Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009014.1 Hibiscus syriacus cultivar Beakdansim tig00112402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3470424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 13
Found at i:1247421 original size:26 final size:26
Alignment explanation
Indices: 1247387--1247470 Score: 81
Period size: 26 Copynumber: 3.5 Consensus size: 26
1247377 TCCTTAATGC
*
1247387 ATCCGTTCATGCATTTTAGTTATGGT
1 ATCCTTTCATGCATTTTAGTTATGGT
* *
1247413 ATTCTTTCATGC--CTTA---AT-GT
1 ATCCTTTCATGCATTTTAGTTATGGT
* *
1247433 ATCCGTTCATGCATTTTAGTTATGGA
1 ATCCTTTCATGCATTTTAGTTATGGT
1247459 ATCCTTTCATGC
1 ATCCTTTCATGC
1247471 CTTAATGCAT
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
20 12 0.27
21 2 0.05
22 3 0.07
24 3 0.07
25 2 0.05
26 22 0.50
ACGTcount: A:0.20, C:0.19, G:0.15, T:0.45
Consensus pattern (26 bp):
ATCCTTTCATGCATTTTAGTTATGGT
Found at i:1247441 original size:20 final size:20
Alignment explanation
Indices: 1247418--1247490 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 20
1247408 ATGGTATTCT
*
1247418 TTCATGCCTTAATGTATCCG
1 TTCATGCCTTAATGAATCCG
* *
1247438 TTCATGCATTTTAGTTATGGAATCCT
1 TTCATGC--CTTA---AT-GAATCCG
*
1247464 TTCATGCCTTAATGCATCCG
1 TTCATGCCTTAATGAATCCG
1247484 TTCATGC
1 TTCATGC
1247491 ATTTTAATTA
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
20 19 0.46
21 2 0.05
22 3 0.07
24 3 0.07
25 2 0.05
26 12 0.29
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (20 bp):
TTCATGCCTTAATGAATCCG
Found at i:1247560 original size:26 final size:26
Alignment explanation
Indices: 1247530--1247700 Score: 108
Period size: 26 Copynumber: 7.3 Consensus size: 26
1247520 AATGCATTCG
1247530 TTCATGCATTTTAGTTATGGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
* * *
1247556 CTCATGC--CTTA---AT-GCATCAT
1 TTCATGCATTTTAGTTATGGCATCCT
**
1247576 TTCATGCATTTTAGTTATGAAATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
* *
1247602 TTCATGC--CTTA---AT-GCATCCG
1 TTCATGCATTTTAGTTATGGCATCCT
*
1247622 TTCATGCATTTTAGTTATGGAATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
* *
1247648 TTCATGC--CTTA---AT-GCATCCA
1 TTCATGCATTTTAGTTATGGCATCCT
* *
1247668 TTAATTCATTTTAGTTATGGCATCCT
1 TTCATGCATTTTAGTTATGGCATCCT
1247694 TTCATGC
1 TTCATGC
1247701 CTTAATGATA
Statistics
Matches: 103, Mismatches: 24, Indels: 36
0.63 0.15 0.22
Matches are distributed among these distances:
20 33 0.32
21 6 0.06
22 9 0.09
24 9 0.09
25 6 0.06
26 40 0.39
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.43
Consensus pattern (26 bp):
TTCATGCATTTTAGTTATGGCATCCT
Found at i:1251666 original size:74 final size:74
Alignment explanation
Indices: 1251533--1251738 Score: 197
Period size: 74 Copynumber: 2.8 Consensus size: 74
1251523 ATGGTGTTAT
* * * *
1251533 ATATTTTT-AT-TTT-TTAATGGAAGAAACAATT-TTTATTTTTATTTATAAACTATAATTTACA
1 ATATTTTTAATATTTGTTAAT-GAAAAAATAATTCTTAATTTTTATTTATAAATTATAATTTACA
1251594 AAAAAATTAC
65 AAAAAATTAC
* ** *
1251604 ATATTTTTAATATTTGTTAATTAAAAAATAATTCTTAATTTTTATTTAGGAATTATAGTTTACAA
1 ATATTTTTAATATTTGTTAATGAAAAAATAATTCTTAATTTTTATTTATAAATTATAATTTACAA
* *** *
1251669 TATTTTTAT
66 AAAAATTAC
* * * * * *
1251678 ATATTTTTACTTTTTGTTAGTGAAAAAATCATTCTTAA-ATTTATTTATTAATTATAATTTA
1 ATATTTTTAATATTTGTTAATGAAAAAATAATTCTTAATTTTTATTTATAAATTATAATTTA
1251739 ATAATTATAT
Statistics
Matches: 109, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
71 8 0.07
72 2 0.02
73 31 0.28
74 68 0.62
ACGTcount: A:0.39, C:0.04, G:0.05, T:0.52
Consensus pattern (74 bp):
ATATTTTTAATATTTGTTAATGAAAAAATAATTCTTAATTTTTATTTATAAATTATAATTTACAA
AAAAATTAC
Found at i:1251892 original size:76 final size:75
Alignment explanation
Indices: 1251808--1251957 Score: 171
Period size: 76 Copynumber: 2.0 Consensus size: 75
1251798 TATTAAATTA
*
1251808 TTAATAAATAGAA-TAAAAAATTATTTCTTT-CATTAAG-AAACATTACAAATATATAAAAAAAT
1 TTAATAAATAAAAGTAAAAAATTATTT-TTTCCATT-AGCAAA-ATTACAAA-ATATAAAAAAAT
*
1251870 ATTTTAAATTATAG
62 ATTGTAAATTATAG
* * ** * *
1251884 TTAATAAATAAAAGTTAAGAATTATTTTTTCCATTAGCAAAATTTTAAAATATATAAAAATGTTG
1 TTAATAAATAAAAGTAAAAAATTATTTTTTCCATTAGCAAAATTACAAAATATAAAAAAATATTG
1251949 TAAATTATA
66 TAAATTATA
1251958 TTCAAATATG
Statistics
Matches: 63, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
75 22 0.35
76 23 0.37
77 18 0.29
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (75 bp):
TTAATAAATAAAAGTAAAAAATTATTTTTTCCATTAGCAAAATTACAAAATATAAAAAAATATTG
TAAATTATAG
Found at i:1254409 original size:95 final size:94
Alignment explanation
Indices: 1254243--1254416 Score: 224
Period size: 95 Copynumber: 1.8 Consensus size: 94
1254233 ACCTAGAATG
* * * *
1254243 TAAAAATTGTATCAATATTGAAAGGGAGTATCAGTACCATAGTTTAGTAGTATCGATACTGATAG
1 TAAAAATGGTATCAATATTGAAAGGGAGTATCAGTACCATAGTATAGAAGTATCAATACTGATAG
*
1254308 AAGGGTATCGATACCATGCAACACATAATA
66 -AGGGTACCGATACCATGCAACACATAATA
** * * *
1254338 TAAAAATGGTATTTATATTGAAAGGGGGTATCGGTACCATAGTATAGAAGTATCAATACCATGGT
1 TAAAAATGGTATCAATATTGAAAGGGAGTATCAGTACCATAGTATAGAAGTATCAATA-C-TGAT
1254403 AG-GGGTACCGATAC
64 AGAGGGTACCGATAC
1254417 TAGTGAGTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
95 61 0.91
96 1 0.01
97 5 0.07
ACGTcount: A:0.38, C:0.12, G:0.22, T:0.28
Consensus pattern (94 bp):
TAAAAATGGTATCAATATTGAAAGGGAGTATCAGTACCATAGTATAGAAGTATCAATACTGATAG
AGGGTACCGATACCATGCAACACATAATA
Found at i:1254897 original size:45 final size:45
Alignment explanation
Indices: 1254833--1255122 Score: 406
Period size: 45 Copynumber: 6.4 Consensus size: 45
1254823 AAAATAATAT
* ** *
1254833 ATGCATATGGGTGCATTATTGGCATGAAAGGATACCATAACTGAA
1 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGAA
* *
1254878 ATGCATATTGGTGCATTATTGGCATGAAAGGATGTCATAATT-AGA
1 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGA-A
* *
1254923 ATGCATATGGGTGCATTATCGGCATGAAATGATGTCATAACTGAA
1 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGAA
* * *
1254968 ATGCATATGGGCGCATTAGT-GGCATGAAAAGATGCCATAATTGAA
1 ATGCATATGGGTGCATTA-TCGGCATGAAAGGATGTCATAATTGAA
1255013 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGAA
1 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGAA
* *
1255058 ATGCATATGGGTGCATTATCAGCATGAAAGGATGTTATAATTGAAA
1 ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTG-AA
1255104 ATGCATAAT-GGTGCATTAT
1 ATGCAT-ATGGGTGCATTAT
1255123 AAGAATGAAT
Statistics
Matches: 222, Mismatches: 17, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
44 2 0.01
45 198 0.89
46 20 0.09
47 2 0.01
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.29
Consensus pattern (45 bp):
ATGCATATGGGTGCATTATCGGCATGAAAGGATGTCATAATTGAA
Found at i:1257554 original size:21 final size:22
Alignment explanation
Indices: 1257529--1257569 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1257519 TTTATAAATA
*
1257529 ATTTTCAT-AAATATTATATTT
1 ATTTTCATAAAATATAATATTT
*
1257550 ATTTTTATAAAATATAATAT
1 ATTTTCATAAAATATAATAT
1257570 AATATGAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
ATTTTCATAAAATATAATATTT
Found at i:1260531 original size:27 final size:26
Alignment explanation
Indices: 1260487--1260546 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
1260477 ATGAGTCTAT
* *
1260487 TAAAAATAATTTTTTAAACTACAAAA
1 TAAAAATAAATTTATAAACTACAAAA
* *
1260513 TAAAAATAAAATTTATAAATTTCAAAA
1 TAAAAAT-AAATTTATAAACTACAAAA
*
1260540 AAAAAAT
1 TAAAAAT
1260547 GATGGGTGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (26 bp):
TAAAAATAAATTTATAAACTACAAAA
Found at i:1262689 original size:13 final size:14
Alignment explanation
Indices: 1262667--1262715 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
1262657 TATGTAATGA
1262667 AATT-TTTAATAAT
1 AATTATTTAATAAT
*
1262680 TA-TATTTAAT-AT
1 AATTATTTAATAAT
1262692 AATTATTTAATAACT
1 AATTATTTAATAA-T
*
1262707 ATTTATTTA
1 AATTATTTA
1262716 TTTATATTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.14
13 15 0.52
14 1 0.03
15 9 0.31
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTATTTAATAAT
Found at i:1262689 original size:25 final size:25
Alignment explanation
Indices: 1262653--1262704 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
1262643 TCATATATTA
1262653 AATTTATGTAATGA-AATT-TTTAAT
1 AATTTATGTAAT-ATAATTATTTAAT
*
1262677 AATTATATTTAATATAATTATTTAAT
1 AATT-TATGTAATATAATTATTTAAT
1262703 AA
1 AA
1262705 CTATTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.21
25 11 0.46
26 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (25 bp):
AATTTATGTAATATAATTATTTAAT
Found at i:1262897 original size:2 final size:2
Alignment explanation
Indices: 1262890--1262915 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
1262880 AACTCTTTAA
1262890 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
1262916 TAATTTTAAC
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:1263968 original size:15 final size:16
Alignment explanation
Indices: 1263948--1264001 Score: 67
Period size: 15 Copynumber: 3.4 Consensus size: 16
1263938 AATAAACAAT
*
1263948 AAATAAAAATAGAG-A
1 AAATAAAAATAAAGTA
1263963 AAATAAAAATAAAGTA
1 AAATAAAAATAAAGTA
*
1263979 AAGATAAAAATGAA-TA
1 AA-ATAAAAATAAAGTA
1263995 AAATAAA
1 AAATAAA
1264002 TAAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 18 0.51
16 7 0.20
17 10 0.29
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (16 bp):
AAATAAAAATAAAGTA
Found at i:1264279 original size:15 final size:17
Alignment explanation
Indices: 1264226--1264283 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 17
1264216 ATAAAATAAG
* *
1264226 AATAAAATAAATAAAAT
1 AATAATATATATAAAAT
*
