTCATATTAGATAGCCGCA
1 AAGGCATCCTACACATATTAGATAGCCACA
* *
38954667 AAGGTATCCAAGCACATA
1 AAGGCATCCTA-CACATA
38954685 CACAAGGTAG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
29 16 0.41
30 7 0.18
31 8 0.21
32 2 0.05
33 6 0.15
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (30 bp):
AAGGCATCCTACACATATTAGATAGCCACA
Found at i:38955185 original size:54 final size:53
Alignment explanation
Indices: 38955115--38955253 Score: 156
Period size: 51 Copynumber: 2.6 Consensus size: 53
38955105 ACATGACATG
* * *
38955115 ATAGTCCCAGAATAGGTCTTACACTATATGGTCTCTTTTCCCCCATATGATGCC
1 ATAGTCTCAGAATAGGTCTTACACTATATGGTCT-ATTTCCCCCATATGATACC
* * * *
38955169 ATAGTCTCAGATTAGGTCTTACACTATATGG--TATTTCCCCTATTTGATATC
1 ATAGTCTCAGAATAGGTCTTACACTATATGGTCTATTTCCCCCATATGATACC
* * * *
38955220 ATAGTTTAAGACTAGGTCTTACACTATATAGTCT
1 ATAGTCTCAGAATAGGTCTTACACTATATGGTCT
38955254 TCTTGCCATG
Statistics
Matches: 72, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
51 41 0.57
52 1 0.01
53 1 0.01
54 29 0.40
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (53 bp):
ATAGTCTCAGAATAGGTCTTACACTATATGGTCTATTTCCCCCATATGATACC
Found at i:38957574 original size:51 final size:51
Alignment explanation
Indices: 38957398--38957579 Score: 197
Period size: 51 Copynumber: 3.6 Consensus size: 51
38957388 GATGGTTACG
** * * * *
38957398 TGTGTAGGGCTATGTGCAGGCTACTACGTGTACCAGA-ATGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGGATAGGTCACA
* * * ** * * *
38957448 TGTGTAGTACTATGTGTAGGCTACAATGCGTACCGGATAGCTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGGATAGGTCACA
* *
38957499 TGTGTAGTACTATGTGTAGGCTACTATGTGTATCGGATAGGGAT-GGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATA-GGATAGGTCACA
38957550 TGTGTAGTACTATGTGCAGGCTACTATGTG
1 TGTGTAGTACTATGTGCAGGCTACTATGTG
38957580 AATCAGTATC
Statistics
Matches: 108, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
50 30 0.28
51 76 0.70
52 2 0.02
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (51 bp):
TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGGATAGGTCACA
Found at i:38964244 original size:51 final size:49
Alignment explanation
Indices: 38964119--38964306 Score: 225
Period size: 51 Copynumber: 3.7 Consensus size: 49
38964109 GATGGTTACG
* * * *
38964119 TGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-ATGATAGGTCGCA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATA-G-TTGGTCACA
* * *
38964169 TGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGATCACG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAG-TT-GGTCACA
*
38964220 TGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATAGTGATGGTCACA
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGT--TGGTCACA
* *
38964271 TGTGTAGTACTATGTGCAGGCTGCTATGTGAACCGG
1 TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGG
38964307 TATCATTAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
50 37 0.31
51 81 0.68
52 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (49 bp):
TGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGATAGTTGGTCACA
Found at i:38964249 original size:26 final size:26
Alignment explanation
Indices: 38964220--38964300 Score: 73
Period size: 26 Copynumber: 3.2 Consensus size: 26
38964210 TTCGATCACG
38964220 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAGGCTACTA
*
38964246 TGTGTA-T-CGGATAGTG-ATGG-TCAC-A
1 TGTGTAGTAC-TAT-GTGCA-GGCT-ACTA
*
38964271 TGTGTAGTACTATGTGCAGGCTGCTA
1 TGTGTAGTACTATGTGCAGGCTACTA
38964297 TGTG
1 TGTG
38964301 AACCGGTATC
Statistics
Matches: 43, Mismatches: 3, Indels: 18
0.67 0.05 0.28
Matches are distributed among these distances:
24 1 0.02
25 18 0.42
26 23 0.53
27 1 0.02
ACGTcount: A:0.21, C:0.14, G:0.31, T:0.35
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAGGCTACTA
Found at i:38964306 original size:102 final size:101
Alignment explanation
Indices: 38964116--38964306 Score: 294
Period size: 102 Copynumber: 1.9 Consensus size: 101
38964106 AGTGATGGTT
*
38964116 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCGCATGTGTAGTACTA
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTACTA
*
38964181 TGTGCAGGCTACTATGCGTACCGGATAGCTTCGATC
66 TGTGCAGGCTACTATGCGAACCGGATAGCTTCGATC
* * *
38964217 ACGTGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATAGTGAT-GGTCACATGTGTAGTAC
1 ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCACATGTGTAGTAC
* *
38964281 TATGTGCAGGCTGCTATGTGAACCGG
64 TATGTGCAGGCTACTATGCGAACCGG
38964307 TATCATTAAT
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
101 37 0.46
102 40 0.49
103 4 0.05
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (101 bp):
ACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGAATGATAGGTCACATGTGTAGTACTA
TGTGCAGGCTACTATGCGAACCGGATAGCTTCGATC
Found at i:38964545 original size:16 final size:16
Alignment explanation
Indices: 38964524--38964555 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
38964514 TGGTTGAAAG
*
38964524 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
38964540 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
38964556 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:38971494 original size:28 final size:28
