Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008504.1 Hibiscus syriacus cultivar Beakdansim tig00111356_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: 2056749
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 10
Found at i:1538924 original size:54 final size:54
Alignment explanation
Indices: 1538817--1539168 Score: 429
Period size: 54 Copynumber: 6.5 Consensus size: 54
1538807 ACATTATAAG
* * ** *
1538817 TTCTCTGGG-TGCACACGTAGTG-CTGATACGGTCGTTCATAAACATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCT-ATACGGTTATTCATCAACATATGATGAA
* * * * ** * * *
1538870 TTTTGTAGGTTACACACTTAGTTCCTATATAGTCATTCATCAATATATAATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTATTCATCAACATATGATGAA
* * * *
1538924 TTCTTTGGGTTGCACACTTAGTGCCTATATGGTCATTTATCAACATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTATTCATCAACATATGATGAA
* * *
1538978 TTCTGTGGGTTGCACAATTAGTGCCTATACGGTTATTTATCAATATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTATTCATCAACATATGATGAA
* * *
1539032 TTCTGTGGGTTGCATAATTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTATTCATCAACATATGATGAA
*
1539086 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAA
1 TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTATTCATCAACATATGATGAA
** *
1539140 TTCCATGGGTTGCACACTTAGTACCTATA
1 TTCTGTGGGTTGCACACTTAGTGCCTATA
1539169 GTACACATAT
Statistics
Matches: 262, Mismatches: 35, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
53 6 0.02
54 254 0.97
55 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.37
Consensus pattern (54 bp):
TTCTGTGGGTTGCACACTTAGTGCCTATACGGTTATTCATCAACATATGATGAA
Found at i:1539631 original size:75 final size:75
Alignment explanation
Indices: 1539508--1539672 Score: 321
Period size: 75 Copynumber: 2.2 Consensus size: 75
1539498 GGTACCACTA
1539508 CTATGGTATCGATACTTCTCTACTATAGTACTGACACTCCCATGAAGTATCAATACCATTTCTGC
1 CTATGGTATCGATACTTCTCTACTATAGTACTGACACTCCCATGAAGTATCAATACCATTTCTGC
1539573 ATTCTGGAAT
66 ATTCTGGAAT
*
1539583 CTATGGTATCGATACTTCTCTACTATAGTACTGACACTCCCTTGAAGTATCAATACCATTTCTGC
1 CTATGGTATCGATACTTCTCTACTATAGTACTGACACTCCCATGAAGTATCAATACCATTTCTGC
1539648 ATTCTGGAAT
66 ATTCTGGAAT
1539658 CTATGGTATCGATAC
1 CTATGGTATCGATAC
1539673 CTTTCTCATA
Statistics
Matches: 89, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 89 1.00
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (75 bp):
CTATGGTATCGATACTTCTCTACTATAGTACTGACACTCCCATGAAGTATCAATACCATTTCTGC
ATTCTGGAAT
Found at i:1540381 original size:54 final size:54
Alignment explanation
Indices: 1540318--1540664 Score: 482
Period size: 54 Copynumber: 6.4 Consensus size: 54
1540308 ATAAGTTCTC
* **
1540318 TGGG-TGCACACGTAGTG-CTGATACGGTCGTTCATCAACATATGATGAATTTTG
1 TGGGTTGCACACTTAGTGCCT-ATACGGTCGTTCATCAACATATGATGAATTCCG
* * * **
1540371 TAGGTTGCACACTTAGTGCCTATATGGTCGTTCATCAACATATAATGAATTATG
1 TGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCG
* *
1540425 TGGGTTGCACACTTAGTGCCTATACGGTCGTTGATCAACATATGATGAATTCTG
1 TGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCG
* ** * *
1540479 TGGGTTGCACAATTAGTGCCTATACGGTTATTTATCAACATATGATGAATTTCG
1 TGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCG
* * *
1540533 TGGGTTGCATAATTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCCG
1 TGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCG
* * *
1540587 TGGGTTGCACACTTAGTGCCTATATGGTTGCTCATCAACATATGATGAATTCCG
1 TGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCG
1540641 TGGGTTGCACACTTAGTGCCTATA
1 TGGGTTGCACACTTAGTGCCTATA
1540665 GTACACATGG
Statistics
Matches: 268, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
53 3 0.01
54 263 0.98
55 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (54 bp):
TGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTCCG
Found at i:1548161 original size:14 final size:15
Alignment explanation
Indices: 1548136--1548164 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1548126 AATAGGGAAT
1548136 AAATACATAAAGAAA
1 AAATACATAAAGAAA
1548151 AAATA-ATAAAGAAA
1 AAATACATAAAGAAA
1548165 CAAGATAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.03, G:0.07, T:0.14
Consensus pattern (15 bp):
AAATACATAAAGAAA
Found at i:1553373 original size:66 final size:66
Alignment explanation
Indices: 1553278--1553403 Score: 198
Period size: 66 Copynumber: 1.9 Consensus size: 66
1553268 ATAAATTCCT
* *
1553278 ACAAAGACACAAGACATATGAATCCCGGAGGCTAATTGCTAGGCTTGACACGGAGAATAATTTAT
1 ACAAAGACACAAGACATATGAATCCCGGAGGCTAAATGCTAGGCCTGACACGGAGAATAATTTAT
1553343 C
66 C
** * *
1553344 ACAAAGACATTAGACATATGAATCTCGGAGTCTAAATGCTAGGCCTGACACGGAGAATAA
1 ACAAAGACACAAGACATATGAATCCCGGAGGCTAAATGCTAGGCCTGACACGGAGAATAA
1553404 ATTCTCACGA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 54 1.00
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.21
Consensus pattern (66 bp):
ACAAAGACACAAGACATATGAATCCCGGAGGCTAAATGCTAGGCCTGACACGGAGAATAATTTAT
C
Found at i:1555388 original size:3 final size:3
Alignment explanation
Indices: 1555380--1555442 Score: 62
Period size: 3 Copynumber: 21.7 Consensus size: 3
1555370 AAAACACAAG
* *
1555380 TAA TAA TAA TATA TAA -AA TAA AAA TAA AAA TAA -AA -AA TTAA -AA
1 TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA
1555423 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
1555443 TTATGTATAC
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
2 8 0.16
3 38 0.75
4 5 0.10
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:1555422 original size:19 final size:19
Alignment explanation
Indices: 1555394--1555431 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
1555384 AATAATATAT
1555394 AAAATAAAAATAAAAATAA
1 AAAATAAAAATAAAAATAA
* *
1555413 AAAATTAAAATAATAATAA
1 AAAATAAAAATAAAAATAA
1555432 TAATAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAATAAAAATAAAAATAA
Found at i:1555500 original size:24 final size:22
Alignment explanation
Indices: 1555467--1555527 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
1555457 CATATATTTA
1555467 AAAAACTATATAATATG-TTTC
1 AAAAACTATATAATATGTTTTC
*
1555488 GAAAAACTATATAACATGTTTTC
1 -AAAAACTATATAATATGTTTTC
1555511 AAAAACTATATATATAT
1 AAAAACTATATA-ATAT
1555528 ATATATATTG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
22 28 0.80
23 7 0.20
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (22 bp):
AAAAACTATATAATATGTTTTC
Found at i:1559713 original size:21 final size:21
Alignment explanation
Indices: 1559682--1559722 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1559672 GTAAATTTCC
1559682 ATGAATAATAAAAATAGAAAAA
1 ATGAATAATAAAAATA-AAAAA
1559704 ATGAA-AATAAAAATAAAAA
1 ATGAATAATAAAAATAAAAA
1559723 TAAATTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 4 0.21
21 10 0.53
22 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (21 bp):
ATGAATAATAAAAATAAAAAA
Found at i:1562867 original size:22 final size:22
Alignment explanation
Indices: 1562828--1562884 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
1562818 GTGCACGAAA
*
1562828 AAGTGTCGAT-ACATTTATAAT
1 AAGTGTCGATCCCATTTATAAT
1562849 AAGTGTCGATCCCATTTATAAT
1 AAGTGTCGATCCCATTTATAAT
1562871 AAGTGTCGATCCCA
1 AAGTGTCGATCCCA
1562885 AAAACATCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 10 0.29
22 24 0.71
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (22 bp):
AAGTGTCGATCCCATTTATAAT
Found at i:1563046 original size:221 final size:221
Alignment explanation
Indices: 1562629--1563083 Score: 750
Period size: 221 Copynumber: 2.1 Consensus size: 221
1562619 GTGCACGAAA
* * *
1562629 AAGTGTCGAT-ACATTAATAACAATTGTCAATCCAAAAAACATCGAAACCCATAATTATAATGTA
1 AAGTGTCGATCCCATTAATAACAAGTGTCAATCCAAAAAACATCGAAACCCATAATTATAATATA
1562693 ATAGGTAAATTAAAAATGTAACAGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAA
66 ATAGGTAAATTAAAAATGTAACAGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAA
* * *
1562758 GTATCGACACAAATAAAACAAGTGTAGATACTTTTGGTCCAGAATGTATTTCTTAACCAAGTGCA
131 GTAACGACACAAATAAAAAAAGTGTAGATACTTTTGGTCCAGAATGTATTTCTGAACCAAGTGCA
1562823 CGAAAAAGTGTCGATACATTTATAAT
196 CGAAAAAGTGTCGATACATTTATAAT
* * * *
1562849 AAGTGTCGATCCCATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATATA
1 AAGTGTCGATCCCATTAATAACAAGTGTCAATCCAAAAAACATCGAAACCCATAATTATAATATA
* * **
1562914 ATAGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACATTTGTACAAAAA
66 ATAGGTAAATTAAAAATGTAACAGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAA
* *
1562979 GTAACGACACAAATAAAAAAAGTTTCGATACTTTTGGTCCAGAATGTATTTCTGAACCAAGTGCA
131 GTAACGACACAAATAAAAAAAGTGTAGATACTTTTGGTCCAGAATGTATTTCTGAACCAAGTGCA
*
1563044 CGAAAAAGTTTCGATACATTTATAAT
196 CGAAAAAGTGTCGATACATTTATAAT
1563070 AAGTGTCGATCCCA
1 AAGTGTCGATCCCA
1563084 AAAATATTGA
Statistics
Matches: 217, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
220 10 0.05
221 207 0.95
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (221 bp):
AAGTGTCGATCCCATTAATAACAAGTGTCAATCCAAAAAACATCGAAACCCATAATTATAATATA
ATAGGTAAATTAAAAATGTAACAGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAA
GTAACGACACAAATAAAAAAAGTGTAGATACTTTTGGTCCAGAATGTATTTCTGAACCAAGTGCA
CGAAAAAGTGTCGATACATTTATAAT
Found at i:1563208 original size:199 final size:199
Alignment explanation
Indices: 1562849--1563351 Score: 781
Period size: 199 Copynumber: 2.5 Consensus size: 199
1562839 CATTTATAAT
* *
1562849 AAGTGTCGATCCCATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATATA
1 AAGTGTCGAT-ACATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTA
* **
1562914 ATAGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACATTTGTACAAAAA
65 ATAGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTGTTTGAGAAAACAGGTGTACAAAAA
* *
1562979 GTAACGACACAAATAAAAAAAGTTTCGATACTTTTGGTCCAGAATGTATTTCTGAACCAAGTGCA
130 GTAACGACACAAATAAAAAAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCA
1563044 CGAAA
195 CGAAA
* * *
1563049 AAGTTTCGATACATTTATAATAAGTGTCGATCCCAAAAATATTGAAACCCATAATTATAATGTAA
1 AAGTGTCGATACATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAA
* *
1563114 TATGTAAATTAACAATGTAACCGGTCTAAATATACCGGTGTTTGAGAAAAGAGGTGTACAAAAAG
66 TAGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTGTTTGAGAAAACAGGTGTACAAAAAG
* *
1563179 TATCGACACAAATAAAATAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCAC
131 TAACGACACAAATAAAAAAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCAC
1563244 GAAA
196 GAAA
* * * *
1563248 ACGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAACATCGAAACCCAAAATTTTAATGTAA
1 AAGTGTCGATACATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAA
* * ** * *
1563313 TAGGTCATTTTGCAATGTAACCGGTATAAATATAGCGGT
66 TAGGTAAATTAACAATGTAACCGGTCTAAATATACCGGT
1563352 TTAATTTGAA
Statistics
Matches: 275, Mismatches: 28, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
199 266 0.97
200 9 0.03
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (199 bp):
AAGTGTCGATACATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAA
TAGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTGTTTGAGAAAACAGGTGTACAAAAAG
TAACGACACAAATAAAAAAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGCAC
GAAA
Found at i:1563238 original size:420 final size:419
Alignment explanation
Indices: 1562433--1563282 Score: 1396
Period size: 420 Copynumber: 2.0 Consensus size: 419
1562423 GTAAACTTAT
* *
1562433 GTGTCGAT-ACATTAATAACAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAAT
1 GTGTCGATCCCATTAATAACAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATATAAT
* * *
1562497 AGGTAAATTAACAATGTAACCGGACTAAATATACTGGTTTTTGAGAAAATAGGTGTACCAAAAGT
66 AGGTAAATTAACAATGTAACCGGACTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGT
* *
1562562 ATCGACACAAATAAAACAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAACCAAGTGCACGA
131 AACGACACAAATAAAAAAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAACCAAGTGCACGA
*
1562627 AAAAGTGTCGATACATTAATAACAATTGTCAATCCAAAAAACATCGAAACCCATAATTATAATGT
196 AAAAGTGTCGATACATTAATAACAAGTGTCAATCCAAAAAACATCGAAACCCATAATTATAATGT
*
1562692 AATAGGTAAATTAAAAATGTAACAGGTCTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAA
261 AATAGGTAAATTAAAAATGTAACAGGTCTAAATATACCGGTGTTTGAGAAAACAGGTGTACAAAA
*
1562757 AGTATCGACACAAATAAAACAAGTGTAGATACTTTTGGTCCAGAATGTATTTCTTAACCAAGTGC
326 AGTATCGACACAAATAAAACAAGTGTAGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGC
*
1562822 ACGAAAAAGTGTCGATACATTTATAATAA
391 ACGAAAAAGTGTCGATACATTTATAACAA
* * *
1562851 GTGTCGATCCCATTTATAATAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATATAAT
1 GTGTCGATCCCATTAATAACAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATATAAT
* **
1562916 AGGTAAATTAACAATGTAACCGGTCTAAATATACCGGTTTTTGAGAAAACATTTGTACAAAAAGT
66 AGGTAAATTAACAATGTAACCGGACTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGT
*
1562981 AACGACACAAATAAAAAAAGTTTCGATACTTTTGGTCCAGAATGTATTTCTGAACCAAGTGCACG
131 AACGACACAAATAAAAAAAGTGTCGATACTTTTGGTCCAGAATGTATTTCT-AACCAAGTGCACG
* * * * * * *
1563046 AAAAAGTTTCGATACATTTATAATAAGTGTCGATCCCAAAAATATTGAAACCCATAATTATAATG
195 AAAAAGTGTCGATACATTAATAACAAGTGTCAATCCAAAAAACATCGAAACCCATAATTATAATG
* * * *
1563111 TAATATGTAAATTAACAATGTAACCGGTCTAAATATACCGGTGTTTGAGAAAAGAGGTGTACAAA
260 TAATAGGTAAATTAAAAATGTAACAGGTCTAAATATACCGGTGTTTGAGAAAACAGGTGTACAAA
* *
1563176 AAGTATCGACACAAATAAAATAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTG
325 AAGTATCGACACAAATAAAACAAGTGTAGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTG
*
1563241 CACGAAAACGTGTCGATACATTTATAACAA
390 CACGAAAAAGTGTCGATACATTTATAACAA
1563271 GTGTCGATCCCA
1 GTGTCGATCCCA
1563283 AAAACATCGA
Statistics
Matches: 398, Mismatches: 32, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
418 8 0.02
419 158 0.40
420 232 0.58
ACGTcount: A:0.41, C:0.16, G:0.15, T:0.28
Consensus pattern (419 bp):
GTGTCGATCCCATTAATAACAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATATAAT
AGGTAAATTAACAATGTAACCGGACTAAATATACCGGTTTTTGAGAAAACAGGTGTACAAAAAGT
AACGACACAAATAAAAAAAGTGTCGATACTTTTGGTCCAGAATGTATTTCTAACCAAGTGCACGA
AAAAGTGTCGATACATTAATAACAAGTGTCAATCCAAAAAACATCGAAACCCATAATTATAATGT
AATAGGTAAATTAAAAATGTAACAGGTCTAAATATACCGGTGTTTGAGAAAACAGGTGTACAAAA
AGTATCGACACAAATAAAACAAGTGTAGATACTTTTGGTCCAGAATGTATTTCTAAACCAAGTGC
ACGAAAAAGTGTCGATACATTTATAACAA
Found at i:1563416 original size:21 final size:21
Alignment explanation
Indices: 1563377--1563416 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1563367 GTCACCATAA
*
1563377 TGTATCGACACGTTATTAACT
1 TGTATCGACACCTTATTAACT
* *
1563398 TGTATCGATACCTTTTTAA
1 TGTATCGACACCTTATTAA
1563417 ATTACTCATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.17, G:0.12, T:0.42
Consensus pattern (21 bp):
TGTATCGACACCTTATTAACT
Found at i:1563724 original size:15 final size:15
Alignment explanation
Indices: 1563704--1563745 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
1563694 TTTCTCAAAG
1563704 CTCTTCTTAACCCAC
1 CTCTTCTTAACCCAC
* *
1563719 CTCTTCCTAACCCAG
1 CTCTTCTTAACCCAC
*
1563734 CTCTTCTCAACC
1 CTCTTCTTAACC
1563746 ACAACCTCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.19, C:0.48, G:0.02, T:0.31
Consensus pattern (15 bp):
CTCTTCTTAACCCAC
Found at i:1566347 original size:24 final size:24
Alignment explanation
Indices: 1566296--1566348 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1566286 TTTCATTTAT
* * *
1566296 AATTAGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATGTA
1566320 AATTTGAGTTTGAATTTAAATGTA
1 AATTTGAGTTTGAATTTAAATGTA
1566344 AATTT
1 AATTT
1566349 CGGCTCCACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATGTA
Found at i:1566892 original size:179 final size:186
Alignment explanation
Indices: 1566521--1567772 Score: 1255
Period size: 200 Copynumber: 6.4 Consensus size: 186
1566511 TAATTCATTC
* * * * * *
1566521 GTGTCGATACATGTTGTCCATAATGTA-TTTCCAAACCAAGTGCACGAAAAAAGCGTTGATACAT
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACG-ACAAAGTGTCGATAC--
*
1566585 TTATAACAAGTGTCGATACTAAAAACATTGAAACACATAGATATAATGTAATAGGTAAAATAACA
63 TTATAACAA--G-CGAT-C--AAAACA-TCAAA-AC----ATATAATGTAATAGGTAAAATAACA
* * *
1566650 ATATAA-CGAGCCTAAATATACCGGTTTTTGAGAAAACAAGTATACATAAAGTATCAACACAAAT
116 ATGTAACCG-GCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAAT
1566714 CCAACAA
180 CCAACAA
* *
1566721 GTGTCGATACTTTTTTTCCAGAATGTATTTTCCAAACCAAGTGTACGACAAAGTGTCGATAC-TA
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACTTA
* * *
1566785 -AA-AA-C-ATCGAAACA-C-AAAGATATAATGTAATAGGTAAAATAACAATGTAACCAGCCTAA
66 TAACAAGCGATCAAAACATCAAAACATATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAA
* * *
1566844 ATATATCAGTTTTTGAGAAAACATGTATACATAAAGTATCGACACAAATCCAACAA
131 ATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAA
*
1566900 GTGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATT
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATAC--T
* *
1566965 TATAACAAGTGTCGATAATAAAAACATCGAAACATATAGATATAATGTAATAGGTAAAATAACAA
64 TATAACAA--G-CG---ATCAAAACATC---A-A-A-ACATATAATGTAATAGGTAAAATAACAA
* * * *
1567030 TGTAATCGGCCTAAATATGCCGGTTTTTGAGAAAACGGGTATACATAAAGTATAGACACAAATCC
117 TGTAACCGGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCC
1567095 AACAA
182 AACAA
1567100 GTGTCGATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATT
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATAC--T
*
1567165 TATAACAAGTGTCGATACTAAAAACATCAAAACACATAGATATAATGTAATATGTAAAATAACAA
64 TATAACAA--G-CGAT-C--AAAACATC-AAA-AC----ATATAATGTAATAGGTAAAATAACAA
* * * *
1567230 TGTAACCGGCCTAAATATACCAGTTTTTAAGAAAACAGGTATACATAAAGTATCAACACAAATTC
117 TGTAACCGGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCC
1567295 AACAA
182 AACAA
* ** *
1567300 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATAC--T
* *
1567365 TATAATAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAAATAACAA
64 TATAACAA--G-CGAT--C-AAAACATC-AAA---A-CA-TATAATGTAATAGGTAAAATAACAA
* *
1567430 TGTAACCGGCCAAAATATATCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCC
117 TGTAACCGGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCC
1567495 AACAA
182 AACAA
* ** * *
1567500 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTATCGATACATT
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATAC--T
*
1567565 TATAACAAGTGTCGATACTAAAAACATCGAAACTCATAATTATAATGTAATAGGTAAAATAACAA
64 TATAACAA--G-CGAT-C--AAAACATC-AAA---A-CA-TATAATGTAATAGGTAAAATAACAA
* * * * *
1567630 TGTAATCAGCCTAAATATATC-GTTTTTGAGAAAATAGGTATACATAAAGTATCGACATAAATCC
117 TGTAACCGGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCC
*
1567694 AACAC
182 AACAA
* ** * ** *
1567699 GTGTCAATACTAATTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1 GTGTCGATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATAC--T
1567764 TATAACAAG
64 TATAACAAG
1567773 TGTCGATCCC
Statistics
Matches: 944, Mismatches: 72, Indels: 75
0.87 0.07 0.07
Matches are distributed among these distances:
179 147 0.16
180 1 0.00
182 2 0.00
183 3 0.00
184 4 0.00
187 5 0.01
188 1 0.00
189 1 0.00
190 2 0.00
191 1 0.00
192 7 0.01
193 1 0.00
195 2 0.00
196 4 0.00
197 6 0.01
198 3 0.00
199 117 0.12
200 616 0.65
201 19 0.02
202 2 0.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.27
Consensus pattern (186 bp):
GTGTCGATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACTTA
TAACAAGCGATCAAAACATCAAAACATATAATGTAATAGGTAAAATAACAATGTAACCGGCCTAA
ATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAA
Found at i:1567114 original size:200 final size:200
Alignment explanation
Indices: 1566771--1567888 Score: 1641
Period size: 200 Copynumber: 5.6 Consensus size: 200
1566761 GTGTACGACA
*
1566771 AAGTGTCGATACTAAAAACATCGAAACACA-AAGATATAATGTAATAGGTAAAATAACAATGTAA
1 AAGTGTCGATACTAAAAACATCGAAACACATAA-TTATAATGTAATAGGTAAAATAACAATGTAA
* * * *
1566835 CCAGCCTAAATATATCAGTTTTTGAGAAAACATGTATACATAAAGTATCGACACAAATCCAACAA
65 CCGGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAA
* * ** *
1566900 GTGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATT
130 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1566965 TATAAC
195 TATAAC
* *
1566971 AAGTGTCGATAATAAAAACATCGAAACATATAGA-TATAATGTAATAGGTAAAATAACAATGTAA
1 AAGTGTCGATACTAAAAACATCGAAACACATA-ATTATAATGTAATAGGTAAAATAACAATGTAA
* * * *
1567035 TCGGCCTAAATATGCCGGTTTTTGAGAAAACGGGTATACATAAAGTATAGACACAAATCCAACAA
65 CCGGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAA
* ** *
1567100 GTGTCGATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATT
130 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
1567165 TATAAC
195 TATAAC
* *
1567171 AAGTGTCGATACTAAAAACATCAAAACACATAGA-TATAATGTAATATGTAAAATAACAATGTAA
1 AAGTGTCGATACTAAAAACATCGAAACACATA-ATTATAATGTAATAGGTAAAATAACAATGTAA
* * * *
1567235 CCGGCCTAAATATACCAGTTTTTAAGAAAACAGGTATACATAAAGTATCAACACAAATTCAACAA
65 CCGGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAA
1567300 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
130 GTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATT
*
1567365 TATAAT
195 TATAAC
* * *
1567371 AAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAAATAACAATGTAAC
1 AAGTGTCGATACTAAAAACATCGAAACACATAATTATAATGTAATAGGTAAAATAACAATGTAAC
* *
1567436 CGGCCAAAATATATCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAAG
66 CGGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAAG
*
1567501 TGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTATCGATACATTT
131 TGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTT
1567566 ATAAC
196 ATAAC
* *
1567571 AAGTGTCGATACTAAAAACATCGAAACTCATAATTATAATGTAATAGGTAAAATAACAATGTAAT
1 AAGTGTCGATACTAAAAACATCGAAACACATAATTATAATGTAATAGGTAAAATAACAATGTAAC
* * * * *
1567636 CAGCCTAAATATATC-GTTTTTGAGAAAATAGGTATACATAAAGTATCGACATAAATCCAACACG
66 CGGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAAG
* **
1567700 TGTCAATACTAATTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTT
131 TGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTT
1567765 ATAAC
196 ATAAC
* * * * * ** * *
1567770 AAGTGTCGATCCCAAAAATATCGAAACCCATAATTATAATGTAATAGGTCACTTTACAATGTAAT
1 AAGTGTCGATACTAAAAACATCGAAACACATAATTATAATGTAATAGGTAAAATAACAATGTAAC
* ** * * * *
1567835 TGGTTTAAATATACCGGTTTTATGAGAAAATAGGTCTAAATAATGTATCGACAC
66 CGGCCTAAATATACCGGTTTT-TGAGAAAACAGGTATACATAAAGTATCGACAC
1567889 TTTATTTATT
Statistics
Matches: 842, Mismatches: 71, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
199 180 0.21
200 632 0.75
201 29 0.03
202 1 0.00
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (200 bp):
AAGTGTCGATACTAAAAACATCGAAACACATAATTATAATGTAATAGGTAAAATAACAATGTAAC
CGGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAAG
TGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTT
ATAAC
Found at i:1567955 original size:600 final size:599
Alignment explanation
Indices: 1566770--1568038 Score: 1674
Period size: 600 Copynumber: 2.1 Consensus size: 599
1566760 AGTGTACGAC
* * *
1566770 AAAGTGTCGATACTAAAAACATCGAAACACAAAGATATAATGTAATAGGTAAAATAACAATGTAA
1 AAAGTGTCGATCCTAAAAACATCGAAACCCAAA-TTATAATGTAATAGGTAAAATAACAATGTAA
* * *
1566835 CCAGCCTAAATATATCAGTTTTTGAGAAAACATGTATACATAAAGTATCGACACAAATCCAACAA
65 CCGGCCAAAATATATCAGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAA
* ** * *
1566900 GTGTCGATACTTTTTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATT
130 GTGTCGATACTTTTTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTATCGATACATT
1566965 TATAACAAGTGTCGATAATAAAAACATCGAAACATATAGATATAATGTAATAGGTAAAATAACAA
195 TATAACAAGTGTCGATAATAAAAACATCGAAACATATAGATATAATGTAATAGGTAAAATAACAA
* * *
1567030 TGTAATCGGCCTAAATATGCCGGTTTTTGAGAAAACGGGTATACATAAAGTATAGACACAAATCC
260 TGTAATCAGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATAGACACAAATCC
* ** ** *
1567095 AACAAGTGTCGATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGAT
325 AACAAGTGTCAATACTAATTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGAT
* *
1567160 ACATTTATAACAAGTGTCGATACTAAAAACATCAAAACACATAGATATAATGTAATATGTAAAAT
390 ACATTTATAACAAGTGTCGATACCAAAAACATCAAAACACATAGATATAATGTAATAGGTAAAAT
*
1567225 AACAATGTAACCGGCCTAAATATACCAGTTTTTAAGAAAACAGGTATACATAAAGTATCAACACA
455 AACAATGTAACCGGCCTAAATATACCAGTTTTTAAGAAAACAGGTATAAATAAAGTATCAACACA
* * * *
1567290 AATTCAACAAGTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTG
520 AATTCAACAAGTGTCGATACTTTTTATCCAGAATGTAATTCAAAAACCAAGTGCACAACAAAGTG
1567355 TCGATACA-TTTATA
585 TCGATACATTTTATA
*
1567369 ATAAGTGTCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAAATAACAATGTA
1 A-AAGTGTCGATCCTAAAAACATCGAAACCCA-AATTATAATGTAATAGGTAAAATAACAATGTA
*
1567434 ACCGGCCAAAATATATCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACA
64 ACCGGCCAAAATATATCAGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACA
*
