Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr9
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: 38630433
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2298367 characters in sequence are not A, C, G, or T
File 3 of 97
Found at i:868680 original size:22 final size:22
Alignment explanation
Indices: 868649--868774 Score: 80
Period size: 22 Copynumber: 5.8 Consensus size: 22
868639 ATTTAAAATT
*
868649 TAATTAAAATATTAATAATTAA
1 TAATTTAAATATTAATAATTAA
*
868671 TAATTTAAATATTAATATTTAA
1 TAATTTAAATATTAATAATTAA
* * * *
868693 TTTAATTTAAGTATT-ATTATGAT
1 --TAATTTAAATATTAATAATTAA
* * * *
868716 TAATTT--TTATT-TTATTTTA
1 TAATTTAAATATTAATAATTAA
** *
868735 TTTTTTAAAATATTAATAATTGA
1 TAATTT-AAATATTAATAATTAA
868758 TAATTTAAATATTAATA
1 TAATTTAAATATTAATA
868775 TTTTATTTAT
Statistics
Matches: 76, Mismatches: 22, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
19 10 0.13
21 6 0.08
22 35 0.46
23 13 0.17
24 12 0.16
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TAATTTAAATATTAATAATTAA
Found at i:868695 original size:19 final size:19
Alignment explanation
Indices: 868641--868697 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 19
868631 TATTAATAAT
* *
868641 TTAAAATTTAATTAAAATA
1 TTAATATTTAATTTAAATA
868660 TTAATAATTAATAATTTAAATA
1 TTAAT-ATT--TAATTTAAATA
868682 TTAATATTTAATTTAA
1 TTAATATTTAATTTAA
868698 TTTAAGTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 12 0.36
20 3 0.09
21 3 0.09
22 15 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
TTAATATTTAATTTAAATA
Found at i:868782 original size:19 final size:19
Alignment explanation
Indices: 868641--868884 Score: 55
Period size: 22 Copynumber: 12.8 Consensus size: 19
868631 TATTAATAAT
* * *
868641 TTAAAATTTAATTAAAATA
1 TTAATATTTTATTTAAATA
*
868660 TTAATAATTAATAATTTAAATA
1 TTAAT-ATT--TTATTTAAATA
*
868682 TTAATATTTAATTT-AAT-
1 TTAATATTTTATTTAAATA
868699 TTAAGTA--TTA-TT--ATGA
1 TTAA-TATTTTATTTAAAT-A
868715 TTAAT-TTTTATTT---TA
1 TTAATATTTTATTTAAATA
* *
868730 TT-TTATTTT-TTAAAATA
1 TTAATATTTTATTTAAATA
*
868747 TTAATAATTGATAATTTAAATA
1 TTAAT-ATT--TTATTTAAATA
868769 TTAATATTTTATTTATAATTTAATTA
1 TTAATATTTTA-TT-T-A---AA-TA
868795 TTAATATTTTATTT-AAT-
1 TTAATATTTTATTTAAATA
868812 TTAAATANTTTTA-TT-AATA
1 TT-AATA-TTTTATTTAAATA
*
868831 --AATGA--TAATTTAAATA
1 TTAAT-ATTTTATTTAAATA
868847 TTAATATTTTATTTTATAAT-
1 TTAATATTTTA-TTTA-AATA
868867 TTAAATATTATTATTTAA
1 TT-AATATT-TTATTTAA
868885 TTAAATTAAT
Statistics
Matches: 175, Mismatches: 11, Indels: 77
0.67 0.04 0.29
Matches are distributed among these distances:
14 7 0.04
15 12 0.07
16 17 0.10
17 14 0.08
18 19 0.11
19 24 0.14
20 12 0.07
21 21 0.12
22 31 0.18
24 1 0.01
25 4 0.02
26 13 0.07
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (19 bp):
TTAATATTTTATTTAAATA
Found at i:868791 original size:113 final size:112
Alignment explanation
Indices: 868612--868815 Score: 284
Period size: 113 Copynumber: 1.8 Consensus size: 112
868602 ATATTTATTT
* *
868612 TTTTATTAAATTTTTTAAATATTAATAATTTAAAATTTAATTAAAATATTAATAATTAATAATTT
1 TTTTATTAAATTTTTTAAATATTAATAATTGAAAATTTAAATAAAATATT-ATAATTAATAATTT
868677 AAATATTAATATTTAATTTAATTTAAGTATTATTATGATTAATTTTTA
65 AAATATTAATATTTAATTTAATTTAAGTATTATTATGATTAATTTTTA
** * * * *
868725 TTTTATTTTATTTTTTAAAATATTAATAATTGATAATTTAAATATTAATATT-TTATTTATAATT
1 TTTTATTAAATTTTTT-AAATATTAATAATTGAAAATTTAAATA-AAATATTATAATTAATAATT
* *
868789 TAATTATTAATATTTTATTTAATTTAA
64 TAAATATTAATATTTAATTTAATTTAA
868816 ATANTTTTAT
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
113 49 0.62
114 24 0.30
115 6 0.08
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (112 bp):
TTTTATTAAATTTTTTAAATATTAATAATTGAAAATTTAAATAAAATATTATAATTAATAATTTA
AATATTAATATTTAATTTAATTTAAGTATTATTATGATTAATTTTTA
Found at i:868838 original size:78 final size:78
Alignment explanation
Indices: 868745--868906 Score: 238
Period size: 78 Copynumber: 2.1 Consensus size: 78
868735 TTTTTTAAAA
* * * *
868745 TATTAATAATTGATAATTTAAATATTAATATTTTA-TTTATAATTTAATTATTAATATTTTATTT
1 TATTAATAAATGATAATTTAAATATTAATATTTTATTTTATAATTTAAATATTAATATTTAATTA
868809 AATTTAAATANTTT
66 AATTTAAATA-TTT
*
868823 TATTAATAAATGATAATTTAAATATTAATATTTTATTTTATAATTTAAATATTATTATTTAATTA
1 TATTAATAAATGATAATTTAAATATTAATATTTTATTTTATAATTTAAATATTAATATTTAATTA
*
868888 AA-TTAATTATTT
66 AATTTAAATATTT
*
868900 AATTAAT
1 TATTAAT
868907 TATTTATTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
77 9 0.12
78 40 0.53
79 27 0.36
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (78 bp):
TATTAATAAATGATAATTTAAATATTAATATTTTATTTTATAATTTAAATATTAATATTTAATTA
AATTTAAATATTT
Found at i:868885 original size:19 final size:19
Alignment explanation
Indices: 868781--868932 Score: 80
Period size: 19 Copynumber: 8.3 Consensus size: 19
868771 AATATTTTAT
* *
868781 TTATAATTTAATTATTAATA
1 TTATTATTTAATT-TAAATA
868801 TT-TTATTTAATTTAAATA
1 TTATTATTTAATTTAAATA
868819 NTT-TTA-TTAA--TAAATGA
1 -TTATTATTTAATTTAAAT-A
*
868836 -TA--ATTTAAATATTAATATT
1 TTATTATTT-AAT-TTAA-ATA
868855 TTATT-TTATAATTTAAATA
1 TTATTATT-TAATTTAAATA
868874 TTATTATTTAA-TTAAAT-
1 TTATTATTTAATTTAAATA
* *
868891 TAATTATTTAA-TTAATTA
1 TTATTATTTAATTTAAATA
*
868909 -T-TTATTTATTTTTAAATA
1 TTATTATTTA-ATTTAAATA
868927 TTATTA
1 TTATTA
868933 ATTAGTAATT
Statistics
Matches: 104, Mismatches: 9, Indels: 38
0.69 0.06 0.25
Matches are distributed among these distances:
14 1 0.01
15 3 0.03
16 14 0.13
17 16 0.15
18 21 0.20
19 28 0.27
20 15 0.14
21 5 0.05
22 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (19 bp):
TTATTATTTAATTTAAATA
Found at i:868892 original size:16 final size:15
Alignment explanation
Indices: 868860--868916 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
868850 ATATTTTATT
* *
868860 TTATAATTTAAAT-A
1 TTATTATTTAATTAA
868874 TTATTATTTAATTAAA
1 TTATTATTTAATT-AA
868890 TTAATTATTTAATTAA
1 TT-ATTATTTAATTAA
868906 TTATTTATTTA
1 TTA-TTATTTA
868917 TTTTTAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
14 11 0.30
15 1 0.03
16 14 0.38
17 11 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTATTATTTAATTAA
Found at i:868931 original size:105 final size:101
Alignment explanation
Indices: 868742--868998 Score: 233
Period size: 105 Copynumber: 2.5 Consensus size: 101
868732 TTATTTTTTA
* *
868742 AAATATTAATAATTGATAATT-TAAATATT-AATATT-TTATTT-A-TAATTTAATTATTAATAT
1 AAATATTAATAATTGATTATTAT-AAT-TTAAATATTATTATTTAATTAAATTAATTATTAATAT
*
868802 TTTATTTAATTTAAATANTTTTATTAATAAATGATAATTT
64 TTTATTTAATTTAAATA--TTTATTAATAAATAATAATTT
* *
868842 AAATATTAATATTTTATT-TTATAATTTAAATATTATTATTTAATTAAATTAATTATTTAATTAA
1 AAATATTAATAATTGATTATTATAATTTAAATATTATTATTTAATTAAATTAATTA-TTAA-T-A
* * * **
868906 TTATTTATTTATTTTTAAATA-TTATTAATTAGTAATTTTTT
63 -T-TTTATTTA-ATTTAAATATTTATTAATAAATAATAATTT
* *
868947 AAATATTAATAATTGATTATT-TAATTATTAATATTATTTATATAATTTAAAT
1 AAATATTAATAATTGATTATTATAATT-TAAATATTA-TTATTTAA-TTAAAT
868999 GTTATTATGC
Statistics
Matches: 128, Mismatches: 14, Indels: 22
0.78 0.09 0.13
Matches are distributed among these distances:
98 2 0.02
99 11 0.09
100 22 0.17
101 1 0.01
102 10 0.08
103 4 0.03
104 1 0.01
105 37 0.29
106 11 0.09
107 15 0.12
108 14 0.11
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (101 bp):
AAATATTAATAATTGATTATTATAATTTAAATATTATTATTTAATTAAATTAATTATTAATATTT
TATTTAATTTAAATATTTATTAATAAATAATAATTT
Found at i:868960 original size:53 final size:51
Alignment explanation
Indices: 868771--868993 Score: 132
Period size: 53 Copynumber: 4.3 Consensus size: 51
868761 TTTAAATATT
* *
868771 AATATT-TTATTT-A-TAATTTAATTATTAAT-A-T-TTTATTTA-ATTTA
1 AATATTATTATTTAATTAATTTAAATATTAATAATTATTTATTTATTTTTA
*
868815 AATANTT-TTATTAATAAATGATAATTTAAATATTAAT-A-T-TTTATTTTATAATTTA
1 AATA-TTATTATT--T-AAT--TAATTTAAATATTAATAATTATTTA-TTTAT-TTTTA
* *
868870 AATATTATTATTTAATTAAATTAATTATTTAATTAATTATTTATTTATTTTTA
1 AATATTATTATTTAATTAATTTAAATA-TTAA-TAATTATTTATTTATTTTTA
* *
868923 AATATTATTAATTAGTAATT-TTTTAAATATTAATAATTGA-TTATTTAATTATT-
1 AATATTATT-ATT--TAATTAATTTAAATATTAATAATT-ATTTATTT-ATTTTTA
*
868976 AATATTATTTATATAATT
1 AATATTA-TTATTTAATT
868994 TAAATGTTAT
Statistics
Matches: 147, Mismatches: 9, Indels: 39
0.75 0.05 0.20
Matches are distributed among these distances:
44 4 0.03
45 7 0.05
47 1 0.01
49 1 0.01
50 9 0.06
51 9 0.06
52 25 0.17
53 39 0.27
54 23 0.16
55 24 0.16
56 5 0.03
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (51 bp):
AATATTATTATTTAATTAATTTAAATATTAATAATTATTTATTTATTTTTA
Found at i:868969 original size:22 final size:22
Alignment explanation
Indices: 868888--868979 Score: 69
Period size: 22 Copynumber: 4.0 Consensus size: 22
868878 TATTTAATTA
* * *
868888 AATTAATTATTTAATTAATTATT
1 AATTGATTATTTAAAT-ATTAAT
* * *
868911 TATTTATT-TTTAAATATTATT
1 AATTGATTATTTAAATATTAAT
*
868932 AATTAGTAATTTTTTAAATATTAAT
1 AATT-G--ATTATTTAAATATTAAT
*
868957 AATTGATTATTTAATTATTAAT
1 AATTGATTATTTAAATATTAAT
868979 A
1 A
868980 TTATTTATAT
Statistics
Matches: 57, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
21 9 0.16
22 22 0.39
23 6 0.11
24 4 0.07
25 16 0.28
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (22 bp):
AATTGATTATTTAAATATTAAT
Found at i:869072 original size:11 final size:11
Alignment explanation
Indices: 869058--869126 Score: 54
Period size: 11 Copynumber: 6.0 Consensus size: 11
869048 ATTTATAATT
869058 TATTTTATTAA
1 TATTTTATTAA
869069 TATTGATTATTTAA