Alignment explanation
Indices: 38971430--38971494 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 28
38971420 CGCCATGAAT
***
38971430 GATACTCTTTCATAATCTTTCACAAAGGC
1 GATACT-TTTCATAATCAACCACAAAGGC
* * *
38971459 TATTCTTTTCATAATCAACCACACAGGC
1 GATACTTTTCATAATCAACCACAAAGGC
38971487 GATACTTT
1 GATACTTT
38971495 CACATTGTGC
Statistics
Matches: 28, Mismatches: 8, Indels: 1
0.76 0.22 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.35
Consensus pattern (28 bp):
GATACTTTTCATAATCAACCACAAAGGC
Found at i:38971594 original size:27 final size:27
Alignment explanation
Indices: 38971530--38971595 Score: 64
Period size: 27 Copynumber: 2.4 Consensus size: 27
38971520 TTCATATTAC
38971530 GCCACAAAGGCTATCACATCAGAATTT
1 GCCACAAAGGCTATCACATCAGAATTT
* * * *
38971557 ACCATAGAGGCTATTC-CTTC-GAAGTTT
1 GCCACAAAGGCTA-TCACATCAGAA-TTT
38971584 GCCACAAAGGCT
1 GCCACAAAGGCT
38971596 CCCTTTTCAG
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
26 3 0.10
27 25 0.83
28 2 0.07
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (27 bp):
GCCACAAAGGCTATCACATCAGAATTT
Found at i:38971614 original size:27 final size:27
Alignment explanation
Indices: 38971584--38972060 Score: 442
Period size: 27 Copynumber: 17.7 Consensus size: 27
38971574 TTCGAAGTTT
* *
38971584 GCCACAAAGGCTCCCTTTTCAGTGTTC
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
* *
38971611 GCCACAAAGGCTTCCTTTTTAGAGTTA
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
* * * *
38971638 GCCACAAAAGTTTCCTTTTTAGAGTTA
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
*
38971665 GCCACAAAGGCTTCCTTTTCAGAGTTA
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
* * * *
38971692 GCGACAAATGCTTTCTTTTCAGTGTTC
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
* * * *
38971719 GCCATAAAGACTTCTTTTTTAGTGTTCA
1 GCCACAAAGGCTTCCTTTTCAGTGTT-A
* * **
38971747 -CCACAAAGGCTTACTTTTTAAAGTTA
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
* * *
38971773 GCCACAAATGCTTCATTTTCAGAGTTA
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
** *
38971800 GCCGTAAAGGCTTCCTTTTCAATGTTCA
1 GCCACAAAGGCTTCCTTTTCAGTGTT-A
*
38971828 -CTACAAAGGCTTCCTTTTCA-TAGTTA
1 GCCACAAAGGCTTCCTTTTCAGT-GTTA
* *
38971854 GCCACAAAGACTTCATTTTCAGTGTTCA
1 GCCACAAAGGCTTCCTTTTCAGTGTT-A
* *
38971882 -CCACAAAGGCTTTCTTTTCAATGTTCA
1 GCCACAAAGGCTTCCTTTTCAGTGTT-A
* ** *
38971909 -CCACAAAGGCTTCTTTTTCAAAGTTC
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
* * *
38971935 GCCGCAAAGTCTTCCTTTTCAGAGTTA
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
*
38971962 GCCATAAAGGCTTCCTTTTCAGTGTTA
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
**
38971989 GCCACAAAGGCTTCCTTTTCAAAGTTA
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
* **
38972016 GCCACAAAAGCTTTATTTTCAGTGTTA
1 GCCACAAAGGCTTCCTTTTCAGTGTTA
* * *
38972043 GCAATAAAGGATTCCTTT
1 GCCACAAAGGCTTCCTTT
38972061 CCTGATGTGT
Statistics
Matches: 366, Mismatches: 76, Indels: 16
0.80 0.17 0.03
Matches are distributed among these distances:
26 3 0.01
27 360 0.98
28 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (27 bp):
GCCACAAAGGCTTCCTTTTCAGTGTTA
Found at i:38972575 original size:42 final size:42
Alignment explanation
Indices: 38972524--38972809 Score: 450
Period size: 42 Copynumber: 6.8 Consensus size: 42
38972514 GTTTACAAAC
* *
38972524 AAAAACGCCGTTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
38972566 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
38972608 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTGTAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAG-AA
* * *
38972650 AAAAATGCCACTAAAGACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
38972692 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
*
38972734 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTA-AGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGA-A
* *
38972776 GAAAACGCCGCTAAAGATCATGTTCTTTAGCGGC
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGC
38972810 ATTTTTTTTC
Statistics
Matches: 227, Mismatches: 14, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
41 4 0.02
42 220 0.97
43 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAGAA
Found at i:38972987 original size:14 final size:14
Alignment explanation
Indices: 38972964--38972997 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
38972954 GCCCTCCTGT
*
38972964 AGCAAAATTTCAAA
1 AGCAACATTTCAAA
38972978 AGCAACATTTCAAA
1 AGCAACATTTCAAA
38972992 AGCAAC
1 AGCAAC
38972998 CAATAGCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.53, C:0.21, G:0.09, T:0.18
Consensus pattern (14 bp):
AGCAACATTTCAAA
Found at i:38978765 original size:18 final size:18
Alignment explanation
Indices: 38978742--38978906 Score: 60
Period size: 18 Copynumber: 9.5 Consensus size: 18
38978732 AATTGCAATG
38978742 GTAAGTTATGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
38978760 GTAAGTTAAATGT-A-TTAT
1 GTAAGTT--ATGTAAGTTAT
*
38978778 ATAAGTTAAATGTAAG-T-T
1 GTAAGTT--ATGTAAGTTAT
*
38978796 GTAAGTTAT-TATGTATTAT
1 GTAAGTTATGTAAG--TTAT
38978815 GTAAG-T-TGTAAGTTAAAT