1567499 AGTGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTATCGATACAT
129 AGTGTCGATACTTTTTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTATCGATACAT
*
1567564 TTATAACAAGTGTCGATACTAAAAACATCGAAAC-TCATA-ATTATAATGTAATAGGTAAAATAA
194 TTATAACAAGTGTCGATAATAAAAACATCGAAACAT-ATAGA-TATAATGTAATAGGTAAAATAA
* * * *
1567627 CAATGTAATCAGCCTAAATATATC-GTTTTTGAGAAAATAGGTATACATAAAGTATCGACATAAA
257 CAATGTAATCAGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATAGACACAAA
* *
1567691 TCCAACACGTGTCAATACTAATTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTC
322 TCCAACAAGTGTCAATACTAATTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTC
* * * * *
1567756 GATACATTTATAACAAGTGTCGATCCCAAAAATATCGAAACCCATA-ATTATAATGTAATAGGTC
387 GATACATTTATAACAAGTGTCGATACCAAAAACATCAAAACACATAGA-TATAATGTAATAGGTA
** * ** ** * * * * * *
1567820 ACTTTACAATGTAATTGGTTTAAATATACCGGTTTTATGAGAAAATAGGTCTAAATAATGTATCG
451 AAATAACAATGTAACCGGCCTAAATATACCAGTTTT-TAAGAAAACAGGTATAAATAAAGTATCA
** * *** * ** * *
1567885 ACACTTTATT-TATTTGTGTCGATACTTTTTATCCATAATG-AATTCCCAAA-CTA-TGTACAAG
515 ACAC-AAATTCAACAAGTGTCGATACTTTTTATCCAGAATGTAATTCAAAAACCAAGTGCACAA-
*
1567946 CTTAAAGTGTCGATACATTTTTTA
578 C--AAAGTGTCGATACATTTTATA
* * * * * * * ** *
1567970 AAAGTATCGAACCTAAATACACCGAGACCGAAAATTATAATGTAATAGGTCACTTTACAATGTAA
1 AAAGTGTCGATCCTAAAAACATCGAAACC-CAAATTATAATGTAATAGGTAAAATAACAATGTAA
1568035 CCGG
65 CCGG
1568039 TTTAAATTTA
Statistics
Matches: 580, Mismatches: 78, Indels: 23
0.85 0.11 0.03
Matches are distributed among these distances:
597 6 0.01
598 4 0.01
599 185 0.32
600 373 0.64
601 12 0.02
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.28
Consensus pattern (599 bp):
AAAGTGTCGATCCTAAAAACATCGAAACCCAAATTATAATGTAATAGGTAAAATAACAATGTAAC
CGGCCAAAATATATCAGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAAG
TGTCGATACTTTTTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTATCGATACATTT
ATAACAAGTGTCGATAATAAAAACATCGAAACATATAGATATAATGTAATAGGTAAAATAACAAT
GTAATCAGCCTAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATAGACACAAATCCA
ACAAGTGTCAATACTAATTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATA
CATTTATAACAAGTGTCGATACCAAAAACATCAAAACACATAGATATAATGTAATAGGTAAAATA
ACAATGTAACCGGCCTAAATATACCAGTTTTTAAGAAAACAGGTATAAATAAAGTATCAACACAA
ATTCAACAAGTGTCGATACTTTTTATCCAGAATGTAATTCAAAAACCAAGTGCACAACAAAGTGT
CGATACATTTTATA
Found at i:1568194 original size:600 final size:598
Alignment explanation
Indices: 1566784--1568234 Score: 1490
Period size: 600 Copynumber: 2.4 Consensus size: 598
1566774 TGTCGATACT
* * * *
1566784 AAAAACATCGAAACACAAAGA-TATAATGTAATAGGTAAAATAACAATGTAACCAGCCTAAATAT
1 AAAAACACCGAAACCCAAA-ATTATAATGTAATAGGTAAAATAACAATGTAACCGGCCAAAATAT
* * *
1566848 ATCAGTTTTTGAGAAAACATGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTT
65 ACCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACAC-AATCCAACAAGTGTCGATACTTT
* * * ** * * * * * *
1566913 TTGTCCATAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAACAAGTGTC
129 ATGTCCAGAATGTA-TATAAAAACCAAGTCCACAACAAAGTATCAATACATTTATAAAAAGTATC
* ** *
1566978 GATAATAAAAACATCGAAACAT-ATAGA-TATAATGTAATAGGTAAAATAACAATGTAATCGGCC
193 GACACCAAAAACATCGAAAC-TCATA-ATTATAATGTAATAGGTAAAATAACAATGTAATCAGCC
* * *
1567041 TAAATATGCCGGTTTTTGAGAAAACGGGTATACATAAAGTATAGACACAAATCCAACAAGTGTCG
256 TAAATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATAGACACAAATCCAACAAGTGTCA
** ** *
1567106 ATACTTTTTGTCCAGAATGTATTTTCCAAACCAAGTGCACGACAAAGTGTCGATACATTTATAAC
321 ATACTAATTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAAC
* *
1567171 AAGTGTCGATACTAAAAACATCAAAACACATAGATATAATGTAATATGTAAAATAACAATGTAAC
386 AAGTGTCGATACCAAAAACATCAAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAAC
*
1567236 CGGCCTAAATATACCAGTTTTTAAGAAAACAGGTATACATAAAGTATCAACACAAATTCAACAAG
451 CGGCCTAAATATACCAGTTTTTAAGAAAACAGGTATAAATAAAGTATCAACACAAATTCAACAAG
* * * *
1567301 TGTCGATACTTTTTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTT
516 TGTCGATACTTTTTATCCAGAATGTAATTCAAAAACCAAGTGCACAACAAAGTGTCGATACATTT
* *
1567366 ATAATAAGTGTCGATCCC
581 ATAATAAGTATCGAACCC
* *
1567384 AAAAACATCGAAACCCATAATTATAATGTAATAGGTAAAATAACAATGTAACCGGCCAAAATATA
1 AAAAACACCGAAACCCAAAATTATAATGTAATAGGTAAAATAACAATGTAACCGGCCAAAATATA
* *
1567449 TCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAAATCCAACAAGTGTCGATACTTTT
66 CCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACAC-AATCCAACAAGTGTCGATACTTTA
* * * * * *
1567514 TGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTATCGATACATTTATAACAAGTGTCG
130 TGTCCAGAATGTA-TATAAAAACCAAGTCCACAACAAAGTATCAATACATTTATAAAAAGTATCG
* *
1567579 ATACTAAAAACATCGAAACTCATAATTATAATGTAATAGGTAAAATAACAATGTAATCAGCCTAA
194 ACACCAAAAACATCGAAACTCATAATTATAATGTAATAGGTAAAATAACAATGTAATCAGCCTAA
* * * * *
1567644 ATATATC-GTTTTTGAGAAAATAGGTATACATAAAGTATCGACATAAATCCAACACGTGTCAATA
259 ATATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATAGACACAAATCCAACAAGTGTCAATA
*
1567708 CTAATTGTCCAGAGTGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAACAAG
324 CTAATTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAACAAG
* * * * * ** * **
1567773 TGTCGATCCCAAAAATATCGAAACCCATA-ATTATAATGTAATAGGTCACTTTACAATGTAATTG
389 TGTCGATACCAAAAACATCAAAACACATAGA-TATAATGTAATAGGTAAAATAACAATGTAACCG
** * * * * * * ** * ***
1567837 GTTTAAATATACCGGTTTTATGAGAAAATAGGTCTAAATAATGTATCGACACTTTATT-TATTTG
453 GCCTAAATATACCAGTTTT-TAAGAAAACAGGTATAAATAAAGTATCAACAC-AAATTCAACAAG
* ** * *
1567901 TGTCGATACTTTTTATCCATAATG-AATTCCCAAA-CTA-TGTACAAGCTTAAAGTGTCGATACA
516 TGTCGATACTTTTTATCCAGAATGTAATTCAAAAACCAAGTGCACAA-C--AAAGTGTCGATACA
* *
1567963 TTTTTTAA-AAGTATCGAACCT
578 -TTTATAATAAGTATCGAACCC
* * * * ** * *** *
1567984 AAATACACCGAGACCGAAAATTATAATGTAATAGGTCACTTTACAATGTAACCGGTTTAAATTTA
1 AAAAACACCGAAACCCAAAATTATAATGTAATAGGTAAAATAACAATGTAACCGGCCAAAATATA
* * * * * * * *** *
1568049 CCGGTTTTATGAGCAAATAGGTCTACATGATGTATCGATAC-TTTGTACATTTGTGTCGATACTT
66 CCGGTTTT-TGAGAAAACAGGTATACATAAAGTATCGACACAATCCAACA--AGTGTCGATACTT
* *** * * * *
1568113 TATGTCCATAATG-A-ATGCCAACCGATGTCCACGCATAAAGTTTCAATACATTTATAAAAAGTA
128 TATGTCCAGAATGTATATAAAAACC-AAGTCCAC-AACAAAGTATCAATACATTTATAAAAAGTA
* * * * * * * *
1568176 TCTACCCCAAATACATCGAGAC-CAGAAATTATAATGTAATAGGTCAATTTACAATGTAA
191 TCGACACCAAAAACATCGAAACTCA-TAATTATAATGTAATAGGTAAAATAACAATGTAA
1568235 CCGGTTGAAA
Statistics
Matches: 717, Mismatches: 118, Indels: 32
0.83 0.14 0.04
Matches are distributed among these distances:
597 6 0.01
598 9 0.01
599 197 0.27
600 448 0.62
601 57 0.08
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (598 bp):
AAAAACACCGAAACCCAAAATTATAATGTAATAGGTAAAATAACAATGTAACCGGCCAAAATATA
CCGGTTTTTGAGAAAACAGGTATACATAAAGTATCGACACAATCCAACAAGTGTCGATACTTTAT
GTCCAGAATGTATATAAAAACCAAGTCCACAACAAAGTATCAATACATTTATAAAAAGTATCGAC
ACCAAAAACATCGAAACTCATAATTATAATGTAATAGGTAAAATAACAATGTAATCAGCCTAAAT
ATACCGGTTTTTGAGAAAACAGGTATACATAAAGTATAGACACAAATCCAACAAGTGTCAATACT
AATTGTCCAGAATGTATTTTAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAACAAGTG
TCGATACCAAAAACATCAAAACACATAGATATAATGTAATAGGTAAAATAACAATGTAACCGGCC
TAAATATACCAGTTTTTAAGAAAACAGGTATAAATAAAGTATCAACACAAATTCAACAAGTGTCG
ATACTTTTTATCCAGAATGTAATTCAAAAACCAAGTGCACAACAAAGTGTCGATACATTTATAAT
AAGTATCGAACCC
Found at i:1568248 original size:200 final size:201
Alignment explanation
Indices: 1567748--1568292 Score: 659
Period size: 201 Copynumber: 2.7 Consensus size: 201
1567738 AGTGCACAAC
* * * * * * *
1567748 AAAGTGTCGATACATTTATAACAAGTGTCGATCCCAAAAATATCGAAACCCA-TAATTATAATGT
1 AAAGTGTCGATACATTTATAAAAAGTATCGAACCCAAATACATCGAGA-CCAGAAATTATAATGT
** *
1567812 AATAGGTCACTTTACAATGTAATTGGTTTAAATATACCGGTTTTATGAGAAAATAGGTCTAAATA
65 AATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTAAATA
** * *
1567877 ATGTATCGACACTTTATTTATTTGTGTCGATACTTTTTATCCATAATGAATTCCCAAACTATGTA
130 ATGTATCGACACTTTATACATTTGTGTCGATACTTTATATCCATAATGAATTCCCAAACGATGTA
*
1567942 CAAGCTT
195 CAAGCAT
* * * *
1567949 AAAGTGTCGATACATTTTTTAAAAGTATCGAACCTAAATACACCGAGACC-GAAAATTATAATGT
1 AAAGTGTCGATACATTTATAAAAAGTATCGAACCCAAATACATCGAGACCAG-AAATTATAATGT
* * *
1568013 AATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGCAAATAGGTCTACATG
65 AATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTAAATA
* * * * * *
1568078 ATGTATCGATACTTTGTACATTTGTGTCGATACTTTATGTCCATAATGAA-TGCCAACCGATGTC
130 ATGTATCGACACTTTATACATTTGTGTCGATACTTTATATCCATAATGAATTCCCAAACGATGTA
*
1568142 CACGCAT
195 CAAGCAT
* * * *
1568149 AAAGTTTCAATACATTTATAAAAAGTATCTACCCCAAATACATCGAGACCAGAAATTATAATGTA
1 AAAGTGTCGATACATTTATAAAAAGTATCGAACCCAAATACATCGAGACCAGAAATTATAATGTA
* * * **
1568214 ATAGGTCAATTTACAATGTAACCGGTTGAAATTTACCGATGTAAAT-AGAAAATAGGTC-AACAT
66 ATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGT-TTTATGAGAAAATAGGTCTAA-AT
* *
1568277 AATGTGTCAACACTTT
129 AATGTATCGACACTTT
1568293 TTAAATCCGT
Statistics
Matches: 291, Mismatches: 48, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
199 1 0.00
200 134 0.46
201 156 0.54
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (201 bp):
AAAGTGTCGATACATTTATAAAAAGTATCGAACCCAAATACATCGAGACCAGAAATTATAATGTA
ATAGGTCACTTTACAATGTAACCGGTTTAAATTTACCGGTTTTATGAGAAAATAGGTCTAAATAA
TGTATCGACACTTTATACATTTGTGTCGATACTTTATATCCATAATGAATTCCCAAACGATGTAC
AAGCAT
Found at i:1572222 original size:180 final size:183
Alignment explanation
Indices: 1571879--1572226 Score: 479
Period size: 180 Copynumber: 1.9 Consensus size: 183
1571869 AACGACAAGC
* *
1571879 ACGCATTAAGTGTCAATACATTTATAAAAACTATCGATCCCAAAAACATCGAGACCGATAATTAT
1 ACGCATAAAGTGTCAATACATTTATAAAAACTATCGATCCCAAAAACATCGAAACCGATAATTAT
* *
1571944 AATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATATACCGGGTTAATGAGATAATAGGTCA
66 AATGTAACAGG---A-TTACAATGTAACCGGTAAAAATATACCGGGTTAATGAGATAATAGGTCA
* *
1572009 ACATAAAGTATCGACACTTTTTAAATTTGTGTCGATACATTTGTCCAGAAGAGGTGT
127 ACATAAAGTATCGACACTCTTTAAATATGTGTCGATACATTTGTCCAGAAGAGGTGT
* * *
1572066 ACGCATAAAGTGTCGATACATTTATAAAAAGTATTGATCCC-AAAACATCGAAACCGATAATTAT
1 ACGCATAAAGTGTCAATACATTTATAAAAACTATCGATCCCAAAAACATCGAAACCGATAATTAT
* * * * *
1572130 TATGTAACAGG-TTACAATGTAACCGGTAAAAATATA-CTGGTTAATTAGCA-AATATGTCTACA
66 AATGTAACAGGATTACAATGTAACCGGTAAAAATATACCGGGTTAATGAG-ATAATAGGTCAACA
* *
1572192 TTATGTATCGACACTCTTTAAATATGTGTCGATAC
130 TAAAGTATCGACACTCTTTAAATATGTGTCGATAC
1572227 TTTTTTTCCA
Statistics
Matches: 144, Mismatches: 16, Indels: 9
0.85 0.09 0.05
Matches are distributed among these distances:
180 51 0.35
181 25 0.17
186 31 0.22
187 37 0.26
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (183 bp):
ACGCATAAAGTGTCAATACATTTATAAAAACTATCGATCCCAAAAACATCGAAACCGATAATTAT
AATGTAACAGGATTACAATGTAACCGGTAAAAATATACCGGGTTAATGAGATAATAGGTCAACAT
AAAGTATCGACACTCTTTAAATATGTGTCGATACATTTGTCCAGAAGAGGTGT
Found at i:1572523 original size:23 final size:23
Alignment explanation
Indices: 1572473--1572517 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
1572463 TGCCTATTTT
*
1572473 ATTATATAAGCGCTACCTATTAC
1 ATTATATAAGCGCTACCTAATAC
1572496 ATTATATAAGCGCTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1572518 TGTTATTGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.33
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1572539 original size:87 final size:87
Alignment explanation
Indices: 1572389--1572551 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
1572379 AAATAAGTCA
*
1572389 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTAATGATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTAATAATATTT
*
1572454 CCGGTTAAATGCCTATTTTATT
66 CCAGTTAAATGCCTATTTTATT
* * *
1572476 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTAATAATATTT
1572541 CCAGTTAAATG
66 CCAGTTAAATG
1572552 ATATAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTATACTTAATAATATTT
CCAGTTAAATGCCTATTTTATT
Found at i:1574163 original size:3 final size:3
Alignment explanation
Indices: 1574155--1574195 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
1574145 ATAAACCTGC
1574155 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1574196 AACCTAGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1576232 original size:28 final size:27
Alignment explanation
Indices: 1576190--1576379 Score: 148
Period size: 29 Copynumber: 6.6 Consensus size: 27
1576180 TCCACATTCG
* *
1576190 AAAATTACCAAAATGTCA-CTTTTTTAA
1 AAAATT-CCCAAATGTCACCTTTTTCAA