1 TATT--TTA-TTAA
869083 -A--TTATTAA
1 TATTTTATTAA
*
869091 TATTTTATTTA
1 TATTTTATTAA
869102 TAATTTAATATTAA
1 T-ATTT--TATTAA
869116 TATTTTATTAA
1 TATTTTATTAA
869127 AAATTAGAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 18
0.70 0.03 0.27
Matches are distributed among these distances:
8 4 0.09
9 4 0.09
11 17 0.36
12 4 0.09
13 8 0.17
14 10 0.21
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:869080 original size:22 final size:20
Alignment explanation
Indices: 869055--869113 Score: 66
Period size: 22 Copynumber: 2.9 Consensus size: 20
869045 ATAATTTATA
*
869055 ATTTATTTTATTAATATTGATT
1 ATTTATATTATTAATATT--TT
*
869077 ATTTAAATTATTAATATTTT
1 ATTTATATTATTAATATTTT
*
869097 ATTTATAAT-TTAATATT
1 ATTTATATTATTAATATT
869114 AATATTTTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
19 8 0.24
20 9 0.27
22 16 0.48
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (20 bp):
ATTTATATTATTAATATTTT
Found at i:869122 original size:14 final size:14
Alignment explanation
Indices: 869065--869122 Score: 50
Period size: 15 Copynumber: 4.2 Consensus size: 14
869055 ATTTATTTTA
*
869065 TTAATATTGATTATT
1 TTAATATT-AATATT
*
869080 TAAATTATTAATATT
1 TTAA-TATTAATATT
*
869095 TT-AT-TT-ATAAT
1 TTAATATTAATATT
869106 TTAATATTAATATT
1 TTAATATTAATATT
869120 TTA
1 TTA
869123 TTAAAAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 9
0.71 0.10 0.19
Matches are distributed among these distances:
11 6 0.18
12 4 0.12
13 3 0.09
14 8 0.24
15 9 0.26
16 4 0.12
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (14 bp):
TTAATATTAATATT
Found at i:878481 original size:54 final size:52
Alignment explanation
Indices: 878399--878507 Score: 182
Period size: 54 Copynumber: 2.1 Consensus size: 52
878389 ATCAGACATT
* *
878399 TAGCAAATTCAAAAACATACATTTACTGATATATCTAACAGAGAGATAGATAGA
1 TAGCAAATTCAAAAACATACATGTACTGATATATCT-A-AGAGAGATAGAAAGA
878453 TAGCAAATTCAAAAACATACATGTACTGATATATCTAAGAGAGATAGAAAGA
1 TAGCAAATTCAAAAACATACATGTACTGATATATCTAAGAGAGATAGAAAGA
878505 TAG
1 TAG
878508 ATAGATATAG
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
52 17 0.32
53 1 0.02
54 35 0.66
ACGTcount: A:0.49, C:0.12, G:0.15, T:0.25
Consensus pattern (52 bp):
TAGCAAATTCAAAAACATACATGTACTGATATATCTAAGAGAGATAGAAAGA
Found at i:879314 original size:5 final size:5
Alignment explanation
Indices: 879304--879333 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
879294 TTTTTTTAGT
879304 TTTTC TTTTC TTTTC TTTT- TTTTC TTTTC T
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC T
879334 CCTCACTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:879326 original size:14 final size:15
Alignment explanation
Indices: 879304--879333 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
879294 TTTTTTTAGT
879304 TTTTCTTTTCTTTTC
1 TTTTCTTTTCTTTTC
879319 TTTT-TTTTCTTTTC
1 TTTTCTTTTCTTTTC
879333 T
1 T
879334 CCTCACTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTCTTTTC
Found at i:885339 original size:12 final size:12
Alignment explanation
Indices: 885322--885351 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
885312 ACTAATTTTT
*
885322 TATATAGTTATA
1 TATATAGTAATA
885334 TATATAGTAATA
1 TATATAGTAATA
885346 TATATA
1 TATATA
885352 ATATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (12 bp):
TATATAGTAATA
Found at i:885682 original size:21 final size:21
Alignment explanation
Indices: 885658--885706 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
885648 TATAAACATA
*
885658 TTATATATACATGTATT-TAAT
1 TTATATAAACAT-TATTATAAT
885679 TTATACATAAACATTATTATAAT
1 TTAT--ATAAACATTATTATAAT
885702 TTATA
1 TTATA
885707 ATCAACTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
21 5 0.21
22 4 0.17
23 15 0.62
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (21 bp):
TTATATAAACATTATTATAAT
Found at i:885717 original size:22 final size:22
Alignment explanation
Indices: 885666--885720 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
885656 TATTATATAT
885666 ACATGTATTTAATTTATACATAA
1 ACAT-TATTTAATTTATACATAA
*
885689 ACATTATTATAATTTATA-ATCA
1 ACATTATT-TAATTTATACATAA
*
885711 ACTTTATTTA
1 ACATTATTTA
885721 TACGATTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 2 0.07
22 14 0.48
23 13 0.45
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.47
Consensus pattern (22 bp):
ACATTATTTAATTTATACATAA
Found at i:887027 original size:3 final size:3
Alignment explanation
Indices: 887021--887068 Score: 53
Period size: 3 Copynumber: 16.3 Consensus size: 3
887011 ATATTTGATG
* * * *
887021 TTA TTA TTA TTA TTA TTA TTA TT- TTG TTA TAA TTA TTT TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
887068 T
1 T
887069 AGATTTTAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:887142 original size:18 final size:18
Alignment explanation
Indices: 887119--887158 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
887109 ATATTTTTAT
887119 TTAATCGTGCTAAACGTG
1 TTAATCGTGCTAAACGTG
* *
887137 TTAATCGTGTTAAACGTT
1 TTAATCGTGCTAAACGTG
887155 TTAA
1 TTAA
887159 ACGTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.40
Consensus pattern (18 bp):
TTAATCGTGCTAAACGTG
Found at i:887158 original size:9 final size:9
Alignment explanation
Indices: 887119--887162 Score: 52
Period size: 9 Copynumber: 4.9 Consensus size: 9
887109 ATATTTTTAT
*
887119 TTAATCGTG
1 TTAAACGTG
*
887128 CTAAACGTG
1 TTAAACGTG
*
887137 TTAATCGTG
1 TTAAACGTG
*
887146 TTAAACGTT
1 TTAAACGTG
887155 TTAAACGT
1 TTAAACGT
887163 ATTATTAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.39
Consensus pattern (9 bp):
TTAAACGTG
Found at i:890330 original size:3 final size:3
Alignment explanation
Indices: 890322--890346 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
890312 ACCATCCTAG
890322 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
890347 CATATTATGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:896588 original size:2 final size:2
Alignment explanation
Indices: 896581--896605 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
896571 CTCCTTCCTA
896581 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
896606 AACAAAGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:901290 original size:2 final size:2
Alignment explanation
Indices: 901283--901314 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
901273 GGAAGTGGGC
901283 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
901315 GCGTTGAGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:903776 original size:13 final size:13
Alignment explanation
Indices: 903758--903785 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
903748 CAAAAAATAT
903758 AACTTATAAAAAA
1 AACTTATAAAAAA
903771 AACTTATAAAAAA
1 AACTTATAAAAAA
903784 AA
1 AA
903786 ATTTACCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.07, G:0.00, T:0.21
Consensus pattern (13 bp):
AACTTATAAAAAA
Found at i:909053 original size:29 final size:30
Alignment explanation
Indices: 908996--909054 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
908986 AATTAAAGCT
* * *
908996 TTTTTATTTTGAATTAAATAAAATTTAATA
1 TTTTTATTTTAAATCAAATAAAACTTAATA
909026 TTTTTATTTTAAATCAAAT-AAACTTAATA
1 TTTTTATTTTAAATCAAATAAAACTTAATA
909055 ATTGATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.35
30 17 0.65
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (30 bp):
TTTTTATTTTAAATCAAATAAAACTTAATA
Found at i:909945 original size:42 final size:42
Alignment explanation
Indices: 909860--909941 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
909850 TGGACAGGGT
909860 CTTAAGGAATTGAAATTAATGAGGAGAGCCGTTACTTCTTTA
1 CTTAAGGAATTGAAATTAATGAGGAGAGCCGTTACTTCTTTA
909902 CTTAAGGAATTGAAATTAATGAGGAGAGCCGTTAC-TCTTT
1 CTTAAGGAATTGAAATTAATGAGGAGAGCCGTTACTTCTTT
909942 TACTAAGTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
41 5 0.12
42 35 0.88
ACGTcount: A:0.33, C:0.12, G:0.22, T:0.33
Consensus pattern (42 bp):
CTTAAGGAATTGAAATTAATGAGGAGAGCCGTTACTTCTTTA
Found at i:910179 original size:30 final size:29
Alignment explanation
Indices: 910123--910181 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
910113 TTTAAAATAT
* *
910123 TTTTTATTTTATTTAATTAAAATTTTATA
1 TTTTTATTTTAATTAAATAAAATTTTATA
**
910152 TTTTTATTTTAAATTAAATAAGTTTTTATA
1 TTTTTATTTT-AATTAAATAAAATTTTATA
910182 ATTAATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (29 bp):
TTTTTATTTTAATTAAATAAAATTTTATA
Found at i:911753 original size:44 final size:44
Alignment explanation
Indices: 911687--911771 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
911677 ATGTATTAAT
*
911687 TTTACCCAGGTCTACCTCTATTAATCTCTTTCCTATTTAGAGTA
1 TTTACCCAGGTCCACCTCTATTAATCTCTTTCCTATTTAGAGTA
* * * *
911731 TTTACCCATGTCCACCTTTATTAATCTTTTTTCTATTTAGA
1 TTTACCCAGGTCCACCTCTATTAATCTCTTTCCTATTTAGA
911772 TACCATATCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.47
Consensus pattern (44 bp):
TTTACCCAGGTCCACCTCTATTAATCTCTTTCCTATTTAGAGTA
Found at i:914281 original size:20 final size:20
Alignment explanation
Indices: 914253--914291 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
914243 TTATATGCTA
*
914253 ACATGGCATTTATCGTGTTG
1 ACATGGCATTTATCATGTTG
*
914273 ACATTGCATTTATCATGTT
1 ACATGGCATTTATCATGTT
914292 AATGTGACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (20 bp):
ACATGGCATTTATCATGTTG
Found at i:921315 original size:9 final size:9
Alignment explanation