1 GTAAGTTATGTAAGTT--AT
*
38978833 GT-A-TTGTGTAAG-T-T
1 GTAAGTTATGTAAGTTAT
38978847 GTAAGTTAAATGT-A-TTAT
1 GTAAGTT--ATGTAAGTTAT
38978865 GTAAG-T-TGTAAGTTAT
1 GTAAGTTATGTAAGTTAT
*
38978881 -TATGTATTATGTAAG-T-T
1 GTAAG--TTATGTAAGTTAT
38978898 GTAAGTTAT
1 GTAAGTTAT
38978907 TATGTATTGT
Statistics
Matches: 114, Mismatches: 7, Indels: 54
0.65 0.04 0.31
Matches are distributed among these distances:
14 6 0.05
15 8 0.07
16 14 0.12
17 8 0.07
18 59 0.52
19 15 0.13
20 4 0.04
ACGTcount: A:0.35, C:0.00, G:0.20, T:0.45
Consensus pattern (18 bp):
GTAAGTTATGTAAGTTAT
Found at i:38978821 original size:26 final size:26
Alignment explanation
Indices: 38978787--38979192 Score: 570
Period size: 26 Copynumber: 16.1 Consensus size: 26
38978777 TATAAGTTAA
38978787 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
38978813 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
38978838 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
38978863 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
38978889 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* * *
38978915 GTGTAAGTTGCAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
38978940 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
38978966 ATGTAAGTTGGAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
38978992 GTGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
38979018 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
38979044 GTGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
* *
38979069 ATGTCA---GTCA---A--ATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
38979087 ATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
38979112 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
*
38979138 ATGTAAGTAATGTAAGTTA-AATGTATT
1 ATGTAAGT--TGTAAGTTATTATGTATT
38979165 ATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTATTATGTATT
38979191 AT
1 AT
38979193 TTAATAAAAT
Statistics
Matches: 343, Mismatches: 24, Indels: 26
0.87 0.06 0.07
Matches are distributed among these distances:
18 12 0.03
19 1 0.00
21 3 0.01
22 3 0.01
24 1 0.00
25 113 0.33
26 186 0.54
27 15 0.04
28 9 0.03
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (26 bp):
ATGTAAGTTGTAAGTTATTATGTATT
Found at i:38978907 original size:19 final size:19
Alignment explanation
Indices: 38978885--38979188 Score: 88
Period size: 19 Copynumber: 16.5 Consensus size: 19
38978875 AGTTATTATG
38978885 TATTATGTAAGTTGTAAGT
1 TATTATGTAAGTTGTAAGT
38978904 TATTATGT-A-TTGT--GT
1 TATTATGTAAGTTGTAAGT
* * * *
38978919 AAGT-TGCAAG-T-TAAAT
1 TATTATGTAAGTTGTAAGT
38978935 GTATTATGTAAGTTGTAAGTTAT
1 -TATTATGTAAGTTGTAAG---T
*
38978958 TATGTATTATGTAAGTTGGAAGT
1 TA----TTATGTAAGTTGTAAGT
38978981 TATTATGT-A-TTGT--GT
1 TATTATGTAAGTTGTAAGT
* * * *
38978996 AAGT-TGTAAGTTATTA-T
1 TATTATGTAAGTTGTAAGT
38979013 GTATTATGTAAGTTGTAAGT
1 -TATTATGTAAGTTGTAAGT
38979033 TATTATGT-A-TTGT--GT
1 TATTATGTAAGTTGTAAGT
* * *
38979048 AAGT-TGTAAG-T-TAAAT
1 TATTATGTAAGTTGTAAGT
* * *
38979064 GTATTATGTCAG-T-CAAAT
1 -TATTATGTAAGTTGTAAGT
38979082 GTATTATGTAAGTTGTAAGTTAAAT
1 -TATTATGTAAGTTGTAAG-----T
38979107 GTATTATGTAAGTTGTAAGT
1 -TATTATGTAAGTTGTAAGT
*
38979127 TATTATGT-ATTATGTAAG-
1 TATTATGTAAGT-TGTAAGT
*
38979145 TA--ATGTAAG-T-TAAAT
1 TATTATGTAAGTTGTAAGT
38979160 GTATTATGTAAGTTGTAAGT
1 -TATTATGTAAGTTGTAAGT
38979180 TATTATGTA
1 TATTATGTA
38979189 TTATTTAATA
Statistics
Matches: 211, Mismatches: 31, Indels: 86
0.64 0.09 0.26
Matches are distributed among these distances:
14 13 0.06
15 18 0.09
16 11 0.05
17 17 0.08
18 42 0.20
19 58 0.27
20 11 0.05
22 2 0.01
23 4 0.02
25 20 0.09
26 15 0.07
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.46
Consensus pattern (19 bp):
TATTATGTAAGTTGTAAGT
Found at i:38979116 original size:18 final size:18
Alignment explanation
Indices: 38979052--38979173 Score: 74
Period size: 18 Copynumber: 6.4 Consensus size: 18
38979042 TTGTGTAAGT
38979052 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
* *
38979070 TGTCAGTCAAATGTATTATGTAA
1 TGTAAGTTAAATG---TAT-T-A
38979093 GTTGTAAGTTAAATGTATTA
1 --TGTAAGTTAAATGTATTA
*
38979113 TGTAAGTTGTAA-GTTATTA
1 TGTAAGTT-AAATG-TATTA
*
38979132 TGT-A-TT--ATGTAAGTAA
1 TGTAAGTTAAATGT-A-TTA
38979148 TGTAAGTTAAATGTATTA
1 TGTAAGTTAAATGTATTA
38979166 TGTAAGTT
1 TGTAAGTT
38979174 GTAAGTTATT
Statistics
Matches: 81, Mismatches: 7, Indels: 32
0.68 0.06 0.27
Matches are distributed among these distances:
14 2 0.02
15 2 0.02
16 5 0.06
17 3 0.04
18 33 0.41
19 11 0.14
20 5 0.06
21 4 0.05
22 4 0.05
23 1 0.01
25 11 0.14
ACGTcount: A:0.35, C:0.02, G:0.19, T:0.44
Consensus pattern (18 bp):
TGTAAGTTAAATGTATTA
Found at i:38979162 original size:53 final size:51
Alignment explanation
Indices: 38978787--38979192 Score: 562
Period size: 51 Copynumber: 8.0 Consensus size: 51
38978777 TATAAGTTAA
* *
38978787 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
*
38978838 GTGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
* * * *
38978889 ATGTAAGTTGTAAGTTATTATGTATTGTGTAAGTTGCAAGTTA-AATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
* *