* * *
1576217 AATAATTCCCATAATGTCACTTTTTTTAC
1 AA-AATTCCCA-AATGTCACCTTTTTCAA
* *
1576246 AAAATTCTCGAAATGTCATCTTTTTCAA
1 AAAATTC-CCAAATGTCACCTTTTTCAA
* * * *
1576274 AAAGCTTTCCAGAATGTCACATTTTTCACT
1 AAA-ATTCCCA-AATGTCACCTTTTTCA-A
1576304 AAAATTCCCGAAATGTCACCTTTTTCAA
1 AAAATTCCC-AAATGTCACCTTTTTCAA
*
1576332 AATAATTCCCAGAATGTCACCTTTATCACA
1 AA-AATTCCCA-AATGTCACCTTTTTCA-A
*
1576362 ATAATTCCCAAAATGTCA
1 AAAATTCCC-AAATGTCA
1576380 TCGAGTCGGG
Statistics
Matches: 131, Mismatches: 20, Indels: 22
0.76 0.12 0.13
Matches are distributed among these distances:
27 5 0.04
28 37 0.28
29 82 0.63
30 7 0.05
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (27 bp):
AAAATTCCCAAATGTCACCTTTTTCAA
Found at i:1576318 original size:58 final size:57
Alignment explanation
Indices: 1576190--1576381 Score: 226
Period size: 58 Copynumber: 3.4 Consensus size: 57
1576180 TCCACATTCG
* * * * *
1576190 AAAATTACCAAAATGTCA-CTTTTTTAAAATAATTCCCATAATGTCACTTTTTTTAC
1 AAAATTCCCAAAATGTCATCTTTTTCAAAATAATTCCCAGAATGTCACATTTTTCAC
* * * *
1576246 AAAATTCTCGAAATGTCATCTTTTTCAAAA-AGCTTTCCAGAATGTCACATTTTTCAC
1 AAAATTCCCAAAATGTCATCTTTTTCAAAATA-ATTCCCAGAATGTCACATTTTTCAC
* * * *
1576303 TAAAATTCCCGAAATGTCACCTTTTTCAAAATAATTCCCAGAATGTCACCTTTATCAC
1 -AAAATTCCCAAAATGTCATCTTTTTCAAAATAATTCCCAGAATGTCACATTTTTCAC
1576361 AATAATTCCCAAAATGTCATC
1 AA-AATTCCCAAAATGTCATC
1576382 GAGTCGGGTT
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
56 16 0.14
57 32 0.28
58 65 0.57
59 1 0.01
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (57 bp):
AAAATTCCCAAAATGTCATCTTTTTCAAAATAATTCCCAGAATGTCACATTTTTCAC
Found at i:1580075 original size:146 final size:146
Alignment explanation
Indices: 1579811--1580104 Score: 570
Period size: 146 Copynumber: 2.0 Consensus size: 146
1579801 TGTCATCTTG
*
1579811 TTCAACTTCCGATAGTTAATACATAGCCTTAGCGACCCATCCTTCTTTTTCACAAACAAAACTGG
1 TTCAACTTCCGATAGTCAATACATAGCCTTAGCGACCCATCCTTCTTTTTCACAAACAAAACTGG
1579876 AGCTCCCCATGGTGAGGTACTATGCCGAATAAATCCTCGATCGAATAATTCTTGCATTGGACCTT
66 AGCTCCCCATGGTGAGGTACTATGCCGAATAAATCCTCGATCGAATAATTCTTGCATTGGACCTT
1579941 CAACTCCTTAAGTTCC
131 CAACTCCTTAAGTTCC
*
1579957 TTCAACTTCTGATAGTCAATACATAGCCTTAGCGACCCATCCTTCTTTTTCACAAACAAAACTGG
1 TTCAACTTCCGATAGTCAATACATAGCCTTAGCGACCCATCCTTCTTTTTCACAAACAAAACTGG
1580022 AGCTCCCCATGGTGAGGTACTATGCCGAATAAATCCTCGATCGAATAATTCTTGCATTGGACCTT
66 AGCTCCCCATGGTGAGGTACTATGCCGAATAAATCCTCGATCGAATAATTCTTGCATTGGACCTT
1580087 CAACTCCTTAAGTTCC
131 CAACTCCTTAAGTTCC
1580103 TT
1 TT
1580105 TGGAGCCATG
Statistics
Matches: 146, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
146 146 1.00
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (146 bp):
TTCAACTTCCGATAGTCAATACATAGCCTTAGCGACCCATCCTTCTTTTTCACAAACAAAACTGG
AGCTCCCCATGGTGAGGTACTATGCCGAATAAATCCTCGATCGAATAATTCTTGCATTGGACCTT
CAACTCCTTAAGTTCC
Found at i:1583859 original size:29 final size:29
Alignment explanation
Indices: 1583826--1583953 Score: 159
Period size: 29 Copynumber: 4.4 Consensus size: 29
1583816 TCGAAAAGTA
* *
1583826 CCAAAATATTACTTTTTTAAAAATAATTC
1 CCAAAATGTCACTTTTTTAAAAATAATTC
* *
1583855 CCAAAATGTCACTTTTTCATAAA-AATTC
1 CCAAAATGTCACTTTTTTAAAAATAATTC
* *
1583883 CCAAATTGTCACTTTTTTCAAAATAATTC
1 CCAAAATGTCACTTTTTTAAAAATAATTC
* * * *
1583912 CCAGAATGTCACCTTTTTCATAATAATTC
1 CCAAAATGTCACTTTTTTAAAAATAATTC
1583941 CCAAAATGTCACT
1 CCAAAATGTCACT
1583954 GGGTCGGGTC
Statistics
Matches: 84, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
28 24 0.29
29 60 0.71
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (29 bp):
CCAAAATGTCACTTTTTTAAAAATAATTC
Found at i:1583914 original size:57 final size:58
Alignment explanation
Indices: 1583826--1583953 Score: 195
Period size: 57 Copynumber: 2.2 Consensus size: 58
1583816 TCGAAAAGTA
* *
1583826 CCAAAATATTACTTTTTTAAAAATAATTCCCAAAATGTCA-CTTTTTCATAAAAATTC
1 CCAAAATGTCACTTTTTTAAAAATAATTCCCAAAATGTCACCTTTTTCATAAAAATTC
* * * *
1583883 CCAAATTGTCACTTTTTTCAAAATAATTCCCAGAATGTCACCTTTTTCATAATAATTC
1 CCAAAATGTCACTTTTTTAAAAATAATTCCCAAAATGTCACCTTTTTCATAAAAATTC
1583941 CCAAAATGTCACT
1 CCAAAATGTCACT
1583954 GGGTCGGGTC
Statistics
Matches: 63, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
57 35 0.56
58 28 0.44
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (58 bp):
CCAAAATGTCACTTTTTTAAAAATAATTCCCAAAATGTCACCTTTTTCATAAAAATTC
Found at i:1585118 original size:2 final size:2
Alignment explanation
Indices: 1585111--1585139 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1585101 CTATTTTCTG
1585111 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1585140 TTGGATTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1587975 original size:17 final size:17
Alignment explanation
Indices: 1587955--1587990 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1587945 TAAAAAAAGT
*
1587955 TAAAATTTTAAAAATAA
1 TAAAATGTTAAAAATAA
1587972 TAAAATGTTAAAAATAA
1 TAAAATGTTAAAAATAA
1587989 TA
1 TA
1587991 TATATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (17 bp):
TAAAATGTTAAAAATAA
Found at i:1587995 original size:2 final size:2
Alignment explanation
Indices: 1587988--1588036 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1587978 GTTAAAAATA
1587988 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1588030 AT AT AT A
1 AT AT AT A
1588037 ATACTCTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1593186 original size:16 final size:17
Alignment explanation
Indices: 1593150--1593187 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
1593140 TTTTCCCCCT
*
1593150 TTTTTCTTTTCTTTTGC
1 TTTTTCTTTTCTTTTGA
*
1593167 TTTTT-TTTTCTTTTTA
1 TTTTTCTTTTCTTTTGA
1593183 TTTTT
1 TTTTT
1593188 GATAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.03, C:0.11, G:0.03, T:0.84
Consensus pattern (17 bp):
TTTTTCTTTTCTTTTGA
Found at i:1601589 original size:17 final size:18
Alignment explanation
Indices: 1601557--1601590 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1601547 TAATTATATG
*
1601557 ATAATATTTGAAATGAAA
1 ATAAAATTTGAAATGAAA
1601575 ATAAAATTT-AAATGAA
1 ATAAAATTTGAAATGAA
1601591 TATATGGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (18 bp):
ATAAAATTTGAAATGAAA
Found at i:1602185 original size:24 final size:23
Alignment explanation
Indices: 1602142--1602217 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 23
1602132 TATTAAAATT
1602142 AAAAATAT-TTT-TAAAGTTA-TA
1 AAAAATATATTTATAAA-TTATTA
1602163 AAAATATATATATTATAAATTATTA
1 AAAA-ATATAT-TTATAAATTATTA
* *
1602188 TAAAAATTTATTTATAAAATATTA
1 -AAAAATATATTTATAAATTATTA
1602212 AAAAAT
1 AAAAAT
1602218 TTAAGTACTT
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
21 4 0.09
22 4 0.09
23 7 0.15
24 17 0.36
25 11 0.23
26 4 0.09
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (23 bp):
AAAAATATATTTATAAATTATTA
Found at i:1602188 original size:27 final size:24
Alignment explanation
Indices: 1602158--1602220 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 24
1602148 ATTTTTAAAG
*
1602158 TTATAAAAATATATATATTATAAATTA
1 TTATAAAAAT-T-TAT-TTATAAAATA
1602185 TTATAAAAATTTATTTATAAAATA
1 TTATAAAAATTTATTTATAAAATA
1602209 TTA-AAAAATTTA
1 TTATAAAAATTTA
1602221 AGTACTTTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
23 9 0.26
24 12 0.34
25 3 0.09
26 1 0.03
27 10 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TTATAAAAATTTATTTATAAAATA
Found at i:1603515 original size:21 final size:21
Alignment explanation
Indices: 1603489--1603538 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
1603479 CACAGTGTAC
1603489 CGATGCACCTTGACCATGCAT
1 CGATGCACCTTGACCATGCAT
1603510 CGATGCACCTTGACCATGCAT
1 CGATGCACCTTGACCATGCAT
1603531 CGATGCAC
1 CGATGCAC
1603539 ACACGCTCCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.34, G:0.20, T:0.22
Consensus pattern (21 bp):
CGATGCACCTTGACCATGCAT
Found at i:1603901 original size:19 final size:19
Alignment explanation
Indices: 1603877--1603921 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
1603867 AAATTTGTAT
*
1603877 TGTTCTCTTTGGTAGAAAG
1 TGTTCTCTTTGGGAGAAAG
*
1603896 TGTTCTCTTTGGGAGAGAG
1 TGTTCTCTTTGGGAGAAAG
1603915 TGTTCTC
1 TGTTCTC
1603922 AAGAATTTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.13, G:0.29, T:0.42
Consensus pattern (19 bp):
TGTTCTCTTTGGGAGAAAG
Found at i:1605581 original size:21 final size:21
Alignment explanation
Indices: 1605535--1605595 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
1605525 TTTATAAATT
*
1605535 TATTTTATTTTTATATTTCTA
1 TATTTTATTTTTAAATTTCTA
*
1605556 TATTTTATTTTTAAATTATGTA
1 TATTTTATTTTTAAATT-TCTA
*
1605578 -ATTTAAATTTTTAAATTT
1 TATTT-TATTTTTAAATTT
1605596 TATGTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 21 0.60
22 14 0.40
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TATTTTATTTTTAAATTTCTA
Found at i:1605597 original size:35 final size:37
Alignment explanation
Indices: 1605557--1605627 Score: 101
Period size: 35 Copynumber: 2.0 Consensus size: 37
1605547 ATATTTCTAT
* * *
1605557 ATTTTATTTTTAAATTATGT-AA-TTTAAATTTTTAA
1 ATTTTATGTTTAAATAATGTAAACTTTAAAATTTTAA
1605592 ATTTTATGTTTAAATAATGTAAACTTTAAAATTTTA
1 ATTTTATGTTTAAATAATGTAAACTTTAAAATTTTA
1605628 TACATTTTGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 18 0.58
36 2 0.06
37 11 0.35
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (37 bp):
ATTTTATGTTTAAATAATGTAAACTTTAAAATTTTAA
Found at i:1613179 original size:31 final size:31
Alignment explanation
Indices: 1613072--1613180 Score: 155
Period size: 31 Copynumber: 3.5 Consensus size: 31
1613062 ATAGATTCCA
* * *
1613072 AAGAACCTAGGTAATCAGTCCACATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
*
1613103 AAGAACATAGGTAAATAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
* * *
1613134 AAAAACATAGGTAAACAGTCTATATATCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCG
1613165 AAGAACATAGGTAAAC
1 AAGAACATAGGTAAAC
1613181 CCTCGACCCT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 69 1.00
ACGTcount: A:0.41, C:0.21, G:0.17, T:0.20
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCG
Found at i:1613870 original size:21 final size:19
Alignment explanation
Indices: 1613844--1613882 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
1613834 CACTTTTGGG
1613844 GGGTATCGGTATCTCCCTATA
1 GGGTATCGGTA-C-CCCTATA
1613865 GGGTATCGGTACCCCTAT
1 GGGTATCGGTACCCCTAT
1613883 TGAAATCTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 1 0.06
21 11 0.61
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.31
Consensus pattern (19 bp):
GGGTATCGGTACCCCTATA
Found at i:1616337 original size:24 final size:24
Alignment explanation
Indices: 1616310--1616361 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
1616300 CATACCAGAT
* *
1616310 TCCATGTCAAGCATCATATAAAAA
1 TCCAGGTCAAGCACCATATAAAAA
* * *
1616334 TCCAGGTCGAGTACCATATCAAAA
1 TCCAGGTCAAGCACCATATAAAAA
1616358 TCCA
1 TCCA
1616362 CAAAAAAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (24 bp):
TCCAGGTCAAGCACCATATAAAAA
Found at i:1621432 original size:17 final size:18
Alignment explanation
Indices: 1621404--1621440 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1621394 TAAGTGATAT
1621404 ATTAGAGTTAGGGTTAGG
1 ATTAGAGTTAGGGTTAGG
*
1621422 ATTAG-GTTAGGGTTTGG
1 ATTAGAGTTAGGGTTAGG
1621439 AT
1 AT
1621441 CTGGGGTTGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.38
Consensus pattern (18 bp):
ATTAGAGTTAGGGTTAGG
Found at i:1621917 original size:117 final size:118
Alignment explanation
Indices: 1621711--1621970 Score: 364
Period size: 117 Copynumber: 2.2 Consensus size: 118
1621701 TTTGAGTTGC
* ** * *
1621711 GAGTTCTTCTCATTATGAACTCT-TAGATGGGGATGTTGATTCATATCCTTCTATGATGAAAATG
1 GAGTTCTTCTCATTATGAACTCTCCAGATGGAAATGTTGATCCACATCCTTCTATGATGAAAATG
* *
1621775 AGTTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-CTCCTCTTCGGAT
66 AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC-CCTCATCGGAT
* * * * * *
1621828 GAGTTCTTCTCATTATGAACTCTCCA-CTGGAAATGTTGATCCACCTCCTTTTGTGATGGAATTG
1 GAGTTCTTCTCATTATGAACTCTCCAGATGGAAATGTTGATCCACATCCTTCTATGATGAAAATG
*
1621892 AGCTAAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGAT
66 AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGAT
1621945 GAGTTCTTCTCATTATGAACTCTCCA
1 GAGTTCTTCTCATTATGAACTCTCCA
1621971 ATGTTGAGCC
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
117 125 0.98
