Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006509.1 Hibiscus syriacus cultivar Beakdansim tig00015853_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: 47754
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Found at i:2948 original size:110 final size:109
Alignment explanation
Indices: 2397--5710 Score: 4176
Period size: 110 Copynumber: 30.3 Consensus size: 109
2387 GAAATTCTTA
* * * * *
2397 TAAAAAAAATGCCATTAAAACTATGGGAAGAACAATAGTCCCAACCTTGCAACAATGAGTTCAAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAAA
* *
2462 TTCATAGCTTTTGACAAGTAAACTGTGC-GCTTACGCATTTTTT
66 TTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* *
2505 TTAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAAAGAGTTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAATGAG-TTCAA
*
2570 ATTCATAGCATTTGACAAGTAAATTGTGCAGCTTACGC--A-TTT
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * * * *
2612 AAAAAAAACGATGCAATTAAAACTGTGGGAAAAAACAACAGTACCAACTTTACAACAATGAGTTC
1 TAAACAAA--ATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTTC
2677 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC--A-TTT
63 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * * *
2721 AAAAAAAACGATGCCATTAAAACTGTGGGATAAAACAACACTACCAACCTTACAACAATGAGTTC
1 TAAACAAA--ATGCCATTAAAACTGTGGGA-AAAACAATAGTGCCAACCTTACAACAATGAGTTC
*
2786 AAATTCATAGCATTTGACAAGT-AACTGTGCAGCTTACGCATTTTTT
63 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * *
2832 CTAAACAAAATGCAATTAAAACTATGGGAAGAACAATAGTGCCAACCTTGCAACAATGAGTTCAA
1 -TAAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
2897 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* *
2942 CTAAACAAAATGCCATTAAAACTGTGGGAAGAACAATAGTGCCAACCTGACAACAATGAGTTCAA
1 -TAAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
* *
3007 ATTCATATCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTTT
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * *
3052 TTAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCATACAACAAAGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
* * **
3117 ATTCATAGCATTTGACAAGTAAATTATGCAGCTTACGCAT-TTAA
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * * * *
3161 AAAAAAAACGATGCAATTAAAACTGTGGGAAAAAACAACAGTACCAACTTTACAACAATGAGTTC
1 TAAACAAA--ATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTTC
*
3226 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC--A-TTG
63 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * * *
3270 AAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACATTACCAACCTTACAACAATGAGTTC
1 TAAACAAA--ATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTTC
3335 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCA-ATTTTT
63 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATA-TTTT
* * *
3382 CTAAACAAAATGCCATTAAAACTATGGGAAGAACAATAGTGCCAACCTTGCAACAATGAGTTCAA
1 -TAAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
*
3447 ATTCATAGCATTTGACAAGTAAATTGTGCAGCTTACGCAT-TTTT
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* *
3491 TTAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAAAGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
3556 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCCAT-TTTT
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACG-CATATTTT
* * * *
3601 TCTAACAAAATGCCATTAAAACTTTGGGAAAAAACAATAGTGCCAACCTTGCAACAAAGAGTTCA
1 T-AAACAAAATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTTCA
3666 AATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCA-ATTTTT
64 AATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATA-TTTT
** * * *
3712 TAAACAAAATGCCGCTAAAACTGTGAGAAAAAATAATAGTGCCAACCTTACAACAAAGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTG-GGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
*
3777 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCAT-TTTA
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * *
3821 AAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTTACAACAATGAGTTC
1 TAAACAAA--ATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTTC
* *
3886 AAATTCATAGCATTTGACAAATAAACTGTGCAGCTTACGCATTTTTT
63 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * * * * *
3933 TAAACAGAATGCCATTAAACCTATGGGAAAAACAATAGTGTCATCCTTACAACAAAGTGTTCAAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAAA
* *