38978940 ATGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGGAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
* *
38978992 GTGTAAGTTGTAAGTTATTATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTA-AATGTATTATGTAAGTTGTAAGTTATTATGTATT
* * *
38979044 GTGTAAGTTGTAAGTTAAATGTATTATGTCA---GTCA---A--ATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
38979087 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
38979138 ATGTAAGTAATGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
1 ATGTAAGT--TGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
38979191 AT
1 AT
38979193 TTAATAAAAT
Statistics
Matches: 323, Mismatches: 19, Indels: 24
0.88 0.05 0.07
Matches are distributed among these distances:
43 36 0.11
45 1 0.00
46 3 0.01
48 3 0.01
49 1 0.00
50 24 0.07
51 114 0.35
52 96 0.30
53 45 0.14
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.47
Consensus pattern (51 bp):
ATGTAAGTTGTAAGTTAAATGTATTATGTAAGTTGTAAGTTATTATGTATT
Found at i:38979312 original size:73 final size:73
Alignment explanation
Indices: 38979229--38979378 Score: 300
Period size: 73 Copynumber: 2.1 Consensus size: 73
38979219 ACATTACTAA
38979229 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
38979294 TATTTTTT
66 TATTTTTT
38979302 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
1 TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
38979367 TATTTTTT
66 TATTTTTT
38979375 TATA
1 TATA
38979379 TTTTATTTAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.41, C:0.07, G:0.01, T:0.51
Consensus pattern (73 bp):
TATAATTATTAATAATATTTAATAAAATAACATTTTATTTTAATAGTCAATTTTAATATTCCACA
TATTTTTT
Found at i:38979372 original size:35 final size:35
Alignment explanation
Indices: 38979260--38979372 Score: 104
Period size: 35 Copynumber: 3.1 Consensus size: 35
38979250 ATAAAATAAC
38979260 ATTTTATTTTAATAGTCAATTTTAATATTCCACAT
1 ATTTTATTTTAATAGTCAATTTTAATATTCCACAT
* * **** *
38979295 ATTTT-TTTATAATTATTAATAATATTTAATAAAATA-AC
1 ATTTTATTT-TAA-TAGT--CAAT-TTTAATATTCCACAT
38979333 ATTTTATTTTAATAGTCAATTTTAATATTCCACAT
1 ATTTTATTTTAATAGTCAATTTTAATATTCCACAT
38979368 ATTTT
1 ATTTT
38979373 TTTATATTTT
Statistics
Matches: 57, Mismatches: 14, Indels: 14
0.67 0.16 0.16
Matches are distributed among these distances:
34 11 0.19
35 17 0.30
36 3 0.05
37 3 0.05
38 12 0.21
39 11 0.19
ACGTcount: A:0.38, C:0.08, G:0.02, T:0.52
Consensus pattern (35 bp):
ATTTTATTTTAATAGTCAATTTTAATATTCCACAT
Found at i:38979542 original size:13 final size:13
Alignment explanation
Indices: 38979524--38979594 Score: 106
Period size: 13 Copynumber: 5.5 Consensus size: 13
38979514 ATTTATAATT
38979524 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
38979537 ATTTAAGTAACAT
1 ATTTAAGTAATAA
38979550 ATTTAAGTAATAA
1 ATTTAAGTAATAA
* *
38979563 ATTTAAGTAACAT
1 ATTTAAGTAATAA
38979576 ATTTAAGTAATAA
1 ATTTAAGTAATAA
38979589 ATTTAA
1 ATTTAA
38979595 ACAAATTTTA
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 50 1.00
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (13 bp):
ATTTAAGTAATAA
Found at i:38979553 original size:26 final size:26
Alignment explanation
Indices: 38979523--38979594 Score: 144
Period size: 26 Copynumber: 2.8 Consensus size: 26
38979513 TATTTATAAT
38979523 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
38979549 TATTTAAGTAATAAATTTAAGTAACA
1 TATTTAAGTAATAAATTTAAGTAACA
38979575 TATTTAAGTAATAAATTTAA
1 TATTTAAGTAATAAATTTAA
38979595 ACAAATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.50, C:0.03, G:0.07, T:0.40
Consensus pattern (26 bp):
TATTTAAGTAATAAATTTAAGTAACA
Found at i:38982534 original size:115 final size:114
Alignment explanation
Indices: 38982396--38982712 Score: 553
Period size: 115 Copynumber: 2.8 Consensus size: 114
38982386 AATAAACACC
38982396 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
1 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
* *
38982461 TAACATTTTTTGCGGCGTTTTAAGATAAGCGCCGCTAAAGTAACATATTT
66 TAACA-TTTTTGCGGCGTTTTAAAAGAAGCGCCGCTAAAGTAACATATTT
* *
38982511 TGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGGTAAACACATA
1 TGCGGCGTTTTAACAAAAACGCCACTAAATACAT-AAAAAACGGTCACGTTTTGGTAAACACAAA
* * *
38982576 ATAACATTTTTGTGGCATTTTAAAAGAAGCGCCGCTAAAGTAACATCTTT
65 ATAACATTTTTGCGGCGTTTTAAAAGAAGCGCCGCTAAAGTAACATATTT
38982626 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
1 TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
38982691 TAACATTTTTGCGGCGTTTTAA
66 TAACATTTTTGCGGCGTTTTAA
38982713 TAAAAATGCC
Statistics
Matches: 190, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
114 50 0.26
115 105 0.55
116 35 0.18
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (114 bp):
TGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
TAACATTTTTGCGGCGTTTTAAAAGAAGCGCCGCTAAAGTAACATATTT
Found at i:38982539 original size:40 final size:40
Alignment explanation
Indices: 38982461--38982539 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
38982451 AAACACAAAA
* * * * * *
38982461 TAACATTTTTTGCGGCGTTTTAAGATAAGCGCCGCTAAAG
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAAG
38982501 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAA
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAA
38982540 TACATAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (40 bp):
TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAAG
Found at i:38982654 original size:40 final size:39
Alignment explanation
Indices: 38982577--38982654 Score: 95
Period size: 40 Copynumber: 2.0 Consensus size: 39
38982567 AAACACATAA
* * *
38982577 TAACATTTTTGTGGCATTTTAAAAGAAGCGCCGCTAAAG
1 TAACATTTTTGCGGCATTTTAAAAGAAACGCCACTAAAG
*
38982616 TAACATCTTTTGCGGCGTTTTAACAA-AAACGCCACTAAA
1 TAACAT-TTTTGCGGCATTTTAA-AAGAAACGCCACTAAA
38982655 TACATAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
39 6 0.18
40 25 0.76
41 2 0.06
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (39 bp):
TAACATTTTTGCGGCATTTTAAAAGAAACGCCACTAAAG
Found at i:38982803 original size:75 final size:74
Alignment explanation
Indices: 38982616--38982787 Score: 299
Period size: 75 Copynumber: 2.3 Consensus size: 74
38982606 GCCGCTAAAG
38982616 TAACATCTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGT
1 TAACAT-TTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGT
38982681 AAACACAAAA
65 AAACACAAAA
* *
38982691 TAACATTTTTGCGGCGTTTTAATAAAAATGCCACTAAATACATAAAAAAACGGTCACGTTTTGGT
1 TAACATTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACAT-AAAAAACGGTCACGTTTTGGT
38982756 AAACACAAAA
65 AAACACAAAA
*
38982766 TAACATTCTTGCGGCGTTTTAA
1 TAACATTTTTGCGGCGTTTTAA
38982788 GATAAGCGCC
Statistics
Matches: 93, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
74 35 0.38
75 58 0.62
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (74 bp):
TAACATTTTTGCGGCGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTA
AACACAAAA
Found at i:38982828 original size:189 final size:189
Alignment explanation
Indices: 38982501--38982879 Score: 580
Period size: 189 Copynumber: 2.0 Consensus size: 189
38982491 GCCGCTAAAG
38982501 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
* * * * *
38982566 TAAACACATAATAACATTTTTGTGGCATTTTAAAAGAAGCGCCGCTAAAGTAACATCTTTTGCGG
66 TAAACACAAAATAACATTCTTGCGGCATTTTAAAAGAAGCGCCGCTAAAGCAACATCTTTTCCGG
* * *
38982631 CGTTTTAACAAAAACGCCACTAAATACATAAAAAACGGTCACGTTTTGGTAAACACAAAA
131 CGTTTTAACAAAAACGCCACTAAAAACAT-AAAAACGATCACGTTTCGGTAAACACAAAA
* * *
38982691 TAACAT-TTTTGCGGCGTTTTAATAAAAATGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
1 TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
* * * *
38982755 TAAACACAAAATAACATTCTTGCGGCGTTTTAAGATAAGCGCCGCTAAAGCAAGATCTTTTCCGG
66 TAAACACAAAATAACATTCTTGCGGCATTTTAAAAGAAGCGCCGCTAAAGCAACATCTTTTCCGG
** *
38982820 CGTTTTAACAAAAACGCCACTAAAAACATAAAAACGATTTCGTTTCGGTCAACACAAAA
131 CGTTTTAACAAAAACGCCACTAAAAACATAAAAACGATCACGTTTCGGTAAACACAAAA
38982879 T
1 T
38982880 CCAACAAAAC
Statistics
Matches: 171, Mismatches: 18, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
188 26 0.15
189 139 0.81
190 6 0.04
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (189 bp):
TAACATATTTTGCGGCATTTTAACAAAAACGCCACTAAATACATAAAAAAACGGTCACGTTTTGG
TAAACACAAAATAACATTCTTGCGGCATTTTAAAAGAAGCGCCGCTAAAGCAACATCTTTTCCGG
CGTTTTAACAAAAACGCCACTAAAAACATAAAAACGATCACGTTTCGGTAAACACAAAA
Found at i:38983076 original size:113 final size:115
Alignment explanation
Indices: 38982876--38983152 Score: 308
Period size: 114 Copynumber: 2.4 Consensus size: 115
38982866 GGTCAACACA
* * * ** * * * * *** **
38982876 AAATCCAACAAAACGGCAACGTTTTTATTATAACCCATTGAAATTTTGTGGCGTTTCCAACGCAG
1 AAATCCTACACAACGGCAACGTTTTTATTAAAACAAAATCACATTTTGCGGCGTTTTTGACATAG
* *
38982941 CGCCGCTAAAGGCTGACGTTTT-CGGCGTTTTACAAAAAACGCCACTAAT
66 CGCCGCTAAAGGATGACGTTTTCCGGCGTTTTACAAAAAACGCCACTAAG
* * *
38982990 AAATCCTACACCACGGCAGCG-TTTTATTAAAACAGAATCACATTTTGCGGCGTTTTTGACATAG
1 AAATCCTACACAACGGCAACGTTTTTATTAAAACAAAATCACATTTTGCGGCGTTTTTGACATAG
* *
38983054 CGCCGCTAAAGGATGATC-TTTTCCGGCGTTTTACCAAAAACGCCAGTAAG
66 CGCCGCTAAAGGATGA-CGTTTTCCGGCGTTTTACAAAAAACGCCACTAAG
* * *
38983104 AAATCTTACAGAACGGCAACGTTTTTATTGAAACAAAATCACATTTTGC
1 AAATCCTACACAACGGCAACGTTTTTATTAAAACAAAATCACATTTTGC
38983153 AGTGTTTTAC
Statistics
Matches: 134, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
113 50 0.37
114 59 0.44
115 25 0.19
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (115 bp):
AAATCCTACACAACGGCAACGTTTTTATTAAAACAAAATCACATTTTGCGGCGTTTTTGACATAG
CGCCGCTAAAGGATGACGTTTTCCGGCGTTTTACAAAAAACGCCACTAAG
Found at i:38983677 original size:7 final size:7
Alignment explanation
Indices: 38983665--38983838 Score: 60
Period size: 7 Copynumber: 25.1 Consensus size: 7
38983655 ACTAATCAAT
38983665 CTAAACC
1 CTAAACC
*
38983672 CTAAACA
1 CTAAACC
38983679 C-ATAACC
1 CTA-AACC
38983686 CTTAAATCC
1 C-TAAA-CC
38983695 CTTAAACC
1 C-TAAACC
38983703 CTAAACC
1 CTAAACC
*
38983710 C-AAATC
1 CTAAACC
* *
38983716 ATAATCC
1 CTAAACC
38983723 CTAAA-C
1 CTAAACC
*
38983729 CT--AGC
1 CTAAACC
*
38983734 CTAGACC
1 CTAAACC
*
38983741 CTGAACC
1 CTAAACC
*
38983748 C-CAACC
1 CTAAACC
38983754 CATAAACC
1 C-TAAACC
*
38983762 TTAAACC
1 CTAAACC
*
38983769 C-CAACC
1 CTAAACC
38983775 CT-AACC
1 CTAAACC
38983781 CGTAAACC
1 C-TAAACC
*
38983789 TTAAACC
1 CTAAACC
*
38983796 C-CAACTC