1264243 AAATATATATATATAAAGT
1 -AATA-ATATATATAAAAT
1264262 AATAATAT-TA-AAAAT
1 AATAATATATATAAAAT
1264277 AATAATA
1 AATAATA
1264284 ATAATGGTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
15 11 0.31
16 2 0.06
17 4 0.11
18 8 0.23
19 10 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
AATAATATATATAAAAT
Found at i:1265411 original size:7 final size:8
Alignment explanation
Indices: 1265398--1265456 Score: 54
Period size: 7 Copynumber: 7.8 Consensus size: 8
1265388 TAACCATGTG
1265398 TATTATAA
1 TATTATAA
1265406 -ATTATAA
1 TATTATAA
*
1265413 TATTATTA
1 TATTATAA
* *
1265421 TATAATAT
1 TATTATAA
1265429 TA-TATACA
1 TATTATA-A
1265437 TATTATAA
1 TATTATAA
1265445 T-TTATAA
1 TATTATAA
1265452 T-TTAT
1 TATTAT
1265457 GTGGTCGAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
7 21 0.50
8 17 0.40
9 4 0.10
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (8 bp):
TATTATAA
Found at i:1266369 original size:43 final size:41
Alignment explanation
Indices: 1266272--1266393 Score: 145
Period size: 43 Copynumber: 2.9 Consensus size: 41
1266262 TGTAGAGTTA
* * *
1266272 GCACGATATCATTCGTCGTGAAGTTGAAATCGTGGATGTGG
1 GCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGG
*
1266313 GCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGCTTTGTGG
1 GCACGATATCCTCCGTCGTGGAGTTGAAATCGTGG--ATGTGG
* ** * *
1266356 GTATTATATCCTCCATCGTGGAGTTAAAATCGTGGATG
1 GCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATG
1266394 GCCCCTTCAT
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 34 0.49
43 35 0.51
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (41 bp):
GCACGATATCCTCCGTCGTGGAGTTGAAATCGTGGATGTGG
Found at i:1271342 original size:13 final size:12
Alignment explanation
Indices: 1271294--1271344 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 12
1271284 CCACCTTATT
1271294 TTTCTTTTCTCTTC
1 TTTCTTTT-T-TTC
*
1271308 TTTCTTTTGTTC
1 TTTCTTTTTTTC
1271320 TTTTCTTTTTTTC
1 -TTTCTTTTTTTC
1271333 TTCTCTTTTTTT
1 TT-TCTTTTTTT
1271345 TCAATTTAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
12 5 0.15
13 20 0.61
14 8 0.24
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTCTTTTTTTC
Found at i:1281770 original size:17 final size:16
Alignment explanation
Indices: 1281737--1281786 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
1281727 TAAACAATAA
*
1281737 AAAAATAGAG-AAAAT
1 AAAAATAAAGTAAAAT
1281752 AAAAATAAAGTAAAGAT
1 AAAAATAAAGTAAA-AT
*
1281769 AAAAATGAA-TAAAAT
1 AAAAATAAAGTAAAAT
1281784 AAA
1 AAA
1281787 TAAAATGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.45
16 7 0.23
17 10 0.32
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (16 bp):
AAAAATAAAGTAAAAT
Found at i:1281771 original size:41 final size:39
Alignment explanation
Indices: 1281719--1281809 Score: 96
Period size: 41 Copynumber: 2.3 Consensus size: 39
1281709 TAAAAAACGA
*
1281719 AAAGAAAATAAACAAT-AAAAAAATAGAGAAAATAAAAAT
1 AAAGAAAATAAA-AATGAAAAAAATAAAGAAAATAAAAAT
* * *
1281758 AAAGTAAAGATAAAAATGAATAAAATAAATAAAATGAAAAT
1 AAAG-AAA-ATAAAAATGAAAAAAATAAAGAAAATAAAAAT
1281799 -AAGAAGAATAA
1 AAAGAA-AATAA
1281810 GAATAAGAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
39 10 0.23
40 10 0.23
41 24 0.55
ACGTcount: A:0.74, C:0.01, G:0.10, T:0.15
Consensus pattern (39 bp):
AAAGAAAATAAAAATGAAAAAAATAAAGAAAATAAAAAT
Found at i:1282052 original size:20 final size:21
Alignment explanation
Indices: 1282006--1282052 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 21
1281996 AACAAAGAAG
1282006 GTAATAAAATAAGAATAAAAA
1 GTAATAAAATAAGAATAAAAA
*
1282027 AT-ATAAAA-AA-ATATAAAAA
1 GTAATAAAATAAGA-ATAAAAA
1282046 GTAATAA
1 GTAATAA
1282053 TATTATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 1 0.05
19 10 0.45
20 10 0.45
21 1 0.05
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.21
Consensus pattern (21 bp):
GTAATAAAATAAGAATAAAAA
Found at i:1289267 original size:30 final size:30
Alignment explanation
Indices: 1289210--1289265 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 30
1289200 TCTTCATTAA
* * *
1289210 TTTTCCAAAATTTACGAAGTTATCCCCAAC
1 TTTTCCAAAACTTACGAAATGATCCCCAAC
1289240 TTTT-CAAAACTTACGAAATGATCCCC
1 TTTTCCAAAACTTACGAAATGATCCCC
1289266 CATTTTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
29 19 0.83
30 4 0.17
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (30 bp):
TTTTCCAAAACTTACGAAATGATCCCCAAC
Found at i:1289272 original size:29 final size:29
Alignment explanation
Indices: 1289208--1289272 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
1289198 GTTCTTCATT
* * * *
1289208 AATTTTCCAAAATTTACGAAGTTATCCCC
1 AATTTTTCAAAACTTACGAAATGATCCCC
*
1289237 AACTTTTCAAAACTTACGAAATGATCCCC
1 AATTTTTCAAAACTTACGAAATGATCCCC
*
1289266 CATTTTT
1 AATTTTT
1289273 ATGAGGTTTG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.25, G:0.06, T:0.35
Consensus pattern (29 bp):
AATTTTTCAAAACTTACGAAATGATCCCC
Found at i:1292443 original size:58 final size:60
Alignment explanation
Indices: 1292352--1292472 Score: 201
Period size: 59 Copynumber: 2.0 Consensus size: 60
1292342 AATAGATGAA
*
1292352 TAAGTGTCCTATCGAACCCTCCCAGTCGCAATGAAAAG-GAAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCGAACCCTCCCAGTCGCAATGAAAAGAAAAAACTCGATAATATGGCTC
* *
1292411 TAAGTGTCTTATCG-ACCCTCCTAGTCGCAATGAAAAGAAAAAACTCGATAATATGGCTC
1 TAAGTGTCCTATCGAACCCTCCCAGTCGCAATGAAAAGAAAAAACTCGATAATATGGCTC
1292470 TAA
1 TAA
1292473 CCAACCCTCC
Statistics
Matches: 58, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
58 22 0.38
59 36 0.62
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (60 bp):
TAAGTGTCCTATCGAACCCTCCCAGTCGCAATGAAAAGAAAAAACTCGATAATATGGCTC
Found at i:1295883 original size:30 final size:31
Alignment explanation
Indices: 1295837--1295895 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
1295827 GTTTTGATTT
1295837 TATTATTATATGAATATGTTCTATGTGAAAA
1 TATTATTATATGAATATGTTCTATGTGAAAA
* *
1295868 TATT-TTATGTGAATATGTTCTATTTGAA
1 TATTATTATATGAATATGTTCTATGTGAA
1295896 CATGGTCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.34, C:0.03, G:0.14, T:0.49
Consensus pattern (31 bp):
TATTATTATATGAATATGTTCTATGTGAAAA
Found at i:1295895 original size:15 final size:15
Alignment explanation
Indices: 1295847--1295912 Score: 78
Period size: 15 Copynumber: 4.4 Consensus size: 15
1295837 TATTATTATA
1295847 TGAATATGTTCTATG
1 TGAATATGTTCTATG
* * *
1295862 TGAAAATATTTTATG
1 TGAATATGTTCTATG
*
1295877 TGAATATGTTCTATT
1 TGAATATGTTCTATG
* *
1295892 TGAACATGGTCTATG
1 TGAATATGTTCTATG
1295907 TGAATA
1 TGAATA
1295913 AATGATACTT
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (15 bp):
TGAATATGTTCTATG
Found at i:1295907 original size:30 final size:30
Alignment explanation
Indices: 1295847--1295912 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 30
1295837 TATTATTATA
* *
1295847 TGAATATGTTCTATGTGAAAATATTTTATG
1 TGAATATGTTCTATGTGAAAATAGTCTATG
* * *
1295877 TGAATATGTTCTATTTGAACATGGTCTATG
1 TGAATATGTTCTATGTGAAAATAGTCTATG
1295907 TGAATA
1 TGAATA
1295913 AATGATACTT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (30 bp):
TGAATATGTTCTATGTGAAAATAGTCTATG
Found at i:1301495 original size:18 final size:18
Alignment explanation
Indices: 1301472--1301508 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1301462 ATATAATACA
*
1301472 TATGTCCCGAATGACCAC
1 TATGTCCCGAAGGACCAC
1301490 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
1301508 T
1 T
1301509 CCTTAAGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.32, G:0.19, T:0.22
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:1301825 original size:8 final size:7
Alignment explanation
Indices: 1301802--1301877 Score: 52
Period size: 8 Copynumber: 10.6 Consensus size: 7
1301792 TACAATGACT
1301802 TATATCA
1 TATATCA
1301809 TATATTCA
1 TATA-TCA
1301817 TTATATCA
1 -TATATCA
1301825 TAT-TCA
1 TATATCA
1301831 TATATTCA
1 TATA-TCA
*
1301839 CAT-TCA
1 TATATCA
1301845 TTATATCA
1 -TATATCA
*
1301853 CATGAT--
1 TAT-ATCA
1301859 TATATCA
1 TATATCA
1301866 TATATTCA
1 TATA-TCA
1301874 TATA
1 TATA
1301878 GACGCATAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
5 2 0.04
6 11 0.20
7 15 0.27
8 23 0.42
9 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.46
Consensus pattern (7 bp):
TATATCA
Found at i:1301829 original size:14 final size:14
Alignment explanation
Indices: 1301810--1301868 Score: 68
Period size: 14 Copynumber: 4.3 Consensus size: 14
1301800 CTTATATCAT
1301810 ATATTCATTATATC
1 ATATTCATTATATC
1301824 ATATTCA-TATATTC
1 ATATTCATTATA-TC
*
1301838 ACATTCATTATATC
1 ATATTCATTATATC
* *
1301852 ACA-TGATTATATC
1 ATATTCATTATATC
1301865 ATAT
1 ATAT
1301869 ATTCATATAG
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
13 15 0.38
14 20 0.51
15 4 0.10
ACGTcount: A:0.37, C:0.15, G:0.02, T:0.46
Consensus pattern (14 bp):
ATATTCATTATATC
Found at i:1301877 original size:28 final size:28
Alignment explanation
Indices: 1301796--1301877 Score: 73
Period size: 28 Copynumber: 2.9 Consensus size: 28
1301786 TGCTCTTACA
1301796 ATGACTTATATCATATATTCAT-TATATC
1 ATGA-TTATATCATATATTCATATATATC
*
1301824 AT-ATTCATAT-ATTCACATTCAT-TATATCAC
1 ATGATT-ATATCA-T-ATATTCATATATAT--C
1301854 ATGATTATATCATATATTCATATA
1 ATGATTATATCATATATTCATATA
1301878 GACGCATAGT
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
26 3 0.07
27 6 0.14
28 14 0.32
29 7 0.16
30 10 0.23
31 4 0.09
ACGTcount: A:0.38, C:0.15, G:0.02, T:0.45
Consensus pattern (28 bp):
ATGATTATATCATATATTCATATATATC
Found at i:1306449 original size:21 final size:21
Alignment explanation