118 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (118 bp):
GAGTTCTTCTCATTATGAACTCTCCAGATGGAAATGTTGATCCACATCCTTCTATGATGAAAATG
AGCTAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGAT
Found at i:1622016 original size:46 final size:49
Alignment explanation
Indices: 1621949--1622063 Score: 148
Period size: 52 Copynumber: 2.3 Consensus size: 49
1621939 TCGGATGAGT
*
1621949 TCTTCTCATTATGAACTCT-C-C-AATGTTGA-GCCAAGGTTGAACAAGC
1 TCTTCTCATTATGAACTCTCCACGAATGTTGATG-AAAGGTTGAACAAGC
*
1621995 TCTTCTCATTATGAACTCTCCACTGGAAATGTTGATGAAAGGTTGAACAAGT
1 TCTTCTCATTATGAACTCTCCAC--G-AATGTTGATGAAAGGTTGAACAAGC
1622047 TCTTCTCATTATGAACT
1 TCTTCTCATTATGAACT
1622064 TCTTCTCCCT
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
46 19 0.32
47 1 0.02
48 1 0.02
52 38 0.63
53 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.34
Consensus pattern (49 bp):
TCTTCTCATTATGAACTCTCCACGAATGTTGATGAAAGGTTGAACAAGC
Found at i:1622056 original size:137 final size:138
Alignment explanation
Indices: 1621896--1622154 Score: 398
Period size: 137 Copynumber: 1.8 Consensus size: 138
1621886 GAATTGAGCT
* *
1621896 AAGGTTGAACAATTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATAAGTTCTTCTCATTAT
1621961 GAACTCTCC-AATGTTGA-GCCAAGGTTGAACAAGC-TCTTCTCATTATGAACTCTCCACTGGAA
66 GAACTCTCCAAATGTTGATG-CAAGGTTGAACAA-CTTCTTCTCATTATGAACTCTCCACTGGAA
1622023 ATGTTGATGA
129 ATGTTGATGA
* *
1622033 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTCGGATAAGTTTTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATAAGTTCTTCTCATTAT
1622098 GAACTCTCCATTGGAAATGTTGATGCAAGGTTGAACAACTTCTTCTCATTATGAACT
66 GAACTCTCC-----AAATGTTGATGCAAGGTTGAACAACTTCTTCTCATTATGAACT
1622155 TTTTCTTCCT
Statistics
Matches: 110, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
137 70 0.64
142 1 0.01
143 38 0.35
144 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (138 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATAAGTTCTTCTCATTAT
GAACTCTCCAAATGTTGATGCAAGGTTGAACAACTTCTTCTCATTATGAACTCTCCACTGGAAAT
GTTGATGA
Found at i:1622152 original size:91 final size:91
Alignment explanation
Indices: 1621997--1622396 Score: 502
Period size: 91 Copynumber: 4.4 Consensus size: 91
1621987 GAACAAGCTC
*
1621997 TTCTCATTATGAACTCTCCACTGGAAATGTTGATGAAAGGTTGAACAAGTTCTTCTCATTATGAA
1 TTCTCATTATGAACTCTCCACTGGAAATGTTGATGCAAGGTTGAACAAGTTCTTCTCATTATGAA
* *
1622062 CTTCTTCTCCCTCGTCGGATAAGTTT
66 CTTCTTCTCCCTCGTCAGATGAGTTT
* *
1622088 TTCTCATTATGAACTCTCCATTGGAAATGTTGATGCAAGGTTGAACAACTTCTTCTCATTATGAA
1 TTCTCATTATGAACTCTCCACTGGAAATGTTGATGCAAGGTTGAACAAGTTCTTCTCATTATGAA
* * * *
1622153 CTTTTTCTTCCTCGTCGGATGAGTTC
66 CTTCTTCTCCCTCGTCAGATGAGTTT
* * *
1622179 TTCTCATTATGAACTCTCCATTGCAAATGTTGATGCATGGTTGAACAAGTTCTTCTCATTATGAA
1 TTCTCATTATGAACTCTCCACTGGAAATGTTGATGCAAGGTTGAACAAGTTCTTCTCATTATGAA
1622244 CTTCTTCTCCCTCGTCAGATGAGTTCT
66 CTTCTTCTCCCTCGTCAGATGAGTT-T
** ** * * *
1622271 TT-TCATTACAAACTC-CCTACCAGAAATTTTGATCCAAGGTTGAACAAGTTATTCTCATTATGA
1 TTCTCATTATGAACTCTCC-ACTGGAAATGTTGATGCAAGGTTGAACAAGTTCTTCTCATTATGA
* *
1622334 ACTTATTC-CTCCTCGTCAAATGA-TTT
65 ACTTCTTCTC-CCTCGTCAGATGAGTTT
* * * *
1622360 CTTCACATTATGAACTCCCCCACTGGACATATTGATG
1 -TTCTCATTATGAACT-CTCCACTGGAAATGTTGATG
1622397 GTCTATCCTC
Statistics
Matches: 268, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
89 1 0.00
90 7 0.03
91 244 0.91
92 14 0.05
93 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.38
Consensus pattern (91 bp):
TTCTCATTATGAACTCTCCACTGGAAATGTTGATGCAAGGTTGAACAAGTTCTTCTCATTATGAA
CTTCTTCTCCCTCGTCAGATGAGTTT
Found at i:1623349 original size:5 final size:5
Alignment explanation
Indices: 1623329--1623418 Score: 60
Period size: 5 Copynumber: 17.8 Consensus size: 5
1623319 GAACCTCTTA
* * * * *
1623329 TTTTC TTTTTA TTTTC TTTTCC TTTTC TTTCC TTTCC TTTCC TTTCC TTTTTC
1 TTTTC -TTTTC TTTTC TTTT-C TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC
* *
1623382 TTTTTC TTTTC TTTGC -ATTC TTTTC -TTT- TTTTC TTTT
1 -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1623419 TAGGCATTGT
Statistics
Matches: 71, Mismatches: 8, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
4 8 0.11
5 44 0.62
6 19 0.27
ACGTcount: A:0.02, C:0.22, G:0.01, T:0.74
Consensus pattern (5 bp):
TTTTC
Found at i:1623381 original size:32 final size:32
Alignment explanation
Indices: 1623345--1623418 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
1623335 TTTTATTTTC
*
1623345 TTTTCCTTTTCTTTCCTTTCCTTTCCTTTCCT
1 TTTTCCTTTTCTTTCCTTTCCATTCCTTTCCT
* * * * *
1623377 TTTTCTTTTTCTTTTCTTTGCATTCTTTTCTT
1 TTTTCCTTTTCTTTCCTTTCCATTCCTTTCCT
*
1623409 TTTTTCTTTT
1 TTTTCCTTTT
1623419 TAGGCATTGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.01, C:0.24, G:0.01, T:0.73
Consensus pattern (32 bp):
TTTTCCTTTTCTTTCCTTTCCATTCCTTTCCT
Found at i:1636375 original size:6 final size:6
Alignment explanation
Indices: 1636364--1636394 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1636354 GAGTGATATA
1636364 TTAGGG TTAGGG TTAGGG TT-GGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
1636395 TGGATCCTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.13, C:0.00, G:0.48, T:0.39
Consensus pattern (6 bp):
TTAGGG
Found at i:1636389 original size:11 final size:12
Alignment explanation
Indices: 1636364--1636394 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
1636354 GAGTGATATA
1636364 TTAGGGTTAGGG
1 TTAGGGTTAGGG
1636376 TTAGGGTT-GGG
1 TTAGGGTTAGGG
1636387 TTAGGGTT
1 TTAGGGTT
1636395 TGGATCCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.58
12 8 0.42
ACGTcount: A:0.13, C:0.00, G:0.48, T:0.39
Consensus pattern (12 bp):
TTAGGGTTAGGG
Found at i:1640987 original size:16 final size:16
Alignment explanation
Indices: 1640968--1641001 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1640958 CAATATACGA
1640968 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
1640984 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
1641000 AT
1 AT
1641002 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:1641075 original size:16 final size:18
Alignment explanation
Indices: 1641043--1641076 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1641033 TATTAATGTA
1641043 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
1641061 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
1641077 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:1641570 original size:17 final size:17
Alignment explanation
Indices: 1641548--1641581 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1641538 AATTTTCTTC
1641548 TAATTAGGTGGTGACAT
1 TAATTAGGTGGTGACAT
1641565 TAATTAGGTGGTGACAT
1 TAATTAGGTGGTGACAT
1641582 GTGTCACCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.29, T:0.35
Consensus pattern (17 bp):
TAATTAGGTGGTGACAT
Found at i:1642265 original size:35 final size:35
Alignment explanation
Indices: 1642204--1642279 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
1642194 AATTGAATTT
* *
1642204 AATTGAATTATTTTAGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
* *
1642239 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
1642274 AATTGA
1 AATTGA
1642280 GGATTATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTAGAAATTAGGGTTTAGAATGA
Found at i:1643068 original size:4 final size:4
Alignment explanation
Indices: 1643059--1643099 Score: 82
Period size: 4 Copynumber: 10.2 Consensus size: 4
1643049 AATGCTGCAA
1643059 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1 TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT TCTT T
1643100 TGATTAACAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TCTT
Found at i:1643529 original size:68 final size:68
Alignment explanation
Indices: 1643413--1643543 Score: 185
Period size: 68 Copynumber: 1.9 Consensus size: 68
1643403 GTGTATATTT
* *
1643413 GAATTTTTCAAAATGATATCGCATTGATGCTTGTGTCATATCAATACGCCGA-TAACTATTTAAT
1 GAATTTTTCAAAACGATATCGCATTGATACTTGTGTCATATCAATACGCC-ATTAACTATTTAAT
1643477 AGAA
65 AGAA
* * *
1643481 GAATTTTTCAAAACGATATC-CTATTGATACTTGTGTCATGTCATTACGCCATTAATTATTTAA
1 GAATTTTTCAAAACGATATCGC-ATTGATACTTGTGTCATATCAATACGCCATTAACTATTTAA
1643544 CGCAGAGTAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 2 0.04
68 54 0.96
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (68 bp):
GAATTTTTCAAAACGATATCGCATTGATACTTGTGTCATATCAATACGCCATTAACTATTTAATA
GAA
Found at i:1654177 original size:25 final size:25
Alignment explanation
Indices: 1654143--1654196 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
1654133 GTATTTGGTT
* * *
1654143 AGATGAAAGGTGTGTGTTGTGTAAG
1 AGATGAAAGGAGTGTATTATGTAAG
1654168 AGATGAAAGGAGTGTATTATGTAAG
1 AGATGAAAGGAGTGTATTATGTAAG
1654193 AGAT
1 AGAT
1654197 TGAAGATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.30
Consensus pattern (25 bp):
AGATGAAAGGAGTGTATTATGTAAG
Found at i:1658834 original size:23 final size:23
Alignment explanation
Indices: 1658808--1658855 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1658798 AATATTGGTT
* *
1658808 GAGTCAACTCGTTGACTTTGACC
1 GAGTCAACCCGTTGACTTTAACC
1658831 GAGTCAACCCGTTGACTTTAACC
1 GAGTCAACCCGTTGACTTTAACC
1658854 GA
1 GA
1658856 AAAAATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (23 bp):
GAGTCAACCCGTTGACTTTAACC
Found at i:1660888 original size:97 final size:97
Alignment explanation
Indices: 1660719--1660913 Score: 291
Period size: 97 Copynumber: 2.0 Consensus size: 97
1660709 GATTTACTGG
* * *
1660719 TTTATGAACTATGATTACGTGAAATGTGTTATCAGGTTTCCTATTTTCACTGGAAAATATGATCG
1 TTTATGAACTATGATTACCTGAAATATATTATCAGGTTTCCTATTTTCACTGGAAAATATGATCG
* *
1660784 TTCCTGATTTATGGATCATGGAACCTACTAGT
66 TTACTGATTTATGGATCATGAAACCTACTAGT
* ** * *
1660816 TTTATGAACTATGGTTACCTGAAATATATTATTGGGTTTCCTGTTTTTACTGGAAAATATGATCG
1 TTTATGAACTATGATTACCTGAAATATATTATCAGGTTTCCTATTTTCACTGGAAAATATGATCG
*
1660881 TTACTGATTTATGGATCATGAAATCTACTAGT
66 TTACTGATTTATGGATCATGAAACCTACTAGT
1660913 T
1 T
1660914 ACTACTTGAA
Statistics
Matches: 87, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 87 1.00
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (97 bp):
TTTATGAACTATGATTACCTGAAATATATTATCAGGTTTCCTATTTTCACTGGAAAATATGATCG
TTACTGATTTATGGATCATGAAACCTACTAGT
Found at i:1661960 original size:250 final size:250
Alignment explanation
Indices: 1661518--1662014 Score: 931
Period size: 250 Copynumber: 2.0 Consensus size: 250
1661508 TAAATCATAT
* *
1661518 TCCAATCTCCTGAAAACATGGTACTCTGAATATTTCTTGTGAACTGAAATCTTCATGACTTTTAC
1 TCCAATCTCCTGAAAACATGGTACTCTGAATATTTCCTGCGAACTGAAATCTTCATGACTTTTAC
*
1661583 TCAAAGGAAATACCAGTGGAACCACAGTTCATCCCGAAAACCTGTAGACATCTGAATCAACAAGA
66 TCAAAGGAAATACCAGTGGAACCACAATTCATCCCGAAAACCTGTAGACATCTGAATCAACAAGA
*
1661648 AAATATTATGTTTTTCCAGTTATCTATAAGTCCTTCAGTATCATATGGTAGTTTTGTATTATTAA
131 AAATATTATGTTTTTCCAGTTATCTATAAGTCCTTCAGTATCATATGGTAGTTTTATATTATTAA
1661713 GCTTCCCAAAGCTCATTATGTTACTCACCTTTTCAGGTTAAAAGGATTGATCAAG
196 GCTTCCCAAAGCTCATTATGTTACTCACCTTTTCAGGTTAAAAGGATTGATCAAG
*
1661768 TCCAATCTCCTGAAAACATGGTACTCTGAATGTTTCCTGCGAACTGAAATCTTCATGACTTTTAC
1 TCCAATCTCCTGAAAACATGGTACTCTGAATATTTCCTGCGAACTGAAATCTTCATGACTTTTAC
1661833 TCAAAGGAAATACCAGTGGAACCACAATTCATCCCGAAAACCTGTAGACATCTGAATCAACAAGA
66 TCAAAGGAAATACCAGTGGAACCACAATTCATCCCGAAAACCTGTAGACATCTGAATCAACAAGA
* *
1661898 AAATATTATGTTTTTCCAGTTATCTATATGTCCTTCAGTATCATATGGTAGTTTTATATTATTGA
131 AAATATTATGTTTTTCCAGTTATCTATAAGTCCTTCAGTATCATATGGTAGTTTTATATTATTAA
1661963 GCTTCCCAAAGCTCATTATGTTACTCACCTTTTCAGGTTAAAAGGATTGATC
196 GCTTCCCAAAGCTCATTATGTTACTCACCTTTTCAGGTTAAAAGGATTGATC
1662015 CAGTGCAACT
Statistics
Matches: 240, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
250 240 1.00
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (250 bp):
TCCAATCTCCTGAAAACATGGTACTCTGAATATTTCCTGCGAACTGAAATCTTCATGACTTTTAC
TCAAAGGAAATACCAGTGGAACCACAATTCATCCCGAAAACCTGTAGACATCTGAATCAACAAGA
AAATATTATGTTTTTCCAGTTATCTATAAGTCCTTCAGTATCATATGGTAGTTTTATATTATTAA
GCTTCCCAAAGCTCATTATGTTACTCACCTTTTCAGGTTAAAAGGATTGATCAAG
Found at i:1663710 original size:30 final size:30
Alignment explanation
Indices: 1663676--1663735 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
1663666 CTGAGTTAAC
* *
1663676 TCGTTAACTTTGATCGAGTCAACCAGTTGA
1 TCGTTAACTTTAACCGAGTCAACCAGTTGA
* *
1663706 TCGTTGACTTTAACCGAGTCAACCCGTTGA
1 TCGTTAACTTTAACCGAGTCAACCAGTTGA