Indices: 921301--921325 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
921291 CATCTGAGAG
921301 AAAATTTTA
1 AAAATTTTA
921310 AAAATTTTA
1 AAAATTTTA
921319 AAAATTT
1 AAAATTT
921326 AATGTTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AAAATTTTA
Found at i:921722 original size:2 final size:2
Alignment explanation
Indices: 921717--921745 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
921707 TGTGTGTGTG
921717 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
921746 GCCTATCTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:922719 original size:26 final size:26
Alignment explanation
Indices: 922683--922734 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
922673 GTCCACAAGT
922683 AAGTCACATGTTTTAGTAAAATAAGC
1 AAGTCACATGTTTTAGTAAAATAAGC
*
922709 AAGTCACATGTTTTAGTGAAATAAGC
1 AAGTCACATGTTTTAGTAAAATAAGC
922735 TTCTTCTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (26 bp):
AAGTCACATGTTTTAGTAAAATAAGC
Found at i:926832 original size:546 final size:544
Alignment explanation
Indices: 925745--926838 Score: 1748
Period size: 546 Copynumber: 2.0 Consensus size: 544
925735 TGCCAAAATT
** * * *
925745 TAGTAGTTGCTTAGTCTGGCTTGCACGGCGCTTCGTTTAGCAGAATACCTTAGAAAATAGCCAGT
1 TAGTAGTTGCACAGTCTGCCTTGCACGGCACTTCATTTAGCAGAATACCTTAGAAAATAGCCAGT
** * * *
925810 ACTGATAGTCAATTGGGTTCTTGAGGGTGTTTTGTATGGATTTGGGTCATGAGAGTTGCCTCTTA
66 ACTGATAGTCAATTGGGCACTTGAGAGCGTTTTGTATGGATTTGGGTCATGAGAGTTGCCACTTA
** * *
925875 ATTGTCTAAGATAGTTTGCTTTGATGGGGCATTCTTTCACTTGGAAGTATATTTAGTACCCCTAG
131 ATTGTCTAAGATAACTTACTTTGATGGGGCATTCTTTCACTTGGAAGTATATTTAATACCCCTAG
*
925940 GGAACATAGTCTGTGCCATATCCAGAAGGCTTTTTATTCCTCCATGGGTCCACTTATGTTAGGAC
196 GGAACAGAGTCTGTGCCATATCCAGAAGGCTTTTTATTCCTCCATGGGTCCACTTATGTTAGGAC
* * * *
926005 AACCATCTGTCAAAAATTGCGTTACTTACAGTGCTTGCCTGTAATTAAGAAATTAAATGTAGGGC
261 AACCATCTGTCAAAAATTCCG-T--TTACAGTGCCTGCCTGTAATTAAGAAATTAAACGAAGGGC
*
926070 AAGAGCAATAGAGTGTTGAAAGTCAGTTGAATGAATTGCTGGCTTACTGAAACCTGTTCCAATGG
323 AAGAGCAATAGAGTGTTGAAAGTCAGTTGAATGAATTACTGGCTTACTGAAACCTGTTCCAATGG
*
926135 CAAAATAGGAGCTGACGTATGCATTGGATCCTTTTTTGGTATTTGCACACAGATTTGTAATAACA
388 CAAAATAGGAGCTGACGTATGCATTGGATCCTTTTTTGGTATTTGCACACAGATTGGTAATAACA
* * *
926200 ATCGGATGTAGATCTGGTTTGGATGTATTTGGAATGGAGAATCCATTTTTTTTCCATTCAATGAA
453 ATCGGATGAACATCCGGTTTGGATGTATTTGGAATGGAGAATCCATTTTTTTTCCATTCAATGAA
926265 TGACATTTAAAACATTGGTAGGTATGA
518 TGACATTTAAAACATTGGTAGGTATGA
* **
926292 TAGTAGTTGCACAGTCTGCCTTGCATGGCACTTCATTTAGCAGAATACCTTGACTAGAAAATATT
1 TAGTAGTTGCACAGTCTGCCTTGCACGGCACTTCATTTAGCAGAATACC-T---TAGAAAATAGC
*
926357 CAGTACTGATAGT-AGATTGGGCACTTGAGAGCGTTTTGTATGGATTTGGGTCGTGAGAGTTGCC
62 CAGTACTGATAGTCA-ATTGGGCACTTGAGAGCGTTTTGTATGGATTTGGGTCATGAGAGTTGCC
*
926421 ACTTAATTGTCTAAGATAACTTACTTTGATGGGGCATTCTTTCATTTGGAAGTATATTTAATACC
126 ACTTAATTGTCTAAGATAACTTACTTTGATGGGGCATTCTTTCACTTGGAAGTATATTTAATACC
**
926486 CCTAGGGAACAGAGTCTGTGCTGTATCCAGAAGGCTTTTTATTCCTCCATGGGTCCAC-TATTGT
191 CCTAGGGAACAGAGTCTGTGCCATATCCAGAAGGCTTTTTATTCCTCCATGGGTCCACTTA-TGT
926550 TAGGACAACCATCTGTCAAAAATTCCG-TTACAGTGCCTG-CTGTAATTAAGAAATTAAACGAAG
255 TAGGACAACCATCTGTCAAAAATTCCGTTTACAGTGCCTGCCTGTAATTAAGAAATTAAACGAAG
*
926613 GTCAAGAGCAATAGAGTGTTGAAAGTCAGTTGAATGAATTACTGGCTTACTGAAACCTGTTCCAA
320 GGCAAGAGCAATAGAGTGTTGAAAGTCAGTTGAATGAATTACTGGCTTACTGAAACCTGTTCCAA
**
926678 TGGCAAAATAGGAGCTGACGTATGCATTGGAT-CTTGTTTTGGTATTTGCACGTAGATTGGTAAT
385 TGGCAAAATAGGAGCTGACGTATGCATTGGATCCTT-TTTTGGTATTTGCACACAGATTGGTAAT
*
926742 AACAATTGGATGAACATCCGGTTTGGATGTATTTGGAATGGAGAATCCATTTTTTTTCCATTCAA
449 AACAATCGGATGAACATCCGGTTTGGATGTATTTGGAATGGAGAATCCATTTTTTTTCCATTCAA
926807 TGAATGACATTTAAAACATTGGTAGGTATGA
514 TGAATGACATTTAAAACATTGGTAGGTATGA
926838 T
1 T
926839 GCCTGAAATG
Statistics
Matches: 505, Mismatches: 35, Indels: 15
0.91 0.06 0.03
Matches are distributed among these distances:
545 3 0.01
546 235 0.47
547 54 0.11
548 1 0.00
550 3 0.01
551 209 0.41
ACGTcount: A:0.28, C:0.15, G:0.23, T:0.34
Consensus pattern (544 bp):
TAGTAGTTGCACAGTCTGCCTTGCACGGCACTTCATTTAGCAGAATACCTTAGAAAATAGCCAGT
ACTGATAGTCAATTGGGCACTTGAGAGCGTTTTGTATGGATTTGGGTCATGAGAGTTGCCACTTA
ATTGTCTAAGATAACTTACTTTGATGGGGCATTCTTTCACTTGGAAGTATATTTAATACCCCTAG
GGAACAGAGTCTGTGCCATATCCAGAAGGCTTTTTATTCCTCCATGGGTCCACTTATGTTAGGAC
AACCATCTGTCAAAAATTCCGTTTACAGTGCCTGCCTGTAATTAAGAAATTAAACGAAGGGCAAG
AGCAATAGAGTGTTGAAAGTCAGTTGAATGAATTACTGGCTTACTGAAACCTGTTCCAATGGCAA
AATAGGAGCTGACGTATGCATTGGATCCTTTTTTGGTATTTGCACACAGATTGGTAATAACAATC
GGATGAACATCCGGTTTGGATGTATTTGGAATGGAGAATCCATTTTTTTTCCATTCAATGAATGA
CATTTAAAACATTGGTAGGTATGA
Found at i:927905 original size:2 final size:2
Alignment explanation
Indices: 927898--927957 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
927888 GTTAATTTCT
*
927898 TC TC TC TC TC TC TC TC TC TC TC TC -C TC TC TC TN TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
927939 TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC T
927958 TATATATATA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:927963 original size:2 final size:2
Alignment explanation
Indices: 927958--928000 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
927948 CTCTCTCTCT
* *
927958 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
928000 T
1 T
928001 GTCAATTACT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:931959 original size:10 final size:9
Alignment explanation
Indices: 931939--931963 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
931929 CCCTCCTCCC
931939 AAAAAATAA
1 AAAAAATAA
931948 AAAAAATAA
1 AAAAAATAA
931957 AAAAAAT
1 AAAAAAT
931964 GGATAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (9 bp):
AAAAAATAA
Found at i:942665 original size:12 final size:12
Alignment explanation
Indices: 942633--942666 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
942623 ATTTAGAGGG
942633 AGGGAGAGAGAA
1 AGGGAGAGAGAA
*
942645 AGAGAGAGAGAA
1 AGGGAGAGAGAA
*
942657 AGGGGGAGAG
1 AGGGAGAGAG
942667 CAAGTGATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (12 bp):
AGGGAGAGAGAA
Found at i:958377 original size:17 final size:17
Alignment explanation
Indices: 958357--958392 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
958347 TTCACTCCCA
958357 TTTCGTTTTTT-TTTCTT
1 TTTC-TTTTTTGTTTCTT
958374 TTTCTTTTTTGTTTCTT
1 TTTCTTTTTTGTTTCTT
958391 TT
1 TT
958393 NACATAGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 12 0.67
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTCTTTTTTGTTTCTT
Found at i:965170 original size:2 final size:2
Alignment explanation
Indices: 965163--965188 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
965153 CTTGCAATAA
965163 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
965189 TTAATATTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:965552 original size:33 final size:34
Alignment explanation
Indices: 965491--965558 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 34
965481 TATATCATCA
*
965491 TCAATTATGATATGTTAACATAAAACATC-ATAC
1 TCAATTATAATATGTTAACATAAAACATCAATAC
* ***
965524 TCAATTATAATATTTTAACATGTCACATCAATAC
1 TCAATTATAATATGTTAACATAAAACATCAATAC
965558 T
1 T
965559 ACACGATATA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
33 24 0.83
34 5 0.17
ACGTcount: A:0.43, C:0.16, G:0.04, T:0.37
Consensus pattern (34 bp):
TCAATTATAATATGTTAACATAAAACATCAATAC
Found at i:976510 original size:10 final size:10
Alignment explanation
Indices: 976495--976519 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
976485 CTTGAAATAT
976495 ATATATATAC
1 ATATATATAC
976505 ATATATATAC
1 ATATATATAC
976515 ATATA
1 ATATA
976520 ATTTAATAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (10 bp):
ATATATATAC
Found at i:977591 original size:2 final size:2
Alignment explanation
Indices: 977586--977630 Score: 81
Period size: 2 Copynumber: 22.0 Consensus size: 2
977576 ATCAAGGAAG
977586 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
977629 AT
1 AT
977631 CTTAAATCAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 40 0.95
3 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:978101 original size:2 final size:2
Alignment explanation
Indices: 978094--978133 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
978084 GCACGTGGTN
978094 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
978134 ATCAGAAGTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:982248 original size:15 final size:15
Alignment explanation
Indices: 982230--982259 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
982220 ATGAGATTCT
982230 ATACACCATGATTGG
1 ATACACCATGATTGG
982245 ATACACCATGATTGG
1 ATACACCATGATTGG
982260 CTTTGACTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (15 bp):
ATACACCATGATTGG
Found at i:1006573 original size:21 final size:21
Alignment explanation
Indices: 1006532--1006598 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
1006522 TATTTTTTAA
* *
1006532 ATTTTAATAATTGAAAT-ATTT
1 ATTTTAA-AATAGTAATAATTT
1006553 ATTTTAAAATAGTAATAATTT
1 ATTTTAAAATAGTAATAATTT
* * *
1006574 AATTT-AAATATTTAATATTTT
1 ATTTTAAAATA-GTAATAATTT
1006595 ATTT
1 ATTT
1006599 ATAATTAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
20 12 0.32
21 26 0.68
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (21 bp):
ATTTTAAAATAGTAATAATTT
Found at i:1006593 original size:20 final size:20
Alignment explanation
Indices: 1006546--1006599 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