Indices: 1306395--1306450 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
1306385 ATAAGTGTAT
* * *
1306395 CAAAGTACCACATATATGTTC
1 CAAAGGACCACATATATATCC
**
1306416 CAAAGGATTACATATATATCC
1 CAAAGGACCACATATATATCC
*
1306437 CGAAGGACCACATA
1 CAAAGGACCACATA
1306451 GAACCCTCTA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.23
Consensus pattern (21 bp):
CAAAGGACCACATATATATCC
Found at i:1310136 original size:15 final size:15
Alignment explanation
Indices: 1310083--1310167 Score: 89
Period size: 15 Copynumber: 5.7 Consensus size: 15
1310073 ATTTTATTAT
**
1310083 TATGTGAATATGTGC
1 TATGTGAATATGTTA
* * * *
1310098 TACGTGAAAATATTC
1 TATGTGAATATGTTA
1310113 TATGTGAATATGTTA
1 TATGTGAATATGTTA
*
1310128 TATGTGAATATGGTA
1 TATGTGAATATGTTA
* *
1310143 TATATGAATATGGTA
1 TATGTGAATATGTTA
1310158 TATGTGAATA
1 TATGTGAATA
1310168 AATGATACTT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.35, C:0.04, G:0.21, T:0.40
Consensus pattern (15 bp):
TATGTGAATATGTTA
Found at i:1310304 original size:23 final size:23
Alignment explanation
Indices: 1310270--1310345 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 23
1310260 TAGTCGAGGG
*
1310270 TTCTATGCGGTCATTCGGGACAA
1 TTCTATGCGGTCCTTCGGGACAA
*
1310293 TTCTATGTGGTCCTTCGAGG-CAA
1 TTCTATGCGGTCCTTCG-GGACAA
** *
1310316 TTCTACACGATCCTTCGGGACAA
1 TTCTATGCGGTCCTTCGGGACAA
*
1310339 ATCTATG
1 TTCTATG
1310346 TGGCACTTCT
Statistics
Matches: 42, Mismatches: 9, Indels: 4
0.76 0.16 0.07
Matches are distributed among these distances:
22 2 0.05
23 38 0.90
24 2 0.05
ACGTcount: A:0.22, C:0.24, G:0.22, T:0.32
Consensus pattern (23 bp):
TTCTATGCGGTCCTTCGGGACAA
Found at i:1313600 original size:42 final size:42
Alignment explanation
Indices: 1313492--1313588 Score: 176
Period size: 42 Copynumber: 2.3 Consensus size: 42
1313482 TCTTCCTACA
* *
1313492 TCTACACTTATACCTATACATTCTACAGAAACACAATTTGCT
1 TCTACACCTATACCTATACATTCTACAGAAACACAATTTGAT
1313534 TCTACACCTATACCTATACATTCTACAGAAACACAATTTGAT
1 TCTACACCTATACCTATACATTCTACAGAAACACAATTTGAT
1313576 TCTACACCTATAC
1 TCTACACCTATAC
1313589 AACCTGCTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 53 1.00
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (42 bp):
TCTACACCTATACCTATACATTCTACAGAAACACAATTTGAT
Found at i:1325464 original size:18 final size:19
Alignment explanation
Indices: 1325437--1325484 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
1325427 GATGCAATTA
* *
1325437 GTATCAATAC-TGAGGTAG
1 GTATCGATACATGAGGAAG
*
1325455 GTATCGATACTATGGGGAAG
1 GTATCGATAC-ATGAGGAAG
1325475 GTATCGATAC
1 GTATCGATAC
1325485 CATTGATTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 9 0.36
20 16 0.64
ACGTcount: A:0.31, C:0.12, G:0.29, T:0.27
Consensus pattern (19 bp):
GTATCGATACATGAGGAAG
Found at i:1325839 original size:15 final size:16
Alignment explanation
Indices: 1325819--1325854 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
1325809 AGCATCTTTT
1325819 AAAAAT-AATTTTAAG
1 AAAAATCAATTTTAAG
*
1325834 AAAAATCATTTTTAAG
1 AAAAATCAATTTTAAG
1325850 AAAAA
1 AAAAA
1325855 AATAGTCTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 6 0.32
16 13 0.68
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAAATCAATTTTAAG
Found at i:1326602 original size:28 final size:29
Alignment explanation
Indices: 1326566--1326624 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
1326556 AAATATGATT
* *
1326566 AACATAAACTTGAGG-ACTAAAATAGCAA
1 AACAAAAACTTAAGGAACTAAAATAGCAA
1326594 AACAAAAACTTAAGGAACTAAAATAGCAA
1 AACAAAAACTTAAGGAACTAAAATAGCAA
1326623 AA
1 AA
1326625 ATAGACATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.59, C:0.14, G:0.12, T:0.15
Consensus pattern (29 bp):
AACAAAAACTTAAGGAACTAAAATAGCAA
Found at i:1328050 original size:3 final size:3
Alignment explanation
Indices: 1328035--1328091 Score: 66
Period size: 3 Copynumber: 19.7 Consensus size: 3
1328025 TGTGATAGGT
*
1328035 ATA ATA TTA ATA ATA A-A AGTA ATA ATA ATA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA
*
1328079 TTA ATA A-A ATA AT
1 ATA ATA ATA ATA AT
1328092 TTTTTTGGTA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 5 0.11
3 39 0.85
4 2 0.04
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1328557 original size:55 final size:55
Alignment explanation
Indices: 1328489--1328904 Score: 563
Period size: 55 Copynumber: 7.6 Consensus size: 55
1328479 TGCGTGCAAT
1328489 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
* * * **
1328544 -TAAAGAAATTCATAATAAGTTGAAT-AATTTTCGTATGGGCATTGTGTGTGGAAAA
1 CT-AAGAAATTCATAATAAGTT-TATGAATTTCCGTATGGGCACTGTGTGTACAAAA
** *
1328599 CTATA-AAATTCATAATAAGTTTATGAATTTATGTATGGGCACTGTGTGTGCAAAA
1 CTA-AGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
*
1328654 CTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTACAAAA
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
* * * *
1328709 CTAAGAAATTCATAATAAGTTGATGAATTTTCGTATGGGCACTATATGTGA-AAAA
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGT-ACAAAA
** * *
1328764 CTATA-AAATTCATAATAAGTTTATGAATTTCTATATGGCCACTATGTGTACAAAA
1 CTA-AGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
* * * *
1328819 CTAAGAAATTCATAATAAGTTTATGAATTTCCATATAGGCATTGTGTGTGCAAAA
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
1328874 CTAAGAAATTCATAATAAGTTTATGAATTTC
1 CTAAGAAATTCATAATAAGTTTATGAATTTC
1328905 TATATTGGTA
Statistics
Matches: 323, Mismatches: 28, Indels: 20
0.87 0.08 0.05
Matches are distributed among these distances:
54 6 0.02
55 311 0.96
56 6 0.02
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (55 bp):
CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA
Found at i:1328766 original size:165 final size:165
Alignment explanation
Indices: 1328489--1328903 Score: 663
Period size: 165 Copynumber: 2.5 Consensus size: 165
1328479 TGCGTGCAAT
1328489 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAA-TAAAGAAAT
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAACT-AAGAAAT
* * * *
1328553 TCATAATAAGTTGAAT-AATTTTCGTATGGGCATTGTGTGTGGAAAACTATAAAATTCATAATAA
65 TCATAATAAGTTG-ATGAATTTTCGTATGGGCACTATATGTGAAAAACTATAAAATTCATAATAA
* * * *
1328617 GTTTATGAATTTATGTATGGGCACTGTGTGTGCAAAA
129 GTTTATGAATTTATATATGGCCACTATGTGTACAAAA
*
1328654 CTAAGAAATTCATAATAAGTTTATGAATTTTCGTATGGGCACTGTGTGTACAAAACTAAGAAATT
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAACTAAGAAATT
1328719 CATAATAAGTTGATGAATTTTCGTATGGGCACTATATGTGAAAAACTATAAAATTCATAATAAGT
66 CATAATAAGTTGATGAATTTTCGTATGGGCACTATATGTGAAAAACTATAAAATTCATAATAAGT
*
1328784 TTATGAATTTCTATATGGCCACTATGTGTACAAAA
131 TTATGAATTTATATATGGCCACTATGTGTACAAAA
* * * *
1328819 CTAAGAAATTCATAATAAGTTTATGAATTTCCATATAGGCATTGTGTGTGCAAAACTAAGAAATT
1 CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAACTAAGAAATT
*
1328884 CATAATAAGTTTATGAATTT
66 CATAATAAGTTGATGAATTT
1328904 CTATATTGGT
Statistics
Matches: 232, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
164 2 0.01
165 229 0.99
166 1 0.00
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (165 bp):
CTAAGAAATTCATAATAAGTTTATGAATTTCCGTATGGGCACTGTGTGTACAAAACTAAGAAATT
CATAATAAGTTGATGAATTTTCGTATGGGCACTATATGTGAAAAACTATAAAATTCATAATAAGT
TTATGAATTTATATATGGCCACTATGTGTACAAAA
Found at i:1331418 original size:2 final size:2
Alignment explanation
Indices: 1331406--1331447 Score: 75
Period size: 2 Copynumber: 20.5 Consensus size: 2
1331396 ATATTTATGT
1331406 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1331448 TACATCATTA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 37 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1337671 original size:55 final size:55
Alignment explanation
Indices: 1337597--1337869 Score: 386
Period size: 55 Copynumber: 5.0 Consensus size: 55
1337587 ATTACTTAAT
* * *
1337597 GGCACTATGCGTGC-AAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATG
1 GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
* * * * *
1337651 GGCACTGTGTGTGTAAAACTAAGAAATTCATAATAAGTTTATAAATTTTCATATG
1 GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
* * * * *
1337706 GGTACTGTATGTGTAAAACTAAGAAATTCATAATAAATTTATGAATTTCTGTATA
1 GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
1337761 GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
1 GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
* * * *
1337816 GACACTGTGTGTACAAAACTAAAAAATTCATAATAAGTTTATGAATTTTCGTAT
1 GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1337870 TGACAGTGGG
Statistics
Matches: 195, Mismatches: 23, Indels: 1
0.89 0.11 0.00
Matches are distributed among these distances:
54 11 0.06
55 184 0.94
ACGTcount: A:0.38, C:0.11, G:0.16, T:0.35
Consensus pattern (55 bp):
GGCACTGTGTGTGCAAAACTAAGAAATTCATAATAAGTTTATGAATTTCCGTATA
Found at i:1342657 original size:26 final size:26
Alignment explanation
Indices: 1342627--1342682 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
1342617 ATGAGAATAT
1342627 AAAGGAGTTGAGGAATTGATAATAAG
1 AAAGGAGTTGAGGAATTGATAATAAG
1342653 AAAGGAGTTGAGGAATTGATAATAAG
1 AAAGGAGTTGAGGAATTGATAATAAG
1342679 AAAG
1 AAAG
1342683 AATTTGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.21
Consensus pattern (26 bp):
AAAGGAGTTGAGGAATTGATAATAAG
Found at i:1347695 original size:30 final size:29
Alignment explanation
Indices: 1347603--1347719 Score: 101
Period size: 30 Copynumber: 3.9 Consensus size: 29
1347593 TCAAAGGACC
* *
1347603 AAAATAGTACAAATAGGAATTTAAAGGACT
1 AAAATAGTAAAAATAGAAATTTAAAGG-CT
* * * * * *
1347633 AATATGGTCAAAACATAAACTTAAATGGCT
1 AAAATAGTAAAAATAGAAATTTAAA-GGCT
*
1347663 AAAATAGTAAAAATAGAAATTTAAGGGTCT