1 CTAAAC-C
*
38983803 GTAAACC
1 CTAAACC
*
38983810 CTAAACT
1 CTAAACC
*
38983817 GTAAACC
1 CTAAACC
* * *
38983824 ATAATCA
1 CTAAACC
38983831 CTAAACC
1 CTAAACC
38983838 C
1 C
38983839 ATAATTTGCA
Statistics
Matches: 121, Mismatches: 31, Indels: 30
0.66 0.17 0.16
Matches are distributed among these distances:
4 1 0.01
5 3 0.02
6 26 0.21
7 66 0.55
8 16 0.13
9 9 0.07
ACGTcount: A:0.40, C:0.39, G:0.03, T:0.18
Consensus pattern (7 bp):
CTAAACC
Found at i:38983774 original size:27 final size:27
Alignment explanation
Indices: 38983744--38983800 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
38983734 CTAGACCCTG
38983744 AACCCCAACCCATAAACCTTAAACCCC
1 AACCCCAACCCATAAACCTTAAACCCC
* *
38983771 AACCCTAACCCGTAAACCTTAAACCCC
1 AACCCCAACCCATAAACCTTAAACCCC
38983798 AAC
1 AAC
38983801 TCGTAAACCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.40, C:0.46, G:0.02, T:0.12
Consensus pattern (27 bp):
AACCCCAACCCATAAACCTTAAACCCC
Found at i:38983788 original size:20 final size:21
Alignment explanation
Indices: 38983744--38983788 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
38983734 CTAGACCCTG
*
38983744 AACCCCAACCCATAAACCTTA
1 AACCCCAACCCATAAACCGTA
*
38983765 AACCCCAACCC-TAACCCGTA
1 AACCCCAACCCATAAACCGTA
38983785 AACC
1 AACC
38983789 TTAAACCCCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.40, C:0.47, G:0.02, T:0.11
Consensus pattern (21 bp):
AACCCCAACCCATAAACCGTA
Found at i:38984365 original size:73 final size:72
Alignment explanation
Indices: 38984270--38984407 Score: 197
Period size: 73 Copynumber: 1.9 Consensus size: 72
38984260 AAAGACTCGA
38984270 AAACTAAGAAAACGATGTCGTTGGGCTTAGGCTTTTTGCGGCG-CTTTTACAAAAACGCCACTAA
1 AAACTAAGAAAACGATGTCGTTGGGCTTAGGCTTTTTGCGGCGACTTTTA-AAAAACGCCACTAA
38984334 AGCCTCCC
65 AGCCTCCC
* * * * * *
38984342 AAACTAAGAAAAACGATGTCGTTGGGCTTCGGTTTTTTGTGGCGATTTTTAAAAAATGCCGCTAA
1 AAACTAAG-AAAACGATGTCGTTGGGCTTAGGCTTTTTGCGGCGACTTTTAAAAAACGCCACTAA
38984407 A
65 A
38984408 ACATTGAGCA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
72 8 0.14
73 45 0.78
74 5 0.09
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (72 bp):
AAACTAAGAAAACGATGTCGTTGGGCTTAGGCTTTTTGCGGCGACTTTTAAAAAACGCCACTAAA
GCCTCCC
Found at i:38984461 original size:114 final size:114
Alignment explanation
Indices: 38984307--38984633 Score: 408
Period size: 113 Copynumber: 2.9 Consensus size: 114
38984297 TAGGCTTTTT
** * ** *
38984307 GCGGCGCTTTTACAAAAACGCCACTAAAGCCTCCCAAACTAAGAAAAACGATGTCGTTGGGCTTC
1 GCGGCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCTTA
* * * * * *
38984372 GGTTTTTTGTGGCGATTTTTAAAAAATGCCGCTAAAACATTGAGCATTA
66 GGTTTTTTGCGGCGCTTTTTAAGAAACGCCGCTAAAACACTGAGAATTA
* *
38984421 GCGGCGCTTTCCCGAAAACGCCACCAAAGCCTCGAAAACTAAG-AAAATGATGTCGTTGGGCTTA
1 GCGGCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCTTA
* * * *
38984485 GGTCTTTTGCGGCGCTTTTTAAGAAACGCTGCTAAAGCCCTGAGAATTA
66 GGTTTTTTGCGGCGCTTTTTAAGAAACGCCGCTAAAACACTGAGAATTA
* * * *
38984534 -CTTGCGC-TTCTCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGACGTCGTTTGGTT
1 GC-GGCGCTTTC-CCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCT
*
38984597 TAGGTTTTTAGCGGCGCTTTTTAAGAAACGCCGCTAA
64 TAGGTTTTTTGCGGCGCTTTTTAAGAAACGCCGCTAA
38984634 TGCTCATTAT
Statistics
Matches: 183, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
112 4 0.02
113 93 0.51
114 86 0.47
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.25
Consensus pattern (114 bp):
GCGGCGCTTTCCCAAAAACGCCACCAAAGCCTCGAAAACTAAGAAAAACGATGTCGTTGGGCTTA
GGTTTTTTGCGGCGCTTTTTAAGAAACGCCGCTAAAACACTGAGAATTA
Found at i:38984647 original size:39 final size:38
Alignment explanation
Indices: 38984604--38984733 Score: 127
Period size: 39 Copynumber: 3.3 Consensus size: 38
38984594 GTTTAGGTTT
* *
38984604 TTAGCGGCGCTTTTTAAGAAACGCCGCTAATGCTCATTA
1 TTAGCGGCGTTTTTTAA-AAACGCCGCTAATGCTAATTA
* * * *
38984643 TTAGCGGCGTTTTTGTAAAAGCGCCGGTAATACTGA-TA
1 TTAGCGGCGTTTTT-TAAAAACGCCGCTAATGCTAATTA
* * *
38984681 TTTAGCGGCGTTTTTTTTAAATCGCCGCTAATGCTTAATTT
1 -TTAGCGGCG-TTTTTTAAAAACGCCGCTAATGC-TAATTA
38984722 TTAGCGGCGTTT
1 TTAGCGGCGTTT
38984734 GTTGTCCAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 10
0.78 0.11 0.10
Matches are distributed among these distances:
38 2 0.03
39 53 0.71
40 19 0.25
41 1 0.01
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (38 bp):
TTAGCGGCGTTTTTTAAAAACGCCGCTAATGCTAATTA
Found at i:38989338 original size:20 final size:20
Alignment explanation
Indices: 38989313--38989350 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
38989303 ACCACTTAAC
*
38989313 GAAAATATCGGTACCCTATT
1 GAAAATATCGATACCCTATT
38989333 GAAAATATCGATACCCTA
1 GAAAATATCGATACCCTA
38989351 GTATCAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.26
Consensus pattern (20 bp):
GAAAATATCGATACCCTATT
Found at i:39003210 original size:14 final size:14
Alignment explanation
Indices: 39003187--39003230 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
39003177 TTGCAATACT
*
39003187 ATAAATGAAGTAAA
1 ATAAAGGAAGTAAA
*
39003201 ATAAAGGAAGTAAGC
1 ATAAAGGAAGTAA-A
39003216 ATAAAGGAAAGTAAA
1 ATAAAGG-AAGTAAA