1006536 TAATAATTGA
*
1006546 AATATTTATTTTAAAATAGT
1 AATATTTAATTTAAAATAGT
*
1006566 AATAATTTAATTT-AAATATTT
1 AAT-ATTTAATTTAAAATA-GT
*
1006587 AATATTTTATTTA
1 AATATTTAATTTA
1006600 TAATTAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
20 16 0.57
21 12 0.43
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (20 bp):
AATATTTAATTTAAAATAGT
Found at i:1006667 original size:63 final size:64
Alignment explanation
Indices: 1006574--1006698 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 64
1006564 GTAATAATTT
1006574 AATTTAAATATTTAATATTTTATTTATAATTAATCATTAATTTTT-AAA-TTAATATTTTTNGAA
1 AATTTAAATATTTAATATTTTATTTATAATTAATCATTAATTTTTAAAAGTTAATATTTTT-GAA
*
1006637 AATTT-AATA-TTAATTATTTTATTTTATAATTAATTATTAATTTTTAAAATGTTAATATTTTT
1 AATTTAAATATTTAA-TATTTTA-TTTATAATTAATCATTAATTTTTAAAA-GTTAATATTTTT
1006699 ATTATTATTT
Statistics
Matches: 56, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
61 4 0.07
62 11 0.20
63 27 0.48
64 3 0.05
66 11 0.20
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (64 bp):
AATTTAAATATTTAATATTTTATTTATAATTAATCATTAATTTTTAAAAGTTAATATTTTTGAA
Found at i:1006681 original size:20 final size:19
Alignment explanation
Indices: 1006596--1006684 Score: 54
Period size: 20 Copynumber: 4.3 Consensus size: 19
1006586 TAATATTTTA
*
1006596 TTTATAATTAATCATTAATT
1 TTTA-AATTAATTATTAATT
* **
1006616 TTTAAATTAATATTTTTNGAAAA
1 TTTAAATT-A-ATTATT--AATT
*
1006639 TTTAATATTAATTATT-TTAT
1 TTTAA-ATTAATTATTAAT-T
1006659 TTTATAATTAATTATTAATT
1 TTTA-AATTAATTATTAATT
1006679 TTTAAA
1 TTTAAA
1006685 ATGTTAATAT
Statistics
Matches: 52, Mismatches: 9, Indels: 17
0.67 0.12 0.22
Matches are distributed among these distances:
19 6 0.12
20 24 0.46
21 6 0.12
22 5 0.10
23 8 0.15
24 3 0.06
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.56
Consensus pattern (19 bp):
TTTAAATTAATTATTAATT
Found at i:1006712 original size:26 final size:26
Alignment explanation
Indices: 1006670--1006765 Score: 72
Period size: 26 Copynumber: 3.6 Consensus size: 26
1006660 TTATAATTAA
*
1006670 TTATTAATT-TTTAAAATGTTAATATTT
1 TTATT-ATTATTT-AAATATTAATATTT
*
1006697 TTATTATTATTTAAATATTATCATGATTA
1 TTATTATTATTTAAATATTA--AT-ATTT
* *
1006726 TT-TTATTTTTTAAATATTAATA-AT
1 TTATTATTATTTAAATATTAATATTT
*
1006750 TTATAATTTATTTAAA
1 TTATTA-TTATTTAAA
1006766 AACTATTACT
Statistics
Matches: 56, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
24 2 0.04
25 3 0.05
26 20 0.36
27 8 0.14
28 18 0.32
29 5 0.09
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (26 bp):
TTATTATTATTTAAATATTAATATTT
Found at i:1006927 original size:16 final size:16
Alignment explanation
Indices: 1006906--1006936 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1006896 TTTATAATTT
*
1006906 AATATTAATATTTTAA
1 AATATTAATACTTTAA
1006922 AATATTAATACTTTA
1 AATATTAATACTTTA
1006937 TTAGAAGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
AATATTAATACTTTAA
Found at i:1012180 original size:55 final size:54
Alignment explanation
Indices: 1012121--1012289 Score: 187
Period size: 55 Copynumber: 3.1 Consensus size: 54
1012111 AATTTTTTTT
* * * * * *
1012121 TTTTTCAAAATGGCATATAGCAAAATTTTTTCGAACATTACATGTAAGAACAATA
1 TTTTTCAAAATAGCATGTAACAAAATTTTTT-GAACATGACATGTAATAATAATA
* * ** *
1012176 TTTTTTCAACATAGCATGTAAC-AAATTTTTTTAACATGACATGTAATAATTTTT
1 -TTTTTCAAAATAGCATGTAACAAAATTTTTTGAACATGACATGTAATAATAATA
* *
1012230 TTTTTCAAAATAGCATGTAATAAAATTTTTTTGAACATGATATGTAATAATAATA
1 TTTTTCAAAATAGCATGTAACAAAA-TTTTTTGAACATGACATGTAATAATAATA
1012285 TTTTT
1 TTTTT
1012290 TTAATATGTC
Statistics
Matches: 93, Mismatches: 18, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
53 19 0.20
54 19 0.20
55 38 0.41
56 17 0.18
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (54 bp):
TTTTTCAAAATAGCATGTAACAAAATTTTTTGAACATGACATGTAATAATAATA
Found at i:1012211 original size:25 final size:27
Alignment explanation
Indices: 1012169--1012267 Score: 98
Period size: 27 Copynumber: 3.7 Consensus size: 27
1012159 TACATGTAAG
1012169 AACAATA-TTTTTTCAACATAGCATGT
1 AACAATATTTTTTTCAACATAGCATGT
1012195 AACAA-ATTTTTTT-AACAT-GACATGT
1 AACAATATTTTTTTCAACATAG-CATGT
* * *
1012220 AATAATTTTTTTTTTCAAAATAGCATGT
1 AACAA-TATTTTTTTCAACATAGCATGT
* * *
1012248 AATAAAATTTTTTTGAACAT
1 AACAATATTTTTTTCAACAT
1012268 GATATGTAAT
Statistics
Matches: 60, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
24 1 0.02
25 15 0.25
26 11 0.18
27 18 0.30
28 14 0.23
29 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.43
Consensus pattern (27 bp):
AACAATATTTTTTTCAACATAGCATGT
Found at i:1012233 original size:28 final size:28
Alignment explanation
Indices: 1012146--1012427 Score: 137
Period size: 26 Copynumber: 10.2 Consensus size: 28
1012136 TATAGCAAAA
* * *
1012146 TTTTTTCGAACATTACATGTAAGAACAAT
1 TTTTTTC-AACATGACATGTAATAATAAT
*
1012175 ATTTTTTCAACAT-AGCATGTAA-CA-AAT
1 -TTTTTTCAACATGA-CATGTAATAATAAT
**
1012202 TTTTTT-AACATGACATGTAATAATTTT
1 TTTTTTCAACATGACATGTAATAATAAT
*
1012229 TTTTTTCAAAAT-AGCATGTAATAA-AAT
1 TTTTTTCAACATGA-CATGTAATAATAAT
* *
1012256 TTTTTTGAACATGATATGTAATAATAAT
1 TTTTTTCAACATGACATGTAATAATAAT
* * * * * *
1012284 ATTTTTTTAATATGTCGTATAACAAGTTTAAAAT
1 -TTTTTTCAACATGACATGTAATAA---T--AAT
* *
1012318 TTTTTTC-ATATGACGTGTAATAACT-A-
1 TTTTTTCAACATGACATGTAATAA-TAAT
*
1012344 TTTTTT-AATATGACA--T-ATAATAAT
1 TTTTTTCAACATGACATGTAATAATAAT
* * *
1012368 TTTTTTTAACATGATATATAATAA-AA-
1 TTTTTTCAACATGACATGTAATAATAAT
* *
1012394 ATTTTTCAACAAT-ACATGTAATAATATT
1 TTTTTTCAAC-ATGACATGTAATAATAAT
1012422 TTTTTT
1 TTTTTT
1012428 TACATGTAAA
Statistics
Matches: 197, Mismatches: 31, Indels: 50
0.71 0.11 0.18
Matches are distributed among these distances:
22 1 0.01
23 5 0.03
24 7 0.04
25 19 0.10
26 38 0.19
27 38 0.19
28 29 0.15
29 29 0.15
30 8 0.04
32 14 0.07
33 6 0.03
34 3 0.02
ACGTcount: A:0.39, C:0.08, G:0.07, T:0.46
Consensus pattern (28 bp):
TTTTTTCAACATGACATGTAATAATAAT
Found at i:1012372 original size:25 final size:26
Alignment explanation
Indices: 1012317--1012391 Score: 89
Period size: 25 Copynumber: 2.9 Consensus size: 26
1012307 AAGTTTAAAA
* * *
1012317 TTTTTTTCATATGACGTGTAATAACT
1 TTTTTTTAATATGACATATAATAACT
*
1012343 ATTTTTTAATATGACATATAATAA-T
1 TTTTTTTAATATGACATATAATAACT
* *
1012368 TTTTTTTAACATGATATATAATAA
1 TTTTTTTAATATGACATATAATAA
1012392 AAATTTTTCA
Statistics
Matches: 42, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
25 22 0.52
26 20 0.48
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (26 bp):
TTTTTTTAATATGACATATAATAACT
Found at i:1012422 original size:25 final size:25
Alignment explanation
Indices: 1012335--1012425 Score: 94
Period size: 25 Copynumber: 3.6 Consensus size: 25
1012325 ATATGACGTG
*
1012335 TAATAACTATTTTTTAATATGACATA
1 TAATAA-TATTTTTTAACATGACATA
* *
1012361 TAATAATTTTTTTTAACATGATATA
1 TAATAATATTTTTTAACATGACATA
* * *
1012386 TAATAAAAATTTTTCAACAAT-ACATG
1 TAAT-AATATTTTTTAAC-ATGACATA
1012412 TAATAATATTTTTT
1 TAATAATATTTTTT
1012426 TTTACATGTA
Statistics
Matches: 53, Mismatches: 10, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
25 28 0.53
26 23 0.43
27 2 0.04
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (25 bp):
TAATAATATTTTTTAACATGACATA
Found at i:1012671 original size:20 final size:20
Alignment explanation
Indices: 1012629--1012673 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
1012619 TGAAAGTTCT
* *
1012629 AAATTTTGCTTAAAGATCAA
1 AAATTTTGCTTAAACATAAA
1012649 AAATTTTGCTTAAACA-AAGA
1 AAATTTTGCTTAAACATAA-A
1012669 AAATT
1 AAATT
1012674 CATGTTAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.33
Consensus pattern (20 bp):
AAATTTTGCTTAAACATAAA
Found at i:1014588 original size:31 final size:29
Alignment explanation
Indices: 1014532--1014592 Score: 70
Period size: 31 Copynumber: 2.0 Consensus size: 29
1014522 TATGCTCATA
*
1014532 TATTTTGATTTAAAGTCAAAATTATCACAT
1 TATTTGGATTTAAAGTCAAAATTATC-CAT
*
1014562 TATTTGGATTTTAAAGT-ATAATTTATCCAT
1 TATTTGGA-TTTAAAGTCA-AAATTATCCAT
1014592 T
1 T
1014593 TAATTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.36, C:0.08, G:0.08, T:0.48
Consensus pattern (29 bp):
TATTTGGATTTAAAGTCAAAATTATCCAT
Found at i:1045836 original size:3 final size:3
Alignment explanation
Indices: 1045828--1045854 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1045818 GTGAATTAGT
1045828 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1045855 TGTCTCCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1051859 original size:3 final size:3
Alignment explanation
Indices: 1051841--1051874 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1051831 TTCATAATTG
* *
1051841 TCA TCA TCG TCT TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1051875 AATATCTCTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.26, C:0.32, G:0.03, T:0.38
Consensus pattern (3 bp):
TCA
Found at i:1061957 original size:2 final size:2
Alignment explanation
Indices: 1061950--1061977 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1061940 TAAGAAAAAC
1061950 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1061978 AGTATTATGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1063625 original size:114 final size:111
Alignment explanation
Indices: 1063437--1063651 Score: 249
Period size: 114 Copynumber: 1.9 Consensus size: 111
1063427 TGTTTATCCC
* *
1063437 ATTTTTATTATTTTTTTTATAATGTTTTTACTTCCCTACAGAAACCGAAAACTTTGATATGTAAG