1 AAAATAGTAAAAATAGAAATTTAAAGG-CT
*
1347693 AAAATA-AATAAAATAGAAATTTAAAGG
1 AAAATAGTA-AAAATAGAAATTTAAAGG
1347720 GCTCAAAGAA
Statistics
Matches: 67, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
29 3 0.04
30 62 0.93
31 2 0.03
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.25
Consensus pattern (29 bp):
AAAATAGTAAAAATAGAAATTTAAAGGCT
Found at i:1349537 original size:40 final size:41
Alignment explanation
Indices: 1349417--1349539 Score: 110
Period size: 43 Copynumber: 3.0 Consensus size: 41
1349407 TAAGGTTTGT
*
1349417 TGGGGACGACAC-TGCTCATACATGATGAAGAGTTCTGGTCG
1 TGGGGATGACACGT-CTCATACATGATGAAGAGTTCTGGTCG
* * * **
1349458 TTTAAGGG-TGACACGGT-TCCTACATGATGAGGAAATCTGGTCG
1 --T-GGGGATGACAC-GTCTCATACATGATGAAGAGTTCTGGTCG
*
1349501 -GGGGATGACACGTCTCATACGTGATGAAGAGTTCTGGTC
1 TGGGGATGACACGTCTCATACATGATGAAGAGTTCTGGTC
1349540 ATCTTTAGGA
Statistics
Matches: 63, Mismatches: 12, Indels: 13
0.72 0.14 0.15
Matches are distributed among these distances:
39 5 0.08
40 26 0.41
43 28 0.44
44 3 0.05
45 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (41 bp):
TGGGGATGACACGTCTCATACATGATGAAGAGTTCTGGTCG
Found at i:1349681 original size:133 final size:134
Alignment explanation
Indices: 1349463--1349784 Score: 466
Period size: 133 Copynumber: 2.4 Consensus size: 134
1349453 GGTCGTTTAA
* * * * *
1349463 GGGTGACACGGTTCCTACATGATGAGGAAATCTGGTCGGGGGATGACACGTCTCATACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACGTGATGA
* * * *
1349528 AGAGTTCTGGTCATCTTTAGGAAGGGTGATAACTCGGTTCCTACGCGATGAGGACGGCTAGATAT
66 AGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACACGATGAGGACGGCTAGATAT
1349593 CTAG
131 CTAG
*
1349597 GGGTGACACGGCTCCTACGCGATGAGGAGATCTGGTC-GGGGATGACACGACTCATACGTGATGA
1 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACGTGATGA
* * * * *
1349661 AGAGTTTTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACATGATGAGGACGTCTGGTTAT
66 AGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACACGATGAGGACGGCTAGATAT
1349726 CTAG
131 CTAG
* * * *
1349730 GGGTGACACGACTCCTACGTGATGAAGAGATCTGGTCAGGAGATGACACAACTCA
1 GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCA
1349785 CACATTACGT
Statistics
Matches: 168, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
133 120 0.71
134 48 0.29
ACGTcount: A:0.25, C:0.19, G:0.32, T:0.24
Consensus pattern (134 bp):
GGGTGACACGGCTCCTACGTGATGAGGAGATCTGGTCAGGGGATGACACGACTCATACGTGATGA
AGAGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACACGATGAGGACGGCTAGATAT
CTAG
Found at i:1349797 original size:45 final size:45
Alignment explanation
Indices: 1349745--1349834 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
1349735 ACACGACTCC
1349745 TACGTGATGAAGAGATCTGGTCAGGAGATGACACAACTCACACAT
1 TACGTGATGAAGAGATCTGGTCAGGAGATGACACAACTCACACAT
1349790 TACGTGATGAAGAGATCTGGTCAGGAGATGACACAACTCACACAT
1 TACGTGATGAAGAGATCTGGTCAGGAGATGACACAACTCACACAT
1349835 GATGAAGAGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.36, C:0.20, G:0.24, T:0.20
Consensus pattern (45 bp):
TACGTGATGAAGAGATCTGGTCAGGAGATGACACAACTCACACAT
Found at i:1349838 original size:40 final size:42
Alignment explanation
Indices: 1349744--1349848 Score: 151
Period size: 45 Copynumber: 2.5 Consensus size: 42
1349734 GACACGACTC
1349744 CTACGTGATGAAGAGATCTGGTCAGGAGATGACACAACTCACA
1 CTAC-TGATGAAGAGATCTGGTCAGGAGATGACACAACTCACA
1349787 CATTACGTGATGAAGAGATCTGGTCAGGAGATGACACAACTCACA
1 C--TAC-TGATGAAGAGATCTGGTCAGGAGATGACACAACTCACA
*
1349832 C-A-TGATGAAGAGTTCTG
1 CTACTGATGAAGAGATCTG
1349849 ACCATCTTTA
Statistics
Matches: 59, Mismatches: 1, Indels: 7
0.88 0.01 0.10
Matches are distributed among these distances:
40 14 0.24
42 1 0.02
43 1 0.02
45 43 0.73
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (42 bp):
CTACTGATGAAGAGATCTGGTCAGGAGATGACACAACTCACA
Found at i:1350171 original size:91 final size:89
Alignment explanation
Indices: 1350069--1350295 Score: 282
Period size: 91 Copynumber: 2.5 Consensus size: 89
1350059 GTTAAGAGGC
*
1350069 ACAATCTCAAAGA-TTTTTCAAAAGGAACAGACTCAAAGATTTTTCTCAAGAAAAACTGTCTCAA
1 ACAAACTCAAAGATTTTTTCAAAAGGAACAGACTCAAAGATTTTT-TCAAG--AAACTGTCTCAA
* *
1350133 GAGAGACAAAACTTTGTTTCAAAAGAA
63 GAGAAACAAAACTTTGGTTCAAAAGAA
* * *
1350160 ACAAACTCAAAGATTTTGGTTTCAAAA-GAA-ATGACTCAAAGATTTTTTCACGAAATTGTCTTA
1 ACAAACTCAAAGA-TTT--TTTCAAAAGGAACA-GACTCAAAGATTTTTTCAAGAAACTGTCTCA
1350223 AGAGAAACAAAACTTTGGTTCAAAAGAA
62 AGAGAAACAAAACTTTGGTTCAAAAGAA
* *
1350251 ACAGACTCAAAGAATTTTTTCAAAAGAAACA-ACTCAAAGATTTTT
1 ACAAACTCAAAG-ATTTTTTCAAAAGGAACAGACTCAAAGATTTTT
1350296 ATTTCAAAAG
Statistics
Matches: 120, Mismatches: 8, Indels: 18
0.82 0.05 0.12
Matches are distributed among these distances:
89 22 0.18
90 2 0.02
91 62 0.52
92 1 0.01
93 7 0.06
94 18 0.15
95 8 0.07
ACGTcount: A:0.45, C:0.15, G:0.13, T:0.27
Consensus pattern (89 bp):
ACAAACTCAAAGATTTTTTCAAAAGGAACAGACTCAAAGATTTTTTCAAGAAACTGTCTCAAGAG
AAACAAAACTTTGGTTCAAAAGAA
Found at i:1350197 original size:29 final size:30
Alignment explanation
Indices: 1350148--1350350 Score: 126
Period size: 29 Copynumber: 6.9 Consensus size: 30
1350138 ACAAAACTTT
1350148 GTTTCAAAAGAAACAAACTCAAAGATTTTG
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
**
1350178 GTTTCAAAAGAAA-TGACTCAAAGA-TTT-
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
* *
1350205 -TTTCACGAAATTGTCTTAAGAGAAA--CAAA-ACTTTG
1 GTTTCA--AAA--G----AA-ACAAACTCAAAGATTTTG
* *
1350240 G-TTCAAAAGAAACAGACTCAAAGAATTT-
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
*
1350268 -TTTCAAAAGAAAC-AACTCAAAGATTTTT
1 GTTTCAAAAGAAACAAACTCAAAGATTTTG
* *
1350296 ATTTCAAAAGAAAC-AACTCATAGACTTTT-
1 GTTTCAAAAGAAACAAACTCAAAGA-TTTTG
* *
1350325 GTTTCAAGAGAAACAAACTTAAAGAT
1 GTTTCAAAAGAAACAAACTCAAAGAT
1350351 AGGTTTTGTT
Statistics
Matches: 138, Mismatches: 14, Indels: 43
0.71 0.07 0.22
Matches are distributed among these distances:
26 8 0.06
27 14 0.10
28 22 0.16
29 48 0.35
30 26 0.19
31 1 0.01
33 4 0.03
34 9 0.07
35 5 0.04
36 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.28
Consensus pattern (30 bp):
GTTTCAAAAGAAACAAACTCAAAGATTTTG
Found at i:1350273 original size:28 final size:29
Alignment explanation
Indices: 1350241--1350349 Score: 132
Period size: 29 Copynumber: 3.8 Consensus size: 29
1350231 AAAACTTTGG
*
1350241 TTCAAAAGAAACAGACTCAAAGA-ATTT-T
1 TTCAAAAGAAACA-ACTCAAAGACTTTTAT
*
1350269 TTCAAAAGAAACAACTCAAAGATTTTTAT
1 TTCAAAAGAAACAACTCAAAGACTTTTAT
* *
1350298 TTCAAAAGAAACAACTCATAGACTTTTGT
1 TTCAAAAGAAACAACTCAAAGACTTTTAT
* *
1350327 TTCAAGAGAAACAAACTTAAAGA
1 TTCAAAAGAAAC-AACTCAAAGA
1350350 TAGGTTTTGT
Statistics
Matches: 71, Mismatches: 7, Indels: 4
0.87 0.09 0.05
Matches are distributed among these distances:
27 9 0.13
28 16 0.23
29 38 0.54
30 8 0.11
ACGTcount: A:0.49, C:0.15, G:0.10, T:0.27
Consensus pattern (29 bp):
TTCAAAAGAAACAACTCAAAGACTTTTAT
Found at i:1350382 original size:33 final size:33
Alignment explanation
Indices: 1350321--1350400 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
1350311 ACTCATAGAC
**
1350321 TTTTGTTTCAAGAGAAACAAACTTAAAGATAGG
1 TTTTGTTTCAAGAGAAACAAACACAAAGATAGG
* *
1350354 TTTTGTTTCAAGGGAAACAATCACAAAGATA--
1 TTTTGTTTCAAGAGAAACAAACACAAAGATAGG
*
1350385 -TTTGTTTTAAGAGAAA
1 TTTTGTTTCAAGAGAAA
1350401 TTGTCTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
30 14 0.34
33 27 0.66
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (33 bp):
TTTTGTTTCAAGAGAAACAAACACAAAGATAGG
Found at i:1350592 original size:37 final size:37
Alignment explanation
Indices: 1350551--1350622 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
1350541 AAGAGACAAA
*
1350551 ATTTTGTTATCA-AAGAAACATACTCAAAGATTTTTTC
1 ATTTTGTT-TCAGAAGAAACAGACTCAAAGATTTTTTC
* * *
1350588 ATTTTGTTTTAGATGAAACAGACTCAAATATTTTT
1 ATTTTGTTTCAGAAGAAACAGACTCAAAGATTTTT
1350623 CAATAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 2 0.07
37 28 0.93
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (37 bp):
ATTTTGTTTCAGAAGAAACAGACTCAAAGATTTTTTC
Found at i:1350688 original size:31 final size:31
Alignment explanation
Indices: 1350653--1350712 Score: 95
Period size: 31 Copynumber: 1.9 Consensus size: 31
1350643 GAGACAAAGT
1350653 TTTGTTTC-AAAAGAAATAGACTCAAAGATCC
1 TTTGTTTCAAAAAGAAA-AGACTCAAAGATCC
*
1350684 TTTGTTTCAAAAAGAAACGACTCAAAGAT
1 TTTGTTTCAAAAAGAAAAGACTCAAAGAT
1350713 AATGTTTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 19 0.70
32 8 0.30
ACGTcount: A:0.43, C:0.15, G:0.13, T:0.28
Consensus pattern (31 bp):
TTTGTTTCAAAAAGAAAAGACTCAAAGATCC
Found at i:1350974 original size:108 final size:104
Alignment explanation
Indices: 1350827--1351135 Score: 381
Period size: 108 Copynumber: 2.9 Consensus size: 104
1350817 TGAGAAAACG
1350827 ATCTCAAGTGAGATTAACTTTGTTTAATGTGAAAACAAATTCAAATTTTGTATCTCAAAGGAAAA
1 ATCTCAAGTGAGATTAACTTTGTTTAATGTG-AAACAAATTCAAATTTTGTATCTCAAAGGAAAA
* *
1350892 ATGTCTCAAACGAGACGAAATTTATTTTGAAAAAAAAATAACA
65 ATGTCTCAAGCGAGACGAAATTTGTTTTGAAAAAAAAAT---A
* * * *
1350935 ATTTCAAGTGAGATTAATTTTTGTTTCAA-GTGAATCAAATTCGAAA-TTTGTATATCAAAGGAA
1 ATCTCAAGTGAGATTAA-CTTTGTTT-AATGTGAAACAAATTC-AAATTTTGTATCTCAAAGG-A
* * * * * *
1350998 AAAATGTCTCAAGCAAGACGAAGTTTGTTTT-AAGAGAAAGTG
62 AAAATGTCTCAAGCGAGACGAAATTTGTTTTGAAAAAAAAATA
* *
1351040 ATCTCAAATGAGATCAACTTTGTTTAATGTGAAACAAATTCAAATTTTGTATCTCAAAGGAAAAA
1 ATCTCAAGTGAGATTAACTTTGTTTAATGTGAAACAAATTCAAATTTTGTATCTCAAAGGAAAAA
* *
1351105 TGTCTCAAGTGAGATGAAATTTGTTTTGAAA
66 TGTCTCAAGCGAGACGAAATTTGTTTTGAAA
1351136 GAAATTGTCT
Statistics
Matches: 171, Mismatches: 23, Indels: 18
0.81 0.11 0.08