1663736 CTTTGGCCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (30 bp):
TCGTTAACTTTAACCGAGTCAACCAGTTGA
Found at i:1665761 original size:96 final size:96
Alignment explanation
Indices: 1665597--1665792 Score: 288
Period size: 96 Copynumber: 2.0 Consensus size: 96
1665587 TTTTTGGATT
*
1665597 TACTGGTTTATGAACTATGGTTACCTGAAATGTGTTATCAGGTTTCATGTTTTCACAGGAAAATA
1 TACTGGTTTATAAACTATGGTTACCTGAAATGTGTTATCAGGTTTCATGTTTTCACAGGAAAATA
**
1665662 TGATCGGTT-CTGATTTATGGATCATGTAATC
66 TGATC-GTTACTGATTTATGGATCATAAAATC
* * * *
1665693 TACTGTTTTATAAACTATGGTTACCTGAAATGTGTTATCGGGTTTCTTGTATTT-ACTGGAAAAT
1 TACTGGTTTATAAACTATGGTTACCTGAAATGTGTTATCAGGTTTCATGT-TTTCACAGGAAAAT
*
1665757 ATGATCGTTACTGATTTATGGGTCATAAAATC
65 ATGATCGTTACTGATTTATGGATCATAAAATC
1665789 TACT
1 TACT
1665793 AGTTACTACA
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
95 3 0.03
96 84 0.93
97 3 0.03
ACGTcount: A:0.28, C:0.12, G:0.19, T:0.41
Consensus pattern (96 bp):
TACTGGTTTATAAACTATGGTTACCTGAAATGTGTTATCAGGTTTCATGTTTTCACAGGAAAATA
TGATCGTTACTGATTTATGGATCATAAAATC
Found at i:1667992 original size:13 final size:13
Alignment explanation
Indices: 1667974--1667998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1667964 AAATCGACTG
1667974 AGTCAACTCATTT
1 AGTCAACTCATTT
1667987 AGTCAACTCATT
1 AGTCAACTCATT
1667999 GATTTAGACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.08, T:0.36
Consensus pattern (13 bp):
AGTCAACTCATTT
Found at i:1668052 original size:30 final size:29
Alignment explanation
Indices: 1668012--1668070 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
1668002 TTAGACCAAG
1668012 TCAACCCGTTGATCGTTAACTTTGACCGAA
1 TCAACCCGTTGA-CGTTAACTTTGACCGAA
* * * *
1668042 TCAACTCGTTGACTTTGACTTTGATCGAA
1 TCAACCCGTTGACGTTAACTTTGACCGAA
1668071 AAAGTCAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (29 bp):
TCAACCCGTTGACGTTAACTTTGACCGAA
Found at i:1670655 original size:2 final size:2
Alignment explanation
Indices: 1670648--1670704 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
1670638 TAATTATTGT
1670648 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
1670690 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
1670705 CTTTTCATTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1675329 original size:16 final size:16
Alignment explanation
Indices: 1675308--1675388 Score: 87
Period size: 16 Copynumber: 5.1 Consensus size: 16
1675298 AGGGGAAGTA
1675308 ATTTTAAAAAATATAT
1 ATTTTAAAAAATATAT
1675324 ATTTTAAAAAATATAT
1 ATTTTAAAAAATATAT
* *
1675340 ATTTTAAATAATATTTTT
1 ATTTTAAA-AA-ATATAT
* *
1675358 ATTTT-TATAA-ATA-
1 ATTTTAAAAAATATAT
1675371 ATTTTAAAAAATATAT
1 ATTTTAAAAAATATAT
1675387 AT
1 AT
1675389 ATACATGATA
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
13 5 0.10
14 4 0.08
15 4 0.08
16 27 0.52
17 3 0.06
18 9 0.17
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTTAAAAAATATAT
Found at i:1676130 original size:32 final size:32
Alignment explanation
Indices: 1676083--1676145 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1676073 ATTAAATTGG
*
1676083 TTGAAATAAAGTGATATATCACTGAAAAGTTA
1 TTGAAATAAAGTGATATATCACTAAAAAGTTA
* *
1676115 TTGAAATGAATTGATATATCACTAAAAAGTT
1 TTGAAATAAAGTGATATATCACTAAAAAGTT
1676146 TAATCATTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.33
Consensus pattern (32 bp):
TTGAAATAAAGTGATATATCACTAAAAAGTTA
Found at i:1679611 original size:2 final size:2
Alignment explanation
Indices: 1679606--1679661 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
1679596 ATAAAAAATA
1679606 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1679648 AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT
1679662 TATTTTAATG
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1680201 original size:2 final size:2
Alignment explanation
Indices: 1680194--1680238 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1680184 TGTTATGAAC
1680194 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1680236 AT A
1 AT A
1680239 AGAAATACGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1680574 original size:181 final size:181
Alignment explanation
Indices: 1680230--1680582 Score: 491
Period size: 181 Copynumber: 2.0 Consensus size: 181
1680220 ATATATATAT
* * *
1680230 ATATATATAAGAAATACGGTTGTGCCCAAGAATGTCATGATTCACTAAGAAAGTAGGTTGTGATT
1 ATATATATAAGAAATACGGTTGTGCCCAAGAATATCATGATTCACTAAGAAAGCAGGTTGCGATT
* *
1680295 TGTAATGTTAATATTTTTATTAATAAAATAGGTTGAGGCTAAAATGTTACTAGAGTTTAAGCTGA
66 TGTAATGTTAATATTTTTATTAATAAAATAGGTTGAGCCTAAAATATTACTAGAGTTTAAGCTGA
* * * *
1680360 TAGGGCCTTGGAAATTCTCCCGATAATAAAATAAGTTAATAGCTGAAAATA
131 TAGGACCTTGAAAATTCTCACGATAACAAAATAAGTTAATAGCTGAAAATA
* * * * *
1680411 ATATCTATAATAAATATGGTT-TCGCCCACGAATATCATGGTTCACTAAGAAAGCAGGTTGCGAT
1 ATATATATAAGAAATACGGTTGT-GCCCAAGAATATCATGATTCACTAAGAAAGCAGGTTGCGAT
*
1680475 CTT-TAAAT-TTAATATTTTTATTAATAAAATAGGTTGTGCCTAAAATATTACTAGAGTTTAAGC
65 -TTGT-AATGTTAATATTTTTATTAATAAAATAGGTTGAGCCTAAAATATTACTAGAGTTTAAGC
1680538 TGAT-GAGACCTT-AAACATTCTCACGATAACAAAATAAGTTAATAG
128 TGATAG-GACCTTGAAA-ATTCTCACGATAACAAAATAAGTTAATAG
1680583 TTAAAAATGT
Statistics
Matches: 152, Mismatches: 15, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
180 4 0.03
181 143 0.94
182 5 0.03
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.33
Consensus pattern (181 bp):
ATATATATAAGAAATACGGTTGTGCCCAAGAATATCATGATTCACTAAGAAAGCAGGTTGCGATT
TGTAATGTTAATATTTTTATTAATAAAATAGGTTGAGCCTAAAATATTACTAGAGTTTAAGCTGA
TAGGACCTTGAAAATTCTCACGATAACAAAATAAGTTAATAGCTGAAAATA
Found at i:1680605 original size:2 final size:2
Alignment explanation
Indices: 1680598--1680640 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1680588 AATGTTATGA
1680598 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1680640 A
1 A
1680641 ATAAATACGG
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1680799 original size:221 final size:220
Alignment explanation
Indices: 1680411--1680835 Score: 557
Period size: 221 Copynumber: 1.9 Consensus size: 220
1680401 GCTGAAAATA
* * * * * * * *
1680411 ATATCTATAATAAATATGGTTTCGCCCACGAATATCATGGTTCACTAAGAAAGCAGGTTGCGATC
1 ATATATATAATAAATACGGTTGCACCCAAGAATATCATGGTTCACTAAAAAAACAGGTTACGATC
* **
1680476 TTTAAATTTAATATTTTTATTAATAAAATAGGTTGTGCCTAAAATATTACTAGAGTTTAAGCTGA
66 TTGAAATTTAATATTTTTATTAATAAAATAGGTTGCACCTAAAATATTACTAGAGTTTAAGCTGA
* * **
1680541 TGAGACCTTAAACATTCTCACGATAACAAAATAAGTTAATAGTTAAAAATGTTATGAATATATAT
131 TGAGACCTTAAACATTCCCACGATAACAAAATAAGTTAAAAGCCAAAAATGTTATGAATATATAT
*
1680606 ATATATATATATATATATATATATAT
196 A-ATAAATATATATATATATATATAT
* * * *
1680632 ATATATATAATAAATACGGTTGCACTCAAGAATGTCATTGTTCACTAAAAAAATAGGTTACGA-C
1 ATATATATAATAAATACGGTTGCACCCAAGAATATCATGGTTCACTAAAAAAACAGGTTACGATC
* *
1680696 TTGGAATGTTAATATTTTTATTAATAAAAT-GGATTGCACCTAAAATATTACTAGAGTTTAAGTT
66 TTGAAAT-TTAATATTTTTATTAATAAAATAGG-TTGCACCTAAAATATTACTAGAGTTTAAGCT
* * * * * *
1680760 GATGGGGCCTTAGACATTCCCACGATAAGAAAATAAGTTAAAAGCCAGAAATGTTATGAATATCT
129 GATGAGACCTTAAACATTCCCACGATAACAAAATAAGTTAAAAGCCAAAAATGTTATGAATATAT
1680825 ATAATAAATAT
194 ATAATAAATAT
1680836 GGTTGCGTCC
Statistics
Matches: 174, Mismatches: 28, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
220 15 0.09
221 159 0.91
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.35
Consensus pattern (220 bp):
ATATATATAATAAATACGGTTGCACCCAAGAATATCATGGTTCACTAAAAAAACAGGTTACGATC
TTGAAATTTAATATTTTTATTAATAAAATAGGTTGCACCTAAAATATTACTAGAGTTTAAGCTGA
TGAGACCTTAAACATTCCCACGATAACAAAATAAGTTAAAAGCCAAAAATGTTATGAATATATAT
AATAAATATATATATATATATATAT
Found at i:1680959 original size:186 final size:186
Alignment explanation
Indices: 1680632--1680988 Score: 472
Period size: 186 Copynumber: 1.9 Consensus size: 186
1680622 ATATATATAT
*
1680632 ATATATATAATAAATACGGTTGCACTCAAGAATGTCATTGTTCACTAAAAAAATAGGTTACGACT
1 ATATATATAATAAATACGGTTGCACTCAAGAATGTCATCGTTCACTAAAAAAATA-GTTACGACT
* * * *
1680697 TGGAATGTTAATATTTTTATTAATAAAATGGATTGCACCTAAAATATTACTAGAGTTTAAGTTGA
65 TGAAATGTTAATATTTTTATCAATAAAATGGATTGCACCTAAAATATTACCAGAGTTTAAGCTGA
* *
1680762 TGGGGCCTTAGACATTCCCACGATAAGAAAATAAGTTAAAAGCCAGAAATGTTATGA
130 TGGGACCTTAGACATTCCCACGATAACAAAATAAGTTAAAAGCCAGAAATGTTATGA
* * * * * *
1680819 ATATCTATAATAAATATGGTTGC-GTCCAAGAATGTCATCGTTCACTAAGAAAGAT-GTTGCTA-
1 ATATATATAATAAATACGGTTGCACT-CAAGAATGTCATCGTTCACTAA-AAAAATAGTTACGAC
* * *
1680881 TCTGAAATGTTAATCTTCTTTA-CAATAAAATTGG-TTGCTCCTAAAATGTTACCAGAGTTTAAG
64 T-TGAAATGTTAATATT-TTTATCAATAAAA-TGGATTGCACCTAAAATATTACCAGAGTTTAAG
*
1680944 CTGATGGGACCTTAGACATTCTCACGATAACAAAATAAGTTAAAA
126 CTGATGGGACCTTAGACATTCCCACGATAACAAAATAAGTTAAAA
1680989 TATTTTAAAT
Statistics
Matches: 148, Mismatches: 17, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
185 1 0.01
186 93 0.63
187 49 0.33
188 5 0.03
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.32
Consensus pattern (186 bp):
ATATATATAATAAATACGGTTGCACTCAAGAATGTCATCGTTCACTAAAAAAATAGTTACGACTT
GAAATGTTAATATTTTTATCAATAAAATGGATTGCACCTAAAATATTACCAGAGTTTAAGCTGAT
GGGACCTTAGACATTCCCACGATAACAAAATAAGTTAAAAGCCAGAAATGTTATGA
Found at i:1681388 original size:37 final size:38
Alignment explanation
Indices: 1681344--1681440 Score: 94
Period size: 36 Copynumber: 2.6 Consensus size: 38
1681334 CAACTTTTTT
1681344 TCAATATTTAAAAGTATCGATCATTATC-TCATAC-ATA
1 TCAATATTTAAAAGTATCGATCATTATCTTCA-ACTATA
* * * * * * *
1681381 TCGATATTT-TAACTTTCGAT-TTTATCTTCAACTTTT
1 TCAATATTTAAAAGTATCGATCATTATCTTCAACTATA
1681417 TCAATATTTAAAAGTATCGATCAT
1 TCAATATTTAAAAGTATCGATCAT
1681441 CATATATAAA
Statistics
Matches: 44, Mismatches: 12, Indels: 7
0.70 0.19 0.11
Matches are distributed among these distances:
35 7 0.16
36 20 0.45
37 16 0.36
38 1 0.02
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.44
Consensus pattern (38 bp):
TCAATATTTAAAAGTATCGATCATTATCTTCAACTATA
Found at i:1681438 original size:73 final size:73
Alignment explanation
Indices: 1681257--1681469 Score: 247
Period size: 73 Copynumber: 2.9 Consensus size: 73
1681247 ATTGGTCATC
**
1681257 TTCATCAACTTTTTCAATATTTAAATTTATCG-T-AGTCATCACATAAGTATCAATATTTTAAAT
1 TTCATCAACTTTTTCAATATTTAAAAGTATCGATCA-TCATCACATAAGTATCAATATTTTAAAT
1681320 TTCGATCTT
65 TTCGATCTT
* * *
1681329 TTCATCAACTTTTTTTCAATATTTAAAAGTATCGATCATTATCTCATACA-TATCGATATTTTAA
1 TTCATCAAC--TTTTTCAATATTTAAAAGTATCGATCATCATCACATA-AGTATCAATATTTTAA
*
1681393 CTTTCGAT-TT
63 ATTTCGATCTT
* * * *
1681403 TATCTTCAACTTTTTCAATATTTAAAAGTATCGATCATCAT-ATATAAAGTATTAATATTTAAAA
1 T-TCATCAACTTTTTCAATATTTAAAAGTATCGATCATCATCACAT-AAGTATCAATATTTTAAA
1681467 TTT
64 TTT
1681470 GAATTGTTTT
Statistics
Matches: 119, Mismatches: 14, Indels: 15
0.80 0.09 0.10
Matches are distributed among these distances:
72 12 0.10
73 45 0.38
74 24 0.20
75 36 0.30
76 2 0.02
ACGTcount: A:0.35, C:0.14, G:0.05, T:0.46
Consensus pattern (73 bp):
TTCATCAACTTTTTCAATATTTAAAAGTATCGATCATCATCACATAAGTATCAATATTTTAAATT
TCGATCTT
Found at i:1683046 original size:186 final size:189
Alignment explanation
Indices: 1682642--1683094 Score: 488
Period size: 186 Copynumber: 2.4 Consensus size: 189
1682632 TATTTATAAC
* * * * * *
1682642 ATTTTAACTTATTTTGTTGTTGTGAGAATGTCTAAGGCCCCATCAGCTTAAACTCT-ATTAACAT
1 ATTTTAATTTATTTTCTTATTGTGAGAATGTCTAAAGCTCTATCAGCTTAAACTCTGA-TAACAT
* * * *
1682706 TTTAGGCGCACCCGAATTTATTATAAAGAAAACTAACATTCCATATCACAACCTACTTTCTTAGT
65 TTTAGGCACAACCGAATTTATTACAAAGAAAACTAACATTCCATATCACAACATACTTTCTTAGT
* * * * *
1682771 GAACCATAACATTCTTAGGCGCAATCAGAATTTTTTTTTATAGATATTCATAATATTTTCAT
130 AAACCAAAACATTCTTAGGCGCAATCAGAA--TTTTCTTATAGATATTCATAACATTTTCAG
* *
1682833 ATTTTAATTTATTTTGC-TATCGTGAGAATGTCTAAAACTCTATCAGCTTAAACTCTGATAACAT
1 ATTTTAATTTATTTT-CTTATTGTGAGAATGTCTAAAGCTCTATCAGCTTAAACTCTGATAACAT
* * * * ** *
1682897 TTTAGGCACAACCGATTTTATT-CAAAGAAAATTAATATTTCATATTGCAACATATTTTCTTAGT
65 TTTAGGCACAACCGAATTTATTACAAAGAAAACTAACATTCCATATCACAACATACTTTCTTAGT
* * * * *
1682961 AAATCAAAACATT-TTTGCGTGCAA-CCGGA-TTTCTTATAGATATTCATAACATTTTCAG
130 AAACCAAAACATTCTTAG-GCGCAATCAGAATTTTCTTATAGATATTCATAACATTTTCAG
* * * * *
1683019 CTTTTAATTTATTTTCTTATTGTGAGAATGTCT-AAGGTCTTATCAGCTCAAACACTGGTAACAT
1 ATTTTAATTTATTTTCTTATTGTGAGAATGTCTAAAGCTC-TATCAGCTTAAACTCTGATAACAT
*
1683083 TTTAGGCTCAAC
65 TTTAGGCACAAC
1683095 ATAAAATATT
Statistics
Matches: 220, Mismatches: 37, Indels: 15
0.81 0.14 0.06
Matches are distributed among these distances:
185 5 0.02
186 87 0.40
189 6 0.03
190 49 0.22