1 ATTTTTATTATTTTTTTTATAATGTTTTTACTTCCATACAGAAACCGAAAACTTT-ATAAGTAAG
1063502 TTCCTAATTTTGC-TTTCTTTTTATCTCATTTGATTTGTTTATTTAA
65 TTCCTAATTTTGCTTTTCTTTTTATCTCATTTGATTTGTTTATTTAA
* *
1063548 ATTTTTATTATTTTTGTTTTTATAATGTTATTTA-TTCCATACATAAATC-ATAAACTTT-TCAA
1 ATTTTTATTA--TTT-TTTTTATAATGTT-TTTACTTCCATACAGAAACCGA-AAACTTTAT-AA
** * * *
1063610 GTAAGTTTTTAAATTTTTCTTTTTTTTTTATCTTATTTGATT
60 GTAAGTTCCT-AATTTTGCTTTTCTTTTTATCTCATTTGATT
1063652 AAATGTGTGA
Statistics
Matches: 87, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
111 10 0.11
112 1 0.01
113 13 0.15
114 39 0.45
115 24 0.28
ACGTcount: A:0.26, C:0.10, G:0.07, T:0.57
Consensus pattern (111 bp):
ATTTTTATTATTTTTTTTATAATGTTTTTACTTCCATACAGAAACCGAAAACTTTATAAGTAAGT
TCCTAATTTTGCTTTTCTTTTTATCTCATTTGATTTGTTTATTTAA
Found at i:1072341 original size:12 final size:12
Alignment explanation
Indices: 1072324--1072348 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1072314 TCTTTTTACT
1072324 TACTTCATTCTG
1 TACTTCATTCTG
1072336 TACTTCATTCTG
1 TACTTCATTCTG
1072348 T
1 T
1072349 CCTTTTATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.08, T:0.52
Consensus pattern (12 bp):
TACTTCATTCTG
Found at i:1093215 original size:18 final size:18
Alignment explanation
Indices: 1093192--1093227 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
1093182 ACGATTCCCT
*
1093192 CCCTTCCCTGACCTCTTC
1 CCCTTCCCCGACCTCTTC
*
1093210 CCCTTCCCCGACTTCTTC
1 CCCTTCCCCGACCTCTTC
1093228 GAGCTAAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.56, G:0.06, T:0.33
Consensus pattern (18 bp):
CCCTTCCCCGACCTCTTC
Found at i:1110078 original size:91 final size:91
Alignment explanation
Indices: 1109923--1110106 Score: 368
Period size: 91 Copynumber: 2.0 Consensus size: 91
1109913 GTAATGACCG
1109923 GAGCGACTCATTTCCAAGGTATTTTTCATTCTTCTCTTCATATACTCTGTCTCCAGGAACCCTTT
1 GAGCGACTCATTTCCAAGGTATTTTTCATTCTTCTCTTCATATACTCTGTCTCCAGGAACCCTTT
1109988 TCACTTCTTTAGAAAATTACTCCGGA
66 TCACTTCTTTAGAAAATTACTCCGGA
1110014 GAGCGACTCATTTCCAAGGTATTTTTCATTCTTCTCTTCATATACTCTGTCTCCAGGAACCCTTT
1 GAGCGACTCATTTCCAAGGTATTTTTCATTCTTCTCTTCATATACTCTGTCTCCAGGAACCCTTT
1110079 TCACTTCTTTAGAAAATTACTCCGGA
66 TCACTTCTTTAGAAAATTACTCCGGA
1110105 GA
1 GA
1110107 AGTAGACTCT
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 93 1.00
ACGTcount: A:0.23, C:0.26, G:0.12, T:0.38
Consensus pattern (91 bp):
GAGCGACTCATTTCCAAGGTATTTTTCATTCTTCTCTTCATATACTCTGTCTCCAGGAACCCTTT
TCACTTCTTTAGAAAATTACTCCGGA
Found at i:1119336 original size:27 final size:27
Alignment explanation
Indices: 1119298--1119376 Score: 149
Period size: 27 Copynumber: 2.9 Consensus size: 27
1119288 TGTTATAGTT
1119298 TAATATCATATTGTATAAAGTAAAGTA
1 TAATATCATATTGTATAAAGTAAAGTA
1119325 TAATATCATATTGTATAAAGTAAAGTA
1 TAATATCATATTGTATAAAGTAAAGTA
*
1119352 TAATATCATATTGTATAAAGGAAAG
1 TAATATCATATTGTATAAAGTAAAG
1119377 GTCCTCATTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (27 bp):
TAATATCATATTGTATAAAGTAAAGTA
Found at i:1132245 original size:573 final size:570
Alignment explanation
Indices: 1130857--1132453 Score: 2256
Period size: 573 Copynumber: 2.8 Consensus size: 570
1130847 TGTGTGGGAT
* * * * * **
1130857 CAATGGTTGAT-TGGTCTAAAATTACATGTCAATCGTATCAACAAATAAAGATAAAAGTATTTGC
1 CAATAGTTGATCT-GTCTAAAATTACGTGTCAGTCTTATCTACAAATAAAGATGGAAGTATTTGC
* * *
1130921 ATATATGTATATAATGACATAAACTTACCTAATAAAAAAACCA-TTTATAATTGTTACAATATTA
65 ATATA--TAT-TAA-GGCATAAATTTACCTGAT-AAAAAACCATTTTATAATTGTTACAATATTA
* *
1130985 TTTGACCACCAACTTAATTTCTCTTTTTAGAGCCAATGCATAACATTGACCAGACTGGACTTAGT
125 TTTAACCACCAACTTAATTTCTCTTTTTAGAGCC-ATGCATAACATTGACCAGACTGAACTTAGT
* * * * * **
1131050 AGTTGTCACATGCTTTCTTTATGAGTGACCTTACACGTTGGGGAGGATTATTGAAATTGCGATGT
189 AGTTGTCACACGCTTTCTCTATGAGTGACCTTACATGTTGAGGAGGACTATTGAAATTGTAATGT
* * ** * * *
1131115 CGGACTAAACTTGATAATTTTACATATGATATGTTATTACATTATGTATATTACACAAAATTAAA
254 TGGACTAGACTTGGCAATTTTATATATGATATGTTA-TACATTATGCATATAACACAAAATTAAA
* * *
1131180 TAGATTTAGATTTAAGATAATTGCATTTCGTGAATTAATCATATACATGACAATTTCGTGTCTTA
318 TAGATTTAGGTTTAAGATAATTGCATTTCGTGTATTAATCGTATACATGACAATTTCGTGTCTTA
** *
1131245 AATGTGTCAACTTACTTGGCTCATTTAAAACCTATTTAACTTGTTTAATTAATCATGTCATCATG
383 AATGTGTCAACTTACTTAACTCATTTAAAACCTATTTAACTTGTTTAATTAATCATGTCACCATG
* *
1131310 TTGATCCATGTAACCCTTTTATTGGTTTATGACTTGTATAAATTACTCATATAATCATTAATATC
448 TCGATCCATGTAACCCTTTTATTGGTTTATGACTTATATAAATTACTCATATAATCATTAATATC
* * *
1131375 TTGAATTTACATAACACTGTTAGGACACACATTTACAAATTACCATATTTATGTGGAT
513 TTGAATTTACATAACACTATTAAGACACACATTTACAAATTACCATATTTATGTGGAC
* * * *
1131433 CAATAGTTGATCGGTCTAAAATTACGTGT-TGATCTTATCTACAGATAAAGATGGAAATATTTGC
1 CAATAGTTGATCTGTCTAAAATTACGTGTCAG-TCTTATCTACAAATAAAGATGGAAGTATTTGC
* *
1131497 ATATATATCAAGGCATAAATTTACCTGATAAAAAACCATTTTATAATTGGTACAATATTATTTAA
65 ATATATATTAAGGCATAAATTTACCTGATAAAAAACCATTTTATAATTGTTACAATATTATTTAA
* * * *
1131562 CCACCAACTTAATTTCTCTTTTTAGAACCATGCATAACATTGACCATACTGTACTTAGTAGTTGC
130 CCACCAACTTAATTTCTCTTTTTAGAGCCATGCATAACATTGACCAGACTGAACTTAGTAGTTGT
* * *
1131627 CACACGCTTTCTCTATGAGTGACCTTGCATGCTAAGGAGGACTATTGAAATTGTAATGTTGGACT
195 CACACGCTTTCTCTATGAGTGACCTTACATGTTGAGGAGGACTATTGAAATTGTAATGTTGGACT
* * *
1131692 AGACTTGGCAATTTTATATATGATATGTTTATACATTCTACATATAACACAAAATTAAATAGAAT
260 AGACTTGGCAATTTTATATATGATATG-TTATACATTATGCATATAACACAAAATTAAATAGATT
** * * * *
1131757 TAGGTTTAAGATAATTGTGTTTCATGTATTCATTGTATACATGACAATTTTGTGTCTTAAATGTG
324 TAGGTTTAAGATAATTGCATTTCGTGTATTAATCGTATACATGACAATTTCGTGTCTTAAATGTG
* *
1131822 TCAACTTACTTAACTCATTGAAAACCTATTTAGA-TTGTTTAATTAATCATGTCACCATGTCGGT
389 TCAACTTACTTAACTCATTTAAAACCTATTTA-ACTTGTTTAATTAATCATGTCACCATGTCGAT
*
1131886 CCATGTAACCCTTTTATTGGTTTATGACTTATATAAATTACTCATATGATCATTAATATCTTGAA
453 CCATGTAACCCTTTTATTGGTTTATGACTTATATAAATTACTCATATAATCATTAATATCTTGAA
* *
1131951 TTTACATATGACATTATTAAGACACACATTTATAAATTACCATATTTATGTGGAC
518 TTTACATA--ACACTATTAAGACACACATTTACAAATTACCATATTTATGTGGAC
* * *
1132006 CAATAGTTGATCTGTCTAAAATTACGTGTCAGTCTTTTCTTCAAATAAAGATGGAAGCATTTGCA
1 CAATAGTTGATCTGTCTAAAATTACGTGTCAGTCTTATCTACAAATAAAGATGGAAGTATTTGCA
1132071 TATATATTAAGGCATAAATTTACCTGATAAAAAACCATTTTATAATTGTTATC-ATATTATTTAA
66 TATATATTAAGGCATAAATTTACCTGATAAAAAACCATTTTATAATTGTTA-CAATATTATTTAA
*
1132135 CCACCAACTTAATTTCTCTTTTTAGAGCCATGCATAACATTGACCAGACTGAACTCAGTAGTTGT
130 CCACCAACTTAATTTCTCTTTTTAGAGCCATGCATAACATTGACCAGACTGAACTTAGTAGTTGT
* * * * *
1132200 CACACACTTGCTCTACT-AGTGACCTTACATGTTGAGGAAGACTATTGAAATTATAATGTTAGAC
195 CACACGCTTTCTCTA-TGAGTGACCTTACATGTTGAGGAGGACTATTGAAATTGTAATGTTGGAC
** * *
1132264 TAGACTTGGCAATTTTACT-TATGATACACTAATACATTATGCATATAACACAAAATTAGATAGA
259 TAGACTTGGCAATTTTA-TATATGATA-TGTTATACATTATGCATATAACACAAAATTAAATAGA
* *
1132328 TTTAGGTTTAAGATAATTGCATTTCGTGTATTAATCGTATACATGATAATTTCGTG-CTTTAAAC
322 TTTAGGTTTAAGATAATTGCATTTCGTGTATTAATCGTATACATGACAATTTCGTGTC-TTAAAT
*
1132392 GTGTCAACTTACTTAACTCATTTAAAACATATTTAACTTGTTTAATTAATCATGTCACCATG
386 GTGTCAACTTACTTAACTCATTTAAAACCTATTTAACTTGTTTAATTAATCATGTCACCATG
1132454 CCTGTTGTCA
Statistics
Matches: 905, Mismatches: 102, Indels: 31
0.87 0.10 0.03
Matches are distributed among these distances:
571 331 0.37
572 73 0.08
573 438 0.48
574 7 0.01
576 56 0.06
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (570 bp):
CAATAGTTGATCTGTCTAAAATTACGTGTCAGTCTTATCTACAAATAAAGATGGAAGTATTTGCA
TATATATTAAGGCATAAATTTACCTGATAAAAAACCATTTTATAATTGTTACAATATTATTTAAC
CACCAACTTAATTTCTCTTTTTAGAGCCATGCATAACATTGACCAGACTGAACTTAGTAGTTGTC
ACACGCTTTCTCTATGAGTGACCTTACATGTTGAGGAGGACTATTGAAATTGTAATGTTGGACTA
GACTTGGCAATTTTATATATGATATGTTATACATTATGCATATAACACAAAATTAAATAGATTTA
GGTTTAAGATAATTGCATTTCGTGTATTAATCGTATACATGACAATTTCGTGTCTTAAATGTGTC
AACTTACTTAACTCATTTAAAACCTATTTAACTTGTTTAATTAATCATGTCACCATGTCGATCCA
TGTAACCCTTTTATTGGTTTATGACTTATATAAATTACTCATATAATCATTAATATCTTGAATTT
ACATAACACTATTAAGACACACATTTACAAATTACCATATTTATGTGGAC
Found at i:1133192 original size:364 final size:362
Alignment explanation
Indices: 1132577--1133483 Score: 1017
Period size: 364 Copynumber: 2.5 Consensus size: 362
1132567 CTCATAGGTC
* * * * * *
1132577 AAAGGTGATGTGAACCCTTATATTCCCAGTATCACTTTAGTACATGGCTAACGTGGGATTCATGG
1 AAAGGTGATGTGAACCCTTATATTTCCAGTATCATTTTAGTACATAGCCAATGTGAGATTCAT-G
* ** * * *
1132642 CTCCTTTCTCTACAACTATGACATCCACCCTTACTCCCCGCTAGGAGTTTCTCTTTGATGTGGGA
65 CTCC-ATCTCTAGGACTATGACATCCACCCTTACTCCCCG-TTGAAGTTTCTCTTCGATGTGGGA
* * * ** * * * *
1132707 CTTTGTGACTCATCTGCTTTGAGCATTATCTTGATTATGTGAGATTCACGTCCAAGCGAGAATCG
128 TTTTGTGACTCACCCGCTAGGAGCATTATCTCGATGATGTGGGATTCACGTCCAAGCAAGAATCG
* * ** * * *
1132772 TGACATCCTCCCCACTTCAACAAGGTTTTACTGTCCTCAGTGGCACATTGCTAGTACTCAAAGTC
193 TGACATCCTCCCCACTTCAACAAAGATCCACTATCCTCAGTAGCACATTACTAGTACTCAAAGTC
* * * *
1132837 TGCTCTGATACCAATAG-TCACAATCCACACTAATCCCTGTGAGGTATTATCCG-TTTTGAATCA
258 TGCTCTGATACCAATAGCT-ACAATCCACACCAACCCCTGTGAGGTATTATCCGCTTTAG-ACCA
* ** * *
1132900 CTAACCTCACGGTTTTATTTCACAAAATGTGCCTCACAAGTT
321 CTAACCTCACGATTTTATCCCACAAAAAGGGCCTCACAAGTT
* * *
1132942 AAAGGTAATGTGAACCCTTATATTTTCAGTATCATTTTAGTTCATAGCCAATGTGAGATTCATAG
1 AAAGGTGATGTGAACCCTTATATTTCCAGTATCATTTTAGTACATAGCCAATGTGAGATTCAT-G
* * * *
1133007 CTCTCATCTCTAGGACTATGACATTCACCTTTACTCCCCGTTGAAGTTTCTATTCAATGTGGGAT
65 CTC-CATCTCTAGGACTATGACATCCACCCTTACTCCCCGTTGAAGTTTCTCTTCGATGTGGGAT
* * * * *
1133072 TTTGTGACTCACCCGCTAGGAGTATTATCTCGATGATATGGGATTTACGTCCACGCAAGGATCGT