Matches are distributed among these distances:
103 33 0.19
104 35 0.20
105 14 0.08
108 46 0.27
109 41 0.24
110 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (104 bp):
ATCTCAAGTGAGATTAACTTTGTTTAATGTGAAACAAATTCAAATTTTGTATCTCAAAGGAAAAA
TGTCTCAAGCGAGACGAAATTTGTTTTGAAAAAAAAATA
Found at i:1351170 original size:104 final size:103
Alignment explanation
Indices: 1350828--1351170 Score: 306
Period size: 103 Copynumber: 3.3 Consensus size: 103
1350818 GAGAAAACGA
* *
1350828 TCTCAAGTGAGATTAACTTTG--TTTAATGTGAAAACAAATTCAAATTTTGTATCTCAAAGGAAA
1 TCTCAAGTGAGA-CAAATTTGTTTTTAATGTG-AAACAAATTCAAATTTTGTATCTCAAAGGAAA
* * * **
1350891 AATGTCTCAAACGAGACGAAATTTATTTTGAAAAAAAAATAACAA
64 AATGTCTCAAGCGAGACGAAATTTGTTTTG--AAAGAAAT---TG
* ** * *
1350936 TTTCAAGTGAGATTAATTT-TTGTTTCAA-GTGAATCAAATTCGAAA-TTTGTATATCAAAGGAA
1 TCTCAAGTGAGACAAATTTGTT-TTT-AATGTGAAACAAATTC-AAATTTTGTATCTCAAAGG-A
* * *
1350998 AAAATGTCTCAAGCAAGACGAAGTTTGTTTT-AAGAGAAAGTG
62 AAAATGTCTCAAGCGAGACGAAATTTGTTTTGAA-AGAAATTG
* *
1351040 ATCTCAAATGAGATCAACTTTG--TTTAATGTGAAACAAATTCAAATTTTGTATCTCAAAGGAAA
1 -TCTCAAGTGAGA-CAAATTTGTTTTTAATGTGAAACAAATTCAAATTTTGTATCTCAAAGGAAA
* *
1351103 AATGTCTCAAGTGAGATGAAATTTGTTTTGAAAGAAATTG
64 AATGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAATTG
**
1351143 TCTCAAGCAAGACAAAATTTGTTTTTAA
1 TCTCAAGTGAGAC-AAATTTGTTTTTAA
1351171 AATTCTCAAA
Statistics
Matches: 190, Mismatches: 29, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
101 1 0.01
102 15 0.08
103 40 0.21
104 36 0.19
105 10 0.05
106 6 0.03
107 9 0.05
108 34 0.18
109 37 0.19
110 2 0.01
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (103 bp):
TCTCAAGTGAGACAAATTTGTTTTTAATGTGAAACAAATTCAAATTTTGTATCTCAAAGGAAAAA
TGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAATTG
Found at i:1351550 original size:16 final size:16
Alignment explanation
Indices: 1351529--1351568 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1351519 CTCATGTAAT
*
1351529 ATGTATGTATGT-GTTG
1 ATGTATGTAT-TCATTG
1351545 ATGTATGTATTCATTG
1 ATGTATGTATTCATTG
1351561 ATGTATGT
1 ATGTATGT
1351569 TTTCTCAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.23, C:0.03, G:0.25, T:0.50
Consensus pattern (16 bp):
ATGTATGTATTCATTG
Found at i:1357244 original size:30 final size:29
Alignment explanation
Indices: 1357152--1357268 Score: 101
Period size: 30 Copynumber: 3.9 Consensus size: 29
1357142 TCAAATGACC
* *
1357152 AAAATAGTACAAATAGGAATTTAAAGGACT
1 AAAATAGTAAAAATAGAAATTTAAAGG-CT
* * * * * *
1357182 AATATGGTCAAAACATAAACTTAAATGGCT
1 AAAATAGTAAAAATAGAAATTTAAA-GGCT
*
1357212 AAAATAGTAAAAATAGAAATTTAAGGGTCT
1 AAAATAGTAAAAATAGAAATTTAAAGG-CT
*
1357242 AAAATA-AATAAAATAGAAATTTAAAGG
1 AAAATAGTA-AAAATAGAAATTTAAAGG
1357269 GCTCAAAGCA
Statistics
Matches: 67, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
29 3 0.04
30 62 0.93
31 2 0.03
ACGTcount: A:0.55, C:0.06, G:0.15, T:0.25
Consensus pattern (29 bp):
AAAATAGTAAAAATAGAAATTTAAAGGCT
Found at i:1358962 original size:3 final size:3
Alignment explanation
Indices: 1358954--1358985 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1358944 TAAATTTTAA
1358954 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1358986 ATTAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1364909 original size:8 final size:9
Alignment explanation
Indices: 1364885--1364913 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1364875 AAAAATATAT
1364885 TAATTTTTA
1 TAATTTTTA
1364894 TAATTTTTA
1 TAATTTTTA
1364903 TAA-TTTTA
1 TAATTTTTA
1364911 TAA
1 TAA
1364914 ATAAGATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TAATTTTTA
Found at i:1366830 original size:3 final size:3
Alignment explanation
Indices: 1366822--1366907 Score: 111
Period size: 3 Copynumber: 28.0 Consensus size: 3
1366812 AATATTTATT
*
1366822 TAA TAA TAA TAA TAAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
1366868 TGTA TAA TAA TAA TAA CAA TAA TAA -AA TAAA TAA TAA TAA
1 T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA
1366908 AAGCAAACTG
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 2 0.03
3 63 0.86
4 8 0.11
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:1366865 original size:34 final size:34
Alignment explanation
Indices: 1366822--1366904 Score: 114
Period size: 34 Copynumber: 2.4 Consensus size: 34
1366812 AATATTTATT
*
1366822 TAATAATAATAATAAATAACAATAATAATAATAA
1 TAATAATAATAATAAATAACAATAATAACAATAA
** *
1366856 TAATAATAATAATGTATAATAATAATAACAATAA
1 TAATAATAATAATAAATAACAATAATAACAATAA
1366890 TAA-AATAAATAATAA
1 TAATAAT-AATAATAA
1366905 TAAAAGCAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
33 3 0.07
34 39 0.93
ACGTcount: A:0.66, C:0.02, G:0.01, T:0.30
Consensus pattern (34 bp):
TAATAATAATAATAAATAACAATAATAACAATAA
Found at i:1367134 original size:45 final size:45
Alignment explanation
Indices: 1367026--1367508 Score: 907
Period size: 45 Copynumber: 10.8 Consensus size: 45
1367016 GATGAAAATG
*
1367026 TTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TT
1367072 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1367117 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1367162 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1367207 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1367252 TTG-AAA-ATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1367295 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
* *
1367340 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCCAAAGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1367385 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1367430 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
*
1367475 TTGAAAACATCATGCACTAAAGGGCTTACAGATG
1 TTGAAAACATCATGCACTGAAGGGCTTACAGATG
1367509 TGGGAAATAG
Statistics
Matches: 429, Mismatches: 6, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
43 40 0.09
44 6 0.01
45 341 0.79
46 42 0.10
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (45 bp):
TTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTT
Found at i:1367423 original size:223 final size:226
Alignment explanation
Indices: 1367026--1367508 Score: 918
Period size: 223 Copynumber: 2.2 Consensus size: 226
1367016 GATGAAAATG
1367026 TTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTG
1 TTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTG
*
1367091 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCG
66 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCC
*
1367156 AAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATG
131 AAAGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATG
1367221 CACTGAAGGGCTTACAGATGACCCGAAGGTT
196 CACTGAAGGGCTTACAGATGACCCGAAGGTT
*
1367252 TTG-AAA-ATCATGCACTGAAGGGCTTACAGATGACCCGAAGG-TTTTGAAAACATCATGCACTG
1 TTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTG
1367314 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCC
66 AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCC
1367379 AAAGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATG
131 AAAGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATG
1367444 CACTGAAGGGCTTACAGATGACCCGAAGGTT
196 CACTGAAGGGCTTACAGATGACCCGAAGGTT
1367475 TTGAAAACATCATGCACTAAAGGGCTTACAGATG
1 TTGAAAACATCATGCACTAAAGGGCTTACAGATG
1367509 TGGGAAATAG
Statistics
Matches: 251, Mismatches: 4, Indels: 5
0.97 0.02 0.02
Matches are distributed among these distances:
223 183 0.73
224 37 0.15
225 28 0.11
226 3 0.01
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.23
Consensus pattern (226 bp):
TTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCATGCACTG
AAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCC
AAAGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCATG
CACTGAAGGGCTTACAGATGACCCGAAGGTT
Found at i:1368181 original size:22 final size:22
Alignment explanation
Indices: 1368156--1368230 Score: 123
Period size: 22 Copynumber: 3.4 Consensus size: 22
1368146 AATAAAGCTT
*
1368156 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
* *
1368178 TCATCTTTGGAGAGAGAATATA
1 TCATCTTTGAAGAGAGAATCTA
1368200 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
1368222 TCATCTTTG
1 TCATCTTTG
1368231 GAGAATGTAG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.35, C:0.13, G:0.17, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:1368741 original size:54 final size:53
Alignment explanation
Indices: 1368593--1368747 Score: 166
Period size: 54 Copynumber: 2.9 Consensus size: 53
1368583 ATAATCACTG
* * * * * * *
1368593 GTTCGTAAAACATGTGACAATACATTCATCCTTTCTCGTGGCTTCTACCCGGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCTTTTCT-GTAGCTTCTGCCCAGAT
* * * **
1368647 TTTCGTAAAGCTTTTGATAACACATTCATCTTTTCTTGTAGCTTCTGGTCAGAT
1 GTTCGTAAAGCATTTGACAACACATTCATCTTTTC-TGTAGCTTCTGCCCAGAT
*
1368701 GTTCGTAAAGCATTTGACAACACATTCATCATTTTCTGTAGTTTCTG
1 GTTCGTAAAGCATTTGACAACACATTCATC-TTTTCTGTAGCTTCTG
1368748 TATAGATTTT
Statistics
Matches: 83, Mismatches: 16, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
54 77 0.93
55 6 0.07
ACGTcount: A:0.24, C:0.21, G:0.15, T:0.39
Consensus pattern (53 bp):
GTTCGTAAAGCATTTGACAACACATTCATCTTTTCTGTAGCTTCTGCCCAGAT
Found at i:1377959 original size:8 final size:9
Alignment explanation
Indices: 1377935--1377963 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
1377925 AAAAATATAT
1377935 TAATTTTTA
1 TAATTTTTA
1377944 TAATTTTTA
1 TAATTTTTA
1377953 TAA-TTTTA
1 TAATTTTTA
1377961 TAA
1 TAA
1377964 ATAAGATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TAATTTTTA
Found at i:1379834 original size:3 final size:3