39003231 TAACAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 12 0.48
15 7 0.28
16 6 0.24
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.16
Consensus pattern (14 bp):
ATAAAGGAAGTAAA
Found at i:39003656 original size:50 final size:50
Alignment explanation
Indices: 39003530--39003778 Score: 209
Period size: 50 Copynumber: 4.9 Consensus size: 50
39003520 GATAATAACA
* ** * * *
39003530 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCTTGTAC--
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGG
* * * * **
39003579 TGCCAATGCCATATCCCTGATATGGTCTTGCATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* ** *
39003629 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * *
39003679 TGCCAACGCCATGTCCAAGACATGGTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * *
39003735 TGCCAATGCCATATTCCAAACATGGTCTTACATGGGA--TCTCATA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
39003779 ACCCAAATGT
Statistics
Matches: 160, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
48 1 0.01
49 37 0.23
50 80 0.50
53 3 0.02
54 6 0.04
56 33 0.21
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:39015269 original size:435 final size:435
Alignment explanation
Indices: 39014459--39015764 Score: 2414
Period size: 435 Copynumber: 3.0 Consensus size: 435
39014449 TGATGTCTCC
39014459 AAATCTTCAACGCAAATACAATGGCAGCTAGCTCTAAATCATGCGTCGGGTAGTTTTTCTCATGT
1 AAATCTTCAACGCAAATACAATGGCAGCTAGCTCTAAATCATGCGTCGGGTAGTTTTTCTCATGT
39014524 AGCTTTAACTGTACGGAAGCATATGCTATTACTTTACCTTCCTACATAATTACACAACCCAATCC
66 AGCTTTAACTGTACGGAAGCATATGCTATTACTTTACCTTCCTACATAATTACACAACCCAATCC
** *
39014589 ATTCAAGGATGCATTACTGTAAATCACAAATTCTTTACCCGGTTCTAGCTGTACTAAAATAGGAG
131 ATTCAAGGATGCATTACTGTAAATCACAAATTCTTTACCTAGTTCTAGCTGTACTAAAACAGGAG
* *
39014654 CTTGAGTGAACAATGCCTTTAACTTGTCAAAACTTTGCTAACACTTCTCAGTCCATTAAAACTTG
196 CTTGAGTGAACAATGCCTTTAACTTGTCAAAACTCTGCTGACACTTCTCAGTCCATTAAAACTTG
* * *
39014719 ATATCTTTCTGGAAAAATATTGTCAATGGGGTAACTATCATGGAAAATTCCTTTACAAACCGTCT
261 ATATCTTTCTGGAACAATCTTGTCAATGGGGTAACTATCATGGAAAATCCCTTTACAAACCGTCT
*
39014784 GTAATAACCAGCTAATCCAAGAAAATTTCTAACCTCTGATACATTCCTAGGTGGTTTCCACTCAA
326 GTAATAACCAGCTAATCCAAGAAAACTTCTAACCTCTGATACATTCCTAGGTGGTTTCCACTCAA
*
39014849 TAATTGCTAAAATTTTACTCGGATCAACTTTAATACCATCACCTG
391 CAATTGCTAAAATTTTACTCGGATCAACTTTAATACCATCACCTG
39014894 AAATCTTCAACGCAAATACAATGGCAGCTAGCTCTAAATCATGCGTCGGGTAGTTTTTCTCATGT
1 AAATCTTCAACGCAAATACAATGGCAGCTAGCTCTAAATCATGCGTCGGGTAGTTTTTCTCATGT
39014959 AGCTTTAACTGTACGGAAGCATATGCTATTACTTTACCTTCCTACATAATTACACAACCCAATCC
66 AGCTTTAACTGTACGGAAGCATATGCTATTACTTTACCTTCCTACATAATTACACAACCCAATCC
*
39015024 ATTCAAGGATGCATTACTATAAATCACAAATTCTTTACCTAGTTCTAGCTGTACTAAAACAGGAG
131 ATTCAAGGATGCATTACTGTAAATCACAAATTCTTTACCTAGTTCTAGCTGTACTAAAACAGGAG
*
39015089 CTTGAGTGAACAATGCCTTTAACTTGTCAAAACTCTGCTGACACTTCTCAGTCTATTAAAACTTG
196 CTTGAGTGAACAATGCCTTTAACTTGTCAAAACTCTGCTGACACTTCTCAGTCCATTAAAACTTG
* *
39015154 ATATCTTTCTGGAACAATCTTTTCAATGGGGTAACTATCATGGAAAATCCCTTTACAAGCCGTCT
261 ATATCTTTCTGGAACAATCTTGTCAATGGGGTAACTATCATGGAAAATCCCTTTACAAACCGTCT
39015219 GTAATAACCAGCTAATCCAAGAAAACTTCTAACCTCTGATACATTCCTAGGTGGTTTCCACTCAA
326 GTAATAACCAGCTAATCCAAGAAAACTTCTAACCTCTGATACATTCCTAGGTGGTTTCCACTCAA
39015284 CAATTGCTAAAATTTTACTCGGATCAACTTTAATACCATCACCTG
391 CAATTGCTAAAATTTTACTCGGATCAACTTTAATACCATCACCTG
*
39015329 AAATCTTCAACGCAAATACAATGGCAGCTAGCTCTAAATCATGTGTCGGGTAGTTTTTCTCATGT
1 AAATCTTCAACGCAAATACAATGGCAGCTAGCTCTAAATCATGCGTCGGGTAGTTTTTCTCATGT
*
39015394 AGCTTTAACTGTACGGAAGCATATGCTATTACTTTACCTTCCTACATAAGTACACAACCCAATCC
66 AGCTTTAACTGTACGGAAGCATATGCTATTACTTTACCTTCCTACATAATTACACAACCCAATCC
39015459 ATTCAAGGATGCATTACTGTAAATCACAAATTCTTTACCTAGTTCTAGCTGTACTAAAACAGGAG
131 ATTCAAGGATGCATTACTGTAAATCACAAATTCTTTACCTAGTTCTAGCTGTACTAAAACAGGAG
* *
39015524 CTTGAGTGAACAATGCCTTTAACTTGTCAAAACTCAGCTGACACTTCTCAGTCCATTAAAACTTT
196 CTTGAGTGAACAATGCCTTTAACTTGTCAAAACTCTGCTGACACTTCTCAGTCCATTAAAACTTG
*
39015589 ATATCTTTCTGGAACAATCTTGTCAATGGGGTAACTATCATTGAAAATCCCTTTACAAACCGTCT
261 ATATCTTTCTGGAACAATCTTGTCAATGGGGTAACTATCATGGAAAATCCCTTTACAAACCGTCT
* *
39015654 GTAATAACCAACTAATCCAAGAAAACTTCTAACCTCTGATACATTCCTAGGTGGTTTTCACTCAA
326 GTAATAACCAGCTAATCCAAGAAAACTTCTAACCTCTGATACATTCCTAGGTGGTTTCCACTCAA
*
39015719 CAATTGCTGAAATTTTACTCGGATCAACTTTAATACCATCACCTG
391 CAATTGCTAAAATTTTACTCGGATCAACTTTAATACCATCACCTG
39015764 A
1 A
39015765 GACAATGTGC
Statistics
Matches: 845, Mismatches: 26, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
435 845 1.00
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (435 bp):
AAATCTTCAACGCAAATACAATGGCAGCTAGCTCTAAATCATGCGTCGGGTAGTTTTTCTCATGT
AGCTTTAACTGTACGGAAGCATATGCTATTACTTTACCTTCCTACATAATTACACAACCCAATCC
ATTCAAGGATGCATTACTGTAAATCACAAATTCTTTACCTAGTTCTAGCTGTACTAAAACAGGAG
CTTGAGTGAACAATGCCTTTAACTTGTCAAAACTCTGCTGACACTTCTCAGTCCATTAAAACTTG
ATATCTTTCTGGAACAATCTTGTCAATGGGGTAACTATCATGGAAAATCCCTTTACAAACCGTCT
GTAATAACCAGCTAATCCAAGAAAACTTCTAACCTCTGATACATTCCTAGGTGGTTTCCACTCAA
CAATTGCTAAAATTTTACTCGGATCAACTTTAATACCATCACCTG
Found at i:39019104 original size:50 final size:50
Alignment explanation