129 TTTGTGACTCACCCGCTAGGAGCATTATCTCGATGATGTGGGATTCACGTCCAAGCAAGAATCGT
* * * *
1133137 GACATCCTCCCCACTTCAACAAAGATCCATTATCCTTAGTAGCACATTACTAGTACTTAGAGTCT
194 GACATCCTCCCCACTTCAACAAAGATCCACTATCCTCAGTAGCACATTACTAGTACTCAAAGTCT
* * * * * *
1133202 GCTCTGATACCAATTGCTAGAGTCCACACCAACCCCTGTGAGGTATTGTCTGCTTTAGCCCACTA
259 GCTCTGATACCAATAGCTACAATCCACACCAACCCCTGTGAGGTATTATCCGCTTTAGACCACTA
* *
1133267 ACCTCATGATTTTATCCCACAAAAAGGGCCTCACAGGTT
324 ACCTCACGATTTTATCCCACAAAAAGGGCCTCACAAGTT
** * * * * *
1133306 AAAAATGGTGTGAACCTTTATATTTCCAGTATCATTCTAGTACATAACCAATGTGATATTCATGA
1 AAAGGTGATGTGAACCCTTATATTTCCAGTATCATTTTAGTACATAGCCAATGTGAGATTCATG-
* * * * *
1133371 CTCCCCTCTCTAGGACCATGACGTCCACCCTTACTCCCAGTTGAGGATTTCTCTTCGATGTGGGA
65 CT-CCATCTCTAGGACTATGACATCCACCCTTACTCCCCGTTGAAG-TTTCTCTTCGATGTGGGA
* * * *
1133436 TTTTGTGACTCACTCGCTGGGAGCATTGTCTCGACGATGTGGGATTCA
128 TTTTGTGACTCACCCGCTAGGAGCATTATCTCGATGATGTGGGATTCA
1133484 TGGTTTTGTC
Statistics
Matches: 448, Mismatches: 88, Indels: 12
0.82 0.16 0.02
Matches are distributed among these distances:
363 1 0.00
364 295 0.66
365 151 0.34
366 1 0.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (362 bp):
AAAGGTGATGTGAACCCTTATATTTCCAGTATCATTTTAGTACATAGCCAATGTGAGATTCATGC
TCCATCTCTAGGACTATGACATCCACCCTTACTCCCCGTTGAAGTTTCTCTTCGATGTGGGATTT
TGTGACTCACCCGCTAGGAGCATTATCTCGATGATGTGGGATTCACGTCCAAGCAAGAATCGTGA
CATCCTCCCCACTTCAACAAAGATCCACTATCCTCAGTAGCACATTACTAGTACTCAAAGTCTGC
TCTGATACCAATAGCTACAATCCACACCAACCCCTGTGAGGTATTATCCGCTTTAGACCACTAAC
CTCACGATTTTATCCCACAAAAAGGGCCTCACAAGTT
Found at i:1133660 original size:211 final size:211
Alignment explanation
Indices: 1133270--1133696 Score: 538
Period size: 211 Copynumber: 2.0 Consensus size: 211
1133260 CCCACTAACC
* * * * *
1133270 TCATGATTTTATCCCACAAAAAGGGCCTCACAGGTTAAAAATGGTGTGAACCTTTATATTTCCAG
1 TCATGATTTTATCCCACAAAAAGGACCTCACAAGTTAAAAATGATATGAACCTTTATATTCCCAG
* * * *
1133335 TATCATTCTAGTACATAACCAATGTGATATTCATGACTCCCCTCTCTAGGACCATGACGTCCACC
66 TATCACTCTAGTACATAACCAATGTGAGATTCATGACTCACCTCTCTAGGACCATGACATCCACC
* * * * * *
1133400 CTTACTCCCAGTTGAGGATTTCTCTTCGATGTGGGATTTTGTGACTCACTCGCTGGGAGCATTGT
131 CTTACTCCCAGCTGAGGATTTCTCTTCGATGTGAGACTTTGTAACTCACTCGCTGAGAGCATTAT
*
1133465 CTCGACGATGTGGGAT
196 CTCGACAATGTGGGAT
* * *
1133481 TCATGGTTTTGTCCCAC-AAAAGGCACCTCACAAGTTAAAAGTGATATGAACCTTTATATTCCCA
1 TCATGATTTTATCCCACAAAAAGG-ACCTCACAAGTTAAAAATGATATGAACCTTTATATTCCCA
* ** * * *
1133545 GTATCACTCTAGTATATAGTCAATGTGAGATTCGTGGCTCACTTCAT-TAGGACCATGACATCCA
65 GTATCACTCTAGTACATAACCAATGTGAGATTCATGACTCACCTC-TCTAGGACCATGACATCCA
* *
1133609 CCCTTACTCCCTA-CTG-GGAGTTTCTCTTTGATGTGAGACTTTGTAACTCACTCGCTGAGAGTA
129 CCCTTACTCCC-AGCTGAGGA-TTTCTCTTCGATGTGAGACTTTGTAACTCACTCGCTGAGAGCA
*
1133672 TTATCTTGACAATGTGGGAT
192 TTATCTCGACAATGTGGGAT
1133692 TCATG
1 TCATG
1133697 TCCACACGAA
Statistics
Matches: 184, Mismatches: 28, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
210 9 0.05
211 173 0.94
212 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (211 bp):
TCATGATTTTATCCCACAAAAAGGACCTCACAAGTTAAAAATGATATGAACCTTTATATTCCCAG
TATCACTCTAGTACATAACCAATGTGAGATTCATGACTCACCTCTCTAGGACCATGACATCCACC
CTTACTCCCAGCTGAGGATTTCTCTTCGATGTGAGACTTTGTAACTCACTCGCTGAGAGCATTAT
CTCGACAATGTGGGAT
Found at i:1136415 original size:20 final size:21
Alignment explanation
Indices: 1136376--1136417 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1136366 CGATCGGTGA
1136376 AAAAACCATAAAATGTTTTTG
1 AAAAACCATAAAATGTTTTTG
**
1136397 AAAAACCATAACCTGTTTTTG
1 AAAAACCATAAAATGTTTTTG
1136418 TTTTTGGTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (21 bp):
AAAAACCATAAAATGTTTTTG
Found at i:1145165 original size:21 final size:21
Alignment explanation
Indices: 1145140--1145186 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
1145130 GCGGCAGTGG
1145140 AGATGAGGATGATGACGATGA
1 AGATGAGGATGATGACGATGA
* *
1145161 GGATGATGATGATGACGATGA
1 AGATGAGGATGATGACGATGA
1145182 AGATG
1 AGATG
1145187 GTGAGGAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.04, G:0.38, T:0.21
Consensus pattern (21 bp):
AGATGAGGATGATGACGATGA
Found at i:1145186 original size:15 final size:15
Alignment explanation
Indices: 1145141--1145193 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
1145131 CGGCAGTGGA
*
1145141 GATGAGGATGATGAC
1 GATGAGGATGATGAT
1145156 GATGAGGATGATGAT
1 GATGAGGATGATGAT
* *
1145171 GATGACGATGAAGAT
1 GATGAGGATGATGAT
*
1145186 GGTGAGGA
1 GATGAGGA
1145194 AGAGGAGGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 33 1.00
ACGTcount: A:0.34, C:0.04, G:0.42, T:0.21
Consensus pattern (15 bp):
GATGAGGATGATGAT
Found at i:1145203 original size:9 final size:9
Alignment explanation
Indices: 1145189--1145218 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1145179 TGAAGATGGT
1145189 GAGGAAGAG
1 GAGGAAGAG
1145198 GAGGAAGAG
1 GAGGAAGAG
*
1145207 GAAGAAGAG
1 GAGGAAGAG
1145216 GAG
1 GAG
1145219 CCGGAAGAAG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (9 bp):
GAGGAAGAG
Found at i:1150223 original size:47 final size:47
Alignment explanation
Indices: 1150149--1150241 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
1150139 ATAAATATGA
* *
1150149 GTAAGAACTCTGCCAGCTCTTTTGGCTATTGTATAACTGATTTTATT
1 GTAAGAACTCTGCCAGCTCTTTTGGCTAATGTATAACTCATTTTATT
* *
1150196 GTAATAACTCTGCCAGCTCTTTTGGCTAATGTATAATTCATTTTAT
1 GTAAGAACTCTGCCAGCTCTTTTGGCTAATGTATAACTCATTTTAT
1150242 ATATTTAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.43
Consensus pattern (47 bp):
GTAAGAACTCTGCCAGCTCTTTTGGCTAATGTATAACTCATTTTATT
Found at i:1155429 original size:20 final size:20
Alignment explanation
Indices: 1155392--1155429 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1155382 GTTCAATATC
*
1155392 AAAATAAAAAAATCTATTAA
1 AAAATAAAAAAATATATTAA
*
1155412 AAAATAAAAATATATATT
1 AAAATAAAAAAATATATT
1155430 TATCATTAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAATAAAAAAATATATTAA
Found at i:1158760 original size:20 final size:19
Alignment explanation
Indices: 1158730--1158767 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1158720 ACAAGCTAGG
1158730 CAAAAAAAAAAAACAAAAA
1 CAAAAAAAAAAAACAAAAA
*
1158749 CAAAACAAAAAATACAAAA
1 CAAAA-AAAAAAAACAAAA
1158768 GAAAAGACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.84, C:0.13, G:0.00, T:0.03
Consensus pattern (19 bp):
CAAAAAAAAAAAACAAAAA
Found at i:1167165 original size:30 final size:30
Alignment explanation
Indices: 1167131--1167205 Score: 132
Period size: 30 Copynumber: 2.5 Consensus size: 30
1167121 ACAACGCTGT
* *
1167131 CTGCTAACTTACGCTAGAAAACGTCACTTC
1 CTGCTATCTTACGCTAGAAAACGTCACTCC
1167161 CTGCTATCTTACGCTAGAAAACGTCACTCC
1 CTGCTATCTTACGCTAGAAAACGTCACTCC
1167191 CTGCTATCTTACGCT
1 CTGCTATCTTACGCT
1167206 TCCCTATTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.29
Consensus pattern (30 bp):
CTGCTATCTTACGCTAGAAAACGTCACTCC
Found at i:1167318 original size:2 final size:2
Alignment explanation
Indices: 1167311--1167347 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
1167301 CGCCTCCCCA
*
1167311 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1167348 TTGCAACATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.03, C:0.46, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:1180018 original size:18 final size:19
Alignment explanation
Indices: 1179982--1180031 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
1179972 TTACATAATT
1179982 ATAAAATTTATAAATAAAA
1 ATAAAATTTATAAATAAAA
1180001 ATAAAA-TTA-AATATAAAA
1 ATAAAATTTATAA-ATAAAA
**
1180019 ATATTATTTATAA
1 ATAAAATTTATAA
1180032 TCGAATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 2 0.08
18 13 0.50
19 9 0.35
20 2 0.08
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAAAATTTATAAATAAAA
Found at i:1182223 original size:23 final size:21
Alignment explanation
Indices: 1182185--1182226 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
1182175 AATATTTATA
1182185 TCATAAAAAAATTTAAAATTT
1 TCATAAAAAAATTTAAAATTT
*
1182206 TCATATAAAATATATTAAAAT
1 TCATA-AAAAAAT-TTAAAAT
1182227 CAAAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 6 0.33
23 7 0.39
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
TCATAAAAAAATTTAAAATTT
Found at i:1182774 original size:15 final size:15
Alignment explanation
Indices: 1182744--1182773 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
1182734 TCTCTTTCTC
1182744 TCTCTGTTTTTTTTT
1 TCTCTGTTTTTTTTT
1182759 TCTCT-TTTTTTTTT
1 TCTCTGTTTTTTTTT
1182773 T
1 T
1182774 TGCATTTTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.83
Consensus pattern (15 bp):
TCTCTGTTTTTTTTT
Found at i:1188976 original size:2 final size:2
Alignment explanation
Indices: 1188969--1189006 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1188959 AGGAAAACAG
1188969 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1189007 TTCTAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1192773 original size:26 final size:26
Alignment explanation
Indices: 1192737--1192809 Score: 69
Period size: 26 Copynumber: 2.8 Consensus size: 26
1192727 AATCCACCTA
* *
1192737 TTTAAATTTAATATATTAATAAATAT
1 TTTAAAATTAATATATTAATAAAAAT
1192763 TTTAAAATTAA-A-ATTAAATAAAAAT
1 TTTAAAATTAATATATT-AATAAAAAT
* * *
1192788 ATTAATTATTAATATAGTAATA
1 TTTAA-AATTAATATATTAATA
1192810 TCTCGAATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
24 3 0.08