191 72 0.33
192 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.39
Consensus pattern (189 bp):
ATTTTAATTTATTTTCTTATTGTGAGAATGTCTAAAGCTCTATCAGCTTAAACTCTGATAACATT
TTAGGCACAACCGAATTTATTACAAAGAAAACTAACATTCCATATCACAACATACTTTCTTAGTA
AACCAAAACATTCTTAGGCGCAATCAGAATTTTCTTATAGATATTCATAACATTTTCAG
Found at i:1684880 original size:39 final size:39
Alignment explanation
Indices: 1684769--1684887 Score: 129
Period size: 39 Copynumber: 3.1 Consensus size: 39
1684759 TTAAATTTGT
* *
1684769 ATTTATAA-TTCTGAAATTATTTCA-GTCTAACATTCTAA
1 ATTTATAATTTCTTAAATTATTTCACAT-TAACATTCTAA
* * *
1684807 ATTCATAATTTCTTAAATT-TTGCCACCA-TGACATTCTAA
1 ATTTATAATTTCTTAAATTATT-TCA-CATTAACATTCTAA
*
1684846 ATTTTTAATTTCTTAAATTATTTCACATTAACATTCTAA
1 ATTTATAATTTCTTAAATTATTTCACATTAACATTCTAA
1684885 ATT
1 ATT
1684888 ATTTTTTAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
38 11 0.17
39 53 0.80
40 2 0.03
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.46
Consensus pattern (39 bp):
ATTTATAATTTCTTAAATTATTTCACATTAACATTCTAA
Found at i:1684923 original size:22 final size:21
Alignment explanation
Indices: 1684882--1684934 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
1684872 ATTAACATTC
* *
1684882 TAAA-TTATTTTTTAAAATAT
1 TAAATTTAATTTTGAAAATAT
* *
1684902 TTATTTTAATTTTGAAACATAT
1 TAAATTTAATTTTGAAA-ATAT
1684924 TAAATTTAATT
1 TAAATTTAATT
1684935 ATAATTTTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
20 2 0.08
21 10 0.40
22 13 0.52
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (21 bp):
TAAATTTAATTTTGAAAATAT
Found at i:1688610 original size:14 final size:14
Alignment explanation
Indices: 1688591--1688629 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1688581 TAATGGGGAG
1688591 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
1688605 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
1688619 GAATCTCTGCA
1 TAATCCCTGCA
1688630 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:1696404 original size:20 final size:20
Alignment explanation
Indices: 1696381--1696477 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
1696371 ATTTGCGTTG
1696381 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
* *
1696401 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-TTTC
* ** *
1696422 AAAATCGCGTTACGATTTTC
1 CATTTCGCGTTGCGATTTTC
1696442 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATTTTC
1696462 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
1696478 AGTCTACAGT
Statistics
Matches: 64, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
20 50 0.78
21 14 0.22
ACGTcount: A:0.15, C:0.23, G:0.22, T:0.40
Consensus pattern (20 bp):
CATTTCGCGTTGCGATTTTC
Found at i:1696497 original size:22 final size:22
Alignment explanation
Indices: 1696469--1696521 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
1696459 TTCCATTTCG
1696469 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
*
1696491 TGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
1696513 CGTTGCGAT
1 CGTTGCGAT
1696522 TTTCCAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.17, C:0.17, G:0.28, T:0.38
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:1696630 original size:6 final size:6
Alignment explanation
Indices: 1696619--1696651 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
1696609 GACATGTATT
1696619 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1696652 CGAGACGGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1697144 original size:6 final size:6
Alignment explanation
Indices: 1697135--1697166 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
1697125 CGCCGCCGCC
*
1697135 GTCGTG GTCGTG GTAGTG GTCGTG GTCGTG GT
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GT
1697167 AGTACGTGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.03, C:0.12, G:0.50, T:0.34
Consensus pattern (6 bp):
GTCGTG
Found at i:1697158 original size:18 final size:18
Alignment explanation
Indices: 1697135--1697169 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1697125 CGCCGCCGCC
1697135 GTCGTGGTCGTGGTAGTG
1 GTCGTGGTCGTGGTAGTG
1697153 GTCGTGGTCGTGGTAGT
1 GTCGTGGTCGTGGTAGT
1697170 ACGTGTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.06, C:0.11, G:0.49, T:0.34
Consensus pattern (18 bp):
GTCGTGGTCGTGGTAGTG
Found at i:1703512 original size:20 final size:20
Alignment explanation
Indices: 1703489--1703535 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
1703479 TGTTTTTCAT
1703489 ATTTTAAA-AGCTTTAAACAC
1 ATTTTAAACA-CTTTAAACAC
*
1703509 ATTTTAAACACTTTAAACAT
1 ATTTTAAACACTTTAAACAC
1703529 ATTTTAA
1 ATTTTAA
1703536 TTAACTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 24 0.96
21 1 0.04
ACGTcount: A:0.45, C:0.13, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTTTAAACACTTTAAACAC
Found at i:1706642 original size:3 final size:3
Alignment explanation
Indices: 1706634--1706703 Score: 140
Period size: 3 Copynumber: 23.3 Consensus size: 3
1706624 ACATACTTTA
1706634 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1706682 TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT T
1706704 GTTTTAATAG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 67 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1710097 original size:19 final size:19
Alignment explanation
Indices: 1710070--1710112 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 19
1710060 TTTATTAAAA
*
1710070 TATTGATTGGTGGGTGTAT
1 TATTAATTGGTGGGTGTAT
*
1710089 TATTAATTGTTGGGTGTAT
1 TATTAATTGGTGGGTGTAT
1710108 TATTA
1 TATTA
1710113 TTCTGCAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (19 bp):
TATTAATTGGTGGGTGTAT
Found at i:1710607 original size:29 final size:28
Alignment explanation
Indices: 1710539--1710697 Score: 178
Period size: 28 Copynumber: 5.6 Consensus size: 28
1710529 GTTATGGTGG
* * *
1710539 TATTTTCGTAAATATTGTT-AAGAAGGTGT
1 TATTTTCGTAATTATT-TTGAA-AAAGTGA
* *
1710568 TAGTTTCGTAAATATTATT-AAACAAGTGA
1 TATTTTCGTAATTATT-TTGAAA-AAGTGA
*
1710597 TATTTTGGTAATTATTTTGAAAAAGTGA
1 TATTTTCGTAATTATTTTGAAAAAGTGA
*
1710625 TATTTTGGTAATTATTTTGAAAAAGTGA
1 TATTTTCGTAATTATTTTGAAAAAGTGA
* *
1710653 TATTTTGGTAATTATTTTGAAAAGGTTGA
1 TATTTTCGTAATTATTTTGAAAAAG-TGA
1710682 TATTTTCGTAATTATT
1 TATTTTCGTAATTATT
1710698 AAAAAAACGG
Statistics
Matches: 118, Mismatches: 9, Indels: 6
0.89 0.07 0.05
Matches are distributed among these distances:
28 61 0.52
29 57 0.48
ACGTcount: A:0.34, C:0.03, G:0.17, T:0.47
Consensus pattern (28 bp):
TATTTTCGTAATTATTTTGAAAAAGTGA
Found at i:1710630 original size:16 final size:16
Alignment explanation
Indices: 1710609--1710659 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
1710599 TTTTGGTAAT
1710609 TATTTTGAAAAAGTGA
1 TATTTTGAAAAAGTGA
**
1710625 TATTTTG-GTAA-T--
1 TATTTTGAAAAAGTGA
1710637 TATTTTGAAAAAGTGA
1 TATTTTGAAAAAGTGA
1710653 TATTTTG
1 TATTTTG
1710660 GTAATTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 8
0.69 0.10 0.21
Matches are distributed among these distances:
12 7 0.26
13 2 0.07
14 2 0.07
15 2 0.07
16 14 0.52
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.47
Consensus pattern (16 bp):
TATTTTGAAAAAGTGA
Found at i:1710704 original size:29 final size:28
Alignment explanation
Indices: 1710591--1710697 Score: 187
Period size: 28 Copynumber: 3.8 Consensus size: 28
1710581 ATTATTAAAC
1710591 AAGTGATATTTTGGTAATTATTTTGAAA
1 AAGTGATATTTTGGTAATTATTTTGAAA
1710619 AAGTGATATTTTGGTAATTATTTTGAAA
1 AAGTGATATTTTGGTAATTATTTTGAAA
1710647 AAGTGATATTTTGGTAATTATTTTGAAA
1 AAGTGATATTTTGGTAATTATTTTGAAA
* *
1710675 AGGTTGATATTTTCGTAATTATT
1 AAG-TGATATTTTGGTAATTATT
1710698 AAAAAAACGG
Statistics
Matches: 76, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
28 58 0.76
29 18 0.24
ACGTcount: A:0.34, C:0.01, G:0.18, T:0.48
Consensus pattern (28 bp):
AAGTGATATTTTGGTAATTATTTTGAAA
Found at i:1713879 original size:2 final size:2
Alignment explanation
Indices: 1713866--1713943 Score: 52
Period size: 2 Copynumber: 44.5 Consensus size: 2
1713856 AGTTAAGGAT
* *
1713866 TA TA TA TT TA TA TA TA TA TA TA TA TA TA -A AA TA -A TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
1713905 TA T- TA T- TA TA TA TT TA -A T- TA T- TA -A TA -A TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1713939 TA TA T
1 TA TA T
1713944 TAAACTTATG
Statistics
Matches: 60, Mismatches: 5, Indels: 22
0.69 0.06 0.25
Matches are distributed among these distances:
1 11 0.18
2 49 0.82
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1713914 original size:29 final size:32
Alignment explanation
Indices: 1713868--1713945 Score: 86
Period size: 35 Copynumber: 2.3 Consensus size: 32
1713858 TTAAGGATTA
1713868 TATATT-TATATATATATATATATATAAAATAATAT
1 TATATTAT-TATATATATA-AT-TAT-AAATAATAT
* *
1713903 TATATTATTATATATTTAATTATTAATAATAT
1 TATATTATTATATATATAATTATAAATAATAT
1713935 TATATATATTA
1 TATAT-TATTA
1713946 AACTTATGGT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
32 13 0.33
33 8 0.21
34 2 0.05
35 15 0.38
36 1 0.03
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (32 bp):
TATATTATTATATATATAATTATAAATAATAT
Found at i:1714625 original size:41 final size:40
Alignment explanation
Indices: 1714549--1714625 Score: 118
Period size: 41 Copynumber: 1.9 Consensus size: 40
1714539 TTTTCTCGAA
* *
1714549 TTTTCGTGTTTGTTTCACGTAATTCTTTTTTCGGAAAATG
1 TTTTCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATG
*
1714589 TTTTCCGTGTTTGTTTCACGTAATTGATTTTCCGGAA
1 TTTT-CGTGTTTGTTTCACGTAATTCATTTTCCGGAA
1714626 TGTAATCTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 4 0.12
41 29 0.88
ACGTcount: A:0.17, C:0.14, G:0.18, T:0.51
Consensus pattern (40 bp):
TTTTCGTGTTTGTTTCACGTAATTCATTTTCCGGAAAATG
Found at i:1714823 original size:14 final size:14
Alignment explanation
Indices: 1714804--1714849 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
1714794 ATCAAAATAT
1714804 TATTTATTTATTAA
1 TATTTATTTATTAA
*
1714818 TATTTA-TAATATAA
1 TATTTATTTAT-TAA
1714832 TATTATATTT-TTAA
1 TATT-TATTTATTAA
1714846 TATT
1 TATT
1714850 ATATAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
13 3 0.11
14 20 0.74
15 3 0.11
16 1 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TATTTATTTATTAA
Found at i:1714836 original size:31 final size:29
Alignment explanation
Indices: 1714797--1714871 Score: 91
Period size: 28 Copynumber: 2.6 Consensus size: 29
1714787 CATTTTCATC
*
1714797 AAAATATTATT-TATTTATTAATATT-TAT
1 AAAATAATATTATATTT-TTAATATTATAT
*
1714825 AATATAATATTATATTTTTAATATTATAT
1 AAAATAATATTATATTTTTAATATTATAT
1714854 AAAATAATCAATTATATT
1 AAAATAAT--ATTATATT
1714872 ATAATAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
28 17 0.43
29 15 0.38
31 8 0.20
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (29 bp):
AAAATAATATTATATTTTTAATATTATAT
Found at i:1714841 original size:19 final size:20
Alignment explanation
Indices: 1714812--1714853 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1714802 ATTATTTATT
1714812 TATTAATATTTATAATATAA
1 TATTAATATTTATAATATAA
* *
1714832 TATT-ATATTTTTAATATTA
1 TATTAATATTTATAATATAA
1714851 TAT
1 TAT
1714854 AAAATAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTAATATTTATAATATAA
Found at i:1714935 original size:31 final size:30
Alignment explanation
Indices: 1714834--1714947 Score: 85
Period size: 29 Copynumber: 3.8 Consensus size: 30
1714824 TAATATAATA
* * *
1714834 TTATATTTTTAATATTATATAA-AATAATCAA
1 TTATA-TTTTAATAATATATAATAAAAATC-T
* * *
1714865 TTATATTATAATAATATA-AGATATTATAT-T
1 TTATATTTTAATAATATATA-ATA-AAAATCT
1714895 TT-TATTTTAATAATATATAATAAAAATCT
1 TTATATTTTAATAATATATAATAAAAATCT
1714924 TTATATATTTAATAATGA-ATAATA
1 TTATAT-TTTAATAAT-ATATAATA
1714948 TTATTTATAT
Statistics
Matches: 66, Mismatches: 9, Indels: 16
0.73 0.10 0.18
Matches are distributed among these distances:
28 3 0.05
29 21 0.32
30 18 0.27
31 21 0.32
32 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
TTATATTTTAATAATATATAATAAAAATCT
Found at i:1714936 original size:28 final size:28
Alignment explanation
Indices: 1714905--1714968 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
1714895 TTTATTTTAA
*
1714905 TAATATAT-AATAAAAATCTTTATATATT
1 TAATA-ATGAATAAAAATATTTATATATT
* *
1714933 TAATAATGAATAATATTATTTATATATT
1 TAATAATGAATAAAAATATTTATATATT
1714961 TAAATAAT
1 T-AATAAT