3998 TTCATAGCATTTGACAAGTAAACTATGCAGCTTACGC--ATTTG
66 TTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * *
4040 AAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTTACAACAATGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
* * *
4105 ATTCATAGCATTTGACAAGTAAATTGTGCAGCTTAGGCATTTTTT
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * *
4150 CTAAACAAAATGCCATTAAAACTGTGAGAAAAAATAATAGTGCCAACCTTACAACAATGACTTCA
1 -TAAACAAAATGCCATTAAAACTGTG-GGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCA
* * *
4215 AATTCATAGCATTTGATAAGTAAACAGTGCAGCGTACGC--ATTTT
64 AATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * * *
4259 TAAAAAAATGATGCCATTAAAACTGTAGGAAAAAACAACAGTACTAACCTTACAACAATGAGTTC
1 TAAACAAA--ATGCCATTAAAACTGT-GGGAAAAACAATAGTGCCAACCTTACAACAATGAGTTC
4324 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCAT-TTCTT
63 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATT-TT
* * *
4371 TATAACAAAATG-CATTAAAACTGTGGAAAAAAATAATAGTGCCAACCTTCCAAC-A-GAGTTCA
1 TA-AACAAAATGCCATTAAAACTGTGG-GAAAAACAATAGTGCCAACCTTACAACAATGAGTTCA
*
4433 AATTCATAGCATTTGACAAGTAAACAGTGCAGCTTACGC--ATTTT
64 AATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * * * *
4477 TAAAAAAATGATGCTATTAAAACTGTGGGAAGAAACAACAGTACCATCCTTACAACAATGTGTTC
1 TAAACAAA--ATGCCATTAAAACTGTGGGAA-AAACAATAGTGCCAACCTTACAACAATGAGTTC
4542 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC--A-TTT
63 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * *
4586 TAAAAAATACGATGCCATTAAAACTGTGGGAAAAAACAACAGTACCGACCTTACAACAATGAGTT
1 TAAACAA-A--ATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTT
4651 CAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
62 CAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * * *
4699 CTAAATAAAATGCCATTAAAACTATGGGAAAAACAATAGTGCCAAACTTACAACAAAGAGTTCGA
1 -TAAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
* *
4764 ATTCATAGCATTTCACAAATAAACTGTGCAGCTTA---ATCA-TTT
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCAT-ATTTT
* * * * * **
4806 AAAAAAAACGATGCCATTAAAACTGTGGGAAAAAAACAACAATACCAACCTTACAACTTTGAGTT
1 TAAACAAA--ATGCCATTAAAACTGTGGG--AAAAACAATAGTGCCAACCTTACAACAATGAGTT
* * *
4871 CAAATTCATAGCATTTGACAAGTGAACAGTGCAGCTTACGCATTTTTT
62 CAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * * *
4919 CTAAACAAAATGTCATT-AAACTGTGAGAAAAATAATAGTGCCAACCTTAAAACAAAGAGTTCAA
1 -TAAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
4983 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC--ATTTT
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * * * *
5026 AAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAATCTTACAACAACGAGTTC
1 TAAACAAA--ATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTTC
5091 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC---TTTT
63 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * * * *
5135 AAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTGACAACAATGAGTTC
1 TAAACAAA--ATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTTC
5200 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
63 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
** * *
5247 CTAAACAAAATGCCATTAAAACCATGGGAAGAACAATAGTGCCAACCTTGCAACAATGAGTTCAA
1 -TAAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
* *
5312 ATTCATATCATTTGAC-----AACTGTGTAGCTTACGCATATTTT
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
* * *
5352 CTAAACAAAATGTCATTAAAACTATGGGAAAAACAATAGTGCCAACCTTACAACAAAGAGTTCAA
1 -TAAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
*
5417 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCCATTTTTT
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACG-CATATTTT
* * * * *
5463 TTAACAAAATGCCATTAAAATTTTGGGAAAAAACAATAGTGCCAACCTTACAATAAAGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
5528 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC--ATTTT
65 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
** * * * *
5571 TAAA-AAAATGCCGCTAAAACTGTGGGGAAAAAATAACAGTACCAACCTGACAACAAAT-AGTTC
1 TAAACAAAATGCCATTAAAACTGT-GGG-AAAAACAATAGTGCCAACCTTACAAC-AATGAGTTC
*
5634 AAACTCATAGCATTTGACAAGT-AACTTGTGCAGCTTACGCAT-TTTT
63 AAATTCATAGCATTTGACAAGTAAAC-TGTGCAGCTTACGCATATTTT
*
5680 TAAAC-AAATGCCGTTAAAACTGTGGGAAAAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAA
5711 ATAACAGTAA
Statistics