25 13 0.34
26 15 0.39
27 5 0.13
28 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (26 bp):
TTTAAAATTAATATATTAATAAAAAT
Found at i:1199633 original size:2 final size:2
Alignment explanation
Indices: 1199626--1199654 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1199616 ATGATGTCAG
1199626 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1199655 TTTGAAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1208392 original size:2 final size:2
Alignment explanation
Indices: 1208385--1208416 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1208375 CATTGCCGCA
1208385 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1208417 TCTTCCGGAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1212785 original size:4 final size:4
Alignment explanation
Indices: 1212776--1212814 Score: 51
Period size: 4 Copynumber: 9.2 Consensus size: 4
1212766 CAAATAATTA
*
1212776 TAAT TAAT TAAAT TAAT TAAT TAAAT TAAT TAAT AAAT T
1 TAAT TAAT T-AAT TAAT TAAT T-AAT TAAT TAAT TAAT T
1212815 TATGATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 23 0.74
5 8 0.26
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
TAAT
Found at i:1212791 original size:9 final size:9
Alignment explanation
Indices: 1212770--1212834 Score: 55
Period size: 9 Copynumber: 7.2 Consensus size: 9
1212760 TAAGGGCAAA
1212770 TAATTATAAT
1 TAATTA-AAT
1212780 TAATTAAAT
1 TAATTAAAT
1212789 TAATT-AAT
1 TAATTAAAT
1212797 TAAATT-AAT
1 T-AATTAAAT
1212806 TAA-TAAAT
1 TAATTAAAT
* * *
1212814 TTATGATTAT
1 TAATTA-AAT
1212824 TAATTAAAT
1 TAATTAAAT
1212833 TA
1 TA
1212835 TAATGTCTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
7 1 0.02
8 11 0.24
9 21 0.47
10 12 0.27
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (9 bp):
TAATTAAAT
Found at i:1212794 original size:13 final size:13
Alignment explanation
Indices: 1212776--1212814 Score: 71
Period size: 13 Copynumber: 3.1 Consensus size: 13
1212766 CAAATAATTA
1212776 TAATTAATTAAAT
1 TAATTAATTAAAT
1212789 TAATTAATTAAAT
1 TAATTAATTAAAT
1212802 TAATTAA-TAAAT
1 TAATTAATTAAAT
1212814 T
1 T
1212815 TATGATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 6 0.23
13 20 0.77
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAATTAATTAAAT
Found at i:1212996 original size:16 final size:17
Alignment explanation
Indices: 1212972--1213006 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
1212962 TATTTTGTGT
1212972 TAACATTATAAAAATTA
1 TAACATTATAAAAATTA
1212989 TAAC-TTATAAAAATTA
1 TAACATTATAAAAATTA
1213005 TA
1 TA
1213007 TTTTTTGTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.37
Consensus pattern (17 bp):
TAACATTATAAAAATTA
Found at i:1213059 original size:41 final size:40
Alignment explanation
Indices: 1213013--1213144 Score: 167
Period size: 39 Copynumber: 3.3 Consensus size: 40
1213003 TATATTTTTT
* *
1213013 GTTATTTAAGTTTATGTTATTTGTTTAGATATTTGTGTTTA
1 GTTATTTAAGTTTATGTT-TTTGTTTGGATATTTATGTTTA
* *
1213054 GTTATTTAAGTTTATGTTTTTATTTGGATATTTATGTATA
1 GTTATTTAAGTTTATGTTTTTGTTTGGATATTTATGTTTA
* ** * *
1213094 GTT-TTTAAGTTTATATCGTTGTATGGATATTTATTTTTA
1 GTTATTTAAGTTTATGTTTTTGTTTGGATATTTATGTTTA
1213133 GTTATTTAAGTT
1 GTTATTTAAGTT
1213145 AATGCTTAAG
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 32 0.41
40 29 0.37
41 18 0.23
ACGTcount: A:0.23, C:0.01, G:0.16, T:0.60
Consensus pattern (40 bp):
GTTATTTAAGTTTATGTTTTTGTTTGGATATTTATGTTTA
Found at i:1213075 original size:22 final size:22
Alignment explanation
Indices: 1213002--1213075 Score: 52
Period size: 22 Copynumber: 3.5 Consensus size: 22
1212992 CTTATAAAAA
* *
1213002 TTATATTTTTTGTTATTTAAGT
1 TTATGTTTTTAGTTATTTAAGT
1213024 TTATGTTATTT-G---TTT-AGAT
1 TTATGTT-TTTAGTTATTTAAG-T
*
1213043 ATT-TGTGTTTAGTTATTTAAGT
1 -TTATGTTTTTAGTTATTTAAGT
1213065 TTATGTTTTTA
1 TTATGTTTTTA
1213076 TTTGGATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 18
0.66 0.05 0.30
Matches are distributed among these distances:
18 5 0.12
19 8 0.20
20 2 0.05
21 2 0.05
22 18 0.45
23 5 0.12
ACGTcount: A:0.22, C:0.00, G:0.14, T:0.65
Consensus pattern (22 bp):
TTATGTTTTTAGTTATTTAAGT
Found at i:1225318 original size:37 final size:37
Alignment explanation
Indices: 1225276--1225349 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
1225266 CCACGTGAAA
*
1225276 GTACGTCATGGGCTCAGAGCGGTTATACAGTTCAAAG
1 GTACGTCATGGGCTCAGAGCGGTTATACAATTCAAAG
*
1225313 GTACGTCATGGGCTCAGAGCGGTTATGCAATTCAAAG
1 GTACGTCATGGGCTCAGAGCGGTTATACAATTCAAAG
1225350 CCTCTTTCCC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (37 bp):
GTACGTCATGGGCTCAGAGCGGTTATACAATTCAAAG
Found at i:1229423 original size:20 final size:20
Alignment explanation
Indices: 1229398--1229437 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
1229388 TACAATAATC
1229398 TAATAAATTTTAGAATTTTA
1 TAATAAATTTTAGAATTTTA
1229418 TAATAAATTTTAGAATTTTA
1 TAATAAATTTTAGAATTTTA
1229438 AGTTATTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TAATAAATTTTAGAATTTTA
Found at i:1234520 original size:77 final size:78
Alignment explanation
Indices: 1234391--1234596 Score: 308
Period size: 77 Copynumber: 2.6 Consensus size: 78
1234381 GTCTGTTTTG
*
1234391 TCCCTTTTCTAATACCTGATTAATATTGTTAAATGAAAGGCTTTGTCACCATCATAGT-AACACC
1 TCCCTTTTCTAATACCTGATTAATATTGATAAATGAAAGGCTTTGTCACCATCATAGTAAACACC
1234455 ATTAATGGACTCC
66 ATTAATGGACTCC
* * *
1234468 TCCCTTTTGTAATACCTGATTAATGTTGATAAATGAAAGGCTTTGTTC-CCATCATGGTAAACAC
1 TCCCTTTTCTAATACCTGATTAATATTGATAAATGAAAGGCTTTG-TCACCATCATAGTAAACAC
*
1234532 CATTAATGGACTTC
65 CATTAATGGACTCC
* * *
1234546 ACCCTTTTCTAATACTTGATTAATATTTGATAAATGAAAGGCTTCGTCACC
1 TCCCTTTTCTAATACCTGATTAATA-TTGATAAATGAAAGGCTTTGTCACC
1234597 TTTAATAGCC
Statistics
Matches: 115, Mismatches: 10, Indels: 6
0.88 0.08 0.05
Matches are distributed among these distances:
77 51 0.44
78 43 0.37
79 21 0.18
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (78 bp):
TCCCTTTTCTAATACCTGATTAATATTGATAAATGAAAGGCTTTGTCACCATCATAGTAAACACC
ATTAATGGACTCC
Found at i:1240601 original size:117 final size:115
Alignment explanation
Indices: 1240424--1240660 Score: 318
Period size: 117 Copynumber: 2.0 Consensus size: 115
1240414 CTCGTATTTC
* * *
1240424 TATATAAAATTGTATTTAATGTAATACATATATAAATTTTATAATTTATTAGTGAATCAAATGTT
1 TATATAAAATTATATTTAATGTAATACATATATAAATTCTATAATTTATTAGTAAATCAAATGTT
* * *
1240489 GTTATCTTATTAATAAATAAATTTTAAAAAATAAATACTCATAAATTAAA
66 ATTATCTTATTAATAAATAAATTTTAAAAAATAAACACTCATAAATGAAA
* *
1240539 -ATATAAAATTTATATTTACTGTAATATCTATGTATAAATTCTATACA-TTACTT-GTAAATCAA
1 TATATAAAA-TTATATTTAATGTAATA-C-ATATATAAATTCTATA-ATTTA-TTAGTAAATCAA
* *
1240601 ATGTTATTTTCTTATTAATAAATAAATTTTAAAAAATCAACACTCATAAATGAAA
61 ATGTTATTATCTTATTAATAAATAAATTTTAAAAAATAAACACTCATAAATGAAA
1240656 TATAT
1 TATAT
1240661 TTATTTAAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
114 8 0.08
115 15 0.14
116 1 0.01
117 75 0.71
118 7 0.07
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.42
Consensus pattern (115 bp):
TATATAAAATTATATTTAATGTAATACATATATAAATTCTATAATTTATTAGTAAATCAAATGTT
ATTATCTTATTAATAAATAAATTTTAAAAAATAAACACTCATAAATGAAA
Found at i:1241588 original size:25 final size:24
Alignment explanation
Indices: 1241560--1241606 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
1241550 TTATAAATTA
*
1241560 TTAAAAATATTAAATAAAACATAAT
1 TTAAAAATA-AAAATAAAACATAAT
1241585 TTAAAAATAAAAATAAAACATA
1 TTAAAAATAAAAATAAAACATA
1241607 TTTTTTTACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (24 bp):
TTAAAAATAAAAATAAAACATAAT
Found at i:1260668 original size:2 final size:2
Alignment explanation
Indices: 1260661--1260694 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
1260651 TCTTTGTGCC
*
1260661 CT CT CT CT CC CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1260695 TTGCTCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:1264135 original size:20 final size:20
Alignment explanation
Indices: 1264110--1264150 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1264100 ATACATGAAA
1264110 CAAAGCAAATACTTCTCAAG
1 CAAAGCAAATACTTCTCAAG
1264130 CAAAGCAAATACTTCTCAAG
1 CAAAGCAAATACTTCTCAAG
1264150 C
1 C
1264151 TTGACGACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.44, C:0.27, G:0.10, T:0.20
Consensus pattern (20 bp):
CAAAGCAAATACTTCTCAAG
Found at i:1264211 original size:23 final size:24
Alignment explanation
Indices: 1264184--1264229 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1264174 TCAATTTTAG
*
1264184 AATTAGACAGTTT-AGATTATATT
1 AATTAAACAGTTTGAGATTATATT
*
1264207 AATTAAACAGTTTGATATTATAT
1 AATTAAACAGTTTGAGATTATAT
1264230 ATATATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.43
Consensus pattern (24 bp):
AATTAAACAGTTTGAGATTATATT
Found at i:1264473 original size:2 final size:2
Alignment explanation
Indices: 1264466--1264508 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1264456 CGCTCCCTCC
1264466 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1264508 T
1 T
1264509 TCTCAGCTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1296990 original size:22 final size:23
Alignment explanation
Indices: 1296969--1297015 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
1296959 ATTTCATATA
1296969 ATAT-ATTAAATTTTT-TATTAT
1 ATATAATTAAATTTTTATATTAT
*
1296990 ATTTAATTAAATTTTTATATT-T
1 ATATAATTAAATTTTTATATTAT
1297012 ATAT
1 ATAT
1297016 TTTATATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 3 0.14