Indices: 39019050--39019223 Score: 240
Period size: 50 Copynumber: 3.5 Consensus size: 50
39019040 TATCTCAAAT
** * * * * *
39019050 ATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATGTCTCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
**
39019100 ATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
* *
39019150 ATGGTCTTACATGGGACCTCTCATCTCGGTGGCAACGCTATGTCCCAGAC
1 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
*
39019200 ATGGTCTTACATGAGACCTCTCAT
1 ATGGTCTTACATGGGACCTCTCAT
39019224 AATCTCAATG
Statistics
Matches: 110, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 110 1.00
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.28
Consensus pattern (50 bp):
ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGAC
Found at i:39023068 original size:27 final size:27
Alignment explanation
Indices: 39023035--39023114 Score: 108
Period size: 27 Copynumber: 3.0 Consensus size: 27
39023025 CACTCAAGCA
*
39023035 TTCCTTTCACT-TTGCGCCATAAAGTCG
1 TTCCTTTCA-TATTGCGCCATAAAGGCG
* *
39023062 TTTCTTTCATATTGCGCCACAAAGGCG
1 TTCCTTTCATATTGCGCCATAAAGGCG
*
39023089 TTCCTTTCATATTGCACCATAAAGGC
1 TTCCTTTCATATTGCGCCATAAAGGC
39023115 TATCATATCA
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
26 1 0.02
27 45 0.98
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.35
Consensus pattern (27 bp):
TTCCTTTCATATTGCGCCATAAAGGCG
Found at i:39023184 original size:27 final size:27
Alignment explanation
Indices: 39023152--39023443 Score: 297
Period size: 27 Copynumber: 10.9 Consensus size: 27
39023142 TATTCCTTTG
* *
39023152 GAGTTCGCCACAATGGCTCCCTTTTCA
1 GAGTTCGCCACAAAGGCTTCCTTTTCA
* *
39023179 GTGTTCGCTACAAAGGCTTCCTTTTCA
1 GAGTTCGCCACAAAGGCTTCCTTTTCA
** * *
39023206 -AAATAGCCACAAAGGCTTCATGTTT-A
1 GAGTTCGCCACAAAGGCTTCCT-TTTCA
* *
39023232 GAGTTAGCCACAAATGCTTCCTTTT-A
1 GAGTTCGCCACAAAGGCTTCCTTTTCA
*
39023258 GAGTTAGCCACAAAGGCTTCCTTTTCA
1 GAGTTCGCCACAAAGGCTTCCTTTTCA
* *
39023285 GTGTTCGCCACAAAGGCTTCCATTTCA
1 GAGTTCGCCACAAAGGCTTCCTTTTCA
39023312 GAGTTCGCCACAAAGGCTTCCTTTTCA
1 GAGTTCGCCACAAAGGCTTCCTTTTCA
* * * **
39023339 GAGTTAGTCATAAAGGCTTAATTTTCA
1 GAGTTCGCCACAAAGGCTTCCTTTTCA
* * * *
39023366 -ATGTTAGCCATAAAAGCTTCCTTTTTA
1 GA-GTTCGCCACAAAGGCTTCCTTTTCA
*
39023393 GAGTTAGCCACAAAGGCTTCCCTTTT-A
1 GAGTTCGCCACAAAGGCTT-CCTTTTCA
* *
39023420 GATTTAGCCACAAAGGCTTCCTTT
1 GAGTTCGCCACAAAGGCTTCCTTT
39023444 CCTAACATGT
Statistics
Matches: 226, Mismatches: 33, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
26 50 0.22
27 169 0.75
28 7 0.03
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (27 bp):
GAGTTCGCCACAAAGGCTTCCTTTTCA
Found at i:39023385 original size:81 final size:80
Alignment explanation
Indices: 39023152--39023443 Score: 345
Period size: 81 Copynumber: 3.6 Consensus size: 80
39023142 TATTCCTTTG
* * * * * * **
39023152 GAGTTCGCCACAATGGCTCCCTTTTCAGTGTTCGCTACAAAGGCTTCCTTTTCAA-AATAGCCAC
1 GAGTTAGCCACAAAGGCTTCCTTTT-AGAGTTAGCCACAAAGGCTTCCTTTTCAATGTTAGCCAC
39023216 AAAGGCTT-CATGTTTA
65 AAAGGCTTCCAT-TTTA
* * *
39023232 GAGTTAGCCACAAATGCTTCCTTTTAGAGTTAGCCACAAAGGCTTCCTTTTCAGTGTTCGCCACA
1 GAGTTAGCCACAAAGGCTTCCTTTTAGAGTTAGCCACAAAGGCTTCCTTTTCAATGTTAGCCACA
*
39023297 AAGGCTTCCATTTCA
66 AAGGCTTCCATTTTA
* * * ** *
39023312 GAGTTCGCCACAAAGGCTTCCTTTTCAGAGTTAGTCATAAAGGCTTAATTTTCAATGTTAGCCAT
1 GAGTTAGCCACAAAGGCTTCCTTTT-AGAGTTAGCCACAAAGGCTTCCTTTTCAATGTTAGCCAC
* *
39023377 AAAAGCTTCCTTTTTA
65 AAAGGCTTCCATTTTA
*
39023393 GAGTTAGCCACAAAGGCTTCCCTTTTAGATTTAGCCACAAAGGCTTCCTTT
1 GAGTTAGCCACAAAGGCTT-CCTTTTAGAGTTAGCCACAAAGGCTTCCTTT
39023444 CCTAACATGT
Statistics
Matches: 178, Mismatches: 30, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
79 25 0.14
80 61 0.34
81 86 0.48
82 6 0.03
ACGTcount: A:0.26, C:0.24, G:0.17, T:0.33
Consensus pattern (80 bp):
GAGTTAGCCACAAAGGCTTCCTTTTAGAGTTAGCCACAAAGGCTTCCTTTTCAATGTTAGCCACA
AAGGCTTCCATTTTA
Found at i:39025803 original size:35 final size:35
Alignment explanation
Indices: 39025744--39025895 Score: 169
Period size: 35 Copynumber: 4.3 Consensus size: 35
39025734 ACTCTCTGTT
* ** *
39025744 TTGGTGTGTTTCAGTTGGACTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* *
39025779 TCGGTGTGTTTCGGGGGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* * *
39025814 TTGGTGTGTTTCGAAGGGATTAACTCTTTTGAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
* * * * *
39025849 TTGGTGTGTTTCGAATGGATTGGCTCTTGTAAGCA
1 TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
39025884 TTTGGTGTGTTT
1 -TTGGTGTGTTT
39025896 TGGTTGGATT
Statistics
Matches: 101, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
35 90 0.89
36 11 0.11
ACGTcount: A:0.16, C:0.12, G:0.32, T:0.41
Consensus pattern (35 bp):
TTGGTGTGTTTCGGAGGGATTAGCTCTTATGAGCA
Found at i:39029811 original size:17 final size:17
Alignment explanation
Indices: 39029791--39029824 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
39029781 TATGCAAAAC
*
39029791 AATTTAAAGTAGATAAT
1 AATTTAAAGTAAATAAT
39029808 AATTTAAAGTAAATAAT
1 AATTTAAAGTAAATAAT
39029825 TTATAAGAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.09, T:0.35
Consensus pattern (17 bp):
AATTTAAAGTAAATAAT
Done.