Matches: 2849, Mismatches: 269, Indels: 177
0.86 0.08 0.05
Matches are distributed among these distances:
105 103 0.04
106 16 0.01
107 72 0.03
108 346 0.12
109 740 0.26
110 980 0.34
111 521 0.18
112 33 0.01
113 26 0.01
114 12 0.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.26
Consensus pattern (109 bp):
TAAACAAAATGCCATTAAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAAA
TTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTT
Found at i:3027 original size:219 final size:218
Alignment explanation
Indices: 2397--5711 Score: 4363
Period size: 219 Copynumber: 15.2 Consensus size: 218
2387 GAAATTCTTA
* * * * *
2397 TAAAAAAAATGCCATTAAAACTATGGG-AAGAACAATAGTCCCAACCTTGCAACAATGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
* * * *
2461 ATTCATAGCTTTTGACAAGTAAACTGTGC-GCTTACGCATTTTTTTTAACAAAATGCCATTAAAA
66 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCA-TTTTCTAAAAAAAATGCCATTAAAA
* * *
2525 CTGTGGGAAAAACAATAGTGCCAACCTTACAACAAAGAGTTTCAAATTCATAGCATTTGACAAGT
130 CTGTGGGAAAAACAACAGTACCAACCTTACAACAATGAG-TTCAAATTCATAGCATTTGACAAGT
*
2590 AAATTGTGCAGCTTACGCA---TTT
194 AAACTGTGCAGCTTACGCATTTTTT
* * * * * *
2612 AAAAAAAACGATGCAATTAAAACTGTGGGAAAAAACAACAGTACCAACTTTACAACAATGAGTTC
1 TAAACAAA--ATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTC
*
2677 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCA-TTT-AAAAAAAACGATGCCATTA
64 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTCTAAAAAAA--ATGCCATTA
*
2740 AAACTGTGGGATAAAACAACACTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACA
127 AAACTGTGGGA-AAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACA
2805 AGT-AACTGTGCAGCTTACGCATTTTTT
191 AGTAAACTGTGCAGCTTACGCATTTTTT
* * * *
2832 CTAAACAAAATGCAATTAAAACTATGGG-AAGAACAATAGTGCCAACCTTGCAACAATGAGTTCA
1 -TAAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCA
*
2896 AATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTTCTAAACAAAATGCCATTAA
65 AATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC--ATTTTCTAAAAAAAATGCCATTAA
* * * * *
2961 AACTGTGGGAAGAACAATAGTGCCAACCTGACAACAATGAGTTCAAATTCATATCATTTGACAAG
128 AACTGTGGGAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAG
3026 TAAACTGTGCAGCTTACGCATTTTTT
193 TAAACTGTGCAGCTTACGCATTTTTT
* * *
3052 TTAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCATACAACAAAGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
* * *** *
3117 ATTCATAGCATTTGACAAGTAAATTATGCAGCTTACGCATTTAAAAAAAAAACGATGCAATTAAA
66 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTCTAAAAAAA--ATGCCATTAAA
*
3182 ACTGTGGGAAAAAACAACAGTACCAACTTTACAACAATGAGTTCAAATTCATAGCATTTGACAAG
129 ACTGTGGG-AAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAG
*
3247 TAAACTGTGCAGCTTACGCA---TTG
193 TAAACTGTGCAGCTTACGCATTTTTT
* * * * *
3270 AAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACATTACCAACCTTACAACAATGAGTTC
1 TAAACAAA--ATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTC
*
3335 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCAATTTTTCTAAACAAAATGCCATTA
64 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC-A-TTTTCTAAAAAAAATGCCATTA
* * * * *
3400 AAACTATGGGAAGAACAATAGTGCCAACCTTGCAACAATGAGTTCAAATTCATAGCATTTGACAA
127 AAACTGTGGGAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAA
*
3465 GTAAATTGTGCAGCTTACGCATTTTTT
192 GTAAACTGTGCAGCTTACGCATTTTTT
*
3492 T-AACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAAAGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
*
3556 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCCATTTTTTCT-AACAAAATGCCATTAA
66 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACG-CA--TTTTCTAAAAAAAATGCCATTAA
* * * * *
3620 AACTTTGGGAAAAAACAATAGTGCCAACCTTGCAACAAAGAGTTCAAATTCATAGCATTTGACAA
128 AACTGTGGG-AAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAA
*
3685 GTAAACTGTGCAGCTTACGCAATTTTT
192 GTAAACTGTGCAGCTTACGCATTTTTT
** * * *
3712 TAAACAAAATGCCGCTAAAACTGTGAGAAAAAATAATAGTGCCAACCTTACAACAAAGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
**
3777 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTAAAAAAAAACGATGCCATTAAA
66 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTCTAAAAAAA--ATGCCATTAAA
*
3842 ACTGTGGGAAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAA
129 ACTGTGGG-AAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAG
3907 TAAACTGTGCAGCTTACGCATTTTTT
193 TAAACTGTGCAGCTTACGCATTTTTT
* * * * * * *
3933 TAAACAGAATGCCATTAAACCTATGGG-AAAAACAATAGTGTCATCCTTACAACAAAGTGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
* **
3997 ATTCATAGCATTTGACAAGTAAACTATGCAGCTTACGCA-TTTGAAAAAAAAATGCCATTAAAAC
66 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTCTAAAAAAAATGCCATTAAAAC
4061 TGTGGGAAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTA
131 TGTGGG-AAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTA
* *
4126 AATTGTGCAGCTTAGGCATTTTTT
195 AACTGTGCAGCTTACGCATTTTTT
* * *
4150 CTAAACAAAATGCCATTAAAACTGTGAGAAAAAATAATAGTGCCAACCTTACAACAATGACTTCA
1 -TAAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCA
* * *
4215 AATTCATAGCATTTGATAAGTAAACAGTGCAGCGTACGCATTTT-TAAAAAAATGATGCCATTAA
65 AATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTCTAAAAAAA--ATGCCATTAA
* *
4279 AACTGTAGGAAAAAACAACAGTACTAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAA
128 AACTGT-GGGAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAA
*
4344 GTAAACTGTGCAGCTTACGCATTTCTT
192 GTAAACTGTGCAGCTTACGCATTTTTT
* * *
4371 TATAACAAAATG-CATTAAAACTGTGGAAAAAAATAATAGTGCCAACCTTCCAAC-A-GAGTTCA
1 TA-AACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCA
* *
4433 AATTCATAGCATTTGACAAGTAAACAGTGCAGCTTACGCATTTT-TAAAAAAATGATGCTATTAA
65 AATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTCTAAAAAAA--ATGCCATTAA
* *
4497 AACTGTGGGAAGAAACAACAGTACCATCCTTACAACAATGTGTTCAAATTCATAGCATTTGACAA
128 AACTGTGGGAA-AAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAA
**
4562 GTAAACTGTGCAGCTTACGCATTTTAA
192 GTAAACTGTGCAGCTTACGCATTTTTT
* * ** * * *
4589 AAAATACGATGCCATTAAAACTGTGGGAAAAAACAACAGTACCGACCTTACAACAATGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
*
4654 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTTCTAAATAAAATGCCATTAAA
66 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC--ATTTTCTAAAAAAAATGCCATTAAA
* * * * * * * *
4719 ACTATGGGAAAAACAATAGTGCCAAACTTACAACAAAGAGTTCGAATTCATAGCATTTCACAAAT
129 ACTGTGGGAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGT
**
4784 AAACTGTGCAGCTTA---ATCATTT
194 AAACTGTGCAGCTTACGCATTTTTT
* * * * * **
4806 AAAAAAAACGATGCCATTAAAACTGTGGGAAAAAAACAACAATACCAACCTTACAACTTTGAGTT
1 TAAACAAA--ATGCCATTAAAACTGTGGG-AAAAAACAATAGTGCCAACCTTACAACAATGAGTT
* * * *
4871 CAAATTCATAGCATTTGACAAGTGAACAGTGCAGCTTACGCATTTTTTCTAAACAAAATGTCATT
63 CAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCA--TTTTCTAAAAAAAATGCCATT
* * * * * *
4936 -AAACTGTGAGAAAAATAATAGTGCCAACCTTAAAACAAAGAGTTCAAATTCATAGCATTTGACA
126 AAAACTGTGGGAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACA
5000 AGTAAACTGTGCAGCTTACGCA--TTTT
191 AGTAAACTGTGCAGCTTACGCATTTTTT
* * * * * *
5026 AAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAATCTTACAACAACGAGTTC
1 TAAACAAA--ATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTC
*
5091 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC-TTTT-AAAAAAAACGATGCCATTA
64 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTCTAAAAAAA--ATGCCATTA
*
5154 AAACTGTGGGAAAAAACAACAGTACCAACCTGACAACAATGAGTTCAAATTCATAGCATTTGACA
127 AAACTGTGGG-AAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACA
*
5219 AGTAAACTGTGCAGCTTACGCATATTTTC
191 AGTAAACTGTGCAGCTTACGCAT-TTTTT
** * *
5248 TAAACAAAATGCCATTAAAACCATGGG-AAGAACAATAGTGCCAACCTTGCAACAATGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
* * * *
5312 ATTCATATCATTTGAC-----AACTGTGTAGCTTACGCATATTTTCTAAACAAAATGTCATTAAA
66 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC--ATTTTCTAAAAAAAATGCCATTAAA
* * * *
5372 ACTATGGGAAAAACAATAGTGCCAACCTTACAACAAAGAGTTCAAATTCATAGCATTTGACAAGT
129 ACTGTGGGAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGT
5437 AAACTGTGCAGCTTACGCCATTTTTT
194 AAACTGTGCAGCTTACG-CATTTTTT
* * * * *
5463 TTAACAAAATGCCATTAAAATTTTGGGAAAAAACAATAGTGCCAACCTTACAATAAAGAGTTCAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
**
5528 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTT-T-AAAAAAATGCCGCTAAAAC
66 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTCTAAAAAAAATGCCATTAAAAC
* * *
5591 TGTGGGGAAAAAATAACAGTACCAACCTGACAACAAAT-AGTTCAAACTCATAGCATTTGACAAG
131 TGT-GGG-AAAAACAACAGTACCAACCTTACAAC-AATGAGTTCAAATTCATAGCATTTGACAAG
5655 T-AACTTGTGCAGCTTACGCA-TTTTT
193 TAAAC-TGTGCAGCTTACGCATTTTTT