Alignment explanation
Indices: 1379826--1379864 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
1379816 AATATTTATT
1379826 TAA TAA TAA TAA TAA TAA -AA TAAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
1379865 AAGCAAACTG
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:1379852 original size:21 final size:21
Alignment explanation
Indices: 1379827--1379866 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
1379817 ATATTTATTT
1379827 AATAATAATAATAATAAAATA
1 AATAATAATAATAATAAAATA
1379848 AATAATAATAATAATAAAA
1 AATAATAATAATAATAAAA
1379867 GCAAACTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
AATAATAATAATAATAAAATA
Found at i:1383469 original size:25 final size:22
Alignment explanation
Indices: 1383427--1383472 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 22
1383417 TTTCATTGCC
1383427 TAAATCCCTAAACTTAAATCCA
1 TAAATCCCTAAACTTAAATCCA
1383449 TAAATCTCCATAAACCTTAAATCC
1 TAAATC-CC-TAAA-CTTAAATCC
1383473 TATGTTCCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 6 0.29
23 2 0.10
24 4 0.19
25 9 0.43
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.28
Consensus pattern (22 bp):
TAAATCCCTAAACTTAAATCCA
Found at i:1393353 original size:6 final size:6
Alignment explanation
Indices: 1393344--1393392 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
1393334 CACATATGCC
** * * *
1393344 ATCATT ATCAAC ATCAAT ATAATT ATCATG ATCATT ATCATT ATCATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
1393392 A
1 A
1393393 ACCCATTTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (6 bp):
ATCATT
Found at i:1393600 original size:30 final size:29
Alignment explanation
Indices: 1393567--1393661 Score: 109
Period size: 30 Copynumber: 3.2 Consensus size: 29
1393557 ATATACTAGT
* *
1393567 CCATGTATACTTTTGATATCTTTTATAAGT
1 CCATGTATA-TTCTGATATCTTTTATAAGC
* *
1393597 CCATGTATATTACTAATATCTTTTATAAAC
1 CCATGTATATT-CTGATATCTTTTATAAGC
* *
1393627 CCATGTACAGTACTGATATCTTTTATAAGC
1 CCATGTATA-TTCTGATATCTTTTATAAGC
1393657 CCATG
1 CCATG
1393662 AACATTACTG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
29 2 0.04
30 52 0.95
31 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.09, T:0.42
Consensus pattern (29 bp):
CCATGTATATTCTGATATCTTTTATAAGC
Found at i:1393671 original size:30 final size:30
Alignment explanation
Indices: 1393580--1393672 Score: 132
Period size: 30 Copynumber: 3.1 Consensus size: 30
1393570 TGTATACTTT
* *
1393580 TGATATCTTTTATAAGTCCATGTATATTAC
1 TGATATCTTTTATAAGCCCATGTACATTAC
* * *
1393610 TAATATCTTTTATAAACCCATGTACAGTAC
1 TGATATCTTTTATAAGCCCATGTACATTAC
*
1393640 TGATATCTTTTATAAGCCCATGAACATTAC
1 TGATATCTTTTATAAGCCCATGTACATTAC
1393670 TGA
1 TGA
1393673 GAACTCAATG
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (30 bp):
TGATATCTTTTATAAGCCCATGTACATTAC
Found at i:1393793 original size:38 final size:37
Alignment explanation
Indices: 1393741--1393906 Score: 189
Period size: 38 Copynumber: 4.5 Consensus size: 37
1393731 GTATAAATTA
* *
1393741 TGTCCCGAATGACCTATCATCCGGAAGGATATCATCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGA-ATCATCTG
* * *
1393779 TGTCCCAAAGGACCTATCATCCCGAATGATATCATATG
1 TGTCCCGAAGGACCTATCATCCCGAAGGA-ATCATCTG
*
1393817 TGTCCCGAAGGACCTATCATCTCGAAGGAAGTC--C-G
1 TGTCCCGAAGGACCTATCATCCCGAAGGAA-TCATCTG
* *
1393852 TCTCCCGAAGGACCTATCATCCCGAAGG-AT-GTCTG
1 TGTCCCGAAGGACCTATCATCCCGAAGGAATCATCTG
*
1393887 TGTCCCGAAGGACCTGTCAT
1 TGTCCCGAAGGACCTATCAT
1393907 ATGTCCCGAA
Statistics
Matches: 111, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
33 1 0.01
34 2 0.02
35 46 0.41
37 1 0.01
38 61 0.55
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (37 bp):
TGTCCCGAAGGACCTATCATCCCGAAGGAATCATCTG
Found at i:1393844 original size:17 final size:17
Alignment explanation
Indices: 1393819--1393880 Score: 65
Period size: 17 Copynumber: 3.6 Consensus size: 17
1393809 ATCATATGTG
1393819 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
* *
1393836 TCTCGAAGGAAGTCC-GTC-
1 TCCCGAAGG-A--CCTATCA
1393854 TCCCGAAGGACCTATCA
1 TCCCGAAGGACCTATCA
1393871 TCCCGAAGGA
1 TCCCGAAGGA
1393881 TGTCTGTGTC
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
15 2 0.06
16 2 0.06
17 19 0.53
18 9 0.25
19 2 0.06
20 2 0.06
ACGTcount: A:0.27, C:0.32, G:0.23, T:0.18
Consensus pattern (17 bp):
TCCCGAAGGACCTATCA
Found at i:1393913 original size:21 final size:18
Alignment explanation
Indices: 1393871--1393916 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
1393861 GGACCTATCA
*
1393871 TCCCGAAGGATGTCTGTG
1 TCCCGAAGGATGTCTATG
1393889 TCCCGAAGGACCTGTCATATG
1 TCCCGAAGGA--TGTC-TATG
1393910 TCCCGAA
1 TCCCGAA
1393917 TGACATATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 10 0.42
20 4 0.17
21 10 0.42
ACGTcount: A:0.22, C:0.28, G:0.26, T:0.24
Consensus pattern (18 bp):
TCCCGAAGGATGTCTATG
Found at i:1396102 original size:30 final size:31
Alignment explanation
Indices: 1396068--1396133 Score: 89
Period size: 31 Copynumber: 2.2 Consensus size: 31
1396058 TTTAGTCCCT
* * *
1396068 AAACTTTTCAAAGT-TTATACTTTGGTCACC
1 AAACTTTACAAAATCTTATAATTTGGTCACC
*
1396098 AAACTTTACAAAATCTTATAATTTGGTCACT
1 AAACTTTACAAAATCTTATAATTTGGTCACC
1396129 AAACT
1 AAACT
1396134 AAATCCATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.36, C:0.18, G:0.08, T:0.38
Consensus pattern (31 bp):
AAACTTTACAAAATCTTATAATTTGGTCACC
Found at i:1396984 original size:9 final size:9
Alignment explanation
Indices: 1396965--1397068 Score: 83
Period size: 9 Copynumber: 11.9 Consensus size: 9
1396955 CATCTCTCAT
1396965 TTTTTTATTC
1 TTTTTT-TTC
1396975 TTTTTTTTC
1 TTTTTTTTC
1396984 ---TTTTTC
1 TTTTTTTTC
*
1396990 TATTTTTTC
1 TTTTTTTTC
*
1396999 TTTCTTTTC
1 TTTTTTTTC
*
1397008 TTTCTTTTC
1 TTTTTTTTC
1397017 --TTTTTTC
1 TTTTTTTTC
*
1397024 TATTTTTTC
1 TTTTTTTTC
* *
1397033 CTTCTTTTC
1 TTTTTTTTC
*
1397042 TTTCTTTTC
1 TTTTTTTTC
*
1397051 TTTTTCTTC
1 TTTTTTTTC
1397060 TTCTTTTTT
1 TT-TTTTTT
1397069 TAGCTCTTAT
Statistics
Matches: 78, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
6 6 0.08
7 6 0.08
9 55 0.71
10 11 0.14
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1397006 original size:25 final size:23
Alignment explanation
Indices: 1396966--1397069 Score: 95
Period size: 25 Copynumber: 4.3 Consensus size: 23
1396956 ATCTCTCATT
*
1396966 TTTTTATTCTTTTTTTTCTTTTTC
1 TTTTT-TTCTTTTTTTTCTTCTTC
* *
1396990 TATTTTTTCTTTCTTTTCTTTCTTT
1 T-TTTTTTCTTTTTTTTC-TTCTTC
*
1397015 TCTTTTTTCTATTTTTTC--CTTC
1 T-TTTTTTCTTTTTTTTCTTCTTC
1397037 TTTTCTTTCTTTTCTTTTTCTTCTTC
1 TTTT-TTTC-TTT-TTTTTCTTCTTC
1397063 TTTTTTT
1 TTTTTTT
1397070 AGCTCTTATG
Statistics
Matches: 65, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.05
22 8 0.12
23 2 0.03
24 18 0.28
25 26 0.40
26 8 0.12
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (23 bp):
TTTTTTTCTTTTTTTTCTTCTTC
Found at i:1397010 original size:33 final size:33
Alignment explanation
Indices: 1396972--1397057 Score: 145
Period size: 34 Copynumber: 2.6 Consensus size: 33
1396962 CATTTTTTTA
* *
1396972 TTCTTTTTTTTCTTTTTCTATTTTTTCTTTCTT
1 TTCTTTCTTTTCTTTTTCTATTTTTTCCTTCTT
1397005 TTCTTTCTTTTCTTTTTTCTATTTTTTCCTTCTT
1 TTCTTTCTTTTC-TTTTTCTATTTTTTCCTTCTT
1397039 TTCTTTCTTTTCTTTTTCT
1 TTCTTTCTTTTCTTTTTCT
1397058 TCTTCTTTTT
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
33 18 0.36
34 32 0.64
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (33 bp):
TTCTTTCTTTTCTTTTTCTATTTTTTCCTTCTT
Found at i:1399795 original size:6 final size:6
Alignment explanation
Indices: 1399786--1399834 Score: 53
Period size: 6 Copynumber: 8.2 Consensus size: 6
1399776 CACATATGCC
** * * *
1399786 ATCATT ATCAAC ATCAAT ATCATT ATCATG ATCTTT ATCATT ATCATT
1 ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT ATCATT
1399834 A
1 A
1399835 ACCCATTTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.02, T:0.43
Consensus pattern (6 bp):
ATCATT
Found at i:1400045 original size:30 final size:29
Alignment explanation
Indices: 1400009--1400109 Score: 121
Period size: 30 Copynumber: 3.4 Consensus size: 29
1399999 ATGTATTAGT
* *
1400009 CCATGTATACTTTTGATATCTTTTATAGGC
1 CCATGTACA-TTTTGATATCTTTTATAAGC
*
1400039 CCATGTACATTATTGATATCTTTTATAAGA
1 CCATGTACATT-TTGATATCTTTTATAAGC
**
1400069 CCATGTACAATACTGATATCTTTTATAAGC
1 CCATGTAC-ATTTTGATATCTTTTATAAGC
*
1400099 CCATGAACATT
1 CCATGTACATT
1400110 ACATAGAACT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
29 4 0.07
30 55 0.90
31 2 0.03
ACGTcount: A:0.31, C:0.18, G:0.11, T:0.41
Consensus pattern (29 bp):
CCATGTACATTTTGATATCTTTTATAAGC
Found at i:1400232 original size:38 final size:37
Alignment explanation
Indices: 1400181--1400287 Score: 160
Period size: 38 Copynumber: 2.8 Consensus size: 37
1400171 TCGTATAAAC
1400181 TGTGTCCCGAAGGACCTATCATACCGAAGGATGTCATA
1 TGTGTCCCGAAGGACCTATCAT-CCGAAGGATGTCATA
* *
1400219 TGTGTCCCGAAGGACCTATCATCCCAAAGGATGTCATC
1 TGTGTCCCGAAGGACCTATCAT-CCGAAGGATGTCATA
*
1400257 TGTGTCCTGAAGGACCTATCATCCTGAAGGA
1 TGTGTCCCGAAGGACCTATCATCC-GAAGGA
1400288 CCTATAATCC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
37 2 0.03
38 61 0.97
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.24
Consensus pattern (37 bp):
TGTGTCCCGAAGGACCTATCATCCGAAGGATGTCATA
Found at i:1400283 original size:17 final size:17
Alignment explanation
Indices: 1400261--1400304 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 17
1400251 GTCATCTGTG
*
1400261 TCCTGAAGGACCTATCA
1 TCCTGAAGGACCTATAA
1400278 TCCTGAAGGACCTATAA
1 TCCTGAAGGACCTATAA
*
1400295 TCCCGAAGGA
1 TCCTGAAGGA