22 15 0.68
23 4 0.18
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
ATATAATTAAATTTTTATATTAT
Found at i:1307658 original size:2 final size:2
Alignment explanation
Indices: 1307651--1307675 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1307641 AAAAGAAAAT
1307651 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
1307676 AAGGGCATGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1309777 original size:21 final size:21
Alignment explanation
Indices: 1309751--1309790 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1309741 ACTTTCAAAG
1309751 AAAAAAACAAAAATTCAAAAA
1 AAAAAAACAAAAATTCAAAAA
* *
1309772 AAAAAAACGAAATTTCAAA
1 AAAAAAACAAAAATTCAAA
1309791 TTTCAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.75, C:0.10, G:0.03, T:0.12
Consensus pattern (21 bp):
AAAAAAACAAAAATTCAAAAA
Found at i:1309784 original size:20 final size:22
Alignment explanation
Indices: 1309743--1309790 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
1309733 CCGATACAAC
*
1309743 TTTC-AAAGAAAAAAACAAAAA
1 TTTCAAAAAAAAAAAACAAAAA
*
1309764 -TTCAAAAAAAAAAAAC-GAAA
1 TTTCAAAAAAAAAAAACAAAAA
1309784 TTTCAAA
1 TTTCAAA
1309791 TTTCAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.69, C:0.10, G:0.04, T:0.17
Consensus pattern (22 bp):
TTTCAAAAAAAAAAAACAAAAA
Found at i:1310019 original size:18 final size:19
Alignment explanation
Indices: 1309996--1310031 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1309986 ATAAGTAGAA
*
1309996 CTTTTCTT-TTTTCTTTTC
1 CTTTTCTTCTTTTATTTTC
1310014 CTTTTCTTCTTTTATTTT
1 CTTTTCTTCTTTTATTTT
1310032 TAGTCTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.03, C:0.19, G:0.00, T:0.78
Consensus pattern (19 bp):
CTTTTCTTCTTTTATTTTC
Found at i:1323614 original size:17 final size:17
Alignment explanation
Indices: 1323594--1323628 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
1323584 TGTTGTGGAC
1323594 AAGTGTTTGGATACTCG
1 AAGTGTTTGGATACTCG
1323611 AAGTGTTTGGATACTCG
1 AAGTGTTTGGATACTCG
1323628 A
1 A
1323629 TTAAGCTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (17 bp):
AAGTGTTTGGATACTCG
Found at i:1332520 original size:21 final size:21
Alignment explanation
Indices: 1332494--1332541 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
1332484 GTTGGTATTC
*
1332494 AGCTTTGGTGGCGGGGACACG
1 AGCTTTGGTGGCGAGGACACG
*
1332515 AGCTTTGGTGGCGAGGACAGG
1 AGCTTTGGTGGCGAGGACACG
1332536 AGCTTT
1 AGCTTT
1332542 TGTGTCAGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.17, G:0.44, T:0.23
Consensus pattern (21 bp):
AGCTTTGGTGGCGAGGACACG
Found at i:1336334 original size:17 final size:18
Alignment explanation
Indices: 1336304--1336337 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1336294 CTTTTTTTTC
*
1336304 TAAAAAGATCCTCCCTCT
1 TAAAAAGATACTCCCTCT
1336322 TAAAAA-ATACTCCCTC
1 TAAAAAGATACTCCCTC
1336338 CCTCTCTCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.38, C:0.32, G:0.03, T:0.26
Consensus pattern (18 bp):
TAAAAAGATACTCCCTCT
Found at i:1339006 original size:33 final size:33
Alignment explanation
Indices: 1338947--1339013 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1338937 AGATTTAAAG
*
1338947 CAGCAATATCAGAAATTTCCTCAATGTCGATAC
1 CAGCAATATCAGAAATTTCCACAATGTCGATAC
* * * *
1338980 CAGCAATATCAGGAATTTTCAGAATGTTGATAC
1 CAGCAATATCAGAAATTTCCACAATGTCGATAC
1339013 C
1 C
1339014 CTTAGTTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (33 bp):
CAGCAATATCAGAAATTTCCACAATGTCGATAC
Found at i:1348578 original size:2 final size:2
Alignment explanation
Indices: 1348571--1348596 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1348561 CTTGTTTTGT
1348571 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
1348597 AAGATTACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1358685 original size:23 final size:22
Alignment explanation
Indices: 1358638--1358687 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 22
1358628 TCTATTTTTG
**
1358638 TATTTATTAAAAATTATAATTT
1 TATTTATTAAAAATTATAAAGT
1358660 TATTTATTAAAAGATTATAAAGT
1 TATTTATTAAAA-ATTATAAAGT
1358683 TATTT
1 TATTT
1358688 TTATATAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 12 0.48
23 13 0.52
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (22 bp):
TATTTATTAAAAATTATAAAGT
Found at i:1365589 original size:32 final size:32
Alignment explanation
Indices: 1365533--1365596 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1365523 CAAAGGTAGG
** *
1365533 TACCCCATAAATTTTATCTCCTTGATTTTTTT
1 TACCCCATAAATTCCATCTCCTTGAGTTTTTT
* *
1365565 TACCCCATGAATTCCATCTTCTTGAGTTTTTT
1 TACCCCATAAATTCCATCTCCTTGAGTTTTTT
1365597 ACTTCTAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.20, C:0.23, G:0.06, T:0.50
Consensus pattern (32 bp):
TACCCCATAAATTCCATCTCCTTGAGTTTTTT
Found at i:1374610 original size:100 final size:100
Alignment explanation
Indices: 1374474--1374653 Score: 247
Period size: 100 Copynumber: 1.8 Consensus size: 100
1374464 TCGATTAGTT
* * * *
1374474 ACTTGTGTCCCTTTTATTAATGAATGAATTTATTATTCACTCATATATTGTTC-ATTACTGAACG
1 ACTTGTGTCCCTTTGATTAATGAATGAACTTATTATTCACTCATATATTG-TCGATTAATGAACA
*
1374538 ACCGATTTAATCAATTGATTACATTCACTTGTGCAC
65 AACGATTTAATCAATTGATTACATTCACTTGTGCAC
* * * *
1374574 ACTTGTGT-CCTGTTGATTAATGGATGAACTTATTATTTACTCATATTTTGTCGATTAATGAATA
1 ACTTGTGTCCCT-TTGATTAATGAATGAACTTATTATTCACTCATATATTGTCGATTAATGAACA
1374638 AACGATTTAATCAATT
65 AACGATTTAATCAATT
1374654 TAATTGATTA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
99 5 0.07
100 64 0.93
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.43
Consensus pattern (100 bp):
ACTTGTGTCCCTTTGATTAATGAATGAACTTATTATTCACTCATATATTGTCGATTAATGAACAA
ACGATTTAATCAATTGATTACATTCACTTGTGCAC
Found at i:1393630 original size:97 final size:97
Alignment explanation
Indices: 1393518--1393734 Score: 258
Period size: 97 Copynumber: 2.2 Consensus size: 97
1393508 CACATGATTG
* * ** **
1393518 ATATGATAATATAAATGAGTTAAACATACTATATACAAGTTAAA-GGAATTTGATTGTTTAAAAT
1 ATATGATAATATAAATGAGTTAAACATACTATAAACAAGTTAAACAG-ATTCAACCGTTT-AAAT
* *
1393582 AACGGATTTAAC-CTTTAAGATATTTATACAATA
64 AACGAATTTAACTATTTAAGATATTTATACAATA
* * ** *
1393615 ATATGATTATATAAATTAGTTAAACATGTTATAAACAGGTTAAACAGATTCAACCGTTTAAATAA
1 ATATGATAATATAAATGAGTTAAACATACTATAAACAAGTTAAACAGATTCAACCGTTTAAATAA
* *
1393680 CGAATTTAACTATTTAAGATATTTGTACGATA
66 CGAATTTAACTATTTAAGATATTTATACAATA
*
1393712 AGATGATAATATAAATGAGTTAA
1 ATATGATAATATAAATGAGTTAA
1393735 CTTGTATATA
Statistics
Matches: 100, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
96 15 0.15
97 84 0.84
98 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.35
Consensus pattern (97 bp):
ATATGATAATATAAATGAGTTAAACATACTATAAACAAGTTAAACAGATTCAACCGTTTAAATAA
CGAATTTAACTATTTAAGATATTTATACAATA
Found at i:1394742 original size:3 final size:3
Alignment explanation
Indices: 1394736--1394770 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1394726 ATCTCCTCCT
1394736 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CCA CC
1394771 GCCATCTCCA
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:0.31, C:0.69, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:1404713 original size:19 final size:19
Alignment explanation
Indices: 1404689--1404727 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
1404679 TCTTACTTTG
1404689 AAGATGGATGGTGAATAGA
1 AAGATGGATGGTGAATAGA
1404708 AAGATGGATGGTGAATAGA
1 AAGATGGATGGTGAATAGA
1404727 A
1 A
1404728 TGCTTACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.21
Consensus pattern (19 bp):
AAGATGGATGGTGAATAGA
Found at i:1413427 original size:2 final size:2
Alignment explanation
Indices: 1413422--1413446 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1413412 ACATTTTTTG
1413422 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
1413447 TCCCTCCTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1432116 original size:95 final size:95
Alignment explanation
Indices: 1431968--1432161 Score: 255
Period size: 95 Copynumber: 2.0 Consensus size: 95
1431958 AAGTGATATT
* * * *
1431968 TTTATTAATTATAATTAATCAATCATTGATTATAAGAATTTATTTGACTCAAATACAAA-TACGA
1 TTTACTAATTATAATTAATCAATCATTAATTATAAGAATTTATTTGACGCAAATA-AAAGTACAA
* *
1432032 GACCTAATTAAACTCAATCAAAAAATAAAAA
65 AACCTAATTAAACTCAATAAAAAAATAAAAA
* * * *
1432063 TTTACTAATTATAATTAATTAATTATTAATTATAAGAGTTTATTTGACGCAAATAAAAGTATAAA
1 TTTACTAATTATAATTAATCAATCATTAATTATAAGAATTTATTTGACGCAAATAAAAGTACAAA
** *
1432128 ATTTTATTAAACTCAATAAAAAAATAAAAA
66 ACCTAATTAAACTCAATAAAAAAATAAAAA
1432158 TTTA
1 TTTA
1432162 TTTAAATATT
Statistics
Matches: 85, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
94 3 0.04
95 82 0.96
ACGTcount: A:0.50, C:0.08, G:0.05, T:0.37
Consensus pattern (95 bp):
TTTACTAATTATAATTAATCAATCATTAATTATAAGAATTTATTTGACGCAAATAAAAGTACAAA
ACCTAATTAAACTCAATAAAAAAATAAAAA
Found at i:1432202 original size:11 final size:11
Alignment explanation
Indices: 1432155--1432202 Score: 50
Period size: 10 Copynumber: 4.7 Consensus size: 11
1432145 AAAAAAATAA
1432155 AAAT-TTATTT
1 AAATATTATTT
1432165 AAATATT-TTT
1 AAATATTATTT
1432175 AAATA--ATTT
1 AAATATTATTT
* *
1432184 AGAGATTATTT
1 AAATATTATTT
1432195 AAATATTA
1 AAATATTA
1432203 CGTCAAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
9 6 0.20
10 12 0.40
11 12 0.40
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (11 bp):
AAATATTATTT
Done.