*
5680 TAAAC-AAATGCCGTTAAAACTGTGGGAAAAAA
1 TAAACAAAATGCCATTAAAACTGTGGGAAAAAA
5712 TAACAGTAAC
Statistics
Matches: 2760, Mismatches: 262, Indels: 155
0.87 0.08 0.05
Matches are distributed among these distances:
214 16 0.01
215 110 0.04
216 101 0.04
217 191 0.07
218 428 0.16
219 748 0.27
220 690 0.25
221 435 0.16
222 34 0.01
223 7 0.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.26
Consensus pattern (218 bp):
TAAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAATGAGTTCAA
ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTCTAAAAAAAATGCCATTAAAAC
TGTGGGAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAA
ACTGTGCAGCTTACGCATTTTTT
Found at i:3528 original size:549 final size:541
Alignment explanation
Indices: 2397--5719 Score: 4479
Period size: 549 Copynumber: 6.1 Consensus size: 541
2387 GAAATTCTTA
* * * *
2397 TAAAAAAAATGCCATTAAAACTATGGG-AAGAACAATAGTCCCAACCTTG-CAACAATGAGTTCA
1 TAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACC-TGACAACAATGAGTTCA
* *
2460 AATTCATAGCTTTTGACAAGTAAACTGTGC-GCTTACGCATTTTTTTTAACAAAATGCCATTAAA
65 AATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTTTTAAACAAAATGCCATTAAA
2524 ACTGTGGGAAAAACAATAGTGCCAACCTTACAACAAAGAGTTTCAAATTCATAGCATTTGACAAG
130 ACTGTGGGAAAAACAATAGTGCCAACCTTACAACAAAGAG-TTCAAATTCATAGCATTTGACAAG
* *
2589 TAAATTGTGCAGCTTACGCATTTAAAAAAAACGATGCAATTAAAACTGTGGGAAAAAACAACAGT
194 TAAACTGTGCAGCTTACGCATTTAAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACAGT
*
2654 ACCAACTTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCA-
259 ACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCAT
* *
2718 TTTAAAAAAAACGATGCCATTAAAACTGTGGGATAAAACAACACTACCAACCTTACAACAATGAG
324 TTTAAAAAAAA--ATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTTACAACAATGAG
*
2783 TTCAAATTCATAGCATTTGACAAGT-AACTGTGCAGCTTACGCATTTTTTCTAAACAAAATGCAA
387 TTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCA--TTTT-TAAACAAAATGCCA
* * * *
2847 TTAAAACTATGGGAAGAACAATAGTGCCAACCTTGCAACAATGAGTTCAAATTCATAGCATTTGA
449 TTAAAACTATGGGAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGA
2912 CAAGTAAACTGTGCAGCTTACGCATATTTT
514 CAAGTAAACTGTGCAGCTTACGC--ATTTT
* * * *
2942 CTAAACAAAATGCCATTAAAACTGTGGG-AAGAACAATAGTGCCAACCTGACAACAATGAGTTCA
1 -TAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTGACAACAATGAGTTCA
* *
3006 AATTCATATCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTTTTTAACAAAATGCCATTAAA
65 AATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTTTTAAACAAAATGCCATTAAA
*
3071 ACTGTGGGAAAAAACAATAGTGCCAACCATACAACAAAGAGTTCAAATTCATAGCATTTGACAAG
130 ACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAAAGAGTTCAAATTCATAGCATTTGACAAG
* * *
3136 TAAATTATGCAGCTTACGCATTTAAAAAAAAAACGATGCAATTAAAACTGTGGGAAAAAACAACA
194 TAAACTGTGCAGCTTACGCATTT--AAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACA
*
3201 GTACCAACTTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC
257 GTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC
* *
3266 A-TTGAAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACATTACCAACCTTACAACAATG
322 ATTTTAAAAAAAA--ATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTTACAACAATG
3330 AGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCAATTTTTCTAAACAAAATGC
385 AGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGC-A-TTTT-TAAACAAAATGC
* * * *
3395 CATTAAAACTATGGGAAGAACAATAGTGCCAACCTTGCAACAATGAGTTCAAATTCATAGCATTT
447 CATTAAAACTATGGGAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTT
*
3460 GACAAGTAAATTGTGCAGCTTACGCATTTTT
512 GACAAGTAAACTGTGCAGCTTACGCA-TTTT
* * * * * *
3491 TTAACAAAATGCCATTAAAACTGTGGGAAAAAACAATAGTGCCAACCTTACAACAAAGAGTTCAA
1 TAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTGACAACAATGAGTTCAA
3556 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCCATTTTTTCT-AACAAAATGCCATTAA
66 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACG-CATTTTTT-TAAACAAAATGCCATTAA
* *
3620 AACTTTGGGAAAAAACAATAGTGCCAACCTTGCAACAAAGAGTTCAAATTCATAGCATTTGACAA
129 AACTGTGGG-AAAAACAATAGTGCCAACCTTACAACAAAGAGTTCAAATTCATAGCATTTGACAA
* * ** * *
3685 GTAAACTGTGCAGCTTACGCAATTTTTTAAACAAA--ATGCCGCTAAAACTGTGAGAAAAAATAA
193 GTAAACTGTGCAGCTTACGC-A--TTTAAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAA
* * *
3748 TAGTGCCAACCTTACAACAAAGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTAC
255 CAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTAC
3813 GCATTTTAAAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTTACAACA
320 GCATTTT-AAAAAAAA--ATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTTACAACA
* *
3878 ATGAGTTCAAATTCATAGCATTTGACAAATAAACTGTGCAGCTTACGCATTTTTTTAAACAGAAT
382 ATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCA--TTTTTAAACAAAAT
* * ** * * *
3943 GCCATTAAACCTATGGGAAAAACAATAGTGTCATCCTTACAACAAAGTGTTCAAATTCATAGCAT
445 GCCATTAAAACTATGGGAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCAT
* *
4008 TTGACAAGTAAACTATGCAGCTTACGCATTTG
510 TTGACAAGTAAACTGTGCAGCTTACGCATTTT
* *
4040 AAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTTACAACAATGAGTTCAA
1 TAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTGACAACAATGAGTTCAA
* *
4105 ATTCATAGCATTTGACAAGTAAATTGTGCAGCTTAGGCATTTTTTCTAAACAAAATGCCATTAAA
66 ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTTT-TAAACAAAATGCCATTAAA
* * * * *
4170 ACTGTGAGAAAAAATAATAGTGCCAACCTTACAACAATGACTTCAAATTCATAGCATTTGATAAG
130 ACTGTG-GGAAAAACAATAGTGCCAACCTTACAACAAAGAGTTCAAATTCATAGCATTTGACAAG
* * * * *
4235 TAAACAGTGCAGCGTACGCATTTTTAAAAAAATGATGCCATTAAAACTGTAGGAAAAAACAACAG
194 TAAACTGTGCAGCTTACGCA-TTTAAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACAG
*
4300 TACTAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCA
258 TACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCA
* * * * * * *
4365 TTTCTTTATAACAAAATG-CATTAAAACTGTGGAAAAAAATAATAGTGCCAACCTTCCAAC-A-G
323 --T-TTTAAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTTACAACAATG
* * *
4427 AGTTCAAATTCATAGCATTTGACAAGTAAACAGTGCAGCTTACGCATTTTTAAAAAAATGATGCT
385 AGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTTAAACAAA--ATGCC
* * *
4492 ATTAAAACTGTGGGAAGAAACAACAGTACCATCCTTACAACAATGTGTTCAAATTCATAGCATTT
448 ATTAAAACTATGGGAA-AAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTT
4557 GACAAGTAAACTGTGCAGCTTACGCA-TTT
512 GACAAGTAAACTGTGCAGCTTACGCATTTT
* *
4586 TAAAAAATACGATGCCATTAAAACTGTGGGAAAAAACAACAGTACCGACCTTACAACAATGAGTT
1 TAAAAAA-A--ATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTGACAACAATGAGTT
* *
4651 CAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTTCTAAATAAAATGCCATT
63 CAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCAT-TTTTTTAAACAAAATGCCATT
* * * *
4716 AAAACTATGGGAAAAACAATAGTGCCAAACTTACAACAAAGAGTTCGAATTCATAGCATTTCACA
127 AAAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAAAGAGTTCAAATTCATAGCATTTGACA
* **
4781 AATAAACTGTGCAGCTTAATCATTTAAAAAAAACGATGCCATTAAAACTGTGGGAAAAAAACAAC
192 AGTAAACTGTGCAGCTTACGCATTTAAAAAAAACGATGCCATTAAAACTGTGGG-AAAAAACAAC
* ** * *
4846 AATACCAACCTTACAACTTTGAGTTCAAATTCATAGCATTTGACAAGTGAACAGTGCAGCTTACG
256 AGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACG
* * * * * * * *
4911 CATTTTTTCTAAACAAAATGTCATT-AAACTGTGAG-AAAAATAATAGTGCCAACCTTAAAACAA
321 CA--TTTT-AAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTTACAACAA
* * *
4974 AGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTAAAAAAAACGATG
383 TGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTTAAACAAA--ATG
* * *
5039 CCATTAAAACTGTGGGAAAAAACAACAGTACCAATCTTACAACAACGAGTTCAAATTCATAGCAT
446 CCATTAAAACTATGGG-AAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCAT
5104 TTGACAAGTAAACTGTGCAGCTTACGC-TTTT
510 TTGACAAGTAAACTGTGCAGCTTACGCATTTT
*
5135 AAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTGACAACAATGAGTTC
1 TAAAAAAA--ATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTGACAACAATGAGTTC
*
5200 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATATTTTCTAAACAAAATGCCATTA
64 AAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCAT-TTTTTTAAACAAAATGCCATTA
** * * * *
5265 AAACCATGGGAAGAACAATAGTGCCAACCTTGCAACAATGAGTTCAAATTCATATCATTTGAC--
128 AAACTGTGGGAAAAACAATAGTGCCAACCTTACAACAAAGAGTTCAAATTCATAGCATTTGACAA
* * * * *
5328 ---AACTGTGTAGCTTACGCATATTTTCTAAACAAA--ATGTCATTAAAACTATGGG-AAAAACA
193 GTAAACTGTGCAGCTTACGC--A-TTT-AAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACA
* * *
5387 ATAGTGCCAACCTTACAACAAAGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTA
254 ACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTA
** * * * * * *
5452 CGCCATTTTTTTTAACAAAATGCCATTAAAATTTTGGGAAAAAACAATAGTGCCAACCTTACAAT