1400305 TGTCTGTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.20
Consensus pattern (17 bp):
TCCTGAAGGACCTATAA
Found at i:1400337 original size:21 final size:20
Alignment explanation
Indices: 1400295--1400365 Score: 83
Period size: 21 Copynumber: 3.5 Consensus size: 20
1400285 GGACCTATAA
*
1400295 TCCCGAAGGA-TGTC-TGTG
1 TCCCGAAGGACTGTCATATG
1400313 TCCCGAAGGACTTGTCATATG
1 TCCCGAAGGAC-TGTCATATG
* *
1400334 TCCCAAAGGACCTATCATATG
1 TCCCGAAGGA-CTGTCATATG
1400355 TCCCGAAGGAC
1 TCCCGAAGGAC
1400366 ATATGTAACC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
18 10 0.22
20 5 0.11
21 29 0.64
22 1 0.02
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (20 bp):
TCCCGAAGGACTGTCATATG
Found at i:1409464 original size:21 final size:22
Alignment explanation
Indices: 1409424--1409469 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
1409414 AAATTTTGGG
1409424 GCCTTTGTTGAAAAACCCATGC
1 GCCTTTGTTGAAAAACCCATGC
*
1409446 GCCTTTGTTG-AAAAGCCATGC
1 GCCTTTGTTGAAAAACCCATGC
1409467 GCC
1 GCC
1409470 CCCTTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.24, C:0.28, G:0.22, T:0.26
Consensus pattern (22 bp):
GCCTTTGTTGAAAAACCCATGC
Found at i:1411616 original size:15 final size:15
Alignment explanation
Indices: 1411596--1411629 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
1411586 TGATCAGGTA
1411596 AGCTGCAGTGTTGAT
1 AGCTGCAGTGTTGAT
1411611 AGCTGCAGTGTTGAT
1 AGCTGCAGTGTTGAT
1411626 AGCT
1 AGCT
1411630 TCAGCCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.21, C:0.15, G:0.32, T:0.32
Consensus pattern (15 bp):
AGCTGCAGTGTTGAT
Found at i:1411664 original size:24 final size:24
Alignment explanation
Indices: 1411637--1411684 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
1411627 GCTTCAGCCC
1411637 ATAGCAATTTGGGCAATTCAGCGT
1 ATAGCAATTTGGGCAATTCAGCGT
1411661 ATAGCAATTTGGGCAATTCAGCGT
1 ATAGCAATTTGGGCAATTCAGCGT
1411685 GTATCCTCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (24 bp):
ATAGCAATTTGGGCAATTCAGCGT
Found at i:1419881 original size:18 final size:18
Alignment explanation
Indices: 1419860--1419902 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1419850 GTTATTTTTA
* *
1419860 AAATAAAATATAAGAATT
1 AAATAAAAGAAAAGAATT
*
1419878 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAAGAATT
1419896 AAATAAA
1 AAATAAA
1419903 CAAATTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:1420588 original size:32 final size:32
Alignment explanation
Indices: 1420550--1420665 Score: 81
Period size: 32 Copynumber: 3.2 Consensus size: 32
1420540 AACTAAAGTA
1420550 CCTAAAACAAAGATAAAATATAAAAATAATAT
1 CCTAAAACAAAGATAAAATATAAAAATAATAT
* *
1420582 CCTAAAACTTAA-TTAAAATACTAAAACCTATTTAAACTAAAAT
1 CCTAAAAC-AAAGATAAAATA-TAAAA---A--T-AA-T---AT
*
1420625 ACCTAAAATAAAGATAAAATATAAAAATAATAT
1 -CCTAAAACAAAGATAAAATATAAAAATAATAT
1420658 CCTAAAAC
1 CCTAAAAC
1420666 TTAATTAAAA
Statistics
Matches: 64, Mismatches: 6, Indels: 28
0.65 0.06 0.29
Matches are distributed among these distances:
32 22 0.34
33 9 0.14
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
40 2 0.03
43 9 0.14
44 14 0.22
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.25
Consensus pattern (32 bp):
CCTAAAACAAAGATAAAATATAAAAATAATAT
Found at i:1420613 original size:76 final size:76
Alignment explanation
Indices: 1420515--1420701 Score: 331
Period size: 76 Copynumber: 2.5 Consensus size: 76
1420505 TCTTAAATCC
* *
1420515 TAATTAAAACACTTAAAA-CTATTTAAACTAAAGTACCTAAAACAAAGATAAAATATAAAAATAA
1 TAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAA
1420579 TATCCTAAAACT
65 TATCCTAAAACT
*
1420591 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAATAAAGATAAAATATAAAAATAAT
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
1420656 ATCCTAAAACT
66 ATCCTAAAACT
1420667 TAATTAAAATACTAAAACCTATTTAAACTAAAATA
1 TAATTAAAATACTAAAACCTATTTAAACTAAAATA
1420702 TAAAGATAAA
Statistics
Matches: 107, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
75 5 0.05
76 102 0.95
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (76 bp):
TAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAAT
ATCCTAAAACT
Found at i:1422389 original size:19 final size:18
Alignment explanation
Indices: 1422365--1422408 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1422355 TGCTGACTCT
1422365 TAAATATAATAATTAACAG
1 TAAATATAAT-ATTAACAG
* *
1422384 TAAATACAATATTAATAG
1 TAAATATAATATTAACAG
*
1422402 TAGATAT
1 TAAATAT
1422409 TTACATGATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.55, C:0.05, G:0.07, T:0.34
Consensus pattern (18 bp):
TAAATATAATATTAACAG
Found at i:1422403 original size:18 final size:19
Alignment explanation
Indices: 1422365--1422403 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
1422355 TGCTGACTCT
*
1422365 TAAATATAATAATTAACAG
1 TAAATACAATAATTAACAG
*
1422384 TAAATACAAT-ATTAATAG
1 TAAATACAATAATTAACAG
1422402 TA
1 TA
1422404 GATATTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.56, C:0.05, G:0.05, T:0.33
Consensus pattern (19 bp):
TAAATACAATAATTAACAG
Found at i:1430783 original size:22 final size:22
Alignment explanation
Indices: 1430743--1430784 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
1430733 AAATTGAATC
* *
1430743 TTTAACAACAAGTATAAATATT
1 TTTAACAACAAATAAAAATATT
*
1430765 TTTAACAATAAATAAAAATA
1 TTTAACAACAAATAAAAATA
1430785 AATTAATTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.33
Consensus pattern (22 bp):
TTTAACAACAAATAAAAATATT
Found at i:1433957 original size:27 final size:27
Alignment explanation
Indices: 1433905--1433956 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
1433895 AGTTATGGTA
* *
1433905 AAAGAGGAGGAGAAAGAAGAATAAAAG
1 AAAGAAGAGAAGAAAGAAGAATAAAAG
1433932 AAAGAAGAGAAGAAAGAA-AATAAAA
1 AAAGAAGAGAAGAAAGAAGAATAAAA
1433957 ACCAAGTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.69, C:0.00, G:0.27, T:0.04
Consensus pattern (27 bp):
AAAGAAGAGAAGAAAGAAGAATAAAAG
Found at i:1435706 original size:13 final size:13
Alignment explanation
Indices: 1435706--1435766 Score: 68
Period size: 13 Copynumber: 4.3 Consensus size: 13
1435696 CCGTTGACCC
1435706 GACCCGACCCGTT
1 GACCCGACCCGTT
*
1435719 TACCCGACCCGTT
1 GACCCGACCCGTT
1435732 GACCCGACCCGACCCGTT
1 -----GACCCGACCCGTT
1435750 GACCCGACCCGTT
1 GACCCGACCCGTT
1435763 GACC
1 GACC
1435767 ATTGACCGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 29 0.71
18 12 0.29
ACGTcount: A:0.16, C:0.48, G:0.21, T:0.15
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:1435707 original size:18 final size:18
Alignment explanation
Indices: 1435684--1435760 Score: 110
Period size: 18 Copynumber: 4.6 Consensus size: 18
1435674 ACCGGTCATA
1435684 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1435702 ACCCGACCCGACCCGTT-
1 ACCCGACCCGACCCGTTG
*
1435719 ----TACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1435733 ACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGTTG
1435751 ACCCGACCCG
1 ACCCGACCCG
1435761 TTGACCATTG
Statistics
Matches: 52, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.23
18 40 0.77
ACGTcount: A:0.17, C:0.51, G:0.21, T:0.12
Consensus pattern (18 bp):
ACCCGACCCGACCCGTTG
Found at i:1435727 original size:31 final size:31
Alignment explanation
Indices: 1435688--1435766 Score: 149
Period size: 31 Copynumber: 2.5 Consensus size: 31
1435678 GTCATAACCC
1435688 GACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
*
1435719 TACCCGACCCGTTGACCCGACCCGACCCGTT
1 GACCCGACCCGTTGACCCGACCCGACCCGTT
1435750 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
1435767 ATTGACCGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 46 1.00
ACGTcount: A:0.16, C:0.48, G:0.22, T:0.14
Consensus pattern (31 bp):
GACCCGACCCGTTGACCCGACCCGACCCGTT
Found at i:1437088 original size:18 final size:18
Alignment explanation
Indices: 1437062--1437096 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1437052 TCGAAAGGAC
*
1437062 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
1437080 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
1437097 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:1450105 original size:25 final size:27
Alignment explanation
Indices: 1450072--1450126 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
1450062 TTATGCAAAG
1450072 GTTTATTAGT-CTTT-T-ACAACTATT
1 GTTTATTAGTGCTTTATGACAACTATT
*
1450096 GTTTCATTAGTGCTTTATGTCAACTATT
1 GTTT-ATTAGTGCTTTATGACAACTATT
1450124 GTT
1 GTT
1450127 ACCCGCTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 4 0.15
25 6 0.23
26 4 0.15
27 1 0.04
28 11 0.42
ACGTcount: A:0.22, C:0.13, G:0.13, T:0.53
Consensus pattern (27 bp):
GTTTATTAGTGCTTTATGACAACTATT
Found at i:1450617 original size:32 final size:32
Alignment explanation
Indices: 1450580--1450668 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 32
1450570 ATACTACAAG
* *
1450580 AACAATATTGGTCATATAACAAG-ATTACTACT
1 AACAATATTGGTAATACAA-AAGTATTACTACT
*
1450612 AACAATATTGGTAATACAAAAGTATTAGTACT
1 AACAATATTGGTAATACAAAAGTATTACTACT
* * * *
1450644 AAGAGTATTGGTACTACAACAGTAT
1 AACAATATTGGTAATACAAAAGTAT
1450669 CGATACTAAC
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
31 3 0.06
32 46 0.94
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.30
Consensus pattern (32 bp):
AACAATATTGGTAATACAAAAGTATTACTACT
Found at i:1450676 original size:32 final size:32
Alignment explanation
Indices: 1450580--1450679 Score: 87
Period size: 32 Copynumber: 3.1 Consensus size: 32
1450570 ATACTACAAG
* * * *
1450580 AACAATATTGGTCATATAACAAG-ATTACTACT
1 AACAATATTGGTAATACAA-AAGTATGAGTACT