1714969 ATTTTAATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 2 0.06
28 23 0.74
29 6 0.19
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (28 bp):
TAATAATGAATAAAAATATTTATATATT
Found at i:1714948 original size:19 final size:19
Alignment explanation
Indices: 1714926--1714978 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
1714916 AAAAATCTTT
*
1714926 ATATATTTAATAATGAATA
1 ATATATTTAATAATAAATA
*
1714945 ATATTATTTATATATTTAAATA
1 ATA-TATTTA-ATA-ATAAATA
1714967 ATAT-TTTAATAA
1 ATATATTTAATAA
1714979 AGATATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 6 0.21
20 10 0.36
21 4 0.14
22 8 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (19 bp):
ATATATTTAATAATAAATA
Found at i:1714999 original size:23 final size:23
Alignment explanation
Indices: 1714973--1715017 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1714963 AATAATATTT
1714973 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
1714996 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
1715018 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:1715168 original size:21 final size:21
Alignment explanation
Indices: 1715105--1715168 Score: 56
Period size: 26 Copynumber: 2.8 Consensus size: 21
1715095 TTTTTATTAA
* * *
1715105 TAAAATTATAAAAATAATATT
1 TAAAATAATAATATTAATATT
1715126 TAATAATAAATAAATTATTTAATATT
1 TAA-AAT-AAT-AA-TA-TTAATATT
1715152 TAAAATAATAATATTAA
1 TAAAATAATAATATTAA
1715169 GTTTTATGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
21 7 0.20
22 5 0.14
23 4 0.11
24 5 0.14
25 4 0.11
26 10 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAATAATAATATTAATATT
Found at i:1715380 original size:14 final size:15
Alignment explanation
Indices: 1715360--1715403 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
1715350 TCCAGAAATT
1715360 TAATTCATTTTCCAG
1 TAATTCATTTTCCAG
**
1715375 -AATTCAAATT-CAG
1 TAATTCATTTTCCAG
1715388 TAATTCATTTTCCAG
1 TAATTCATTTTCCAG
1715403 T
1 T
1715404 TCCAGTAATT
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
13 3 0.13
14 16 0.70
15 4 0.17
ACGTcount: A:0.32, C:0.18, G:0.07, T:0.43
Consensus pattern (15 bp):
TAATTCATTTTCCAG
Found at i:1715384 original size:20 final size:20
Alignment explanation
Indices: 1715347--1715386 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
1715337 CCGGAAAACG
*
1715347 TTTTCCAGAAATTTAATTCA
1 TTTTCCAGAAATTAAATTCA
1715367 TTTTCCAG-AATTCAAATTCA
1 TTTTCCAGAAATT-AAATTCA
1715387 GTAATTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.42
Consensus pattern (20 bp):
TTTTCCAGAAATTAAATTCA
Found at i:1715607 original size:21 final size:21
Alignment explanation
Indices: 1715577--1715618 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1715567 TAACTGACCC
1715577 TATTCCCATATGTAATGGGGT
1 TATTCCCATATGTAATGGGGT
*
1715598 TATTCTCATATGTAATGGGGT
1 TATTCCCATATGTAATGGGGT
1715619 AAGGGGAGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.40
Consensus pattern (21 bp):
TATTCCCATATGTAATGGGGT
Found at i:1716307 original size:3 final size:3
Alignment explanation
Indices: 1716299--1716444 Score: 292
Period size: 3 Copynumber: 48.7 Consensus size: 3
1716289 ACTACAAAAC
1716299 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1716347 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1716395 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1716443 AT
1 AT
1716445 CAAACCATGG
Statistics
Matches: 143, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 143 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:1718078 original size:22 final size:22
Alignment explanation
Indices: 1718043--1718093 Score: 75
Period size: 22 Copynumber: 2.3 Consensus size: 22
1718033 CTGAGTGGCA
* *
1718043 TATGAGATTTGTCCCGAGGGACC
1 TATGA-ATATGTCCCGAAGGACC
1718066 TATGAATATGTCCCGAAGGACC
1 TATGAATATGTCCCGAAGGACC
1718088 TATGAA
1 TATGAA
1718094 ACCCTCGACT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 21 0.81
23 5 0.19
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (22 bp):
TATGAATATGTCCCGAAGGACC
Found at i:1718658 original size:20 final size:20
Alignment explanation
Indices: 1718633--1718704 Score: 117
Period size: 20 Copynumber: 3.6 Consensus size: 20
1718623 GACTAAGGTA
1718633 GGTATCGGTACACTCTATAG
1 GGTATCGGTACACTCTATAG
*
1718653 GGTATCAGTACACTCTATAG
1 GGTATCGGTACACTCTATAG
*
1718673 GGTATTGGTACACTCTATAG
1 GGTATCGGTACACTCTATAG
*
1718693 GGTATCGATACA
1 GGTATCGGTACA
1718705 TCCCTTAACG
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.31
Consensus pattern (20 bp):
GGTATCGGTACACTCTATAG
Found at i:1718784 original size:63 final size:64
Alignment explanation
Indices: 1718716--1718862 Score: 185
Period size: 63 Copynumber: 2.3 Consensus size: 64
1718706 CCCTTAACGT
* * * *
1718716 GTGTATCGATACACTACCTATA-TATCGATACACAAATTACATTCAAAGTTT-TC-ATTTTAAGG
1 GTGTATCGATACACT-CCTA-AGTATCGATACACAAATTACACTAAAAATTTGTCTATTTCAAGG
1718778 G
64 G
*
1718779 GTGTATCGATACACTGCCTAAGTATCGATACCCAAATTACACTAAAAATTTGTCTATTTCAAGGG
1 GTGTATCGATACACT-CCTAAGTATCGATACACAAATTACACTAAAAATTTGTCTATTTCAAGGG
*
1718844 G-GTATTGATACACTCCTAA
1 GTGTATCGATACACTCCTAA
1718863 AGGTATCGGT
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
62 1 0.01
63 49 0.66
64 14 0.19
65 10 0.14
ACGTcount: A:0.34, C:0.19, G:0.14, T:0.33
Consensus pattern (64 bp):
GTGTATCGATACACTCCTAAGTATCGATACACAAATTACACTAAAAATTTGTCTATTTCAAGGG
Found at i:1725741 original size:62 final size:64
Alignment explanation
Indices: 1725635--1725773 Score: 183
Period size: 62 Copynumber: 2.2 Consensus size: 64
1725625 CTTAACGTGT
* * * * * * *
1725635 GTATCGATACACTACCTATGTATTGGTACACAAATTGCATTCGAAGTTT-TC-ATTTTAAGGGG
1 GTATCGATACACTACCTAGGTATCGATACACAAATTACACTCGAAATTTCTCTATTTCAAGGGG
* *
1725697 GTATCGATACACTGCCTAGGTATCGATACCCAAATTACACTCGAAATTTCTCTATTTCAAGGGG
1 GTATCGATACACTACCTAGGTATCGATACACAAATTACACTCGAAATTTCTCTATTTCAAGGGG
1725761 GTATCGATACACT
1 GTATCGATACACT
1725774 CCTGAAGGTA
Statistics
Matches: 66, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
62 41 0.62
63 2 0.03
64 23 0.35
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (64 bp):
GTATCGATACACTACCTAGGTATCGATACACAAATTACACTCGAAATTTCTCTATTTCAAGGGG
Found at i:1733091 original size:26 final size:24
Alignment explanation
Indices: 1733055--1733107 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 24
1733045 TGTAAATATA
* *
1733055 ATAATAATAATGCTACTATATATTAT
1 ATAATAATAAT-ATAAT-TATATTAT
1733081 ATAATAATAATATAATTATATTAT
1 ATAATAATAATATAATTATATTAT
1733105 ATA
1 ATA
1733108 GAAACAACAC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 11 0.44
25 3 0.12
26 11 0.44
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (24 bp):
ATAATAATAATATAATTATATTAT
Found at i:1733365 original size:36 final size:34
Alignment explanation
Indices: 1733283--1733554 Score: 202
Period size: 36 Copynumber: 7.6 Consensus size: 34
1733273 TATAATCTTG
* * *
1733283 CTTCACTACTCTTCCGTGAAGGCTAGATTGAATCA
1 CTTCACTACTCTTCCGTGAAGGATAAATTG-ATTA
* * *
1733318 CTTCATTACTCTTTCGTGAAGGATAAATTTGTATTT
1 CTTCACTACTCTTCCGTGAAGGATAAA-TTG-ATTA
* *
1733354 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATTAA
1 CTTCACTACTCTTCCGTGAAGGAT-AAATTGATT-A
* * * *
1733390 CTTCACTACTCTTTCGTGAAGGTTGAAAATGATGAA
1 CTTCACTACTCTTCCGTGAAGGAT-AAATTGAT-TA
* * *
1733426 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATGAA
1 CTTCACTACTCTTCCGTGAAGGAT-AAATTGAT-TA
* * * * *
1733462 CTTCACTACTTTTCCTTGAAGGTTGAAAATGATGAA
1 CTTCACTACTCTTCCGTGAAGGAT-AAATTGAT-TA
* * * * *
1733498 CTTCATTACTCTTTCGTGAAGGTTGAAAATGATGAA
1 CTTCACTACTCTTCCGTGAAGGAT-AAATTGAT-TA
1733534 CTTCACTACTCTTCCGTGAAG
1 CTTCACTACTCTTCCGTGAAG
1733555 ATCAGATTTG
Statistics
Matches: 210, Mismatches: 23, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
35 26 0.12
36 181 0.86
37 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (34 bp):
CTTCACTACTCTTCCGTGAAGGATAAATTGATTA
Found at i:1733411 original size:72 final size:72
Alignment explanation
Indices: 1733283--1733554 Score: 347
Period size: 72 Copynumber: 3.8 Consensus size: 72
1733273 TATAATCTTG
* * * * * *
1733283 CTTCACTACTCTTCCGTGAAGGCT-AGATTGAAT-CACTTCATTACTCTTTCGTGAAGGAT-AAA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATG-ATGAACTTCACTACTCTTTCGTGAAGGTTGAAA
* **
1733345 TTTGTAT-TT
65 -ATG-ATGAA
*
1733354 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATTAACTTCACTACTCTTTCGTGAAGGTTGAAAA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATGAACTTCACTACTCTTTCGTGAAGGTTGAAAA
1733419 TGATGAA
66 TGATGAA
*
1733426 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATGAACTTCACTACT-TTTCCTTGAAGGTTGAAA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATGAACTTCACTACTCTTT-CGTGAAGGTTGAAA
1733490 ATGATGAA
65 ATGATGAA
* * *
1733498 CTTCATTACTCTTTCGTGAAGGTTGAAAATGATGAACTTCACTACTCTTCCGTGAAG
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATGAACTTCACTACTCTTTCGTGAAG
1733555 ATCAGATTTG
Statistics
Matches: 180, Mismatches: 15, Indels: 11
0.87 0.07 0.05
Matches are distributed among these distances:
71 30 0.17
72 145 0.81
73 5 0.03
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.35
Consensus pattern (72 bp):
CTTCACTACTCTTCCGTGAAGGTTGAAAATGATGAACTTCACTACTCTTTCGTGAAGGTTGAAAA
TGATGAA
Found at i:1733444 original size:108 final size:108
Alignment explanation
Indices: 1733354--1733554 Score: 357
Period size: 108 Copynumber: 1.9 Consensus size: 108
1733344 ATTTGTATTT
*
1733354 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATTAACTTCACTACTCTTTCGTGAAGGTTGAAAA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATGAACTTCACTACTCTTTCGTGAAGGTTGAAAA
*
1733419 TGATGAACTTCACTACTCTTCCGTGAAGGTTGAAAATGATGAA
66 TGATGAACTTCACTACTCTTCCGTGAAGGATGAAAATGATGAA
* * *
1733462 CTTCACTACTTTTCCTTGAAGGTTGAAAATGATGAACTTCATTACTCTTTCGTGAAGGTTGAAAA
1 CTTCACTACTCTTCCGTGAAGGTTGAAAATGATGAACTTCACTACTCTTTCGTGAAGGTTGAAAA
1733527 TGATGAACTTCACTACTCTTCCGTGAAG
66 TGATGAACTTCACTACTCTTCCGTGAAG
1733555 ATCAGATTTG
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
108 89 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (108 bp):
CTTCACTACTCTTCCGTGAAGGTTGAAAATGATGAACTTCACTACTCTTTCGTGAAGGTTGAAAA
TGATGAACTTCACTACTCTTCCGTGAAGGATGAAAATGATGAA
Found at i:1733631 original size:20 final size:20
Alignment explanation
Indices: 1733606--1733646 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
1733596 TCATCTAGCT
*
1733606 CAAAAGACTTACAGATAACC
1 CAAAAGACTTACAAATAACC
*
1733626 CAAAAGATTTACAAATAACC
1 CAAAAGACTTACAAATAACC
1733646 C
1 C
1733647 GAAGGTTTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.51, C:0.24, G:0.07, T:0.17
Consensus pattern (20 bp):
CAAAAGACTTACAAATAACC
Found at i:1733681 original size:20 final size:20
Alignment explanation
Indices: 1733614--1733700 Score: 113
Period size: 20 Copynumber: 4.4 Consensus size: 20
1733604 CTCAAAAGAC
* * * *
1733614 TTACAGATAACCCAAAAGAT
1 TTACAAATAACCCGAAGGTT
1733634 TTACAAATAACCCGAAGGTT
1 TTACAAATAACCCGAAGGTT
* *
1733654 TT-CAAATAACCCGTACGTT
1 TTACAAATAACCCGAAGGTT
1733673 TTACAAATAACCCGAAGGTT
1 TTACAAATAACCCGAAGGTT
1733693 TTACAAAT
1 TTACAAAT
1733701 TTGTCGGAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 17 0.29
20 41 0.71
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.26
Consensus pattern (20 bp):
TTACAAATAACCCGAAGGTT
Found at i:1742235 original size:26 final size:25
Alignment explanation
Indices: 1742191--1742251 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 25
1742181 GGTTTTGTAA
* *
1742191 ATATAATA-ATAATAATAATGCTACT
1 ATATATTATATAATAATAATACTA-T
*
1742216 ATATATTATATAATAATAATATTAT
1 ATATATTATATAATAATAATACTAT
1742241 -TATATTATATA
1 ATATATTATATA
1742252 GAAACAACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.34
25 8 0.25
26 13 0.41
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (25 bp):
ATATATTATATAATAATAATACTAT
Found at i:1745429 original size:37 final size:37
Alignment explanation
Indices: 1745359--1745429 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
1745349 ATTTAAACAT
* *
1745359 ATAAAATTAAAATATAAATAAATAATGAGTAAAATAA
1 ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
1745396 ATAAAATTAAAACTA-AATATAAAAAAT-AATAAAA
1 ATAAAATTAAAA-TATAA-ATAAAAAATGAATAAAA
1745430 ACTTACAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
37 20 0.67
38 10 0.33
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATATAAATAAAAAATGAATAAAATAA
Done.