319 CG-CA--TTTTAAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTTACAAC
*
5517 AAAGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTTAAA-AAAATG
381 AATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTTAAACAAAATG
** * * * *
5581 CCGCTAAAACTGTGGGGAAAAAATAACAGTACCAACCTGACAACAAAT-AGTTCAAACTCATAGC
446 CCATTAAAACTAT-GGG-AAAAACAACAGTACCAACCTTACAAC-AATGAGTTCAAATTCATAGC
5645 ATTTGACAAGT-AACTTGTGCAGCTTACGCATTTT
508 ATTTGACAAGTAAAC-TGTGCAGCTTACGCATTTT
* * * *
5679 TTAAACAAATGCCGTTAAAACTGTGGGAAAAAATAACAGTA
1 TAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTA
5720 ACTACCTGTC
Statistics
Matches: 2543, Mismatches: 185, Indels: 102
0.90 0.07 0.04
Matches are distributed among these distances:
542 48 0.02
543 161 0.06
544 39 0.02
545 100 0.04
546 159 0.06
547 232 0.09
548 438 0.17
549 906 0.36
550 330 0.13
551 124 0.05
552 3 0.00
553 3 0.00
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.26
Consensus pattern (541 bp):
TAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTGACAACAATGAGTTCAA
ATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTTTTAAACAAAATGCCATTAAAA
CTGTGGGAAAAACAATAGTGCCAACCTTACAACAAAGAGTTCAAATTCATAGCATTTGACAAGTA
AACTGTGCAGCTTACGCATTTAAAAAAAACGATGCCATTAAAACTGTGGGAAAAAACAACAGTAC
CAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTT
TAAAAAAAAATGCCATTAAAACTGTGGGAAAAAACAACAGTACCAACCTTACAACAATGAGTTCA
AATTCATAGCATTTGACAAGTAAACTGTGCAGCTTACGCATTTTTAAACAAAATGCCATTAAAAC
TATGGGAAAAACAACAGTACCAACCTTACAACAATGAGTTCAAATTCATAGCATTTGACAAGTAA
ACTGTGCAGCTTACGCATTTT
Found at i:7244 original size:24 final size:24
Alignment explanation
Indices: 7215--7265 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
7205 CCCAATTTAC
*
7215 TCTCCCAAATCCCTAACCCTTCTT
1 TCTCCCAAATCCCTAACCCTCCTT
7239 TCTCCCAAATCCCTAACCCTCCTT
1 TCTCCCAAATCCCTAACCCTCCTT
7263 TCT
1 TCT
7266 TCATTCCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.20, C:0.47, G:0.00, T:0.33
Consensus pattern (24 bp):
TCTCCCAAATCCCTAACCCTCCTT
Found at i:24116 original size:20 final size:21
Alignment explanation
Indices: 24091--24183 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
24081 TTTTCCCAAT
*
24091 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
24111 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
24132 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
24152 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
24173 TCGCAATGCGA
1 TCGCAATGCGA
24184 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:24136 original size:41 final size:41
Alignment explanation
Indices: 24091--24183 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
24081 TTTTCCCAAT
24091 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
24132 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
24173 TCGCAATGCGA
1 TCGCAATGCGA
24184 TACTGACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:24196 original size:41 final size:41
Alignment explanation
Indices: 24110--24243 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
24100 GAATAAGTAA
* *
24110 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
24151 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * * * * *
24192 ATCGCAATGCGATAAT--AAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
24232 TTCGCAACGCGA
1 ATCGCAACGCGA
24244 TACTGTCTTT
Statistics
Matches: 80, Mismatches: 10, Indels: 7
0.82 0.10 0.07
Matches are distributed among these distances:
40 34 0.43
41 44 0.55
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.22, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:24197 original size:20 final size:20
Alignment explanation
Indices: 24172--24261 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
24162 AATTGGGAAA
*
24172 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
24192 ATCGCAATGCGATAATAAAA
1 ATCGCAACGCGATACTGACT
* *
24212 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
* *
24232 TTCGCAACGCGATACTGTCT
1 ATCGCAACGCGATACTGACT
*
24252 TTCGCAACGC
1 ATCGCAACGC
24262 AATAATACAT
Statistics
Matches: 56, Mismatches: 14, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 56 1.00
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:24226 original size:40 final size:40
Alignment explanation
Indices: 24169--24245 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