*
1450612 AACAATATTGGTAATACAAAAGTATTAGTACT
1 AACAATATTGGTAATACAAAAGTATGAGTACT
* * * *
1450644 AAGAGTATTGGTACTACAACAGTATCGA-TACT
1 AACAATATTGGTAATACAAAAGTAT-GAGTACT
1450676 AACA
1 AACA
1450680 TTACCGATAC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
31 3 0.05
32 53 0.93
33 1 0.02
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (32 bp):
AACAATATTGGTAATACAAAAGTATGAGTACT
Found at i:1454793 original size:3 final size:3
Alignment explanation
Indices: 1454785--1454869 Score: 161
Period size: 3 Copynumber: 28.0 Consensus size: 3
1454775 AATTATTTTA
1454785 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
1454831 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1454870 TCAAACCTTC
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 78 0.96
4 3 0.04
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1456654 original size:2 final size:2
Alignment explanation
Indices: 1456647--1456674 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1456637 ATTTAACCTA
1456647 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
1456675 GACATGTGGA
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):
AT
Found at i:1456826 original size:62 final size:61
Alignment explanation
Indices: 1456760--1456875 Score: 162
Period size: 62 Copynumber: 1.9 Consensus size: 61
1456750 TTCATACTAT
*
1456760 TTTTATAAAATGATATT-TGAATGATTTTGGGTATAAATTACCCAATACAATTTTACATGGTA
1 TTTTATAAAATGAT-TTATCAATGATTTTGGGTATAAATTACCCAATAC-ATTTTACATGGTA
** * *
1456822 TTTTATTTAATGATTTATCAATGATTTTGGGTTTTAATTACCCAATACATTTTA
1 TTTTATAAAATGATTTATCAATGATTTTGGGTATAAATTACCCAATACATTTTA
1456876 TATGATACTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
61 8 0.17
62 40 0.83
ACGTcount: A:0.34, C:0.09, G:0.11, T:0.47
Consensus pattern (61 bp):
TTTTATAAAATGATTTATCAATGATTTTGGGTATAAATTACCCAATACATTTTACATGGTA
Found at i:1457908 original size:2 final size:2
Alignment explanation
Indices: 1457859--1457892 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1457849 AAACGAGTCA
1457859 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
1457893 TAGTTAGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1461979 original size:14 final size:14
Alignment explanation
Indices: 1461960--1462019 Score: 93
Period size: 14 Copynumber: 4.2 Consensus size: 14
1461950 TAGTTCATGA
1461960 ATGATGTAAGGATG
1 ATGATGTAAGGATG
1461974 ATGATGTAAGGATG
1 ATGATGTAAGGATG
*
1461988 ATGATGTAAGGATA
1 ATGATGTAAGGATG
*
1462002 ATGATATAAGGAATG
1 ATGATGTAAGG-ATG
1462017 ATG
1 ATG
1462020 TCATGATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 37 0.88
15 5 0.12
ACGTcount: A:0.40, C:0.00, G:0.32, T:0.28
Consensus pattern (14 bp):
ATGATGTAAGGATG
Found at i:1465380 original size:29 final size:29
Alignment explanation
Indices: 1465335--1465405 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
1465325 ATATATAATT
* * *
1465335 TTTTAAAATTTTGTACTTT-TCCCTAAAC
1 TTTTAAAAGTTTATACTTTGCCCCTAAAC
1465363 TTTTATAAAGTTTATACTTTGGCCCCTAAAC
1 TTTTA-AAAGTTTATACTTT-GCCCCTAAAC
*
1465394 TTTCAAAA-TTTA
1 TTTTAAAAGTTTA
1465406 CATTTTTATC
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
28 5 0.14
29 16 0.44
30 3 0.08
31 12 0.33
ACGTcount: A:0.31, C:0.17, G:0.06, T:0.46
Consensus pattern (29 bp):
TTTTAAAAGTTTATACTTTGCCCCTAAAC
Found at i:1465786 original size:26 final size:26
Alignment explanation
Indices: 1465738--1465787 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1465728 ACAATTAAAC
*
1465738 TTATGTTTTAGGATATTATTTTAATT
1 TTATGTTTTAGGATATTAGTTTAATT
*
1465764 TTAT-TTTTAGGAATTTTAGTTTAA
1 TTATGTTTTAGG-ATATTAGTTTAA
1465788 ATAGTTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (26 bp):
TTATGTTTTAGGATATTAGTTTAATT
Found at i:1468148 original size:21 final size:21
Alignment explanation
Indices: 1468124--1468194 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 21
1468114 AGCAATTTCA
*
1468124 CAAGAAAAGATGGTTACATCC
1 CAAGAAAAGATAGTTACATCC
* * *
1468145 CAAGAAAAGCTAGTTACGTCT
1 CAAGAAAAGATAGTTACATCC
* * *
1468166 CAAGAAAAGCTAATTGCATCC
1 CAAGAAAAGATAGTTACATCC
*
1468187 CAGGAAAA
1 CAAGAAAA
1468195 ATTCCAAAGC
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.44, C:0.20, G:0.18, T:0.18
Consensus pattern (21 bp):
CAAGAAAAGATAGTTACATCC
Found at i:1477794 original size:20 final size:21
Alignment explanation
Indices: 1477751--1477794 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
1477741 TATTTACTTG
* *
1477751 TATTTATTTAAGTATATATTA
1 TATTTATTTAAGTACATATGA
*
1477772 TATTTATTT-TGTACATATGA
1 TATTTATTTAAGTACATATGA
1477792 TAT
1 TAT
1477795 ATACAATTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.34, C:0.02, G:0.07, T:0.57
Consensus pattern (21 bp):
TATTTATTTAAGTACATATGA
Found at i:1481829 original size:3 final size:3
Alignment explanation
Indices: 1481823--1481864 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
1481813 TATTTTTATT
* *
1481823 TAA TAA TAA TAA TAA TAC TAA TAT TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1481865 AACGAAATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1485389 original size:24 final size:25
Alignment explanation
Indices: 1485362--1485417 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 25
1485352 TGGTGTGGGT
*
1485362 TATTTATGGAT-GATTAAGTGTTTA
1 TATTTATGAATGGATTAAGTGTTTA
* * *
1485386 TATTAATGAATGGTTTAAGTTTTTA
1 TATTTATGAATGGATTAAGTGTTTA
*
1485411 TGTTTAT
1 TATTTAT
1485418 TATTTGATTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.29, C:0.00, G:0.18, T:0.54
Consensus pattern (25 bp):
TATTTATGAATGGATTAAGTGTTTA
Found at i:1488185 original size:90 final size:88
Alignment explanation
Indices: 1488067--1488240 Score: 276
Period size: 89 Copynumber: 2.0 Consensus size: 88
1488057 TCCCGAATAT
* * *
1488067 TTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAACAAAATCCCTGATATGATTAG
1 TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAACAAAA-CCCTAATATGACTAG
1488132 GGTAACTTGGATATAAAAGGATTA
65 GGTAACTTGGATATAAAAGGATTA
* *
1488156 TTAAATTCTAATTAATTAAATATATATTTAATTAATTTGAAATAATAAAACCCTAATATGACTAG
1 TTAAATTC-AATTAATTAAATATAGATTTAATTAATTTGAAATAACAAAACCCTAATATGACTAG
*
1488221 GGTAACTTGGCTATAAAAGG
65 GGTAACTTGGATATAAAAGG
1488241 GTGTGTTTAG
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
89 39 0.50
90 39 0.50
ACGTcount: A:0.44, C:0.07, G:0.11, T:0.37
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAGATTTAATTAATTTGAAATAACAAAACCCTAATATGACTAGG
GTAACTTGGATATAAAAGGATTA
Found at i:1492422 original size:2 final size:2
Alignment explanation
Indices: 1492411--1492511 Score: 170
Period size: 2 Copynumber: 51.5 Consensus size: 2
1492401 TTACACCATT
1492411 TA TA -A 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
*
1492452 TA TA TA TA TA T- TA TA TA TA TA TA TG 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
*
1492493 TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
1492512 TATTACTATA
Statistics
Matches: 93, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
1 2 0.02
2 91 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1492965 original size:23 final size:24
Alignment explanation
Indices: 1492938--1492994 Score: 59
Period size: 23 Copynumber: 2.5 Consensus size: 24
1492928 ATATGCATTT
*
1492938 AAACTCAAAGCA-AAATACACAAG
1 AAACTCAAAGCAGAAACACACAAG
*
1492961 AAACT-ATGAG-AGAAACACACAAG
1 AAACTCA-AAGCAGAAACACACAAG
1492984 AAA-TCAAAGCA
1 AAACTCAAAGCA
1492995 CTTGAAAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 8
0.71 0.08 0.21
Matches are distributed among these distances:
22 5 0.19
23 22 0.81
ACGTcount: A:0.60, C:0.19, G:0.12, T:0.09
Consensus pattern (24 bp):
AAACTCAAAGCAGAAACACACAAG
Found at i:1493757 original size:12 final size:12
Alignment explanation
Indices: 1493740--1493780 Score: 75
Period size: 12 Copynumber: 3.5 Consensus size: 12
1493730 ATTTTTCTCC
1493740 TTTTTAATGTTT
1 TTTTTAATGTTT
1493752 TTTTTAATG-TT
1 TTTTTAATGTTT
1493763 TTTTTAATGTTT
1 TTTTTAATGTTT
1493775 TTTTTA
1 TTTTTA
1493781 TCTTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.39
12 17 0.61
ACGTcount: A:0.17, C:0.00, G:0.07, T:0.76
Consensus pattern (12 bp):
TTTTTAATGTTT
Found at i:1493764 original size:11 final size:11
Alignment explanation
Indices: 1493740--1493778 Score: 69
Period size: 11 Copynumber: 3.5 Consensus size: 11
1493730 ATTTTTCTCC
1493740 TTTTTAATGTTT
1 TTTTTAATG-TT
1493752 TTTTTAATGTT
1 TTTTTAATGTT
1493763 TTTTTAATGTT
1 TTTTTAATGTT
1493774 TTTTT
1 TTTTT
1493779 TATCTTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 18 0.67
12 9 0.33
ACGTcount: A:0.15, C:0.00, G:0.08, T:0.77
Consensus pattern (11 bp):
TTTTTAATGTT
Found at i:1494889 original size:27 final size:27
Alignment explanation
Indices: 1494858--1494912 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
1494848 GATATCTAGA
1494858 TCGGAATTTGCATACCATGGGGATAAC
1 TCGGAATTTGCATACCATGGGGATAAC
1494885 TCGGAATTTGCATACCATGGGGATAAC
1 TCGGAATTTGCATACCATGGGGATAAC
1494912 T
1 T
1494913 ACAAGAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (27 bp):
TCGGAATTTGCATACCATGGGGATAAC
Found at i:1499246 original size:18 final size:19
Alignment explanation
Indices: 1499223--1499264 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
1499213 GTAAGAAAAT
*
1499223 ATTAAAATAA-TAAAAGCG
1 ATTAAAATAAGTAAAAGCA
1499241 ATT-AAATAAGTAAAAGCA
1 ATTAAAATAAGTAAAAGCA
1499259 ATTAAA
1 ATTAAA
1499265 GTAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 6 0.29
18 13 0.62
19 2 0.10
ACGTcount: A:0.62, C:0.05, G:0.10, T:0.24
Consensus pattern (19 bp):
ATTAAAATAAGTAAAAGCA
Done.