24159 GCGAATTGGG
* * *
24169 AAAATCGCAATGCGATACTGACTATCGCAATGCGATAATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATA
* *
24209 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
24246 CTGTCTTTCG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.39, C:0.22, G:0.17, T:0.22
Consensus pattern (40 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATA
Found at i:24481 original size:22 final size:22
Alignment explanation
Indices: 24453--24496 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
24443 CACTCTCTCA
24453 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
24475 CCCATCTTCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
24497 TATCTAAATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:24785 original size:20 final size:20
Alignment explanation
Indices: 24760--24797 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
24750 CGATTCTCTC
24760 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
24780 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
24798 AGAAACTATC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:28788 original size:12 final size:12
Alignment explanation
Indices: 28771--28796 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
28761 GTCTCTGTAC
28771 TCTCCTCCATTG
1 TCTCCTCCATTG
28783 TCTCCTCCATTG
1 TCTCCTCCATTG
28795 TC
1 TC
28797 AAACCTCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.42, G:0.08, T:0.42
Consensus pattern (12 bp):
TCTCCTCCATTG
Found at i:30498 original size:16 final size:16
Alignment explanation
Indices: 30474--30507 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
30464 TATTGTCGAC
*
30474 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
30490 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
30506 CG
1 CG
30508 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:32551 original size:12 final size:11
Alignment explanation
Indices: 32530--32570 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
32520 GTAGAAGACT
32530 ACAAATTTAGTG
1 ACAAA-TTAGTG
32542 ACAAAGTTAGTG
1 ACAAA-TTAGTG
32554 ACAAATTAGATG
1 ACAAATTAG-TG
32566 ACAAA
1 ACAAA
32571 ATTTATGTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 4 0.15
12 23 0.85
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (11 bp):
ACAAATTAGTG
Found at i:35256 original size:15 final size:15
Alignment explanation
Indices: 35228--35260 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
35218 TAATTGATTT
35228 TTTTAAATATTTTATA
1 TTTTAAATATTTTA-A
35244 TTTTAAA-ATTTTAA
1 TTTTAAATATTTTAA
35258 TTT
1 TTT
35261 AAACTATACA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 6 0.35
16 7 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTAAATATTTTAA
Found at i:35443 original size:14 final size:14
Alignment explanation
Indices: 35424--35456 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
35414 TTTTGCTTAT
35424 ATTTTAT-TTTTAAA
1 ATTTTATATTTT-AA
35438 ATTTTATATTTTAA
1 ATTTTATATTTTAA
35452 ATTTT
1 ATTTT
35457 TTTGGAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
ATTTTATATTTTAA
Found at i:45800 original size:34 final size:35
Alignment explanation
Indices: 45757--45833 Score: 104
Period size: 36 Copynumber: 2.2 Consensus size: 35
45747 TTGCTCCAGA
45757 ACCCTCTGGTGCAAGATA-C-CAGCTGGTGCAAGAT
1 ACCCTCTGGTGCAAG-TACCTCAGCTGGTGCAAGAT
* *
45791 ACCCTCTGGTGCAAGTACCCTCTGGTGGTGCAAGAT
1 ACCCTCTGGTGCAAGTA-CCTCAGCTGGTGCAAGAT
45827 ACCCTCT
1 ACCCTCT
45834 TACTATTTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
33 2 0.05
34 15 0.39
35 1 0.03
36 20 0.53
ACGTcount: A:0.22, C:0.30, G:0.25, T:0.23
Consensus pattern (35 bp):
ACCCTCTGGTGCAAGTACCTCAGCTGGTGCAAGAT
Found at i:45811 original size:16 final size:17
Alignment explanation
Indices: 45757--45833 Score: 102
Period size: 17 Copynumber: 4.4 Consensus size: 17
45747 TTGCTCCAGA
45757 ACCCTCTGGTGCAAGAT
1 ACCCTCTGGTGCAAGAT
**
45774 ACCAGCTGGTGCAAGAT
1 ACCCTCTGGTGCAAGAT
45791 ACCCTCTGGTGCAAG-T
1 ACCCTCTGGTGCAAGAT
45807 ACCCTCTGGTGGTGCAAGAT
1 ACCCTC---TGGTGCAAGAT
45827 ACCCTCT
1 ACCCTCT
45834 TACTATTTGG
Statistics
Matches: 52, Mismatches: 4, Indels: 8
0.81 0.06 0.12
Matches are distributed among these distances:
16 7 0.13
17 29 0.56
19 9 0.17
20 7 0.13
ACGTcount: A:0.22, C:0.30, G:0.25, T:0.23
Consensus pattern (17 bp):
ACCCTCTGGTGCAAGAT
Done.